diff --git a/MCdata/124d_MC b/MCdata/124d_MC deleted file mode 100644 index f841ad838986ec8f5aeca0155a672739130ec2df..0000000000000000000000000000000000000000 --- a/MCdata/124d_MC +++ /dev/null @@ -1,45 +0,0 @@ -Residue conformations ------------------------------------------- -A1 : G C1p_exo anti -A2 : T O4p_endo anti -A3 : C O4p_endo anti -A4 : A C1p_exo anti -A5 : C O4p_endo anti -A6 : A C1p_exo anti -A7 : T C1p_exo anti -A8 : G O4p_endo anti -B9 : C C3p_endo anti -B10 : A C3p_endo anti -B11 : U C3p_endo anti -B12 : G C3p_endo anti -B13 : U C2p_exo anti -B14 : G C3p_endo anti -B15 : A C3p_endo anti -B16 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -B9-B10 : adjacent_5p upward -B10-B11 : adjacent_5p upward -B12-B13 : adjacent_5p upward -B14-B15 : adjacent_5p upward -B15-B16 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-B14 : outward -A6-B12 : outward -A8-B10 : outward -Number of stackings = 14 -Number of adjacent stackings = 11 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -A1-B16 : G-C Ww/Ww pairing antiparallel cis XIX -A2-B15 : T-A Ww/Ww pairing antiparallel cis -A3-B14 : C-G Ww/Ww pairing antiparallel cis XIX -A4-B13 : A-U Ww/Ww pairing antiparallel cis XX -A5-B12 : C-G Ww/Ww pairing antiparallel cis XIX -A6-B11 : A-U Ww/Ww pairing antiparallel cis XX -A7-B10 : T-A Ww/Ww pairing antiparallel cis -A8-B9 : G-C Ww/Ww pairing antiparallel cis XIX diff --git a/MCdata/157d_MC b/MCdata/157d_MC deleted file mode 100644 index 40f19fffbf3225fb4ac69e3f371e1ac2171879ba..0000000000000000000000000000000000000000 --- a/MCdata/157d_MC +++ /dev/null @@ -1,162 +0,0 @@ -Residue conformations ------------------------------------------- -A1 : C C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C3p_endo anti -A5 : A C4p_exo anti -A6 : A C3p_endo anti -A7 : U C3p_endo anti -A8 : U C2p_exo anti -A9 : A C3p_endo anti -A10 : G C3p_endo anti -A11 : C C3p_endo anti -A12 : G C3p_endo anti -B13 : C C2p_exo anti -B14 : G C3p_endo anti -B15 : C C2p_exo anti -B16 : G C3p_endo anti -B17 : A C3p_endo anti -B18 : A C2p_exo anti -B19 : U C4p_exo anti -B20 : U C3p_endo anti -B21 : A C3p_endo anti -B22 : G C3p_endo anti -B23 : C C3p_endo anti -B24 : G C3p_endo anti -A25 : HOH -A26 : HOH -A31 : HOH -A33 : HOH -A42 : HOH -A43 : HOH -A44 : HOH -A45 : HOH -A46 : HOH -A47 : HOH -A48 : HOH -A49 : HOH -A50 : HOH -A51 : HOH -A52 : HOH -A53 : HOH -A56 : HOH -A61 : HOH -A62 : HOH -A70 : HOH -A75 : HOH -A76 : HOH -A77 : HOH -A78 : HOH -A80 : HOH -A81 : HOH -A82 : HOH -A83 : HOH -A84 : HOH -A85 : HOH -A86 : HOH -A87 : HOH -A88 : HOH -A89 : HOH -A91 : HOH -A94 : HOH -A96 : HOH -A98 : HOH -A99 : HOH -A100 : HOH -A103 : HOH -A104 : HOH -A105 : HOH -A106 : HOH -A107 : HOH -A111 : HOH -A112 : HOH -A113 : HOH -A114 : HOH -A116 : HOH -A117 : HOH -A120 : HOH -A121 : HOH -B27 : HOH -B28 : HOH -B29 : HOH -B30 : HOH -B32 : HOH -B34 : HOH -B35 : HOH -B36 : HOH -B37 : HOH -B38 : HOH -B39 : HOH -B40 : HOH -B41 : HOH -B54 : HOH -B55 : HOH -B57 : HOH -B58 : HOH -B59 : HOH -B60 : HOH -B63 : HOH -B64 : HOH -B65 : HOH -B66 : HOH -B67 : HOH -B68 : HOH -B69 : HOH -B71 : HOH -B72 : HOH -B73 : HOH -B74 : HOH -B79 : HOH -B90 : HOH -B92 : HOH -B93 : HOH -B95 : HOH -B97 : HOH -B101 : HOH -B102 : HOH -B108 : HOH -B109 : HOH -B110 : HOH -B115 : HOH -B118 : HOH -B119 : HOH -Adjacent stackings ---------------------------------------------- -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -B14-B15 : adjacent_5p upward -B15-B16 : adjacent_5p upward -B16-B17 : adjacent_5p upward -B17-B18 : adjacent_5p upward -B18-B19 : adjacent_5p upward -B19-B20 : adjacent_5p upward -B20-B21 : adjacent_5p upward -B21-B22 : adjacent_5p upward -B22-B23 : adjacent_5p upward -B23-B24 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A2-B24 : outward -A12-B14 : outward -Number of stackings = 22 -Number of adjacent stackings = 20 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A1-B24 : C-G Ww/Ww pairing antiparallel cis XIX -A2-B23 : G-C Ww/Ww pairing antiparallel cis XIX -A3-B22 : C-G Ww/Ww pairing antiparallel cis XIX -A4-B21 : G-A Ww/Ww pairing antiparallel cis VIII -A5-B20 : A-U Ww/Ww pairing antiparallel cis XX -A6-B19 : A-U Ww/Ww pairing antiparallel cis XX -A7-B18 : U-A Ww/Ww pairing antiparallel cis XX -A8-B17 : U-A Ww/Ww pairing antiparallel cis XX -A9-B16 : A-G Ww/Ww pairing antiparallel cis VIII -A10-B15 : G-C Ww/Ww pairing antiparallel cis XIX -A11-B14 : C-G Ww/Ww pairing antiparallel cis XIX -A12-B13 : G-C Ww/Ww pairing antiparallel cis XIX diff --git a/MCdata/165d_MC b/MCdata/165d_MC deleted file mode 100644 index 1f11523fe7c32ecd0ca67872e030d2dc2bcc5f8f..0000000000000000000000000000000000000000 --- a/MCdata/165d_MC +++ /dev/null @@ -1,103 +0,0 @@ -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : C C3p_endo anti -A3 : U C3p_endo anti -A4 : U C3p_endo anti -A5 : C C3p_endo anti -A6 : G C3p_endo anti -A7 : G C3p_endo anti -A8 : C C3p_endo anti -A9 : BRU -B10 : G C3p_endo anti -B11 : C C3p_endo anti -B12 : U C3p_endo anti -B13 : U C2p_exo anti -B14 : C C3p_endo anti -B15 : G C3p_endo anti -B16 : G C3p_endo anti -B17 : C C3p_endo anti -B18 : BRU -A19 : RHD -A20 : RHD -A22 : RHD -B21 : RHD -A23 : HOH -A25 : HOH -A26 : HOH -A27 : HOH -A28 : HOH -A29 : HOH -A30 : HOH -A31 : HOH -A33 : HOH -A35 : HOH -A36 : HOH -A37 : HOH -A38 : HOH -A41 : HOH -A43 : HOH -A47 : HOH -A48 : HOH -A51 : HOH -A53 : HOH -A54 : HOH -A56 : HOH -A57 : HOH -A59 : HOH -A60 : HOH -A61 : HOH -A63 : HOH -A64 : HOH -A65 : HOH -A66 : HOH -A73 : HOH -A74 : HOH -B24 : HOH -B32 : HOH -B34 : HOH -B39 : HOH -B40 : HOH -B42 : HOH -B44 : HOH -B45 : HOH -B46 : HOH -B49 : HOH -B50 : HOH -B52 : HOH -B55 : HOH -B58 : HOH -B62 : HOH -B67 : HOH -B68 : HOH -B69 : HOH -B70 : HOH -B71 : HOH -B72 : HOH -B75 : HOH -B76 : HOH -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -B10-B11 : adjacent_5p upward -B11-B12 : adjacent_5p upward -B13-B14 : adjacent_5p upward -B14-B15 : adjacent_5p upward -B15-B16 : adjacent_5p upward -B16-B17 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 12 -Number of adjacent stackings = 12 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-B17 : G-C Ww/Ww pairing antiparallel cis XIX -A2-B16 : C-G Ww/Ww pairing antiparallel cis XIX -A3-B15 : U-G Ws/Ww pairing antiparallel cis XXVIII -A4-B14 : U-C Wh/Wh pairing antiparallel cis one_hbond -A5-B13 : C-U Wh/Wh pairing antiparallel cis one_hbond -A6-B12 : G-U Ww/Ws pairing antiparallel cis XXVIII -A7-B11 : G-C Ww/Ww pairing antiparallel cis XIX -A8-B10 : C-G Ww/Ww pairing antiparallel cis XIX diff --git a/MCdata/176d_MC b/MCdata/176d_MC deleted file mode 100644 index 53aaf008b2a59b09423466df8ec74ee3bec3e4ef..0000000000000000000000000000000000000000 --- a/MCdata/176d_MC +++ /dev/null @@ -1,239 +0,0 @@ -Residue conformations ------------------------------------------- -A1 : GPN -A2 : APN -A3 : APN -A4 : CPN -A5 : TPN -A6 : CPN -B7 : G C2p_exo anti -B8 : A C2p_exo anti -B9 : G C3p_endo anti -B10 : U C3p_endo anti -B11 : U C3p_endo anti -B12 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -B7-B8 : adjacent_5p upward -B8-B9 : adjacent_5p upward -B9-B10 : adjacent_5p upward -B11-B12 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 4 -Number of adjacent stackings = 4 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-B12 : GPN-C pairing parallel one_hbond -Residue conformations ------------------------------------------- -A1 : GPN -A2 : APN -A3 : APN -A4 : CPN -A5 : TPN -A6 : CPN -B7 : G C2p_exo anti -B8 : A C3p_endo anti -B9 : G C3p_endo anti -B10 : U C3p_endo anti -B11 : U C3p_endo anti -B12 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -B7-B8 : adjacent_5p upward -B8-B9 : adjacent_5p upward -B9-B10 : adjacent_5p upward -B11-B12 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 4 -Number of adjacent stackings = 4 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-B12 : GPN-C pairing parallel one_hbond -Residue conformations ------------------------------------------- -A1 : GPN -A2 : APN -A3 : APN -A4 : CPN -A5 : TPN -A6 : CPN -B7 : G C2p_exo anti -B8 : A C3p_endo anti -B9 : G C3p_endo anti -B10 : U C3p_endo anti -B11 : U C3p_endo anti -B12 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -B7-B8 : adjacent_5p upward -B8-B9 : adjacent_5p upward -B9-B10 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 3 -Number of adjacent stackings = 3 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-B12 : GPN-C pairing parallel one_hbond -Residue conformations ------------------------------------------- -A1 : GPN -A2 : APN -A3 : APN -A4 : CPN -A5 : TPN -A6 : CPN -B7 : G C2p_exo anti -B8 : A C3p_endo anti -B9 : G C2p_exo anti -B10 : U C3p_endo anti -B11 : U C3p_endo anti -B12 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -B7-B8 : adjacent_5p upward -B8-B9 : adjacent_5p upward -B9-B10 : adjacent_5p upward -B11-B12 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 4 -Number of adjacent stackings = 4 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-B12 : GPN-C pairing parallel one_hbond -Residue conformations ------------------------------------------- -A1 : GPN -A2 : APN -A3 : APN -A4 : CPN -A5 : TPN -A6 : CPN -B7 : G C2p_exo anti -B8 : A C3p_endo anti -B9 : G C2p_exo anti -B10 : U C3p_endo anti -B11 : U C3p_endo anti -B12 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -B7-B8 : adjacent_5p upward -B8-B9 : adjacent_5p upward -B9-B10 : adjacent_5p upward -B10-B11 : adjacent_5p upward -B11-B12 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 5 -Number of adjacent stackings = 5 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-B12 : GPN-C pairing parallel one_hbond -Residue conformations ------------------------------------------- -A1 : GPN -A2 : APN -A3 : APN -A4 : CPN -A5 : TPN -A6 : CPN -B7 : G C2p_exo anti -B8 : A C3p_endo anti -B9 : G C2p_exo anti -B10 : U C3p_endo anti -B11 : U C3p_endo anti -B12 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -B7-B8 : adjacent_5p upward -B8-B9 : adjacent_5p upward -B9-B10 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 3 -Number of adjacent stackings = 3 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-B12 : GPN-C pairing parallel one_hbond -Residue conformations ------------------------------------------- -A1 : GPN -A2 : APN -A3 : APN -A4 : CPN -A5 : TPN -A6 : CPN -B7 : G C2p_exo anti -B8 : A C3p_endo anti -B9 : G C3p_endo anti -B10 : U C3p_endo anti -B11 : U C3p_endo anti -B12 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -B7-B8 : adjacent_5p upward -B8-B9 : adjacent_5p upward -B9-B10 : adjacent_5p upward -B11-B12 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 4 -Number of adjacent stackings = 4 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-B12 : GPN-C pairing parallel one_hbond -Residue conformations ------------------------------------------- -A1 : GPN -A2 : APN -A3 : APN -A4 : CPN -A5 : TPN -A6 : CPN -B7 : G C2p_exo anti -B8 : A C3p_endo anti -B9 : G C2p_exo anti -B10 : U C3p_endo anti -B11 : U C3p_endo anti -B12 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -B7-B8 : adjacent_5p upward -B8-B9 : adjacent_5p upward -B9-B10 : adjacent_5p upward -B10-B11 : adjacent_5p upward -B11-B12 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 5 -Number of adjacent stackings = 5 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-B12 : GPN-C pairing parallel one_hbond -Residue conformations ------------------------------------------- -A1 : GPN -A2 : APN -A3 : APN -A4 : CPN -A5 : TPN -A6 : CPN -B7 : G C2p_exo anti -B8 : A C3p_endo anti -B9 : G C3p_endo anti -B10 : U C3p_endo anti -B11 : U C3p_endo anti -B12 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -B7-B8 : adjacent_5p upward -B8-B9 : adjacent_5p upward -B9-B10 : adjacent_5p upward -B11-B12 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 4 -Number of adjacent stackings = 4 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-B12 : GPN-C pairing parallel one_hbond -Residue conformations ------------------------------------------- -A1 : GPN -A2 : APN -A3 : APN -A4 : CPN -A5 : TPN -A6 : CPN -B7 : G C2p_exo anti -B8 : A C2p_exo anti -B9 : G C3p_endo anti -B10 : U C3p_endo anti -B11 : U C3p_endo anti -B12 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -B7-B8 : adjacent_5p upward -B8-B9 : adjacent_5p upward -B9-B10 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 3 -Number of adjacent stackings = 3 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-B12 : GPN-C pairing parallel one_hbond diff --git a/MCdata/17ra_MC b/MCdata/17ra_MC deleted file mode 100644 index 3653fe4dd70e4c1c6a825769dbee4cb8f7879747..0000000000000000000000000000000000000000 --- a/MCdata/17ra_MC +++ /dev/null @@ -1,571 +0,0 @@ -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : A O4p_endo anti -A7 : A C3p_endo anti -A8 : G C3p_endo anti -A9 : G C3p_endo anti -A10 : A C3p_endo anti -A11 : U C3p_exo anti -A12 : U C3p_exo anti -A13 : A C3p_exo anti -A14 : C C3p_endo anti -A15 : C C3p_endo anti -A16 : U C3p_endo anti -A17 : A C3p_endo anti -A18 : U C3p_endo anti -A19 : G C3p_endo anti -A20 : C C3p_endo anti -A21 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A19-A20 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A19 : outward -A6-A17 : outward -A9-A15 : outward -Number of stackings = 12 -Number of adjacent stackings = 9 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -A1-A21 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A20 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A19 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A18 : G-U Ww/Ws pairing antiparallel cis XXVIII -A5-A17 : U-A Ww/Ww pairing antiparallel cis XX -A8-A15 : G-C Ww/Ww pairing antiparallel cis XIX -A9-A14 : G-C Ww/Ww pairing antiparallel cis -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : A C4p_exo anti -A7 : A C3p_endo anti -A8 : G C3p_endo anti -A9 : G C3p_endo anti -A10 : A C3p_endo anti -A11 : U C3p_exo anti -A12 : U C3p_exo anti -A13 : A C3p_exo anti -A14 : C C3p_endo anti -A15 : C C3p_endo anti -A16 : U C3p_endo anti -A17 : A C3p_endo anti -A18 : U C3p_endo anti -A19 : G C3p_endo anti -A20 : C C3p_endo anti -A21 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A19-A20 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A19 : outward -A6-A17 : outward -A9-A15 : outward -Number of stackings = 11 -Number of adjacent stackings = 8 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -A1-A21 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A20 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A19 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A18 : G-U Ww/Ws pairing antiparallel cis XXVIII -A5-A17 : U-A Ww/Ww pairing antiparallel cis XX -A8-A15 : G-C Ww/Ww pairing antiparallel cis XIX -A9-A14 : G-C Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : A C4p_exo anti -A7 : A C3p_endo anti -A8 : G C3p_endo anti -A9 : G C3p_endo anti -A10 : A C3p_endo anti -A11 : U C3p_exo anti -A12 : U C3p_exo anti -A13 : A C3p_exo anti -A14 : C C3p_endo anti -A15 : C C3p_endo anti -A16 : U C3p_endo anti -A17 : A C3p_endo anti -A18 : U C3p_endo anti -A19 : G C3p_endo anti -A20 : C C3p_endo anti -A21 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A19-A20 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A19 : outward -A6-A17 : outward -A9-A15 : outward -Number of stackings = 12 -Number of adjacent stackings = 9 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -A1-A21 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A20 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A19 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A18 : G-U Ww/Ws pairing antiparallel cis XXVIII -A5-A17 : U-A Ww/Ww pairing antiparallel cis XX -A8-A15 : G-C Ww/Ww pairing antiparallel cis XIX -A9-A14 : G-C Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : A C4p_exo anti -A7 : A C3p_endo anti -A8 : G C3p_endo anti -A9 : G C3p_endo anti -A10 : A C3p_endo anti -A11 : U C3p_exo anti -A12 : U C3p_exo anti -A13 : A C3p_exo anti -A14 : C C3p_endo anti -A15 : C C3p_endo anti -A16 : U C3p_endo anti -A17 : A C3p_endo anti -A18 : U C3p_endo anti -A19 : G C3p_endo anti -A20 : C C3p_endo anti -A21 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A19-A20 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A19 : outward -A6-A17 : outward -Number of stackings = 13 -Number of adjacent stackings = 11 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A1-A21 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A20 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A19 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A18 : G-U Ww/Ws pairing antiparallel cis XXVIII -A5-A17 : U-A Ww/Ww pairing antiparallel cis XX -A8-A15 : G-C Ww/Ww pairing antiparallel cis XIX -A9-A14 : G-C Ww/Ww pairing antiparallel cis -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : A O4p_endo anti -A7 : A C3p_endo anti -A8 : G C3p_endo anti -A9 : G C3p_endo anti -A10 : A C3p_endo anti -A11 : U C3p_exo anti -A12 : U C3p_exo anti -A13 : A C3p_exo anti -A14 : C C3p_endo anti -A15 : C C3p_endo anti -A16 : U C3p_endo anti -A17 : A C3p_endo anti -A18 : U C3p_endo anti -A19 : G C3p_endo anti -A20 : C C3p_endo anti -A21 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A19-A20 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A19 : outward -A6-A17 : outward -A9-A15 : outward -Number of stackings = 13 -Number of adjacent stackings = 10 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -A1-A21 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A20 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A19 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A18 : G-U Ww/Ws pairing antiparallel cis XXVIII -A5-A17 : U-A Ww/Ww pairing antiparallel cis XX -A8-A15 : G-C Ww/Ww pairing antiparallel cis XIX -A9-A14 : G-C Ww/Ww pairing antiparallel cis -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : A O4p_endo anti -A7 : A C3p_endo anti -A8 : G C3p_endo anti -A9 : G C3p_endo anti -A10 : A C3p_endo anti -A11 : U C3p_exo anti -A12 : U C3p_exo anti -A13 : A C3p_exo anti -A14 : C C3p_endo anti -A15 : C C3p_endo anti -A16 : U C3p_endo anti -A17 : A C3p_endo anti -A18 : U C3p_endo anti -A19 : G C3p_endo anti -A20 : C C3p_endo anti -A21 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A19-A20 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A19 : outward -A6-A17 : outward -Number of stackings = 11 -Number of adjacent stackings = 9 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A1-A21 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A20 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A19 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A18 : G-U Ww/Ws pairing antiparallel cis XXVIII -A5-A17 : U-A Ww/Ww pairing antiparallel cis XX -A8-A15 : G-C Ww/Ww pairing antiparallel cis XIX -A9-A14 : G-C Ww/Ww pairing antiparallel cis -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : A C3p_endo anti -A7 : A C3p_endo anti -A8 : G C3p_endo anti -A9 : G C3p_endo anti -A10 : A C3p_endo anti -A11 : U C3p_exo anti -A12 : U C3p_exo anti -A13 : A C3p_exo anti -A14 : C C3p_endo anti -A15 : C C3p_endo anti -A16 : U C3p_endo anti -A17 : A C3p_endo anti -A18 : U C3p_endo anti -A19 : G C3p_endo anti -A20 : C C3p_endo anti -A21 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A19-A20 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A19 : outward -A6-A17 : outward -Number of stackings = 12 -Number of adjacent stackings = 10 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A1-A21 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A20 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A19 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A18 : G-U Ww/Ws pairing antiparallel cis XXVIII -A5-A17 : U-A Ww/Ww pairing antiparallel cis XX -A6-A16 : A-U Ww/Ww pairing antiparallel cis XX -A8-A15 : G-C Ww/Ww pairing antiparallel cis XIX -A9-A14 : G-C Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : A C3p_endo anti -A7 : A C3p_endo anti -A8 : G C3p_endo anti -A9 : G C3p_endo anti -A10 : A C3p_endo anti -A11 : U C3p_exo anti -A12 : U C3p_exo anti -A13 : A C3p_exo anti -A14 : C C3p_endo anti -A15 : C C3p_endo anti -A16 : U C3p_endo anti -A17 : A C3p_endo anti -A18 : U C3p_endo anti -A19 : G C3p_endo anti -A20 : C C3p_endo anti -A21 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A19-A20 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A19 : outward -A6-A17 : outward -Number of stackings = 13 -Number of adjacent stackings = 11 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A1-A21 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A20 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A19 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A18 : G-U Ww/Ws pairing antiparallel cis XXVIII -A5-A17 : U-A Ww/Ww pairing antiparallel cis XX -A6-A16 : A-U Ww/Ww pairing antiparallel cis XX -A8-A15 : G-C Ww/Ww pairing antiparallel cis XIX -A9-A14 : G-C Ww/Ww pairing antiparallel cis -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : A C3p_endo anti -A7 : A C3p_endo anti -A8 : G C3p_endo anti -A9 : G C3p_endo anti -A10 : A C3p_endo anti -A11 : U C3p_exo anti -A12 : U C3p_exo anti -A13 : A C3p_exo anti -A14 : C C3p_endo anti -A15 : C C3p_endo anti -A16 : U C3p_endo anti -A17 : A C3p_endo anti -A18 : U C3p_endo anti -A19 : G C3p_endo anti -A20 : C C3p_endo anti -A21 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A19-A20 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A19 : outward -A6-A17 : outward -Number of stackings = 12 -Number of adjacent stackings = 10 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A1-A21 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A20 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A19 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A18 : G-U Ww/Ws pairing antiparallel cis XXVIII -A5-A17 : U-A Ww/Ww pairing antiparallel cis XX -A6-A16 : A-U Ww/Ww pairing antiparallel cis XX -A8-A15 : G-C Ww/Ww pairing antiparallel cis XIX -A9-A14 : G-C Ww/Ww pairing antiparallel cis -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : A C3p_endo anti -A7 : A C3p_endo anti -A8 : G C3p_endo anti -A9 : G C3p_endo anti -A10 : A C3p_endo anti -A11 : U C3p_exo anti -A12 : U C3p_exo anti -A13 : A C3p_exo anti -A14 : C C3p_endo anti -A15 : C C3p_endo anti -A16 : U C3p_endo anti -A17 : A C3p_endo anti -A18 : U C3p_endo anti -A19 : G C3p_endo anti -A20 : C C3p_endo anti -A21 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A19-A20 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A19 : outward -A6-A17 : outward -Number of stackings = 12 -Number of adjacent stackings = 10 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A1-A21 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A20 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A19 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A18 : G-U Ww/Ws pairing antiparallel cis XXVIII -A5-A17 : U-A Ww/Ww pairing antiparallel cis XX -A6-A16 : A-U Ww/Ww pairing antiparallel cis XX -A8-A15 : G-C Ww/Ww pairing antiparallel cis XIX -A9-A14 : G-C Ww/Ww pairing antiparallel cis -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : A C3p_endo anti -A7 : A C3p_endo anti -A8 : G C3p_endo anti -A9 : G C3p_endo anti -A10 : A C3p_endo anti -A11 : U C3p_exo anti -A12 : U C3p_exo anti -A13 : A C3p_exo anti -A14 : C C3p_endo anti -A15 : C C3p_endo anti -A16 : U C3p_endo anti -A17 : A C3p_endo anti -A18 : U C3p_endo anti -A19 : G C3p_endo anti -A20 : C C3p_endo anti -A21 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A19-A20 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A19 : outward -A6-A17 : outward -Number of stackings = 12 -Number of adjacent stackings = 10 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A1-A21 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A20 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A19 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A18 : G-U Ww/Ws pairing antiparallel cis XXVIII -A5-A17 : U-A Ww/Ww pairing antiparallel cis XX -A6-A16 : A-U Ww/Ww pairing antiparallel cis XX -A8-A15 : G-C Ww/Ww pairing antiparallel cis XIX -A9-A14 : G-C Ww/Ww pairing antiparallel cis -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : A C3p_endo anti -A7 : A C3p_endo anti -A8 : G C3p_endo anti -A9 : G C3p_endo anti -A10 : A C3p_endo anti -A11 : U C3p_exo anti -A12 : U C3p_exo anti -A13 : A C3p_exo anti -A14 : C C3p_endo anti -A15 : C C3p_endo anti -A16 : U C3p_endo anti -A17 : A C3p_endo anti -A18 : U C3p_endo anti -A19 : G C3p_endo anti -A20 : C C3p_endo anti -A21 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A19-A20 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A19 : outward -A6-A17 : outward -Number of stackings = 12 -Number of adjacent stackings = 10 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A1-A21 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A20 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A19 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A18 : G-U Ww/Ws pairing antiparallel cis XXVIII -A5-A17 : U-A Ww/Ww pairing antiparallel cis XX -A6-A16 : A-U Ww/Ww pairing antiparallel cis XX -A8-A15 : G-C Ww/Ww pairing antiparallel cis XIX -A9-A14 : G-C Ww/Ww pairing antiparallel cis XIX diff --git a/MCdata/1a1t_MC b/MCdata/1a1t_MC deleted file mode 100644 index 9904d7d6fab8775c47ce93e61809444fb3cc470f..0000000000000000000000000000000000000000 --- a/MCdata/1a1t_MC +++ /dev/null @@ -1,2627 +0,0 @@ -Residue conformations ------------------------------------------- -B201 : G C2p_exo anti -B202 : G C2p_exo anti -B203 : A C3p_endo anti -B204 : C O4p_exo anti -B205 : U C3p_endo anti -B206 : A C3p_endo anti -B207 : G C3p_endo anti -B208 : C O4p_exo anti -B209 : G O4p_exo anti -B210 : G C4p_endo anti -B211 : A C2p_endo anti -B212 : G O4p_endo anti -B213 : G C2p_exo anti -B214 : C C2p_exo anti -B215 : U C4p_exo anti -B216 : A C4p_exo anti -B217 : G C4p_exo anti -B218 : U C3p_endo anti -B219 : C C3p_endo anti -B220 : C C3p_endo anti -A1 : MET -A2 : GLN -A3 : LYS -A4 : GLY -A5 : ASN -A6 : PHE -A7 : ARG -A8 : ASN -A9 : GLN -A10 : ARG -A11 : LYS -A12 : THR -A13 : VAL -A14 : LYS -A15 : CYS -A16 : PHE -A17 : ASN -A18 : CYS -A19 : GLY -A20 : LYS -A21 : GLU -A22 : GLY -A23 : HIS -A24 : ILE -A25 : ALA -A26 : LYS -A27 : ASN -A28 : CYS -A29 : ARG -A30 : ALA -A31 : PRO -A32 : ARG -A33 : LYS -A34 : LYS -A35 : GLY -A36 : CYS -A37 : TRP -A38 : LYS -A39 : CYS -A40 : GLY -A41 : LYS -A42 : GLU -A43 : GLY -A44 : HIS -A45 : GLN -A46 : MET -A47 : LYS -A48 : ASP -A49 : CYS -A50 : THR -A51 : GLU -A52 : ARG -A53 : GLN -A54 : ALA -A55 : ASN -A56 : ZN -A57 : ZN -Adjacent stackings ---------------------------------------------- -B201-B202 : adjacent_5p upward -B202-B203 : adjacent_5p upward -B203-B204 : adjacent_5p upward -B204-B205 : adjacent_5p upward -B205-B206 : adjacent_5p upward -B206-B207 : adjacent_5p upward -B207-B208 : adjacent_5p upward -B213-B214 : adjacent_5p upward -B214-B215 : adjacent_5p upward -B216-B217 : adjacent_5p upward -B217-B218 : adjacent_5p upward -B218-B219 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 12 -Number of adjacent stackings = 12 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A32-B211 : ARG-A pairing one_hbond -A46-B210 : MET-G pairing one_hbond -B201-B220 : G-C Ww/Ww pairing antiparallel cis XIX -B202-B219 : G-C Ww/Ww pairing antiparallel cis XIX -B203-B218 : A-U Ww/Ww pairing antiparallel cis XX -B204-B217 : C-G Ww/Ww pairing antiparallel cis XIX -B205-B216 : U-A Ww/Ww pairing antiparallel cis XX -B206-B215 : A-U Ww/Ww pairing antiparallel cis XX -B207-B214 : G-C Ww/Ww pairing antiparallel cis -B208-B213 : C-G Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -B201 : G C3p_endo anti -B202 : G C3p_endo anti -B203 : A C3p_endo anti -B204 : C C3p_endo anti -B205 : U C4p_exo anti -B206 : A C4p_exo anti -B207 : G C4p_exo anti -B208 : C C3p_endo anti -B209 : G C3p_endo anti -B210 : G C4p_endo anti -B211 : A C2p_endo anti -B212 : G C3p_endo anti -B213 : G C2p_exo anti -B214 : C C2p_exo anti -B215 : U C4p_endo anti -B216 : A C4p_exo anti -B217 : G C4p_exo anti -B218 : U C4p_exo anti -B219 : C C3p_endo anti -B220 : C C3p_endo anti -A1 : MET -A2 : GLN -A3 : LYS -A4 : GLY -A5 : ASN -A6 : PHE -A7 : ARG -A8 : ASN -A9 : GLN -A10 : ARG -A11 : LYS -A12 : THR -A13 : VAL -A14 : LYS -A15 : CYS -A16 : PHE -A17 : ASN -A18 : CYS -A19 : GLY -A20 : LYS -A21 : GLU -A22 : GLY -A23 : HIS -A24 : ILE -A25 : ALA -A26 : LYS -A27 : ASN -A28 : CYS -A29 : ARG -A30 : ALA -A31 : PRO -A32 : ARG -A33 : LYS -A34 : LYS -A35 : GLY -A36 : CYS -A37 : TRP -A38 : LYS -A39 : CYS -A40 : GLY -A41 : LYS -A42 : GLU -A43 : GLY -A44 : HIS -A45 : GLN -A46 : MET -A47 : LYS -A48 : ASP -A49 : CYS -A50 : THR -A51 : GLU -A52 : ARG -A53 : GLN -A54 : ALA -A55 : ASN -A56 : ZN -A57 : ZN -Adjacent stackings ---------------------------------------------- -B202-B203 : adjacent_5p upward -B203-B204 : adjacent_5p upward -B204-B205 : adjacent_5p upward -B206-B207 : adjacent_5p upward -B207-B208 : adjacent_5p upward -B208-B209 : adjacent_5p upward -B213-B214 : adjacent_5p upward -B214-B215 : adjacent_5p upward -B216-B217 : adjacent_5p upward -B217-B218 : adjacent_5p upward -B218-B219 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -B209-B213 : outward -Number of stackings = 12 -Number of adjacent stackings = 11 -Number of non adjacent stackings = 1 -Base-pairs ------------------------------------------------------ -A32-B211 : ARG-A pairing one_hbond -B201-B220 : G-C Ww/Ww pairing antiparallel cis XIX -B202-B219 : G-C Ww/Ww pairing antiparallel cis XIX -B203-B218 : A-U Ww/Ww pairing antiparallel cis XX -B204-B217 : C-G Ww/Ww pairing antiparallel cis -B205-B216 : U-A Ww/Ww pairing antiparallel cis XX -B206-B215 : A-U Ww/Ww pairing antiparallel cis XX -B207-B214 : G-C Ww/Ww pairing antiparallel cis XIX -B208-B213 : C-G Ww/Ww pairing antiparallel cis one_hbond -B209-B212 : G-G Bs/O2P pairing -Residue conformations ------------------------------------------- -B201 : G C3p_endo anti -B202 : G C3p_endo anti -B203 : A C4p_exo anti -B204 : C C3p_endo anti -B205 : U C4p_exo anti -B206 : A C4p_exo anti -B207 : G C4p_exo anti -B208 : C C3p_endo anti -B209 : G C2p_exo anti -B210 : G C4p_endo anti -B211 : A C2p_endo anti -B212 : G C4p_exo anti -B213 : G C1p_endo anti -B214 : C C2p_exo anti -B215 : U O4p_exo anti -B216 : A C4p_exo anti -B217 : G C3p_endo anti -B218 : U C3p_endo anti -B219 : C C3p_endo anti -B220 : C C3p_endo anti -A1 : MET -A2 : GLN -A3 : LYS -A4 : GLY -A5 : ASN -A6 : PHE -A7 : ARG -A8 : ASN -A9 : GLN -A10 : ARG -A11 : LYS -A12 : THR -A13 : VAL -A14 : LYS -A15 : CYS -A16 : PHE -A17 : ASN -A18 : CYS -A19 : GLY -A20 : LYS -A21 : GLU -A22 : GLY -A23 : HIS -A24 : ILE -A25 : ALA -A26 : LYS -A27 : ASN -A28 : CYS -A29 : ARG -A30 : ALA -A31 : PRO -A32 : ARG -A33 : LYS -A34 : LYS -A35 : GLY -A36 : CYS -A37 : TRP -A38 : LYS -A39 : CYS -A40 : GLY -A41 : LYS -A42 : GLU -A43 : GLY -A44 : HIS -A45 : GLN -A46 : MET -A47 : LYS -A48 : ASP -A49 : CYS -A50 : THR -A51 : GLU -A52 : ARG -A53 : GLN -A54 : ALA -A55 : ASN -A56 : ZN -A57 : ZN -Adjacent stackings ---------------------------------------------- -B203-B204 : adjacent_5p upward -B204-B205 : adjacent_5p upward -B205-B206 : adjacent_5p upward -B206-B207 : adjacent_5p upward -B207-B208 : adjacent_5p upward -B213-B214 : adjacent_5p upward -B214-B215 : adjacent_5p upward -B216-B217 : adjacent_5p upward -B217-B218 : adjacent_5p upward -B218-B219 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -B209-B213 : outward -Number of stackings = 11 -Number of adjacent stackings = 10 -Number of non adjacent stackings = 1 -Base-pairs ------------------------------------------------------ -A32-B211 : ARG-A pairing one_hbond -B201-B220 : G-C Ww/Ww pairing antiparallel cis XIX -B202-B219 : G-C Ww/Ww pairing antiparallel cis XIX -B203-B218 : A-U Ww/Ww pairing antiparallel cis XX -B204-B217 : C-G Ww/Ww pairing antiparallel cis XIX -B205-B216 : U-A Ww/Ww pairing antiparallel cis XX -B206-B215 : A-U Ww/Ww pairing antiparallel cis XX -B207-B214 : G-C Ww/Ww pairing antiparallel cis XIX -B208-B213 : C-G Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -B201 : G C3p_endo anti -B202 : G C3p_endo anti -B203 : A C3p_endo anti -B204 : C O4p_exo anti -B205 : U C2p_exo anti -B206 : A C3p_endo anti -B207 : G C4p_exo anti -B208 : C C4p_exo anti -B209 : G C3p_endo anti -B210 : G C4p_endo anti -B211 : A C2p_endo anti -B212 : G C4p_exo anti -B213 : G C1p_endo anti -B214 : C C2p_exo anti -B215 : U C4p_exo anti -B216 : A C4p_exo anti -B217 : G C4p_exo anti -B218 : U C4p_exo anti -B219 : C C3p_endo anti -B220 : C C3p_endo anti -A1 : MET -A2 : GLN -A3 : LYS -A4 : GLY -A5 : ASN -A6 : PHE -A7 : ARG -A8 : ASN -A9 : GLN -A10 : ARG -A11 : LYS -A12 : THR -A13 : VAL -A14 : LYS -A15 : CYS -A16 : PHE -A17 : ASN -A18 : CYS -A19 : GLY -A20 : LYS -A21 : GLU -A22 : GLY -A23 : HIS -A24 : ILE -A25 : ALA -A26 : LYS -A27 : ASN -A28 : CYS -A29 : ARG -A30 : ALA -A31 : PRO -A32 : ARG -A33 : LYS -A34 : LYS -A35 : GLY -A36 : CYS -A37 : TRP -A38 : LYS -A39 : CYS -A40 : GLY -A41 : LYS -A42 : GLU -A43 : GLY -A44 : HIS -A45 : GLN -A46 : MET -A47 : LYS -A48 : ASP -A49 : CYS -A50 : THR -A51 : GLU -A52 : ARG -A53 : GLN -A54 : ALA -A55 : ASN -A56 : ZN -A57 : ZN -Adjacent stackings ---------------------------------------------- -B201-B202 : adjacent_5p upward -B203-B204 : adjacent_5p upward -B204-B205 : adjacent_5p upward -B206-B207 : adjacent_5p upward -B208-B209 : adjacent_5p upward -B213-B214 : adjacent_5p upward -B214-B215 : adjacent_5p upward -B216-B217 : adjacent_5p upward -B217-B218 : adjacent_5p upward -B218-B219 : adjacent_5p upward -B219-B220 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -B206-B216 : outward -Number of stackings = 12 -Number of adjacent stackings = 11 -Number of non adjacent stackings = 1 -Base-pairs ------------------------------------------------------ -A32-B211 : ARG-A pairing one_hbond -B201-B220 : G-C Ww/Ww pairing antiparallel cis XIX -B202-B219 : G-C Ww/Ww pairing antiparallel cis XIX -B203-B218 : A-U Ww/Ww pairing antiparallel cis XX -B204-B217 : C-G Ww/Ww pairing antiparallel cis XIX -B205-B216 : U-A Ww/Ww pairing antiparallel cis XX -B206-B215 : A-U Ww/Ww pairing antiparallel cis XX -B207-B214 : G-C Ww/Ww pairing antiparallel cis XIX -B208-B213 : C-G Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -B201 : G C3p_endo anti -B202 : G C3p_endo anti -B203 : A C4p_exo anti -B204 : C C4p_exo anti -B205 : U C4p_exo anti -B206 : A C4p_exo anti -B207 : G C4p_exo anti -B208 : C C4p_exo anti -B209 : G C4p_exo anti -B210 : G C4p_endo anti -B211 : A C3p_exo anti -B212 : G C1p_exo anti -B213 : G C2p_exo anti -B214 : C C2p_exo anti -B215 : U C2p_exo anti -B216 : A C4p_exo anti -B217 : G C4p_exo anti -B218 : U C3p_endo anti -B219 : C C3p_endo anti -B220 : C C3p_endo anti -A1 : MET -A2 : GLN -A3 : LYS -A4 : GLY -A5 : ASN -A6 : PHE -A7 : ARG -A8 : ASN -A9 : GLN -A10 : ARG -A11 : LYS -A12 : THR -A13 : VAL -A14 : LYS -A15 : CYS -A16 : PHE -A17 : ASN -A18 : CYS -A19 : GLY -A20 : LYS -A21 : GLU -A22 : GLY -A23 : HIS -A24 : ILE -A25 : ALA -A26 : LYS -A27 : ASN -A28 : CYS -A29 : ARG -A30 : ALA -A31 : PRO -A32 : ARG -A33 : LYS -A34 : LYS -A35 : GLY -A36 : CYS -A37 : TRP -A38 : LYS -A39 : CYS -A40 : GLY -A41 : LYS -A42 : GLU -A43 : GLY -A44 : HIS -A45 : GLN -A46 : MET -A47 : LYS -A48 : ASP -A49 : CYS -A50 : THR -A51 : GLU -A52 : ARG -A53 : GLN -A54 : ALA -A55 : ASN -A56 : ZN -A57 : ZN -Adjacent stackings ---------------------------------------------- -B201-B202 : adjacent_5p upward -B202-B203 : adjacent_5p upward -B203-B204 : adjacent_5p upward -B204-B205 : adjacent_5p upward -B205-B206 : adjacent_5p upward -B206-B207 : adjacent_5p upward -B207-B208 : adjacent_5p upward pairing -B208-B209 : adjacent_5p upward -B213-B214 : adjacent_5p upward -B214-B215 : adjacent_5p upward -B216-B217 : adjacent_5p upward -B217-B218 : adjacent_5p upward -B218-B219 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 13 -Number of adjacent stackings = 13 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A32-B211 : ARG-A pairing one_hbond -A46-B210 : MET-G pairing one_hbond -B201-B220 : G-C Ww/Ww pairing antiparallel cis XIX -B202-B219 : G-C Ww/Ww pairing antiparallel cis XIX -B203-B218 : A-U Ww/Ww pairing antiparallel cis XX -B204-B217 : C-G Ww/Ww pairing antiparallel cis -B205-B216 : U-A Ww/Ww pairing antiparallel cis XX -B206-B215 : A-U Ww/Ww pairing antiparallel cis XX -B207-B208 : G-C O2'/Hh adjacent_5p upward pairing -B207-B214 : G-C Ww/Ww pairing antiparallel cis XIX -B208-B213 : C-G Ww/Ww pairing antiparallel cis -Residue conformations ------------------------------------------- -B201 : G C3p_endo anti -B202 : G C3p_endo anti -B203 : A C3p_endo anti -B204 : C C3p_endo anti -B205 : U C4p_exo anti -B206 : A C3p_endo anti -B207 : G C4p_exo anti -B208 : C C4p_exo anti -B209 : G C3p_endo anti -B210 : G C4p_endo anti -B211 : A C2p_endo anti -B212 : G O4p_endo anti -B213 : G C2p_exo anti -B214 : C C2p_exo anti -B215 : U C4p_exo anti -B216 : A C4p_exo anti -B217 : G C4p_exo anti -B218 : U C4p_exo anti -B219 : C C3p_endo anti -B220 : C C3p_endo anti -A1 : MET -A2 : GLN -A3 : LYS -A4 : GLY -A5 : ASN -A6 : PHE -A7 : ARG -A8 : ASN -A9 : GLN -A10 : ARG -A11 : LYS -A12 : THR -A13 : VAL -A14 : LYS -A15 : CYS -A16 : PHE -A17 : ASN -A18 : CYS -A19 : GLY -A20 : LYS -A21 : GLU -A22 : GLY -A23 : HIS -A24 : ILE -A25 : ALA -A26 : LYS -A27 : ASN -A28 : CYS -A29 : ARG -A30 : ALA -A31 : PRO -A32 : ARG -A33 : LYS -A34 : LYS -A35 : GLY -A36 : CYS -A37 : TRP -A38 : LYS -A39 : CYS -A40 : GLY -A41 : LYS -A42 : GLU -A43 : GLY -A44 : HIS -A45 : GLN -A46 : MET -A47 : LYS -A48 : ASP -A49 : CYS -A50 : THR -A51 : GLU -A52 : ARG -A53 : GLN -A54 : ALA -A55 : ASN -A56 : ZN -A57 : ZN -Adjacent stackings ---------------------------------------------- -B203-B204 : adjacent_5p upward -B204-B205 : adjacent_5p upward -B205-B206 : adjacent_5p upward -B206-B207 : adjacent_5p upward -B207-B208 : adjacent_5p upward -B208-B209 : adjacent_5p upward -B213-B214 : adjacent_5p upward -B214-B215 : adjacent_5p upward -B216-B217 : adjacent_5p upward -B217-B218 : adjacent_5p upward -B218-B219 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 11 -Number of adjacent stackings = 11 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A32-B211 : ARG-A pairing one_hbond -A46-B210 : MET-G pairing one_hbond -B201-B220 : G-C Ww/Ww pairing antiparallel cis XIX -B202-B219 : G-C Ww/Ww pairing antiparallel cis XIX -B203-B218 : A-U Ww/Ww pairing antiparallel cis XX -B204-B217 : C-G Ww/Ww pairing antiparallel cis -B205-B216 : U-A Ww/Ww pairing antiparallel cis XX -B206-B215 : A-U Ww/Ww pairing antiparallel cis XX -B207-B214 : G-C Ww/Ww pairing antiparallel cis -B208-B213 : C-G Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -B201 : G C3p_endo anti -B202 : G C3p_endo anti -B203 : A C3p_endo anti -B204 : C C3p_endo anti -B205 : U C4p_exo anti -B206 : A C3p_endo anti -B207 : G C3p_endo anti -B208 : C O4p_exo anti -B209 : G C2p_exo anti -B210 : G C4p_endo anti -B211 : A C2p_endo anti -B212 : G C4p_exo anti -B213 : G C2p_exo anti -B214 : C C3p_endo anti -B215 : U C3p_endo anti -B216 : A C4p_exo anti -B217 : G C4p_exo anti -B218 : U C4p_exo anti -B219 : C C4p_exo anti -B220 : C C3p_endo anti -A1 : MET -A2 : GLN -A3 : LYS -A4 : GLY -A5 : ASN -A6 : PHE -A7 : ARG -A8 : ASN -A9 : GLN -A10 : ARG -A11 : LYS -A12 : THR -A13 : VAL -A14 : LYS -A15 : CYS -A16 : PHE -A17 : ASN -A18 : CYS -A19 : GLY -A20 : LYS -A21 : GLU -A22 : GLY -A23 : HIS -A24 : ILE -A25 : ALA -A26 : LYS -A27 : ASN -A28 : CYS -A29 : ARG -A30 : ALA -A31 : PRO -A32 : ARG -A33 : LYS -A34 : LYS -A35 : GLY -A36 : CYS -A37 : TRP -A38 : LYS -A39 : CYS -A40 : GLY -A41 : LYS -A42 : GLU -A43 : GLY -A44 : HIS -A45 : GLN -A46 : MET -A47 : LYS -A48 : ASP -A49 : CYS -A50 : THR -A51 : GLU -A52 : ARG -A53 : GLN -A54 : ALA -A55 : ASN -A56 : ZN -A57 : ZN -Adjacent stackings ---------------------------------------------- -B202-B203 : adjacent_5p upward -B203-B204 : adjacent_5p upward -B204-B205 : adjacent_5p upward -B206-B207 : adjacent_5p upward -B207-B208 : adjacent_5p upward -B213-B214 : adjacent_5p upward -B214-B215 : adjacent_5p upward -B216-B217 : adjacent_5p upward -B217-B218 : adjacent_5p upward -B218-B219 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 10 -Number of adjacent stackings = 10 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A32-B211 : ARG-A pairing one_hbond -A46-B210 : MET-G pairing one_hbond -B201-B220 : G-C Ww/Ww pairing antiparallel cis XIX -B202-B219 : G-C Ww/Ww pairing antiparallel cis XIX -B203-B218 : A-U Ww/Ww pairing antiparallel cis XX -B204-B217 : C-G Ww/Ww pairing antiparallel cis -B205-B216 : U-A Ww/Ww pairing antiparallel cis XX -B206-B215 : A-U Ww/Ww pairing antiparallel cis XX -B207-B214 : G-C Ww/Ww pairing antiparallel cis XIX -B208-B213 : C-G Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -B201 : G C3p_endo anti -B202 : G C3p_endo anti -B203 : A C3p_endo anti -B204 : C C3p_endo anti -B205 : U C4p_exo anti -B206 : A C4p_exo anti -B207 : G C4p_exo anti -B208 : C C4p_exo anti -B209 : G C2p_exo anti -B210 : G O4p_exo anti -B211 : A C2p_endo anti -B212 : G C3p_endo anti -B213 : G C2p_exo anti -B214 : C C3p_endo anti -B215 : U C4p_exo anti -B216 : A C4p_exo anti -B217 : G C4p_exo anti -B218 : U C3p_endo anti -B219 : C C3p_endo anti -B220 : C C3p_endo anti -A1 : MET -A2 : GLN -A3 : LYS -A4 : GLY -A5 : ASN -A6 : PHE -A7 : ARG -A8 : ASN -A9 : GLN -A10 : ARG -A11 : LYS -A12 : THR -A13 : VAL -A14 : LYS -A15 : CYS -A16 : PHE -A17 : ASN -A18 : CYS -A19 : GLY -A20 : LYS -A21 : GLU -A22 : GLY -A23 : HIS -A24 : ILE -A25 : ALA -A26 : LYS -A27 : ASN -A28 : CYS -A29 : ARG -A30 : ALA -A31 : PRO -A32 : ARG -A33 : LYS -A34 : LYS -A35 : GLY -A36 : CYS -A37 : TRP -A38 : LYS -A39 : CYS -A40 : GLY -A41 : LYS -A42 : GLU -A43 : GLY -A44 : HIS -A45 : GLN -A46 : MET -A47 : LYS -A48 : ASP -A49 : CYS -A50 : THR -A51 : GLU -A52 : ARG -A53 : GLN -A54 : ALA -A55 : ASN -A56 : ZN -A57 : ZN -Adjacent stackings ---------------------------------------------- -B201-B202 : adjacent_5p upward -B203-B204 : adjacent_5p upward -B204-B205 : adjacent_5p upward -B206-B207 : adjacent_5p upward -B207-B208 : adjacent_5p upward -B208-B209 : adjacent_5p upward -B213-B214 : adjacent_5p upward -B214-B215 : adjacent_5p upward -B216-B217 : adjacent_5p upward -B217-B218 : adjacent_5p upward -B218-B219 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 11 -Number of adjacent stackings = 11 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A32-B211 : ARG-A pairing one_hbond -A46-B210 : MET-G pairing one_hbond -B201-B220 : G-C Ww/Ww pairing antiparallel cis XIX -B202-B219 : G-C Ww/Ww pairing antiparallel cis XIX -B203-B218 : A-U Ww/Ww pairing antiparallel cis XX -B204-B217 : C-G Ww/Ww pairing antiparallel cis XIX -B205-B216 : U-A Ww/Ww pairing antiparallel cis XX -B206-B215 : A-U Ww/Ww pairing antiparallel cis XX -B207-B214 : G-C Ww/Ww pairing antiparallel cis XIX -B208-B213 : C-G Wh/Wh pairing antiparallel cis one_hbond -Residue conformations ------------------------------------------- -B201 : G C4p_exo syn -B202 : G C2p_exo anti -B203 : A C4p_exo anti -B204 : C C4p_exo anti -B205 : U C3p_endo anti -B206 : A C4p_exo anti -B207 : G C3p_endo anti -B208 : C O4p_exo anti -B209 : G C2p_exo anti -B210 : G C4p_endo anti -B211 : A C2p_endo anti -B212 : G C4p_exo anti -B213 : G O4p_exo anti -B214 : C C2p_exo anti -B215 : U C4p_exo anti -B216 : A C4p_exo anti -B217 : G C4p_exo anti -B218 : U C4p_exo anti -B219 : C C3p_endo anti -B220 : C C1p_endo anti -A1 : MET -A2 : GLN -A3 : LYS -A4 : GLY -A5 : ASN -A6 : PHE -A7 : ARG -A8 : ASN -A9 : GLN -A10 : ARG -A11 : LYS -A12 : THR -A13 : VAL -A14 : LYS -A15 : CYS -A16 : PHE -A17 : ASN -A18 : CYS -A19 : GLY -A20 : LYS -A21 : GLU -A22 : GLY -A23 : HIS -A24 : ILE -A25 : ALA -A26 : LYS -A27 : ASN -A28 : CYS -A29 : ARG -A30 : ALA -A31 : PRO -A32 : ARG -A33 : LYS -A34 : LYS -A35 : GLY -A36 : CYS -A37 : TRP -A38 : LYS -A39 : CYS -A40 : GLY -A41 : LYS -A42 : GLU -A43 : GLY -A44 : HIS -A45 : GLN -A46 : MET -A47 : LYS -A48 : ASP -A49 : CYS -A50 : THR -A51 : GLU -A52 : ARG -A53 : GLN -A54 : ALA -A55 : ASN -A56 : ZN -A57 : ZN -Adjacent stackings ---------------------------------------------- -B202-B203 : adjacent_5p upward -B203-B204 : adjacent_5p upward -B204-B205 : adjacent_5p upward -B206-B207 : adjacent_5p upward -B207-B208 : adjacent_5p upward -B208-B209 : adjacent_5p upward -B213-B214 : adjacent_5p upward -B214-B215 : adjacent_5p upward -B216-B217 : adjacent_5p upward -B217-B218 : adjacent_5p upward -B218-B219 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 11 -Number of adjacent stackings = 11 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A32-B211 : ARG-A pairing one_hbond -A46-B210 : MET-G pairing one_hbond -B201-B220 : G-C Ww/Ww pairing antiparallel cis XIX -B202-B219 : G-C Ww/Ww pairing antiparallel cis XIX -B203-B218 : A-U Ww/Ww pairing antiparallel cis XX -B204-B217 : C-G Ww/Ww pairing antiparallel cis XIX -B205-B216 : U-A Ww/Ww pairing antiparallel cis XX -B206-B215 : A-U Ww/Ww pairing antiparallel cis XX -B207-B214 : G-C Ww/Ww pairing antiparallel cis XIX -B208-B213 : C-G Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -B201 : G C3p_endo anti -B202 : G C3p_endo anti -B203 : A C3p_endo anti -B204 : C C3p_endo anti -B205 : U C3p_endo anti -B206 : A C4p_exo anti -B207 : G C4p_exo anti -B208 : C O4p_exo anti -B209 : G C1p_endo anti -B210 : G C4p_endo anti -B211 : A C2p_endo anti -B212 : G C3p_endo anti -B213 : G C2p_exo anti -B214 : C C2p_exo anti -B215 : U C3p_endo anti -B216 : A C4p_exo anti -B217 : G C4p_exo anti -B218 : U C4p_exo anti -B219 : C C4p_exo anti -B220 : C C3p_endo anti -A1 : MET -A2 : GLN -A3 : LYS -A4 : GLY -A5 : ASN -A6 : PHE -A7 : ARG -A8 : ASN -A9 : GLN -A10 : ARG -A11 : LYS -A12 : THR -A13 : VAL -A14 : LYS -A15 : CYS -A16 : PHE -A17 : ASN -A18 : CYS -A19 : GLY -A20 : LYS -A21 : GLU -A22 : GLY -A23 : HIS -A24 : ILE -A25 : ALA -A26 : LYS -A27 : ASN -A28 : CYS -A29 : ARG -A30 : ALA -A31 : PRO -A32 : ARG -A33 : LYS -A34 : LYS -A35 : GLY -A36 : CYS -A37 : TRP -A38 : LYS -A39 : CYS -A40 : GLY -A41 : LYS -A42 : GLU -A43 : GLY -A44 : HIS -A45 : GLN -A46 : MET -A47 : LYS -A48 : ASP -A49 : CYS -A50 : THR -A51 : GLU -A52 : ARG -A53 : GLN -A54 : ALA -A55 : ASN -A56 : ZN -A57 : ZN -Adjacent stackings ---------------------------------------------- -B201-B202 : adjacent_5p upward -B202-B203 : adjacent_5p upward -B203-B204 : adjacent_5p upward -B206-B207 : adjacent_5p upward -B207-B208 : adjacent_5p upward -B213-B214 : adjacent_5p upward -B214-B215 : adjacent_5p upward -B216-B217 : adjacent_5p upward -B217-B218 : adjacent_5p upward -B218-B219 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 10 -Number of adjacent stackings = 10 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A32-B211 : ARG-A pairing one_hbond -A46-B210 : MET-G pairing one_hbond -B201-B220 : G-C Ww/Ww pairing antiparallel cis XIX -B202-B219 : G-C Ww/Ww pairing antiparallel cis XIX -B203-B218 : A-U Ww/Ww pairing antiparallel cis XX -B204-B217 : C-G Ww/Ww pairing antiparallel cis -B205-B216 : U-A Ww/Ww pairing antiparallel cis XX -B206-B215 : A-U Ww/Ww pairing antiparallel cis XX -B207-B214 : G-C Ww/Ww pairing antiparallel cis XIX -B208-B213 : C-G Ww/Ww pairing antiparallel cis -B209-B212 : G-G Bs/O2P pairing -Residue conformations ------------------------------------------- -B201 : G C3p_endo anti -B202 : G C3p_endo anti -B203 : A C3p_endo anti -B204 : C C3p_endo anti -B205 : U O4p_exo anti -B206 : A C4p_exo anti -B207 : G C3p_endo anti -B208 : C C4p_exo anti -B209 : G C2p_exo anti -B210 : G C4p_endo anti -B211 : A C3p_exo anti -B212 : G O4p_endo anti -B213 : G C2p_exo anti -B214 : C C3p_endo anti -B215 : U C3p_endo anti -B216 : A C4p_exo anti -B217 : G C4p_exo anti -B218 : U C4p_exo anti -B219 : C C4p_exo anti -B220 : C C3p_endo anti -A1 : MET -A2 : GLN -A3 : LYS -A4 : GLY -A5 : ASN -A6 : PHE -A7 : ARG -A8 : ASN -A9 : GLN -A10 : ARG -A11 : LYS -A12 : THR -A13 : VAL -A14 : LYS -A15 : CYS -A16 : PHE -A17 : ASN -A18 : CYS -A19 : GLY -A20 : LYS -A21 : GLU -A22 : GLY -A23 : HIS -A24 : ILE -A25 : ALA -A26 : LYS -A27 : ASN -A28 : CYS -A29 : ARG -A30 : ALA -A31 : PRO -A32 : ARG -A33 : LYS -A34 : LYS -A35 : GLY -A36 : CYS -A37 : TRP -A38 : LYS -A39 : CYS -A40 : GLY -A41 : LYS -A42 : GLU -A43 : GLY -A44 : HIS -A45 : GLN -A46 : MET -A47 : LYS -A48 : ASP -A49 : CYS -A50 : THR -A51 : GLU -A52 : ARG -A53 : GLN -A54 : ALA -A55 : ASN -A56 : ZN -A57 : ZN -Adjacent stackings ---------------------------------------------- -B201-B202 : adjacent_5p upward -B202-B203 : adjacent_5p upward -B203-B204 : adjacent_5p upward -B204-B205 : adjacent_5p upward -B206-B207 : adjacent_5p upward -B207-B208 : adjacent_5p upward -B208-B209 : adjacent_5p upward -B213-B214 : adjacent_5p upward -B214-B215 : adjacent_5p upward -B216-B217 : adjacent_5p upward -B217-B218 : adjacent_5p upward -B218-B219 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 12 -Number of adjacent stackings = 12 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A32-B211 : ARG-A pairing one_hbond -B201-B220 : G-C Ww/Ww pairing antiparallel cis XIX -B202-B219 : G-C Ww/Ww pairing antiparallel cis XIX -B203-B218 : A-U Ww/Ww pairing antiparallel cis XX -B204-B217 : C-G Ww/Ww pairing antiparallel cis XIX -B205-B216 : U-A Ww/Ww pairing antiparallel cis XX -B206-B215 : A-U Ww/Ww pairing antiparallel cis XX -B207-B214 : G-C Ww/Ww pairing antiparallel cis XIX -B208-B213 : C-G Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -B201 : G C3p_endo anti -B202 : G C3p_endo anti -B203 : A C4p_exo anti -B204 : C C3p_endo anti -B205 : U C4p_exo anti -B206 : A C3p_endo anti -B207 : G C3p_endo anti -B208 : C C2p_exo anti -B209 : G O4p_exo anti -B210 : G C4p_endo anti -B211 : A C2p_endo anti -B212 : G C4p_exo anti -B213 : G C2p_exo anti -B214 : C C2p_exo anti -B215 : U C1p_endo anti -B216 : A C4p_exo anti -B217 : G C3p_endo anti -B218 : U C4p_exo anti -B219 : C C4p_exo anti -B220 : C C3p_endo anti -A1 : MET -A2 : GLN -A3 : LYS -A4 : GLY -A5 : ASN -A6 : PHE -A7 : ARG -A8 : ASN -A9 : GLN -A10 : ARG -A11 : LYS -A12 : THR -A13 : VAL -A14 : LYS -A15 : CYS -A16 : PHE -A17 : ASN -A18 : CYS -A19 : GLY -A20 : LYS -A21 : GLU -A22 : GLY -A23 : HIS -A24 : ILE -A25 : ALA -A26 : LYS -A27 : ASN -A28 : CYS -A29 : ARG -A30 : ALA -A31 : PRO -A32 : ARG -A33 : LYS -A34 : LYS -A35 : GLY -A36 : CYS -A37 : TRP -A38 : LYS -A39 : CYS -A40 : GLY -A41 : LYS -A42 : GLU -A43 : GLY -A44 : HIS -A45 : GLN -A46 : MET -A47 : LYS -A48 : ASP -A49 : CYS -A50 : THR -A51 : GLU -A52 : ARG -A53 : GLN -A54 : ALA -A55 : ASN -A56 : ZN -A57 : ZN -Adjacent stackings ---------------------------------------------- -B201-B202 : adjacent_5p upward -B202-B203 : adjacent_5p upward -B203-B204 : adjacent_5p upward -B204-B205 : adjacent_5p upward -B206-B207 : adjacent_5p upward -B207-B208 : adjacent_5p upward -B208-B209 : adjacent_5p upward -B213-B214 : adjacent_5p upward -B214-B215 : adjacent_5p upward -B216-B217 : adjacent_5p upward -B217-B218 : adjacent_5p upward -B218-B219 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 12 -Number of adjacent stackings = 12 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A32-B211 : ARG-A pairing one_hbond -A46-B210 : MET-G pairing one_hbond -B201-B220 : G-C Ww/Ww pairing antiparallel cis XIX -B202-B219 : G-C Ww/Ww pairing antiparallel cis XIX -B203-B218 : A-U Ww/Ww pairing antiparallel cis XX -B204-B217 : C-G Ww/Ww pairing antiparallel cis XIX -B205-B216 : U-A Ww/Ww pairing antiparallel cis XX -B206-B215 : A-U Ww/Ww pairing antiparallel cis XX -B207-B214 : G-C Ww/Ww pairing antiparallel cis XIX -B208-B213 : C-G Ww/Ww pairing antiparallel cis -B209-B212 : G-G Bs/O2P pairing -Residue conformations ------------------------------------------- -B201 : G C3p_endo anti -B202 : G C3p_endo anti -B203 : A C3p_endo anti -B204 : C C3p_endo anti -B205 : U C3p_endo anti -B206 : A C3p_endo anti -B207 : G C3p_endo anti -B208 : C O4p_exo anti -B209 : G C1p_endo anti -B210 : G C4p_endo anti -B211 : A C2p_endo anti -B212 : G C4p_exo anti -B213 : G C2p_exo anti -B214 : C C3p_endo anti -B215 : U C4p_exo anti -B216 : A C4p_exo anti -B217 : G C4p_exo anti -B218 : U C3p_endo anti -B219 : C C2p_exo anti -B220 : C C3p_endo anti -A1 : MET -A2 : GLN -A3 : LYS -A4 : GLY -A5 : ASN -A6 : PHE -A7 : ARG -A8 : ASN -A9 : GLN -A10 : ARG -A11 : LYS -A12 : THR -A13 : VAL -A14 : LYS -A15 : CYS -A16 : PHE -A17 : ASN -A18 : CYS -A19 : GLY -A20 : LYS -A21 : GLU -A22 : GLY -A23 : HIS -A24 : ILE -A25 : ALA -A26 : LYS -A27 : ASN -A28 : CYS -A29 : ARG -A30 : ALA -A31 : PRO -A32 : ARG -A33 : LYS -A34 : LYS -A35 : GLY -A36 : CYS -A37 : TRP -A38 : LYS -A39 : CYS -A40 : GLY -A41 : LYS -A42 : GLU -A43 : GLY -A44 : HIS -A45 : GLN -A46 : MET -A47 : LYS -A48 : ASP -A49 : CYS -A50 : THR -A51 : GLU -A52 : ARG -A53 : GLN -A54 : ALA -A55 : ASN -A56 : ZN -A57 : ZN -Adjacent stackings ---------------------------------------------- -B202-B203 : adjacent_5p upward -B203-B204 : adjacent_5p upward -B204-B205 : adjacent_5p upward -B206-B207 : adjacent_5p upward -B207-B208 : adjacent_5p upward -B208-B209 : adjacent_5p upward -B213-B214 : adjacent_5p upward -B214-B215 : adjacent_5p upward -B216-B217 : adjacent_5p upward -B217-B218 : adjacent_5p upward -B218-B219 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 11 -Number of adjacent stackings = 11 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A32-B211 : ARG-A pairing one_hbond -B201-B220 : G-C Ww/Ww pairing antiparallel cis XIX -B202-B219 : G-C Ww/Ww pairing antiparallel cis XIX -B203-B218 : A-U Ww/Ww pairing antiparallel cis XX -B204-B217 : C-G Ww/Ww pairing antiparallel cis -B205-B216 : U-A Ww/Ww pairing antiparallel cis XX -B206-B215 : A-U Ww/Ww pairing antiparallel cis XX -B207-B214 : G-C Ww/Ww pairing antiparallel cis XIX -B208-B213 : C-G Ww/Ww pairing antiparallel cis XIX -B209-B212 : G-G Wh/Sw pairing parallel cis one_hbond 114 -Residue conformations ------------------------------------------- -B201 : G C3p_endo anti -B202 : G C3p_endo anti -B203 : A C3p_endo anti -B204 : C O4p_exo anti -B205 : U C3p_endo anti -B206 : A C4p_exo anti -B207 : G C4p_exo anti -B208 : C C4p_exo anti -B209 : G C3p_endo anti -B210 : G C4p_endo anti -B211 : A C2p_endo anti -B212 : G C4p_exo anti -B213 : G C1p_endo anti -B214 : C C3p_endo anti -B215 : U C2p_exo anti -B216 : A C4p_exo anti -B217 : G C4p_exo anti -B218 : U C4p_exo anti -B219 : C C4p_exo anti -B220 : C C4p_exo anti -A1 : MET -A2 : GLN -A3 : LYS -A4 : GLY -A5 : ASN -A6 : PHE -A7 : ARG -A8 : ASN -A9 : GLN -A10 : ARG -A11 : LYS -A12 : THR -A13 : VAL -A14 : LYS -A15 : CYS -A16 : PHE -A17 : ASN -A18 : CYS -A19 : GLY -A20 : LYS -A21 : GLU -A22 : GLY -A23 : HIS -A24 : ILE -A25 : ALA -A26 : LYS -A27 : ASN -A28 : CYS -A29 : ARG -A30 : ALA -A31 : PRO -A32 : ARG -A33 : LYS -A34 : LYS -A35 : GLY -A36 : CYS -A37 : TRP -A38 : LYS -A39 : CYS -A40 : GLY -A41 : LYS -A42 : GLU -A43 : GLY -A44 : HIS -A45 : GLN -A46 : MET -A47 : LYS -A48 : ASP -A49 : CYS -A50 : THR -A51 : GLU -A52 : ARG -A53 : GLN -A54 : ALA -A55 : ASN -A56 : ZN -A57 : ZN -Adjacent stackings ---------------------------------------------- -B202-B203 : adjacent_5p upward -B203-B204 : adjacent_5p upward -B205-B206 : adjacent_5p upward -B206-B207 : adjacent_5p upward -B207-B208 : adjacent_5p upward -B208-B209 : adjacent_5p upward -B213-B214 : adjacent_5p upward -B214-B215 : adjacent_5p upward -B216-B217 : adjacent_5p upward -B217-B218 : adjacent_5p upward -B218-B219 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 11 -Number of adjacent stackings = 11 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A32-B211 : ARG-A pairing one_hbond -A46-B210 : MET-G pairing one_hbond -B201-B220 : G-C Ww/Ww pairing antiparallel cis XIX -B202-B219 : G-C Ww/Ww pairing antiparallel cis XIX -B203-B218 : A-U Ww/Ww pairing antiparallel cis XX -B204-B217 : C-G Ww/Ww pairing antiparallel cis XIX -B205-B216 : U-A Ww/Ww pairing antiparallel cis XX -B206-B215 : A-U Ww/Ww pairing antiparallel cis XX -B207-B214 : G-C Ww/Ww pairing antiparallel cis XIX -B208-B213 : C-G Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -B201 : G C3p_endo anti -B202 : G C3p_endo anti -B203 : A C3p_endo anti -B204 : C C4p_exo anti -B205 : U C4p_exo anti -B206 : A C3p_endo anti -B207 : G C3p_endo anti -B208 : C C1p_endo anti -B209 : G C4p_exo anti -B210 : G C4p_endo anti -B211 : A C3p_exo anti -B212 : G C4p_exo anti -B213 : G C2p_exo anti -B214 : C C2p_exo anti -B215 : U C4p_endo anti -B216 : A C4p_exo anti -B217 : G C3p_endo anti -B218 : U C3p_endo anti -B219 : C C4p_endo anti -B220 : C C4p_exo anti -A1 : MET -A2 : GLN -A3 : LYS -A4 : GLY -A5 : ASN -A6 : PHE -A7 : ARG -A8 : ASN -A9 : GLN -A10 : ARG -A11 : LYS -A12 : THR -A13 : VAL -A14 : LYS -A15 : CYS -A16 : PHE -A17 : ASN -A18 : CYS -A19 : GLY -A20 : LYS -A21 : GLU -A22 : GLY -A23 : HIS -A24 : ILE -A25 : ALA -A26 : LYS -A27 : ASN -A28 : CYS -A29 : ARG -A30 : ALA -A31 : PRO -A32 : ARG -A33 : LYS -A34 : LYS -A35 : GLY -A36 : CYS -A37 : TRP -A38 : LYS -A39 : CYS -A40 : GLY -A41 : LYS -A42 : GLU -A43 : GLY -A44 : HIS -A45 : GLN -A46 : MET -A47 : LYS -A48 : ASP -A49 : CYS -A50 : THR -A51 : GLU -A52 : ARG -A53 : GLN -A54 : ALA -A55 : ASN -A56 : ZN -A57 : ZN -Adjacent stackings ---------------------------------------------- -B201-B202 : adjacent_5p upward -B202-B203 : adjacent_5p upward -B203-B204 : adjacent_5p upward -B204-B205 : adjacent_5p upward -B206-B207 : adjacent_5p upward -B207-B208 : adjacent_5p upward -B213-B214 : adjacent_5p upward -B214-B215 : adjacent_5p upward -B216-B217 : adjacent_5p upward -B217-B218 : adjacent_5p upward -B218-B219 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 11 -Number of adjacent stackings = 11 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A32-B211 : ARG-A pairing one_hbond -A46-B210 : MET-G pairing -B201-B220 : G-C Ww/Ww pairing antiparallel cis XIX -B202-B219 : G-C Ww/Ww pairing antiparallel cis XIX -B203-B218 : A-U Ww/Ww pairing antiparallel cis XX -B204-B217 : C-G Ww/Ww pairing antiparallel cis -B205-B216 : U-A Ww/Ww pairing antiparallel cis XX -B206-B215 : A-U Ww/Ww pairing antiparallel cis XX -B207-B214 : G-C Ww/Ww pairing antiparallel cis XIX -B208-B213 : C-G Ww/Ww pairing antiparallel cis XIX -B209-B212 : G-G Hw/Sw pairing antiparallel trans one_hbond 112 -Residue conformations ------------------------------------------- -B201 : G C3p_endo anti -B202 : G C3p_endo anti -B203 : A C2p_exo anti -B204 : C C3p_endo anti -B205 : U C3p_endo anti -B206 : A C4p_exo anti -B207 : G C4p_exo anti -B208 : C C4p_exo anti -B209 : G C3p_endo anti -B210 : G C4p_endo anti -B211 : A C1p_exo anti -B212 : G O4p_endo anti -B213 : G C2p_exo anti -B214 : C C3p_endo anti -B215 : U C4p_endo anti -B216 : A C4p_exo anti -B217 : G C4p_exo anti -B218 : U C3p_endo anti -B219 : C C2p_exo anti -B220 : C C4p_endo anti -A1 : MET -A2 : GLN -A3 : LYS -A4 : GLY -A5 : ASN -A6 : PHE -A7 : ARG -A8 : ASN -A9 : GLN -A10 : ARG -A11 : LYS -A12 : THR -A13 : VAL -A14 : LYS -A15 : CYS -A16 : PHE -A17 : ASN -A18 : CYS -A19 : GLY -A20 : LYS -A21 : GLU -A22 : GLY -A23 : HIS -A24 : ILE -A25 : ALA -A26 : LYS -A27 : ASN -A28 : CYS -A29 : ARG -A30 : ALA -A31 : PRO -A32 : ARG -A33 : LYS -A34 : LYS -A35 : GLY -A36 : CYS -A37 : TRP -A38 : LYS -A39 : CYS -A40 : GLY -A41 : LYS -A42 : GLU -A43 : GLY -A44 : HIS -A45 : GLN -A46 : MET -A47 : LYS -A48 : ASP -A49 : CYS -A50 : THR -A51 : GLU -A52 : ARG -A53 : GLN -A54 : ALA -A55 : ASN -A56 : ZN -A57 : ZN -Adjacent stackings ---------------------------------------------- -B201-B202 : adjacent_5p upward -B202-B203 : adjacent_5p upward -B203-B204 : adjacent_5p upward -B204-B205 : adjacent_5p upward -B205-B206 : adjacent_5p upward -B206-B207 : adjacent_5p upward -B207-B208 : adjacent_5p upward -B208-B209 : adjacent_5p upward -B213-B214 : adjacent_5p upward -B214-B215 : adjacent_5p upward -B216-B217 : adjacent_5p upward -B217-B218 : adjacent_5p upward -B218-B219 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 13 -Number of adjacent stackings = 13 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A32-B211 : ARG-A pairing one_hbond -B201-B220 : G-C Ww/Ww pairing antiparallel cis XIX -B202-B219 : G-C Ww/Ww pairing antiparallel cis XIX -B203-B218 : A-U Ww/Ww pairing antiparallel cis XX -B204-B217 : C-G Ww/Ww pairing antiparallel cis -B205-B216 : U-A Ww/Ww pairing antiparallel cis XX -B206-B215 : A-U Ww/Ww pairing antiparallel cis XX -B207-B214 : G-C Ww/Ww pairing antiparallel cis XIX -B208-B213 : C-G Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -B201 : G C3p_endo anti -B202 : G C3p_endo anti -B203 : A C3p_endo anti -B204 : C C3p_endo anti -B205 : U C4p_exo anti -B206 : A C4p_exo anti -B207 : G C4p_exo anti -B208 : C C4p_exo anti -B209 : G C4p_exo anti -B210 : G C4p_endo anti -B211 : A C2p_endo anti -B212 : G C4p_exo anti -B213 : G C2p_exo anti -B214 : C C2p_exo anti -B215 : U O4p_exo anti -B216 : A C4p_exo anti -B217 : G C4p_exo anti -B218 : U C4p_exo anti -B219 : C C4p_exo anti -B220 : C C3p_endo anti -A1 : MET -A2 : GLN -A3 : LYS -A4 : GLY -A5 : ASN -A6 : PHE -A7 : ARG -A8 : ASN -A9 : GLN -A10 : ARG -A11 : LYS -A12 : THR -A13 : VAL -A14 : LYS -A15 : CYS -A16 : PHE -A17 : ASN -A18 : CYS -A19 : GLY -A20 : LYS -A21 : GLU -A22 : GLY -A23 : HIS -A24 : ILE -A25 : ALA -A26 : LYS -A27 : ASN -A28 : CYS -A29 : ARG -A30 : ALA -A31 : PRO -A32 : ARG -A33 : LYS -A34 : LYS -A35 : GLY -A36 : CYS -A37 : TRP -A38 : LYS -A39 : CYS -A40 : GLY -A41 : LYS -A42 : GLU -A43 : GLY -A44 : HIS -A45 : GLN -A46 : MET -A47 : LYS -A48 : ASP -A49 : CYS -A50 : THR -A51 : GLU -A52 : ARG -A53 : GLN -A54 : ALA -A55 : ASN -A56 : ZN -A57 : ZN -Adjacent stackings ---------------------------------------------- -B201-B202 : adjacent_5p upward -B202-B203 : adjacent_5p upward -B203-B204 : adjacent_5p upward -B204-B205 : adjacent_5p upward -B205-B206 : adjacent_5p upward -B206-B207 : adjacent_5p upward -B208-B209 : adjacent_5p upward -B213-B214 : adjacent_5p upward -B214-B215 : adjacent_5p upward -B216-B217 : adjacent_5p upward -B217-B218 : adjacent_5p upward -B218-B219 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 12 -Number of adjacent stackings = 12 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A32-B211 : ARG-A pairing one_hbond -A46-B210 : MET-G pairing one_hbond -B201-B220 : G-C Ww/Ww pairing antiparallel cis XIX -B202-B219 : G-C Ww/Ww pairing antiparallel cis XIX -B203-B218 : A-U Ww/Ww pairing antiparallel cis XX -B204-B217 : C-G Ww/Ww pairing antiparallel cis -B205-B216 : U-A Ww/Ww pairing antiparallel cis XX -B206-B215 : A-U Ww/Ww pairing antiparallel cis XX -B207-B214 : G-C Ww/Ww pairing antiparallel cis XIX -B208-B213 : C-G Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -B201 : G C3p_endo anti -B202 : G C3p_endo anti -B203 : A C3p_endo anti -B204 : C C3p_endo anti -B205 : U C4p_exo anti -B206 : A C3p_endo anti -B207 : G C3p_endo anti -B208 : C C1p_endo anti -B209 : G O4p_exo anti -B210 : G C4p_endo anti -B211 : A C2p_endo anti -B212 : G O4p_endo anti -B213 : G C2p_exo anti -B214 : C C3p_endo anti -B215 : U C4p_exo anti -B216 : A C4p_exo anti -B217 : G C4p_exo anti -B218 : U C3p_endo anti -B219 : C C4p_endo anti -B220 : C C4p_exo anti -A1 : MET -A2 : GLN -A3 : LYS -A4 : GLY -A5 : ASN -A6 : PHE -A7 : ARG -A8 : ASN -A9 : GLN -A10 : ARG -A11 : LYS -A12 : THR -A13 : VAL -A14 : LYS -A15 : CYS -A16 : PHE -A17 : ASN -A18 : CYS -A19 : GLY -A20 : LYS -A21 : GLU -A22 : GLY -A23 : HIS -A24 : ILE -A25 : ALA -A26 : LYS -A27 : ASN -A28 : CYS -A29 : ARG -A30 : ALA -A31 : PRO -A32 : ARG -A33 : LYS -A34 : LYS -A35 : GLY -A36 : CYS -A37 : TRP -A38 : LYS -A39 : CYS -A40 : GLY -A41 : LYS -A42 : GLU -A43 : GLY -A44 : HIS -A45 : GLN -A46 : MET -A47 : LYS -A48 : ASP -A49 : CYS -A50 : THR -A51 : GLU -A52 : ARG -A53 : GLN -A54 : ALA -A55 : ASN -A56 : ZN -A57 : ZN -Adjacent stackings ---------------------------------------------- -B201-B202 : adjacent_5p upward -B202-B203 : adjacent_5p upward -B203-B204 : adjacent_5p upward -B205-B206 : adjacent_5p upward -B206-B207 : adjacent_5p upward -B207-B208 : adjacent_5p upward -B208-B209 : adjacent_5p upward -B213-B214 : adjacent_5p upward -B214-B215 : adjacent_5p upward -B216-B217 : adjacent_5p upward -B217-B218 : adjacent_5p upward -B218-B219 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 12 -Number of adjacent stackings = 12 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A32-B211 : ARG-A pairing one_hbond -B201-B220 : G-C Ww/Ww pairing antiparallel cis XIX -B202-B219 : G-C Ww/Ww pairing antiparallel cis XIX -B203-B218 : A-U Ww/Ww pairing antiparallel cis XX -B204-B217 : C-G Ww/Ww pairing antiparallel cis XIX -B205-B216 : U-A Ww/Ww pairing antiparallel cis XX -B206-B215 : A-U Ww/Ww pairing antiparallel cis XX -B207-B214 : G-C Ww/Ww pairing antiparallel cis XIX -B208-B213 : C-G Ww/Ww pairing antiparallel cis XIX -B209-B212 : G-G Bs/O2P pairing -Residue conformations ------------------------------------------- -B201 : G C3p_endo anti -B202 : G C3p_endo anti -B203 : A C3p_endo anti -B204 : C C3p_endo anti -B205 : U C3p_endo anti -B206 : A C3p_endo anti -B207 : G C4p_exo anti -B208 : C O4p_exo anti -B209 : G O4p_exo anti -B210 : G C4p_endo anti -B211 : A C2p_endo anti -B212 : G C3p_endo anti -B213 : G C2p_exo anti -B214 : C C3p_endo anti -B215 : U C3p_endo anti -B216 : A C4p_exo anti -B217 : G C4p_exo anti -B218 : U C4p_exo anti -B219 : C C3p_endo anti -B220 : C C4p_endo anti -A1 : MET -A2 : GLN -A3 : LYS -A4 : GLY -A5 : ASN -A6 : PHE -A7 : ARG -A8 : ASN -A9 : GLN -A10 : ARG -A11 : LYS -A12 : THR -A13 : VAL -A14 : LYS -A15 : CYS -A16 : PHE -A17 : ASN -A18 : CYS -A19 : GLY -A20 : LYS -A21 : GLU -A22 : GLY -A23 : HIS -A24 : ILE -A25 : ALA -A26 : LYS -A27 : ASN -A28 : CYS -A29 : ARG -A30 : ALA -A31 : PRO -A32 : ARG -A33 : LYS -A34 : LYS -A35 : GLY -A36 : CYS -A37 : TRP -A38 : LYS -A39 : CYS -A40 : GLY -A41 : LYS -A42 : GLU -A43 : GLY -A44 : HIS -A45 : GLN -A46 : MET -A47 : LYS -A48 : ASP -A49 : CYS -A50 : THR -A51 : GLU -A52 : ARG -A53 : GLN -A54 : ALA -A55 : ASN -A56 : ZN -A57 : ZN -Adjacent stackings ---------------------------------------------- -B201-B202 : adjacent_5p upward -B202-B203 : adjacent_5p upward -B203-B204 : adjacent_5p upward -B204-B205 : adjacent_5p upward -B206-B207 : adjacent_5p upward -B207-B208 : adjacent_5p upward -B213-B214 : adjacent_5p upward -B214-B215 : adjacent_5p upward -B216-B217 : adjacent_5p upward -B217-B218 : adjacent_5p upward -B218-B219 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 11 -Number of adjacent stackings = 11 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A32-B211 : ARG-A pairing one_hbond -A46-B210 : MET-G pairing one_hbond -B201-B220 : G-C Ww/Ww pairing antiparallel cis XIX -B202-B219 : G-C Ww/Ww pairing antiparallel cis XIX -B203-B218 : A-U Ww/Ww pairing antiparallel cis XX -B204-B217 : C-G Ww/Ww pairing antiparallel cis XIX -B205-B216 : U-A Ww/Ww pairing antiparallel cis XX -B206-B215 : A-U Ww/Ww pairing antiparallel cis XX -B207-B214 : G-C Ww/Ww pairing antiparallel cis XIX -B208-B213 : C-G Ww/Ww pairing antiparallel cis -Residue conformations ------------------------------------------- -B201 : G C3p_endo anti -B202 : G C3p_endo anti -B203 : A C3p_endo anti -B204 : C C3p_endo anti -B205 : U C4p_exo anti -B206 : A C4p_exo anti -B207 : G C4p_exo anti -B208 : C C3p_endo anti -B209 : G C3p_endo anti -B210 : G O4p_exo anti -B211 : A C2p_endo anti -B212 : G C4p_exo anti -B213 : G C1p_endo anti -B214 : C C3p_endo anti -B215 : U C4p_endo anti -B216 : A C4p_exo anti -B217 : G C3p_endo anti -B218 : U C3p_endo anti -B219 : C C3p_endo anti -B220 : C C3p_endo anti -A1 : MET -A2 : GLN -A3 : LYS -A4 : GLY -A5 : ASN -A6 : PHE -A7 : ARG -A8 : ASN -A9 : GLN -A10 : ARG -A11 : LYS -A12 : THR -A13 : VAL -A14 : LYS -A15 : CYS -A16 : PHE -A17 : ASN -A18 : CYS -A19 : GLY -A20 : LYS -A21 : GLU -A22 : GLY -A23 : HIS -A24 : ILE -A25 : ALA -A26 : LYS -A27 : ASN -A28 : CYS -A29 : ARG -A30 : ALA -A31 : PRO -A32 : ARG -A33 : LYS -A34 : LYS -A35 : GLY -A36 : CYS -A37 : TRP -A38 : LYS -A39 : CYS -A40 : GLY -A41 : LYS -A42 : GLU -A43 : GLY -A44 : HIS -A45 : GLN -A46 : MET -A47 : LYS -A48 : ASP -A49 : CYS -A50 : THR -A51 : GLU -A52 : ARG -A53 : GLN -A54 : ALA -A55 : ASN -A56 : ZN -A57 : ZN -Adjacent stackings ---------------------------------------------- -B203-B204 : adjacent_5p upward -B206-B207 : adjacent_5p upward -B207-B208 : adjacent_5p upward -B208-B209 : adjacent_5p upward -B213-B214 : adjacent_5p upward -B214-B215 : adjacent_5p upward -B216-B217 : adjacent_5p upward -B217-B218 : adjacent_5p upward -B218-B219 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -B206-B216 : outward -Number of stackings = 10 -Number of adjacent stackings = 9 -Number of non adjacent stackings = 1 -Base-pairs ------------------------------------------------------ -A32-B211 : ARG-A pairing one_hbond -A46-B210 : MET-G pairing one_hbond -B201-B219 : G-C Hw/Wh pairing antiparallel cis one_hbond 122 -B201-B220 : G-C Ww/Ww pairing antiparallel cis XIX -B202-B219 : G-C Ww/Ww pairing antiparallel cis XIX -B203-B218 : A-U Ww/Ww pairing antiparallel cis XX -B204-B217 : C-G Ww/Ww pairing antiparallel cis -B205-B216 : U-A Ww/Ww pairing antiparallel cis XX -B206-B215 : A-U Ww/Ww pairing antiparallel cis XX -B207-B214 : G-C Ww/Ww pairing antiparallel cis XIX -B208-B213 : C-G Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -B201 : G C3p_endo anti -B202 : G C3p_endo anti -B203 : A C3p_endo anti -B204 : C C3p_endo anti -B205 : U C3p_endo anti -B206 : A C4p_exo anti -B207 : G C3p_endo anti -B208 : C O4p_exo anti -B209 : G C3p_endo anti -B210 : G C4p_endo anti -B211 : A C2p_endo anti -B212 : G O4p_endo anti -B213 : G C2p_exo anti -B214 : C C2p_exo anti -B215 : U C2p_exo anti -B216 : A C4p_exo anti -B217 : G C4p_exo anti -B218 : U C4p_exo anti -B219 : C C4p_exo anti -B220 : C C4p_exo anti -A1 : MET -A2 : GLN -A3 : LYS -A4 : GLY -A5 : ASN -A6 : PHE -A7 : ARG -A8 : ASN -A9 : GLN -A10 : ARG -A11 : LYS -A12 : THR -A13 : VAL -A14 : LYS -A15 : CYS -A16 : PHE -A17 : ASN -A18 : CYS -A19 : GLY -A20 : LYS -A21 : GLU -A22 : GLY -A23 : HIS -A24 : ILE -A25 : ALA -A26 : LYS -A27 : ASN -A28 : CYS -A29 : ARG -A30 : ALA -A31 : PRO -A32 : ARG -A33 : LYS -A34 : LYS -A35 : GLY -A36 : CYS -A37 : TRP -A38 : LYS -A39 : CYS -A40 : GLY -A41 : LYS -A42 : GLU -A43 : GLY -A44 : HIS -A45 : GLN -A46 : MET -A47 : LYS -A48 : ASP -A49 : CYS -A50 : THR -A51 : GLU -A52 : ARG -A53 : GLN -A54 : ALA -A55 : ASN -A56 : ZN -A57 : ZN -Adjacent stackings ---------------------------------------------- -B202-B203 : adjacent_5p upward -B203-B204 : adjacent_5p upward -B204-B205 : adjacent_5p upward -B206-B207 : adjacent_5p upward -B207-B208 : adjacent_5p upward -B208-B209 : adjacent_5p upward -B213-B214 : adjacent_5p upward -B214-B215 : adjacent_5p upward -B216-B217 : adjacent_5p upward -B217-B218 : adjacent_5p upward -B218-B219 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 11 -Number of adjacent stackings = 11 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A32-B211 : ARG-A pairing one_hbond -A46-B210 : MET-G pairing one_hbond -B201-B220 : G-C Ww/Ww pairing antiparallel cis XIX -B202-B219 : G-C Ww/Ww pairing antiparallel cis XIX -B203-B218 : A-U Ww/Ww pairing antiparallel cis XX -B204-B217 : C-G Ww/Ww pairing antiparallel cis XIX -B205-B216 : U-A Ww/Ww pairing antiparallel cis XX -B206-B215 : A-U Ww/Ww pairing antiparallel cis XX -B207-B214 : G-C Ww/Ww pairing antiparallel cis XIX -B208-B213 : C-G Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -B201 : G C3p_endo anti -B202 : G C3p_endo anti -B203 : A C3p_endo anti -B204 : C C3p_endo anti -B205 : U C4p_exo anti -B206 : A C4p_exo anti -B207 : G C3p_endo anti -B208 : C C3p_endo anti -B209 : G C4p_exo anti -B210 : G C4p_endo anti -B211 : A C2p_endo anti -B212 : G O4p_endo anti -B213 : G O4p_exo anti -B214 : C C2p_exo anti -B215 : U O4p_exo anti -B216 : A C4p_exo anti -B217 : G C3p_endo anti -B218 : U C4p_exo anti -B219 : C C3p_endo anti -B220 : C C3p_endo anti -A1 : MET -A2 : GLN -A3 : LYS -A4 : GLY -A5 : ASN -A6 : PHE -A7 : ARG -A8 : ASN -A9 : GLN -A10 : ARG -A11 : LYS -A12 : THR -A13 : VAL -A14 : LYS -A15 : CYS -A16 : PHE -A17 : ASN -A18 : CYS -A19 : GLY -A20 : LYS -A21 : GLU -A22 : GLY -A23 : HIS -A24 : ILE -A25 : ALA -A26 : LYS -A27 : ASN -A28 : CYS -A29 : ARG -A30 : ALA -A31 : PRO -A32 : ARG -A33 : LYS -A34 : LYS -A35 : GLY -A36 : CYS -A37 : TRP -A38 : LYS -A39 : CYS -A40 : GLY -A41 : LYS -A42 : GLU -A43 : GLY -A44 : HIS -A45 : GLN -A46 : MET -A47 : LYS -A48 : ASP -A49 : CYS -A50 : THR -A51 : GLU -A52 : ARG -A53 : GLN -A54 : ALA -A55 : ASN -A56 : ZN -A57 : ZN -Adjacent stackings ---------------------------------------------- -B203-B204 : adjacent_5p upward -B206-B207 : adjacent_5p upward -B208-B209 : adjacent_5p upward -B213-B214 : adjacent_5p upward -B214-B215 : adjacent_5p upward -B216-B217 : adjacent_5p upward -B218-B219 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 7 -Number of adjacent stackings = 7 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A32-B211 : ARG-A pairing one_hbond -A46-B210 : MET-G pairing one_hbond -B201-B220 : G-C Ww/Ww pairing antiparallel cis XIX -B202-B219 : G-C Ww/Ww pairing antiparallel cis XIX -B203-B218 : A-U Ww/Ww pairing antiparallel cis XX -B204-B217 : C-G Ww/Ww pairing antiparallel cis XIX -B205-B216 : U-A Ww/Ww pairing antiparallel cis XX -B206-B215 : A-U Ww/Ww pairing antiparallel cis XX -B207-B214 : G-C Ww/Ww pairing antiparallel cis XIX -B208-B213 : C-G Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -B201 : G C3p_endo anti -B202 : G C3p_endo anti -B203 : A C3p_endo anti -B204 : C C3p_endo anti -B205 : U C4p_exo anti -B206 : A C3p_endo anti -B207 : G C4p_exo anti -B208 : C C4p_exo anti -B209 : G C4p_exo anti -B210 : G C4p_endo anti -B211 : A C3p_exo anti -B212 : G O4p_endo anti -B213 : G C2p_exo anti -B214 : C C3p_endo anti -B215 : U C3p_endo anti -B216 : A C4p_exo anti -B217 : G C3p_endo anti -B218 : U C4p_exo anti -B219 : C C4p_exo anti -B220 : C C3p_endo anti -A1 : MET -A2 : GLN -A3 : LYS -A4 : GLY -A5 : ASN -A6 : PHE -A7 : ARG -A8 : ASN -A9 : GLN -A10 : ARG -A11 : LYS -A12 : THR -A13 : VAL -A14 : LYS -A15 : CYS -A16 : PHE -A17 : ASN -A18 : CYS -A19 : GLY -A20 : LYS -A21 : GLU -A22 : GLY -A23 : HIS -A24 : ILE -A25 : ALA -A26 : LYS -A27 : ASN -A28 : CYS -A29 : ARG -A30 : ALA -A31 : PRO -A32 : ARG -A33 : LYS -A34 : LYS -A35 : GLY -A36 : CYS -A37 : TRP -A38 : LYS -A39 : CYS -A40 : GLY -A41 : LYS -A42 : GLU -A43 : GLY -A44 : HIS -A45 : GLN -A46 : MET -A47 : LYS -A48 : ASP -A49 : CYS -A50 : THR -A51 : GLU -A52 : ARG -A53 : GLN -A54 : ALA -A55 : ASN -A56 : ZN -A57 : ZN -Adjacent stackings ---------------------------------------------- -B202-B203 : adjacent_5p upward -B203-B204 : adjacent_5p upward -B206-B207 : adjacent_5p upward -B207-B208 : adjacent_5p upward -B213-B214 : adjacent_5p upward -B214-B215 : adjacent_5p upward -B216-B217 : adjacent_5p upward -B217-B218 : adjacent_5p upward -B218-B219 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 9 -Number of adjacent stackings = 9 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A32-B211 : ARG-A pairing one_hbond -B201-B220 : G-C Ww/Ww pairing antiparallel cis XIX -B202-B219 : G-C Ww/Ww pairing antiparallel cis XIX -B203-B218 : A-U Ww/Ww pairing antiparallel cis XX -B204-B217 : C-G Ww/Ww pairing antiparallel cis XIX -B205-B216 : U-A Ww/Ww pairing antiparallel cis XX -B206-B215 : A-U Ww/Ww pairing antiparallel cis XX -B207-B214 : G-C Ww/Ww pairing antiparallel cis XIX -B208-B213 : C-G Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -B201 : G C3p_endo anti -B202 : G C3p_endo anti -B203 : A C3p_endo anti -B204 : C C3p_endo anti -B205 : U C4p_exo anti -B206 : A C4p_exo anti -B207 : G C4p_exo anti -B208 : C C4p_exo anti -B209 : G C2p_exo anti -B210 : G C4p_endo anti -B211 : A C2p_endo anti -B212 : G C3p_exo anti -B213 : G C2p_exo anti -B214 : C C3p_endo anti -B215 : U C4p_exo anti -B216 : A C4p_exo anti -B217 : G C4p_exo anti -B218 : U C4p_exo anti -B219 : C C3p_endo anti -B220 : C C3p_endo anti -A1 : MET -A2 : GLN -A3 : LYS -A4 : GLY -A5 : ASN -A6 : PHE -A7 : ARG -A8 : ASN -A9 : GLN -A10 : ARG -A11 : LYS -A12 : THR -A13 : VAL -A14 : LYS -A15 : CYS -A16 : PHE -A17 : ASN -A18 : CYS -A19 : GLY -A20 : LYS -A21 : GLU -A22 : GLY -A23 : HIS -A24 : ILE -A25 : ALA -A26 : LYS -A27 : ASN -A28 : CYS -A29 : ARG -A30 : ALA -A31 : PRO -A32 : ARG -A33 : LYS -A34 : LYS -A35 : GLY -A36 : CYS -A37 : TRP -A38 : LYS -A39 : CYS -A40 : GLY -A41 : LYS -A42 : GLU -A43 : GLY -A44 : HIS -A45 : GLN -A46 : MET -A47 : LYS -A48 : ASP -A49 : CYS -A50 : THR -A51 : GLU -A52 : ARG -A53 : GLN -A54 : ALA -A55 : ASN -A56 : ZN -A57 : ZN -Adjacent stackings ---------------------------------------------- -B202-B203 : adjacent_5p upward -B203-B204 : adjacent_5p upward -B204-B205 : adjacent_5p upward -B206-B207 : adjacent_5p upward -B207-B208 : adjacent_5p upward -B208-B209 : adjacent_5p upward -B213-B214 : adjacent_5p upward -B214-B215 : adjacent_5p upward -B216-B217 : adjacent_5p upward -B217-B218 : adjacent_5p upward -B218-B219 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 11 -Number of adjacent stackings = 11 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A32-B211 : ARG-A pairing one_hbond -A46-B210 : MET-G pairing one_hbond -B201-B220 : G-C Ww/Ww pairing antiparallel cis XIX -B202-B219 : G-C Ww/Ww pairing antiparallel cis XIX -B203-B218 : A-U Ww/Ww pairing antiparallel cis XX -B204-B217 : C-G Ww/Ww pairing antiparallel cis XIX -B205-B216 : U-A Ww/Ww pairing antiparallel cis XX -B206-B215 : A-U Ww/Ww pairing antiparallel cis XX -B207-B214 : G-C Ww/Ww pairing antiparallel cis XIX -B208-B213 : C-G Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -B201 : G C3p_endo anti -B202 : G C3p_endo anti -B203 : A C3p_endo anti -B204 : C C3p_endo anti -B205 : U C3p_endo anti -B206 : A C4p_exo anti -B207 : G C4p_exo anti -B208 : C C4p_exo anti -B209 : G C2p_exo anti -B210 : G O4p_exo anti -B211 : A C2p_endo anti -B212 : G O4p_endo anti -B213 : G C2p_exo anti -B214 : C C3p_endo anti -B215 : U C4p_exo anti -B216 : A C4p_exo anti -B217 : G C4p_exo anti -B218 : U C3p_endo anti -B219 : C C3p_endo anti -B220 : C C3p_endo anti -A1 : MET -A2 : GLN -A3 : LYS -A4 : GLY -A5 : ASN -A6 : PHE -A7 : ARG -A8 : ASN -A9 : GLN -A10 : ARG -A11 : LYS -A12 : THR -A13 : VAL -A14 : LYS -A15 : CYS -A16 : PHE -A17 : ASN -A18 : CYS -A19 : GLY -A20 : LYS -A21 : GLU -A22 : GLY -A23 : HIS -A24 : ILE -A25 : ALA -A26 : LYS -A27 : ASN -A28 : CYS -A29 : ARG -A30 : ALA -A31 : PRO -A32 : ARG -A33 : LYS -A34 : LYS -A35 : GLY -A36 : CYS -A37 : TRP -A38 : LYS -A39 : CYS -A40 : GLY -A41 : LYS -A42 : GLU -A43 : GLY -A44 : HIS -A45 : GLN -A46 : MET -A47 : LYS -A48 : ASP -A49 : CYS -A50 : THR -A51 : GLU -A52 : ARG -A53 : GLN -A54 : ALA -A55 : ASN -A56 : ZN -A57 : ZN -Adjacent stackings ---------------------------------------------- -B203-B204 : adjacent_5p upward -B204-B205 : adjacent_5p upward -B206-B207 : adjacent_5p upward -B207-B208 : adjacent_5p upward pairing -B208-B209 : adjacent_5p upward -B213-B214 : adjacent_5p upward -B214-B215 : adjacent_5p upward -B216-B217 : adjacent_5p upward -B217-B218 : adjacent_5p upward -B218-B219 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 10 -Number of adjacent stackings = 10 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A32-B211 : ARG-A pairing one_hbond -A46-B210 : MET-G pairing one_hbond -B201-B220 : G-C Ww/Ww pairing antiparallel cis XIX -B202-B219 : G-C Ww/Ww pairing antiparallel cis XIX -B203-B218 : A-U Ww/Ww pairing antiparallel cis XX -B204-B217 : C-G Ww/Ww pairing antiparallel cis XIX -B205-B216 : U-A Ww/Ww pairing antiparallel cis XX -B206-B215 : A-U Ww/Ww pairing antiparallel cis XX -B207-B208 : G-C O2'/Hh adjacent_5p upward pairing -B207-B214 : G-C Ww/Ww pairing antiparallel cis XIX -B208-B213 : C-G Ww/Ww pairing antiparallel cis one_hbond diff --git a/MCdata/1a34_MC b/MCdata/1a34_MC deleted file mode 100644 index 3130011119aa29260726c264869b0852bfeceb81..0000000000000000000000000000000000000000 --- a/MCdata/1a34_MC +++ /dev/null @@ -1,365 +0,0 @@ -Residue conformations ------------------------------------------- -A13 : THR -A14 : GLY -A15 : ASP -A16 : ASN -A17 : SER -A18 : ASN -A19 : VAL -A20 : VAL -A21 : THR -A22 : MET -A23 : ILE -A24 : ARG -A25 : ALA -A26 : GLY -A27 : SER -A28 : TYR -A29 : PRO -A30 : LYS -A31 : VAL -A32 : ASN -A33 : PRO -A34 : THR -A35 : PRO -A36 : THR -A37 : TRP -A38 : VAL -A39 : ARG -A40 : ALA -A41 : ILE -A42 : PRO -A43 : PHE -A44 : GLU -A45 : VAL -A46 : SER -A47 : VAL -A48 : GLN -A49 : SER -A50 : GLY -A51 : ILE -A52 : ALA -A53 : PHE -A54 : LYS -A55 : VAL -A56 : PRO -A57 : VAL -A58 : GLY -A59 : SER -A60 : LEU -A61 : PHE -A62 : SER -A63 : ALA -A64 : ASN -A65 : PHE -A66 : ARG -A67 : THR -A68 : ASP -A69 : SER -A70 : PHE -A71 : THR -A72 : SER -A73 : VAL -A74 : THR -A75 : VAL -A76 : MET -A77 : SER -A78 : VAL -A79 : ARG -A80 : ALA -A81 : TRP -A82 : THR -A83 : GLN -A84 : LEU -A85 : THR -A86 : PRO -A87 : PRO -A88 : VAL -A89 : ASN -A90 : GLU -A91 : TYR -A92 : SER -A93 : PHE -A94 : VAL -A95 : ARG -A96 : LEU -A97 : LYS -A98 : PRO -A99 : LEU -A100 : PHE -A101 : LYS -A102 : THR -A103 : GLY -A104 : ASP -A105 : SER -A106 : THR -A107 : GLU -A108 : GLU -A109 : PHE -A110 : GLU -A111 : GLY -A112 : ARG -A113 : ALA -A114 : SER -A115 : ASN -A116 : ILE -A117 : ASN -A118 : THR -A119 : ARG -A120 : ALA -A121 : SER -A122 : VAL -A123 : GLY -A124 : TYR -A125 : ARG -A126 : ILE -A127 : PRO -A128 : THR -A129 : ASN -A130 : LEU -A131 : ARG -A132 : GLN -A133 : ASN -A134 : THR -A135 : VAL -A136 : ALA -A137 : ALA -A138 : ASP -A139 : ASN -A140 : VAL -A141 : CYS -A142 : GLU -A143 : VAL -A144 : ARG -A145 : SER -A146 : ASN -A147 : CYS -A148 : ARG -A149 : GLN -A150 : VAL -A151 : ALA -A152 : LEU -A153 : VAL -A154 : ILE -A155 : SER -A156 : CYS -A157 : CYS -A158 : PHE -A159 : ASN -B1 : A C3p_endo anti -B2 : A C3p_endo anti -B3 : A C3p_endo anti -B4 : A C3p_endo anti -B5 : A C3p_endo anti -B6 : A C3p_endo anti -B7 : A C3p_endo anti -B8 : A C3p_endo anti -B9 : A C3p_endo anti -B10 : A C3p_endo anti -C1 : U C2p_exo anti -C2 : U C3p_endo anti -C3 : U C3p_endo anti -C4 : U C3p_endo anti -C5 : U C3p_endo anti -C6 : U C3p_endo anti -C7 : U C3p_endo anti -C8 : U C3p_endo anti -C9 : U C3p_endo anti -C10 : U C3p_endo anti -A3001 : SO4 -B11 : U C2p_endo unknown -A2001 : HOH -A2002 : HOH -A2003 : HOH -A2004 : HOH -A2005 : HOH -A2006 : HOH -A2007 : HOH -A2008 : HOH -A2009 : HOH -A2010 : HOH -A2011 : HOH -A2012 : HOH -A2013 : HOH -A2014 : HOH -A2015 : HOH -A2016 : HOH -A2017 : HOH -A2018 : HOH -A2019 : HOH -A2020 : HOH -A2021 : HOH -A2022 : HOH -A2023 : HOH -A2024 : HOH -A2101 : HOH -A2102 : HOH -A2103 : HOH -A2104 : HOH -A2105 : HOH -A2106 : HOH -A2107 : HOH -A2108 : HOH -A2109 : HOH -A2110 : HOH -A2111 : HOH -A2112 : HOH -A2113 : HOH -A2114 : HOH -A2115 : HOH -A2116 : HOH -A2117 : HOH -A2118 : HOH -A2119 : HOH -A2120 : HOH -A2121 : HOH -A2122 : HOH -A2123 : HOH -A2124 : HOH -A2125 : HOH -A2126 : HOH -A2127 : HOH -A2128 : HOH -A2129 : HOH -A2130 : HOH -A2131 : HOH -A2132 : HOH -A2133 : HOH -A2134 : HOH -A2135 : HOH -A2136 : HOH -A2137 : HOH -A2138 : HOH -A2139 : HOH -A2140 : HOH -A2141 : HOH -A2142 : HOH -A2143 : HOH -A2144 : HOH -A2145 : HOH -A2146 : HOH -A2147 : HOH -A2148 : HOH -A2149 : HOH -A2150 : HOH -A2151 : HOH -A2152 : HOH -A2153 : HOH -A2154 : HOH -A2155 : HOH -A2156 : HOH -A2157 : HOH -A2158 : HOH -A2159 : HOH -A2160 : HOH -A2161 : HOH -A2162 : HOH -A2163 : HOH -A2164 : HOH -A2165 : HOH -A2166 : HOH -A2167 : HOH -A2168 : HOH -A2169 : HOH -A2170 : HOH -A2171 : HOH -A2172 : HOH -A2173 : HOH -A2174 : HOH -A2175 : HOH -A2176 : HOH -A2177 : HOH -A2178 : HOH -A2179 : HOH -A2180 : HOH -A2181 : HOH -A2182 : HOH -A2183 : HOH -A2184 : HOH -A2185 : HOH -A2186 : HOH -A2187 : HOH -A2188 : HOH -A2189 : HOH -A2190 : HOH -A2191 : HOH -A2192 : HOH -A2193 : HOH -A2194 : HOH -A2195 : HOH -A2196 : HOH -A2197 : HOH -A2198 : HOH -A2199 : HOH -A2207 : HOH -A2301 : HOH -A2302 : HOH -A2303 : HOH -A2304 : HOH -A2305 : HOH -A2306 : HOH -A2401 : HOH -A2402 : HOH -A2403 : HOH -A2404 : HOH -A2405 : HOH -A2501 : HOH -A2502 : HOH -A2503 : HOH -A2504 : HOH -A2505 : HOH -A2506 : HOH -A2507 : HOH -A2508 : HOH -A2509 : HOH -A2601 : HOH -A2606 : HOH -A2607 : HOH -A2701 : HOH -A2901 : HOH -B2201 : HOH -B2202 : HOH -B2203 : HOH -B2204 : HOH -B2210 : HOH -B2211 : HOH -B2602 : HOH -B2603 : HOH -B2604 : HOH -B2605 : HOH -B2801 : HOH -C2205 : HOH -C2206 : HOH -C2208 : HOH -C2209 : HOH -C2212 : HOH -C2608 : HOH -C2609 : HOH -C2610 : HOH -Adjacent stackings ---------------------------------------------- -B1-B2 : adjacent_5p upward -B2-B3 : adjacent_5p upward -B3-B4 : adjacent_5p upward -B4-B5 : adjacent_5p upward -B5-B6 : adjacent_5p upward -B6-B7 : adjacent_5p upward -B7-B8 : adjacent_5p upward -B8-B9 : adjacent_5p upward -C1-C2 : adjacent_5p upward -C4-C5 : adjacent_5p upward -C5-C6 : adjacent_5p upward -C6-C7 : adjacent_5p upward -C7-C8 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 13 -Number of adjacent stackings = 13 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -B1-C9 : A-U Ww/Ww pairing antiparallel cis XX -B3-C7 : A-U Ww/Ww pairing antiparallel cis XX -B4-C6 : A-U Ww/Ww pairing antiparallel cis XX -B5-C5 : A-U Ww/Ww pairing antiparallel cis XX -B6-C4 : A-U Ww/Ww pairing antiparallel cis XX -B7-C3 : A-U Ww/Ww pairing antiparallel cis XX -B8-C2 : A-U Ww/Ww pairing antiparallel cis XX -B9-C1 : A-U Ww/Ww pairing antiparallel cis XX diff --git a/MCdata/1a3m_MC b/MCdata/1a3m_MC deleted file mode 100644 index 6471fc9f49d8a7fb05c7c7fd6e696526f22c02b0..0000000000000000000000000000000000000000 --- a/MCdata/1a3m_MC +++ /dev/null @@ -1,1385 +0,0 @@ -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : C C3p_endo anti -A7 : A C3p_endo anti -A8 : C C3p_endo anti -A9 : A C3p_endo anti -A10 : C C3p_endo anti -A11 : C C3p_endo anti -A12 : U C3p_endo anti -A13 : U C1p_exo anti -A14 : C C2p_endo anti -B15 : G C3p_endo syn -B16 : G C3p_endo anti -B17 : G C3p_endo anti -B18 : U C3p_endo anti -B19 : G C4p_exo anti -B20 : A C3p_endo anti -B21 : A C2p_exo anti -B22 : G C2p_exo anti -B23 : U C3p_endo anti -B24 : C C3p_endo anti -B25 : G C3p_endo anti -B26 : C C1p_exo anti -B27 : C O4p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -B15-B16 : adjacent_5p outward -B16-B17 : adjacent_5p upward -B17-B18 : adjacent_5p upward -B18-B19 : adjacent_5p upward -B20-B21 : adjacent_5p upward -B21-B22 : adjacent_5p upward -B22-B23 : adjacent_5p upward -B23-B24 : adjacent_5p upward -B24-B25 : adjacent_5p upward -B25-B26 : adjacent_5p upward -B26-B27 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-B25 : outward -A9-B19 : outward -A12-A14 : upward -Number of stackings = 24 -Number of adjacent stackings = 21 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -A1-B27 : G-C Ww/Ww pairing antiparallel cis XIX -A2-B26 : G-C Ww/Ww pairing antiparallel cis XIX -A3-B25 : C-G Ww/Ww pairing antiparallel cis XIX -A4-B24 : G-C Ww/Ww pairing antiparallel cis XIX -A6-B22 : C-G Ww/Ww pairing antiparallel cis XIX -A8-B19 : C-G Ww/Ww pairing antiparallel cis XIX -A9-B18 : A-U Ww/Ww pairing antiparallel cis XX -A10-B17 : C-G Ww/Ww pairing antiparallel cis XIX -A11-B16 : C-G Ww/Ww pairing antiparallel cis XIX -A12-B15 : U-G Bs/Ww pairing parallel trans 87 -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : C C3p_endo anti -A7 : A C3p_endo anti -A8 : C C3p_endo anti -A9 : A C3p_endo anti -A10 : C C3p_endo anti -A11 : C C3p_endo anti -A12 : U C3p_endo anti -A13 : U C1p_exo anti -A14 : C C2p_endo anti -B15 : G C3p_endo syn -B16 : G C3p_endo anti -B17 : G C3p_endo anti -B18 : U C3p_endo anti -B19 : G C4p_exo anti -B20 : A C3p_endo anti -B21 : A C2p_exo anti -B22 : G C3p_endo anti -B23 : U C3p_endo anti -B24 : C C3p_endo anti -B25 : G C3p_endo anti -B26 : C C1p_exo anti -B27 : C O4p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -B15-B16 : adjacent_5p outward -B16-B17 : adjacent_5p upward -B17-B18 : adjacent_5p upward -B18-B19 : adjacent_5p upward -B20-B21 : adjacent_5p upward -B21-B22 : adjacent_5p upward -B22-B23 : adjacent_5p upward -B23-B24 : adjacent_5p upward -B24-B25 : adjacent_5p upward -B25-B26 : adjacent_5p upward -B26-B27 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-B25 : outward -A7-B22 : outward -A9-B19 : outward -A12-A14 : upward -Number of stackings = 26 -Number of adjacent stackings = 22 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A1-B27 : G-C Ww/Ww pairing antiparallel cis XIX -A2-B26 : G-C Ww/Ww pairing antiparallel cis XIX -A3-B25 : C-G Ww/Ww pairing antiparallel cis XIX -A4-B24 : G-C Ww/Ww pairing antiparallel cis XIX -A6-B22 : C-G Ww/Ww pairing antiparallel cis XIX -A8-B19 : C-G Ww/Ww pairing antiparallel cis XIX -A9-B18 : A-U Ww/Ww pairing antiparallel cis XX -A10-B17 : C-G Ww/Ww pairing antiparallel cis XIX -A11-B16 : C-G Ww/Ww pairing antiparallel cis XIX -A12-B15 : U-G Bs/Ww pairing parallel trans 87 -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : C C3p_endo anti -A7 : A C3p_endo anti -A8 : C C3p_endo anti -A9 : A C3p_endo anti -A10 : C C3p_endo anti -A11 : C C3p_endo anti -A12 : U C3p_endo anti -A13 : U C1p_exo anti -A14 : C C2p_endo anti -B15 : G C3p_endo syn -B16 : G C2p_exo anti -B17 : G C3p_endo anti -B18 : U C3p_endo anti -B19 : G C3p_endo anti -B20 : A C4p_exo anti -B21 : A C2p_endo anti -B22 : G C3p_endo anti -B23 : U C3p_endo anti -B24 : C C3p_endo anti -B25 : G C3p_endo anti -B26 : C C1p_exo anti -B27 : C O4p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -B15-B16 : adjacent_5p outward -B16-B17 : adjacent_5p upward -B17-B18 : adjacent_5p upward -B18-B19 : adjacent_5p upward -B20-B21 : adjacent_5p upward -B21-B22 : adjacent_5p upward -B22-B23 : adjacent_5p upward -B23-B24 : adjacent_5p upward -B24-B25 : adjacent_5p upward -B25-B26 : adjacent_5p upward -B26-B27 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-B25 : outward -A9-B19 : outward -A12-A14 : upward -Number of stackings = 25 -Number of adjacent stackings = 22 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -A1-B27 : G-C Ww/Ww pairing antiparallel cis XIX -A2-B26 : G-C Ww/Ww pairing antiparallel cis XIX -A3-B25 : C-G Ww/Ww pairing antiparallel cis XIX -A4-B24 : G-C Ww/Ww pairing antiparallel cis XIX -A6-B22 : C-G Ww/Ww pairing antiparallel cis XIX -A8-B19 : C-G Ww/Ww pairing antiparallel cis XIX -A9-B18 : A-U Ww/Ww pairing antiparallel cis XX -A10-B17 : C-G Ww/Ww pairing antiparallel cis XIX -A11-B16 : C-G Ww/Ww pairing antiparallel cis XIX -A12-B15 : U-G Bs/Ww pairing parallel trans 87 -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : C C3p_endo anti -A7 : A C3p_endo anti -A8 : C C3p_endo anti -A9 : A C3p_endo anti -A10 : C C3p_endo anti -A11 : C C3p_endo anti -A12 : U C3p_endo anti -A13 : U C1p_exo anti -A14 : C C2p_endo anti -B15 : G C3p_endo syn -B16 : G C3p_endo anti -B17 : G C3p_endo anti -B18 : U C3p_endo anti -B19 : G C2p_exo anti -B20 : A C3p_endo anti -B21 : A C3p_exo anti -B22 : G C3p_endo anti -B23 : U C3p_endo anti -B24 : C C3p_endo anti -B25 : G C3p_endo anti -B26 : C C1p_exo anti -B27 : C O4p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -B15-B16 : adjacent_5p outward -B16-B17 : adjacent_5p upward -B17-B18 : adjacent_5p upward -B18-B19 : adjacent_5p upward -B20-B21 : adjacent_5p upward -B22-B23 : adjacent_5p upward -B23-B24 : adjacent_5p upward -B24-B25 : adjacent_5p upward -B25-B26 : adjacent_5p upward -B26-B27 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-B25 : outward -A7-B22 : outward -A9-B19 : outward -A12-A14 : upward -Number of stackings = 24 -Number of adjacent stackings = 20 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A1-B27 : G-C Ww/Ww pairing antiparallel cis XIX -A2-B26 : G-C Ww/Ww pairing antiparallel cis XIX -A3-B25 : C-G Ww/Ww pairing antiparallel cis XIX -A4-B24 : G-C Ww/Ww pairing antiparallel cis XIX -A6-B22 : C-G Ww/Ww pairing antiparallel cis XIX -A8-B19 : C-G Ww/Ww pairing antiparallel cis XIX -A9-B18 : A-U Ww/Ww pairing antiparallel cis XX -A10-B17 : C-G Ww/Ww pairing antiparallel cis XIX -A11-B16 : C-G Ww/Ww pairing antiparallel cis XIX -A12-B15 : U-G Bs/Ww pairing parallel trans 87 -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : C C3p_endo anti -A7 : A C3p_endo anti -A8 : C C3p_endo anti -A9 : A C3p_endo anti -A10 : C C3p_endo anti -A11 : C C3p_endo anti -A12 : U C3p_endo anti -A13 : U C1p_exo anti -A14 : C C2p_endo anti -B15 : G C3p_endo syn -B16 : G C3p_endo anti -B17 : G C3p_endo anti -B18 : U C3p_endo anti -B19 : G C3p_endo anti -B20 : A C4p_exo anti -B21 : A C3p_endo anti -B22 : G C2p_exo anti -B23 : U C3p_endo anti -B24 : C C3p_endo anti -B25 : G C3p_endo anti -B26 : C C1p_exo anti -B27 : C O4p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -B15-B16 : adjacent_5p outward -B16-B17 : adjacent_5p upward -B17-B18 : adjacent_5p upward -B18-B19 : adjacent_5p upward -B21-B22 : adjacent_5p upward -B22-B23 : adjacent_5p upward -B23-B24 : adjacent_5p upward -B24-B25 : adjacent_5p upward -B25-B26 : adjacent_5p upward -B26-B27 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-B25 : outward -A7-B22 : outward -A9-B19 : outward -A12-A14 : upward -Number of stackings = 24 -Number of adjacent stackings = 20 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A1-B27 : G-C Ww/Ww pairing antiparallel cis XIX -A2-B26 : G-C Ww/Ww pairing antiparallel cis XIX -A3-B25 : C-G Ww/Ww pairing antiparallel cis XIX -A4-B24 : G-C Ww/Ww pairing antiparallel cis XIX -A6-B22 : C-G Ww/Ww pairing antiparallel cis XIX -A8-B19 : C-G Ww/Ww pairing antiparallel cis XIX -A9-B18 : A-U Ww/Ww pairing antiparallel cis XX -A10-B17 : C-G Ww/Ww pairing antiparallel cis XIX -A11-B16 : C-G Ww/Ww pairing antiparallel cis XIX -A12-B15 : U-G Bs/Ww pairing parallel trans 87 -B20-B21 : A-A O2'/C8 adjacent_5p pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : C C3p_endo anti -A7 : A C3p_endo anti -A8 : C C3p_endo anti -A9 : A C3p_endo anti -A10 : C C3p_endo anti -A11 : C C3p_endo anti -A12 : U C3p_endo anti -A13 : U C1p_exo anti -A14 : C C2p_endo anti -B15 : G C3p_endo syn -B16 : G C3p_endo anti -B17 : G C3p_endo anti -B18 : U C3p_endo anti -B19 : G C2p_exo anti -B20 : A C3p_endo anti -B21 : A C2p_endo anti -B22 : G C3p_endo anti -B23 : U C3p_endo anti -B24 : C C3p_endo anti -B25 : G C3p_endo anti -B26 : C C1p_exo anti -B27 : C O4p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -B15-B16 : adjacent_5p outward -B16-B17 : adjacent_5p upward -B17-B18 : adjacent_5p upward -B18-B19 : adjacent_5p upward -B20-B21 : adjacent_5p upward -B21-B22 : adjacent_5p upward -B22-B23 : adjacent_5p upward -B23-B24 : adjacent_5p upward -B24-B25 : adjacent_5p upward -B25-B26 : adjacent_5p upward -B26-B27 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-B25 : outward -A7-B22 : outward -A9-B19 : outward -A12-A14 : upward -Number of stackings = 26 -Number of adjacent stackings = 22 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A1-B27 : G-C Ww/Ww pairing antiparallel cis XIX -A2-B26 : G-C Ww/Ww pairing antiparallel cis XIX -A3-B25 : C-G Ww/Ww pairing antiparallel cis XIX -A4-B24 : G-C Ww/Ww pairing antiparallel cis XIX -A6-B22 : C-G Ww/Ww pairing antiparallel cis XIX -A8-B19 : C-G Ww/Ww pairing antiparallel cis XIX -A9-B18 : A-U Ww/Ww pairing antiparallel cis XX -A10-B17 : C-G Ww/Ww pairing antiparallel cis XIX -A11-B16 : C-G Ww/Ww pairing antiparallel cis XIX -A12-B15 : U-G Bs/Ww pairing parallel trans 87 -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : C C3p_endo anti -A7 : A C3p_endo anti -A8 : C C3p_endo anti -A9 : A C3p_endo anti -A10 : C C3p_endo anti -A11 : C C3p_endo anti -A12 : U C3p_endo anti -A13 : U C1p_exo anti -A14 : C C2p_endo anti -B15 : G C3p_endo syn -B16 : G C3p_endo anti -B17 : G C3p_endo anti -B18 : U C3p_endo anti -B19 : G C2p_exo anti -B20 : A C3p_endo anti -B21 : A C2p_exo anti -B22 : G C3p_endo anti -B23 : U C3p_endo anti -B24 : C C3p_endo anti -B25 : G C3p_endo anti -B26 : C C1p_exo anti -B27 : C O4p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -B15-B16 : adjacent_5p outward -B16-B17 : adjacent_5p upward -B17-B18 : adjacent_5p upward -B18-B19 : adjacent_5p upward -B20-B21 : adjacent_5p upward -B21-B22 : adjacent_5p upward -B22-B23 : adjacent_5p upward -B23-B24 : adjacent_5p upward -B24-B25 : adjacent_5p upward -B25-B26 : adjacent_5p upward -B26-B27 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-B25 : outward -A7-B22 : outward -A9-B19 : outward -A12-A14 : upward -Number of stackings = 26 -Number of adjacent stackings = 22 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A1-B27 : G-C Ww/Ww pairing antiparallel cis -A2-B26 : G-C Ww/Ww pairing antiparallel cis XIX -A3-B25 : C-G Ww/Ww pairing antiparallel cis XIX -A4-B24 : G-C Ww/Ww pairing antiparallel cis XIX -A6-B22 : C-G Ww/Ww pairing antiparallel cis XIX -A8-B19 : C-G Ww/Ww pairing antiparallel cis XIX -A9-B18 : A-U Ww/Ww pairing antiparallel cis XX -A10-B17 : C-G Ww/Ww pairing antiparallel cis XIX -A11-B16 : C-G Ww/Ww pairing antiparallel cis XIX -A12-B15 : U-G Bs/Ww pairing parallel trans 87 -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : C C3p_endo anti -A7 : A C3p_endo anti -A8 : C C3p_endo anti -A9 : A C3p_endo anti -A10 : C C3p_endo anti -A11 : C C3p_endo anti -A12 : U C3p_endo anti -A13 : U C1p_exo anti -A14 : C C2p_endo anti -B15 : G C3p_endo syn -B16 : G C3p_endo anti -B17 : G C3p_endo anti -B18 : U C3p_endo anti -B19 : G C2p_exo anti -B20 : A C3p_endo anti -B21 : A C2p_exo anti -B22 : G C3p_endo anti -B23 : U C3p_endo anti -B24 : C C3p_endo anti -B25 : G C3p_endo anti -B26 : C C1p_exo anti -B27 : C O4p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -B15-B16 : adjacent_5p outward -B16-B17 : adjacent_5p upward -B17-B18 : adjacent_5p upward -B18-B19 : adjacent_5p upward -B20-B21 : adjacent_5p upward -B21-B22 : adjacent_5p upward -B22-B23 : adjacent_5p upward -B23-B24 : adjacent_5p upward -B24-B25 : adjacent_5p upward -B25-B26 : adjacent_5p upward -B26-B27 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-B25 : outward -A7-B22 : outward -A9-B19 : outward -A12-A14 : upward -Number of stackings = 26 -Number of adjacent stackings = 22 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A1-B27 : G-C Ww/Ww pairing antiparallel cis XIX -A2-B26 : G-C Ww/Ww pairing antiparallel cis XIX -A3-B25 : C-G Ww/Ww pairing antiparallel cis XIX -A4-B24 : G-C Ww/Ww pairing antiparallel cis XIX -A6-B22 : C-G Ww/Ww pairing antiparallel cis XIX -A8-B19 : C-G Ww/Ww pairing antiparallel cis XIX -A9-B18 : A-U Ww/Ww pairing antiparallel cis XX -A10-B17 : C-G Ww/Ww pairing antiparallel cis XIX -A11-B16 : C-G Ww/Ww pairing antiparallel cis XIX -A12-B15 : U-G Bs/Ww pairing parallel trans 87 -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : C C3p_endo anti -A7 : A C3p_endo anti -A8 : C C3p_endo anti -A9 : A C3p_endo anti -A10 : C C3p_endo anti -A11 : C C3p_endo anti -A12 : U C3p_endo anti -A13 : U C1p_exo anti -A14 : C C2p_endo anti -B15 : G C3p_endo syn -B16 : G C3p_endo anti -B17 : G C3p_endo anti -B18 : U C3p_endo anti -B19 : G C2p_exo anti -B20 : A C3p_endo anti -B21 : A C3p_endo anti -B22 : G C3p_endo anti -B23 : U C3p_endo anti -B24 : C C3p_endo anti -B25 : G C3p_endo anti -B26 : C C1p_exo anti -B27 : C O4p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -B15-B16 : adjacent_5p outward -B16-B17 : adjacent_5p upward -B17-B18 : adjacent_5p upward -B18-B19 : adjacent_5p upward -B20-B21 : adjacent_5p upward -B22-B23 : adjacent_5p upward -B23-B24 : adjacent_5p upward -B24-B25 : adjacent_5p upward -B25-B26 : adjacent_5p upward -B26-B27 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-B25 : outward -A7-B22 : outward -A9-B19 : outward -A12-A14 : upward -Number of stackings = 24 -Number of adjacent stackings = 20 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A1-B27 : G-C Ww/Ww pairing antiparallel cis XIX -A2-B26 : G-C Ww/Ww pairing antiparallel cis XIX -A3-B25 : C-G Ww/Ww pairing antiparallel cis XIX -A4-B24 : G-C Ww/Ww pairing antiparallel cis XIX -A6-B22 : C-G Ww/Ww pairing antiparallel cis XIX -A8-B19 : C-G Ww/Ww pairing antiparallel cis XIX -A9-B18 : A-U Ww/Ww pairing antiparallel cis XX -A10-B17 : C-G Ww/Ww pairing antiparallel cis XIX -A11-B16 : C-G Ww/Ww pairing antiparallel cis XIX -A12-B15 : U-G Bs/Ww pairing parallel trans 87 -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : C C3p_endo anti -A7 : A C3p_endo anti -A8 : C C3p_endo anti -A9 : A C3p_endo anti -A10 : C C3p_endo anti -A11 : C C3p_endo anti -A12 : U C3p_endo anti -A13 : U C1p_exo anti -A14 : C C2p_endo anti -B15 : G C3p_endo syn -B16 : G C3p_endo anti -B17 : G C3p_endo anti -B18 : U C3p_endo anti -B19 : G C3p_endo anti -B20 : A C3p_endo anti -B21 : A C2p_exo anti -B22 : G C2p_exo anti -B23 : U C3p_endo anti -B24 : C C3p_endo anti -B25 : G C3p_endo anti -B26 : C C1p_exo anti -B27 : C O4p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -B15-B16 : adjacent_5p outward -B16-B17 : adjacent_5p upward -B17-B18 : adjacent_5p upward -B18-B19 : adjacent_5p upward -B20-B21 : adjacent_5p upward -B21-B22 : adjacent_5p upward -B22-B23 : adjacent_5p upward -B23-B24 : adjacent_5p upward -B24-B25 : adjacent_5p upward -B25-B26 : adjacent_5p upward -B26-B27 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-B25 : outward -A7-B22 : outward -A9-B19 : outward -A12-A14 : upward -Number of stackings = 25 -Number of adjacent stackings = 21 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A1-B27 : G-C Ww/Ww pairing antiparallel cis XIX -A2-B26 : G-C Ww/Ww pairing antiparallel cis XIX -A3-B25 : C-G Ww/Ww pairing antiparallel cis XIX -A4-B24 : G-C Ww/Ww pairing antiparallel cis XIX -A6-B22 : C-G Ww/Ww pairing antiparallel cis XIX -A8-B19 : C-G Ww/Ww pairing antiparallel cis XIX -A9-B18 : A-U Ww/Ww pairing antiparallel cis XX -A10-B17 : C-G Ww/Ww pairing antiparallel cis XIX -A11-B16 : C-G Ww/Ww pairing antiparallel cis XIX -A12-B15 : U-G Bs/Ww pairing parallel trans 87 -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : C C3p_endo anti -A7 : A C3p_endo anti -A8 : C C3p_endo anti -A9 : A C3p_endo anti -A10 : C C3p_endo anti -A11 : C C3p_endo anti -A12 : U C3p_endo anti -A13 : U C1p_exo anti -A14 : C C2p_endo anti -B15 : G C3p_endo syn -B16 : G C3p_endo anti -B17 : G C3p_endo anti -B18 : U C3p_endo anti -B19 : G C2p_exo anti -B20 : A C3p_endo anti -B21 : A C2p_endo anti -B22 : G C3p_endo anti -B23 : U C3p_endo anti -B24 : C C3p_endo anti -B25 : G C3p_endo anti -B26 : C C1p_exo anti -B27 : C O4p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -B15-B16 : adjacent_5p outward -B16-B17 : adjacent_5p upward -B17-B18 : adjacent_5p upward -B18-B19 : adjacent_5p upward -B20-B21 : adjacent_5p upward -B21-B22 : adjacent_5p upward -B22-B23 : adjacent_5p upward -B23-B24 : adjacent_5p upward -B24-B25 : adjacent_5p upward -B25-B26 : adjacent_5p upward -B26-B27 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-B25 : outward -A7-B22 : outward -A9-B19 : outward -A12-A14 : upward -Number of stackings = 26 -Number of adjacent stackings = 22 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A1-B27 : G-C Ww/Ww pairing antiparallel cis XIX -A2-B26 : G-C Ww/Ww pairing antiparallel cis XIX -A3-B25 : C-G Ww/Ww pairing antiparallel cis XIX -A4-B24 : G-C Ww/Ww pairing antiparallel cis XIX -A6-B22 : C-G Ww/Ww pairing antiparallel cis XIX -A8-B19 : C-G Ww/Ww pairing antiparallel cis XIX -A9-B18 : A-U Ww/Ww pairing antiparallel cis XX -A10-B17 : C-G Ww/Ww pairing antiparallel cis XIX -A11-B16 : C-G Ww/Ww pairing antiparallel cis XIX -A12-B15 : U-G Bs/Ww pairing parallel trans 87 -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : C C3p_endo anti -A7 : A C3p_endo anti -A8 : C C3p_endo anti -A9 : A C3p_endo anti -A10 : C C3p_endo anti -A11 : C C3p_endo anti -A12 : U C3p_endo anti -A13 : U C1p_exo anti -A14 : C C2p_endo anti -B15 : G C3p_endo syn -B16 : G C3p_endo anti -B17 : G C3p_endo anti -B18 : U C3p_endo anti -B19 : G C3p_endo anti -B20 : A O4p_endo anti -B21 : A C2p_endo anti -B22 : G C3p_endo anti -B23 : U C3p_endo anti -B24 : C C3p_endo anti -B25 : G C3p_endo anti -B26 : C C1p_exo anti -B27 : C O4p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -B15-B16 : adjacent_5p outward -B16-B17 : adjacent_5p upward -B17-B18 : adjacent_5p upward -B18-B19 : adjacent_5p upward -B20-B21 : adjacent_5p upward -B21-B22 : adjacent_5p upward -B22-B23 : adjacent_5p upward -B23-B24 : adjacent_5p upward -B24-B25 : adjacent_5p upward -B25-B26 : adjacent_5p upward -B26-B27 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-B25 : outward -A9-B19 : outward -A12-A14 : upward -Number of stackings = 25 -Number of adjacent stackings = 22 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -A1-B27 : G-C Ww/Ww pairing antiparallel cis XIX -A2-B26 : G-C Ww/Ww pairing antiparallel cis XIX -A3-B25 : C-G Ww/Ww pairing antiparallel cis XIX -A4-B24 : G-C Ww/Ww pairing antiparallel cis XIX -A6-B22 : C-G Ww/Ww pairing antiparallel cis XIX -A8-B19 : C-G Ww/Ww pairing antiparallel cis XIX -A9-B18 : A-U Ww/Ww pairing antiparallel cis XX -A10-B17 : C-G Ww/Ww pairing antiparallel cis -A11-B16 : C-G Ww/Ww pairing antiparallel cis XIX -A12-B15 : U-G Bs/Ww pairing parallel trans 87 -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : C C3p_endo anti -A7 : A C3p_endo anti -A8 : C C3p_endo anti -A9 : A C3p_endo anti -A10 : C C3p_endo anti -A11 : C C3p_endo anti -A12 : U C3p_endo anti -A13 : U C1p_exo anti -A14 : C C2p_endo anti -B15 : G C3p_endo syn -B16 : G C2p_exo anti -B17 : G C3p_endo anti -B18 : U C3p_endo anti -B19 : G C4p_exo anti -B20 : A C3p_endo anti -B21 : A C3p_endo anti -B22 : G C3p_endo anti -B23 : U C3p_endo anti -B24 : C C3p_endo anti -B25 : G C3p_endo anti -B26 : C C1p_exo anti -B27 : C O4p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -B15-B16 : adjacent_5p outward -B16-B17 : adjacent_5p upward -B17-B18 : adjacent_5p upward -B18-B19 : adjacent_5p upward -B20-B21 : adjacent_5p upward -B21-B22 : adjacent_5p upward -B22-B23 : adjacent_5p upward -B23-B24 : adjacent_5p upward -B24-B25 : adjacent_5p upward -B25-B26 : adjacent_5p upward -B26-B27 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-B25 : outward -A7-B22 : outward -A9-B19 : outward -A12-A14 : upward -Number of stackings = 25 -Number of adjacent stackings = 21 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A1-B27 : G-C Ww/Ww pairing antiparallel cis XIX -A2-B26 : G-C Ww/Ww pairing antiparallel cis XIX -A3-B25 : C-G Ww/Ww pairing antiparallel cis XIX -A4-B24 : G-C Ww/Ww pairing antiparallel cis XIX -A6-B22 : C-G Ww/Ww pairing antiparallel cis XIX -A8-B19 : C-G Ww/Ww pairing antiparallel cis XIX -A9-B18 : A-U Ww/Ww pairing antiparallel cis XX -A10-B17 : C-G Ww/Ww pairing antiparallel cis XIX -A11-B16 : C-G Ww/Ww pairing antiparallel cis XIX -A12-B15 : U-G Bs/Ww pairing parallel trans 87 -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : C C3p_endo anti -A7 : A C3p_endo anti -A8 : C C3p_endo anti -A9 : A C3p_endo anti -A10 : C C3p_endo anti -A11 : C C3p_endo anti -A12 : U C3p_endo anti -A13 : U C1p_exo anti -A14 : C C2p_endo anti -B15 : G C3p_endo syn -B16 : G C3p_endo anti -B17 : G C3p_endo anti -B18 : U C3p_endo anti -B19 : G C4p_exo anti -B20 : A C3p_endo anti -B21 : A C3p_endo anti -B22 : G C3p_endo anti -B23 : U C3p_endo anti -B24 : C C3p_endo anti -B25 : G C3p_endo anti -B26 : C C1p_exo anti -B27 : C O4p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -B15-B16 : adjacent_5p outward -B16-B17 : adjacent_5p upward -B17-B18 : adjacent_5p upward -B18-B19 : adjacent_5p upward -B20-B21 : adjacent_5p upward -B21-B22 : adjacent_5p upward -B22-B23 : adjacent_5p upward -B23-B24 : adjacent_5p upward -B24-B25 : adjacent_5p upward -B25-B26 : adjacent_5p upward -B26-B27 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-B25 : outward -A7-B22 : outward -A9-B19 : outward -A12-A14 : upward -Number of stackings = 25 -Number of adjacent stackings = 21 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A1-B27 : G-C Ww/Ww pairing antiparallel cis XIX -A2-B26 : G-C Ww/Ww pairing antiparallel cis XIX -A3-B25 : C-G Ww/Ww pairing antiparallel cis XIX -A4-B24 : G-C Ww/Ww pairing antiparallel cis XIX -A6-B22 : C-G Ww/Ww pairing antiparallel cis XIX -A8-B19 : C-G Ww/Ww pairing antiparallel cis XIX -A9-B18 : A-U Ww/Ww pairing antiparallel cis XX -A10-B17 : C-G Ww/Ww pairing antiparallel cis XIX -A11-B16 : C-G Ww/Ww pairing antiparallel cis XIX -A12-B15 : U-G Bs/Ww pairing parallel trans 87 -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : C C3p_endo anti -A7 : A C3p_endo anti -A8 : C C3p_endo anti -A9 : A C3p_endo anti -A10 : C C3p_endo anti -A11 : C C3p_endo anti -A12 : U C3p_endo anti -A13 : U C1p_exo anti -A14 : C C2p_endo anti -B15 : G C3p_endo syn -B16 : G C3p_endo anti -B17 : G C3p_endo anti -B18 : U C3p_endo anti -B19 : G C3p_endo anti -B20 : A C3p_endo anti -B21 : A C2p_exo anti -B22 : G C2p_exo anti -B23 : U C3p_endo anti -B24 : C C3p_endo anti -B25 : G C3p_endo anti -B26 : C C1p_exo anti -B27 : C O4p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -B15-B16 : adjacent_5p outward -B16-B17 : adjacent_5p upward -B17-B18 : adjacent_5p upward -B18-B19 : adjacent_5p upward -B20-B21 : adjacent_5p upward -B21-B22 : adjacent_5p upward -B22-B23 : adjacent_5p upward -B23-B24 : adjacent_5p upward -B24-B25 : adjacent_5p upward -B25-B26 : adjacent_5p upward -B26-B27 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-B25 : outward -A7-B22 : outward -A9-B19 : outward -A12-A14 : upward -Number of stackings = 26 -Number of adjacent stackings = 22 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A1-B27 : G-C Ww/Ww pairing antiparallel cis -A2-B26 : G-C Ww/Ww pairing antiparallel cis XIX -A3-B25 : C-G Ww/Ww pairing antiparallel cis XIX -A4-B24 : G-C Ww/Ww pairing antiparallel cis XIX -A6-B22 : C-G Ww/Ww pairing antiparallel cis XIX -A8-B19 : C-G Ww/Ww pairing antiparallel cis XIX -A9-B18 : A-U Ww/Ww pairing antiparallel cis XX -A10-B17 : C-G Ww/Ww pairing antiparallel cis XIX -A11-B16 : C-G Ww/Ww pairing antiparallel cis XIX -A12-B15 : U-G Bs/Ww pairing parallel trans 87 -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : C C3p_endo anti -A7 : A C3p_endo anti -A8 : C C3p_endo anti -A9 : A C3p_endo anti -A10 : C C3p_endo anti -A11 : C C3p_endo anti -A12 : U C3p_endo anti -A13 : U C1p_exo anti -A14 : C C2p_endo anti -B15 : G C3p_endo syn -B16 : G C3p_endo anti -B17 : G C3p_endo anti -B18 : U C3p_endo anti -B19 : G C2p_exo anti -B20 : A C3p_endo anti -B21 : A C2p_endo anti -B22 : G C3p_endo anti -B23 : U C3p_endo anti -B24 : C C3p_endo anti -B25 : G C3p_endo anti -B26 : C C1p_exo anti -B27 : C O4p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -B15-B16 : adjacent_5p outward -B16-B17 : adjacent_5p upward -B17-B18 : adjacent_5p upward -B18-B19 : adjacent_5p upward -B20-B21 : adjacent_5p upward -B21-B22 : adjacent_5p upward -B22-B23 : adjacent_5p upward -B23-B24 : adjacent_5p upward -B24-B25 : adjacent_5p upward -B25-B26 : adjacent_5p upward -B26-B27 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-B25 : outward -A7-B22 : outward -A9-B19 : outward -A12-A14 : upward -Number of stackings = 26 -Number of adjacent stackings = 22 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A1-B27 : G-C Ww/Ww pairing antiparallel cis XIX -A2-B26 : G-C Ww/Ww pairing antiparallel cis XIX -A3-B25 : C-G Ww/Ww pairing antiparallel cis XIX -A4-B24 : G-C Ww/Ww pairing antiparallel cis XIX -A6-B22 : C-G Ww/Ww pairing antiparallel cis XIX -A8-B19 : C-G Ww/Ww pairing antiparallel cis XIX -A9-B18 : A-U Ww/Ww pairing antiparallel cis XX -A10-B17 : C-G Ww/Ww pairing antiparallel cis XIX -A11-B16 : C-G Ww/Ww pairing antiparallel cis XIX -A12-B15 : U-G Bs/Ww pairing parallel trans 87 -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : C C3p_endo anti -A7 : A C3p_endo anti -A8 : C C3p_endo anti -A9 : A C3p_endo anti -A10 : C C3p_endo anti -A11 : C C3p_endo anti -A12 : U C3p_endo anti -A13 : U C1p_exo anti -A14 : C C2p_endo anti -B15 : G C3p_endo syn -B16 : G C3p_endo anti -B17 : G C3p_endo anti -B18 : U C3p_endo anti -B19 : G C2p_exo anti -B20 : A C3p_endo anti -B21 : A C2p_exo anti -B22 : G C3p_endo anti -B23 : U C3p_endo anti -B24 : C C3p_endo anti -B25 : G C3p_endo anti -B26 : C C1p_exo anti -B27 : C O4p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -B15-B16 : adjacent_5p outward -B16-B17 : adjacent_5p upward -B17-B18 : adjacent_5p upward -B18-B19 : adjacent_5p upward -B20-B21 : adjacent_5p upward -B21-B22 : adjacent_5p upward -B22-B23 : adjacent_5p upward -B23-B24 : adjacent_5p upward -B24-B25 : adjacent_5p upward -B25-B26 : adjacent_5p upward -B26-B27 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-B25 : outward -A7-B22 : outward -A9-B19 : outward -A12-A14 : upward -Number of stackings = 26 -Number of adjacent stackings = 22 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A1-B27 : G-C Ww/Ww pairing antiparallel cis XIX -A2-B26 : G-C Ww/Ww pairing antiparallel cis XIX -A3-B25 : C-G Ww/Ww pairing antiparallel cis XIX -A4-B24 : G-C Ww/Ww pairing antiparallel cis -A6-B22 : C-G Ww/Ww pairing antiparallel cis XIX -A8-B19 : C-G Ww/Ww pairing antiparallel cis XIX -A9-B18 : A-U Ww/Ww pairing antiparallel cis XX -A10-B17 : C-G Ww/Ww pairing antiparallel cis XIX -A11-B16 : C-G Ww/Ww pairing antiparallel cis XIX -A12-B15 : U-G Bs/Ww pairing parallel trans 87 -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : C C3p_endo anti -A7 : A C3p_endo anti -A8 : C C3p_endo anti -A9 : A C3p_endo anti -A10 : C C3p_endo anti -A11 : C C3p_endo anti -A12 : U C3p_endo anti -A13 : U C1p_exo anti -A14 : C C2p_endo anti -B15 : G C3p_endo syn -B16 : G C3p_endo anti -B17 : G C3p_endo anti -B18 : U C3p_endo anti -B19 : G C2p_exo anti -B20 : A C3p_endo anti -B21 : A C2p_endo anti -B22 : G C3p_endo anti -B23 : U C3p_endo anti -B24 : C C3p_endo anti -B25 : G C3p_endo anti -B26 : C C1p_exo anti -B27 : C O4p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -B15-B16 : adjacent_5p outward -B16-B17 : adjacent_5p upward -B17-B18 : adjacent_5p upward -B18-B19 : adjacent_5p upward -B20-B21 : adjacent_5p upward -B21-B22 : adjacent_5p upward -B22-B23 : adjacent_5p upward -B23-B24 : adjacent_5p upward -B24-B25 : adjacent_5p upward -B25-B26 : adjacent_5p upward -B26-B27 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-B25 : outward -A7-B22 : outward -A9-B19 : outward -A12-A14 : upward -Number of stackings = 26 -Number of adjacent stackings = 22 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A1-B27 : G-C Ww/Ww pairing antiparallel cis XIX -A2-B26 : G-C Ww/Ww pairing antiparallel cis XIX -A3-B25 : C-G Ww/Ww pairing antiparallel cis XIX -A4-B24 : G-C Ww/Ww pairing antiparallel cis XIX -A6-B22 : C-G Ww/Ww pairing antiparallel cis XIX -A8-B19 : C-G Ww/Ww pairing antiparallel cis XIX -A9-B18 : A-U Ww/Ww pairing antiparallel cis XX -A10-B17 : C-G Ww/Ww pairing antiparallel cis XIX -A11-B16 : C-G Ww/Ww pairing antiparallel cis XIX -A12-B15 : U-G Bs/Ww pairing parallel trans 87 -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : C C3p_endo anti -A7 : A C3p_endo anti -A8 : C C3p_endo anti -A9 : A C3p_endo anti -A10 : C C3p_endo anti -A11 : C C3p_endo anti -A12 : U C3p_endo anti -A13 : U C1p_exo anti -A14 : C C2p_endo anti -B15 : G C3p_endo syn -B16 : G C3p_endo anti -B17 : G C3p_endo anti -B18 : U C3p_endo anti -B19 : G C2p_exo anti -B20 : A C3p_endo anti -B21 : A C2p_exo anti -B22 : G C3p_endo anti -B23 : U C3p_endo anti -B24 : C C3p_endo anti -B25 : G C3p_endo anti -B26 : C C1p_exo anti -B27 : C O4p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -B15-B16 : adjacent_5p outward -B16-B17 : adjacent_5p upward -B17-B18 : adjacent_5p upward -B18-B19 : adjacent_5p upward -B20-B21 : adjacent_5p upward -B21-B22 : adjacent_5p upward -B22-B23 : adjacent_5p upward -B23-B24 : adjacent_5p upward -B24-B25 : adjacent_5p upward -B25-B26 : adjacent_5p upward -B26-B27 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-B25 : outward -A7-B22 : outward -A9-B19 : outward -A12-A14 : upward -Number of stackings = 25 -Number of adjacent stackings = 21 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A1-B27 : G-C Ww/Ww pairing antiparallel cis XIX -A2-B26 : G-C Ww/Ww pairing antiparallel cis XIX -A3-B25 : C-G Ww/Ww pairing antiparallel cis XIX -A4-B24 : G-C Ww/Ww pairing antiparallel cis XIX -A6-B22 : C-G Ww/Ww pairing antiparallel cis XIX -A8-B19 : C-G Ww/Ww pairing antiparallel cis XIX -A9-B18 : A-U Ww/Ww pairing antiparallel cis XX -A10-B17 : C-G Ww/Ww pairing antiparallel cis XIX -A11-B16 : C-G Ww/Ww pairing antiparallel cis XIX -A12-B15 : U-G Bs/Ww pairing parallel trans 87 -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : C C3p_endo anti -A7 : A C3p_endo anti -A8 : C C3p_endo anti -A9 : A C3p_endo anti -A10 : C C3p_endo anti -A11 : C C3p_endo anti -A12 : U C3p_endo anti -A13 : U C1p_exo anti -A14 : C C2p_endo anti -B15 : G C3p_endo syn -B16 : G C3p_endo anti -B17 : G C3p_endo anti -B18 : U C3p_endo anti -B19 : G C3p_endo anti -B20 : A C4p_exo anti -B21 : A C4p_exo anti -B22 : G C2p_exo anti -B23 : U C3p_endo anti -B24 : C C3p_endo anti -B25 : G C3p_endo anti -B26 : C C1p_exo anti -B27 : C O4p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -B15-B16 : adjacent_5p outward -B16-B17 : adjacent_5p upward -B17-B18 : adjacent_5p upward -B18-B19 : adjacent_5p upward -B22-B23 : adjacent_5p upward -B23-B24 : adjacent_5p upward -B24-B25 : adjacent_5p upward -B25-B26 : adjacent_5p upward -B26-B27 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-B25 : outward -A7-B22 : outward -A9-B19 : outward -A12-A14 : upward -Number of stackings = 24 -Number of adjacent stackings = 20 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A1-B27 : G-C Ww/Ww pairing antiparallel cis XIX -A2-B26 : G-C Ww/Ww pairing antiparallel cis XIX -A3-B25 : C-G Ww/Ww pairing antiparallel cis XIX -A4-B24 : G-C Ww/Ww pairing antiparallel cis XIX -A6-B22 : C-G Ww/Ww pairing antiparallel cis XIX -A8-B19 : C-G Ww/Ww pairing antiparallel cis XIX -A9-B18 : A-U Ww/Ww pairing antiparallel cis XX -A10-B17 : C-G Ww/Ww pairing antiparallel cis XIX -A11-B16 : C-G Ww/Ww pairing antiparallel cis XIX -A12-B15 : U-G Bs/Ww pairing parallel trans 87 diff --git a/MCdata/1a4d_MC b/MCdata/1a4d_MC deleted file mode 100644 index c5ce1d35abf3e16b5636af86840dcaa592df122e..0000000000000000000000000000000000000000 --- a/MCdata/1a4d_MC +++ /dev/null @@ -1,101 +0,0 @@ -Residue conformations ------------------------------------------- -A68 : G C3p_endo anti -A69 : G C3p_endo anti -A70 : C C3p_endo anti -A71 : C C3p_endo anti -A72 : G C3p_endo anti -A73 : A C2p_exo anti -A74 : U C3p_endo anti -A75 : G C3p_endo anti -A76 : G C3p_endo anti -A77 : U C3p_endo anti -A78 : A C3p_endo anti -A79 : G C3p_endo anti -A80 : U C3p_endo anti -A81 : G C3p_endo anti -A82 : U C3p_endo anti -A83 : G C3p_endo anti -A84 : G C3p_endo anti -A85 : G C3p_endo anti -A86 : G C3p_endo anti -A87 : U C4p_exo anti -A88 : C C2p_endo anti -B89 : U C3p_endo anti -B90 : C C2p_exo anti -B91 : C C3p_endo anti -B92 : C C3p_endo anti -B93 : C C3p_endo anti -B94 : A C3p_endo anti -B95 : U C3p_endo anti -B96 : G C3p_endo anti -B97 : C C3p_endo anti -B98 : G C3p_endo anti -B99 : A C2p_exo anti -B100 : G C3p_endo anti -B101 : A C2p_exo anti -B102 : G C3p_endo anti -B103 : U C3p_endo anti -B104 : A C3p_endo anti -B105 : G C3p_endo anti -B106 : G C3p_endo anti -B107 : C C3p_endo anti -B108 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A68-A69 : adjacent_5p upward -A69-A70 : adjacent_5p upward -A71-A72 : adjacent_5p upward -A73-A74 : adjacent_5p upward -A74-A75 : adjacent_5p upward -A75-A76 : adjacent_5p upward -A76-A77 : adjacent_5p upward -A77-A78 : adjacent_5p upward -A78-A79 : adjacent_5p upward -A79-A80 : adjacent_5p upward -A81-A82 : adjacent_5p upward -A82-A83 : adjacent_5p upward -A83-A84 : adjacent_5p upward -A84-A85 : adjacent_5p upward -A85-A86 : adjacent_5p upward -B93-B94 : adjacent_5p upward -B94-B95 : adjacent_5p upward -B96-B97 : adjacent_5p upward -B97-B98 : adjacent_5p upward -B99-B100 : adjacent_5p upward -B100-B101 : adjacent_5p upward -B101-B102 : adjacent_5p upward -B102-B103 : adjacent_5p upward -B103-B104 : adjacent_5p upward -B104-B105 : adjacent_5p upward -B105-B106 : adjacent_5p upward -B106-B107 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A73-B104 : outward -A78-B99 : outward -A81-B96 : outward -A83-B94 : outward -Number of stackings = 31 -Number of adjacent stackings = 27 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A68-B108 : G-C Ww/Ww pairing antiparallel cis XIX -A69-B107 : G-C Ww/Ww pairing antiparallel cis XIX -A70-B106 : C-G Ww/Ww pairing antiparallel cis XIX -A71-B105 : C-G Ww/Ww pairing antiparallel cis XIX -A72-B102 : G-G Hh/O2P pairing -A72-B103 : G-U Ww/O2P Bs/O2P pairing -A72-B104 : G-A Ss/Hh pairing antiparallel trans XI -A73-B103 : A-U Hh/Ws pairing antiparallel trans XXIV -A74-B102 : U-G Hh/Ww pairing antiparallel trans one_hbond 91 -A75-B101 : G-A Hw/Wh pairing antiparallel cis one_hbond 64 -A76-B100 : G-G Ww/Bh pairing antiparallel trans 115 -A77-B99 : U-A Ws/Hh pairing antiparallel trans XXIV -A78-B98 : A-G Hh/Ss Bh/O2' pairing antiparallel trans XI -A79-B97 : G-C Ww/Ww pairing antiparallel cis XIX -A80-B96 : U-G Ws/Ww pairing antiparallel cis XXVIII -A81-B95 : G-U Ww/Ws pairing antiparallel cis XXVIII -A82-B94 : U-A Ww/Ww pairing antiparallel cis XX -A83-B93 : G-C Ww/Ww pairing antiparallel cis XIX -A84-B92 : G-C Ww/Ww pairing antiparallel cis XIX -A85-B91 : G-C Ww/Ww pairing antiparallel cis XIX -A86-B90 : G-C Bs/Ww pairing antiparallel cis 128 -B89-B90 : U-C O2P/Ww O2P/Bh adjacent_5p pairing diff --git a/MCdata/1a4t_MC b/MCdata/1a4t_MC deleted file mode 100644 index 878eae5e404eeb242fb10e4dca1fc01af744b404..0000000000000000000000000000000000000000 --- a/MCdata/1a4t_MC +++ /dev/null @@ -1,1186 +0,0 @@ -Residue conformations ------------------------------------------- -A4 : G C4p_exo anti -A5 : C C2p_exo anti -A6 : G C2p_exo anti -A7 : C C3p_endo anti -A8 : U C2p_exo anti -A9 : G C3p_endo anti -A10 : A C2p_endo anti -A11 : C C1p_exo anti -A12 : A C3p_endo anti -A13 : A C3p_endo anti -A14 : A C2p_exo anti -A15 : G C2p_exo anti -A16 : C C3p_endo anti -A17 : G C2p_exo anti -A18 : C C3p_endo anti -B1 : ASN -B2 : ALA -B3 : LYS -B4 : THR -B5 : ARG -B6 : ARG -B7 : HIS -B8 : GLU -B9 : ARG -B10 : ARG -B11 : ARG -B12 : LYS -B13 : LEU -B14 : ALA -B15 : ILE -B16 : GLU -B17 : ARG -B18 : ASP -B19 : THR -Adjacent stackings ---------------------------------------------- -A4-A5 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A17-A18 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A6-A17 : outward -A10-A12 : upward -Number of stackings = 10 -Number of adjacent stackings = 8 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A4-A18 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A6-A16 : G-C Ww/Ww pairing antiparallel cis XIX -A7-A15 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A14 : U-A Ww/Ww pairing antiparallel cis XX -A9-A12 : G-A O2'/Hh Ww/O2P pairing -A9-A13 : G-A Bs/Hh Bs/O2P pairing antiparallel trans one_hbond -A9-B6 : G-ARG pairing one_hbond -A15-B3 : G-LYS pairing one_hbond -Residue conformations ------------------------------------------- -A4 : G C3p_endo anti -A5 : C C3p_endo anti -A6 : G C2p_exo anti -A7 : C C3p_endo anti -A8 : U C2p_exo anti -A9 : G C3p_endo anti -A10 : A C1p_exo anti -A11 : C C1p_exo anti -A12 : A C3p_endo anti -A13 : A C3p_endo anti -A14 : A C2p_exo anti -A15 : G C2p_exo anti -A16 : C C3p_endo anti -A17 : G C3p_endo anti -A18 : C C3p_endo anti -B1 : ASN -B2 : ALA -B3 : LYS -B4 : THR -B5 : ARG -B6 : ARG -B7 : HIS -B8 : GLU -B9 : ARG -B10 : ARG -B11 : ARG -B12 : LYS -B13 : LEU -B14 : ALA -B15 : ILE -B16 : GLU -B17 : ARG -B18 : ASP -B19 : THR -Adjacent stackings ---------------------------------------------- -A4-A5 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A17-A18 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A6-A17 : outward -A10-A12 : upward -Number of stackings = 10 -Number of adjacent stackings = 8 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A4-A18 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A6-A16 : G-C Ww/Ww pairing antiparallel cis XIX -A7-A15 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A14 : U-A Ww/Ww pairing antiparallel cis XX -A9-A12 : G-A O2'/Hh pairing -A9-A13 : G-A Bs/O2P pairing -A9-B6 : G-ARG pairing one_hbond -A14-B3 : A-LYS pairing one_hbond -Residue conformations ------------------------------------------- -A4 : G C4p_exo anti -A5 : C C3p_endo anti -A6 : G C2p_exo anti -A7 : C C3p_endo anti -A8 : U C2p_exo anti -A9 : G C3p_endo anti -A10 : A O4p_endo anti -A11 : C C1p_exo anti -A12 : A C3p_endo anti -A13 : A C3p_endo anti -A14 : A C2p_exo anti -A15 : G C2p_exo anti -A16 : C C3p_endo anti -A17 : G C3p_endo anti -A18 : C C3p_endo anti -B1 : ASN -B2 : ALA -B3 : LYS -B4 : THR -B5 : ARG -B6 : ARG -B7 : HIS -B8 : GLU -B9 : ARG -B10 : ARG -B11 : ARG -B12 : LYS -B13 : LEU -B14 : ALA -B15 : ILE -B16 : GLU -B17 : ARG -B18 : ASP -B19 : THR -Adjacent stackings ---------------------------------------------- -A4-A5 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A17-A18 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A6-A17 : outward -A10-A12 : upward -Number of stackings = 10 -Number of adjacent stackings = 8 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A4-A18 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A6-A16 : G-C Ww/Ww pairing antiparallel cis XIX -A7-A15 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A14 : U-A Ww/Ww pairing antiparallel cis XX -A9-A12 : G-A O2'/Hh pairing -A9-A13 : G-A Bs/O2P pairing -A9-B6 : G-ARG pairing one_hbond -A14-B3 : A-LYS pairing one_hbond -Residue conformations ------------------------------------------- -A4 : G C4p_exo anti -A5 : C C3p_endo anti -A6 : G C2p_exo anti -A7 : C C3p_endo anti -A8 : U C2p_exo anti -A9 : G C3p_endo anti -A10 : A C1p_exo anti -A11 : C C1p_exo anti -A12 : A C3p_endo anti -A13 : A C3p_endo anti -A14 : A C2p_exo anti -A15 : G C2p_exo anti -A16 : C C3p_endo anti -A17 : G C3p_endo anti -A18 : C C3p_endo anti -B1 : ASN -B2 : ALA -B3 : LYS -B4 : THR -B5 : ARG -B6 : ARG -B7 : HIS -B8 : GLU -B9 : ARG -B10 : ARG -B11 : ARG -B12 : LYS -B13 : LEU -B14 : ALA -B15 : ILE -B16 : GLU -B17 : ARG -B18 : ASP -B19 : THR -Adjacent stackings ---------------------------------------------- -A4-A5 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A17-A18 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A6-A17 : outward -A10-A12 : upward -Number of stackings = 10 -Number of adjacent stackings = 8 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A4-A18 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A6-A16 : G-C Ww/Ww pairing antiparallel cis XIX -A7-A15 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A14 : U-A Ww/Ww pairing antiparallel cis XX -A9-A12 : G-A O2'/Hh Ww/O2P pairing -A9-A13 : G-A Bs/Hh Ws/O2P pairing antiparallel trans one_hbond -A9-B6 : G-ARG pairing one_hbond -A15-B3 : G-LYS pairing -Residue conformations ------------------------------------------- -A4 : G C3p_endo anti -A5 : C C2p_exo anti -A6 : G C2p_exo anti -A7 : C C3p_endo anti -A8 : U C2p_exo anti -A9 : G C3p_endo anti -A10 : A C3p_exo anti -A11 : C C2p_endo anti -A12 : A C3p_endo anti -A13 : A C3p_endo anti -A14 : A C2p_exo anti -A15 : G C2p_exo anti -A16 : C C3p_endo anti -A17 : G C2p_exo anti -A18 : C C3p_endo anti -B1 : ASN -B2 : ALA -B3 : LYS -B4 : THR -B5 : ARG -B6 : ARG -B7 : HIS -B8 : GLU -B9 : ARG -B10 : ARG -B11 : ARG -B12 : LYS -B13 : LEU -B14 : ALA -B15 : ILE -B16 : GLU -B17 : ARG -B18 : ASP -B19 : THR -Adjacent stackings ---------------------------------------------- -A4-A5 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A17-A18 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A6-A17 : outward -A10-A12 : upward -Number of stackings = 9 -Number of adjacent stackings = 7 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A4-A18 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A6-A16 : G-C Ww/Ww pairing antiparallel cis XIX -A7-A15 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A14 : U-A Ww/Ww pairing antiparallel cis XX -A9-A12 : G-A O2'/Hh Bs/O2P pairing -A9-A13 : G-A Bs/O2P pairing -A9-B6 : G-ARG pairing one_hbond -A15-B3 : G-LYS pairing one_hbond -Residue conformations ------------------------------------------- -A4 : G C4p_exo anti -A5 : C C3p_endo anti -A6 : G C2p_exo anti -A7 : C C3p_endo anti -A8 : U C3p_endo anti -A9 : G C3p_endo anti -A10 : A O4p_endo anti -A11 : C C1p_exo anti -A12 : A C3p_endo anti -A13 : A C2p_exo anti -A14 : A C2p_exo anti -A15 : G C2p_exo anti -A16 : C C2p_exo anti -A17 : G C3p_endo anti -A18 : C C3p_endo anti -B1 : ASN -B2 : ALA -B3 : LYS -B4 : THR -B5 : ARG -B6 : ARG -B7 : HIS -B8 : GLU -B9 : ARG -B10 : ARG -B11 : ARG -B12 : LYS -B13 : LEU -B14 : ALA -B15 : ILE -B16 : GLU -B17 : ARG -B18 : ASP -B19 : THR -Adjacent stackings ---------------------------------------------- -A4-A5 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A17-A18 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A6-A17 : outward -A10-A12 : upward -Number of stackings = 10 -Number of adjacent stackings = 8 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A4-A18 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A6-A16 : G-C Ww/Ww pairing antiparallel cis XIX -A7-A15 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A14 : U-A Ww/Ww pairing antiparallel cis XX -A9-A12 : G-A O2'/Hh pairing -A9-A13 : G-A Bs/O2P pairing -A9-B6 : G-ARG pairing one_hbond -A14-B3 : A-LYS pairing one_hbond -Residue conformations ------------------------------------------- -A4 : G C4p_exo anti -A5 : C C3p_endo anti -A6 : G C2p_exo anti -A7 : C C3p_endo anti -A8 : U C3p_endo anti -A9 : G C3p_endo anti -A10 : A C1p_exo anti -A11 : C C1p_exo anti -A12 : A C3p_endo anti -A13 : A C3p_endo anti -A14 : A C2p_exo anti -A15 : G C2p_exo anti -A16 : C C2p_exo anti -A17 : G C3p_endo anti -A18 : C C3p_endo anti -B1 : ASN -B2 : ALA -B3 : LYS -B4 : THR -B5 : ARG -B6 : ARG -B7 : HIS -B8 : GLU -B9 : ARG -B10 : ARG -B11 : ARG -B12 : LYS -B13 : LEU -B14 : ALA -B15 : ILE -B16 : GLU -B17 : ARG -B18 : ASP -B19 : THR -Adjacent stackings ---------------------------------------------- -A4-A5 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A17-A18 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A6-A17 : outward -A10-A12 : upward -Number of stackings = 10 -Number of adjacent stackings = 8 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A4-A18 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A6-A16 : G-C Ww/Ww pairing antiparallel cis XIX -A7-A15 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A14 : U-A Ww/Ww pairing antiparallel cis XX -A9-A13 : G-A Bs/Hh pairing antiparallel trans one_hbond -A9-B6 : G-ARG pairing one_hbond -Residue conformations ------------------------------------------- -A4 : G C4p_exo anti -A5 : C C3p_endo anti -A6 : G C2p_exo anti -A7 : C C3p_endo anti -A8 : U C3p_endo anti -A9 : G C3p_endo anti -A10 : A C1p_exo anti -A11 : C C1p_exo anti -A12 : A C2p_exo anti -A13 : A C3p_endo anti -A14 : A C2p_exo anti -A15 : G C2p_exo anti -A16 : C C3p_endo anti -A17 : G C3p_endo anti -A18 : C C3p_endo anti -B1 : ASN -B2 : ALA -B3 : LYS -B4 : THR -B5 : ARG -B6 : ARG -B7 : HIS -B8 : GLU -B9 : ARG -B10 : ARG -B11 : ARG -B12 : LYS -B13 : LEU -B14 : ALA -B15 : ILE -B16 : GLU -B17 : ARG -B18 : ASP -B19 : THR -Adjacent stackings ---------------------------------------------- -A4-A5 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A17-A18 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A6-A17 : outward -A10-A12 : upward -Number of stackings = 10 -Number of adjacent stackings = 8 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A4-A18 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A6-A16 : G-C Ww/Ww pairing antiparallel cis XIX -A7-A15 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A14 : U-A Ww/Ww pairing antiparallel cis XX -A9-A12 : G-A O2'/Hh pairing -A9-A13 : G-A Bs/Hh Ws/O2P pairing antiparallel trans one_hbond -Residue conformations ------------------------------------------- -A4 : G C4p_exo anti -A5 : C C3p_endo anti -A6 : G C2p_exo anti -A7 : C C3p_endo anti -A8 : U C2p_exo anti -A9 : G C3p_endo anti -A10 : A C1p_exo anti -A11 : C C1p_exo anti -A12 : A C3p_endo anti -A13 : A C3p_endo anti -A14 : A C2p_exo anti -A15 : G C2p_exo anti -A16 : C C2p_exo anti -A17 : G C3p_endo anti -A18 : C C3p_endo anti -B1 : ASN -B2 : ALA -B3 : LYS -B4 : THR -B5 : ARG -B6 : ARG -B7 : HIS -B8 : GLU -B9 : ARG -B10 : ARG -B11 : ARG -B12 : LYS -B13 : LEU -B14 : ALA -B15 : ILE -B16 : GLU -B17 : ARG -B18 : ASP -B19 : THR -Adjacent stackings ---------------------------------------------- -A4-A5 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A17-A18 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A6-A17 : outward -A10-A12 : upward -Number of stackings = 10 -Number of adjacent stackings = 8 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A4-A18 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A6-A16 : G-C Ww/Ww pairing antiparallel cis XIX -A7-A15 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A14 : U-A Ww/Ww pairing antiparallel cis XX -A9-A12 : G-A Ww/O2P pairing -A9-A13 : G-A Ws/O2P pairing -A9-B6 : G-ARG pairing one_hbond -Residue conformations ------------------------------------------- -A4 : G C4p_exo anti -A5 : C C3p_endo anti -A6 : G C2p_exo anti -A7 : C C3p_endo anti -A8 : U C3p_endo anti -A9 : G C3p_endo anti -A10 : A C2p_endo anti -A11 : C C1p_exo anti -A12 : A C3p_endo anti -A13 : A C3p_endo anti -A14 : A C2p_exo anti -A15 : G C2p_exo anti -A16 : C C3p_endo anti -A17 : G C2p_exo anti -A18 : C C3p_endo anti -B1 : ASN -B2 : ALA -B3 : LYS -B4 : THR -B5 : ARG -B6 : ARG -B7 : HIS -B8 : GLU -B9 : ARG -B10 : ARG -B11 : ARG -B12 : LYS -B13 : LEU -B14 : ALA -B15 : ILE -B16 : GLU -B17 : ARG -B18 : ASP -B19 : THR -Adjacent stackings ---------------------------------------------- -A4-A5 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A17-A18 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A6-A17 : outward -A10-A12 : upward -Number of stackings = 10 -Number of adjacent stackings = 8 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A4-A18 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A6-A16 : G-C Ww/Ww pairing antiparallel cis XIX -A7-A15 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A14 : U-A Ww/Ww pairing antiparallel cis XX -A9-A12 : G-A O2'/Hh pairing -A9-A13 : G-A Ws/O2P pairing -A9-B6 : G-ARG pairing one_hbond -Residue conformations ------------------------------------------- -A4 : G C4p_exo anti -A5 : C C2p_exo anti -A6 : G C2p_exo anti -A7 : C C3p_endo anti -A8 : U C3p_endo anti -A9 : G C3p_endo anti -A10 : A C2p_endo anti -A11 : C C1p_exo anti -A12 : A C3p_endo anti -A13 : A C3p_endo anti -A14 : A C2p_exo anti -A15 : G C2p_exo anti -A16 : C C2p_exo anti -A17 : G C3p_endo anti -A18 : C C3p_endo anti -B1 : ASN -B2 : ALA -B3 : LYS -B4 : THR -B5 : ARG -B6 : ARG -B7 : HIS -B8 : GLU -B9 : ARG -B10 : ARG -B11 : ARG -B12 : LYS -B13 : LEU -B14 : ALA -B15 : ILE -B16 : GLU -B17 : ARG -B18 : ASP -B19 : THR -Adjacent stackings ---------------------------------------------- -A4-A5 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A17-A18 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A6-A17 : outward -A10-A12 : upward -Number of stackings = 10 -Number of adjacent stackings = 8 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A4-A18 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A6-A16 : G-C Ww/Ww pairing antiparallel cis XIX -A7-A15 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A14 : U-A Ww/Ww pairing antiparallel cis XX -A9-A12 : G-A O2'/Hh Ww/O2P pairing -A9-A13 : G-A Bs/O2P pairing -A9-B6 : G-ARG pairing one_hbond -Residue conformations ------------------------------------------- -A4 : G C4p_exo anti -A5 : C C3p_endo anti -A6 : G C2p_exo anti -A7 : C C3p_endo anti -A8 : U C3p_endo anti -A9 : G C3p_endo anti -A10 : A O4p_endo anti -A11 : C C1p_exo anti -A12 : A C3p_endo anti -A13 : A C3p_endo anti -A14 : A C2p_exo anti -A15 : G C2p_exo anti -A16 : C C3p_endo anti -A17 : G C3p_endo anti -A18 : C C3p_endo anti -B1 : ASN -B2 : ALA -B3 : LYS -B4 : THR -B5 : ARG -B6 : ARG -B7 : HIS -B8 : GLU -B9 : ARG -B10 : ARG -B11 : ARG -B12 : LYS -B13 : LEU -B14 : ALA -B15 : ILE -B16 : GLU -B17 : ARG -B18 : ASP -B19 : THR -Adjacent stackings ---------------------------------------------- -A4-A5 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A17-A18 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A6-A17 : outward -A10-A12 : upward -Number of stackings = 10 -Number of adjacent stackings = 8 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A4-A18 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A6-A16 : G-C Ww/Ww pairing antiparallel cis XIX -A7-A15 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A14 : U-A Ww/Ww pairing antiparallel cis XX -A9-A12 : G-A Ww/O2P pairing -A9-A13 : G-A Ws/O2P pairing -A9-B6 : G-ARG pairing one_hbond -A14-B3 : A-LYS pairing one_hbond -Residue conformations ------------------------------------------- -A4 : G C4p_exo anti -A5 : C C3p_endo anti -A6 : G C2p_exo anti -A7 : C C3p_endo anti -A8 : U C3p_endo anti -A9 : G C3p_endo anti -A10 : A C2p_endo anti -A11 : C C1p_exo anti -A12 : A C3p_endo anti -A13 : A C3p_endo anti -A14 : A C2p_exo anti -A15 : G C2p_exo anti -A16 : C C3p_endo anti -A17 : G C2p_exo anti -A18 : C C3p_endo anti -B1 : ASN -B2 : ALA -B3 : LYS -B4 : THR -B5 : ARG -B6 : ARG -B7 : HIS -B8 : GLU -B9 : ARG -B10 : ARG -B11 : ARG -B12 : LYS -B13 : LEU -B14 : ALA -B15 : ILE -B16 : GLU -B17 : ARG -B18 : ASP -B19 : THR -Adjacent stackings ---------------------------------------------- -A4-A5 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A17-A18 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A6-A17 : outward -A10-A12 : upward -Number of stackings = 10 -Number of adjacent stackings = 8 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A4-A18 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A6-A16 : G-C Ww/Ww pairing antiparallel cis XIX -A7-A15 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A14 : U-A Ww/Ww pairing antiparallel cis XX -A9-A13 : G-A Bs/Hh Ws/O2P pairing antiparallel trans one_hbond -A9-B6 : G-ARG pairing one_hbond -Residue conformations ------------------------------------------- -A4 : G C4p_exo anti -A5 : C C3p_endo anti -A6 : G C2p_exo anti -A7 : C C3p_endo anti -A8 : U C2p_exo anti -A9 : G C3p_endo anti -A10 : A O4p_endo anti -A11 : C C1p_exo anti -A12 : A C3p_endo anti -A13 : A C3p_endo anti -A14 : A C2p_exo anti -A15 : G C2p_exo anti -A16 : C C3p_endo anti -A17 : G C2p_exo anti -A18 : C C3p_endo anti -B1 : ASN -B2 : ALA -B3 : LYS -B4 : THR -B5 : ARG -B6 : ARG -B7 : HIS -B8 : GLU -B9 : ARG -B10 : ARG -B11 : ARG -B12 : LYS -B13 : LEU -B14 : ALA -B15 : ILE -B16 : GLU -B17 : ARG -B18 : ASP -B19 : THR -Adjacent stackings ---------------------------------------------- -A4-A5 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A17-A18 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A6-A17 : outward -A10-A12 : upward -Number of stackings = 10 -Number of adjacent stackings = 8 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A4-A18 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A6-A16 : G-C Ww/Ww pairing antiparallel cis XIX -A7-A15 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A14 : U-A Ww/Ww pairing antiparallel cis XX -A9-A12 : G-A O2'/Hh Ww/O2P pairing -A9-A13 : G-A Bs/O2P pairing -A9-B6 : G-ARG pairing one_hbond -A14-B3 : A-LYS pairing one_hbond -Residue conformations ------------------------------------------- -A4 : G C4p_exo anti -A5 : C C3p_endo anti -A6 : G C2p_exo anti -A7 : C C3p_endo anti -A8 : U C3p_endo anti -A9 : G C3p_endo anti -A10 : A O4p_endo anti -A11 : C C1p_exo anti -A12 : A C3p_endo anti -A13 : A C3p_endo anti -A14 : A C2p_exo anti -A15 : G C2p_exo anti -A16 : C C3p_endo anti -A17 : G C3p_endo anti -A18 : C C3p_endo anti -B1 : ASN -B2 : ALA -B3 : LYS -B4 : THR -B5 : ARG -B6 : ARG -B7 : HIS -B8 : GLU -B9 : ARG -B10 : ARG -B11 : ARG -B12 : LYS -B13 : LEU -B14 : ALA -B15 : ILE -B16 : GLU -B17 : ARG -B18 : ASP -B19 : THR -Adjacent stackings ---------------------------------------------- -A4-A5 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A17-A18 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A6-A17 : outward -A10-A12 : upward -Number of stackings = 10 -Number of adjacent stackings = 8 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A4-A18 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A6-A16 : G-C Ww/Ww pairing antiparallel cis XIX -A7-A15 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A14 : U-A Ww/Ww pairing antiparallel cis XX -A9-A12 : G-A O2'/Hh Bs/O2P pairing -A9-A13 : G-A Bs/O2P pairing -A9-B6 : G-ARG pairing one_hbond -Residue conformations ------------------------------------------- -A4 : G C4p_exo anti -A5 : C C3p_endo anti -A6 : G C2p_exo anti -A7 : C C3p_endo anti -A8 : U C3p_endo anti -A9 : G C3p_endo anti -A10 : A O4p_endo anti -A11 : C C1p_exo anti -A12 : A C3p_endo anti -A13 : A C3p_endo anti -A14 : A C2p_exo anti -A15 : G C2p_exo anti -A16 : C C3p_endo anti -A17 : G C2p_exo anti -A18 : C C3p_endo anti -B1 : ASN -B2 : ALA -B3 : LYS -B4 : THR -B5 : ARG -B6 : ARG -B7 : HIS -B8 : GLU -B9 : ARG -B10 : ARG -B11 : ARG -B12 : LYS -B13 : LEU -B14 : ALA -B15 : ILE -B16 : GLU -B17 : ARG -B18 : ASP -B19 : THR -Adjacent stackings ---------------------------------------------- -A4-A5 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A17-A18 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A6-A17 : outward -A10-A12 : upward -Number of stackings = 10 -Number of adjacent stackings = 8 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A4-A18 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A6-A16 : G-C Ww/Ww pairing antiparallel cis XIX -A7-A15 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A14 : U-A Ww/Ww pairing antiparallel cis XX -A9-A12 : G-A O2'/Hh pairing -A9-A13 : G-A Bs/O2P pairing -A9-B6 : G-ARG pairing one_hbond -A14-B3 : A-LYS pairing one_hbond -Residue conformations ------------------------------------------- -A4 : G C4p_exo anti -A5 : C C3p_endo anti -A6 : G C2p_exo anti -A7 : C C3p_endo anti -A8 : U C3p_endo anti -A9 : G C3p_endo anti -A10 : A C1p_exo anti -A11 : C C1p_exo anti -A12 : A C2p_exo anti -A13 : A C3p_endo anti -A14 : A C2p_exo anti -A15 : G C2p_exo anti -A16 : C C3p_endo anti -A17 : G C3p_endo anti -A18 : C C3p_endo anti -B1 : ASN -B2 : ALA -B3 : LYS -B4 : THR -B5 : ARG -B6 : ARG -B7 : HIS -B8 : GLU -B9 : ARG -B10 : ARG -B11 : ARG -B12 : LYS -B13 : LEU -B14 : ALA -B15 : ILE -B16 : GLU -B17 : ARG -B18 : ASP -B19 : THR -Adjacent stackings ---------------------------------------------- -A4-A5 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A17-A18 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A6-A17 : outward -A10-A12 : upward -Number of stackings = 10 -Number of adjacent stackings = 8 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A4-A18 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A6-A16 : G-C Ww/Ww pairing antiparallel cis XIX -A7-A15 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A14 : U-A Ww/Ww pairing antiparallel cis XX -A9-A12 : G-A O2'/Hh pairing -A9-A13 : G-A Bs/Hh pairing antiparallel trans one_hbond -A9-B6 : G-ARG pairing one_hbond -A14-B3 : A-LYS pairing one_hbond -Residue conformations ------------------------------------------- -A4 : G C3p_endo anti -A5 : C C3p_endo anti -A6 : G C2p_exo anti -A7 : C C3p_endo anti -A8 : U C2p_exo anti -A9 : G C3p_endo anti -A10 : A C1p_exo anti -A11 : C C1p_exo anti -A12 : A C3p_endo anti -A13 : A C3p_endo anti -A14 : A C2p_exo anti -A15 : G C2p_exo anti -A16 : C C2p_exo anti -A17 : G C3p_endo anti -A18 : C C3p_endo anti -B1 : ASN -B2 : ALA -B3 : LYS -B4 : THR -B5 : ARG -B6 : ARG -B7 : HIS -B8 : GLU -B9 : ARG -B10 : ARG -B11 : ARG -B12 : LYS -B13 : LEU -B14 : ALA -B15 : ILE -B16 : GLU -B17 : ARG -B18 : ASP -B19 : THR -Adjacent stackings ---------------------------------------------- -A4-A5 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A17-A18 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A6-A17 : outward -A10-A12 : upward -Number of stackings = 10 -Number of adjacent stackings = 8 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A4-A18 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A6-A16 : G-C Ww/Ww pairing antiparallel cis XIX -A7-A15 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A14 : U-A Ww/Ww pairing antiparallel cis XX -A9-A12 : G-A Ww/O2P pairing -A9-A13 : G-A Bs/Hh Ws/O2P pairing antiparallel trans one_hbond -Residue conformations ------------------------------------------- -A4 : G C4p_exo anti -A5 : C C3p_endo anti -A6 : G C2p_exo anti -A7 : C C3p_endo anti -A8 : U C2p_exo anti -A9 : G C3p_endo anti -A10 : A O4p_endo anti -A11 : C C1p_exo anti -A12 : A C3p_endo anti -A13 : A C3p_endo anti -A14 : A C2p_exo anti -A15 : G C2p_exo anti -A16 : C C3p_endo anti -A17 : G C2p_exo anti -A18 : C C3p_endo anti -B1 : ASN -B2 : ALA -B3 : LYS -B4 : THR -B5 : ARG -B6 : ARG -B7 : HIS -B8 : GLU -B9 : ARG -B10 : ARG -B11 : ARG -B12 : LYS -B13 : LEU -B14 : ALA -B15 : ILE -B16 : GLU -B17 : ARG -B18 : ASP -B19 : THR -Adjacent stackings ---------------------------------------------- -A4-A5 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A17-A18 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A6-A17 : outward -A10-A12 : upward -Number of stackings = 10 -Number of adjacent stackings = 8 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A4-A18 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A6-A16 : G-C Ww/Ww pairing antiparallel cis XIX -A7-A15 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A14 : U-A Ww/Ww pairing antiparallel cis XX -A9-A12 : G-A O2'/Hh Ww/O2P pairing -A9-A13 : G-A Ws/O2P pairing -A9-B6 : G-ARG pairing one_hbond -A15-B3 : G-LYS pairing one_hbond -Residue conformations ------------------------------------------- -A4 : G C4p_exo anti -A5 : C C2p_exo anti -A6 : G C2p_exo anti -A7 : C C3p_endo anti -A8 : U C2p_exo anti -A9 : G C3p_endo anti -A10 : A O4p_endo anti -A11 : C C1p_exo anti -A12 : A C3p_endo anti -A13 : A C3p_endo anti -A14 : A C2p_exo anti -A15 : G C2p_exo anti -A16 : C C2p_exo anti -A17 : G C3p_endo anti -A18 : C C3p_endo anti -B1 : ASN -B2 : ALA -B3 : LYS -B4 : THR -B5 : ARG -B6 : ARG -B7 : HIS -B8 : GLU -B9 : ARG -B10 : ARG -B11 : ARG -B12 : LYS -B13 : LEU -B14 : ALA -B15 : ILE -B16 : GLU -B17 : ARG -B18 : ASP -B19 : THR -Adjacent stackings ---------------------------------------------- -A4-A5 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A17-A18 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A6-A17 : outward -A10-A12 : upward -Number of stackings = 10 -Number of adjacent stackings = 8 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A4-A18 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A6-A16 : G-C Ww/Ww pairing antiparallel cis XIX -A7-A15 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A14 : U-A Ww/Ww pairing antiparallel cis XX -A9-A12 : G-A O2'/Hh pairing -A9-A13 : G-A Bs/O2P pairing -A9-B6 : G-ARG pairing one_hbond diff --git a/MCdata/1a51_MC b/MCdata/1a51_MC deleted file mode 100644 index d38ae2ef91028b71ceb3bd37e9d7241f0ba6d989..0000000000000000000000000000000000000000 --- a/MCdata/1a51_MC +++ /dev/null @@ -1,897 +0,0 @@ -Residue conformations ------------------------------------------- -A68 : G C3p_endo anti -A69 : G C3p_endo anti -A70 : C C3p_endo anti -A71 : C C3p_endo anti -A72 : G C3p_endo anti -A73 : A C2p_exo anti -A74 : U C3p_endo anti -A75 : G C3p_endo anti -A76 : G C3p_endo anti -A77 : U C3p_endo anti -A78 : A C3p_endo anti -A79 : G C3p_endo anti -A80 : U C3p_endo anti -A81 : G C3p_endo anti -A82 : U C3p_endo anti -A83 : G C3p_endo anti -A84 : G C3p_endo anti -A85 : G C3p_endo anti -A86 : G C3p_endo anti -A87 : U C4p_exo anti -A88 : C C2p_endo anti -A89 : U C3p_endo anti -A90 : C C2p_exo anti -A91 : C C3p_endo anti -A92 : C C3p_endo anti -A93 : C C3p_endo anti -A94 : A C3p_endo anti -A95 : U C3p_endo anti -A96 : G C3p_endo anti -A97 : C C3p_endo anti -A98 : G C3p_endo anti -A99 : A C2p_exo anti -A100 : G C3p_endo anti -A101 : A C2p_exo anti -A102 : G C3p_endo anti -A103 : U C3p_endo anti -A104 : A C3p_endo anti -A105 : G C3p_endo anti -A106 : G C3p_endo anti -A107 : C C3p_endo anti -A108 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A68-A69 : adjacent_5p upward -A69-A70 : adjacent_5p upward -A71-A72 : adjacent_5p upward -A73-A74 : adjacent_5p upward -A74-A75 : adjacent_5p upward -A75-A76 : adjacent_5p upward -A76-A77 : adjacent_5p upward -A77-A78 : adjacent_5p upward -A78-A79 : adjacent_5p upward -A79-A80 : adjacent_5p upward -A81-A82 : adjacent_5p upward -A82-A83 : adjacent_5p upward -A83-A84 : adjacent_5p upward -A84-A85 : adjacent_5p upward -A85-A86 : adjacent_5p upward -A93-A94 : adjacent_5p upward -A94-A95 : adjacent_5p upward -A96-A97 : adjacent_5p upward -A97-A98 : adjacent_5p upward -A99-A100 : adjacent_5p upward -A100-A101 : adjacent_5p upward -A101-A102 : adjacent_5p upward -A102-A103 : adjacent_5p upward -A103-A104 : adjacent_5p upward -A104-A105 : adjacent_5p upward -A105-A106 : adjacent_5p upward -A106-A107 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A73-A104 : outward -A78-A99 : outward -A81-A96 : outward -A83-A94 : outward -Number of stackings = 31 -Number of adjacent stackings = 27 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A68-A108 : G-C Ww/Ww pairing antiparallel cis XIX -A69-A107 : G-C Ww/Ww pairing antiparallel cis XIX -A70-A106 : C-G Ww/Ww pairing antiparallel cis XIX -A71-A105 : C-G Ww/Ww pairing antiparallel cis XIX -A72-A102 : G-G Hh/O2P pairing -A72-A103 : G-U Ww/O2P Bs/O2P pairing -A72-A104 : G-A Ss/Hh pairing antiparallel trans XI -A73-A103 : A-U Hh/Ws pairing antiparallel trans XXIV -A74-A102 : U-G Hh/Ww pairing antiparallel trans one_hbond 91 -A75-A101 : G-A Hw/Wh pairing antiparallel cis one_hbond 64 -A76-A100 : G-G Ww/Bh pairing antiparallel trans 115 -A77-A99 : U-A Ws/Hh pairing antiparallel trans XXIV -A78-A98 : A-G Hh/Ss Bh/O2' pairing antiparallel trans XI -A79-A97 : G-C Ww/Ww pairing antiparallel cis XIX -A80-A96 : U-G Ws/Ww pairing antiparallel cis XXVIII -A81-A95 : G-U Ww/Ws pairing antiparallel cis XXVIII -A82-A94 : U-A Ww/Ww pairing antiparallel cis XX -A83-A93 : G-C Ww/Ww pairing antiparallel cis XIX -A84-A92 : G-C Ww/Ww pairing antiparallel cis XIX -A85-A91 : G-C Ww/Ww pairing antiparallel cis XIX -A86-A90 : G-C Bs/Ww pairing antiparallel cis 128 -A89-A90 : U-C O2P/Ww O2P/Bh adjacent_5p pairing -Residue conformations ------------------------------------------- -A68 : G C2p_exo anti -A69 : G C3p_endo anti -A70 : C C3p_endo anti -A71 : C C3p_endo anti -A72 : G C3p_endo anti -A73 : A C2p_exo anti -A74 : U C3p_endo anti -A75 : G C3p_endo anti -A76 : G C3p_endo anti -A77 : U C3p_endo anti -A78 : A C3p_endo anti -A79 : G C3p_endo anti -A80 : U C3p_endo anti -A81 : G C3p_endo anti -A82 : U C3p_endo anti -A83 : G C3p_endo anti -A84 : G C3p_endo anti -A85 : G C3p_endo anti -A86 : G C3p_endo anti -A87 : U C4p_exo anti -A88 : C C2p_endo anti -A89 : U C4p_exo anti -A90 : C C2p_exo anti -A91 : C C3p_endo anti -A92 : C C3p_endo anti -A93 : C C3p_endo anti -A94 : A C3p_endo anti -A95 : U C3p_endo anti -A96 : G C3p_endo anti -A97 : C C3p_endo anti -A98 : G C3p_endo anti -A99 : A C2p_exo anti -A100 : G C3p_endo anti -A101 : A C3p_endo anti -A102 : G C3p_endo anti -A103 : U C3p_endo anti -A104 : A C3p_endo anti -A105 : G C3p_endo anti -A106 : G C3p_endo anti -A107 : C C3p_endo anti -A108 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A68-A69 : adjacent_5p upward -A69-A70 : adjacent_5p upward -A70-A71 : adjacent_5p upward -A71-A72 : adjacent_5p upward -A73-A74 : adjacent_5p upward -A74-A75 : adjacent_5p upward -A75-A76 : adjacent_5p upward -A76-A77 : adjacent_5p upward -A77-A78 : adjacent_5p upward -A78-A79 : adjacent_5p upward -A79-A80 : adjacent_5p upward -A81-A82 : adjacent_5p upward -A82-A83 : adjacent_5p upward -A83-A84 : adjacent_5p upward -A84-A85 : adjacent_5p upward -A85-A86 : adjacent_5p upward -A91-A92 : adjacent_5p upward -A93-A94 : adjacent_5p upward -A94-A95 : adjacent_5p upward -A96-A97 : adjacent_5p upward -A97-A98 : adjacent_5p upward -A99-A100 : adjacent_5p upward -A100-A101 : adjacent_5p upward -A101-A102 : adjacent_5p upward -A102-A103 : adjacent_5p upward -A103-A104 : adjacent_5p upward -A104-A105 : adjacent_5p upward -A105-A106 : adjacent_5p upward -A106-A107 : adjacent_5p upward -A107-A108 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A73-A104 : outward -A78-A99 : outward -A81-A96 : outward -A83-A94 : outward -Number of stackings = 34 -Number of adjacent stackings = 30 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A68-A108 : G-C Ww/Ww pairing antiparallel cis XIX -A69-A107 : G-C Ww/Ww pairing antiparallel cis XIX -A70-A106 : C-G Ww/Ww pairing antiparallel cis XIX -A71-A105 : C-G Ww/Ww pairing antiparallel cis XIX -A72-A104 : G-A Ss/Hh O2'/Bh pairing antiparallel trans XI -A73-A103 : A-U Hh/Ws pairing antiparallel trans XXIV -A74-A102 : U-G Bh/Ww pairing antiparallel trans 91 -A76-A100 : G-G Ww/Bh pairing antiparallel trans 115 -A77-A99 : U-A Ws/Hh pairing antiparallel trans XXIV -A78-A98 : A-G Hh/Ss Bh/O2' pairing antiparallel trans XI -A79-A97 : G-C Ww/Ww pairing antiparallel cis XIX -A80-A96 : U-G Ws/Ww pairing antiparallel cis XXVIII -A81-A95 : G-U Ww/Ws pairing antiparallel cis XXVIII -A82-A94 : U-A Ww/Ww pairing antiparallel cis XX -A83-A93 : G-C Ww/Ww pairing antiparallel cis XIX -A84-A92 : G-C Ww/Ww pairing antiparallel cis XIX -A85-A91 : G-C Ww/Ww pairing antiparallel cis XIX -A86-A90 : G-C Bs/Ww pairing antiparallel cis 128 -A89-A90 : U-C O2P/Ww adjacent_5p pairing -Residue conformations ------------------------------------------- -A68 : G C3p_endo anti -A69 : G C3p_endo anti -A70 : C C3p_endo anti -A71 : C C3p_endo anti -A72 : G C3p_endo anti -A73 : A C2p_exo anti -A74 : U C3p_endo anti -A75 : G C3p_endo anti -A76 : G C3p_endo anti -A77 : U C3p_endo anti -A78 : A C3p_endo anti -A79 : G C3p_endo anti -A80 : U C3p_endo anti -A81 : G C3p_endo anti -A82 : U C3p_endo anti -A83 : G C3p_endo anti -A84 : G C3p_endo anti -A85 : G C3p_endo anti -A86 : G C3p_endo anti -A87 : U C4p_exo anti -A88 : C C2p_endo anti -A89 : U C4p_exo anti -A90 : C C2p_exo anti -A91 : C C3p_endo anti -A92 : C C3p_endo anti -A93 : C C3p_endo anti -A94 : A C3p_endo anti -A95 : U C3p_endo anti -A96 : G C3p_endo anti -A97 : C C3p_endo anti -A98 : G C3p_endo anti -A99 : A C2p_exo anti -A100 : G C3p_endo anti -A101 : A C3p_endo anti -A102 : G C3p_endo anti -A103 : U C3p_endo anti -A104 : A C3p_endo anti -A105 : G C3p_endo anti -A106 : G C3p_endo anti -A107 : C C3p_endo anti -A108 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A68-A69 : adjacent_5p upward -A69-A70 : adjacent_5p upward -A71-A72 : adjacent_5p upward -A73-A74 : adjacent_5p upward -A74-A75 : adjacent_5p upward -A75-A76 : adjacent_5p upward -A76-A77 : adjacent_5p upward -A77-A78 : adjacent_5p upward -A78-A79 : adjacent_5p upward -A79-A80 : adjacent_5p upward -A81-A82 : adjacent_5p upward -A83-A84 : adjacent_5p upward -A84-A85 : adjacent_5p upward -A85-A86 : adjacent_5p upward -A91-A92 : adjacent_5p upward -A94-A95 : adjacent_5p upward -A96-A97 : adjacent_5p upward -A97-A98 : adjacent_5p upward -A99-A100 : adjacent_5p upward -A100-A101 : adjacent_5p upward -A101-A102 : adjacent_5p upward -A102-A103 : adjacent_5p upward -A103-A104 : adjacent_5p upward -A104-A105 : adjacent_5p upward -A105-A106 : adjacent_5p upward -A106-A107 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A73-A104 : outward -A78-A99 : outward -A81-A96 : outward -A83-A94 : outward -Number of stackings = 30 -Number of adjacent stackings = 26 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A68-A108 : G-C Ww/Ww pairing antiparallel cis XIX -A69-A107 : G-C Ww/Ww pairing antiparallel cis XIX -A70-A106 : C-G Ww/Ww pairing antiparallel cis XIX -A71-A105 : C-G Ww/Ww pairing antiparallel cis XIX -A72-A104 : G-A Ss/Hh O2'/Bh pairing antiparallel trans XI -A73-A103 : A-U Hh/Ws pairing antiparallel trans XXIV -A74-A102 : U-G Bh/Ww pairing antiparallel trans 91 -A76-A100 : G-G Ww/Bh pairing antiparallel trans 115 -A77-A99 : U-A Ws/Hh pairing antiparallel trans XXIV -A78-A98 : A-G Hh/Ss Bh/O2' pairing antiparallel trans XI -A79-A97 : G-C Ww/Ww pairing antiparallel cis XIX -A80-A96 : U-G Ws/Ww pairing antiparallel cis XXVIII -A81-A95 : G-U Ww/Ws pairing antiparallel cis XXVIII -A82-A94 : U-A Ww/Ww pairing antiparallel cis XX -A83-A93 : G-C Ww/Ww pairing antiparallel cis XIX -A84-A92 : G-C Ww/Ww pairing antiparallel cis XIX -A85-A91 : G-C Ww/Ww pairing antiparallel cis XIX -A86-A90 : G-C Bs/Ww pairing antiparallel cis 128 -A89-A90 : U-C O2P/Ww O2P/Bh adjacent_5p pairing -Residue conformations ------------------------------------------- -A68 : G C2p_exo anti -A69 : G C3p_endo anti -A70 : C C3p_endo anti -A71 : C C3p_endo anti -A72 : G C3p_endo anti -A73 : A C2p_exo anti -A74 : U C3p_endo anti -A75 : G C3p_endo anti -A76 : G C3p_endo anti -A77 : U C3p_endo anti -A78 : A C3p_endo anti -A79 : G C3p_endo anti -A80 : U C3p_endo anti -A81 : G C3p_endo anti -A82 : U C3p_endo anti -A83 : G C3p_endo anti -A84 : G C3p_endo anti -A85 : G C3p_endo anti -A86 : G C3p_endo anti -A87 : U C4p_exo anti -A88 : C C2p_endo anti -A89 : U C4p_exo anti -A90 : C C2p_exo anti -A91 : C C3p_endo anti -A92 : C C3p_endo anti -A93 : C C3p_endo anti -A94 : A C3p_endo anti -A95 : U C3p_endo anti -A96 : G C3p_endo anti -A97 : C C3p_endo anti -A98 : G C3p_endo anti -A99 : A C3p_endo anti -A100 : G C3p_endo anti -A101 : A C3p_endo anti -A102 : G C3p_endo anti -A103 : U C3p_endo anti -A104 : A C3p_endo anti -A105 : G C3p_endo anti -A106 : G C3p_endo anti -A107 : C C3p_endo anti -A108 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A68-A69 : adjacent_5p upward -A69-A70 : adjacent_5p upward -A70-A71 : adjacent_5p upward -A71-A72 : adjacent_5p upward -A73-A74 : adjacent_5p upward -A74-A75 : adjacent_5p upward -A75-A76 : adjacent_5p upward -A76-A77 : adjacent_5p upward -A78-A79 : adjacent_5p upward -A79-A80 : adjacent_5p upward -A81-A82 : adjacent_5p upward -A83-A84 : adjacent_5p upward -A84-A85 : adjacent_5p upward -A85-A86 : adjacent_5p upward -A91-A92 : adjacent_5p upward -A93-A94 : adjacent_5p upward -A94-A95 : adjacent_5p upward -A96-A97 : adjacent_5p upward -A97-A98 : adjacent_5p upward -A99-A100 : adjacent_5p upward -A100-A101 : adjacent_5p upward -A101-A102 : adjacent_5p upward -A102-A103 : adjacent_5p upward -A103-A104 : adjacent_5p upward -A104-A105 : adjacent_5p upward -A105-A106 : adjacent_5p upward -A106-A107 : adjacent_5p upward -A107-A108 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A73-A104 : outward -A78-A99 : outward -A81-A96 : outward -A83-A94 : outward -Number of stackings = 32 -Number of adjacent stackings = 28 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A68-A108 : G-C Ww/Ww pairing antiparallel cis XIX -A69-A107 : G-C Ww/Ww pairing antiparallel cis XIX -A70-A106 : C-G Ww/Ww pairing antiparallel cis XIX -A71-A105 : C-G Ww/Ww pairing antiparallel cis XIX -A72-A104 : G-A Ss/Hh O2'/Bh pairing antiparallel trans XI -A73-A103 : A-U Hh/Ws pairing antiparallel trans XXIV -A74-A102 : U-G Bh/Ww pairing antiparallel trans 91 -A75-A101 : G-A Hw/Wh pairing antiparallel cis one_hbond 64 -A76-A100 : G-G Ww/Bh pairing antiparallel trans 115 -A77-A99 : U-A Ws/Hh pairing antiparallel trans XXIV -A78-A98 : A-G Hh/Ss Bh/O2' pairing antiparallel trans XI -A79-A97 : G-C Ww/Ww pairing antiparallel cis XIX -A80-A96 : U-G Ws/Ww pairing antiparallel cis XXVIII -A81-A95 : G-U Ww/Ws pairing antiparallel cis XXVIII -A82-A94 : U-A Ww/Ww pairing antiparallel cis XX -A83-A93 : G-C Ww/Ww pairing antiparallel cis XIX -A84-A92 : G-C Ww/Ww pairing antiparallel cis XIX -A85-A91 : G-C Ww/Ww pairing antiparallel cis XIX -A86-A90 : G-C Bs/Ww pairing antiparallel cis 128 -A89-A90 : U-C O2P/Ww adjacent_5p pairing -Residue conformations ------------------------------------------- -A68 : G C2p_exo anti -A69 : G C3p_endo anti -A70 : C C3p_endo anti -A71 : C C3p_endo anti -A72 : G C3p_endo anti -A73 : A C2p_exo anti -A74 : U C3p_endo anti -A75 : G C3p_endo anti -A76 : G C3p_endo anti -A77 : U C3p_endo anti -A78 : A C3p_endo anti -A79 : G C3p_endo anti -A80 : U C3p_endo anti -A81 : G C3p_endo anti -A82 : U C3p_endo anti -A83 : G C3p_endo anti -A84 : G C3p_endo anti -A85 : G C3p_endo anti -A86 : G C3p_endo anti -A87 : U C4p_exo anti -A88 : C C2p_endo anti -A89 : U C4p_exo anti -A90 : C C2p_exo anti -A91 : C C3p_endo anti -A92 : C C3p_endo anti -A93 : C C3p_endo anti -A94 : A C3p_endo anti -A95 : U C3p_endo anti -A96 : G C3p_endo anti -A97 : C C3p_endo anti -A98 : G C2p_exo anti -A99 : A C3p_endo anti -A100 : G C3p_endo anti -A101 : A C3p_endo anti -A102 : G C3p_endo anti -A103 : U C3p_endo anti -A104 : A C3p_endo anti -A105 : G C3p_endo anti -A106 : G C3p_endo anti -A107 : C C3p_endo anti -A108 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A68-A69 : adjacent_5p upward -A69-A70 : adjacent_5p upward -A70-A71 : adjacent_5p upward -A71-A72 : adjacent_5p upward -A73-A74 : adjacent_5p upward -A74-A75 : adjacent_5p upward -A75-A76 : adjacent_5p upward -A76-A77 : adjacent_5p upward -A77-A78 : adjacent_5p upward -A78-A79 : adjacent_5p upward -A79-A80 : adjacent_5p upward -A81-A82 : adjacent_5p upward -A83-A84 : adjacent_5p upward -A84-A85 : adjacent_5p upward -A85-A86 : adjacent_5p upward -A93-A94 : adjacent_5p upward -A94-A95 : adjacent_5p upward -A96-A97 : adjacent_5p upward -A97-A98 : adjacent_5p upward -A99-A100 : adjacent_5p upward -A100-A101 : adjacent_5p upward -A101-A102 : adjacent_5p upward -A102-A103 : adjacent_5p upward -A103-A104 : adjacent_5p upward -A104-A105 : adjacent_5p upward -A105-A106 : adjacent_5p upward -A106-A107 : adjacent_5p upward -A107-A108 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A73-A104 : outward -A78-A99 : outward -A81-A96 : outward -A83-A94 : outward -Number of stackings = 32 -Number of adjacent stackings = 28 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A68-A108 : G-C Ww/Ww pairing antiparallel cis XIX -A69-A107 : G-C Ww/Ww pairing antiparallel cis XIX -A70-A106 : C-G Ww/Ww pairing antiparallel cis XIX -A71-A105 : C-G Ww/Ww pairing antiparallel cis XIX -A72-A104 : G-A Ss/Hh O2'/Bh pairing antiparallel trans XI -A73-A103 : A-U Hh/Ws pairing antiparallel trans XXIV -A74-A102 : U-G Bh/Ww pairing antiparallel trans 91 -A76-A100 : G-G Ww/Bh pairing antiparallel trans 115 -A77-A98 : U-G O2P/Ww pairing -A77-A99 : U-A Ws/Hh pairing antiparallel trans XXIV -A78-A98 : A-G Hh/Ss pairing antiparallel trans XI -A79-A97 : G-C Ww/Ww pairing antiparallel cis XIX -A80-A96 : U-G Ws/Ww pairing antiparallel cis XXVIII -A81-A95 : G-U Ww/Ws pairing antiparallel cis XXVIII -A82-A94 : U-A Ww/Ww pairing antiparallel cis XX -A83-A93 : G-C Ww/Ww pairing antiparallel cis XIX -A84-A92 : G-C Ww/Ww pairing antiparallel cis XIX -A85-A91 : G-C Ww/Ww pairing antiparallel cis XIX -A86-A90 : G-C Bs/Ww pairing antiparallel cis 128 -A89-A90 : U-C O2P/Ww O2P/Bh adjacent_5p pairing -Residue conformations ------------------------------------------- -A68 : G C3p_endo anti -A69 : G C3p_endo anti -A70 : C C3p_endo anti -A71 : C C3p_endo anti -A72 : G C3p_endo anti -A73 : A C3p_endo anti -A74 : U C3p_endo anti -A75 : G C3p_endo anti -A76 : G C3p_endo anti -A77 : U C3p_endo anti -A78 : A C3p_endo anti -A79 : G C3p_endo anti -A80 : U C3p_endo anti -A81 : G C3p_endo anti -A82 : U C3p_endo anti -A83 : G C3p_endo anti -A84 : G C3p_endo anti -A85 : G C3p_endo anti -A86 : G C3p_endo anti -A87 : U C4p_exo anti -A88 : C C2p_endo anti -A89 : U C4p_exo anti -A90 : C C2p_exo anti -A91 : C C3p_endo anti -A92 : C C3p_endo anti -A93 : C C3p_endo anti -A94 : A C3p_endo anti -A95 : U C3p_endo anti -A96 : G C3p_endo anti -A97 : C C3p_endo anti -A98 : G C2p_exo anti -A99 : A C3p_endo anti -A100 : G C3p_endo anti -A101 : A C3p_endo anti -A102 : G C3p_endo anti -A103 : U C3p_endo anti -A104 : A C3p_endo anti -A105 : G C3p_endo anti -A106 : G C3p_endo anti -A107 : C C3p_endo anti -A108 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A68-A69 : adjacent_5p upward -A69-A70 : adjacent_5p upward -A71-A72 : adjacent_5p upward -A73-A74 : adjacent_5p upward -A74-A75 : adjacent_5p upward -A75-A76 : adjacent_5p upward -A76-A77 : adjacent_5p upward -A77-A78 : adjacent_5p upward -A78-A79 : adjacent_5p upward -A79-A80 : adjacent_5p upward -A81-A82 : adjacent_5p upward -A83-A84 : adjacent_5p upward -A84-A85 : adjacent_5p upward -A85-A86 : adjacent_5p upward -A90-A91 : adjacent_5p upward -A91-A92 : adjacent_5p upward -A94-A95 : adjacent_5p upward -A96-A97 : adjacent_5p upward -A97-A98 : adjacent_5p upward -A99-A100 : adjacent_5p upward -A100-A101 : adjacent_5p upward -A101-A102 : adjacent_5p upward -A102-A103 : adjacent_5p upward -A103-A104 : adjacent_5p upward -A104-A105 : adjacent_5p upward -A105-A106 : adjacent_5p upward -A106-A107 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A73-A104 : outward -A78-A99 : outward -A81-A96 : outward -A83-A94 : outward -Number of stackings = 31 -Number of adjacent stackings = 27 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A68-A108 : G-C Ww/Ww pairing antiparallel cis XIX -A69-A107 : G-C Ww/Ww pairing antiparallel cis XIX -A70-A106 : C-G Ww/Ww pairing antiparallel cis XIX -A71-A105 : C-G Ww/Ww pairing antiparallel cis XIX -A72-A104 : G-A Ss/Hh pairing antiparallel trans XI -A73-A103 : A-U Hh/Ws pairing antiparallel trans XXIV -A74-A102 : U-G Bh/Ww pairing antiparallel trans 91 -A75-A101 : G-A Wh/Wh pairing antiparallel cis one_hbond -A76-A100 : G-G Ww/Bh pairing antiparallel trans 115 -A77-A98 : U-G O2P/Ww O2P/Bs pairing -A77-A99 : U-A Ws/Hh pairing antiparallel trans XXIV -A78-A98 : A-G Hh/Ss pairing antiparallel trans XI -A79-A97 : G-C Ww/Ww pairing antiparallel cis XIX -A80-A96 : U-G Ws/Ww pairing antiparallel cis XXVIII -A81-A95 : G-U Ww/Ws pairing antiparallel cis XXVIII -A82-A94 : U-A Ww/Ww pairing antiparallel cis XX -A83-A93 : G-C Ww/Ww pairing antiparallel cis XIX -A84-A92 : G-C Ww/Ww pairing antiparallel cis XIX -A85-A91 : G-C Ww/Ww pairing antiparallel cis XIX -A86-A90 : G-C Bs/Ww pairing antiparallel cis one_hbond 128 -A89-A90 : U-C O2P/Ww adjacent_5p pairing -Residue conformations ------------------------------------------- -A68 : G C2p_exo anti -A69 : G C3p_endo anti -A70 : C C3p_endo anti -A71 : C C3p_endo anti -A72 : G C3p_endo anti -A73 : A C2p_exo anti -A74 : U C3p_endo anti -A75 : G C3p_endo anti -A76 : G C3p_endo anti -A77 : U C3p_endo anti -A78 : A C3p_endo anti -A79 : G C3p_endo anti -A80 : U C3p_endo anti -A81 : G C3p_endo anti -A82 : U C3p_endo anti -A83 : G C3p_endo anti -A84 : G C3p_endo anti -A85 : G C3p_endo anti -A86 : G C3p_endo anti -A87 : U C4p_exo anti -A88 : C C2p_endo anti -A89 : U C4p_exo anti -A90 : C C2p_exo anti -A91 : C C3p_endo anti -A92 : C C3p_endo anti -A93 : C C3p_endo anti -A94 : A C3p_endo anti -A95 : U C3p_endo anti -A96 : G C3p_endo anti -A97 : C C3p_endo anti -A98 : G C3p_endo anti -A99 : A C2p_exo anti -A100 : G C3p_endo anti -A101 : A C3p_endo anti -A102 : G C3p_endo anti -A103 : U C3p_endo anti -A104 : A C3p_endo anti -A105 : G C3p_endo anti -A106 : G C3p_endo anti -A107 : C C3p_endo anti -A108 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A68-A69 : adjacent_5p upward -A69-A70 : adjacent_5p upward -A70-A71 : adjacent_5p upward -A71-A72 : adjacent_5p upward -A73-A74 : adjacent_5p upward -A74-A75 : adjacent_5p upward -A75-A76 : adjacent_5p upward -A76-A77 : adjacent_5p upward -A77-A78 : adjacent_5p upward -A78-A79 : adjacent_5p upward -A79-A80 : adjacent_5p upward -A81-A82 : adjacent_5p upward -A83-A84 : adjacent_5p upward -A84-A85 : adjacent_5p upward -A85-A86 : adjacent_5p upward -A91-A92 : adjacent_5p upward -A93-A94 : adjacent_5p upward -A94-A95 : adjacent_5p upward -A96-A97 : adjacent_5p upward -A97-A98 : adjacent_5p upward -A99-A100 : adjacent_5p upward -A100-A101 : adjacent_5p upward -A101-A102 : adjacent_5p upward -A102-A103 : adjacent_5p upward -A103-A104 : adjacent_5p upward -A104-A105 : adjacent_5p upward -A105-A106 : adjacent_5p upward -A106-A107 : adjacent_5p upward -A107-A108 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A73-A104 : outward -A78-A99 : outward -A81-A96 : outward -A83-A94 : outward -Number of stackings = 33 -Number of adjacent stackings = 29 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A68-A108 : G-C Ww/Ww pairing antiparallel cis XIX -A69-A107 : G-C Ww/Ww pairing antiparallel cis XIX -A70-A106 : C-G Ww/Ww pairing antiparallel cis XIX -A71-A105 : C-G Ww/Ww pairing antiparallel cis XIX -A72-A104 : G-A Ss/Hh O2'/Bh pairing antiparallel trans XI -A73-A103 : A-U Hh/Ws pairing antiparallel trans XXIV -A74-A102 : U-G Bh/Ww pairing antiparallel trans 91 -A76-A100 : G-G Ww/Bh pairing antiparallel trans 115 -A77-A99 : U-A Ws/Hh pairing antiparallel trans XXIV -A78-A98 : A-G Hh/Ss Bh/O2' pairing antiparallel trans XI -A79-A97 : G-C Ww/Ww pairing antiparallel cis XIX -A80-A96 : U-G Ws/Ww pairing antiparallel cis XXVIII -A81-A95 : G-U Ww/Ws pairing antiparallel cis XXVIII -A82-A94 : U-A Ww/Ww pairing antiparallel cis XX -A83-A93 : G-C Ww/Ww pairing antiparallel cis XIX -A84-A92 : G-C Ww/Ww pairing antiparallel cis XIX -A85-A91 : G-C Ww/Ww pairing antiparallel cis XIX -A86-A90 : G-C Bs/Ww pairing antiparallel cis 128 -A89-A90 : U-C O2P/Ww adjacent_5p pairing -Residue conformations ------------------------------------------- -A68 : G C3p_endo anti -A69 : G C3p_endo anti -A70 : C C3p_endo anti -A71 : C C3p_endo anti -A72 : G C3p_endo anti -A73 : A C2p_exo anti -A74 : U C3p_endo anti -A75 : G C3p_endo anti -A76 : G C3p_endo anti -A77 : U C3p_endo anti -A78 : A C3p_endo anti -A79 : G C3p_endo anti -A80 : U C3p_endo anti -A81 : G C3p_endo anti -A82 : U C3p_endo anti -A83 : G C3p_endo anti -A84 : G C3p_endo anti -A85 : G C3p_endo anti -A86 : G C3p_endo anti -A87 : U C4p_exo anti -A88 : C C2p_endo anti -A89 : U C4p_exo anti -A90 : C C2p_exo anti -A91 : C C3p_endo anti -A92 : C C3p_endo anti -A93 : C C3p_endo anti -A94 : A C3p_endo anti -A95 : U C3p_endo anti -A96 : G C3p_endo anti -A97 : C C3p_endo anti -A98 : G C3p_endo anti -A99 : A C3p_endo anti -A100 : G C3p_endo anti -A101 : A C3p_endo anti -A102 : G C3p_endo anti -A103 : U C3p_endo anti -A104 : A C3p_endo anti -A105 : G C3p_endo anti -A106 : G C3p_endo anti -A107 : C C3p_endo anti -A108 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A68-A69 : adjacent_5p upward -A69-A70 : adjacent_5p upward -A70-A71 : adjacent_5p upward -A71-A72 : adjacent_5p upward -A73-A74 : adjacent_5p upward -A74-A75 : adjacent_5p upward -A75-A76 : adjacent_5p upward -A76-A77 : adjacent_5p upward -A78-A79 : adjacent_5p upward -A79-A80 : adjacent_5p upward -A81-A82 : adjacent_5p upward -A83-A84 : adjacent_5p upward -A84-A85 : adjacent_5p upward -A85-A86 : adjacent_5p upward -A90-A91 : adjacent_5p upward -A91-A92 : adjacent_5p upward -A93-A94 : adjacent_5p upward -A94-A95 : adjacent_5p upward -A96-A97 : adjacent_5p upward -A97-A98 : adjacent_5p upward -A99-A100 : adjacent_5p upward -A100-A101 : adjacent_5p upward -A101-A102 : adjacent_5p upward -A102-A103 : adjacent_5p upward -A103-A104 : adjacent_5p upward -A104-A105 : adjacent_5p upward -A105-A106 : adjacent_5p upward -A106-A107 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A73-A104 : outward -A78-A99 : outward -A81-A96 : outward -A83-A94 : outward -Number of stackings = 32 -Number of adjacent stackings = 28 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A68-A108 : G-C Ww/Ww pairing antiparallel cis XIX -A69-A107 : G-C Ww/Ww pairing antiparallel cis XIX -A70-A106 : C-G Ww/Ww pairing antiparallel cis XIX -A71-A105 : C-G Ww/Ww pairing antiparallel cis XIX -A72-A104 : G-A Ss/Hh O2'/Bh pairing antiparallel trans XI -A73-A103 : A-U Hh/Ws pairing antiparallel trans XXIV -A74-A102 : U-G Bh/Ww pairing antiparallel trans 91 -A76-A100 : G-G Ww/Bh pairing antiparallel trans 115 -A77-A99 : U-A Ws/Hh pairing antiparallel trans XXIV -A78-A98 : A-G Hh/Ss Bh/O2' pairing antiparallel trans XI -A79-A97 : G-C Ww/Ww pairing antiparallel cis XIX -A80-A96 : U-G Ws/Ww pairing antiparallel cis XXVIII -A81-A95 : G-U Ww/Ws pairing antiparallel cis XXVIII -A82-A94 : U-A Ww/Ww pairing antiparallel cis XX -A83-A93 : G-C Ww/Ww pairing antiparallel cis XIX -A84-A92 : G-C Ww/Ww pairing antiparallel cis XIX -A85-A91 : G-C Ww/Ww pairing antiparallel cis XIX -A86-A90 : G-C Bs/Ww pairing antiparallel cis 128 -A89-A90 : U-C O2P/Ww adjacent_5p pairing -Residue conformations ------------------------------------------- -A68 : G C3p_endo anti -A69 : G C3p_endo anti -A70 : C C3p_endo anti -A71 : C C3p_endo anti -A72 : G C3p_endo anti -A73 : A C2p_exo anti -A74 : U C3p_endo anti -A75 : G C3p_endo anti -A76 : G C3p_endo anti -A77 : U C3p_endo anti -A78 : A C3p_endo anti -A79 : G C3p_endo anti -A80 : U C3p_endo anti -A81 : G C3p_endo anti -A82 : U C3p_endo anti -A83 : G C3p_endo anti -A84 : G C3p_endo anti -A85 : G C3p_endo anti -A86 : G C3p_endo anti -A87 : U C4p_exo anti -A88 : C C2p_endo anti -A89 : U C4p_exo anti -A90 : C C2p_exo anti -A91 : C C3p_endo anti -A92 : C C3p_endo anti -A93 : C C3p_endo anti -A94 : A C3p_endo anti -A95 : U C3p_endo anti -A96 : G C3p_endo anti -A97 : C C3p_endo anti -A98 : G C3p_endo anti -A99 : A C3p_endo anti -A100 : G C3p_endo anti -A101 : A C3p_endo anti -A102 : G C3p_endo anti -A103 : U C3p_endo anti -A104 : A C3p_endo anti -A105 : G C3p_endo anti -A106 : G C3p_endo anti -A107 : C C3p_endo anti -A108 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A68-A69 : adjacent_5p upward -A69-A70 : adjacent_5p upward -A70-A71 : adjacent_5p upward -A71-A72 : adjacent_5p upward -A73-A74 : adjacent_5p upward -A74-A75 : adjacent_5p upward -A75-A76 : adjacent_5p upward -A76-A77 : adjacent_5p upward -A77-A78 : adjacent_5p upward -A78-A79 : adjacent_5p upward -A79-A80 : adjacent_5p upward -A81-A82 : adjacent_5p upward -A83-A84 : adjacent_5p upward -A84-A85 : adjacent_5p upward -A85-A86 : adjacent_5p upward -A91-A92 : adjacent_5p upward -A94-A95 : adjacent_5p upward -A96-A97 : adjacent_5p upward -A97-A98 : adjacent_5p upward -A99-A100 : adjacent_5p upward -A100-A101 : adjacent_5p upward -A101-A102 : adjacent_5p upward -A102-A103 : adjacent_5p upward -A103-A104 : adjacent_5p upward -A104-A105 : adjacent_5p upward -A105-A106 : adjacent_5p upward -A106-A107 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A73-A104 : outward -A78-A99 : outward -A81-A96 : outward -A83-A94 : outward -Number of stackings = 31 -Number of adjacent stackings = 27 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A68-A108 : G-C Ww/Ww pairing antiparallel cis XIX -A69-A107 : G-C Ww/Ww pairing antiparallel cis XIX -A70-A106 : C-G Ww/Ww pairing antiparallel cis XIX -A71-A105 : C-G Ww/Ww pairing antiparallel cis XIX -A72-A104 : G-A Ss/Hh O2'/Bh pairing antiparallel trans XI -A73-A103 : A-U Hh/Ws pairing antiparallel trans XXIV -A74-A102 : U-G Bh/Ww pairing antiparallel trans 91 -A75-A101 : G-A Hw/Wh pairing antiparallel cis one_hbond 64 -A76-A100 : G-G Ww/Bh pairing antiparallel trans 115 -A77-A99 : U-A Ws/Hh pairing antiparallel trans XXIV -A78-A98 : A-G Hh/Ss pairing antiparallel trans XI -A79-A97 : G-C Ww/Ww pairing antiparallel cis XIX -A80-A96 : U-G Ws/Ww pairing antiparallel cis XXVIII -A81-A95 : G-U Ww/Ws pairing antiparallel cis XXVIII -A82-A94 : U-A Ww/Ww pairing antiparallel cis XX -A83-A93 : G-C Ww/Ww pairing antiparallel cis XIX -A84-A92 : G-C Ww/Ww pairing antiparallel cis XIX -A85-A91 : G-C Ww/Ww pairing antiparallel cis XIX -A86-A90 : G-C Bs/Ww pairing antiparallel cis 128 -A89-A90 : U-C O2P/Ww adjacent_5p pairing diff --git a/MCdata/1a60_MC b/MCdata/1a60_MC deleted file mode 100644 index 8700dc0c5361ce33624b88c85595c252899080b3..0000000000000000000000000000000000000000 --- a/MCdata/1a60_MC +++ /dev/null @@ -1,2298 +0,0 @@ -Residue conformations ------------------------------------------- -A1 : G C2p_exo anti -A2 : G C4p_exo anti -A3 : G C3p_endo anti -A4 : A C2p_exo anti -A5 : G C3p_endo anti -A6 : C C3p_endo anti -A7 : U C3p_endo anti -A8 : C C2p_endo anti -A9 : A C3p_endo anti -A10 : A C3p_endo anti -A11 : C C3p_endo anti -A12 : U C3p_endo anti -A13 : C C2p_exo anti -A14 : U C3p_endo anti -A15 : C C3p_endo anti -A16 : C C3p_endo anti -A17 : C C3p_endo anti -A18 : C C3p_endo anti -A19 : C C3p_endo anti -A20 : C C3p_endo anti -A21 : C C3p_endo anti -A22 : U C2p_endo anti -A23 : U C3p_endo anti -A24 : U C2p_exo anti -A25 : U C3p_endo anti -A26 : C C3p_endo anti -A27 : C C3p_endo anti -A28 : G C3p_endo anti -A29 : A C3p_endo anti -A30 : G C3p_endo anti -A31 : G C2p_exo anti -A32 : G C2p_exo anti -A33 : U C2p_endo anti -A34 : C C3p_endo anti -A35 : A C2p_endo anti -A36 : U C3p_endo anti -A37 : C C3p_endo anti -A38 : G C3p_endo anti -A39 : G C4p_exo anti -A40 : A C2p_exo anti -A41 : A C3p_endo anti -A42 : C C3p_endo anti -A43 : C C3p_endo anti -A44 : A O4p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A28-A29 : adjacent_5p upward -A29-A30 : adjacent_5p upward -A30-A31 : adjacent_5p upward -A31-A32 : adjacent_5p upward -A36-A37 : adjacent_5p upward -A38-A39 : adjacent_5p upward -A39-A40 : adjacent_5p upward pairing -A40-A41 : adjacent_5p upward -A41-A42 : adjacent_5p upward -A42-A43 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A28-A38 : outward -Number of stackings = 24 -Number of adjacent stackings = 23 -Number of non adjacent stackings = 1 -Base-pairs ------------------------------------------------------ -A1-A17 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A16 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A15 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A14 : A-U Ww/Ww pairing antiparallel cis XX -A5-A13 : G-C Ww/Ww pairing antiparallel cis XIX -A6-A11 : C-C Ww/Wh pairing antiparallel cis one_hbond 131 -A18-A32 : C-G Ww/Ww pairing antiparallel cis XIX -A19-A31 : C-G Ww/Ww pairing antiparallel cis XIX -A20-A30 : C-G Ww/Ww pairing antiparallel cis XIX -A20-A35 : C-A Ws/Bs pairing parallel cis one_hbond -A21-A37 : C-C Ss/Hw O2'/Bh pairing parallel cis one_hbond -A22-A24 : U-U Hh/O2P pairing -A24-A41 : U-A Ww/Ww pairing antiparallel cis one_hbond -A25-A40 : U-A Ww/Ww pairing antiparallel cis XX -A26-A39 : C-G Ww/Ww pairing antiparallel cis XIX -A27-A38 : C-G Ww/Ww pairing antiparallel cis XIX -A28-A37 : G-C Ww/Ww pairing antiparallel cis XIX -A29-A36 : A-U Ww/Ww pairing antiparallel cis XX -A30-A35 : G-A Bs/Ww pairing antiparallel cis one_hbond -A39-A40 : G-A O2'/Hh adjacent_5p upward pairing -Residue conformations ------------------------------------------- -A1 : G C2p_exo anti -A2 : G C4p_exo anti -A3 : G C3p_endo anti -A4 : A C2p_exo anti -A5 : G C3p_endo anti -A6 : C C3p_endo anti -A7 : U C3p_endo anti -A8 : C C3p_endo anti -A9 : A C3p_endo anti -A10 : A C3p_endo anti -A11 : C C3p_endo anti -A12 : U C3p_endo anti -A13 : C C2p_exo anti -A14 : U C3p_endo anti -A15 : C C3p_endo anti -A16 : C C3p_endo anti -A17 : C C3p_endo anti -A18 : C C3p_endo anti -A19 : C C3p_endo anti -A20 : C C3p_endo anti -A21 : C C4p_exo anti -A22 : U C2p_endo anti -A23 : U C3p_endo anti -A24 : U C3p_endo anti -A25 : U C3p_endo anti -A26 : C C3p_endo anti -A27 : C C3p_endo anti -A28 : G C3p_endo anti -A29 : A C3p_endo anti -A30 : G C3p_endo anti -A31 : G C4p_exo anti -A32 : G C3p_endo anti -A33 : U C2p_endo anti -A34 : C C3p_endo anti -A35 : A C2p_endo anti -A36 : U C3p_endo anti -A37 : C C4p_exo anti -A38 : G C3p_endo anti -A39 : G C4p_exo anti -A40 : A C2p_exo anti -A41 : A C3p_endo anti -A42 : C C3p_endo anti -A43 : C C3p_endo anti -A44 : A O4p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A28-A29 : adjacent_5p upward -A29-A30 : adjacent_5p upward -A30-A31 : adjacent_5p upward -A31-A32 : adjacent_5p upward -A36-A37 : adjacent_5p upward -A38-A39 : adjacent_5p upward -A39-A40 : adjacent_5p upward pairing -A40-A41 : adjacent_5p upward -A41-A42 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A28-A38 : outward -Number of stackings = 24 -Number of adjacent stackings = 23 -Number of non adjacent stackings = 1 -Base-pairs ------------------------------------------------------ -A1-A17 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A16 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A15 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A14 : A-U Ww/Ww pairing antiparallel cis XX -A5-A13 : G-C Ww/Ww pairing antiparallel cis XIX -A7-A9 : U-A Hh/O2P pairing -A18-A32 : C-G Ww/Ww pairing antiparallel cis XIX -A19-A31 : C-G Ww/Ww pairing antiparallel cis XIX -A20-A30 : C-G Ww/Ww pairing antiparallel cis XIX -A21-A27 : C-C Ws/Hh pairing parallel trans one_hbond -A25-A40 : U-A Ww/Ww pairing antiparallel cis XX -A26-A39 : C-G Ww/Ww pairing antiparallel cis XIX -A27-A38 : C-G Ww/Ww pairing antiparallel cis XIX -A28-A37 : G-C Ww/Ww pairing antiparallel cis XIX -A29-A36 : A-U Ww/Ww pairing antiparallel cis XX -A30-A35 : G-A Ws/Ww pairing antiparallel cis one_hbond -A31-A35 : G-A Ss/Wh O2'/Bh pairing parallel trans one_hbond -A39-A40 : G-A O2'/Hh adjacent_5p upward pairing -Residue conformations ------------------------------------------- -A1 : G C1p_exo anti -A2 : G C3p_endo anti -A3 : G C3p_endo anti -A4 : A C3p_endo anti -A5 : G C3p_endo anti -A6 : C C3p_endo anti -A7 : U C3p_endo anti -A8 : C C1p_exo anti -A9 : A C3p_endo anti -A10 : A C3p_endo anti -A11 : C C3p_endo anti -A12 : U C3p_endo anti -A13 : C C2p_exo anti -A14 : U C3p_endo anti -A15 : C C3p_endo anti -A16 : C C3p_endo anti -A17 : C C3p_endo anti -A18 : C C4p_exo anti -A19 : C C3p_endo anti -A20 : C C3p_endo anti -A21 : C C3p_endo anti -A22 : U C2p_endo anti -A23 : U C3p_endo anti -A24 : U C3p_endo anti -A25 : U C3p_endo anti -A26 : C C3p_endo anti -A27 : C C3p_endo anti -A28 : G C3p_endo anti -A29 : A C3p_endo anti -A30 : G C3p_endo anti -A31 : G C3p_endo anti -A32 : G C4p_exo anti -A33 : U C2p_endo anti -A34 : C C3p_endo anti -A35 : A C2p_endo anti -A36 : U C3p_endo anti -A37 : C C4p_exo anti -A38 : G C3p_endo anti -A39 : G C3p_endo anti -A40 : A C3p_endo anti -A41 : A C3p_endo anti -A42 : C C3p_endo anti -A43 : C C3p_endo anti -A44 : A O4p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward pairing -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A24-A25 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A28-A29 : adjacent_5p upward -A29-A30 : adjacent_5p upward -A30-A31 : adjacent_5p upward -A31-A32 : adjacent_5p upward -A36-A37 : adjacent_5p upward -A38-A39 : adjacent_5p upward -A39-A40 : adjacent_5p upward -A40-A41 : adjacent_5p upward -A42-A43 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A28-A38 : outward -Number of stackings = 26 -Number of adjacent stackings = 25 -Number of non adjacent stackings = 1 -Base-pairs ------------------------------------------------------ -A1-A2 : G-G O2'/Hh adjacent_5p upward pairing -A1-A17 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A16 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A15 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A14 : A-U Ww/Ww pairing antiparallel cis XX -A5-A13 : G-C Ww/Ww pairing antiparallel cis XIX -A6-A10 : C-A Ws/Hw pairing antiparallel trans one_hbond -A7-A9 : U-A Hh/O2P pairing -A7-A10 : U-A Ww/O2P pairing -A18-A32 : C-G Ww/Ww pairing antiparallel cis XIX -A19-A31 : C-G Ww/Ww pairing antiparallel cis XIX -A20-A30 : C-G Ww/Ww pairing antiparallel cis XIX -A20-A35 : C-A Ws/Bs pairing parallel cis one_hbond -A21-A37 : C-C Ss/Hw O2'/Bh pairing parallel cis one_hbond -A22-A24 : U-U Hh/O2P pairing -A25-A40 : U-A Ww/Ww pairing antiparallel cis XX -A26-A39 : C-G Ww/Ww pairing antiparallel cis XIX -A27-A38 : C-G Ww/Ww pairing antiparallel cis XIX -A28-A37 : G-C Ww/Ww pairing antiparallel cis XIX -A29-A36 : A-U Ww/Ww pairing antiparallel cis XX -A32-A34 : G-C O2P/Bh pairing -A32-A35 : G-A O2'/Bh pairing -Residue conformations ------------------------------------------- -A1 : G C1p_exo anti -A2 : G C3p_endo anti -A3 : G C3p_endo anti -A4 : A C3p_endo anti -A5 : G C3p_endo anti -A6 : C C3p_endo anti -A7 : U C3p_endo anti -A8 : C C1p_exo anti -A9 : A C3p_endo anti -A10 : A C3p_endo anti -A11 : C C3p_endo anti -A12 : U C3p_endo anti -A13 : C C2p_exo anti -A14 : U C3p_endo anti -A15 : C C3p_endo anti -A16 : C C3p_endo anti -A17 : C C3p_endo anti -A18 : C C3p_endo anti -A19 : C C3p_endo anti -A20 : C C3p_endo anti -A21 : C C3p_endo anti -A22 : U C2p_endo anti -A23 : U C3p_endo anti -A24 : U C3p_endo anti -A25 : U C3p_endo anti -A26 : C C3p_endo anti -A27 : C C3p_endo anti -A28 : G C3p_endo anti -A29 : A C3p_endo anti -A30 : G C3p_endo anti -A31 : G C3p_endo anti -A32 : G C4p_exo anti -A33 : U C2p_endo anti -A34 : C C3p_endo anti -A35 : A C2p_endo anti -A36 : U C3p_endo anti -A37 : C C4p_exo anti -A38 : G C3p_endo anti -A39 : G C3p_endo anti -A40 : A C3p_endo anti -A41 : A C3p_endo anti -A42 : C C3p_endo anti -A43 : C C3p_endo anti -A44 : A O4p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward pairing -A2-A3 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A28-A29 : adjacent_5p upward -A29-A30 : adjacent_5p upward -A30-A31 : adjacent_5p upward -A31-A32 : adjacent_5p upward -A36-A37 : adjacent_5p upward -A38-A39 : adjacent_5p upward -A39-A40 : adjacent_5p upward -A40-A41 : adjacent_5p upward -A41-A42 : adjacent_5p upward -A42-A43 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A28-A38 : outward -Number of stackings = 26 -Number of adjacent stackings = 25 -Number of non adjacent stackings = 1 -Base-pairs ------------------------------------------------------ -A1-A2 : G-G O2'/Hh O2'/C8 adjacent_5p upward pairing -A1-A17 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A16 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A15 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A14 : A-U Ww/Ww pairing antiparallel cis XX -A5-A13 : G-C Ww/Ww pairing antiparallel cis XIX -A6-A11 : C-C Ww/Bh pairing antiparallel trans one_hbond -A7-A9 : U-A Hh/O2P pairing -A18-A32 : C-G Ww/Ww pairing antiparallel cis XIX -A19-A31 : C-G Ww/Ww pairing antiparallel cis XIX -A20-A30 : C-G Ww/Ww pairing antiparallel cis XIX -A20-A35 : C-A Ws/Bs pairing parallel cis one_hbond -A21-A37 : C-C Ss/Hw O2'/Bh pairing parallel cis one_hbond -A25-A40 : U-A Ww/Ww pairing antiparallel cis XX -A26-A39 : C-G Ww/Ww pairing antiparallel cis XIX -A27-A38 : C-G Ww/Ww pairing antiparallel cis XIX -A28-A37 : G-C Ww/Ww pairing antiparallel cis XIX -A29-A36 : A-U Ww/Ww pairing antiparallel cis XX -A32-A34 : G-C O2P/Bh pairing -A32-A35 : G-A O2'/Bh pairing -Residue conformations ------------------------------------------- -A1 : G O4p_endo anti -A2 : G C3p_endo anti -A3 : G C3p_endo anti -A4 : A C2p_exo anti -A5 : G C3p_endo anti -A6 : C C3p_endo anti -A7 : U C3p_endo anti -A8 : C C4p_exo anti -A9 : A C3p_endo anti -A10 : A C3p_endo anti -A11 : C C3p_endo anti -A12 : U C3p_endo anti -A13 : C C2p_exo anti -A14 : U C3p_endo anti -A15 : C C3p_endo anti -A16 : C C3p_endo anti -A17 : C C3p_endo anti -A18 : C C3p_endo anti -A19 : C C3p_endo anti -A20 : C C3p_endo anti -A21 : C C3p_endo anti -A22 : U C2p_endo anti -A23 : U C3p_endo anti -A24 : U C3p_endo anti -A25 : U C3p_endo anti -A26 : C C4p_exo anti -A27 : C C3p_endo anti -A28 : G C3p_endo anti -A29 : A C3p_endo anti -A30 : G C3p_endo anti -A31 : G C3p_endo anti -A32 : G C2p_exo anti -A33 : U C2p_endo anti -A34 : C C3p_endo anti -A35 : A C1p_exo anti -A36 : U C3p_endo anti -A37 : C C3p_endo anti -A38 : G C3p_endo anti -A39 : G C4p_exo anti -A40 : A C3p_endo anti -A41 : A C3p_endo anti -A42 : C C3p_endo anti -A43 : C C3p_endo anti -A44 : A O4p_endo anti -Adjacent stackings ---------------------------------------------- -A2-A3 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A28-A29 : adjacent_5p upward -A29-A30 : adjacent_5p upward -A30-A31 : adjacent_5p upward -A31-A32 : adjacent_5p upward -A36-A37 : adjacent_5p upward -A38-A39 : adjacent_5p upward -A40-A41 : adjacent_5p upward -A41-A42 : adjacent_5p upward -A42-A43 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A28-A38 : outward -Number of stackings = 27 -Number of adjacent stackings = 26 -Number of non adjacent stackings = 1 -Base-pairs ------------------------------------------------------ -A1-A2 : G-G O2'/Hh adjacent_5p pairing -A1-A17 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A16 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A15 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A14 : A-U Ww/Ww pairing antiparallel cis XX -A5-A13 : G-C Ww/Ww pairing antiparallel cis XIX -A6-A11 : C-C Ww/Wh pairing antiparallel cis one_hbond 131 -A7-A9 : U-A Hh/O2P pairing -A18-A32 : C-G Ww/Ww pairing antiparallel cis XIX -A19-A31 : C-G Ww/Ww pairing antiparallel cis XIX -A20-A30 : C-G Ww/Ww pairing antiparallel cis XIX -A20-A35 : C-A O2'/Ss pairing -A21-A37 : C-C Ss/Hw O2'/Bh pairing parallel cis one_hbond -A22-A24 : U-U Hh/O2P pairing -A22-A25 : U-U Ww/O2P pairing -A24-A41 : U-A Ws/Wh pairing antiparallel cis one_hbond 46 -A25-A40 : U-A Ww/Ww pairing antiparallel cis XX -A26-A39 : C-G Ww/Ww pairing antiparallel cis XIX -A27-A38 : C-G Ww/Ww pairing antiparallel cis XIX -A28-A37 : G-C Ww/Ww pairing antiparallel cis XIX -A29-A36 : A-U Ww/Ww pairing antiparallel cis XX -A30-A35 : G-A Ws/Ww pairing antiparallel cis one_hbond -A39-A40 : G-A O2'/Hh adjacent_5p pairing -A43-A44 : C-A O2'/Hh adjacent_5p pairing -Residue conformations ------------------------------------------- -A1 : G C1p_exo anti -A2 : G C3p_endo anti -A3 : G C4p_exo anti -A4 : A C2p_exo anti -A5 : G C3p_endo anti -A6 : C C3p_endo anti -A7 : U C3p_endo anti -A8 : C C2p_endo anti -A9 : A C3p_endo anti -A10 : A C3p_endo anti -A11 : C C3p_endo anti -A12 : U C3p_endo anti -A13 : C C2p_exo anti -A14 : U C3p_endo anti -A15 : C C3p_endo anti -A16 : C C3p_endo anti -A17 : C C3p_endo anti -A18 : C C3p_endo anti -A19 : C C3p_endo anti -A20 : C C3p_endo anti -A21 : C C3p_endo anti -A22 : U C2p_endo anti -A23 : U C3p_endo anti -A24 : U C3p_endo anti -A25 : U C3p_endo anti -A26 : C C3p_endo anti -A27 : C C3p_endo anti -A28 : G C3p_endo anti -A29 : A C3p_endo anti -A30 : G C3p_endo anti -A31 : G C2p_exo anti -A32 : G C4p_exo anti -A33 : U C2p_endo anti -A34 : C C3p_endo anti -A35 : A C1p_exo anti -A36 : U C3p_endo anti -A37 : C C3p_endo anti -A38 : G C3p_endo anti -A39 : G C3p_endo anti -A40 : A C3p_endo anti -A41 : A C3p_endo anti -A42 : C C3p_endo anti -A43 : C C3p_endo anti -A44 : A O4p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward pairing -A2-A3 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A28-A29 : adjacent_5p upward -A29-A30 : adjacent_5p upward -A30-A31 : adjacent_5p upward -A31-A32 : adjacent_5p upward -A36-A37 : adjacent_5p upward -A38-A39 : adjacent_5p upward -A39-A40 : adjacent_5p upward -A41-A42 : adjacent_5p upward -A42-A43 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A28-A38 : outward -Number of stackings = 24 -Number of adjacent stackings = 23 -Number of non adjacent stackings = 1 -Base-pairs ------------------------------------------------------ -A1-A2 : G-G O2'/Hh adjacent_5p upward pairing -A1-A17 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A16 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A4 : G-A O2'/Hh adjacent_5p pairing -A3-A15 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A14 : A-U Ww/Ww pairing antiparallel cis XX -A5-A13 : G-C Ww/Ww pairing antiparallel cis XIX -A6-A11 : C-C Ww/Bh pairing antiparallel trans 137 -A7-A9 : U-A Hh/O2P pairing -A18-A32 : C-G Ww/Ww pairing antiparallel cis XIX -A19-A31 : C-G Ww/Ww pairing antiparallel cis XIX -A20-A30 : C-G Ww/Ww pairing antiparallel cis XIX -A20-A35 : C-A Ws/Bs pairing parallel cis one_hbond -A21-A37 : C-C Ss/Hw pairing parallel cis one_hbond -A25-A40 : U-A Ww/Ww pairing antiparallel cis XX -A26-A39 : C-G Ww/Ww pairing antiparallel cis XIX -A27-A38 : C-G Ww/Ww pairing antiparallel cis XIX -A28-A37 : G-C Ww/Ww pairing antiparallel cis XIX -A29-A36 : A-U Ww/Ww pairing antiparallel cis XX -A32-A35 : G-A O2'/Bh pairing -Residue conformations ------------------------------------------- -A1 : G C2p_exo anti -A2 : G C4p_exo anti -A3 : G C3p_endo anti -A4 : A C3p_endo anti -A5 : G C3p_endo anti -A6 : C C3p_endo anti -A7 : U C3p_endo anti -A8 : C O4p_endo anti -A9 : A C3p_endo anti -A10 : A C3p_endo anti -A11 : C C3p_endo anti -A12 : U C3p_endo anti -A13 : C C2p_exo anti -A14 : U C3p_endo anti -A15 : C C3p_endo anti -A16 : C C3p_endo anti -A17 : C C3p_endo anti -A18 : C C3p_endo anti -A19 : C C3p_endo anti -A20 : C C3p_endo anti -A21 : C C3p_endo anti -A22 : U C2p_endo anti -A23 : U C3p_endo anti -A24 : U C3p_endo anti -A25 : U C3p_endo anti -A26 : C C4p_exo anti -A27 : C C3p_endo anti -A28 : G C3p_endo anti -A29 : A C3p_endo anti -A30 : G C3p_endo anti -A31 : G C3p_endo anti -A32 : G C4p_exo anti -A33 : U C2p_endo anti -A34 : C C3p_endo anti -A35 : A C2p_endo anti -A36 : U C3p_endo anti -A37 : C C4p_exo anti -A38 : G C3p_endo anti -A39 : G C4p_exo anti -A40 : A C2p_exo anti -A41 : A C3p_endo anti -A42 : C C3p_endo anti -A43 : C C3p_endo anti -A44 : A O4p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A24-A25 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A28-A29 : adjacent_5p upward -A29-A30 : adjacent_5p upward -A30-A31 : adjacent_5p upward -A31-A32 : adjacent_5p upward -A36-A37 : adjacent_5p upward -A38-A39 : adjacent_5p upward -A40-A41 : adjacent_5p upward -A41-A42 : adjacent_5p upward -A42-A43 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A28-A38 : outward -Number of stackings = 24 -Number of adjacent stackings = 23 -Number of non adjacent stackings = 1 -Base-pairs ------------------------------------------------------ -A1-A17 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A16 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A15 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A14 : A-U Ww/Ww pairing antiparallel cis XX -A5-A13 : G-C Ww/Ww pairing antiparallel cis XIX -A6-A11 : C-C Ww/Wh pairing antiparallel cis one_hbond 131 -A7-A9 : U-A Hh/O2P pairing -A18-A32 : C-G Ww/Ww pairing antiparallel cis XIX -A19-A31 : C-G Ww/Ww pairing antiparallel cis XIX -A20-A30 : C-G Ww/Ww pairing antiparallel cis XIX -A20-A35 : C-A Ws/Bs pairing parallel cis one_hbond -A21-A37 : C-C Ss/Hw pairing parallel cis one_hbond -A22-A24 : U-U Hh/O2P pairing -A24-A41 : U-A Ws/Wh pairing antiparallel trans one_hbond 46 -A25-A40 : U-A Ww/Ww pairing antiparallel cis XX -A26-A39 : C-G Ww/Ww pairing antiparallel cis XIX -A27-A38 : C-G Ww/Ww pairing antiparallel cis XIX -A28-A37 : G-C Ww/Ww pairing antiparallel cis XIX -A29-A36 : A-U Ww/Ww pairing antiparallel cis XX -A32-A35 : G-A O2'/Bh pairing -A39-A40 : G-A O2'/Hh adjacent_5p pairing -Residue conformations ------------------------------------------- -A1 : G C1p_exo anti -A2 : G C3p_endo anti -A3 : G C3p_endo anti -A4 : A C3p_endo anti -A5 : G C3p_endo anti -A6 : C C3p_endo anti -A7 : U C3p_endo anti -A8 : C C1p_exo anti -A9 : A C3p_endo anti -A10 : A C3p_endo anti -A11 : C C3p_endo anti -A12 : U C3p_endo anti -A13 : C C2p_exo anti -A14 : U C3p_endo anti -A15 : C C3p_endo anti -A16 : C C3p_endo anti -A17 : C C3p_endo anti -A18 : C C3p_endo anti -A19 : C C3p_endo anti -A20 : C C3p_endo anti -A21 : C C3p_endo anti -A22 : U C2p_endo anti -A23 : U C3p_endo anti -A24 : U C2p_exo anti -A25 : U C3p_endo anti -A26 : C C3p_endo anti -A27 : C C3p_endo anti -A28 : G C3p_endo anti -A29 : A C3p_endo anti -A30 : G C3p_endo anti -A31 : G C3p_endo anti -A32 : G C4p_exo anti -A33 : U C2p_endo anti -A34 : C C2p_exo anti -A35 : A C1p_exo anti -A36 : U C3p_endo anti -A37 : C C3p_endo anti -A38 : G C3p_endo anti -A39 : G C4p_exo anti -A40 : A C3p_endo anti -A41 : A C3p_endo anti -A42 : C C3p_endo anti -A43 : C C3p_endo anti -A44 : A O4p_endo anti -Adjacent stackings ---------------------------------------------- -A2-A3 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A28-A29 : adjacent_5p upward -A29-A30 : adjacent_5p upward -A30-A31 : adjacent_5p upward -A31-A32 : adjacent_5p upward -A36-A37 : adjacent_5p upward -A38-A39 : adjacent_5p upward -A40-A41 : adjacent_5p upward -A41-A42 : adjacent_5p upward -A42-A43 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A28-A38 : outward -Number of stackings = 25 -Number of adjacent stackings = 24 -Number of non adjacent stackings = 1 -Base-pairs ------------------------------------------------------ -A1-A2 : G-G O2'/Hh adjacent_5p pairing -A1-A17 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A16 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A15 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A14 : A-U Ww/Ww pairing antiparallel cis XX -A5-A13 : G-C Ww/Ww pairing antiparallel cis XIX -A6-A11 : C-C Ww/Bh pairing antiparallel cis one_hbond 131 -A7-A9 : U-A Hh/O2P pairing -A18-A32 : C-G Ww/Ww pairing antiparallel cis XIX -A19-A31 : C-G Ww/Ww pairing antiparallel cis XIX -A20-A30 : C-G Ww/Ww pairing antiparallel cis XIX -A20-A35 : C-A Ws/Bs pairing parallel cis one_hbond -A21-A37 : C-C Ss/Hw O2'/Bh pairing parallel cis one_hbond -A22-A24 : U-U Hh/O2P pairing -A24-A41 : U-A Ws/Wh pairing antiparallel trans one_hbond 46 -A25-A40 : U-A Ww/Ww pairing antiparallel cis XX -A26-A39 : C-G Ww/Ww pairing antiparallel cis XIX -A27-A38 : C-G Ww/Ww pairing antiparallel cis XIX -A28-A37 : G-C Ww/Ww pairing antiparallel cis XIX -A29-A36 : A-U Ww/Ww pairing antiparallel cis XX -A30-A35 : G-A Ws/Ww pairing antiparallel cis one_hbond -A32-A35 : G-A O2'/Bh pairing -A39-A40 : G-A O2'/Hh adjacent_5p pairing -Residue conformations ------------------------------------------- -A1 : G C1p_exo anti -A2 : G C3p_endo anti -A3 : G C4p_exo anti -A4 : A C2p_exo anti -A5 : G C3p_endo anti -A6 : C C3p_endo anti -A7 : U C3p_endo anti -A8 : C C2p_endo anti -A9 : A C3p_endo anti -A10 : A C3p_endo anti -A11 : C C3p_endo anti -A12 : U C3p_endo anti -A13 : C C2p_exo anti -A14 : U C3p_endo anti -A15 : C C3p_endo anti -A16 : C C3p_endo anti -A17 : C C3p_endo anti -A18 : C C3p_endo anti -A19 : C C3p_endo anti -A20 : C C3p_endo anti -A21 : C C3p_endo anti -A22 : U C2p_endo anti -A23 : U C3p_endo anti -A24 : U C2p_exo anti -A25 : U C3p_endo anti -A26 : C C3p_endo anti -A27 : C C3p_endo anti -A28 : G C3p_endo anti -A29 : A C3p_endo anti -A30 : G C2p_exo anti -A31 : G C3p_endo anti -A32 : G C4p_exo anti -A33 : U C2p_endo anti -A34 : C C3p_endo anti -A35 : A C1p_exo anti -A36 : U C3p_endo anti -A37 : C C4p_exo anti -A38 : G C3p_endo anti -A39 : G C3p_endo anti -A40 : A C3p_endo anti -A41 : A C3p_endo anti -A42 : C C3p_endo anti -A43 : C C3p_endo anti -A44 : A O4p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward pairing -A2-A3 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A28-A29 : adjacent_5p upward -A29-A30 : adjacent_5p upward -A30-A31 : adjacent_5p upward -A31-A32 : adjacent_5p upward -A36-A37 : adjacent_5p upward -A38-A39 : adjacent_5p upward -A39-A40 : adjacent_5p upward -A40-A41 : adjacent_5p upward -A42-A43 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A28-A38 : outward -Number of stackings = 23 -Number of adjacent stackings = 22 -Number of non adjacent stackings = 1 -Base-pairs ------------------------------------------------------ -A1-A2 : G-G O2'/Hh adjacent_5p upward pairing -A1-A17 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A16 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A4 : G-A O2'/Hh adjacent_5p pairing -A3-A15 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A14 : A-U Ww/Ww pairing antiparallel cis XX -A5-A13 : G-C Ww/Ww pairing antiparallel cis XIX -A6-A11 : C-C Ww/Wh pairing antiparallel cis one_hbond 131 -A7-A9 : U-A Hh/O2P pairing -A18-A32 : C-G Ww/Ww pairing antiparallel cis XIX -A19-A31 : C-G Ww/Ww pairing antiparallel cis XIX -A20-A30 : C-G Ww/Ww pairing antiparallel cis XIX -A20-A35 : C-A Ws/Bs pairing parallel cis one_hbond -A21-A37 : C-C Ss/Bh O2'/Bh pairing parallel trans one_hbond -A25-A40 : U-A Ww/Ww pairing antiparallel cis XX -A26-A39 : C-G Ww/Ww pairing antiparallel cis XIX -A27-A38 : C-G Ww/Ww pairing antiparallel cis XIX -A28-A37 : G-C Ww/Ww pairing antiparallel cis XIX -A29-A36 : A-U Ww/Ww pairing antiparallel cis XX -A32-A35 : G-A O2'/Bh pairing -A43-A44 : C-A O2'/Hh adjacent_5p pairing -Residue conformations ------------------------------------------- -A1 : G C1p_exo anti -A2 : G C3p_endo anti -A3 : G C4p_exo anti -A4 : A C2p_exo anti -A5 : G C3p_endo anti -A6 : C C3p_endo anti -A7 : U C3p_endo anti -A8 : C C4p_exo anti -A9 : A C3p_endo anti -A10 : A C3p_endo anti -A11 : C C3p_endo anti -A12 : U C3p_endo anti -A13 : C C2p_exo anti -A14 : U C3p_endo anti -A15 : C C3p_endo anti -A16 : C C3p_endo anti -A17 : C C3p_endo anti -A18 : C C3p_endo anti -A19 : C C3p_endo anti -A20 : C C3p_endo anti -A21 : C C3p_endo anti -A22 : U C2p_endo anti -A23 : U C3p_endo anti -A24 : U C3p_endo anti -A25 : U C3p_endo anti -A26 : C C3p_endo anti -A27 : C C3p_endo anti -A28 : G C3p_endo anti -A29 : A C3p_endo anti -A30 : G C3p_endo anti -A31 : G C3p_endo anti -A32 : G C4p_exo anti -A33 : U C2p_endo anti -A34 : C C3p_endo anti -A35 : A C2p_endo anti -A36 : U C3p_endo anti -A37 : C C4p_exo anti -A38 : G C2p_exo anti -A39 : G C3p_endo anti -A40 : A C2p_exo anti -A41 : A C3p_endo anti -A42 : C C3p_endo anti -A43 : C C3p_endo anti -A44 : A O4p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward pairing -A2-A3 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A24-A25 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A28-A29 : adjacent_5p upward -A29-A30 : adjacent_5p upward -A30-A31 : adjacent_5p upward -A31-A32 : adjacent_5p upward -A36-A37 : adjacent_5p upward -A38-A39 : adjacent_5p upward -A39-A40 : adjacent_5p upward -A40-A41 : adjacent_5p upward -A41-A42 : adjacent_5p upward -A42-A43 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 25 -Number of adjacent stackings = 25 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-A2 : G-G O2'/Hh adjacent_5p upward pairing -A1-A17 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A16 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A4 : G-A O2'/Hh adjacent_5p pairing -A3-A15 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A14 : A-U Ww/Ww pairing antiparallel cis XX -A5-A13 : G-C Ww/Ww pairing antiparallel cis XIX -A6-A11 : C-C Ww/Bh pairing antiparallel cis 137 -A7-A9 : U-A Hh/O2P pairing -A18-A32 : C-G Ww/Ww pairing antiparallel cis XIX -A19-A31 : C-G Ww/Ww pairing antiparallel cis XIX -A20-A30 : C-G Ww/Ww pairing antiparallel cis XIX -A20-A35 : C-A Ws/Bs pairing parallel cis one_hbond -A21-A37 : C-C Ss/Bh O2'/Bh pairing parallel trans one_hbond -A24-A41 : U-A Ww/Ww pairing antiparallel cis XX -A25-A40 : U-A Ww/Ww pairing antiparallel cis XX -A26-A39 : C-G Ww/Ww pairing antiparallel cis XIX -A27-A38 : C-G Ww/Ww pairing antiparallel cis XIX -A28-A37 : G-C Ww/Ww pairing antiparallel cis XIX -A29-A36 : A-U Ww/Ww pairing antiparallel cis XX -A32-A35 : G-A O2'/Bh pairing -Residue conformations ------------------------------------------- -A1 : G O4p_endo anti -A2 : G C3p_endo anti -A3 : G C3p_endo anti -A4 : A C2p_exo anti -A5 : G C3p_endo anti -A6 : C C3p_endo anti -A7 : U C3p_endo anti -A8 : C C1p_exo anti -A9 : A C3p_endo anti -A10 : A C3p_endo anti -A11 : C C3p_endo anti -A12 : U C3p_endo anti -A13 : C C2p_exo anti -A14 : U C3p_endo anti -A15 : C C3p_endo anti -A16 : C C3p_endo anti -A17 : C C3p_endo anti -A18 : C C3p_endo anti -A19 : C C3p_endo anti -A20 : C C4p_exo anti -A21 : C C3p_endo anti -A22 : U C2p_endo anti -A23 : U C3p_endo anti -A24 : U C3p_endo anti -A25 : U C3p_endo anti -A26 : C C3p_endo anti -A27 : C C3p_endo anti -A28 : G C3p_endo anti -A29 : A C3p_endo anti -A30 : G C3p_endo anti -A31 : G C2p_exo anti -A32 : G C4p_exo anti -A33 : U C2p_endo anti -A34 : C C3p_endo anti -A35 : A C2p_endo anti -A36 : U C3p_endo anti -A37 : C C4p_exo anti -A38 : G C3p_endo anti -A39 : G C3p_endo anti -A40 : A C3p_endo anti -A41 : A C3p_endo anti -A42 : C C3p_endo anti -A43 : C C3p_endo anti -A44 : A O4p_endo anti -Adjacent stackings ---------------------------------------------- -A2-A3 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A24-A25 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A28-A29 : adjacent_5p upward -A29-A30 : adjacent_5p upward -A30-A31 : adjacent_5p upward -A31-A32 : adjacent_5p upward -A36-A37 : adjacent_5p upward -A38-A39 : adjacent_5p upward -A39-A40 : adjacent_5p upward -A40-A41 : adjacent_5p upward -A42-A43 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A28-A38 : outward -Number of stackings = 25 -Number of adjacent stackings = 24 -Number of non adjacent stackings = 1 -Base-pairs ------------------------------------------------------ -A1-A2 : G-G O2'/Hh adjacent_5p pairing -A1-A17 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A16 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A15 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A14 : A-U Ww/Ww pairing antiparallel cis XX -A5-A13 : G-C Ww/Ww pairing antiparallel cis XIX -A6-A11 : C-C Ww/Bh pairing antiparallel trans one_hbond -A7-A9 : U-A Hh/O2P pairing -A18-A32 : C-G Ww/Ww pairing antiparallel cis XIX -A19-A31 : C-G Ww/Ww pairing antiparallel cis XIX -A20-A30 : C-G Ww/Ww pairing antiparallel cis XIX -A20-A35 : C-A Ws/Bs pairing parallel cis one_hbond -A21-A37 : C-C Ss/Hw pairing parallel cis one_hbond -A22-A24 : U-U Hh/O2P pairing -A24-A41 : U-A Ww/Ww pairing antiparallel cis one_hbond -A25-A40 : U-A Ww/Ww pairing antiparallel cis XX -A26-A39 : C-G Ww/Ww pairing antiparallel cis XIX -A27-A38 : C-G Ww/Ww pairing antiparallel cis XIX -A28-A37 : G-C Ww/Ww pairing antiparallel cis XIX -A29-A36 : A-U Ww/Ww pairing antiparallel cis XX -A32-A35 : G-A O2'/Bh pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C4p_exo anti -A3 : G C4p_exo anti -A4 : A C3p_endo anti -A5 : G C3p_endo anti -A6 : C C3p_endo anti -A7 : U C3p_endo anti -A8 : C C3p_endo anti -A9 : A C3p_endo anti -A10 : A C3p_endo anti -A11 : C C3p_endo anti -A12 : U C3p_endo anti -A13 : C C2p_exo anti -A14 : U C3p_endo anti -A15 : C C3p_endo anti -A16 : C C3p_endo anti -A17 : C C3p_endo anti -A18 : C C3p_endo anti -A19 : C C3p_endo anti -A20 : C C3p_endo anti -A21 : C C4p_exo anti -A22 : U C2p_endo anti -A23 : U C3p_endo anti -A24 : U C4p_exo anti -A25 : U C3p_endo anti -A26 : C C3p_endo anti -A27 : C C3p_endo anti -A28 : G C3p_endo anti -A29 : A C3p_endo anti -A30 : G C3p_endo anti -A31 : G C4p_exo anti -A32 : G C3p_endo anti -A33 : U C2p_endo anti -A34 : C C3p_endo anti -A35 : A C2p_endo anti -A36 : U C3p_endo anti -A37 : C C3p_endo anti -A38 : G C3p_endo anti -A39 : G C4p_exo anti -A40 : A C2p_exo anti -A41 : A C3p_endo anti -A42 : C C3p_endo anti -A43 : C C3p_endo anti -A44 : A O4p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A28-A29 : adjacent_5p upward -A29-A30 : adjacent_5p upward -A30-A31 : adjacent_5p upward -A36-A37 : adjacent_5p upward -A38-A39 : adjacent_5p upward -A40-A41 : adjacent_5p upward -A41-A42 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A28-A38 : outward -Number of stackings = 22 -Number of adjacent stackings = 21 -Number of non adjacent stackings = 1 -Base-pairs ------------------------------------------------------ -A1-A17 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A3 : G-G O2'/C8 adjacent_5p pairing -A2-A16 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A15 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A14 : A-U Ww/Ww pairing antiparallel cis XX -A5-A13 : G-C Ww/Ww pairing antiparallel cis XIX -A7-A9 : U-A Hh/O2P Ww/O2P pairing -A18-A32 : C-G Ww/Ww pairing antiparallel cis XIX -A19-A31 : C-G Ww/Ww pairing antiparallel cis XIX -A20-A30 : C-G Ww/Ww pairing antiparallel cis XIX -A21-A37 : C-C O2'/Bh pairing -A24-A41 : U-A Ww/Ww pairing antiparallel cis XX -A25-A40 : U-A Ww/Ww pairing antiparallel cis XX -A26-A39 : C-G Ww/Ww pairing antiparallel cis XIX -A27-A38 : C-G Ww/Ww pairing antiparallel cis XIX -A28-A37 : G-C Ww/Ww pairing antiparallel cis XIX -A29-A36 : A-U Ww/Ww pairing antiparallel cis XX -A39-A40 : G-A O2'/Hh adjacent_5p pairing -Residue conformations ------------------------------------------- -A1 : G O4p_endo anti -A2 : G C3p_endo anti -A3 : G C3p_endo anti -A4 : A C3p_endo anti -A5 : G C3p_endo anti -A6 : C C3p_endo anti -A7 : U C3p_endo anti -A8 : C O4p_endo anti -A9 : A C3p_endo anti -A10 : A C3p_endo anti -A11 : C C2p_exo anti -A12 : U C3p_endo anti -A13 : C C2p_exo anti -A14 : U C3p_endo anti -A15 : C C3p_endo anti -A16 : C C3p_endo anti -A17 : C C3p_endo anti -A18 : C C3p_endo anti -A19 : C C3p_endo anti -A20 : C C3p_endo anti -A21 : C C3p_endo anti -A22 : U C2p_endo anti -A23 : U C3p_endo anti -A24 : U C3p_endo anti -A25 : U C3p_endo anti -A26 : C C4p_exo anti -A27 : C C3p_endo anti -A28 : G C3p_endo anti -A29 : A C3p_endo anti -A30 : G C3p_endo anti -A31 : G C2p_exo anti -A32 : G C4p_exo anti -A33 : U C2p_endo anti -A34 : C C3p_endo anti -A35 : A C2p_endo anti -A36 : U C3p_endo anti -A37 : C C4p_exo anti -A38 : G C3p_endo anti -A39 : G C4p_exo anti -A40 : A C2p_exo anti -A41 : A C3p_endo anti -A42 : C C3p_endo anti -A43 : C C3p_endo anti -A44 : A O4p_endo anti -Adjacent stackings ---------------------------------------------- -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A28-A29 : adjacent_5p upward -A29-A30 : adjacent_5p upward -A30-A31 : adjacent_5p upward -A31-A32 : adjacent_5p upward -A36-A37 : adjacent_5p upward -A38-A39 : adjacent_5p upward -A40-A41 : adjacent_5p upward -A41-A42 : adjacent_5p upward -A42-A43 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A28-A38 : outward -Number of stackings = 22 -Number of adjacent stackings = 21 -Number of non adjacent stackings = 1 -Base-pairs ------------------------------------------------------ -A1-A2 : G-G O2'/Hh adjacent_5p pairing -A1-A17 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A16 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A15 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A14 : A-U Ww/Ww pairing antiparallel cis XX -A5-A13 : G-C Ww/Ww pairing antiparallel cis XIX -A6-A10 : C-A Bh/O2P Bh/O2P pairing -A7-A9 : U-A Hh/O2P pairing -A7-A10 : U-A Ww/O2P pairing -A8-A9 : C-A O2'/Hh adjacent_5p pairing -A18-A32 : C-G Ww/Ww pairing antiparallel cis XIX -A19-A31 : C-G Ww/Ww pairing antiparallel cis XIX -A20-A30 : C-G Ww/Ww pairing antiparallel cis XIX -A20-A35 : C-A Ws/Bs pairing parallel cis one_hbond -A21-A37 : C-C Ss/Hw pairing parallel cis one_hbond -A25-A40 : U-A Ww/Ww pairing antiparallel cis XX -A26-A39 : C-G Ww/Ww pairing antiparallel cis XIX -A27-A38 : C-G Ww/Ww pairing antiparallel cis XIX -A28-A37 : G-C Ww/Ww pairing antiparallel cis XIX -A29-A36 : A-U Ww/Ww pairing antiparallel cis XX -A30-A35 : G-A Ws/Ww pairing antiparallel cis one_hbond -A39-A40 : G-A O2'/Hh adjacent_5p pairing -A43-A44 : C-A O2'/Hh adjacent_5p pairing -Residue conformations ------------------------------------------- -A1 : G O4p_endo anti -A2 : G C3p_endo anti -A3 : G C3p_endo anti -A4 : A C3p_endo anti -A5 : G C3p_endo anti -A6 : C C3p_endo anti -A7 : U C3p_endo anti -A8 : C C1p_exo anti -A9 : A C3p_endo anti -A10 : A C3p_endo anti -A11 : C C3p_endo anti -A12 : U C3p_endo anti -A13 : C C2p_exo anti -A14 : U C3p_endo anti -A15 : C C3p_endo anti -A16 : C C3p_endo anti -A17 : C C3p_endo anti -A18 : C C3p_endo anti -A19 : C C3p_endo anti -A20 : C C3p_endo anti -A21 : C C3p_endo anti -A22 : U C2p_endo anti -A23 : U C3p_endo anti -A24 : U C3p_endo anti -A25 : U C3p_endo anti -A26 : C C3p_endo anti -A27 : C C3p_endo anti -A28 : G C2p_exo anti -A29 : A C3p_endo anti -A30 : G C3p_endo anti -A31 : G C4p_exo anti -A32 : G C3p_endo anti -A33 : U C2p_endo anti -A34 : C C3p_endo anti -A35 : A C1p_exo anti -A36 : U C3p_endo anti -A37 : C C3p_endo anti -A38 : G C2p_exo anti -A39 : G C3p_endo anti -A40 : A C3p_endo anti -A41 : A C3p_endo anti -A42 : C C3p_endo anti -A43 : C C3p_endo anti -A44 : A O4p_endo anti -Adjacent stackings ---------------------------------------------- -A2-A3 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A24-A25 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A28-A29 : adjacent_5p upward -A29-A30 : adjacent_5p upward -A30-A31 : adjacent_5p upward -A36-A37 : adjacent_5p upward -A38-A39 : adjacent_5p upward -A39-A40 : adjacent_5p upward -A40-A41 : adjacent_5p upward -A42-A43 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A28-A38 : outward -Number of stackings = 23 -Number of adjacent stackings = 22 -Number of non adjacent stackings = 1 -Base-pairs ------------------------------------------------------ -A1-A2 : G-G O2'/Hh adjacent_5p pairing -A1-A17 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A16 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A15 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A14 : A-U Ww/Ww pairing antiparallel cis XX -A5-A13 : G-C Ww/Ww pairing antiparallel cis XIX -A7-A9 : U-A Hh/O2P pairing -A18-A32 : C-G Ww/Ww pairing antiparallel cis XIX -A19-A31 : C-G Ww/Ww pairing antiparallel cis XIX -A20-A30 : C-G Ww/Ww pairing antiparallel cis XIX -A20-A35 : C-A Ws/Bs O2'/Ss pairing parallel cis one_hbond -A21-A27 : C-C Ws/Wh pairing antiparallel trans one_hbond 137 -A24-A41 : U-A Ww/Ww pairing antiparallel cis XX -A25-A40 : U-A Ww/Ww pairing antiparallel cis XX -A26-A39 : C-G Ww/Ww pairing antiparallel cis XIX -A27-A38 : C-G Ww/Ww pairing antiparallel cis XIX -A28-A37 : G-C Ww/Ww pairing antiparallel cis XIX -A29-A36 : A-U Ww/Ww pairing antiparallel cis XX -A30-A35 : G-A Ws/Ww pairing antiparallel cis one_hbond -A32-A34 : G-C O2P/Bh pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C2p_exo anti -A3 : G C3p_endo anti -A4 : A C2p_exo anti -A5 : G C3p_endo anti -A6 : C C3p_endo anti -A7 : U C3p_endo anti -A8 : C C1p_exo anti -A9 : A C3p_endo anti -A10 : A C3p_endo anti -A11 : C C2p_exo anti -A12 : U C3p_endo anti -A13 : C C2p_exo anti -A14 : U C3p_endo anti -A15 : C C3p_endo anti -A16 : C C4p_exo anti -A17 : C C3p_endo anti -A18 : C C3p_endo anti -A19 : C C3p_endo anti -A20 : C C3p_endo anti -A21 : C C3p_endo anti -A22 : U C2p_endo anti -A23 : U C3p_endo anti -A24 : U C3p_endo anti -A25 : U C3p_endo anti -A26 : C C3p_endo anti -A27 : C C3p_endo anti -A28 : G C3p_endo anti -A29 : A C3p_endo anti -A30 : G C3p_endo anti -A31 : G C3p_endo anti -A32 : G C4p_exo anti -A33 : U C2p_endo anti -A34 : C C3p_endo anti -A35 : A C2p_endo anti -A36 : U C3p_endo anti -A37 : C C4p_exo anti -A38 : G C3p_endo anti -A39 : G C3p_endo anti -A40 : A C3p_endo anti -A41 : A C3p_endo anti -A42 : C C3p_endo anti -A43 : C C3p_endo anti -A44 : A O4p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward pairing -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A17-A18 : adjacent_5p upward pairing -A19-A20 : adjacent_5p upward -A24-A25 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A28-A29 : adjacent_5p upward -A29-A30 : adjacent_5p upward -A30-A31 : adjacent_5p upward -A31-A32 : adjacent_5p upward -A36-A37 : adjacent_5p upward -A38-A39 : adjacent_5p upward -A39-A40 : adjacent_5p upward -A40-A41 : adjacent_5p upward -A41-A42 : adjacent_5p upward -A42-A43 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A28-A38 : outward -Number of stackings = 24 -Number of adjacent stackings = 23 -Number of non adjacent stackings = 1 -Base-pairs ------------------------------------------------------ -A1-A2 : G-G O2'/Hh O2'/C8 adjacent_5p upward pairing -A1-A17 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A16 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A15 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A14 : A-U Ww/Ww pairing antiparallel cis XX -A5-A13 : G-C Ww/Ww pairing antiparallel cis XIX -A7-A10 : U-A Ww/O2P pairing -A16-A17 : C-C O2'/Hh adjacent_5p pairing -A17-A18 : C-C O2P/Bh adjacent_5p upward pairing -A18-A32 : C-G Ww/Ww pairing antiparallel cis XIX -A19-A31 : C-G Ww/Ww pairing antiparallel cis XIX -A20-A30 : C-G Ww/Ww pairing antiparallel cis XIX -A20-A35 : C-A Ws/Bs pairing parallel cis one_hbond -A21-A22 : C-U O2'/Hh adjacent_5p pairing -A21-A37 : C-C Ss/Hw O2'/Bh pairing parallel cis one_hbond -A24-A41 : U-A Ww/Ww pairing antiparallel cis one_hbond -A25-A40 : U-A Ww/Ww pairing antiparallel cis XX -A26-A39 : C-G Ww/Ww pairing antiparallel cis XIX -A27-A38 : C-G Ww/Ww pairing antiparallel cis XIX -A28-A37 : G-C Ww/Ww pairing antiparallel cis XIX -A29-A36 : A-U Ww/Ww pairing antiparallel cis XX -Residue conformations ------------------------------------------- -A1 : G C1p_exo anti -A2 : G C3p_endo anti -A3 : G C3p_endo anti -A4 : A C3p_endo anti -A5 : G C3p_endo anti -A6 : C C3p_endo anti -A7 : U C3p_endo anti -A8 : C C2p_endo anti -A9 : A C3p_endo anti -A10 : A C3p_endo anti -A11 : C C3p_endo anti -A12 : U C3p_endo anti -A13 : C C2p_exo anti -A14 : U C3p_endo anti -A15 : C C3p_endo anti -A16 : C C3p_endo anti -A17 : C C3p_endo anti -A18 : C C4p_exo anti -A19 : C C3p_endo anti -A20 : C C3p_endo anti -A21 : C C3p_endo anti -A22 : U C2p_endo anti -A23 : U C3p_endo anti -A24 : U C3p_endo anti -A25 : U C3p_endo anti -A26 : C C4p_exo anti -A27 : C C3p_endo anti -A28 : G C3p_endo anti -A29 : A C3p_endo anti -A30 : G C3p_endo anti -A31 : G C3p_endo anti -A32 : G C4p_exo anti -A33 : U C2p_endo anti -A34 : C C3p_endo anti -A35 : A C2p_endo anti -A36 : U C3p_endo anti -A37 : C C4p_exo anti -A38 : G C3p_endo anti -A39 : G C4p_exo anti -A40 : A C2p_exo anti -A41 : A C3p_endo anti -A42 : C C3p_endo anti -A43 : C C3p_endo anti -A44 : A O4p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward pairing -A2-A3 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A28-A29 : adjacent_5p upward -A29-A30 : adjacent_5p upward -A30-A31 : adjacent_5p upward -A31-A32 : adjacent_5p upward -A36-A37 : adjacent_5p upward -A38-A39 : adjacent_5p upward -A40-A41 : adjacent_5p upward -A41-A42 : adjacent_5p upward -A42-A43 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A28-A38 : outward -Number of stackings = 21 -Number of adjacent stackings = 20 -Number of non adjacent stackings = 1 -Base-pairs ------------------------------------------------------ -A1-A2 : G-G O2'/Hh adjacent_5p upward pairing -A1-A17 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A16 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A15 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A14 : A-U Ww/Ww pairing antiparallel cis XX -A5-A13 : G-C Ww/Ww pairing antiparallel cis XIX -A6-A11 : C-C Ww/Wh pairing antiparallel cis one_hbond 131 -A7-A9 : U-A Hh/O2P pairing -A18-A32 : C-G Ww/Ww pairing antiparallel cis XIX -A19-A31 : C-G Ww/Ww pairing antiparallel cis XIX -A20-A30 : C-G Ww/Ww pairing antiparallel cis XIX -A20-A35 : C-A Ws/Bs pairing parallel cis one_hbond -A21-A37 : C-C Ss/Hw pairing parallel cis one_hbond -A22-A24 : U-U Hh/O2P pairing -A24-A41 : U-A Ww/Ww pairing antiparallel cis one_hbond -A25-A40 : U-A Ww/Ww pairing antiparallel cis XX -A26-A39 : C-G Ww/Ww pairing antiparallel cis XIX -A27-A38 : C-G Ww/Ww pairing antiparallel cis XIX -A28-A37 : G-C Ww/Ww pairing antiparallel cis XIX -A29-A36 : A-U Ww/Ww pairing antiparallel cis XX -A32-A34 : G-C O2P/Bh pairing -A32-A35 : G-A O2'/Bh pairing -A39-A40 : G-A O2'/Hh adjacent_5p pairing -A43-A44 : C-A O2'/Hh adjacent_5p pairing -Residue conformations ------------------------------------------- -A1 : G C2p_exo anti -A2 : G C3p_endo anti -A3 : G C3p_endo anti -A4 : A C3p_endo anti -A5 : G C3p_endo anti -A6 : C C3p_endo anti -A7 : U C3p_endo anti -A8 : C C1p_exo anti -A9 : A C3p_endo anti -A10 : A C3p_endo anti -A11 : C C3p_endo anti -A12 : U C3p_endo anti -A13 : C C2p_exo anti -A14 : U C3p_endo anti -A15 : C C3p_endo anti -A16 : C C3p_endo anti -A17 : C C3p_endo anti -A18 : C C3p_endo anti -A19 : C C3p_endo anti -A20 : C C3p_endo anti -A21 : C C3p_endo anti -A22 : U C2p_endo anti -A23 : U C3p_endo anti -A24 : U C2p_exo anti -A25 : U C3p_endo anti -A26 : C C4p_exo anti -A27 : C C4p_exo anti -A28 : G C3p_endo anti -A29 : A C3p_endo anti -A30 : G C2p_exo anti -A31 : G C3p_endo anti -A32 : G C4p_exo anti -A33 : U C2p_endo anti -A34 : C C3p_endo anti -A35 : A C1p_exo anti -A36 : U C3p_endo anti -A37 : C C3p_endo anti -A38 : G C3p_endo anti -A39 : G C3p_endo anti -A40 : A C3p_endo anti -A41 : A C3p_endo anti -A42 : C C3p_endo anti -A43 : C C3p_endo anti -A44 : A O4p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A28-A29 : adjacent_5p upward -A29-A30 : adjacent_5p upward -A30-A31 : adjacent_5p upward -A31-A32 : adjacent_5p upward -A36-A37 : adjacent_5p upward -A38-A39 : adjacent_5p upward -A39-A40 : adjacent_5p upward -A40-A41 : adjacent_5p upward -A41-A42 : adjacent_5p upward -A42-A43 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A28-A38 : outward -Number of stackings = 24 -Number of adjacent stackings = 23 -Number of non adjacent stackings = 1 -Base-pairs ------------------------------------------------------ -A1-A17 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A16 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A15 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A14 : A-U Ww/Ww pairing antiparallel cis XX -A5-A13 : G-C Ww/Ww pairing antiparallel cis XIX -A6-A10 : C-A Ws/Hw pairing antiparallel trans one_hbond -A7-A9 : U-A Hh/O2P pairing -A18-A32 : C-G Ww/Ww pairing antiparallel cis XIX -A19-A31 : C-G Ww/Ww pairing antiparallel cis XIX -A20-A30 : C-G Ww/Ww pairing antiparallel cis XIX -A20-A35 : C-A Ws/Bs pairing parallel cis one_hbond -A25-A40 : U-A Ww/Ww pairing antiparallel cis XX -A26-A39 : C-G Ww/Ww pairing antiparallel cis XIX -A27-A38 : C-G Ww/Ww pairing antiparallel cis XIX -A28-A37 : G-C Ww/Ww pairing antiparallel cis XIX -A29-A36 : A-U Ww/Ww pairing antiparallel cis XX -A32-A35 : G-A O2'/Bh pairing -Residue conformations ------------------------------------------- -A1 : G C2p_exo anti -A2 : G C4p_exo anti -A3 : G C3p_endo anti -A4 : A C2p_exo anti -A5 : G C3p_endo anti -A6 : C C3p_endo anti -A7 : U C3p_endo anti -A8 : C O4p_endo anti -A9 : A C3p_endo anti -A10 : A C3p_endo anti -A11 : C C3p_endo anti -A12 : U C3p_endo anti -A13 : C C2p_exo anti -A14 : U C3p_endo anti -A15 : C C3p_endo anti -A16 : C C3p_endo anti -A17 : C C3p_endo anti -A18 : C C3p_endo anti -A19 : C C2p_exo anti -A20 : C C3p_endo anti -A21 : C C3p_endo anti -A22 : U C2p_endo anti -A23 : U C3p_endo anti -A24 : U C3p_endo anti -A25 : U C3p_endo anti -A26 : C C3p_endo anti -A27 : C C3p_endo anti -A28 : G C3p_endo anti -A29 : A C3p_endo anti -A30 : G C3p_endo anti -A31 : G C2p_exo anti -A32 : G C3p_endo anti -A33 : U C2p_endo anti -A34 : C C3p_endo anti -A35 : A C2p_endo anti -A36 : U C3p_endo anti -A37 : C C3p_endo anti -A38 : G C3p_endo anti -A39 : G C4p_exo anti -A40 : A C2p_exo anti -A41 : A C3p_endo anti -A42 : C C3p_endo anti -A43 : C C3p_endo anti -A44 : A O4p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A24-A25 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A28-A29 : adjacent_5p upward -A29-A30 : adjacent_5p upward -A30-A31 : adjacent_5p upward -A31-A32 : adjacent_5p upward -A36-A37 : adjacent_5p upward -A38-A39 : adjacent_5p upward -A39-A40 : adjacent_5p upward pairing -A40-A41 : adjacent_5p upward -A41-A42 : adjacent_5p upward -A42-A43 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A28-A38 : outward -Number of stackings = 28 -Number of adjacent stackings = 27 -Number of non adjacent stackings = 1 -Base-pairs ------------------------------------------------------ -A1-A17 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A16 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A15 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A14 : A-U Ww/Ww pairing antiparallel cis XX -A5-A13 : G-C Ww/Ww pairing antiparallel cis XIX -A6-A11 : C-C Ww/Bh pairing antiparallel trans 137 -A7-A9 : U-A Hh/O2P pairing -A18-A32 : C-G Ww/Ww pairing antiparallel cis XIX -A19-A31 : C-G Ww/Ww pairing antiparallel cis XIX -A19-A35 : C-A Ws/Wh pairing parallel trans one_hbond 79 -A20-A30 : C-G Ww/Ww pairing antiparallel cis XIX -A20-A35 : C-A Ws/Bs O2'/Ss pairing parallel cis one_hbond -A21-A37 : C-C Ss/Hw O2'/Bh pairing parallel cis one_hbond -A22-A36 : U-U Ww/O2P pairing -A24-A41 : U-A Ws/Wh pairing antiparallel trans one_hbond 46 -A25-A40 : U-A Ww/Ww pairing antiparallel cis XX -A26-A39 : C-G Ww/Ww pairing antiparallel cis XIX -A27-A38 : C-G Ww/Ww pairing antiparallel cis XIX -A28-A37 : G-C Ww/Ww pairing antiparallel cis XIX -A29-A36 : A-U Ww/Ww pairing antiparallel cis XX -A39-A40 : G-A O2'/Hh adjacent_5p upward pairing -Residue conformations ------------------------------------------- -A1 : G C2p_exo anti -A2 : G C4p_exo anti -A3 : G C3p_endo anti -A4 : A C2p_exo anti -A5 : G C3p_endo anti -A6 : C C3p_endo anti -A7 : U C3p_endo anti -A8 : C C1p_exo anti -A9 : A C3p_endo anti -A10 : A C2p_exo anti -A11 : C C3p_endo anti -A12 : U C3p_endo anti -A13 : C C2p_exo anti -A14 : U C3p_endo anti -A15 : C C3p_endo anti -A16 : C C3p_endo anti -A17 : C C3p_endo anti -A18 : C C3p_endo anti -A19 : C C3p_endo anti -A20 : C C3p_endo anti -A21 : C C3p_endo anti -A22 : U C2p_endo anti -A23 : U C3p_endo anti -A24 : U C3p_endo anti -A25 : U C3p_endo anti -A26 : C C3p_endo anti -A27 : C C3p_endo anti -A28 : G C3p_endo anti -A29 : A C3p_endo anti -A30 : G C3p_endo anti -A31 : G C3p_endo anti -A32 : G C3p_endo anti -A33 : U C3p_exo anti -A34 : C C3p_endo anti -A35 : A C2p_endo anti -A36 : U C3p_endo anti -A37 : C C3p_endo anti -A38 : G C3p_endo anti -A39 : G C3p_endo anti -A40 : A C3p_endo anti -A41 : A C3p_endo anti -A42 : C C3p_endo anti -A43 : C C3p_endo anti -A44 : A O4p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A28-A29 : adjacent_5p upward -A29-A30 : adjacent_5p upward -A30-A31 : adjacent_5p upward -A31-A32 : adjacent_5p upward -A36-A37 : adjacent_5p upward -A38-A39 : adjacent_5p upward -A39-A40 : adjacent_5p upward -A41-A42 : adjacent_5p upward -A42-A43 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 21 -Number of adjacent stackings = 21 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-A17 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A16 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A15 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A14 : A-U Ww/Ww pairing antiparallel cis XX -A5-A13 : G-C Ww/Ww pairing antiparallel cis XIX -A6-A10 : C-A Ws/Wh pairing antiparallel trans one_hbond 78 -A7-A9 : U-A Hh/O2P pairing -A7-A10 : U-A Ww/O2P pairing -A18-A32 : C-G Ww/Ww pairing antiparallel cis XIX -A19-A31 : C-G Ww/Ww pairing antiparallel cis XIX -A20-A30 : C-G Ww/Ww pairing antiparallel cis XIX -A20-A35 : C-A Ws/Bs pairing parallel cis one_hbond -A21-A27 : C-C Ws/Hw pairing antiparallel trans one_hbond -A21-A37 : C-C Ss/Hw O2'/Bh pairing parallel cis one_hbond -A25-A40 : U-A Ww/Ww pairing antiparallel cis XX -A26-A39 : C-G Ww/Ww pairing antiparallel cis XIX -A27-A38 : C-G Ww/Ww pairing antiparallel cis XIX -A28-A37 : G-C Ww/Ww pairing antiparallel cis XIX -A29-A36 : A-U Ww/Ww pairing antiparallel cis XX -A30-A35 : G-A Ws/Ww pairing antiparallel cis one_hbond -A43-A44 : C-A O2'/Hh adjacent_5p pairing -Residue conformations ------------------------------------------- -A1 : G C2p_exo anti -A2 : G C4p_exo anti -A3 : G C4p_exo anti -A4 : A C2p_exo anti -A5 : G C3p_endo anti -A6 : C C3p_endo anti -A7 : U C3p_endo anti -A8 : C C1p_exo anti -A9 : A C3p_endo anti -A10 : A C3p_endo anti -A11 : C C3p_endo anti -A12 : U C3p_endo anti -A13 : C C2p_exo anti -A14 : U C3p_endo anti -A15 : C C3p_endo anti -A16 : C C3p_endo anti -A17 : C C3p_endo anti -A18 : C C3p_endo anti -A19 : C C3p_endo anti -A20 : C C3p_endo anti -A21 : C C4p_exo anti -A22 : U C2p_endo anti -A23 : U C3p_endo anti -A24 : U C3p_endo anti -A25 : U C3p_endo anti -A26 : C C3p_endo anti -A27 : C C3p_endo anti -A28 : G C3p_endo anti -A29 : A C3p_endo anti -A30 : G C3p_endo anti -A31 : G C2p_exo anti -A32 : G C3p_endo anti -A33 : U C3p_exo anti -A34 : C C3p_endo anti -A35 : A C2p_endo anti -A36 : U C3p_endo anti -A37 : C C3p_endo anti -A38 : G C3p_endo anti -A39 : G C3p_endo anti -A40 : A C3p_endo anti -A41 : A C3p_endo anti -A42 : C C3p_endo anti -A43 : C C3p_endo anti -A44 : A O4p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A28-A29 : adjacent_5p upward -A29-A30 : adjacent_5p upward -A30-A31 : adjacent_5p upward -A31-A32 : adjacent_5p upward -A36-A37 : adjacent_5p upward -A38-A39 : adjacent_5p upward -A39-A40 : adjacent_5p upward -A41-A42 : adjacent_5p upward -A42-A43 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 25 -Number of adjacent stackings = 25 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-A17 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A16 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A4 : G-A O2'/Hh adjacent_5p pairing -A3-A15 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A14 : A-U Ww/Ww pairing antiparallel cis XX -A5-A13 : G-C Ww/Ww pairing antiparallel cis XIX -A6-A11 : C-C Ww/Hw pairing antiparallel trans one_hbond -A7-A9 : U-A Hh/O2P pairing -A18-A32 : C-G Ww/Ww pairing antiparallel cis XIX -A19-A31 : C-G Ww/Ww pairing antiparallel cis XIX -A19-A35 : C-A Ws/Wh pairing parallel trans one_hbond 79 -A20-A30 : C-G Ww/Ww pairing antiparallel cis XIX -A20-A35 : C-A Bs/Bs pairing parallel cis one_hbond -A21-A27 : C-C O2'/Bh pairing -A21-A37 : C-C O2'/Bh pairing -A22-A37 : U-C O2P/Bh pairing -A23-A26 : U-C O2P/Bh pairing -A25-A40 : U-A Ww/Ww pairing antiparallel cis XX -A26-A39 : C-G Ww/Ww pairing antiparallel cis XIX -A27-A38 : C-G Ww/Ww pairing antiparallel cis XIX -A28-A37 : G-C Ww/Ww pairing antiparallel cis XIX -A29-A36 : A-U Ww/Ww pairing antiparallel cis XX -A43-A44 : C-A O2'/Hh adjacent_5p pairing -Residue conformations ------------------------------------------- -A1 : G C2p_exo anti -A2 : G C4p_exo anti -A3 : G C3p_endo anti -A4 : A C3p_endo anti -A5 : G C3p_endo anti -A6 : C C3p_endo anti -A7 : U C3p_endo anti -A8 : C C3p_endo anti -A9 : A C3p_endo anti -A10 : A C3p_endo anti -A11 : C C3p_endo anti -A12 : U C3p_endo anti -A13 : C C2p_exo anti -A14 : U C3p_endo anti -A15 : C C3p_endo anti -A16 : C C3p_endo anti -A17 : C C3p_endo anti -A18 : C C3p_endo anti -A19 : C C3p_endo anti -A20 : C C3p_endo anti -A21 : C C4p_exo anti -A22 : U C2p_endo anti -A23 : U C3p_endo anti -A24 : U C3p_endo anti -A25 : U C3p_endo anti -A26 : C C4p_exo anti -A27 : C C3p_endo anti -A28 : G C3p_endo anti -A29 : A C3p_endo anti -A30 : G C3p_endo anti -A31 : G C3p_endo anti -A32 : G C3p_endo anti -A33 : U C2p_endo anti -A34 : C C3p_endo anti -A35 : A C2p_endo anti -A36 : U C3p_endo anti -A37 : C C3p_endo anti -A38 : G C3p_endo anti -A39 : G C4p_exo anti -A40 : A C2p_exo anti -A41 : A C3p_endo anti -A42 : C C3p_endo anti -A43 : C C3p_endo anti -A44 : A O4p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A28-A29 : adjacent_5p upward -A29-A30 : adjacent_5p upward -A30-A31 : adjacent_5p upward -A36-A37 : adjacent_5p upward -A38-A39 : adjacent_5p upward -A40-A41 : adjacent_5p upward -A41-A42 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A28-A38 : outward -Number of stackings = 20 -Number of adjacent stackings = 19 -Number of non adjacent stackings = 1 -Base-pairs ------------------------------------------------------ -A1-A17 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A16 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A15 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A14 : A-U Ww/Ww pairing antiparallel cis XX -A5-A13 : G-C Ww/Ww pairing antiparallel cis XIX -A6-A11 : C-C Ww/Wh pairing antiparallel cis one_hbond 131 -A18-A32 : C-G Ww/Ww pairing antiparallel cis XIX -A19-A31 : C-G Ww/Ww pairing antiparallel cis XIX -A20-A30 : C-G Ww/Ww pairing antiparallel cis XIX -A21-A37 : C-C O2'/Bh pairing -A25-A40 : U-A Ww/Ww pairing antiparallel cis XX -A26-A39 : C-G Ww/Ww pairing antiparallel cis XIX -A27-A38 : C-G Ww/Ww pairing antiparallel cis XIX -A28-A37 : G-C Ww/Ww pairing antiparallel cis XIX -A29-A36 : A-U Ww/Ww pairing antiparallel cis XX -A30-A35 : G-A Bs/Ww pairing antiparallel cis one_hbond -A31-A35 : G-A Ss/Wh pairing antiparallel trans one_hbond 63 -A35-A36 : A-U O2'/Hh adjacent_5p pairing -A39-A40 : G-A O2'/Hh adjacent_5p pairing -A43-A44 : C-A O2'/Hh adjacent_5p pairing -Residue conformations ------------------------------------------- -A1 : G C2p_exo anti -A2 : G C4p_exo anti -A3 : G C3p_endo anti -A4 : A C2p_exo anti -A5 : G C3p_endo anti -A6 : C C3p_endo anti -A7 : U C3p_endo anti -A8 : C C2p_endo anti -A9 : A C3p_endo anti -A10 : A C3p_endo anti -A11 : C C3p_endo anti -A12 : U C3p_endo anti -A13 : C C2p_exo anti -A14 : U C3p_endo anti -A15 : C C3p_endo anti -A16 : C C3p_endo anti -A17 : C C3p_endo anti -A18 : C C3p_endo anti -A19 : C C2p_exo anti -A20 : C C3p_endo anti -A21 : C C4p_exo anti -A22 : U C2p_endo anti -A23 : U C3p_endo anti -A24 : U C3p_endo anti -A25 : U C3p_endo anti -A26 : C C3p_endo anti -A27 : C C3p_endo anti -A28 : G C3p_endo anti -A29 : A C3p_endo anti -A30 : G C3p_endo anti -A31 : G C2p_exo anti -A32 : G C2p_exo anti -A33 : U C3p_exo anti -A34 : C C2p_exo anti -A35 : A C2p_endo anti -A36 : U C3p_endo anti -A37 : C C3p_endo anti -A38 : G C3p_endo anti -A39 : G C3p_endo anti -A40 : A C3p_endo anti -A41 : A C3p_endo anti -A42 : C C3p_endo anti -A43 : C C3p_endo anti -A44 : A O4p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A28-A29 : adjacent_5p upward -A29-A30 : adjacent_5p upward -A30-A31 : adjacent_5p upward -A31-A32 : adjacent_5p upward -A36-A37 : adjacent_5p upward -A38-A39 : adjacent_5p upward -A39-A40 : adjacent_5p upward -A41-A42 : adjacent_5p upward -A42-A43 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 23 -Number of adjacent stackings = 23 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-A17 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A16 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A15 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A14 : A-U Ww/Ww pairing antiparallel cis XX -A5-A13 : G-C Ww/Ww pairing antiparallel cis XIX -A6-A11 : C-C Ww/Wh pairing antiparallel cis one_hbond 131 -A18-A32 : C-G Ww/Ww pairing antiparallel cis XIX -A19-A31 : C-G Ww/Ww pairing antiparallel cis XIX -A20-A30 : C-G Ww/Ww pairing antiparallel cis XIX -A20-A35 : C-A Ws/Bs pairing parallel cis one_hbond -A21-A27 : C-C O2'/Bh pairing -A21-A37 : C-C O2'/Bh pairing -A24-A25 : U-U Hh/Hw adjacent_5p pairing parallel cis one_hbond -A25-A40 : U-A Ww/Ww pairing antiparallel cis XX -A26-A39 : C-G Ww/Ww pairing antiparallel cis XIX -A27-A38 : C-G Ww/Ww pairing antiparallel cis XIX -A28-A37 : G-C Ww/Ww pairing antiparallel cis XIX -A29-A36 : A-U Ww/Ww pairing antiparallel cis XX -A30-A35 : G-A Bs/Ww pairing antiparallel cis one_hbond -A34-A35 : C-A O2P/Hh adjacent_5p pairing -A35-A36 : A-U O2'/Hh adjacent_5p pairing -A43-A44 : C-A O2'/Hh adjacent_5p pairing -Residue conformations ------------------------------------------- -A1 : G C2p_exo anti -A2 : G C4p_exo anti -A3 : G C3p_endo anti -A4 : A C3p_endo anti -A5 : G C3p_endo anti -A6 : C C3p_endo anti -A7 : U C3p_endo anti -A8 : C C3p_endo anti -A9 : A C3p_endo anti -A10 : A C3p_endo anti -A11 : C C3p_endo anti -A12 : U C3p_endo anti -A13 : C C3p_endo anti -A14 : U C3p_endo anti -A15 : C C3p_endo anti -A16 : C C3p_endo anti -A17 : C C3p_endo anti -A18 : C C3p_endo anti -A19 : C C3p_endo anti -A20 : C C3p_endo anti -A21 : C C4p_exo anti -A22 : U C2p_endo anti -A23 : U C3p_endo anti -A24 : U C3p_endo anti -A25 : U C3p_endo anti -A26 : C C3p_endo anti -A27 : C C3p_endo anti -A28 : G C3p_endo anti -A29 : A C3p_endo anti -A30 : G C3p_endo anti -A31 : G C3p_endo anti -A32 : G C3p_endo anti -A33 : U C2p_endo anti -A34 : C C3p_endo anti -A35 : A C2p_endo anti -A36 : U C3p_endo anti -A37 : C C4p_exo anti -A38 : G C3p_endo anti -A39 : G C4p_exo anti -A40 : A C2p_exo anti -A41 : A C3p_endo anti -A42 : C C3p_endo anti -A43 : C C3p_endo anti -A44 : A O4p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A28-A29 : adjacent_5p upward -A29-A30 : adjacent_5p upward -A30-A31 : adjacent_5p upward -A31-A32 : adjacent_5p upward -A36-A37 : adjacent_5p upward -A38-A39 : adjacent_5p upward -A39-A40 : adjacent_5p upward pairing -A40-A41 : adjacent_5p upward -A41-A42 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A28-A38 : outward -Number of stackings = 23 -Number of adjacent stackings = 22 -Number of non adjacent stackings = 1 -Base-pairs ------------------------------------------------------ -A1-A17 : G-C Ww/Ww pairing antiparallel cis XIX -A1-A18 : G-C Bs/O2' pairing -A2-A16 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A15 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A14 : A-U Ww/Ww pairing antiparallel cis XX -A5-A13 : G-C Ww/Ww pairing antiparallel cis XIX -A6-A11 : C-C Ww/Bh pairing antiparallel trans 137 -A18-A32 : C-G Ww/Ww pairing antiparallel cis XIX -A19-A31 : C-G Ww/Ww pairing antiparallel cis XIX -A20-A30 : C-G Ww/Ww pairing antiparallel cis XIX -A21-A37 : C-C Ss/Hw O2'/Bh pairing parallel cis one_hbond -A25-A40 : U-A Ww/Ww pairing antiparallel cis XX -A26-A39 : C-G Ww/Ww pairing antiparallel cis XIX -A27-A38 : C-G Ww/Ww pairing antiparallel cis XIX -A28-A37 : G-C Ww/Ww pairing antiparallel cis XIX -A29-A36 : A-U Ww/Ww pairing antiparallel cis XX -A30-A35 : G-A Bs/Ww pairing parallel cis one_hbond 56 -A31-A35 : G-A Ss/Wh O2'/Bh pairing parallel trans one_hbond -A39-A40 : G-A O2'/Hh adjacent_5p upward pairing -Residue conformations ------------------------------------------- -A1 : G C2p_exo anti -A2 : G C4p_exo anti -A3 : G C3p_endo anti -A4 : A C3p_endo anti -A5 : G C3p_endo anti -A6 : C C3p_endo anti -A7 : U C3p_endo anti -A8 : C O4p_endo anti -A9 : A C3p_endo anti -A10 : A C3p_endo anti -A11 : C C3p_endo anti -A12 : U C3p_endo anti -A13 : C C2p_exo anti -A14 : U C3p_endo anti -A15 : C C3p_endo anti -A16 : C C3p_endo anti -A17 : C C3p_endo anti -A18 : C C3p_endo anti -A19 : C C3p_endo anti -A20 : C C3p_endo anti -A21 : C C3p_endo anti -A22 : U C2p_endo anti -A23 : U C3p_endo anti -A24 : U C3p_endo anti -A25 : U C3p_endo anti -A26 : C C3p_endo anti -A27 : C C3p_endo anti -A28 : G C3p_endo anti -A29 : A C3p_endo anti -A30 : G C3p_endo anti -A31 : G C2p_exo anti -A32 : G C3p_endo anti -A33 : U C2p_endo anti -A34 : C C3p_endo anti -A35 : A C2p_endo anti -A36 : U C3p_endo anti -A37 : C C3p_endo anti -A38 : G C3p_endo anti -A39 : G C3p_endo anti -A40 : A C3p_endo anti -A41 : A C3p_endo anti -A42 : C C3p_endo anti -A43 : C C3p_endo anti -A44 : A O4p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A28-A29 : adjacent_5p upward -A29-A30 : adjacent_5p upward -A30-A31 : adjacent_5p upward -A31-A32 : adjacent_5p upward -A36-A37 : adjacent_5p upward -A38-A39 : adjacent_5p upward -A39-A40 : adjacent_5p upward -A41-A42 : adjacent_5p upward -A42-A43 : adjacent_5p upward -A43-A44 : adjacent_5p inward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 25 -Number of adjacent stackings = 25 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-A17 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A16 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A15 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A14 : A-U Ww/Ww pairing antiparallel cis XX -A5-A13 : G-C Ww/Ww pairing antiparallel cis XIX -A7-A9 : U-A Hh/O2P pairing -A7-A10 : U-A Ww/O2P pairing -A18-A32 : C-G Ww/Ww pairing antiparallel cis XIX -A19-A31 : C-G Ww/Ww pairing antiparallel cis XIX -A19-A35 : C-A Ws/Wh pairing parallel trans one_hbond 79 -A20-A30 : C-G Ww/Ww pairing antiparallel cis XIX -A20-A35 : C-A Bs/Bs O2'/Ss pairing parallel cis one_hbond -A21-A37 : C-C Ss/Hw O2'/Bh pairing parallel trans one_hbond -A22-A24 : U-U Hh/O2P pairing -A24-A25 : U-U Hh/Hw adjacent_5p pairing parallel cis one_hbond -A25-A40 : U-A Ww/Ww pairing antiparallel cis XX -A26-A39 : C-G Ww/Ww pairing antiparallel cis XIX -A27-A38 : C-G Ww/Ww pairing antiparallel cis XIX -A28-A37 : G-C Ww/Ww pairing antiparallel cis XIX -A29-A36 : A-U Ww/Ww pairing antiparallel cis XX diff --git a/MCdata/1a9l_MC b/MCdata/1a9l_MC deleted file mode 100644 index 8ddd8e65f90ad600e3da499137b6f83eb3036dfe..0000000000000000000000000000000000000000 --- a/MCdata/1a9l_MC +++ /dev/null @@ -1,1086 +0,0 @@ -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : G C3p_endo anti -A4 : U C3p_endo anti -A5 : G C3p_endo anti -A6 : A C2p_endo anti -A7 : C C3p_endo anti -A8 : U C3p_endo anti -A9 : C C3p_endo anti -A10 : C C3p_endo anti -A11 : A C2p_exo anti -A12 : G C1p_exo anti -A13 : A C2p_endo anti -A14 : G C3p_endo anti -A15 : G C3p_endo anti -A16 : U C3p_endo anti -A17 : C C3p_endo anti -A18 : G C3p_endo anti -A19 : A C4p_exo anti -A20 : G C3p_endo anti -A21 : A C2p_exo anti -A22 : G C3p_endo anti -A23 : A C3p_endo anti -A24 : C C3p_endo anti -A25 : C C3p_exo anti -A26 : G C2p_exo anti -A27 : G C2p_exo anti -A28 : A C3p_endo anti -A29 : G C3p_endo anti -A30 : A C3p_endo anti -A31 : U C4p_exo anti -A32 : A C2p_endo anti -A33 : U C3p_endo anti -A34 : C C3p_endo anti -A35 : A C3p_endo anti -A36 : C C3p_endo anti -A37 : C C3p_endo anti -A38 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A19-A20 : adjacent_5p upward pairing -A20-A21 : adjacent_5p upward -A22-A23 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A24-A25 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A28-A29 : adjacent_5p upward -A29-A30 : adjacent_5p upward -A30-A31 : adjacent_5p upward -A32-A33 : adjacent_5p upward -A34-A35 : adjacent_5p upward -A35-A36 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A5-A35 : outward -A11-A26 : outward -A18-A22 : outward -Number of stackings = 26 -Number of adjacent stackings = 23 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -A1-A38 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A37 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A36 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A35 : U-A Ww/Ww pairing antiparallel cis XX -A5-A34 : G-C Ww/Ww pairing antiparallel cis XIX -A6-A33 : A-U Ww/Ww pairing antiparallel cis XX -A7-A29 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A28 : U-A Ww/Ww pairing antiparallel cis XX -A9-A27 : C-G Ww/Ww pairing antiparallel cis XIX -A10-A26 : C-G Ww/Ww pairing antiparallel cis XIX -A11-A12 : A-G O2'/C8 adjacent_5p pairing -A13-A14 : A-G O2'/Hh adjacent_5p pairing -A13-A26 : A-G Ww/O2' pairing -A14-A25 : G-C Ww/Ww pairing antiparallel cis XIX -A14-A26 : G-G Bs/O2' pairing -A15-A24 : G-C Ww/Ww pairing antiparallel cis XIX -A16-A23 : U-A Ww/Ww pairing antiparallel cis XX -A17-A22 : C-G Ww/Ww pairing antiparallel cis XIX -A18-A20 : G-G O2'/Hh pairing -A19-A20 : A-G O2P/Hh adjacent_5p upward pairing -A31-A32 : U-A O2'/C8 adjacent_5p pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : G C3p_endo anti -A4 : U C3p_endo anti -A5 : G C3p_endo anti -A6 : A C2p_endo anti -A7 : C C3p_endo anti -A8 : U C3p_endo anti -A9 : C C3p_endo anti -A10 : C C3p_endo anti -A11 : A C3p_endo anti -A12 : G C1p_exo syn -A13 : A C2p_endo anti -A14 : G C2p_exo anti -A15 : G C3p_endo anti -A16 : U C3p_endo anti -A17 : C C3p_endo anti -A18 : G C3p_endo anti -A19 : A C4p_exo anti -A20 : G C3p_endo anti -A21 : A C2p_exo anti -A22 : G C3p_endo anti -A23 : A C3p_endo anti -A24 : C C3p_endo anti -A25 : C C3p_exo anti -A26 : G C2p_exo anti -A27 : G C3p_endo anti -A28 : A C3p_endo anti -A29 : G C3p_endo anti -A30 : A C3p_endo anti -A31 : U C3p_exo anti -A32 : A C4p_exo anti -A33 : U C3p_endo anti -A34 : C C3p_endo anti -A35 : A C3p_endo anti -A36 : C C3p_endo anti -A37 : C C3p_endo anti -A38 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A19-A20 : adjacent_5p upward pairing -A20-A21 : adjacent_5p upward -A22-A23 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A24-A25 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A28-A29 : adjacent_5p upward -A29-A30 : adjacent_5p upward -A32-A33 : adjacent_5p upward -A33-A34 : adjacent_5p upward -A34-A35 : adjacent_5p upward -A35-A36 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A5-A35 : outward -A10-A27 : outward -A18-A22 : outward -Number of stackings = 25 -Number of adjacent stackings = 22 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -A1-A38 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A37 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A36 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A35 : U-A Ww/Ww pairing antiparallel cis XX -A5-A34 : G-C Ww/Ww pairing antiparallel cis XIX -A6-A33 : A-U Ww/Ww pairing antiparallel cis XX -A7-A29 : C-G Ww/Ww pairing antiparallel cis XIX -A7-A32 : C-A Ss/Wh O2'/Ww pairing parallel trans one_hbond 76 -A8-A28 : U-A Ww/Ww pairing antiparallel cis XX -A9-A27 : C-G Ww/Ww pairing antiparallel cis XIX -A10-A26 : C-G Ww/Ww pairing antiparallel cis XIX -A12-A13 : G-A O2'/Ss adjacent_5p pairing -A13-A14 : A-G O2'/Hh adjacent_5p pairing -A13-A26 : A-G Ww/O2' pairing -A14-A25 : G-C Ww/Ww pairing antiparallel cis XIX -A14-A26 : G-G Bs/O2' pairing -A15-A24 : G-C Ww/Ww pairing antiparallel cis XIX -A16-A23 : U-A Ww/Ww pairing antiparallel cis XX -A17-A22 : C-G Ww/Ww pairing antiparallel cis XIX -A18-A20 : G-G O2'/Hh pairing -A19-A20 : A-G O2P/Hh adjacent_5p upward pairing -A30-A31 : A-U O2'/Hh adjacent_5p pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : G C3p_endo anti -A4 : U C3p_endo anti -A5 : G C3p_endo anti -A6 : A C2p_endo anti -A7 : C C3p_endo anti -A8 : U C3p_endo anti -A9 : C C3p_endo anti -A10 : C C3p_endo anti -A11 : A C2p_exo anti -A12 : G C1p_exo anti -A13 : A C2p_endo anti -A14 : G C3p_endo anti -A15 : G C3p_endo anti -A16 : U C3p_endo anti -A17 : C C3p_endo anti -A18 : G C4p_exo anti -A19 : A C3p_exo anti -A20 : G C3p_endo anti -A21 : A C3p_endo anti -A22 : G C3p_endo anti -A23 : A C3p_endo anti -A24 : C C3p_endo anti -A25 : C C3p_endo anti -A26 : G C4p_endo anti -A27 : G C3p_endo anti -A28 : A C3p_endo anti -A29 : G C3p_endo anti -A30 : A C3p_endo anti -A31 : U C3p_endo anti -A32 : A C2p_endo syn -A33 : U C3p_endo anti -A34 : C C3p_endo anti -A35 : A C3p_endo anti -A36 : C C3p_endo anti -A37 : C C3p_endo anti -A38 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A13-A14 : adjacent_5p upward pairing -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A20-A21 : adjacent_5p outward -A22-A23 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A24-A25 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A28-A29 : adjacent_5p upward -A29-A30 : adjacent_5p upward -A32-A33 : adjacent_5p upward -A35-A36 : adjacent_5p upward -A37-A38 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A5-A35 : outward -A9-A28 : outward -A11-A26 : outward -A18-A22 : outward -Number of stackings = 24 -Number of adjacent stackings = 20 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A1-A38 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A37 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A36 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A35 : U-A Ww/Ww pairing antiparallel cis XX -A5-A34 : G-C Ww/Ww pairing antiparallel cis XIX -A6-A33 : A-U Ww/Ww pairing antiparallel cis XX -A7-A29 : C-G Ww/Ww pairing antiparallel cis XIX -A7-A32 : C-A O2'/Ww pairing -A8-A28 : U-A Ww/Ww pairing antiparallel cis XX -A9-A27 : C-G Ww/Ww pairing antiparallel cis XIX -A10-A26 : C-G Ww/Ww pairing antiparallel cis XIX -A12-A13 : G-A O2'/Ss adjacent_5p pairing -A12-A14 : G-G Ww/O2' pairing -A13-A14 : A-G O2'/Hh adjacent_5p upward pairing -A13-A26 : A-G Wh/Ss Ww/O2' pairing parallel cis one_hbond -A14-A25 : G-C Ww/Ww pairing antiparallel cis XIX -A14-A26 : G-G Ws/O2' pairing -A14-A27 : G-G Ws/O2P pairing -A15-A24 : G-C Ww/Ww pairing antiparallel cis XIX -A16-A23 : U-A Ww/Ww pairing antiparallel cis XX -A17-A22 : C-G Ww/Ww pairing antiparallel cis XIX -A18-A20 : G-G O2'/Hh pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : G C3p_endo anti -A4 : U C3p_endo anti -A5 : G C3p_endo anti -A6 : A C2p_endo anti -A7 : C C3p_endo anti -A8 : U C3p_endo anti -A9 : C C3p_endo anti -A10 : C C3p_endo anti -A11 : A C2p_exo anti -A12 : G C1p_exo anti -A13 : A C2p_endo anti -A14 : G C3p_endo anti -A15 : G C3p_endo anti -A16 : U C3p_endo anti -A17 : C C3p_endo anti -A18 : G C3p_exo anti -A19 : A C4p_exo anti -A20 : G C4p_exo anti -A21 : A C3p_endo anti -A22 : G C3p_endo anti -A23 : A C3p_endo anti -A24 : C C3p_endo anti -A25 : C C3p_exo anti -A26 : G C2p_exo anti -A27 : G C2p_exo anti -A28 : A C3p_endo anti -A29 : G C3p_endo anti -A30 : A C3p_endo anti -A31 : U C3p_endo anti -A32 : A C4p_exo anti -A33 : U C3p_endo anti -A34 : C C3p_endo anti -A35 : A C3p_endo anti -A36 : C C3p_endo anti -A37 : C C3p_endo anti -A38 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A22-A23 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A24-A25 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A28-A29 : adjacent_5p upward -A29-A30 : adjacent_5p upward -A32-A33 : adjacent_5p upward -A34-A35 : adjacent_5p upward -A35-A36 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A5-A35 : outward -A8-A29 : outward -A9-A28 : outward -A11-A26 : outward -A18-A22 : outward -Number of stackings = 24 -Number of adjacent stackings = 19 -Number of non adjacent stackings = 5 -Base-pairs ------------------------------------------------------ -A1-A38 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A37 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A36 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A35 : U-A Ww/Ww pairing antiparallel cis XX -A5-A34 : G-C Ww/Ww pairing antiparallel cis XIX -A6-A33 : A-U Ww/Ww pairing antiparallel cis XX -A7-A29 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A28 : U-A Ww/Ww pairing antiparallel cis XX -A9-A27 : C-G Ww/Ww pairing antiparallel cis XIX -A10-A26 : C-G Ww/Ww pairing antiparallel cis XIX -A13-A14 : A-G O2'/Hh adjacent_5p pairing -A13-A26 : A-G Wh/Ss Ww/O2' pairing parallel trans one_hbond -A14-A25 : G-C Ww/Ww pairing antiparallel cis XIX -A14-A26 : G-G Bs/O2' pairing -A15-A24 : G-C Ww/Ww pairing antiparallel cis XIX -A16-A23 : U-A Ww/Ww pairing antiparallel cis XX -A17-A22 : C-G Ww/Ww pairing antiparallel cis XIX -A18-A21 : G-A O2'/Bh pairing -A20-A21 : G-A O2'/C8 adjacent_5p pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : G C3p_endo anti -A4 : U C3p_endo anti -A5 : G C3p_endo anti -A6 : A C2p_endo anti -A7 : C C3p_endo anti -A8 : U C3p_endo anti -A9 : C C3p_endo anti -A10 : C C3p_endo anti -A11 : A C3p_endo anti -A12 : G C1p_exo anti -A13 : A C3p_exo anti -A14 : G C3p_endo anti -A15 : G C3p_endo anti -A16 : U C3p_endo anti -A17 : C C3p_endo anti -A18 : G C4p_exo anti -A19 : A C3p_endo anti -A20 : G C2p_exo anti -A21 : A C3p_endo anti -A22 : G C3p_endo anti -A23 : A C3p_endo anti -A24 : C C3p_endo anti -A25 : C C3p_exo anti -A26 : G C2p_exo anti -A27 : G C2p_exo anti -A28 : A C3p_endo anti -A29 : G C3p_endo anti -A30 : A C3p_endo anti -A31 : U C3p_endo anti -A32 : A C4p_exo anti -A33 : U C3p_endo anti -A34 : C C3p_endo anti -A35 : A C3p_endo anti -A36 : C C3p_endo anti -A37 : C C3p_endo anti -A38 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A20-A21 : adjacent_5p outward -A22-A23 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A24-A25 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A28-A29 : adjacent_5p upward -A29-A30 : adjacent_5p upward -A32-A33 : adjacent_5p upward -A34-A35 : adjacent_5p upward -A35-A36 : adjacent_5p upward -A36-A37 : adjacent_5p upward -A37-A38 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A5-A35 : outward -A11-A26 : outward -A18-A20 : upward pairing -A18-A22 : outward -Number of stackings = 28 -Number of adjacent stackings = 24 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A1-A38 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A37 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A36 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A35 : U-A Ww/Ww pairing antiparallel cis XX -A5-A34 : G-C Ww/Ww pairing antiparallel cis XIX -A6-A33 : A-U Ww/Ww pairing antiparallel cis XX -A7-A29 : C-G Ww/Ww pairing antiparallel cis XIX -A7-A32 : C-A O2'/Ww pairing -A8-A28 : U-A Ww/Ww pairing antiparallel cis XX -A9-A27 : C-G Ww/Ww pairing antiparallel cis XIX -A10-A26 : C-G Ww/Ww pairing antiparallel cis XIX -A13-A14 : A-G O2'/Hh adjacent_5p pairing -A13-A26 : A-G Ww/O2' pairing -A14-A25 : G-C Ww/Ww pairing antiparallel cis XIX -A14-A26 : G-G Bs/O2' pairing -A15-A24 : G-C Ww/Ww pairing antiparallel cis XIX -A16-A23 : U-A Ww/Ww pairing antiparallel cis XX -A17-A22 : C-G Ww/Ww pairing antiparallel cis XIX -A18-A20 : G-G O2'/Hh upward pairing -A19-A20 : A-G O2P/Hh adjacent_5p pairing -A31-A32 : U-A O2'/C8 adjacent_5p pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : G C3p_endo anti -A4 : U C3p_endo anti -A5 : G C3p_endo anti -A6 : A C2p_endo anti -A7 : C C3p_endo anti -A8 : U C3p_endo anti -A9 : C C3p_endo anti -A10 : C C3p_endo anti -A11 : A C3p_endo anti -A12 : G C1p_exo anti -A13 : A C3p_exo anti -A14 : G C3p_endo anti -A15 : G C3p_endo anti -A16 : U C3p_endo anti -A17 : C C3p_endo anti -A18 : G C3p_endo anti -A19 : A C3p_endo anti -A20 : G C3p_endo anti -A21 : A C2p_exo anti -A22 : G C3p_endo anti -A23 : A C3p_endo anti -A24 : C C3p_endo anti -A25 : C C3p_exo anti -A26 : G C3p_endo anti -A27 : G C3p_endo anti -A28 : A C3p_endo anti -A29 : G C3p_endo anti -A30 : A C3p_endo anti -A31 : U C2p_endo anti -A32 : A C3p_exo anti -A33 : U C3p_endo anti -A34 : C C3p_endo anti -A35 : A C3p_endo anti -A36 : C C3p_endo anti -A37 : C C3p_endo anti -A38 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A22-A23 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A28-A29 : adjacent_5p upward -A29-A30 : adjacent_5p upward -A32-A33 : adjacent_5p upward -A34-A35 : adjacent_5p upward -A35-A36 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A5-A35 : outward -A8-A29 : outward -A9-A28 : outward -A18-A22 : outward -Number of stackings = 25 -Number of adjacent stackings = 21 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A1-A38 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A37 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A36 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A35 : U-A Ww/Ww pairing antiparallel cis XX -A5-A34 : G-C Ww/Ww pairing antiparallel cis XIX -A6-A33 : A-U Ww/Ww pairing antiparallel cis XX -A7-A29 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A28 : U-A Ww/Ww pairing antiparallel cis XX -A9-A27 : C-G Ww/Ww pairing antiparallel cis XIX -A10-A26 : C-G Ww/Ww pairing antiparallel cis XIX -A13-A14 : A-G O2'/Hh adjacent_5p pairing -A14-A25 : G-C Ww/Ww pairing antiparallel cis XIX -A14-A26 : G-G Bs/O2' pairing -A15-A24 : G-C Ww/Ww pairing antiparallel cis XIX -A16-A23 : U-A Ww/Ww pairing antiparallel cis XX -A17-A22 : C-G Ww/Ww pairing antiparallel cis XIX -A18-A20 : G-G O2'/Hh pairing -A30-A31 : A-U O2'/Hh adjacent_5p pairing -A31-A32 : U-A O2'/C8 adjacent_5p pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : G C3p_endo anti -A4 : U C3p_endo anti -A5 : G C3p_endo anti -A6 : A C2p_endo anti -A7 : C C3p_endo anti -A8 : U C3p_endo anti -A9 : C C3p_endo anti -A10 : C C3p_endo anti -A11 : A C2p_exo anti -A12 : G C3p_exo syn -A13 : A C2p_endo anti -A14 : G C2p_exo anti -A15 : G C3p_endo anti -A16 : U C3p_endo anti -A17 : C C3p_endo anti -A18 : G C3p_endo anti -A19 : A C3p_endo anti -A20 : G C3p_endo anti -A21 : A C2p_exo anti -A22 : G C3p_endo anti -A23 : A C3p_endo anti -A24 : C C3p_endo anti -A25 : C C3p_exo anti -A26 : G C2p_exo anti -A27 : G C2p_exo anti -A28 : A C3p_endo anti -A29 : G C3p_endo anti -A30 : A C3p_endo anti -A31 : U C2p_endo anti -A32 : A C3p_exo anti -A33 : U C3p_endo anti -A34 : C C3p_endo anti -A35 : A C3p_endo anti -A36 : C C3p_endo anti -A37 : C C3p_endo anti -A38 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A22-A23 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A28-A29 : adjacent_5p upward -A29-A30 : adjacent_5p upward -A32-A33 : adjacent_5p upward -A33-A34 : adjacent_5p upward -A34-A35 : adjacent_5p upward -A35-A36 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A5-A35 : outward -A8-A29 : outward -A18-A22 : outward -Number of stackings = 26 -Number of adjacent stackings = 23 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -A1-A38 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A37 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A36 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A35 : U-A Ww/Ww pairing antiparallel cis XX -A5-A34 : G-C Ww/Ww pairing antiparallel cis XIX -A6-A33 : A-U Ww/Ww pairing antiparallel cis XX -A7-A29 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A28 : U-A Ww/Ww pairing antiparallel cis XX -A9-A27 : C-G Ww/Ww pairing antiparallel cis XIX -A10-A26 : C-G Ww/Ww pairing antiparallel cis XIX -A12-A13 : G-A O2'/Ss adjacent_5p pairing -A13-A14 : A-G O2'/Hh adjacent_5p pairing -A14-A25 : G-C Ww/Ww pairing antiparallel cis XIX -A14-A26 : G-G Bs/O2' pairing -A15-A24 : G-C Ww/Ww pairing antiparallel cis XIX -A16-A23 : U-A Ww/Ww pairing antiparallel cis XX -A17-A22 : C-G Ww/Ww pairing antiparallel cis XIX -A18-A20 : G-G O2'/Hh pairing -A30-A31 : A-U O2'/Hh adjacent_5p pairing -A31-A32 : U-A O2'/C8 adjacent_5p pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : G C3p_endo anti -A4 : U C3p_endo anti -A5 : G C3p_endo anti -A6 : A C2p_endo anti -A7 : C C3p_endo anti -A8 : U C3p_endo anti -A9 : C C3p_endo anti -A10 : C C3p_endo anti -A11 : A C3p_endo anti -A12 : G C1p_exo anti -A13 : A C3p_exo anti -A14 : G C3p_endo anti -A15 : G C3p_endo anti -A16 : U C3p_endo anti -A17 : C C3p_endo anti -A18 : G C4p_exo anti -A19 : A C3p_endo anti -A20 : G C2p_exo anti -A21 : A C3p_endo anti -A22 : G C3p_endo anti -A23 : A C3p_endo anti -A24 : C C3p_endo anti -A25 : C C3p_exo anti -A26 : G C2p_exo anti -A27 : G C3p_endo anti -A28 : A C3p_endo anti -A29 : G C3p_endo anti -A30 : A C3p_endo anti -A31 : U C3p_endo anti -A32 : A C4p_exo anti -A33 : U C3p_endo anti -A34 : C C3p_endo anti -A35 : A C3p_endo anti -A36 : C C3p_endo anti -A37 : C C3p_endo anti -A38 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A22-A23 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A24-A25 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A28-A29 : adjacent_5p upward -A29-A30 : adjacent_5p upward -A32-A33 : adjacent_5p upward -A33-A34 : adjacent_5p upward -A35-A36 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A5-A35 : outward -A9-A28 : outward -A11-A26 : outward -A18-A20 : upward pairing -A18-A22 : outward -Number of stackings = 24 -Number of adjacent stackings = 19 -Number of non adjacent stackings = 5 -Base-pairs ------------------------------------------------------ -A1-A38 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A37 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A36 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A35 : U-A Ww/Ww pairing antiparallel cis XX -A5-A34 : G-C Ww/Ww pairing antiparallel cis XIX -A6-A33 : A-U Ww/Ww pairing antiparallel cis XX -A7-A29 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A28 : U-A Ww/Ww pairing antiparallel cis XX -A9-A27 : C-G Ww/Ww pairing antiparallel cis XIX -A10-A26 : C-G Ww/Ww pairing antiparallel cis XIX -A12-A14 : G-G Hh/O2' pairing -A13-A14 : A-G O2'/Hh adjacent_5p pairing -A14-A25 : G-C Ww/Ww pairing antiparallel cis XIX -A14-A26 : G-G Bs/O2' pairing -A15-A24 : G-C Ww/Ww pairing antiparallel cis XIX -A16-A23 : U-A Ww/Ww pairing antiparallel cis XX -A17-A22 : C-G Ww/Ww pairing antiparallel cis XIX -A18-A20 : G-G O2'/Hh upward pairing -A19-A20 : A-G O2P/Hh adjacent_5p pairing -A31-A32 : U-A O2'/C8 adjacent_5p pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : G C3p_endo anti -A4 : U C3p_endo anti -A5 : G C3p_endo anti -A6 : A C2p_endo anti -A7 : C C3p_endo anti -A8 : U C3p_endo anti -A9 : C C3p_endo anti -A10 : C C3p_endo anti -A11 : A C2p_exo anti -A12 : G C1p_exo syn -A13 : A C3p_exo anti -A14 : G C3p_endo anti -A15 : G C3p_endo anti -A16 : U C3p_endo anti -A17 : C C3p_endo anti -A18 : G C4p_exo anti -A19 : A C4p_exo anti -A20 : G C3p_endo anti -A21 : A C3p_endo anti -A22 : G C3p_endo anti -A23 : A C3p_endo anti -A24 : C C3p_endo anti -A25 : C C3p_exo anti -A26 : G C3p_endo anti -A27 : G C3p_endo anti -A28 : A C3p_endo anti -A29 : G C3p_endo anti -A30 : A C3p_endo anti -A31 : U C3p_endo anti -A32 : A C3p_exo syn -A33 : U C3p_endo anti -A34 : C C3p_endo anti -A35 : A C3p_endo anti -A36 : C C3p_endo anti -A37 : C C3p_endo anti -A38 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A19-A20 : adjacent_5p upward pairing -A20-A21 : adjacent_5p upward -A22-A23 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A24-A25 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A28-A29 : adjacent_5p upward -A29-A30 : adjacent_5p upward -A32-A33 : adjacent_5p upward -A34-A35 : adjacent_5p upward -A35-A36 : adjacent_5p upward -A36-A37 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A5-A35 : outward -A9-A28 : outward -A11-A26 : outward -A18-A22 : outward -Number of stackings = 25 -Number of adjacent stackings = 21 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A1-A38 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A37 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A36 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A35 : U-A Ww/Ww pairing antiparallel cis XX -A5-A34 : G-C Ww/Ww pairing antiparallel cis XIX -A6-A33 : A-U Ww/Ww pairing antiparallel cis XX -A7-A29 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A28 : U-A Ww/Ww pairing antiparallel cis XX -A9-A27 : C-G Ww/Ww pairing antiparallel cis XIX -A10-A26 : C-G Ww/Ww pairing antiparallel cis XIX -A12-A14 : G-G Hh/O2' pairing -A13-A14 : A-G O2'/Hh adjacent_5p pairing -A13-A26 : A-G Wh/Ss pairing parallel trans one_hbond -A14-A25 : G-C Ww/Ww pairing antiparallel cis XIX -A15-A24 : G-C Ww/Ww pairing antiparallel cis XIX -A16-A23 : U-A Ww/Ww pairing antiparallel cis XX -A17-A22 : C-G Ww/Ww pairing antiparallel cis XIX -A18-A20 : G-G O2'/Hh pairing -A19-A20 : A-G O2P/Hh adjacent_5p upward pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : G C3p_endo anti -A4 : U C3p_endo anti -A5 : G C3p_endo anti -A6 : A C2p_endo anti -A7 : C C3p_endo anti -A8 : U C3p_endo anti -A9 : C C3p_endo anti -A10 : C C3p_endo anti -A11 : A C2p_exo anti -A12 : G C1p_exo anti -A13 : A C2p_endo anti -A14 : G C3p_endo anti -A15 : G C3p_endo anti -A16 : U C3p_endo anti -A17 : C C3p_endo anti -A18 : G C3p_endo anti -A19 : A C3p_endo anti -A20 : G C3p_endo anti -A21 : A C3p_endo anti -A22 : G C3p_endo anti -A23 : A C3p_endo anti -A24 : C C3p_endo anti -A25 : C C3p_exo anti -A26 : G C2p_exo anti -A27 : G C2p_exo anti -A28 : A C3p_endo anti -A29 : G C3p_endo anti -A30 : A C3p_endo anti -A31 : U C4p_exo anti -A32 : A C4p_exo anti -A33 : U C3p_endo anti -A34 : C C3p_endo anti -A35 : A C3p_endo anti -A36 : C C3p_endo anti -A37 : C C3p_endo anti -A38 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A22-A23 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A24-A25 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A28-A29 : adjacent_5p upward -A29-A30 : adjacent_5p upward -A31-A32 : adjacent_5p upward -A32-A33 : adjacent_5p upward -A33-A34 : adjacent_5p upward -A35-A36 : adjacent_5p upward -A36-A37 : adjacent_5p upward -A37-A38 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A5-A35 : outward -A11-A26 : outward -A18-A22 : outward -Number of stackings = 28 -Number of adjacent stackings = 25 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -A1-A38 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A37 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A36 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A35 : U-A Ww/Ww pairing antiparallel cis XX -A5-A34 : G-C Ww/Ww pairing antiparallel cis XIX -A6-A33 : A-U Ww/Ww pairing antiparallel cis XX -A7-A29 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A28 : U-A Ww/Ww pairing antiparallel cis XX -A9-A27 : C-G Ww/Ww pairing antiparallel cis XIX -A10-A26 : C-G Ww/Ww pairing antiparallel cis XIX -A12-A27 : G-G Hh/O2' pairing -A13-A14 : A-G O2'/Hh adjacent_5p pairing -A13-A26 : A-G Ww/O2' pairing -A14-A25 : G-C Ww/Ww pairing antiparallel cis XIX -A14-A26 : G-G Bs/O2' pairing -A15-A24 : G-C Ww/Ww pairing antiparallel cis XIX -A16-A23 : U-A Ww/Ww pairing antiparallel cis XX -A17-A22 : C-G Ww/Ww pairing antiparallel cis XIX -A18-A20 : G-G O2'/Hh pairing -A30-A32 : A-A O2'/Hh pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : G C3p_endo anti -A4 : U C3p_endo anti -A5 : G C3p_endo anti -A6 : A C2p_endo anti -A7 : C C3p_endo anti -A8 : U C3p_endo anti -A9 : C C3p_endo anti -A10 : C C3p_endo anti -A11 : A C2p_exo anti -A12 : G C1p_exo anti -A13 : A C2p_endo anti -A14 : G C3p_endo anti -A15 : G C3p_endo anti -A16 : U C3p_endo anti -A17 : C C3p_endo anti -A18 : G C3p_endo anti -A19 : A C3p_endo anti -A20 : G C3p_endo anti -A21 : A C2p_exo anti -A22 : G C3p_endo anti -A23 : A C3p_endo anti -A24 : C C3p_endo anti -A25 : C C3p_exo anti -A26 : G C2p_exo anti -A27 : G C2p_exo anti -A28 : A C3p_endo anti -A29 : G C3p_endo anti -A30 : A C3p_endo anti -A31 : U C3p_endo anti -A32 : A C3p_exo syn -A33 : U C3p_endo anti -A34 : C C3p_endo anti -A35 : A C3p_endo anti -A36 : C C3p_endo anti -A37 : C C3p_endo anti -A38 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A22-A23 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A24-A25 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A28-A29 : adjacent_5p upward -A29-A30 : adjacent_5p upward -A32-A33 : adjacent_5p upward -A33-A34 : adjacent_5p upward -A34-A35 : adjacent_5p upward -A35-A36 : adjacent_5p upward -A37-A38 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A5-A35 : outward -A7-A30 : outward -A9-A28 : outward -A11-A26 : outward -A18-A22 : outward -Number of stackings = 27 -Number of adjacent stackings = 22 -Number of non adjacent stackings = 5 -Base-pairs ------------------------------------------------------ -A1-A38 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A37 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A36 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A35 : U-A Ww/Ww pairing antiparallel cis XX -A5-A34 : G-C Ww/Ww pairing antiparallel cis XIX -A6-A33 : A-U Ww/Ww pairing antiparallel cis XX -A7-A29 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A28 : U-A Ww/Ww pairing antiparallel cis XX -A9-A27 : C-G Ww/Ww pairing antiparallel cis XIX -A10-A26 : C-G Ww/Ww pairing antiparallel cis XIX -A13-A14 : A-G O2'/Hh adjacent_5p pairing -A13-A26 : A-G Ww/O2' pairing -A14-A25 : G-C Ww/Ww pairing antiparallel cis XIX -A14-A26 : G-G Bs/O2' pairing -A15-A24 : G-C Ww/Ww pairing antiparallel cis XIX -A16-A23 : U-A Ww/Ww pairing antiparallel cis XX -A17-A22 : C-G Ww/Ww pairing antiparallel cis XIX -A18-A20 : G-G O2'/Hh pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : G C3p_endo anti -A4 : U C3p_endo anti -A5 : G C3p_endo anti -A6 : A C2p_endo anti -A7 : C C3p_endo anti -A8 : U C3p_endo anti -A9 : C C3p_endo anti -A10 : C C3p_endo anti -A11 : A C3p_endo anti -A12 : G C1p_exo syn -A13 : A C2p_endo anti -A14 : G C2p_exo anti -A15 : G C3p_endo anti -A16 : U C3p_endo anti -A17 : C C3p_endo anti -A18 : G C3p_endo anti -A19 : A C3p_endo anti -A20 : G C3p_endo anti -A21 : A C3p_endo anti -A22 : G C3p_endo anti -A23 : A C3p_endo anti -A24 : C C3p_endo anti -A25 : C C3p_exo anti -A26 : G C2p_exo anti -A27 : G C3p_endo anti -A28 : A C3p_endo anti -A29 : G C3p_endo anti -A30 : A C3p_endo anti -A31 : U C4p_exo anti -A32 : A C4p_exo anti -A33 : U C3p_endo anti -A34 : C C3p_endo anti -A35 : A C3p_endo anti -A36 : C C3p_endo anti -A37 : C C3p_endo anti -A38 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A22-A23 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A28-A29 : adjacent_5p upward -A29-A30 : adjacent_5p upward -A31-A32 : adjacent_5p upward -A32-A33 : adjacent_5p upward -A33-A34 : adjacent_5p upward -A35-A36 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A5-A35 : outward -A7-A30 : outward -A18-A22 : outward -Number of stackings = 24 -Number of adjacent stackings = 21 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -A1-A38 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A37 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A36 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A35 : U-A Ww/Ww pairing antiparallel cis XX -A5-A34 : G-C Ww/Ww pairing antiparallel cis XIX -A6-A33 : A-U Ww/Ww pairing antiparallel cis XX -A7-A29 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A28 : U-A Ww/Ww pairing antiparallel cis XX -A9-A27 : C-G Ww/Ww pairing antiparallel cis XIX -A10-A26 : C-G Ww/Ww pairing antiparallel cis XIX -A12-A13 : G-A O2'/Ss adjacent_5p pairing -A13-A14 : A-G O2'/Hh adjacent_5p pairing -A13-A26 : A-G Ww/O2' pairing -A14-A25 : G-C Ww/Ww pairing antiparallel cis XIX -A14-A26 : G-G Bs/O2' pairing -A15-A24 : G-C Ww/Ww pairing antiparallel cis XIX -A16-A23 : U-A Ww/Ww pairing antiparallel cis XX -A17-A22 : C-G Ww/Ww pairing antiparallel cis XIX -A18-A20 : G-G O2'/Hh pairing diff --git a/MCdata/1a9n_MC b/MCdata/1a9n_MC deleted file mode 100644 index fb219792900a1ac3c9a47590547b012d61899d81..0000000000000000000000000000000000000000 --- a/MCdata/1a9n_MC +++ /dev/null @@ -1,621 +0,0 @@ -Residue conformations ------------------------------------------- -Q0 : C C3p_endo anti -Q1 : C C3p_endo anti -Q2 : U C1p_endo anti -Q3 : G C2p_exo anti -Q4 : G C3p_endo anti -Q5 : U C3p_endo anti -Q6 : A C3p_endo anti -Q7 : U C3p_endo anti -Q8 : U C2p_endo anti -Q9 : G C3p_endo anti -Q10 : C C3p_exo anti -Q11 : A C3p_endo anti -Q12 : G C2p_endo syn -Q13 : U C2p_endo anti -Q14 : A C1p_endo anti -Q15 : C C3p_endo anti -Q16 : C C1p_exo anti -Q17 : U C3p_endo anti -Q18 : C C3p_endo anti -Q19 : C C3p_endo anti -Q20 : A C3p_endo anti -Q21 : G C3p_endo anti -Q22 : G C3p_endo anti -Q23 : U C2p_exo anti -R0 : C C3p_endo anti -R1 : C C3p_endo anti -R2 : U C1p_endo anti -R3 : G C2p_exo anti -R4 : G C3p_endo anti -R5 : U C3p_endo anti -R6 : A C3p_endo anti -R7 : U C3p_endo anti -R8 : U C2p_endo anti -R9 : G C3p_endo anti -R10 : C C3p_exo anti -R11 : A C3p_endo anti -R12 : G C1p_exo syn -R13 : U C2p_endo anti -R14 : A C1p_endo anti -R15 : C C3p_endo anti -R16 : C C2p_endo anti -R17 : U C3p_endo anti -R18 : C C3p_endo anti -R19 : C C3p_endo anti -R20 : A C3p_endo anti -R21 : G C3p_endo anti -R22 : G C3p_endo anti -R23 : U C1p_endo anti -A2 : VAL -A3 : LYS -A4 : LEU -A5 : THR -A6 : ALA -A7 : GLU -A8 : LEU -A9 : ILE -A10 : GLU -A11 : GLN -A12 : ALA -A13 : ALA -A14 : GLN -A15 : TYR -A16 : THR -A17 : ASN -A18 : ALA -A19 : VAL -A20 : ARG -A21 : ASP -A22 : ARG -A23 : GLU -A24 : LEU -A25 : ASP -A26 : LEU -A27 : ARG -A28 : GLY -A29 : TYR -A30 : LYS -A31 : ILE -A32 : PRO -A33 : VAL -A34 : ILE -A35 : GLU -A36 : ASN -A37 : LEU -A38 : GLY -A39 : ALA -A40 : THR -A41 : LEU -A42 : ASP -A43 : GLN -A44 : PHE -A45 : ASP -A46 : ALA -A47 : ILE -A48 : ASP -A49 : PHE -A50 : SER -A51 : ASP -A52 : ASN -A53 : GLU -A54 : ILE -A55 : ARG -A56 : LYS -A57 : LEU -A58 : ASP -A59 : GLY -A60 : PHE -A61 : PRO -A62 : LEU -A63 : LEU -A64 : ARG -A65 : ARG -A66 : LEU -A67 : LYS -A68 : THR -A69 : LEU -A70 : LEU -A71 : VAL -A72 : ASN -A73 : ASN -A74 : ASN -A75 : ARG -A76 : ILE -A77 : CYS -A78 : ARG -A79 : ILE -A80 : GLY -A81 : GLU -A82 : GLY -A83 : LEU -A84 : ASP -A85 : GLN -A86 : ALA -A87 : LEU -A88 : PRO -A89 : ASP -A90 : LEU -A91 : THR -A92 : GLU -A93 : LEU -A94 : ILE -A95 : LEU -A96 : THR -A97 : ASN -A98 : ASN -A99 : SER -A100 : LEU -A101 : VAL -A102 : GLU -A103 : LEU -A104 : GLY -A105 : ASP -A106 : LEU -A107 : ASP -A108 : PRO -A109 : LEU -A110 : ALA -A111 : SER -A112 : LEU -A113 : LYS -A114 : SER -A115 : LEU -A116 : THR -A117 : TYR -A118 : LEU -A119 : CYS -A120 : ILE -A121 : LEU -A122 : ARG -A123 : ASN -A124 : PRO -A125 : VAL -A126 : THR -A127 : ASN -A128 : LYS -A129 : LYS -A130 : HIS -A131 : TYR -A132 : ARG -A133 : LEU -A134 : TYR -A135 : VAL -A136 : ILE -A137 : TYR -A138 : LYS -A139 : VAL -A140 : PRO -A141 : GLN -A142 : VAL -A143 : ARG -A144 : VAL -A145 : LEU -A146 : ASP -A147 : PHE -A148 : GLN -A149 : LYS -A150 : VAL -A151 : LYS -A152 : LEU -A153 : LYS -A154 : GLU -A155 : ARG -A156 : GLN -A157 : GLU -A158 : ALA -A159 : GLU -A160 : LYS -A161 : MET -A162 : PHE -A163 : LYS -C2 : VAL -C3 : LYS -C4 : LEU -C5 : THR -C6 : ALA -C7 : GLU -C8 : LEU -C9 : ILE -C10 : GLU -C11 : GLN -C12 : ALA -C13 : ALA -C14 : GLN -C15 : TYR -C16 : THR -C17 : ASN -C18 : ALA -C19 : VAL -C20 : ARG -C21 : ASP -C22 : ARG -C23 : GLU -C24 : LEU -C25 : ASP -C26 : LEU -C27 : ARG -C28 : GLY -C29 : TYR -C30 : LYS -C31 : ILE -C32 : PRO -C33 : VAL -C34 : ILE -C35 : GLU -C36 : ASN -C37 : LEU -C38 : GLY -C39 : ALA -C40 : THR -C41 : LEU -C42 : ASP -C43 : GLN -C44 : PHE -C45 : ASP -C46 : ALA -C47 : ILE -C48 : ASP -C49 : PHE -C50 : SER -C51 : ASP -C52 : ASN -C53 : GLU -C54 : ILE -C55 : ARG -C56 : LYS -C57 : LEU -C58 : ASP -C59 : GLY -C60 : PHE -C61 : PRO -C62 : LEU -C63 : LEU -C64 : ARG -C65 : ARG -C66 : LEU -C67 : LYS -C68 : THR -C69 : LEU -C70 : LEU -C71 : VAL -C72 : ASN -C73 : ASN -C74 : ASN -C75 : ARG -C76 : ILE -C77 : CYS -C78 : ARG -C79 : ILE -C80 : GLY -C81 : GLU -C82 : GLY -C83 : LEU -C84 : ASP -C85 : GLN -C86 : ALA -C87 : LEU -C88 : PRO -C89 : ASP -C90 : LEU -C91 : THR -C92 : GLU -C93 : LEU -C94 : ILE -C95 : LEU -C96 : THR -C97 : ASN -C98 : ASN -C99 : SER -C100 : LEU -C101 : VAL -C102 : GLU -C103 : LEU -C104 : GLY -C105 : ASP -C106 : LEU -C107 : ASP -C108 : PRO -C109 : LEU -C110 : ALA -C111 : SER -C112 : LEU -C113 : LYS -C114 : SER -C115 : LEU -C116 : THR -C117 : TYR -C118 : LEU -C119 : CYS -C120 : ILE -C121 : LEU -C122 : ARG -C123 : ASN -C124 : PRO -C125 : VAL -C126 : THR -C127 : ASN -C128 : LYS -C129 : LYS -C130 : HIS -C131 : TYR -C132 : ARG -C133 : LEU -C134 : TYR -C135 : VAL -C136 : ILE -C137 : TYR -C138 : LYS -C139 : VAL -C140 : PRO -C141 : GLN -C142 : VAL -C143 : ARG -C144 : VAL -C145 : LEU -C146 : ASP -C147 : PHE -C148 : GLN -C149 : LYS -C150 : VAL -C151 : LYS -C152 : LEU -C153 : LYS -C154 : GLU -C155 : ARG -C156 : GLN -C157 : GLU -C158 : ALA -C159 : GLU -C160 : LYS -C161 : MET -C162 : PHE -C163 : LYS -C164 : GLY -C165 : LYS -C166 : ARG -C167 : GLY -C168 : ALA -C169 : GLN -C170 : LEU -C171 : ALA -C172 : LYS -C173 : ASP -C174 : ILE -C175 : ALA -B6 : ILE -B7 : ARG -B8 : PRO -B9 : ASN -B10 : HIS -B11 : THR -B12 : ILE -B13 : TYR -B14 : ILE -B15 : ASN -B16 : ASN -B17 : MET -B18 : ASN -B19 : ASP -B20 : LYS -B21 : ILE -B22 : LYS -B23 : LYS -B24 : GLU -B25 : GLU -B26 : LEU -B27 : LYS -B28 : ARG -B29 : SER -B30 : LEU -B31 : TYR -B32 : ALA -B33 : LEU -B34 : PHE -B35 : SER -B36 : GLN -B37 : PHE -B38 : GLY -B39 : HIS -B40 : VAL -B41 : VAL -B42 : ASP -B43 : ILE -B44 : VAL -B45 : ALA -B46 : LEU -B47 : LYS -B48 : THR -B49 : MET -B50 : LYS -B51 : MET -B52 : ARG -B53 : GLY -B54 : GLN -B55 : ALA -B56 : PHE -B57 : VAL -B58 : ILE -B59 : PHE -B60 : LYS -B61 : GLU -B62 : LEU -B63 : GLY -B64 : SER -B65 : SER -B66 : THR -B67 : ASN -B68 : ALA -B69 : LEU -B70 : ARG -B71 : GLN -B72 : LEU -B73 : GLN -B74 : GLY -B75 : PHE -B76 : PRO -B77 : PHE -B78 : TYR -B79 : GLY -B80 : LYS -B81 : PRO -B82 : MET -B83 : ARG -B84 : ILE -B85 : GLN -B86 : TYR -B87 : ALA -B88 : LYS -B89 : THR -B90 : ASP -B91 : SER -B92 : ASP -B93 : ILE -B94 : ILE -B95 : SER -B96 : LYS -B97 : MET -B98 : ARG -B99 : GLY -D6 : ILE -D7 : ARG -D8 : PRO -D9 : ASN -D10 : HIS -D11 : THR -D12 : ILE -D13 : TYR -D14 : ILE -D15 : ASN -D16 : ASN -D17 : MET -D18 : ASN -D19 : ASP -D20 : LYS -D21 : ILE -D22 : LYS -D23 : LYS -D24 : GLU -D25 : GLU -D26 : LEU -D27 : LYS -D28 : ARG -D29 : SER -D30 : LEU -D31 : TYR -D32 : ALA -D33 : LEU -D34 : PHE -D35 : SER -D36 : GLN -D37 : PHE -D38 : GLY -D39 : HIS -D40 : VAL -D41 : VAL -D42 : ASP -D43 : ILE -D44 : VAL -D45 : ALA -D46 : LEU -D47 : LYS -D48 : THR -D49 : MET -D50 : LYS -D51 : MET -D52 : ARG -D53 : GLY -D54 : GLN -D55 : ALA -D56 : PHE -D57 : VAL -D58 : ILE -D59 : PHE -D60 : LYS -D61 : GLU -D62 : LEU -D63 : GLY -D64 : SER -D65 : SER -D66 : THR -D67 : ASN -D68 : ALA -D69 : LEU -D70 : ARG -D71 : GLN -D72 : LEU -D73 : GLN -D74 : GLY -D75 : PHE -D76 : PRO -D77 : PHE -D78 : TYR -D79 : GLY -D80 : LYS -D81 : PRO -D82 : MET -D83 : ARG -D84 : ILE -D85 : GLN -D86 : TYR -D87 : ALA -D88 : LYS -D89 : THR -D90 : ASP -D91 : SER -D92 : ASP -D93 : ILE -D94 : ILE -D95 : SER -D96 : LYS -D97 : MET -D98 : ARG -Adjacent stackings ---------------------------------------------- -Q0-Q1 : adjacent_5p upward -Q1-Q2 : adjacent_5p upward -Q3-Q4 : adjacent_5p upward -Q4-Q5 : adjacent_5p upward -Q6-Q7 : adjacent_5p upward -Q11-Q12 : adjacent_5p inward -Q14-Q15 : adjacent_5p upward -Q15-Q16 : adjacent_5p upward -Q17-Q18 : adjacent_5p upward -Q19-Q20 : adjacent_5p upward -Q20-Q21 : adjacent_5p upward -Q21-Q22 : adjacent_5p upward -Q22-Q23 : adjacent_5p upward -R0-R1 : adjacent_5p upward -R1-R2 : adjacent_5p upward -R2-R3 : adjacent_5p upward -R3-R4 : adjacent_5p upward -R4-R5 : adjacent_5p upward -R6-R7 : adjacent_5p upward -R11-R12 : adjacent_5p inward -R14-R15 : adjacent_5p upward -R15-R16 : adjacent_5p upward -R17-R18 : adjacent_5p upward -R19-R20 : adjacent_5p upward -R20-R21 : adjacent_5p upward -R21-R22 : adjacent_5p upward -R22-R23 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Q3-Q20 : outward -Q6-Q17 : outward -R3-R20 : outward -R6-R17 : outward -Number of stackings = 31 -Number of adjacent stackings = 27 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -Q0-Q22 : C-G Ww/Ww pairing antiparallel cis XIX -Q1-Q21 : C-G Ww/Ww pairing antiparallel cis XIX -Q2-Q20 : U-A Ww/Ww pairing antiparallel cis XX -Q3-Q19 : G-C Ww/Ww pairing antiparallel cis XIX -Q4-Q18 : G-C Ww/Ww pairing antiparallel cis XIX -Q5-Q17 : U-U Ws/Ww pairing antiparallel cis XVI -R0-R22 : C-G Ww/Ww pairing antiparallel cis XIX -R1-R21 : C-G Ww/Ww pairing antiparallel cis XIX -R2-R20 : U-A Ww/Ww pairing antiparallel cis XX -R3-R19 : G-C Ww/Ww pairing antiparallel cis XIX -R4-R18 : G-C Ww/Ww pairing antiparallel cis XIX -R5-R17 : U-U Ws/Ww pairing antiparallel cis XVI diff --git a/MCdata/1ac3_MC b/MCdata/1ac3_MC deleted file mode 100644 index edd00a909d1e32d031dc4befcb1564a91a157aaa..0000000000000000000000000000000000000000 --- a/MCdata/1ac3_MC +++ /dev/null @@ -1,497 +0,0 @@ -Residue conformations ------------------------------------------- -A1 : C O4p_endo anti -A2 : G C1p_exo anti -A3 : C O4p_endo anti -A4 : G O4p_endo anti -A5 : T O4p_endo anti -A6 : TSP -A7 : TCP -A8 : T O4p_endo anti -A9 : G O4p_endo anti -A10 : C O4p_endo anti -A11 : G O4p_endo anti -A12 : C O4p_endo anti -B13 : G C4p_exo anti -B14 : C C3p_endo anti -B15 : G C3p_endo anti -B16 : C C3p_endo anti -B17 : A C3p_endo anti -B18 : A C3p_endo anti -B19 : A C3p_endo anti -B20 : A C3p_endo anti -B21 : C C3p_endo anti -B22 : G C3p_endo anti -B23 : C C3p_endo anti -B24 : G O4p_endo anti -Adjacent stackings ---------------------------------------------- -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -B13-B14 : adjacent_5p upward -B14-B15 : adjacent_5p upward -B15-B16 : adjacent_5p upward -B16-B17 : adjacent_5p upward -B17-B18 : adjacent_5p upward -B18-B19 : adjacent_5p upward -B19-B20 : adjacent_5p upward -B20-B21 : adjacent_5p upward -B21-B22 : adjacent_5p upward -B22-B23 : adjacent_5p upward -B23-B24 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A2-B24 : outward -A4-B22 : outward -A9-B17 : outward -A11-B15 : outward -Number of stackings = 21 -Number of adjacent stackings = 17 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A1-B24 : C-G Ww/Ww pairing antiparallel cis XIX -A2-B23 : G-C Ww/Ww pairing antiparallel cis XIX -A3-B22 : C-G Ww/Ww pairing antiparallel cis XIX -A4-B21 : G-C Ww/Ww pairing antiparallel cis XIX -A5-B20 : T-A Ww/Ww pairing antiparallel cis -A8-B17 : T-A Ww/Ww pairing antiparallel cis -A9-B16 : G-C Ww/Ww pairing antiparallel cis XIX -A10-B15 : C-G Ww/Ww pairing antiparallel cis XIX -A11-B14 : G-C Ww/Ww pairing antiparallel cis XIX -A12-B13 : C-G Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -A1 : C O4p_endo anti -A2 : G C1p_exo anti -A3 : C O4p_endo anti -A4 : G O4p_endo anti -A5 : T O4p_endo anti -A6 : TSP -A7 : TCP -A8 : T O4p_endo anti -A9 : G O4p_endo anti -A10 : C O4p_endo anti -A11 : G O4p_endo anti -A12 : C O4p_endo anti -B13 : G C4p_exo anti -B14 : C C3p_endo anti -B15 : G C3p_endo anti -B16 : C C3p_endo anti -B17 : A C3p_endo anti -B18 : A C3p_endo anti -B19 : A C3p_endo anti -B20 : A C3p_endo anti -B21 : C C3p_endo anti -B22 : G C3p_endo anti -B23 : C C3p_endo anti -B24 : G C4p_exo anti -Adjacent stackings ---------------------------------------------- -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -B13-B14 : adjacent_5p upward -B14-B15 : adjacent_5p upward -B15-B16 : adjacent_5p upward -B16-B17 : adjacent_5p upward -B17-B18 : adjacent_5p upward -B18-B19 : adjacent_5p upward -B19-B20 : adjacent_5p upward -B20-B21 : adjacent_5p upward -B21-B22 : adjacent_5p upward -B22-B23 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A2-B24 : outward -A4-B22 : outward -A9-B17 : outward -A11-B15 : outward -Number of stackings = 21 -Number of adjacent stackings = 17 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A1-B24 : C-G Ww/Ww pairing antiparallel cis XIX -A2-B23 : G-C Ww/Ww pairing antiparallel cis XIX -A3-B22 : C-G Ww/Ww pairing antiparallel cis XIX -A4-B21 : G-C Ww/Ww pairing antiparallel cis XIX -A5-B20 : T-A Ww/Ww pairing antiparallel cis -A8-B17 : T-A Ww/Ww pairing antiparallel cis -A9-B16 : G-C Ww/Ww pairing antiparallel cis XIX -A10-B15 : C-G Ww/Ww pairing antiparallel cis XIX -A11-B14 : G-C Ww/Ww pairing antiparallel cis XIX -A12-B13 : C-G Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -A1 : C O4p_endo anti -A2 : G C1p_exo anti -A3 : C O4p_endo anti -A4 : G O4p_endo anti -A5 : T O4p_endo anti -A6 : TSP -A7 : TCP -A8 : T O4p_endo anti -A9 : G O4p_endo anti -A10 : C O4p_endo anti -A11 : G O4p_endo anti -A12 : C O4p_endo anti -B13 : G C4p_exo anti -B14 : C C3p_endo anti -B15 : G C3p_endo anti -B16 : C C3p_endo anti -B17 : A C3p_endo anti -B18 : A C3p_endo anti -B19 : A C3p_endo anti -B20 : A C3p_endo anti -B21 : C C3p_endo anti -B22 : G C3p_endo anti -B23 : C C3p_endo anti -B24 : G C4p_exo anti -Adjacent stackings ---------------------------------------------- -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -B13-B14 : adjacent_5p upward -B14-B15 : adjacent_5p upward -B15-B16 : adjacent_5p upward -B16-B17 : adjacent_5p upward -B17-B18 : adjacent_5p upward -B18-B19 : adjacent_5p upward -B19-B20 : adjacent_5p upward -B20-B21 : adjacent_5p upward -B21-B22 : adjacent_5p upward -B22-B23 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A2-B24 : outward -A4-B22 : outward -A9-B17 : outward -A11-B15 : outward -Number of stackings = 21 -Number of adjacent stackings = 17 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A1-B24 : C-G Ww/Ww pairing antiparallel cis XIX -A2-B23 : G-C Ww/Ww pairing antiparallel cis XIX -A3-B22 : C-G Ww/Ww pairing antiparallel cis XIX -A4-B21 : G-C Ww/Ww pairing antiparallel cis XIX -A5-B20 : T-A Ww/Ww pairing antiparallel cis -A8-B17 : T-A Ww/Ww pairing antiparallel cis -A9-B16 : G-C Ww/Ww pairing antiparallel cis XIX -A10-B15 : C-G Ww/Ww pairing antiparallel cis XIX -A11-B14 : G-C Ww/Ww pairing antiparallel cis XIX -A12-B13 : C-G Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -A1 : C O4p_endo anti -A2 : G C1p_exo anti -A3 : C O4p_endo anti -A4 : G O4p_endo anti -A5 : T O4p_endo anti -A6 : TSP -A7 : TCP -A8 : T O4p_endo anti -A9 : G O4p_endo anti -A10 : C O4p_endo anti -A11 : G O4p_endo anti -A12 : C O4p_endo anti -B13 : G C4p_exo anti -B14 : C C3p_endo anti -B15 : G C3p_endo anti -B16 : C C3p_endo anti -B17 : A C3p_endo anti -B18 : A C3p_endo anti -B19 : A C3p_endo anti -B20 : A C3p_endo anti -B21 : C C3p_endo anti -B22 : G C3p_endo anti -B23 : C C3p_endo anti -B24 : G C4p_exo anti -Adjacent stackings ---------------------------------------------- -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -B13-B14 : adjacent_5p upward -B14-B15 : adjacent_5p upward -B15-B16 : adjacent_5p upward -B16-B17 : adjacent_5p upward -B17-B18 : adjacent_5p upward -B18-B19 : adjacent_5p upward -B19-B20 : adjacent_5p upward -B20-B21 : adjacent_5p upward -B21-B22 : adjacent_5p upward -B22-B23 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A2-B24 : outward -A4-B22 : outward -A9-B17 : outward -A11-B15 : outward -Number of stackings = 21 -Number of adjacent stackings = 17 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A1-B24 : C-G Ww/Ww pairing antiparallel cis XIX -A2-B23 : G-C Ww/Ww pairing antiparallel cis XIX -A3-B22 : C-G Ww/Ww pairing antiparallel cis XIX -A4-B21 : G-C Ww/Ww pairing antiparallel cis XIX -A5-B20 : T-A Ww/Ww pairing antiparallel cis -A8-B17 : T-A Ww/Ww pairing antiparallel cis -A9-B16 : G-C Ww/Ww pairing antiparallel cis XIX -A10-B15 : C-G Ww/Ww pairing antiparallel cis XIX -A11-B14 : G-C Ww/Ww pairing antiparallel cis XIX -A12-B13 : C-G Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -A1 : C O4p_endo anti -A2 : G C1p_exo anti -A3 : C O4p_endo anti -A4 : G O4p_endo anti -A5 : T O4p_endo anti -A6 : TSP -A7 : TCP -A8 : T O4p_endo anti -A9 : G O4p_endo anti -A10 : C O4p_endo anti -A11 : G O4p_endo anti -A12 : C O4p_endo anti -B13 : G C4p_exo anti -B14 : C C3p_endo anti -B15 : G C3p_endo anti -B16 : C C3p_endo anti -B17 : A C3p_endo anti -B18 : A C3p_endo anti -B19 : A C3p_endo anti -B20 : A C3p_endo anti -B21 : C C3p_endo anti -B22 : G C3p_endo anti -B23 : C C3p_endo anti -B24 : G C4p_exo anti -Adjacent stackings ---------------------------------------------- -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -B13-B14 : adjacent_5p upward -B14-B15 : adjacent_5p upward -B15-B16 : adjacent_5p upward -B16-B17 : adjacent_5p upward -B17-B18 : adjacent_5p upward -B18-B19 : adjacent_5p upward -B19-B20 : adjacent_5p upward -B20-B21 : adjacent_5p upward -B21-B22 : adjacent_5p upward -B22-B23 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A2-B24 : outward -A4-B22 : outward -A9-B17 : outward -A11-B15 : outward -Number of stackings = 21 -Number of adjacent stackings = 17 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A1-B24 : C-G Ww/Ww pairing antiparallel cis XIX -A2-B23 : G-C Ww/Ww pairing antiparallel cis XIX -A3-B22 : C-G Ww/Ww pairing antiparallel cis XIX -A4-B21 : G-C Ww/Ww pairing antiparallel cis XIX -A5-B20 : T-A Ww/Ww pairing antiparallel cis -A8-B17 : T-A Ww/Ww pairing antiparallel cis -A9-B16 : G-C Ww/Ww pairing antiparallel cis XIX -A10-B15 : C-G Ww/Ww pairing antiparallel cis XIX -A11-B14 : G-C Ww/Ww pairing antiparallel cis XIX -A12-B13 : C-G Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -A1 : C O4p_endo anti -A2 : G C1p_exo anti -A3 : C O4p_endo anti -A4 : G O4p_endo anti -A5 : T O4p_endo anti -A6 : TSP -A7 : TCP -A8 : T O4p_endo anti -A9 : G O4p_endo anti -A10 : C O4p_endo anti -A11 : G O4p_endo anti -A12 : C O4p_endo anti -B13 : G C4p_exo anti -B14 : C C3p_endo anti -B15 : G C3p_endo anti -B16 : C C3p_endo anti -B17 : A C3p_endo anti -B18 : A C3p_endo anti -B19 : A C3p_endo anti -B20 : A C3p_endo anti -B21 : C C3p_endo anti -B22 : G C3p_endo anti -B23 : C C3p_endo anti -B24 : G C4p_exo anti -Adjacent stackings ---------------------------------------------- -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -B13-B14 : adjacent_5p upward -B14-B15 : adjacent_5p upward -B15-B16 : adjacent_5p upward -B16-B17 : adjacent_5p upward -B17-B18 : adjacent_5p upward -B18-B19 : adjacent_5p upward -B19-B20 : adjacent_5p upward -B20-B21 : adjacent_5p upward -B21-B22 : adjacent_5p upward -B22-B23 : adjacent_5p upward -B23-B24 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A2-B24 : outward -A4-B22 : outward -A9-B17 : outward -A11-B15 : outward -Number of stackings = 21 -Number of adjacent stackings = 17 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A1-B24 : C-G Ww/Ww pairing antiparallel cis XIX -A2-B23 : G-C Ww/Ww pairing antiparallel cis XIX -A3-B22 : C-G Ww/Ww pairing antiparallel cis XIX -A4-B21 : G-C Ww/Ww pairing antiparallel cis XIX -A5-B20 : T-A Ww/Ww pairing antiparallel cis -A8-B17 : T-A Ww/Ww pairing antiparallel cis -A9-B16 : G-C Ww/Ww pairing antiparallel cis XIX -A10-B15 : C-G Ww/Ww pairing antiparallel cis XIX -A11-B14 : G-C Ww/Ww pairing antiparallel cis XIX -A12-B13 : C-G Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -A1 : C O4p_endo anti -A2 : G C1p_exo anti -A3 : C O4p_endo anti -A4 : G O4p_endo anti -A5 : T O4p_endo anti -A6 : TSP -A7 : TCP -A8 : T O4p_endo anti -A9 : G O4p_endo anti -A10 : C O4p_endo anti -A11 : G O4p_endo anti -A12 : C O4p_endo anti -B13 : G C4p_exo anti -B14 : C C3p_endo anti -B15 : G C3p_endo anti -B16 : C C3p_endo anti -B17 : A C3p_endo anti -B18 : A C3p_endo anti -B19 : A C3p_endo anti -B20 : A C3p_endo anti -B21 : C C3p_endo anti -B22 : G C3p_endo anti -B23 : C C3p_endo anti -B24 : G C4p_exo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -B13-B14 : adjacent_5p upward -B14-B15 : adjacent_5p upward -B15-B16 : adjacent_5p upward -B16-B17 : adjacent_5p upward -B17-B18 : adjacent_5p upward -B18-B19 : adjacent_5p upward -B19-B20 : adjacent_5p upward -B20-B21 : adjacent_5p upward -B21-B22 : adjacent_5p upward -B22-B23 : adjacent_5p upward -B23-B24 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A2-B24 : outward -A4-B22 : outward -A9-B17 : outward -A11-B15 : outward -Number of stackings = 22 -Number of adjacent stackings = 18 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A1-B24 : C-G Ww/Ww pairing antiparallel cis XIX -A2-B23 : G-C Ww/Ww pairing antiparallel cis XIX -A3-B22 : C-G Ww/Ww pairing antiparallel cis XIX -A4-B21 : G-C Ww/Ww pairing antiparallel cis XIX -A5-B20 : T-A Ww/Ww pairing antiparallel cis -A8-B17 : T-A Ww/Ww pairing antiparallel cis -A9-B16 : G-C Ww/Ww pairing antiparallel cis XIX -A10-B15 : C-G Ww/Ww pairing antiparallel cis XIX -A11-B14 : G-C Ww/Ww pairing antiparallel cis XIX -A12-B13 : C-G Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -A1 : C O4p_endo anti -A2 : G C1p_exo anti -A3 : C O4p_endo anti -A4 : G O4p_endo anti -A5 : T O4p_endo anti -A6 : TSP -A7 : TCP -A8 : T O4p_endo anti -A9 : G O4p_endo anti -A10 : C O4p_endo anti -A11 : G O4p_endo anti -A12 : C O4p_endo anti -B13 : G C4p_exo anti -B14 : C C3p_endo anti -B15 : G C3p_endo anti -B16 : C C3p_endo anti -B17 : A C3p_endo anti -B18 : A C3p_endo anti -B19 : A C3p_endo anti -B20 : A C3p_endo anti -B21 : C C3p_endo anti -B22 : G C3p_endo anti -B23 : C C3p_endo anti -B24 : G C4p_exo anti -Adjacent stackings ---------------------------------------------- -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -B13-B14 : adjacent_5p upward -B14-B15 : adjacent_5p upward -B15-B16 : adjacent_5p upward -B16-B17 : adjacent_5p upward -B17-B18 : adjacent_5p upward -B18-B19 : adjacent_5p upward -B19-B20 : adjacent_5p upward -B20-B21 : adjacent_5p upward -B21-B22 : adjacent_5p upward -B22-B23 : adjacent_5p upward -B23-B24 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A2-B24 : outward -A4-B22 : outward -A9-B17 : outward -A11-B15 : outward -Number of stackings = 21 -Number of adjacent stackings = 17 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A1-B24 : C-G Ww/Ww pairing antiparallel cis XIX -A2-B23 : G-C Ww/Ww pairing antiparallel cis XIX -A3-B22 : C-G Ww/Ww pairing antiparallel cis XIX -A4-B21 : G-C Ww/Ww pairing antiparallel cis XIX -A5-B20 : T-A Ww/Ww pairing antiparallel cis -A8-B17 : T-A Ww/Ww pairing antiparallel cis -A9-B16 : G-C Ww/Ww pairing antiparallel cis XIX -A10-B15 : C-G Ww/Ww pairing antiparallel cis XIX -A11-B14 : G-C Ww/Ww pairing antiparallel cis XIX -A12-B13 : C-G Ww/Ww pairing antiparallel cis XIX diff --git a/MCdata/1afx_MC b/MCdata/1afx_MC deleted file mode 100644 index 5f1e1c3eaca93cb7f22981f2798d39f06150ef93..0000000000000000000000000000000000000000 --- a/MCdata/1afx_MC +++ /dev/null @@ -1,459 +0,0 @@ -Residue conformations ------------------------------------------- -A1 : G O4p_exo anti -A2 : G C3p_endo anti -A3 : U C3p_endo anti -A4 : G C4p_exo anti -A5 : U C3p_endo anti -A6 : G C4p_exo syn -A7 : A C3p_exo syn -A8 : A C2p_endo syn -A9 : C C3p_endo anti -A10 : A C2p_exo anti -A11 : C C3p_endo anti -A12 : C C4p_exo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p inward -A7-A8 : adjacent_5p upward pairing -A8-A9 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 9 -Number of adjacent stackings = 9 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-A12 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A11 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A10 : U-A Ww/Ww pairing antiparallel cis XX -A4-A9 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A8 : U-A O2'/Bh pairing -A6-A7 : G-A O2P/Bh O2P/Hh adjacent_5p pairing -A7-A8 : A-A O2'/Hh O2'/C8 adjacent_5p upward pairing -A9-A10 : C-A O2'/C8 adjacent_5p pairing -Residue conformations ------------------------------------------- -A1 : G O4p_exo anti -A2 : G C3p_endo anti -A3 : U C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : G C3p_endo syn -A7 : A C3p_exo syn -A8 : A C2p_endo syn -A9 : C C4p_exo anti -A10 : A C3p_endo anti -A11 : C C3p_endo anti -A12 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p inward -A7-A8 : adjacent_5p upward pairing -A8-A9 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 9 -Number of adjacent stackings = 9 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-A12 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A11 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A10 : U-A Ww/Ww pairing antiparallel cis XX -A4-A9 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A8 : U-A O2'/Ww O2'/Bh pairing -A6-A7 : G-A O2P/Bh adjacent_5p pairing -A7-A8 : A-A O2'/Hh O2'/C8 adjacent_5p upward pairing -Residue conformations ------------------------------------------- -A1 : G O4p_exo anti -A2 : G C3p_endo anti -A3 : U C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : G C3p_endo syn -A7 : A C3p_exo syn -A8 : A C2p_endo syn -A9 : C C4p_exo anti -A10 : A C3p_endo anti -A11 : C C3p_endo anti -A12 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p inward -A8-A9 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 8 -Number of adjacent stackings = 8 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-A12 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A11 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A10 : U-A Ww/Ww pairing antiparallel cis XX -A4-A9 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A8 : U-A Ss/Wh O2'/Ww O2'/Bh pairing antiparallel cis one_hbond -A6-A7 : G-A O2P/Bh adjacent_5p pairing -A7-A8 : A-A O2'/Hh O2'/C8 adjacent_5p pairing -A9-A10 : C-A O2'/C8 adjacent_5p pairing -Residue conformations ------------------------------------------- -A1 : G O4p_exo anti -A2 : G C3p_endo anti -A3 : U C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : G C3p_endo syn -A7 : A C3p_exo syn -A8 : A C2p_endo syn -A9 : C C4p_exo anti -A10 : A C3p_endo anti -A11 : C C3p_endo anti -A12 : C C4p_exo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p inward -A7-A8 : adjacent_5p upward pairing -A8-A9 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 9 -Number of adjacent stackings = 9 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-A12 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A11 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A10 : U-A Ww/Ww pairing antiparallel cis XX -A4-A9 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A8 : U-A O2'/Bh pairing -A6-A7 : G-A O2P/Bh adjacent_5p pairing -A7-A8 : A-A O2'/Hh O2'/C8 adjacent_5p upward pairing -A9-A10 : C-A O2'/C8 adjacent_5p pairing -Residue conformations ------------------------------------------- -A1 : G O4p_exo anti -A2 : G C3p_endo anti -A3 : U C2p_exo anti -A4 : G C4p_exo anti -A5 : U C3p_endo anti -A6 : G C3p_endo syn -A7 : A C3p_exo syn -A8 : A C2p_endo syn -A9 : C C4p_exo anti -A10 : A C3p_endo anti -A11 : C C3p_endo anti -A12 : C O4p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p inward -A8-A9 : adjacent_5p upward -A10-A11 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 6 -Number of adjacent stackings = 6 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-A12 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A11 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A10 : U-A Ww/Ww pairing antiparallel cis XX -A4-A9 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A8 : U-A O2'/Ww O2'/Bh pairing -A6-A7 : G-A O2P/Bh adjacent_5p pairing -A7-A8 : A-A O2'/Hh O2'/C8 adjacent_5p pairing -A9-A10 : C-A O2'/C8 adjacent_5p pairing -Residue conformations ------------------------------------------- -A1 : G O4p_exo anti -A2 : G C3p_endo anti -A3 : U C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : G C3p_endo syn -A7 : A C3p_exo syn -A8 : A C2p_endo syn -A9 : C C4p_exo anti -A10 : A C2p_exo anti -A11 : C C3p_endo anti -A12 : C C4p_exo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p inward -A8-A9 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 8 -Number of adjacent stackings = 8 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-A12 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A11 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A10 : U-A Ww/Ww pairing antiparallel cis XX -A4-A9 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A8 : U-A O2'/Ww O2'/Bh pairing -A6-A7 : G-A O2P/Bh adjacent_5p pairing -A7-A8 : A-A O2'/Hh O2'/C8 adjacent_5p pairing -A9-A10 : C-A O2'/C8 adjacent_5p pairing -Residue conformations ------------------------------------------- -A1 : G O4p_exo anti -A2 : G C3p_endo anti -A3 : U C2p_exo anti -A4 : G C4p_exo anti -A5 : U C3p_endo anti -A6 : G C3p_endo syn -A7 : A C3p_exo syn -A8 : A C2p_endo syn -A9 : C C3p_endo anti -A10 : A C2p_exo anti -A11 : C C3p_endo anti -A12 : C C4p_exo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p inward -A7-A8 : adjacent_5p upward pairing -A8-A9 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 9 -Number of adjacent stackings = 9 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-A12 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A11 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A10 : U-A Ww/Ww pairing antiparallel cis XX -A4-A9 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A8 : U-A O2'/Bh pairing -A6-A7 : G-A O2P/Bh O2P/Hh adjacent_5p pairing -A7-A8 : A-A O2'/Hh O2'/C8 adjacent_5p upward pairing -A9-A10 : C-A O2'/C8 adjacent_5p pairing -Residue conformations ------------------------------------------- -A1 : G O4p_exo anti -A2 : G C3p_endo anti -A3 : U C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : G C3p_endo syn -A7 : A C3p_exo syn -A8 : A C2p_endo syn -A9 : C C3p_endo anti -A10 : A C2p_exo anti -A11 : C C3p_endo anti -A12 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p inward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 9 -Number of adjacent stackings = 9 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-A12 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A11 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A10 : U-A Ww/Ww pairing antiparallel cis XX -A4-A9 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A7 : U-A O2'/Hh pairing -A5-A8 : U-A Ss/Wh O2'/Ww pairing antiparallel cis one_hbond -A7-A8 : A-A O2'/Hh O2'/C8 adjacent_5p pairing -Residue conformations ------------------------------------------- -A1 : G O4p_exo anti -A2 : G C3p_endo anti -A3 : U C3p_endo anti -A4 : G C4p_exo anti -A5 : U C3p_endo anti -A6 : G C3p_endo syn -A7 : A C3p_exo syn -A8 : A C2p_endo syn -A9 : C C4p_exo anti -A10 : A C3p_endo anti -A11 : C C3p_endo anti -A12 : C C4p_exo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 7 -Number of adjacent stackings = 7 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-A12 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A11 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A10 : U-A Ww/Ww pairing antiparallel cis XX -A4-A9 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A7 : U-A O2'/Hh pairing -A5-A8 : U-A Bs/Wh O2'/Ww pairing antiparallel cis one_hbond 46 -A6-A7 : G-A O2P/Hh adjacent_5p pairing -A7-A8 : A-A O2'/Hh O2'/C8 adjacent_5p pairing -A9-A10 : C-A O2'/C8 adjacent_5p pairing -Residue conformations ------------------------------------------- -A1 : G O4p_exo anti -A2 : G C3p_endo anti -A3 : U C3p_endo anti -A4 : G C4p_exo anti -A5 : U C3p_endo anti -A6 : G C3p_endo syn -A7 : A C2p_endo syn -A8 : A C2p_endo syn -A9 : C C4p_exo anti -A10 : A C3p_endo anti -A11 : C C3p_endo anti -A12 : C C4p_exo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 7 -Number of adjacent stackings = 7 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-A12 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A11 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A10 : U-A Ww/Ww pairing antiparallel cis XX -A4-A9 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A7 : U-A O2'/Hh pairing -A5-A8 : U-A Bs/Wh O2'/Ww pairing antiparallel cis one_hbond 46 -A6-A7 : G-A O2P/Hh adjacent_5p pairing -A7-A8 : A-A O2'/Hh O2'/C8 adjacent_5p pairing -A9-A10 : C-A O2'/C8 adjacent_5p pairing -Residue conformations ------------------------------------------- -A1 : G O4p_exo anti -A2 : G C3p_endo anti -A3 : U C3p_endo anti -A4 : G C4p_exo anti -A5 : U C3p_endo anti -A6 : G O4p_endo syn -A7 : A C3p_exo syn -A8 : A C2p_endo syn -A9 : C C4p_exo anti -A10 : A C2p_exo anti -A11 : C C3p_endo anti -A12 : C C4p_exo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p inward pairing -A7-A8 : adjacent_5p upward pairing -A8-A9 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 9 -Number of adjacent stackings = 9 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-A12 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A11 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A10 : U-A Ww/Ww pairing antiparallel cis XX -A4-A9 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A6 : U-G O2P/Ww adjacent_5p inward pairing -A5-A7 : U-A O2'/Hh pairing -A5-A8 : U-A Ss/Wh O2'/Ww pairing antiparallel cis one_hbond -A6-A7 : G-A O2P/Bh O2P/Hh adjacent_5p pairing -A7-A8 : A-A O2'/Hh O2'/C8 adjacent_5p upward pairing -A9-A10 : C-A O2'/C8 adjacent_5p pairing -Residue conformations ------------------------------------------- -A1 : G O4p_exo anti -A2 : G C3p_endo anti -A3 : U C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : G C3p_endo syn -A7 : A C3p_exo syn -A8 : A C3p_exo anti -A9 : C C4p_exo anti -A10 : A C3p_endo anti -A11 : C C3p_endo anti -A12 : C O4p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p inward pairing -A7-A8 : adjacent_5p upward pairing -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward pairing -A10-A11 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 8 -Number of adjacent stackings = 8 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-A12 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A11 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A10 : U-A Ww/Ww pairing antiparallel cis XX -A4-A9 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A6 : U-G O2'/C8 adjacent_5p inward pairing -A5-A8 : U-A O2'/Ww O2'/Bh pairing -A7-A8 : A-A O2'/Hh O2'/C8 adjacent_5p upward pairing -A7-A9 : A-C Ss/O2P pairing -A9-A10 : C-A O2'/C8 adjacent_5p upward pairing -Residue conformations ------------------------------------------- -A1 : G O4p_exo anti -A2 : G C3p_endo anti -A3 : U C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : G C3p_endo syn -A7 : A C3p_exo syn -A8 : A C2p_endo syn -A9 : C C4p_exo anti -A10 : A C3p_endo anti -A11 : C C3p_endo anti -A12 : C C4p_exo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p inward -A8-A9 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 7 -Number of adjacent stackings = 7 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-A12 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A11 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A10 : U-A Ww/Ww pairing antiparallel cis XX -A4-A9 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A8 : U-A Ss/Wh O2'/Ww O2'/Bh pairing antiparallel cis one_hbond -A6-A7 : G-A O2P/Bh adjacent_5p pairing -A7-A8 : A-A O2'/Hh O2'/C8 adjacent_5p pairing -A9-A10 : C-A O2'/C8 adjacent_5p pairing diff --git a/MCdata/1ajf_MC b/MCdata/1ajf_MC deleted file mode 100644 index 996f642010258afd5b7d9d326603b815c4b0344c..0000000000000000000000000000000000000000 --- a/MCdata/1ajf_MC +++ /dev/null @@ -1,52 +0,0 @@ -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : A C3p_endo anti -A3 : C C3p_endo anti -A4 : A C3p_endo anti -A5 : G C3p_endo anti -A6 : G C3p_endo anti -A7 : G C3p_endo anti -A8 : G C3p_endo anti -A9 : A C3p_endo anti -A10 : A C3p_endo anti -A11 : A C3p_endo anti -A12 : C C3p_endo anti -A13 : U C3p_endo anti -A14 : U C3p_endo anti -A15 : U C3p_endo anti -A16 : G C3p_endo anti -A17 : U C3p_endo anti -A18 : C C3p_endo anti -A19 : NCO -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A16 : outward -Number of stackings = 17 -Number of adjacent stackings = 16 -Number of non adjacent stackings = 1 -Base-pairs ------------------------------------------------------ -A1-A18 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A17 : A-U Ww/Ww pairing antiparallel cis XX -A3-A16 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A15 : A-U Ww/Ww pairing antiparallel cis XX -A5-A14 : G-U Ww/Ws pairing antiparallel cis XXVIII -A6-A13 : G-U Ww/Ws pairing antiparallel cis XXVIII -A7-A12 : G-C Ww/Ww pairing antiparallel cis XIX -A8-A10 : G-A Ss/O2P pairing -A8-A11 : G-A Ss/Hh O2'/Bh Bs/O2P pairing antiparallel trans XI diff --git a/MCdata/1ajl_MC b/MCdata/1ajl_MC deleted file mode 100644 index 43e17ea89c187827b9a0203c0d4a16c3601973a9..0000000000000000000000000000000000000000 --- a/MCdata/1ajl_MC +++ /dev/null @@ -1,48 +0,0 @@ -Residue conformations ------------------------------------------- -A2 : G C3p_endo anti -A3 : G C3p_endo anti -A4 : U C3p_endo anti -A5 : A C3p_endo anti -A6 : A O4p_endo anti -A7 : U C2p_endo anti -A8 : A C2p_endo anti -A9 : A O4p_endo anti -A10 : G C3p_endo anti -A11 : C C3p_endo anti -A12 : U C3p_endo anti -A13 : C C3p_endo anti -B18 : G C3p_endo anti -B19 : A C3p_endo anti -B20 : G C3p_endo anti -B21 : U C3p_endo anti -B22 : A C3p_endo anti -B23 : C C3p_endo anti -B24 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A3-A4 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A12-A13 : adjacent_5p upward -B18-B19 : adjacent_5p upward -B19-B20 : adjacent_5p upward -B20-B21 : adjacent_5p upward -B22-B23 : adjacent_5p upward pairing -B23-B24 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A5-B22 : outward -Number of stackings = 11 -Number of adjacent stackings = 10 -Number of non adjacent stackings = 1 -Base-pairs ------------------------------------------------------ -A2-B21 : G-U Hh/O2P pairing -A2-B24 : G-C Ww/Ww pairing antiparallel cis XIX -A3-B23 : G-C Ww/Ww pairing antiparallel cis XIX -A4-B22 : U-A Ws/Wh pairing antiparallel cis one_hbond 46 -A6-A9 : A-A O2'/Bh pairing -A7-A8 : U-A O2P/Bh adjacent_5p pairing -A10-B21 : G-U Ww/Ws pairing antiparallel cis XXVIII -A11-B20 : C-G Ww/Ww pairing antiparallel cis -A12-B19 : U-A Ww/Ww pairing antiparallel cis XX -A13-B18 : C-G Ww/Ww pairing antiparallel cis XIX -B22-B23 : A-C O2P/Bh adjacent_5p upward pairing diff --git a/MCdata/1ajt_MC b/MCdata/1ajt_MC deleted file mode 100644 index aa0fa26c8482373463d2b870dd07d593f27203ad..0000000000000000000000000000000000000000 --- a/MCdata/1ajt_MC +++ /dev/null @@ -1,46 +0,0 @@ -Residue conformations ------------------------------------------- -A2 : G C3p_endo anti -A3 : G C3p_endo anti -A4 : U C3p_endo anti -A5 : A C3p_endo anti -A6 : A C3p_exo anti -A7 : U C2p_endo anti -A8 : A C2p_endo anti -A9 : A O4p_endo anti -A10 : G C3p_endo anti -A11 : C C2p_exo anti -A12 : U C3p_endo anti -A13 : C C3p_endo anti -B18 : G C3p_endo anti -B19 : A C3p_endo anti -B20 : G C3p_endo anti -B21 : U C3p_endo anti -B22 : A C3p_endo anti -B23 : C C3p_endo anti -B24 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A3-A4 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward pairing -A12-A13 : adjacent_5p upward -B18-B19 : adjacent_5p upward -B19-B20 : adjacent_5p upward -B20-B21 : adjacent_5p upward -B22-B23 : adjacent_5p upward pairing -B23-B24 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 10 -Number of adjacent stackings = 10 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A2-B24 : G-C Ww/Ww pairing antiparallel cis XIX -A3-B23 : G-C Ww/Ww pairing antiparallel cis -A4-B22 : U-A Ws/Wh pairing antiparallel cis one_hbond 46 -A7-A8 : U-A O2P/Bh O2P/Hh adjacent_5p pairing -A9-A10 : A-G O2'/C8 adjacent_5p upward pairing -A10-B21 : G-U Ww/Ws pairing antiparallel cis XXVIII -A11-B20 : C-G Ww/Ww pairing antiparallel cis XIX -A12-B19 : U-A Ww/Ww pairing antiparallel cis XX -A13-B18 : C-G Ww/Ww pairing antiparallel cis XIX -B22-B23 : A-C O2P/Bh adjacent_5p upward pairing diff --git a/MCdata/1aju_MC b/MCdata/1aju_MC deleted file mode 100644 index 3f5c9d4c1077f2b9e5f10a4deecacab947c1696e..0000000000000000000000000000000000000000 --- a/MCdata/1aju_MC +++ /dev/null @@ -1,1409 +0,0 @@ -Residue conformations ------------------------------------------- -A16 : G C3p_endo anti -A17 : G C2p_exo anti -A18 : C C3p_endo anti -A19 : C C2p_exo anti -A20 : A C3p_endo anti -A21 : G C3p_endo anti -A22 : A C3p_endo anti -A23 : U C2p_endo anti -A25 : U C2p_endo anti -A26 : G C3p_endo anti -A27 : A C3p_endo anti -A28 : G C3p_endo anti -A29 : C C3p_endo anti -A30 : C C2p_endo anti -A31 : U C2p_endo anti -A32 : G C2p_endo anti -A33 : G C2p_endo anti -A34 : G C2p_endo syn -A35 : A C3p_exo anti -A36 : G C2p_exo anti -A37 : C C3p_endo anti -A38 : U C3p_endo anti -A39 : C C3p_endo anti -A40 : U C3p_endo anti -A41 : C C3p_endo anti -A42 : U C3p_endo anti -A43 : G C3p_endo anti -A44 : G C3p_endo anti -A45 : C C3p_endo anti -A46 : C C3p_endo anti -A47 : ARG -Adjacent stackings ---------------------------------------------- -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A28-A29 : adjacent_5p upward -A29-A30 : adjacent_5p upward -A36-A37 : adjacent_5p upward -A38-A39 : adjacent_5p upward -A39-A40 : adjacent_5p upward -A41-A42 : adjacent_5p upward -A42-A43 : adjacent_5p upward -A43-A44 : adjacent_5p upward -A44-A45 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A20-A43 : outward -A30-A34 : inward pairing -A30-A36 : outward -Number of stackings = 19 -Number of adjacent stackings = 16 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -A16-A46 : G-C Ww/Ww pairing antiparallel cis XIX -A17-A45 : G-C Ww/Ww pairing antiparallel cis XIX -A18-A44 : C-G Ww/Ww pairing antiparallel cis -A19-A43 : C-G Ww/Ww pairing antiparallel cis XIX -A20-A42 : A-U Ww/Ww pairing antiparallel cis XX -A21-A41 : G-C Ww/Ww pairing antiparallel cis XIX -A22-A25 : A-U O2'/Hh pairing -A22-A40 : A-U Ww/Ww pairing antiparallel cis one_hbond -A26-A39 : G-C Ww/Ww pairing antiparallel cis XIX -A27-A38 : A-U Ww/Ww pairing antiparallel cis XX -A28-A37 : G-C Ww/Ww pairing antiparallel cis XIX -A29-A36 : C-G Ww/Ww pairing antiparallel cis XIX -A30-A34 : C-G O2'/Ss O2'/C8 inward pairing -A34-A35 : G-A O2'/C8 adjacent_5p pairing -A38-A47 : U-ARG pairing one_hbond -Residue conformations ------------------------------------------- -A16 : G C3p_endo anti -A17 : G C2p_exo anti -A18 : C C3p_endo anti -A19 : C C3p_endo anti -A20 : A C3p_endo anti -A21 : G C2p_exo anti -A22 : A C3p_endo anti -A23 : U C2p_endo anti -A25 : U C2p_endo anti -A26 : G C3p_endo anti -A27 : A C3p_endo anti -A28 : G C3p_endo anti -A29 : C C3p_endo anti -A30 : C C2p_endo anti -A31 : U C2p_endo anti -A32 : G C2p_endo anti -A33 : G C2p_endo anti -A34 : G C2p_endo syn -A35 : A C2p_endo anti -A36 : G C3p_endo anti -A37 : C C3p_endo anti -A38 : U C3p_endo anti -A39 : C C3p_endo anti -A40 : U C3p_endo anti -A41 : C C3p_endo anti -A42 : U C3p_endo anti -A43 : G C3p_endo anti -A44 : G C3p_endo anti -A45 : C C3p_endo anti -A46 : C C3p_endo anti -A47 : ARG -Adjacent stackings ---------------------------------------------- -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A28-A29 : adjacent_5p upward -A29-A30 : adjacent_5p upward -A36-A37 : adjacent_5p upward -A38-A39 : adjacent_5p upward -A39-A40 : adjacent_5p upward -A43-A44 : adjacent_5p upward -A44-A45 : adjacent_5p upward -A45-A46 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A20-A43 : outward -A21-A42 : outward -Number of stackings = 17 -Number of adjacent stackings = 15 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A16-A46 : G-C Ww/Ww pairing antiparallel cis XIX -A17-A45 : G-C Ww/Ww pairing antiparallel cis XIX -A18-A44 : C-G Ww/Ww pairing antiparallel cis XIX -A19-A43 : C-G Ww/Ww pairing antiparallel cis XIX -A20-A42 : A-U Ww/Ww pairing antiparallel cis XX -A21-A41 : G-C Ww/Ww pairing antiparallel cis XIX -A22-A40 : A-U Ww/Ww pairing antiparallel cis XX -A23-A27 : U-A Ws/Hh pairing parallel cis one_hbond -A25-A42 : U-U Hh/O2' pairing -A26-A39 : G-C Ww/Ww pairing antiparallel cis XIX -A27-A38 : A-U Ww/Ww pairing antiparallel cis XX -A28-A37 : G-C Ww/Ww pairing antiparallel cis XIX -A29-A36 : C-G Ww/Ww pairing antiparallel cis XIX -A31-A34 : U-G O2P/Bs pairing -Residue conformations ------------------------------------------- -A16 : G C3p_endo anti -A17 : G C3p_endo anti -A18 : C C3p_endo anti -A19 : C C2p_exo anti -A20 : A C3p_endo anti -A21 : G C3p_endo anti -A22 : A C3p_endo anti -A23 : U C2p_endo anti -A25 : U C2p_endo anti -A26 : G C3p_endo anti -A27 : A C3p_endo anti -A28 : G C3p_endo anti -A29 : C C3p_endo anti -A30 : C C2p_endo anti -A31 : U C2p_endo anti -A32 : G C2p_endo anti -A33 : G C2p_endo anti -A34 : G C2p_endo syn -A35 : A C3p_endo anti -A36 : G C3p_endo anti -A37 : C C3p_endo anti -A38 : U C3p_endo anti -A39 : C C3p_endo anti -A40 : U C3p_endo anti -A41 : C C3p_endo anti -A42 : U C3p_endo anti -A43 : G C2p_exo anti -A44 : G C3p_endo anti -A45 : C C3p_endo anti -A46 : C C3p_endo anti -A47 : ARG -Adjacent stackings ---------------------------------------------- -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A28-A29 : adjacent_5p upward -A29-A30 : adjacent_5p upward -A36-A37 : adjacent_5p upward -A37-A38 : adjacent_5p upward -A38-A39 : adjacent_5p upward -A39-A40 : adjacent_5p upward -A43-A44 : adjacent_5p upward -A44-A45 : adjacent_5p upward -A45-A46 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A19-A44 : outward -A20-A43 : outward -A30-A36 : outward -Number of stackings = 19 -Number of adjacent stackings = 16 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -A16-A46 : G-C Ww/Ww pairing antiparallel cis -A17-A45 : G-C Ww/Ww pairing antiparallel cis XIX -A18-A44 : C-G Ww/Ww pairing antiparallel cis XIX -A19-A43 : C-G Ww/Ww pairing antiparallel cis XIX -A20-A42 : A-U Ww/Ww pairing antiparallel cis one_hbond -A21-A25 : G-U O2'/Hh Ss/O2' pairing -A21-A26 : G-G Bs/O2P pairing -A21-A41 : G-C Ww/Ww pairing antiparallel cis XIX -A22-A40 : A-U Ww/Ww pairing antiparallel cis XX -A26-A39 : G-C Ww/Ww pairing antiparallel cis -A27-A38 : A-U Ww/Ww pairing antiparallel cis XX -A28-A37 : G-C Ww/Ww pairing antiparallel cis XIX -A29-A36 : C-G Ww/Ww pairing antiparallel cis XIX -A31-A34 : U-G O2P/Hh pairing -A32-A34 : G-G O2'/Ww pairing -A33-A34 : G-G O2'/Bs O2P/Ss adjacent_5p pairing -A34-A35 : G-A O2P/Bh adjacent_5p pairing -Residue conformations ------------------------------------------- -A16 : G C3p_endo anti -A17 : G C3p_endo anti -A18 : C C3p_endo anti -A19 : C C3p_endo anti -A20 : A C3p_endo anti -A21 : G C3p_endo anti -A22 : A C3p_endo anti -A23 : U C2p_endo anti -A25 : U C2p_endo anti -A26 : G C2p_exo anti -A27 : A C2p_exo anti -A28 : G C3p_endo anti -A29 : C C3p_endo anti -A30 : C C2p_endo anti -A31 : U C2p_endo anti -A32 : G C2p_endo anti -A33 : G C2p_endo anti -A34 : G C2p_endo syn -A35 : A C2p_endo anti -A36 : G C3p_endo anti -A37 : C C3p_endo anti -A38 : U C3p_endo anti -A39 : C C3p_endo anti -A40 : U C3p_endo anti -A41 : C C3p_endo anti -A42 : U C3p_endo anti -A43 : G C3p_endo anti -A44 : G C3p_endo anti -A45 : C C3p_endo anti -A46 : C C3p_endo anti -A47 : ARG -Adjacent stackings ---------------------------------------------- -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A28-A29 : adjacent_5p upward -A29-A30 : adjacent_5p upward -A36-A37 : adjacent_5p upward -A37-A38 : adjacent_5p upward -A38-A39 : adjacent_5p upward -A39-A40 : adjacent_5p upward -A43-A44 : adjacent_5p upward -A44-A45 : adjacent_5p upward -A45-A46 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A20-A43 : outward -Number of stackings = 16 -Number of adjacent stackings = 15 -Number of non adjacent stackings = 1 -Base-pairs ------------------------------------------------------ -A17-A45 : G-C Ww/Ww pairing antiparallel cis XIX -A18-A44 : C-G Ww/Ww pairing antiparallel cis XIX -A19-A43 : C-G Ww/Ww pairing antiparallel cis XIX -A20-A42 : A-U Ww/Ww pairing antiparallel cis XX -A21-A41 : G-C Ww/Ww pairing antiparallel cis XIX -A22-A40 : A-U Ww/Ww pairing antiparallel cis XX -A26-A39 : G-C Ww/Ww pairing antiparallel cis XIX -A27-A38 : A-U Ww/Ww pairing antiparallel cis XX -A28-A37 : G-C Ww/Ww pairing antiparallel cis XIX -A29-A36 : C-G Ww/Ww pairing antiparallel cis one_hbond -A30-A34 : C-G O2'/Hh pairing -A31-A34 : U-G O2P/Ww pairing -A32-A33 : G-G O2'/Hh adjacent_5p pairing -A32-A34 : G-G O2'/Ww O2'/Bs pairing -A34-A36 : G-G O2'/Hh O2'/C8 pairing -Residue conformations ------------------------------------------- -A16 : G C3p_endo anti -A17 : G C3p_endo anti -A18 : C C2p_exo anti -A19 : C C3p_endo anti -A20 : A C3p_endo anti -A21 : G C2p_exo anti -A22 : A C3p_endo anti -A23 : U C2p_endo anti -A25 : U C2p_endo anti -A26 : G C3p_endo anti -A27 : A C3p_endo anti -A28 : G C3p_endo anti -A29 : C C3p_endo anti -A30 : C C2p_endo anti -A31 : U C2p_endo anti -A32 : G C2p_endo anti -A33 : G C2p_endo anti -A34 : G C2p_endo syn -A35 : A C2p_endo anti -A36 : G C3p_endo anti -A37 : C C3p_endo anti -A38 : U C3p_endo anti -A39 : C C3p_endo anti -A40 : U C3p_endo anti -A41 : C C3p_endo anti -A42 : U C3p_endo anti -A43 : G C3p_endo anti -A44 : G C3p_endo anti -A45 : C C3p_endo anti -A46 : C C3p_endo anti -A47 : ARG -Adjacent stackings ---------------------------------------------- -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A28-A29 : adjacent_5p upward -A36-A37 : adjacent_5p upward -A38-A39 : adjacent_5p upward -A39-A40 : adjacent_5p upward -A40-A41 : adjacent_5p upward -A42-A43 : adjacent_5p upward -A43-A44 : adjacent_5p upward -A44-A45 : adjacent_5p upward -A45-A46 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A20-A43 : outward -A21-A42 : outward -A30-A36 : outward -Number of stackings = 20 -Number of adjacent stackings = 17 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -A16-A46 : G-C Ww/Ww pairing antiparallel cis XIX -A17-A45 : G-C Ww/Ww pairing antiparallel cis XIX -A18-A44 : C-G Ww/Ww pairing antiparallel cis XIX -A19-A43 : C-G Ww/Ww pairing antiparallel cis XIX -A20-A42 : A-U Ww/Ww pairing antiparallel cis XX -A21-A41 : G-C Ww/Ww pairing antiparallel cis XIX -A22-A40 : A-U Ww/Ww pairing antiparallel cis XX -A23-A27 : U-A Ww/Hh pairing parallel cis one_hbond -A26-A39 : G-C Ww/Ww pairing antiparallel cis XIX -A26-A40 : G-U Bs/O2' pairing -A27-A38 : A-U Ww/Ww pairing antiparallel cis XX -A28-A37 : G-C Ww/Ww pairing antiparallel cis XIX -A29-A36 : C-G Ww/Ww pairing antiparallel cis XIX -A30-A34 : C-G O2'/Ww pairing -A32-A33 : G-G Sw/Hh adjacent_5p pairing parallel cis one_hbond 109 -A33-A34 : G-G O2P/Bs adjacent_5p pairing -Residue conformations ------------------------------------------- -A16 : G C3p_endo anti -A17 : G C2p_exo anti -A18 : C C3p_endo anti -A19 : C C2p_exo anti -A20 : A C3p_endo anti -A21 : G C3p_endo anti -A22 : A C3p_endo anti -A23 : U C2p_endo anti -A25 : U C2p_endo anti -A26 : G C3p_endo anti -A27 : A C3p_endo anti -A28 : G C3p_endo anti -A29 : C C3p_endo anti -A30 : C C2p_endo anti -A31 : U C2p_endo anti -A32 : G C2p_endo anti -A33 : G C2p_endo anti -A34 : G C2p_endo anti -A35 : A C2p_endo anti -A36 : G C2p_exo anti -A37 : C C3p_endo anti -A38 : U C3p_endo anti -A39 : C C3p_endo anti -A40 : U C3p_endo anti -A41 : C C3p_endo anti -A42 : U C2p_exo anti -A43 : G C3p_endo anti -A44 : G C3p_endo anti -A45 : C C3p_endo anti -A46 : C C3p_endo anti -A47 : ARG -Adjacent stackings ---------------------------------------------- -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A28-A29 : adjacent_5p upward -A36-A37 : adjacent_5p upward -A37-A38 : adjacent_5p upward -A38-A39 : adjacent_5p upward -A39-A40 : adjacent_5p upward -A43-A44 : adjacent_5p upward -A44-A45 : adjacent_5p upward -A45-A46 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A20-A43 : outward -A30-A36 : outward -Number of stackings = 17 -Number of adjacent stackings = 15 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A16-A46 : G-C Ww/Ww pairing antiparallel cis -A17-A45 : G-C Ww/Ww pairing antiparallel cis XIX -A18-A44 : C-G Ww/Ww pairing antiparallel cis XIX -A19-A43 : C-G Ww/Ww pairing antiparallel cis XIX -A20-A42 : A-U Ww/Ww pairing antiparallel cis XX -A21-A41 : G-C Ww/Ww pairing antiparallel cis XIX -A22-A40 : A-U Ww/Ww pairing antiparallel cis XX -A23-A27 : U-A Ww/Hh pairing parallel cis XXIII -A26-A39 : G-C Ww/Ww pairing antiparallel cis XIX -A27-A38 : A-U Ww/Ww pairing antiparallel cis one_hbond -A28-A37 : G-C Ww/Ww pairing antiparallel cis -A29-A36 : C-G Ww/Ww pairing antiparallel cis XIX -A30-A34 : C-G O2'/Hh pairing -A34-A36 : G-G Ww/O2' pairing -A34-A37 : G-C Ww/O2P pairing -Residue conformations ------------------------------------------- -A16 : G C3p_endo anti -A17 : G C3p_endo anti -A18 : C C3p_endo anti -A19 : C C2p_exo anti -A20 : A C3p_endo anti -A21 : G C3p_endo anti -A22 : A C2p_exo anti -A23 : U C2p_endo anti -A25 : U C2p_endo anti -A26 : G C3p_endo anti -A27 : A C3p_endo anti -A28 : G C3p_endo anti -A29 : C C3p_endo anti -A30 : C C2p_endo anti -A31 : U C2p_endo anti -A32 : G C2p_endo anti -A33 : G C2p_endo anti -A34 : G C2p_endo syn -A35 : A C3p_exo anti -A36 : G C3p_endo anti -A37 : C C3p_endo anti -A38 : U C3p_endo anti -A39 : C C3p_endo anti -A40 : U C3p_endo anti -A41 : C C3p_endo anti -A42 : U C3p_endo anti -A43 : G C3p_endo anti -A44 : G C3p_endo anti -A45 : C C3p_endo anti -A46 : C C3p_endo anti -A47 : ARG -Adjacent stackings ---------------------------------------------- -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A28-A29 : adjacent_5p upward -A36-A37 : adjacent_5p upward -A38-A39 : adjacent_5p upward -A39-A40 : adjacent_5p upward -A40-A41 : adjacent_5p upward -A42-A43 : adjacent_5p upward -A43-A44 : adjacent_5p upward -A44-A45 : adjacent_5p upward -A45-A46 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A20-A43 : outward -Number of stackings = 17 -Number of adjacent stackings = 16 -Number of non adjacent stackings = 1 -Base-pairs ------------------------------------------------------ -A16-A46 : G-C Ww/Ww pairing antiparallel cis XIX -A17-A45 : G-C Ww/Ww pairing antiparallel cis XIX -A18-A44 : C-G Ww/Ww pairing antiparallel cis XIX -A19-A43 : C-G Ww/Ww pairing antiparallel cis XIX -A20-A42 : A-U Ww/Ww pairing antiparallel cis one_hbond -A21-A41 : G-C Ww/Ww pairing antiparallel cis XIX -A22-A40 : A-U Ww/Ww pairing antiparallel cis XX -A25-A42 : U-U Hh/O2' pairing -A26-A39 : G-C Ww/Ww pairing antiparallel cis XIX -A26-A40 : G-U Bs/O2' pairing -A27-A38 : A-U Ww/Ww pairing antiparallel cis XX -A28-A37 : G-C Ww/Ww pairing antiparallel cis XIX -A29-A36 : C-G Ww/Ww pairing antiparallel cis XIX -A30-A32 : C-G O2'/Hh pairing -A32-A34 : G-G Bs/O2P Ss/O2P pairing -A34-A36 : G-G Ss/O2' pairing -Residue conformations ------------------------------------------- -A16 : G C3p_endo anti -A17 : G C2p_exo anti -A18 : C C3p_endo anti -A19 : C C3p_endo anti -A20 : A C3p_endo anti -A21 : G C2p_exo anti -A22 : A C3p_endo anti -A23 : U C2p_endo anti -A25 : U C2p_endo anti -A26 : G C2p_exo anti -A27 : A C3p_endo anti -A28 : G C3p_endo anti -A29 : C C3p_endo anti -A30 : C C2p_endo syn -A31 : U C2p_endo anti -A32 : G C2p_endo anti -A33 : G C2p_endo anti -A34 : G C2p_endo syn -A35 : A C3p_exo anti -A36 : G C2p_exo anti -A37 : C C3p_endo anti -A38 : U C3p_endo anti -A39 : C C3p_endo anti -A40 : U C2p_exo anti -A41 : C C3p_endo anti -A42 : U C3p_endo anti -A43 : G C3p_endo anti -A44 : G C3p_endo anti -A45 : C C2p_exo anti -A46 : C C3p_endo anti -A47 : ARG -Adjacent stackings ---------------------------------------------- -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A28-A29 : adjacent_5p upward -A32-A33 : adjacent_5p outward -A36-A37 : adjacent_5p upward -A37-A38 : adjacent_5p upward -A38-A39 : adjacent_5p upward -A39-A40 : adjacent_5p upward -A41-A42 : adjacent_5p upward -A43-A44 : adjacent_5p upward -A44-A45 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A20-A43 : outward -Number of stackings = 17 -Number of adjacent stackings = 16 -Number of non adjacent stackings = 1 -Base-pairs ------------------------------------------------------ -A16-A46 : G-C Ww/Ww pairing antiparallel cis XIX -A17-A45 : G-C Ww/Ww pairing antiparallel cis XIX -A18-A44 : C-G Ww/Ww pairing antiparallel cis XIX -A19-A43 : C-G Ww/Ww pairing antiparallel cis XIX -A20-A42 : A-U Ww/Ww pairing antiparallel cis XX -A21-A41 : G-C Ww/Ww pairing antiparallel cis XIX -A22-A40 : A-U Ww/Ww pairing antiparallel cis XX -A25-A42 : U-U Hh/O2' pairing -A26-A39 : G-C Ww/Ww pairing antiparallel cis XIX -A26-A40 : G-U Bs/O2' pairing -A27-A38 : A-U Ww/Ww pairing antiparallel cis XX -A28-A37 : G-C Ww/Ww pairing antiparallel cis XIX -A29-A36 : C-G Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -A16 : G C3p_endo anti -A17 : G C2p_exo anti -A18 : C C3p_endo anti -A19 : C C2p_exo anti -A20 : A C3p_endo anti -A21 : G C2p_exo anti -A22 : A C3p_endo anti -A23 : U C2p_endo anti -A25 : U C2p_endo anti -A26 : G C3p_endo anti -A27 : A C3p_endo anti -A28 : G C3p_endo anti -A29 : C C2p_exo anti -A30 : C C2p_endo anti -A31 : U C2p_endo anti -A32 : G C3p_exo anti -A33 : G C2p_endo anti -A34 : G C2p_endo syn -A35 : A C3p_endo anti -A36 : G C2p_exo anti -A37 : C C3p_endo anti -A38 : U C3p_endo anti -A39 : C C3p_endo anti -A40 : U C3p_endo anti -A41 : C C3p_endo anti -A42 : U C3p_endo anti -A43 : G C3p_endo anti -A44 : G C3p_endo anti -A45 : C C3p_endo anti -A46 : C C3p_endo anti -A47 : ARG -Adjacent stackings ---------------------------------------------- -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A28-A29 : adjacent_5p upward -A36-A37 : adjacent_5p upward -A37-A38 : adjacent_5p upward -A38-A39 : adjacent_5p upward -A39-A40 : adjacent_5p upward -A40-A41 : adjacent_5p upward -A41-A42 : adjacent_5p upward -A42-A43 : adjacent_5p upward -A43-A44 : adjacent_5p upward -A44-A45 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A20-A43 : outward -A30-A36 : outward -Number of stackings = 19 -Number of adjacent stackings = 17 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A16-A46 : G-C Ww/Ww pairing antiparallel cis XIX -A17-A45 : G-C Ww/Ww pairing antiparallel cis XIX -A18-A44 : C-G Ww/Ww pairing antiparallel cis XIX -A19-A43 : C-G Ww/Ww pairing antiparallel cis XIX -A20-A42 : A-U Ww/Ww pairing antiparallel cis XX -A21-A41 : G-C Ww/Ww pairing antiparallel cis XIX -A22-A40 : A-U Ww/Ww pairing antiparallel cis XX -A23-A27 : U-A Ww/Hh pairing parallel cis one_hbond -A26-A39 : G-C Ww/Ww pairing antiparallel cis XIX -A27-A38 : A-U Ww/Ww pairing antiparallel cis XX -A28-A37 : G-C Ww/Ww pairing antiparallel cis XIX -A29-A36 : C-G Ww/Ww pairing antiparallel cis XIX -A30-A34 : C-G O2'/Ww pairing -A30-A35 : C-A O2'/Bh pairing -A32-A33 : G-G O2'/Hh adjacent_5p pairing -A33-A34 : G-G O2P/Bs adjacent_5p pairing -Residue conformations ------------------------------------------- -A16 : G C3p_endo anti -A17 : G C3p_endo anti -A18 : C C3p_endo anti -A19 : C C3p_endo anti -A20 : A C3p_endo anti -A21 : G C3p_endo anti -A22 : A C3p_endo anti -A23 : U C2p_endo anti -A25 : U C2p_endo anti -A26 : G C3p_endo anti -A27 : A C3p_endo anti -A28 : G C3p_endo anti -A29 : C C3p_endo anti -A30 : C C2p_endo anti -A31 : U C2p_endo anti -A32 : G C3p_exo anti -A33 : G C2p_endo anti -A34 : G C2p_endo anti -A35 : A C2p_exo anti -A36 : G C3p_endo anti -A37 : C C3p_endo anti -A38 : U C3p_endo anti -A39 : C C3p_endo anti -A40 : U C3p_endo anti -A41 : C C3p_endo anti -A42 : U C3p_endo anti -A43 : G C3p_endo anti -A44 : G C3p_endo anti -A45 : C C3p_endo anti -A46 : C C3p_endo anti -A47 : ARG -Adjacent stackings ---------------------------------------------- -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A28-A29 : adjacent_5p upward -A32-A33 : adjacent_5p outward pairing -A36-A37 : adjacent_5p upward -A38-A39 : adjacent_5p upward -A39-A40 : adjacent_5p upward -A40-A41 : adjacent_5p upward -A43-A44 : adjacent_5p upward -A44-A45 : adjacent_5p upward -A45-A46 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A20-A43 : outward -A34-A36 : outward -Number of stackings = 19 -Number of adjacent stackings = 17 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A16-A46 : G-C Ww/Ww pairing antiparallel cis XIX -A17-A45 : G-C Ww/Ww pairing antiparallel cis XIX -A18-A44 : C-G Ww/Ww pairing antiparallel cis XIX -A19-A43 : C-G Ww/Ww pairing antiparallel cis XIX -A20-A42 : A-U Ww/Ww pairing antiparallel cis XX -A21-A41 : G-C Ww/Ww pairing antiparallel cis XIX -A22-A40 : A-U Ww/Ww pairing antiparallel cis XX -A23-A27 : U-A Ws/Hh pairing parallel cis one_hbond -A26-A39 : G-C Ww/Ww pairing antiparallel cis XIX -A27-A38 : A-U Ww/Ww pairing antiparallel cis XX -A28-A37 : G-C Ww/Ww pairing antiparallel cis -A29-A30 : C-C Ss/Hh adjacent_5p pairing parallel cis one_hbond -A29-A36 : C-G Ww/Ww pairing antiparallel cis XIX -A30-A37 : C-C Ww/O2' Bh/O2' pairing -A32-A33 : G-G O2P/Bs adjacent_5p outward pairing -Residue conformations ------------------------------------------- -A16 : G C3p_endo anti -A17 : G C3p_endo anti -A18 : C C3p_endo anti -A19 : C C3p_endo anti -A20 : A C3p_endo anti -A21 : G C3p_endo anti -A22 : A C3p_endo anti -A23 : U C2p_endo anti -A25 : U C2p_endo anti -A26 : G C3p_endo anti -A27 : A C2p_exo anti -A28 : G C3p_endo anti -A29 : C C2p_exo anti -A30 : C C2p_endo anti -A31 : U C2p_endo anti -A32 : G C2p_endo anti -A33 : G C2p_endo anti -A34 : G C2p_endo syn -A35 : A C2p_endo anti -A36 : G C2p_exo anti -A37 : C C3p_endo anti -A38 : U C3p_endo anti -A39 : C C3p_endo anti -A40 : U C3p_endo anti -A41 : C C2p_exo anti -A42 : U C3p_endo anti -A43 : G C3p_endo anti -A44 : G C3p_endo anti -A45 : C C3p_endo anti -A46 : C C2p_exo anti -A47 : ARG -Adjacent stackings ---------------------------------------------- -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A28-A29 : adjacent_5p upward -A29-A30 : adjacent_5p upward -A36-A37 : adjacent_5p upward -A37-A38 : adjacent_5p upward -A38-A39 : adjacent_5p upward -A39-A40 : adjacent_5p upward -A43-A44 : adjacent_5p upward -A44-A45 : adjacent_5p upward -A45-A46 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A17-A46 : outward -A20-A43 : outward -A30-A36 : outward -Number of stackings = 20 -Number of adjacent stackings = 17 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -A16-A46 : G-C Ww/Ww pairing antiparallel cis XIX -A17-A45 : G-C Ww/Ww pairing antiparallel cis XIX -A18-A44 : C-G Ww/Ww pairing antiparallel cis XIX -A19-A43 : C-G Ww/Ww pairing antiparallel cis XIX -A20-A42 : A-U Ww/Ww pairing antiparallel cis XX -A21-A41 : G-C Ww/Ww pairing antiparallel cis XIX -A22-A40 : A-U Ww/Ww pairing antiparallel cis XX -A26-A39 : G-C Ww/Ww pairing antiparallel cis XIX -A27-A38 : A-U Ww/Ww pairing antiparallel cis XX -A28-A37 : G-C Ww/Ww pairing antiparallel cis XIX -A29-A36 : C-G Ww/Ww pairing antiparallel cis XIX -A33-A34 : G-G O2'/Ss adjacent_5p pairing -A34-A36 : G-G Ww/O2' Ss/O2' pairing -Residue conformations ------------------------------------------- -A16 : G C3p_endo anti -A17 : G C3p_endo anti -A18 : C C3p_endo anti -A19 : C C3p_endo anti -A20 : A C3p_endo anti -A21 : G C2p_exo anti -A22 : A C2p_exo anti -A23 : U C2p_endo anti -A25 : U C2p_endo anti -A26 : G C3p_endo anti -A27 : A C3p_endo anti -A28 : G C3p_endo anti -A29 : C C3p_endo anti -A30 : C C2p_endo syn -A31 : U C2p_endo anti -A32 : G C2p_endo anti -A33 : G C2p_endo anti -A34 : G C2p_endo syn -A35 : A C2p_exo anti -A36 : G C2p_exo anti -A37 : C C3p_endo anti -A38 : U C3p_endo anti -A39 : C C3p_endo anti -A40 : U C2p_exo anti -A41 : C C3p_endo anti -A42 : U C3p_endo anti -A43 : G C3p_endo anti -A44 : G C3p_endo anti -A45 : C C3p_endo anti -A46 : C C3p_endo anti -A47 : ARG -Adjacent stackings ---------------------------------------------- -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A28-A29 : adjacent_5p upward -A36-A37 : adjacent_5p upward -A37-A38 : adjacent_5p upward -A38-A39 : adjacent_5p upward -A39-A40 : adjacent_5p upward -A40-A41 : adjacent_5p upward -A43-A44 : adjacent_5p upward -A44-A45 : adjacent_5p upward -A45-A46 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A20-A43 : outward -Number of stackings = 17 -Number of adjacent stackings = 16 -Number of non adjacent stackings = 1 -Base-pairs ------------------------------------------------------ -A16-A46 : G-C Ww/Ww pairing antiparallel cis XIX -A17-A45 : G-C Ww/Ww pairing antiparallel cis XIX -A18-A44 : C-G Ww/Ww pairing antiparallel cis XIX -A19-A43 : C-G Ww/Ww pairing antiparallel cis XIX -A20-A42 : A-U Ww/Ww pairing antiparallel cis XX -A21-A41 : G-C Ww/Ww pairing antiparallel cis XIX -A22-A40 : A-U Ww/Ww pairing antiparallel cis XX -A26-A39 : G-C Ww/Ww pairing antiparallel cis XIX -A27-A38 : A-U Ww/Ww pairing antiparallel cis XX -A28-A37 : G-C Ww/Ww pairing antiparallel cis XIX -A29-A36 : C-G Ww/Ww pairing antiparallel cis XIX -A34-A36 : G-G O2'/C8 pairing -A35-A36 : A-G O2P/Hh adjacent_5p pairing -Residue conformations ------------------------------------------- -A16 : G C3p_endo anti -A17 : G C3p_endo anti -A18 : C C3p_endo anti -A19 : C C2p_exo anti -A20 : A C3p_endo anti -A21 : G C2p_exo anti -A22 : A C3p_endo anti -A23 : U C2p_endo anti -A25 : U C2p_endo anti -A26 : G C3p_endo anti -A27 : A C3p_endo anti -A28 : G C3p_endo anti -A29 : C C3p_endo anti -A30 : C C2p_endo anti -A31 : U C2p_endo anti -A32 : G C2p_endo anti -A33 : G C2p_endo anti -A34 : G C2p_endo anti -A35 : A C2p_exo anti -A36 : G C2p_exo anti -A37 : C C3p_endo anti -A38 : U C3p_endo anti -A39 : C C3p_endo anti -A40 : U C3p_endo anti -A41 : C C3p_endo anti -A42 : U C3p_endo anti -A43 : G C3p_endo anti -A44 : G C3p_endo anti -A45 : C C3p_endo anti -A46 : C C3p_endo anti -A47 : ARG -Adjacent stackings ---------------------------------------------- -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A28-A29 : adjacent_5p upward -A36-A37 : adjacent_5p upward -A38-A39 : adjacent_5p upward -A39-A40 : adjacent_5p upward -A40-A41 : adjacent_5p upward -A42-A43 : adjacent_5p upward -A43-A44 : adjacent_5p upward -A44-A45 : adjacent_5p upward -A45-A46 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A20-A43 : outward -Number of stackings = 16 -Number of adjacent stackings = 15 -Number of non adjacent stackings = 1 -Base-pairs ------------------------------------------------------ -A16-A45 : G-C Wh/Wh pairing antiparallel cis one_hbond -A16-A46 : G-C Ww/Ww pairing antiparallel cis XIX -A17-A45 : G-C Ww/Ww pairing antiparallel cis XIX -A18-A44 : C-G Ww/Ww pairing antiparallel cis XIX -A19-A43 : C-G Ww/Ww pairing antiparallel cis XIX -A20-A42 : A-U Ww/Ww pairing antiparallel cis one_hbond -A21-A41 : G-C Ww/Ww pairing antiparallel cis XIX -A22-A40 : A-U Ww/Ww pairing antiparallel cis XX -A25-A42 : U-U Hh/O2' pairing -A26-A39 : G-C Ww/Ww pairing antiparallel cis XIX -A27-A38 : A-U Ww/Ww pairing antiparallel cis XX -A28-A37 : G-C Ww/Ww pairing antiparallel cis XIX -A29-A36 : C-G Ww/Ww pairing antiparallel cis XIX -A34-A35 : G-A O2'/C8 adjacent_5p pairing -A38-A47 : U-ARG pairing one_hbond -Residue conformations ------------------------------------------- -A16 : G C3p_endo anti -A17 : G C3p_endo anti -A18 : C C3p_endo anti -A19 : C C3p_endo anti -A20 : A C3p_endo anti -A21 : G C3p_endo anti -A22 : A C2p_exo anti -A23 : U C2p_endo anti -A25 : U C2p_endo anti -A26 : G C2p_exo anti -A27 : A C2p_exo anti -A28 : G C3p_endo anti -A29 : C C3p_endo anti -A30 : C C2p_endo anti -A31 : U C2p_endo anti -A32 : G C2p_endo anti -A33 : G C2p_endo anti -A34 : G C2p_endo syn -A35 : A C2p_endo anti -A36 : G C2p_exo anti -A37 : C C3p_endo anti -A38 : U C3p_endo anti -A39 : C C3p_endo anti -A40 : U C3p_endo anti -A41 : C C2p_exo anti -A42 : U C3p_endo anti -A43 : G C3p_endo anti -A44 : G C3p_endo anti -A45 : C C3p_endo anti -A46 : C C3p_endo anti -A47 : ARG -Adjacent stackings ---------------------------------------------- -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A28-A29 : adjacent_5p upward -A36-A37 : adjacent_5p upward -A38-A39 : adjacent_5p upward -A39-A40 : adjacent_5p upward -A43-A44 : adjacent_5p upward -A44-A45 : adjacent_5p upward -A45-A46 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A20-A43 : outward -Number of stackings = 15 -Number of adjacent stackings = 14 -Number of non adjacent stackings = 1 -Base-pairs ------------------------------------------------------ -A16-A46 : G-C Ww/Ww pairing antiparallel cis XIX -A17-A45 : G-C Ww/Ww pairing antiparallel cis XIX -A18-A44 : C-G Ww/Ww pairing antiparallel cis XIX -A19-A43 : C-G Ww/Ww pairing antiparallel cis XIX -A20-A42 : A-U Ww/Ww pairing antiparallel cis XX -A21-A41 : G-C Ww/Ww pairing antiparallel cis XIX -A22-A40 : A-U Ww/Ww pairing antiparallel cis XX -A26-A39 : G-C Ww/Ww pairing antiparallel cis XIX -A27-A38 : A-U Ww/Ww pairing antiparallel cis XX -A28-A37 : G-C Ww/Ww pairing antiparallel cis XIX -A29-A36 : C-G Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -A16 : G C3p_endo anti -A17 : G C3p_endo anti -A18 : C C3p_endo anti -A19 : C C2p_exo anti -A20 : A C3p_endo anti -A21 : G C3p_endo anti -A22 : A C3p_endo anti -A23 : U C2p_endo anti -A25 : U C2p_endo anti -A26 : G C3p_endo anti -A27 : A C2p_exo anti -A28 : G C3p_endo anti -A29 : C C2p_exo anti -A30 : C C2p_endo syn -A31 : U C2p_endo anti -A32 : G C2p_endo anti -A33 : G C2p_endo anti -A34 : G C2p_endo syn -A35 : A C2p_endo anti -A36 : G C3p_endo anti -A37 : C C3p_endo anti -A38 : U C3p_endo anti -A39 : C C2p_exo anti -A40 : U C3p_endo anti -A41 : C C3p_endo anti -A42 : U C3p_endo anti -A43 : G C3p_endo anti -A44 : G C3p_endo anti -A45 : C C3p_endo anti -A46 : C C3p_endo anti -A47 : ARG -Adjacent stackings ---------------------------------------------- -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A28-A29 : adjacent_5p upward -A36-A37 : adjacent_5p upward -A37-A38 : adjacent_5p upward -A38-A39 : adjacent_5p upward -A39-A40 : adjacent_5p upward -A40-A41 : adjacent_5p upward -A41-A42 : adjacent_5p upward -A43-A44 : adjacent_5p upward -A44-A45 : adjacent_5p upward -A45-A46 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A19-A44 : outward -A20-A43 : outward -A23-A26 : downward -Number of stackings = 21 -Number of adjacent stackings = 18 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -A16-A46 : G-C Ww/Ww pairing antiparallel cis XIX -A17-A45 : G-C Ww/Ww pairing antiparallel cis XIX -A18-A44 : C-G Ww/Ww pairing antiparallel cis XIX -A19-A43 : C-G Ww/Ww pairing antiparallel cis XIX -A20-A42 : A-U Ww/Ww pairing antiparallel cis XX -A21-A41 : G-C Ww/Ww pairing antiparallel cis XIX -A22-A40 : A-U Ww/Ww pairing antiparallel cis XX -A25-A42 : U-U Hh/O2' pairing -A26-A39 : G-C Ww/Ww pairing antiparallel cis XIX -A27-A38 : A-U Ww/Ww pairing antiparallel cis XX -A28-A30 : G-C Ss/Hw O2'/Bh pairing antiparallel trans one_hbond -A28-A37 : G-C Ww/Ww pairing antiparallel cis XIX -A29-A30 : C-C O2'/Hh adjacent_5p pairing -A29-A36 : C-G Ww/Ww pairing antiparallel cis -A30-A36 : C-G O2'/Bs pairing -A31-A34 : U-G O2P/Hh pairing -A32-A34 : G-G O2P/Bs O2P/Ss O2P/Bs pairing -Residue conformations ------------------------------------------- -A16 : G C3p_endo anti -A17 : G C2p_exo anti -A18 : C C3p_endo anti -A19 : C C3p_endo anti -A20 : A C2p_exo anti -A21 : G C3p_endo anti -A22 : A C3p_endo anti -A23 : U C2p_endo anti -A25 : U C2p_endo anti -A26 : G C3p_endo anti -A27 : A C3p_endo anti -A28 : G C3p_endo anti -A29 : C C3p_endo anti -A30 : C C2p_endo anti -A31 : U C2p_endo anti -A32 : G C2p_endo anti -A33 : G C2p_endo anti -A34 : G C2p_endo syn -A35 : A C3p_exo anti -A36 : G C2p_exo anti -A37 : C C3p_endo anti -A38 : U C3p_endo anti -A39 : C C3p_endo anti -A40 : U C3p_endo anti -A41 : C C3p_endo anti -A42 : U C3p_endo anti -A43 : G C3p_endo anti -A44 : G C3p_endo anti -A45 : C C3p_endo anti -A46 : C C3p_endo anti -A47 : ARG -Adjacent stackings ---------------------------------------------- -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A28-A29 : adjacent_5p upward -A29-A30 : adjacent_5p upward -A36-A37 : adjacent_5p upward -A38-A39 : adjacent_5p upward -A39-A40 : adjacent_5p upward -A40-A41 : adjacent_5p upward -A41-A42 : adjacent_5p upward -A43-A44 : adjacent_5p upward -A44-A45 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A20-A43 : outward -A22-A26 : upward -Number of stackings = 19 -Number of adjacent stackings = 17 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A16-A46 : G-C Ww/Ww pairing antiparallel cis XIX -A17-A45 : G-C Ww/Ww pairing antiparallel cis XIX -A18-A44 : C-G Ww/Ww pairing antiparallel cis XIX -A19-A43 : C-G Ww/Ww pairing antiparallel cis XIX -A20-A42 : A-U Ww/Ww pairing antiparallel cis XX -A21-A41 : G-C Ww/Ww pairing antiparallel cis XIX -A22-A40 : A-U Ww/Ww pairing antiparallel cis XX -A26-A39 : G-C Ww/Ww pairing antiparallel cis XIX -A27-A38 : A-U Ww/Ww pairing antiparallel cis XX -A28-A37 : G-C Ww/Ww pairing antiparallel cis XIX -A29-A36 : C-G Ww/Ww pairing antiparallel cis -A31-A34 : U-G Hh/Hh O2P/Ss O2P/C8 pairing parallel trans one_hbond -A32-A33 : G-G Sw/Hw adjacent_5p pairing parallel cis one_hbond -A32-A34 : G-G O2'/Ww O2'/Bs pairing -A33-A34 : G-G O2'/Bs O2'/Ss adjacent_5p pairing -A33-A35 : G-A Ss/Wh O2'/Bh pairing parallel trans one_hbond -A34-A36 : G-G O2'/C8 pairing -Residue conformations ------------------------------------------- -A16 : G C3p_endo anti -A17 : G C3p_endo anti -A18 : C C3p_endo anti -A19 : C C2p_exo anti -A20 : A C3p_endo anti -A21 : G C3p_endo anti -A22 : A C2p_exo anti -A23 : U C2p_endo anti -A25 : U C2p_endo anti -A26 : G C3p_endo anti -A27 : A C3p_endo anti -A28 : G C3p_endo anti -A29 : C C2p_exo anti -A30 : C C2p_endo syn -A31 : U C2p_endo anti -A32 : G C3p_exo anti -A33 : G C2p_endo anti -A34 : G C2p_endo syn -A35 : A C2p_endo anti -A36 : G C2p_exo anti -A37 : C C3p_endo anti -A38 : U C3p_endo anti -A39 : C C3p_endo anti -A40 : U C3p_endo anti -A41 : C C3p_endo anti -A42 : U C3p_endo anti -A43 : G C2p_exo anti -A44 : G C3p_endo anti -A45 : C C3p_endo anti -A46 : C C3p_endo anti -A47 : ARG -Adjacent stackings ---------------------------------------------- -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A28-A29 : adjacent_5p upward -A36-A37 : adjacent_5p upward -A38-A39 : adjacent_5p upward -A39-A40 : adjacent_5p upward -A42-A43 : adjacent_5p upward -A43-A44 : adjacent_5p upward -A44-A45 : adjacent_5p upward -A45-A46 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A20-A43 : outward -A31-A34 : outward -Number of stackings = 16 -Number of adjacent stackings = 14 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A16-A46 : G-C Ww/Ww pairing antiparallel cis XIX -A17-A45 : G-C Ww/Ww pairing antiparallel cis XIX -A18-A44 : C-G Ww/Ww pairing antiparallel cis XIX -A19-A43 : C-G Ww/Ww pairing antiparallel cis XIX -A20-A42 : A-U Ww/Ww pairing antiparallel cis XX -A21-A41 : G-C Ww/Ww pairing antiparallel cis XIX -A22-A40 : A-U Ww/Ww pairing antiparallel cis XX -A26-A39 : G-C Ww/Ww pairing antiparallel cis XIX -A27-A38 : A-U Ww/Ww pairing antiparallel cis XX -A28-A37 : G-C Ww/Ww pairing antiparallel cis XIX -A29-A30 : C-C O2'/Hh adjacent_5p pairing -A29-A36 : C-G Ww/Ww pairing antiparallel cis one_hbond -A30-A36 : C-G O2'/Bs pairing -A33-A34 : G-G O2P/Bs adjacent_5p pairing -A34-A36 : G-G O2'/Ss O2'/C8 pairing -Residue conformations ------------------------------------------- -A16 : G C3p_endo anti -A17 : G C3p_endo anti -A18 : C C3p_endo anti -A19 : C C2p_exo anti -A20 : A C3p_endo anti -A21 : G C2p_exo anti -A22 : A C2p_exo anti -A23 : U C2p_endo anti -A25 : U C2p_endo anti -A26 : G C3p_endo anti -A27 : A C3p_endo anti -A28 : G C3p_endo anti -A29 : C C3p_endo anti -A30 : C C2p_endo syn -A31 : U C2p_endo anti -A32 : G C2p_endo anti -A33 : G C2p_endo anti -A34 : G C2p_endo anti -A35 : A C2p_exo syn -A36 : G C3p_endo anti -A37 : C C2p_exo anti -A38 : U C3p_endo anti -A39 : C C3p_endo anti -A40 : U C3p_endo anti -A41 : C C3p_endo anti -A42 : U C3p_endo anti -A43 : G C2p_exo anti -A44 : G C3p_endo anti -A45 : C C3p_endo anti -A46 : C C3p_endo anti -A47 : ARG -Adjacent stackings ---------------------------------------------- -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A28-A29 : adjacent_5p upward -A36-A37 : adjacent_5p upward -A38-A39 : adjacent_5p upward -A39-A40 : adjacent_5p upward -A40-A41 : adjacent_5p upward -A42-A43 : adjacent_5p upward -A43-A44 : adjacent_5p upward -A44-A45 : adjacent_5p upward -A45-A46 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A19-A44 : outward -A20-A43 : outward -Number of stackings = 17 -Number of adjacent stackings = 15 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A16-A46 : G-C Ww/Ww pairing antiparallel cis XIX -A17-A45 : G-C Ww/Ww pairing antiparallel cis XIX -A18-A44 : C-G Ww/Ww pairing antiparallel cis XIX -A19-A43 : C-G Ww/Ww pairing antiparallel cis XIX -A20-A42 : A-U Ww/Ww pairing antiparallel cis XX -A21-A41 : G-C Ww/Ww pairing antiparallel cis XIX -A22-A40 : A-U Ww/Ww pairing antiparallel cis XX -A26-A39 : G-C Ww/Ww pairing antiparallel cis XIX -A26-A40 : G-U Bs/O2' pairing -A27-A38 : A-U Ww/Ww pairing antiparallel cis XX -A28-A37 : G-C Ww/Ww pairing antiparallel cis XIX -A29-A36 : C-G Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -A16 : G C3p_endo anti -A17 : G C3p_endo anti -A18 : C C3p_endo anti -A19 : C C2p_exo anti -A20 : A C3p_endo anti -A21 : G C2p_exo anti -A22 : A C3p_endo anti -A23 : U C2p_endo anti -A25 : U C2p_endo anti -A26 : G C3p_endo anti -A27 : A C2p_exo anti -A28 : G C3p_endo anti -A29 : C C2p_exo anti -A30 : C C2p_endo syn -A31 : U C2p_endo anti -A32 : G C2p_endo anti -A33 : G C2p_endo anti -A34 : G C2p_endo anti -A35 : A C2p_endo anti -A36 : G C3p_endo anti -A37 : C C3p_endo anti -A38 : U C3p_endo anti -A39 : C C3p_endo anti -A40 : U C2p_exo anti -A41 : C C3p_endo anti -A42 : U C3p_endo anti -A43 : G C3p_endo anti -A44 : G C3p_endo anti -A45 : C C3p_endo anti -A46 : C C3p_endo anti -A47 : ARG -Adjacent stackings ---------------------------------------------- -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A28-A29 : adjacent_5p upward -A36-A37 : adjacent_5p upward -A38-A39 : adjacent_5p upward -A39-A40 : adjacent_5p upward -A43-A44 : adjacent_5p upward -A44-A45 : adjacent_5p upward -A45-A46 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A20-A43 : outward -A21-A42 : outward -Number of stackings = 15 -Number of adjacent stackings = 13 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A16-A46 : G-C Ww/Ww pairing antiparallel cis XIX -A17-A45 : G-C Ww/Ww pairing antiparallel cis XIX -A18-A44 : C-G Ww/Ww pairing antiparallel cis XIX -A19-A43 : C-G Ww/Ww pairing antiparallel cis XIX -A20-A42 : A-U Ww/Ww pairing antiparallel cis XX -A21-A41 : G-C Ww/Ww pairing antiparallel cis XIX -A22-A40 : A-U Ww/Ww pairing antiparallel cis XX -A26-A39 : G-C Ww/Ww pairing antiparallel cis XIX -A26-A40 : G-U Bs/O2' pairing -A27-A38 : A-U Ww/Ww pairing antiparallel cis XX -A28-A37 : G-C Ww/Ww pairing antiparallel cis XIX -A29-A30 : C-C O2'/Hh adjacent_5p pairing -A29-A36 : C-G Ww/Ww pairing antiparallel cis -A30-A36 : C-G O2'/Bs pairing -Residue conformations ------------------------------------------- -A16 : G C3p_endo anti -A17 : G C3p_endo anti -A18 : C C3p_endo anti -A19 : C C3p_endo anti -A20 : A C3p_endo anti -A21 : G C3p_endo anti -A22 : A C3p_endo anti -A23 : U C2p_endo anti -A25 : U C2p_endo anti -A26 : G C3p_endo anti -A27 : A C2p_exo anti -A28 : G C3p_endo anti -A29 : C C2p_exo anti -A30 : C C2p_endo syn -A31 : U C2p_endo anti -A32 : G C2p_endo anti -A33 : G C2p_endo anti -A34 : G C2p_endo syn -A35 : A C2p_exo anti -A36 : G C3p_endo anti -A37 : C C3p_endo anti -A38 : U C2p_exo anti -A39 : C C3p_endo anti -A40 : U C3p_endo anti -A41 : C C2p_exo anti -A42 : U C3p_endo anti -A43 : G C3p_endo anti -A44 : G C2p_exo anti -A45 : C C3p_endo anti -A46 : C C3p_endo anti -A47 : ARG -Adjacent stackings ---------------------------------------------- -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A28-A29 : adjacent_5p upward -A36-A37 : adjacent_5p upward -A38-A39 : adjacent_5p upward -A39-A40 : adjacent_5p upward -A40-A41 : adjacent_5p upward -A41-A42 : adjacent_5p upward -A42-A43 : adjacent_5p upward -A43-A44 : adjacent_5p upward -A44-A45 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A20-A43 : outward -Number of stackings = 18 -Number of adjacent stackings = 17 -Number of non adjacent stackings = 1 -Base-pairs ------------------------------------------------------ -A16-A46 : G-C Ww/Ww pairing antiparallel cis XIX -A17-A45 : G-C Ww/Ww pairing antiparallel cis XIX -A18-A44 : C-G Ww/Ww pairing antiparallel cis XIX -A19-A43 : C-G Ww/Ww pairing antiparallel cis XIX -A20-A42 : A-U Ww/Ww pairing antiparallel cis XX -A21-A41 : G-C Ww/Ww pairing antiparallel cis XIX -A22-A40 : A-U Ww/Ww pairing antiparallel cis XX -A25-A42 : U-U Hh/O2' pairing -A26-A39 : G-C Ww/Ww pairing antiparallel cis XIX -A27-A38 : A-U Ww/Ww pairing antiparallel cis XX -A28-A37 : G-C Ww/Ww pairing antiparallel cis XIX -A29-A30 : C-C O2'/Hh adjacent_5p pairing -A29-A36 : C-G Ww/Ww pairing antiparallel cis -A30-A31 : C-U O2P/Ww adjacent_5p pairing -A30-A36 : C-G O2'/Bs pairing -A34-A35 : G-A O2P/Hh adjacent_5p pairing diff --git a/MCdata/1akx_MC b/MCdata/1akx_MC deleted file mode 100644 index f212302f2c76782a0434125601fd38bd02ff8e75..0000000000000000000000000000000000000000 --- a/MCdata/1akx_MC +++ /dev/null @@ -1,68 +0,0 @@ -Residue conformations ------------------------------------------- -A16 : G C3p_endo anti -A17 : G C2p_exo anti -A18 : C C3p_endo anti -A19 : C C3p_endo anti -A20 : A C3p_endo anti -A21 : G C3p_endo anti -A22 : A C3p_endo anti -A23 : U C2p_endo anti -A25 : U C2p_endo anti -A26 : G C2p_exo anti -A27 : A C2p_exo anti -A28 : G C3p_endo anti -A29 : C C3p_endo anti -A30 : C C2p_endo anti -A31 : U C2p_endo anti -A32 : G C3p_exo anti -A33 : G C2p_endo anti -A34 : G C2p_endo syn -A35 : A C2p_endo anti -A36 : G C2p_exo anti -A37 : C C3p_endo anti -A38 : U C3p_endo anti -A39 : C C3p_endo anti -A40 : U C3p_endo anti -A41 : C C3p_endo anti -A42 : U C3p_endo anti -A43 : G C3p_endo anti -A44 : G C3p_endo anti -A45 : C C3p_endo anti -A46 : C C3p_endo anti -A47 : ARG -Adjacent stackings ---------------------------------------------- -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A28-A29 : adjacent_5p upward -A29-A30 : adjacent_5p upward -A36-A37 : adjacent_5p upward -A37-A38 : adjacent_5p upward -A38-A39 : adjacent_5p upward -A39-A40 : adjacent_5p upward -A40-A41 : adjacent_5p upward -A42-A43 : adjacent_5p upward -A43-A44 : adjacent_5p upward -A44-A45 : adjacent_5p upward -A45-A46 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A20-A43 : outward -Number of stackings = 18 -Number of adjacent stackings = 17 -Number of non adjacent stackings = 1 -Base-pairs ------------------------------------------------------ -A16-A46 : G-C Ww/Ww pairing antiparallel cis XIX -A17-A45 : G-C Ww/Ww pairing antiparallel cis XIX -A18-A44 : C-G Ww/Ww pairing antiparallel cis XIX -A19-A43 : C-G Ww/Ww pairing antiparallel cis XIX -A20-A42 : A-U Ww/Ww pairing antiparallel cis XX -A21-A41 : G-C Ww/Ww pairing antiparallel cis XIX -A22-A40 : A-U Ww/Ww pairing antiparallel cis XX -A26-A39 : G-C Ww/Ww pairing antiparallel cis XIX -A27-A38 : A-U Ww/Ww pairing antiparallel cis XX -A28-A37 : G-C Ww/Ww pairing antiparallel cis XIX -A29-A36 : C-G Ww/Ww pairing antiparallel cis XIX -A30-A31 : C-U O2P/Ww adjacent_5p pairing diff --git a/MCdata/1al5_MC b/MCdata/1al5_MC deleted file mode 100644 index a2ea30f88fb146fe6d3e986c0e962d98b865b7b1..0000000000000000000000000000000000000000 --- a/MCdata/1al5_MC +++ /dev/null @@ -1,794 +0,0 @@ -Residue conformations ------------------------------------------- -A1 : C C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : A C3p_endo anti -A5 : A C3p_endo anti -A6 : A C3p_endo anti -A7 : U C3p_endo anti -A8 : U C3p_endo anti -A9 : U C3p_endo anti -A10 : G C3p_endo anti -A11 : C C3p_endo anti -A12 : G C3p_endo anti -B1 : C C3p_endo anti -B2 : G C3p_endo anti -B3 : C C3p_endo anti -B4 : A C3p_endo anti -B5 : A C3p_endo anti -B6 : A C3p_endo anti -B7 : U C3p_endo anti -B8 : U C3p_endo anti -B9 : U C3p_endo anti -B10 : G C3p_endo anti -B11 : C C3p_endo anti -B12 : G C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -B1-B2 : adjacent_5p upward -B2-B3 : adjacent_5p upward -B3-B4 : adjacent_5p upward -B4-B5 : adjacent_5p upward -B5-B6 : adjacent_5p upward -B6-B7 : adjacent_5p upward -B10-B11 : adjacent_5p upward -B11-B12 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A2-B12 : outward -A4-B10 : outward -A10-B4 : outward -A12-B2 : outward -Number of stackings = 23 -Number of adjacent stackings = 19 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A1-B12 : C-G Ww/Ww pairing antiparallel cis XIX -A2-B11 : G-C Ww/Ww pairing antiparallel cis XIX -A3-B10 : C-G Ww/Ww pairing antiparallel cis XIX -A4-B9 : A-U Ww/Ww pairing antiparallel cis XX -A5-B8 : A-U Ww/Ww pairing antiparallel cis XX -A6-B7 : A-U Ww/Ww pairing antiparallel cis XX -A7-B6 : U-A Ww/Ww pairing antiparallel cis XX -A8-B5 : U-A Ww/Ww pairing antiparallel cis XX -A9-B4 : U-A Ww/Ww pairing antiparallel cis XX -A10-B3 : G-C Ww/Ww pairing antiparallel cis XIX -A11-B2 : C-G Ww/Ww pairing antiparallel cis XIX -A12-B1 : G-C Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -A1 : C C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : A C3p_endo anti -A5 : A C3p_endo anti -A6 : A C3p_endo anti -A7 : U C3p_endo anti -A8 : U C3p_endo anti -A9 : U C3p_endo anti -A10 : G C3p_endo anti -A11 : C C3p_endo anti -A12 : G C3p_endo anti -B1 : C C3p_endo anti -B2 : G C3p_endo anti -B3 : C C3p_endo anti -B4 : A C3p_endo anti -B5 : A C3p_endo anti -B6 : A C3p_endo anti -B7 : U C3p_endo anti -B8 : U C3p_endo anti -B9 : U C3p_endo anti -B10 : G C3p_endo anti -B11 : C C3p_endo anti -B12 : G C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -B1-B2 : adjacent_5p upward -B2-B3 : adjacent_5p upward -B3-B4 : adjacent_5p upward -B4-B5 : adjacent_5p upward -B5-B6 : adjacent_5p upward -B6-B7 : adjacent_5p upward -B10-B11 : adjacent_5p upward -B11-B12 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A2-B12 : outward -A4-B10 : outward -A10-B4 : outward -A12-B2 : outward -Number of stackings = 23 -Number of adjacent stackings = 19 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A1-B12 : C-G Ww/Ww pairing antiparallel cis XIX -A2-B11 : G-C Ww/Ww pairing antiparallel cis XIX -A3-B10 : C-G Ww/Ww pairing antiparallel cis XIX -A4-B9 : A-U Ww/Ww pairing antiparallel cis XX -A5-B8 : A-U Ww/Ww pairing antiparallel cis XX -A6-B7 : A-U Ww/Ww pairing antiparallel cis XX -A7-B6 : U-A Ww/Ww pairing antiparallel cis XX -A8-B5 : U-A Ww/Ww pairing antiparallel cis XX -A9-B4 : U-A Ww/Ww pairing antiparallel cis XX -A10-B3 : G-C Ww/Ww pairing antiparallel cis XIX -A11-B2 : C-G Ww/Ww pairing antiparallel cis XIX -A12-B1 : G-C Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -A1 : C C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : A C3p_endo anti -A5 : A C3p_endo anti -A6 : A C3p_endo anti -A7 : U C3p_endo anti -A8 : U C3p_endo anti -A9 : U C3p_endo anti -A10 : G C3p_endo anti -A11 : C C3p_endo anti -A12 : G C3p_endo anti -B1 : C C3p_endo anti -B2 : G C3p_endo anti -B3 : C C3p_endo anti -B4 : A C3p_endo anti -B5 : A C3p_endo anti -B6 : A C3p_endo anti -B7 : U C3p_endo anti -B8 : U C3p_endo anti -B9 : U C3p_endo anti -B10 : G C3p_endo anti -B11 : C C3p_endo anti -B12 : G C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -B1-B2 : adjacent_5p upward -B2-B3 : adjacent_5p upward -B3-B4 : adjacent_5p upward -B4-B5 : adjacent_5p upward -B5-B6 : adjacent_5p upward -B6-B7 : adjacent_5p upward -B10-B11 : adjacent_5p upward -B11-B12 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A2-B12 : outward -A4-B10 : outward -A10-B4 : outward -A12-B2 : outward -Number of stackings = 23 -Number of adjacent stackings = 19 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A1-B12 : C-G Ww/Ww pairing antiparallel cis XIX -A2-B11 : G-C Ww/Ww pairing antiparallel cis XIX -A3-B10 : C-G Ww/Ww pairing antiparallel cis XIX -A4-B9 : A-U Ww/Ww pairing antiparallel cis XX -A5-B8 : A-U Ww/Ww pairing antiparallel cis XX -A6-B7 : A-U Ww/Ww pairing antiparallel cis XX -A7-B6 : U-A Ww/Ww pairing antiparallel cis XX -A8-B5 : U-A Ww/Ww pairing antiparallel cis XX -A9-B4 : U-A Ww/Ww pairing antiparallel cis XX -A10-B3 : G-C Ww/Ww pairing antiparallel cis XIX -A11-B2 : C-G Ww/Ww pairing antiparallel cis XIX -A12-B1 : G-C Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -A1 : C C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : A C3p_endo anti -A5 : A C3p_endo anti -A6 : A C3p_endo anti -A7 : U C3p_endo anti -A8 : U C3p_endo anti -A9 : U C3p_endo anti -A10 : G C3p_endo anti -A11 : C C3p_endo anti -A12 : G C3p_endo anti -B1 : C C3p_endo anti -B2 : G C3p_endo anti -B3 : C C3p_endo anti -B4 : A C3p_endo anti -B5 : A C3p_endo anti -B6 : A C3p_endo anti -B7 : U C3p_endo anti -B8 : U C3p_endo anti -B9 : U C3p_endo anti -B10 : G C3p_endo anti -B11 : C C3p_endo anti -B12 : G C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -B1-B2 : adjacent_5p upward -B2-B3 : adjacent_5p upward -B3-B4 : adjacent_5p upward -B4-B5 : adjacent_5p upward -B5-B6 : adjacent_5p upward -B6-B7 : adjacent_5p upward -B7-B8 : adjacent_5p upward -B8-B9 : adjacent_5p upward -B9-B10 : adjacent_5p upward -B10-B11 : adjacent_5p upward -B11-B12 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A2-B12 : outward -A4-B10 : outward -A10-B4 : outward -A12-B2 : outward -Number of stackings = 26 -Number of adjacent stackings = 22 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A1-B12 : C-G Ww/Ww pairing antiparallel cis XIX -A2-B11 : G-C Ww/Ww pairing antiparallel cis XIX -A3-B10 : C-G Ww/Ww pairing antiparallel cis XIX -A4-B9 : A-U Ww/Ww pairing antiparallel cis XX -A5-B8 : A-U Ww/Ww pairing antiparallel cis XX -A6-B7 : A-U Ww/Ww pairing antiparallel cis XX -A7-B6 : U-A Ww/Ww pairing antiparallel cis XX -A8-B5 : U-A Ww/Ww pairing antiparallel cis XX -A9-B4 : U-A Ww/Ww pairing antiparallel cis XX -A10-B3 : G-C Ww/Ww pairing antiparallel cis XIX -A11-B2 : C-G Ww/Ww pairing antiparallel cis XIX -A12-B1 : G-C Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -A1 : C C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : A C3p_endo anti -A5 : A C3p_endo anti -A6 : A C3p_endo anti -A7 : U C3p_endo anti -A8 : U C3p_endo anti -A9 : U C3p_endo anti -A10 : G C3p_endo anti -A11 : C C3p_endo anti -A12 : G C3p_endo anti -B1 : C C3p_endo anti -B2 : G C3p_endo anti -B3 : C C3p_endo anti -B4 : A C3p_endo anti -B5 : A C3p_endo anti -B6 : A C2p_exo anti -B7 : U C3p_endo anti -B8 : U C3p_endo anti -B9 : U C3p_endo anti -B10 : G C3p_endo anti -B11 : C C3p_endo anti -B12 : G C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -B1-B2 : adjacent_5p upward -B2-B3 : adjacent_5p upward -B3-B4 : adjacent_5p upward -B4-B5 : adjacent_5p upward -B5-B6 : adjacent_5p upward -B6-B7 : adjacent_5p upward -B8-B9 : adjacent_5p upward -B9-B10 : adjacent_5p upward -B10-B11 : adjacent_5p upward -B11-B12 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A2-B12 : outward -A4-B10 : outward -A10-B4 : outward -A12-B2 : outward -Number of stackings = 24 -Number of adjacent stackings = 20 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A1-B12 : C-G Ww/Ww pairing antiparallel cis XIX -A2-B11 : G-C Ww/Ww pairing antiparallel cis XIX -A3-B10 : C-G Ww/Ww pairing antiparallel cis XIX -A4-B9 : A-U Ww/Ww pairing antiparallel cis XX -A5-B8 : A-U Ww/Ww pairing antiparallel cis XX -A6-B7 : A-U Ww/Ww pairing antiparallel cis XX -A7-B6 : U-A Ww/Ww pairing antiparallel cis XX -A8-B5 : U-A Ww/Ww pairing antiparallel cis XX -A9-B4 : U-A Ww/Ww pairing antiparallel cis XX -A10-B3 : G-C Ww/Ww pairing antiparallel cis XIX -A11-B2 : C-G Ww/Ww pairing antiparallel cis XIX -A12-B1 : G-C Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -A1 : C C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : A C3p_endo anti -A5 : A C3p_endo anti -A6 : A C3p_endo anti -A7 : U C3p_endo anti -A8 : U C3p_endo anti -A9 : U C3p_endo anti -A10 : G C3p_endo anti -A11 : C C3p_endo anti -A12 : G C3p_endo anti -B1 : C C3p_endo anti -B2 : G C3p_endo anti -B3 : C C3p_endo anti -B4 : A C3p_endo anti -B5 : A C3p_endo anti -B6 : A C3p_endo anti -B7 : U C3p_endo anti -B8 : U C3p_endo anti -B9 : U C3p_endo anti -B10 : G C3p_endo anti -B11 : C C3p_endo anti -B12 : G C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -B1-B2 : adjacent_5p upward -B2-B3 : adjacent_5p upward -B3-B4 : adjacent_5p upward -B4-B5 : adjacent_5p upward -B5-B6 : adjacent_5p upward -B6-B7 : adjacent_5p upward -B8-B9 : adjacent_5p upward -B9-B10 : adjacent_5p upward -B10-B11 : adjacent_5p upward -B11-B12 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A2-B12 : outward -A4-B10 : outward -A10-B4 : outward -A12-B2 : outward -Number of stackings = 24 -Number of adjacent stackings = 20 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A1-B12 : C-G Ww/Ww pairing antiparallel cis XIX -A2-B11 : G-C Ww/Ww pairing antiparallel cis XIX -A3-B10 : C-G Ww/Ww pairing antiparallel cis XIX -A4-B9 : A-U Ww/Ww pairing antiparallel cis XX -A5-B8 : A-U Ww/Ww pairing antiparallel cis XX -A6-B7 : A-U Ww/Ww pairing antiparallel cis XX -A7-B6 : U-A Ww/Ww pairing antiparallel cis XX -A8-B5 : U-A Ww/Ww pairing antiparallel cis XX -A9-B4 : U-A Ww/Ww pairing antiparallel cis XX -A10-B3 : G-C Ww/Ww pairing antiparallel cis XIX -A11-B2 : C-G Ww/Ww pairing antiparallel cis XIX -A12-B1 : G-C Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -A1 : C C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : A C3p_endo anti -A5 : A C3p_endo anti -A6 : A C3p_endo anti -A7 : U C3p_endo anti -A8 : U C3p_endo anti -A9 : U C3p_endo anti -A10 : G C3p_endo anti -A11 : C C3p_endo anti -A12 : G C3p_endo anti -B1 : C C3p_endo anti -B2 : G C3p_endo anti -B3 : C C3p_endo anti -B4 : A C3p_endo anti -B5 : A C3p_endo anti -B6 : A C2p_exo anti -B7 : U C3p_endo anti -B8 : U C3p_endo anti -B9 : U C3p_endo anti -B10 : G C3p_endo anti -B11 : C C3p_endo anti -B12 : G C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -B1-B2 : adjacent_5p upward -B2-B3 : adjacent_5p upward -B3-B4 : adjacent_5p upward -B4-B5 : adjacent_5p upward -B5-B6 : adjacent_5p upward -B6-B7 : adjacent_5p upward -B9-B10 : adjacent_5p upward -B10-B11 : adjacent_5p upward -B11-B12 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A2-B12 : outward -A4-B10 : outward -A10-B4 : outward -A12-B2 : outward -Number of stackings = 21 -Number of adjacent stackings = 17 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A1-B12 : C-G Ww/Ww pairing antiparallel cis XIX -A2-B11 : G-C Ww/Ww pairing antiparallel cis XIX -A3-B10 : C-G Ww/Ww pairing antiparallel cis XIX -A4-B9 : A-U Ww/Ww pairing antiparallel cis XX -A5-B8 : A-U Ww/Ww pairing antiparallel cis XX -A6-B7 : A-U Ww/Ww pairing antiparallel cis XX -A7-B6 : U-A Ww/Ww pairing antiparallel cis XX -A8-B5 : U-A Ww/Ww pairing antiparallel cis XX -A9-B4 : U-A Ww/Ww pairing antiparallel cis XX -A10-B3 : G-C Ww/Ww pairing antiparallel cis XIX -A11-B2 : C-G Ww/Ww pairing antiparallel cis XIX -A12-B1 : G-C Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -A1 : C C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : A C3p_endo anti -A5 : A C3p_endo anti -A6 : A C3p_endo anti -A7 : U C3p_endo anti -A8 : U C3p_endo anti -A9 : U C3p_endo anti -A10 : G C3p_endo anti -A11 : C C3p_endo anti -A12 : G C3p_endo anti -B1 : C C3p_endo anti -B2 : G C3p_endo anti -B3 : C C3p_endo anti -B4 : A C3p_endo anti -B5 : A C3p_endo anti -B6 : A C2p_exo anti -B7 : U C3p_endo anti -B8 : U C3p_endo anti -B9 : U C3p_endo anti -B10 : G C3p_endo anti -B11 : C C3p_endo anti -B12 : G C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -B1-B2 : adjacent_5p upward -B2-B3 : adjacent_5p upward -B3-B4 : adjacent_5p upward -B4-B5 : adjacent_5p upward -B5-B6 : adjacent_5p upward -B6-B7 : adjacent_5p upward -B9-B10 : adjacent_5p upward -B10-B11 : adjacent_5p upward -B11-B12 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A2-B12 : outward -A4-B10 : outward -A10-B4 : outward -A12-B2 : outward -Number of stackings = 21 -Number of adjacent stackings = 17 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A1-B12 : C-G Ww/Ww pairing antiparallel cis XIX -A2-B11 : G-C Ww/Ww pairing antiparallel cis XIX -A3-B10 : C-G Ww/Ww pairing antiparallel cis XIX -A4-B9 : A-U Ww/Ww pairing antiparallel cis XX -A5-B8 : A-U Ww/Ww pairing antiparallel cis XX -A6-B7 : A-U Ww/Ww pairing antiparallel cis XX -A7-B6 : U-A Ww/Ww pairing antiparallel cis XX -A8-B5 : U-A Ww/Ww pairing antiparallel cis XX -A9-B4 : U-A Ww/Ww pairing antiparallel cis XX -A10-B3 : G-C Ww/Ww pairing antiparallel cis XIX -A11-B2 : C-G Ww/Ww pairing antiparallel cis XIX -A12-B1 : G-C Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -A1 : C C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : A C3p_endo anti -A5 : A C3p_endo anti -A6 : A C2p_exo anti -A7 : U C3p_endo anti -A8 : U C3p_endo anti -A9 : U C3p_endo anti -A10 : G C3p_endo anti -A11 : C C3p_endo anti -A12 : G C3p_endo anti -B1 : C C3p_endo anti -B2 : G C3p_endo anti -B3 : C C3p_endo anti -B4 : A C3p_endo anti -B5 : A C3p_endo anti -B6 : A C2p_exo anti -B7 : U C3p_endo anti -B8 : U C3p_endo anti -B9 : U C3p_endo anti -B10 : G C3p_endo anti -B11 : C C3p_endo anti -B12 : G C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -B1-B2 : adjacent_5p upward -B2-B3 : adjacent_5p upward -B3-B4 : adjacent_5p upward -B4-B5 : adjacent_5p upward -B5-B6 : adjacent_5p upward -B6-B7 : adjacent_5p upward -B8-B9 : adjacent_5p upward -B9-B10 : adjacent_5p upward -B10-B11 : adjacent_5p upward -B11-B12 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A2-B12 : outward -A4-B10 : outward -A10-B4 : outward -A12-B2 : outward -Number of stackings = 24 -Number of adjacent stackings = 20 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A1-B12 : C-G Ww/Ww pairing antiparallel cis XIX -A2-B11 : G-C Ww/Ww pairing antiparallel cis XIX -A3-B10 : C-G Ww/Ww pairing antiparallel cis XIX -A4-B9 : A-U Ww/Ww pairing antiparallel cis XX -A5-B8 : A-U Ww/Ww pairing antiparallel cis XX -A6-B7 : A-U Ww/Ww pairing antiparallel cis XX -A7-B6 : U-A Ww/Ww pairing antiparallel cis XX -A8-B5 : U-A Ww/Ww pairing antiparallel cis XX -A9-B4 : U-A Ww/Ww pairing antiparallel cis XX -A10-B3 : G-C Ww/Ww pairing antiparallel cis XIX -A11-B2 : C-G Ww/Ww pairing antiparallel cis XIX -A12-B1 : G-C Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -A1 : C C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : A C3p_endo anti -A5 : A C3p_endo anti -A6 : A C2p_exo anti -A7 : U C3p_endo anti -A8 : U C3p_endo anti -A9 : U C3p_endo anti -A10 : G C3p_endo anti -A11 : C C3p_endo anti -A12 : G C3p_endo anti -B1 : C C3p_endo anti -B2 : G C3p_endo anti -B3 : C C3p_endo anti -B4 : A C3p_endo anti -B5 : A C3p_endo anti -B6 : A C2p_exo anti -B7 : U C3p_endo anti -B8 : U C3p_endo anti -B9 : U C3p_endo anti -B10 : G C3p_endo anti -B11 : C C3p_endo anti -B12 : G C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -B1-B2 : adjacent_5p upward -B2-B3 : adjacent_5p upward -B3-B4 : adjacent_5p upward -B4-B5 : adjacent_5p upward -B5-B6 : adjacent_5p upward -B6-B7 : adjacent_5p upward -B9-B10 : adjacent_5p upward -B10-B11 : adjacent_5p upward -B11-B12 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A2-B12 : outward -A4-B10 : outward -A10-B4 : outward -A12-B2 : outward -Number of stackings = 23 -Number of adjacent stackings = 19 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A1-B12 : C-G Ww/Ww pairing antiparallel cis XIX -A2-B11 : G-C Ww/Ww pairing antiparallel cis XIX -A3-B10 : C-G Ww/Ww pairing antiparallel cis XIX -A4-B9 : A-U Ww/Ww pairing antiparallel cis XX -A5-B8 : A-U Ww/Ww pairing antiparallel cis XX -A6-B7 : A-U Ww/Ww pairing antiparallel cis XX -A7-B6 : U-A Ww/Ww pairing antiparallel cis XX -A8-B5 : U-A Ww/Ww pairing antiparallel cis XX -A9-B4 : U-A Ww/Ww pairing antiparallel cis XX -A10-B3 : G-C Ww/Ww pairing antiparallel cis XIX -A11-B2 : C-G Ww/Ww pairing antiparallel cis XIX -A12-B1 : G-C Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -A1 : C C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : A C3p_endo anti -A5 : A C3p_endo anti -A6 : A C3p_endo anti -A7 : U C3p_endo anti -A8 : U C3p_endo anti -A9 : U C3p_endo anti -A10 : G C3p_endo anti -A11 : C C3p_endo anti -A12 : G C3p_endo anti -B1 : C C3p_endo anti -B2 : G C3p_endo anti -B3 : C C3p_endo anti -B4 : A C3p_endo anti -B5 : A C3p_endo anti -B6 : A C2p_exo anti -B7 : U C3p_endo anti -B8 : U C3p_endo anti -B9 : U C3p_endo anti -B10 : G C3p_endo anti -B11 : C C3p_endo anti -B12 : G C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -B1-B2 : adjacent_5p upward -B2-B3 : adjacent_5p upward -B3-B4 : adjacent_5p upward -B4-B5 : adjacent_5p upward -B5-B6 : adjacent_5p upward -B6-B7 : adjacent_5p upward -B8-B9 : adjacent_5p upward -B9-B10 : adjacent_5p upward -B10-B11 : adjacent_5p upward -B11-B12 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A2-B12 : outward -A4-B10 : outward -A10-B4 : outward -A12-B2 : outward -Number of stackings = 24 -Number of adjacent stackings = 20 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A1-B12 : C-G Ww/Ww pairing antiparallel cis XIX -A2-B11 : G-C Ww/Ww pairing antiparallel cis XIX -A3-B10 : C-G Ww/Ww pairing antiparallel cis XIX -A4-B9 : A-U Ww/Ww pairing antiparallel cis XX -A5-B8 : A-U Ww/Ww pairing antiparallel cis XX -A6-B7 : A-U Ww/Ww pairing antiparallel cis XX -A7-B6 : U-A Ww/Ww pairing antiparallel cis XX -A8-B5 : U-A Ww/Ww pairing antiparallel cis XX -A9-B4 : U-A Ww/Ww pairing antiparallel cis XX -A10-B3 : G-C Ww/Ww pairing antiparallel cis XIX -A11-B2 : C-G Ww/Ww pairing antiparallel cis XIX -A12-B1 : G-C Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -A1 : C C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : A C3p_endo anti -A5 : A C3p_endo anti -A6 : A C2p_exo anti -A7 : U C3p_endo anti -A8 : U C3p_endo anti -A9 : U C3p_endo anti -A10 : G C3p_endo anti -A11 : C C3p_endo anti -A12 : G C3p_endo anti -B1 : C C3p_endo anti -B2 : G C3p_endo anti -B3 : C C3p_endo anti -B4 : A C3p_endo anti -B5 : A C3p_endo anti -B6 : A C3p_endo anti -B7 : U C3p_endo anti -B8 : U C3p_endo anti -B9 : U C3p_endo anti -B10 : G C3p_endo anti -B11 : C C3p_endo anti -B12 : G C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -B1-B2 : adjacent_5p upward -B2-B3 : adjacent_5p upward -B3-B4 : adjacent_5p upward -B4-B5 : adjacent_5p upward -B5-B6 : adjacent_5p upward -B6-B7 : adjacent_5p upward -B8-B9 : adjacent_5p upward -B9-B10 : adjacent_5p upward -B10-B11 : adjacent_5p upward -B11-B12 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A2-B12 : outward -A4-B10 : outward -A10-B4 : outward -A12-B2 : outward -Number of stackings = 22 -Number of adjacent stackings = 18 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A1-B12 : C-G Ww/Ww pairing antiparallel cis XIX -A2-B11 : G-C Ww/Ww pairing antiparallel cis XIX -A3-B10 : C-G Ww/Ww pairing antiparallel cis XIX -A4-B9 : A-U Ww/Ww pairing antiparallel cis XX -A5-B8 : A-U Ww/Ww pairing antiparallel cis XX -A6-B7 : A-U Ww/Ww pairing antiparallel cis XX -A7-B6 : U-A Ww/Ww pairing antiparallel cis XX -A8-B5 : U-A Ww/Ww pairing antiparallel cis XX -A9-B4 : U-A Ww/Ww pairing antiparallel cis XX -A10-B3 : G-C Ww/Ww pairing antiparallel cis XIX -A11-B2 : C-G Ww/Ww pairing antiparallel cis XIX -A12-B1 : G-C Ww/Ww pairing antiparallel cis XIX diff --git a/MCdata/1am0_MC b/MCdata/1am0_MC deleted file mode 100644 index 39b935208f7c6995a44751ccfd5bac2512590639..0000000000000000000000000000000000000000 --- a/MCdata/1am0_MC +++ /dev/null @@ -1,384 +0,0 @@ -Residue conformations ------------------------------------------- -A6 : G O4p_endo anti -A7 : G O4p_endo anti -A8 : G C3p_endo anti -A9 : A C3p_exo anti -A10 : A C4p_exo anti -A11 : G O4p_endo anti -A12 : A O4p_endo anti -A13 : A C3p_exo anti -A14 : A C4p_exo anti -A15 : C C2p_endo anti -A16 : U C3p_endo anti -A17 : G C3p_endo anti -A18 : U C3p_endo anti -A33 : A C2p_exo anti -A34 : G C1p_exo syn -A35 : C C2p_exo anti -A41 : AMP -Adjacent stackings ---------------------------------------------- -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward pairing -A16-A17 : adjacent_5p upward -A33-A34 : adjacent_5p inward -Non-Adjacent stackings ------------------------------------------ -A11-A35 : upward pairing -A12-A34 : upward pairing -Number of stackings = 10 -Number of adjacent stackings = 8 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A6-A35 : G-C Ww/Ww pairing antiparallel cis XIX -A7-A11 : G-G Ww/Hh pairing antiparallel trans -A8-A9 : G-A Ww/O2' Ss/O2' adjacent_5p pairing -A8-A10 : G-A O2'/Hh pairing -A8-A11 : G-G Ww/O2P pairing -A9-A16 : A-U Bs/Ss pairing parallel trans one_hbond -A10-A15 : A-C O2'/Bh pairing -A10-A17 : A-G Bs/Ss Ww/O2' pairing parallel trans one_hbond -A11-A12 : G-A O2'/Hh adjacent_5p pairing -A11-A13 : G-A O2P/Bh O2P/Hh pairing -A11-A34 : G-G Bs/O2' Ss/O2' pairing -A11-A35 : G-C O2'/Bh Bs/O2P upward pairing -A12-A16 : A-U Bs/Wh pairing parallel trans one_hbond -A12-A34 : A-G O2'/Bs Bh/O2' Hh/O2' upward pairing -A15-A16 : C-U O2'/Hh adjacent_5p upward pairing -A17-A34 : G-G Ww/Hh pairing parallel cis one_hbond -A18-A33 : U-A Ww/Ww pairing antiparallel cis XX -Residue conformations ------------------------------------------- -A6 : G O4p_endo anti -A7 : G O4p_endo anti -A8 : G C2p_exo anti -A9 : A C3p_exo anti -A10 : A O4p_endo anti -A11 : G O4p_endo anti -A12 : A O4p_endo anti -A13 : A C3p_exo anti -A14 : A O4p_endo anti -A15 : C O4p_endo anti -A16 : U C3p_endo anti -A17 : G C3p_endo anti -A18 : U C3p_endo anti -A33 : A C2p_exo anti -A34 : G C1p_exo syn -A35 : C C2p_exo anti -A41 : AMP -Adjacent stackings ---------------------------------------------- -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A33-A34 : adjacent_5p inward -Non-Adjacent stackings ------------------------------------------ -A11-A35 : upward pairing -A12-A34 : upward pairing -Number of stackings = 10 -Number of adjacent stackings = 8 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A6-A35 : G-C Ww/Ww pairing antiparallel cis XIX -A7-A11 : G-G Ww/Hh pairing antiparallel trans VII -A8-A9 : G-A Ww/O2' Ss/O2' adjacent_5p pairing -A8-A10 : G-A O2'/Hh pairing -A8-A11 : G-G Ww/O2P pairing -A9-A16 : A-U Bs/Ss pairing antiparallel trans one_hbond -A10-A15 : A-C O2'/Bh pairing -A10-A17 : A-G Bs/Ss pairing parallel trans one_hbond -A11-A14 : G-A O2P/Bh pairing -A11-A34 : G-G Bs/O2' Ss/O2' pairing -A11-A35 : G-C O2'/Bh Bs/O2P upward pairing -A12-A16 : A-U Bs/Wh pairing parallel trans one_hbond -A12-A34 : A-G O2'/Bs Hh/O2' upward pairing -A17-A34 : G-G Ww/Hh pairing parallel cis VI -A18-A33 : U-A Ww/Ww pairing antiparallel cis XX -Residue conformations ------------------------------------------- -A6 : G O4p_endo anti -A7 : G O4p_endo anti -A8 : G C3p_endo anti -A9 : A C3p_exo anti -A10 : A C3p_endo anti -A11 : G O4p_endo anti -A12 : A O4p_endo anti -A13 : A C3p_exo anti -A14 : A O4p_endo anti -A15 : C O4p_endo anti -A16 : U C3p_endo anti -A17 : G C3p_endo anti -A18 : U C2p_exo anti -A33 : A C1p_endo anti -A34 : G C3p_exo syn -A35 : C C2p_exo anti -A41 : AMP -Adjacent stackings ---------------------------------------------- -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A33-A34 : adjacent_5p inward -Non-Adjacent stackings ------------------------------------------ -A11-A35 : upward pairing -A12-A34 : upward pairing -Number of stackings = 11 -Number of adjacent stackings = 9 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A6-A35 : G-C Ww/Ww pairing antiparallel cis XIX -A7-A11 : G-G Ww/Hh pairing antiparallel trans VII -A8-A9 : G-A Ww/O2' Ss/O2' adjacent_5p pairing -A8-A10 : G-A O2'/Hh pairing -A8-A11 : G-G Ww/O2P pairing -A9-A16 : A-U Bs/Ss pairing parallel trans one_hbond -A10-A15 : A-C O2'/Ww O2'/Bh pairing -A10-A16 : A-U O2'/Ww pairing -A10-A17 : A-G Bs/Ss Ww/O2' pairing parallel trans one_hbond -A11-A12 : G-A Ss/Hw adjacent_5p pairing antiparallel cis one_hbond -A11-A34 : G-G Bs/O2' Ss/O2' pairing -A11-A35 : G-C O2'/Bh upward pairing -A12-A16 : A-U Bs/Wh pairing parallel trans one_hbond -A12-A34 : A-G O2'/Bs upward pairing -A17-A34 : G-G Ww/Hw pairing parallel cis one_hbond -A18-A33 : U-A Ww/Ww pairing antiparallel cis XX -Residue conformations ------------------------------------------- -A6 : G O4p_endo anti -A7 : G O4p_endo anti -A8 : G C3p_endo anti -A9 : A C2p_exo anti -A10 : A C4p_exo anti -A11 : G O4p_endo anti -A12 : A O4p_endo anti -A13 : A C4p_exo anti -A14 : A O4p_endo anti -A15 : C C2p_endo anti -A16 : U C3p_endo anti -A17 : G C2p_exo anti -A18 : U C2p_exo anti -A33 : A C2p_exo anti -A34 : G C2p_endo syn -A35 : C C2p_exo anti -A41 : AMP -Adjacent stackings ---------------------------------------------- -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A33-A34 : adjacent_5p inward -Non-Adjacent stackings ------------------------------------------ -A11-A35 : upward pairing -A12-A34 : upward pairing -Number of stackings = 8 -Number of adjacent stackings = 6 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A6-A35 : G-C Ww/Ww pairing antiparallel cis XIX -A7-A11 : G-G Ww/Hh pairing antiparallel trans one_hbond -A8-A9 : G-A O2'/Bh O2'/Hh adjacent_5p pairing -A8-A10 : G-A O2'/Hh Hh/O2P pairing -A8-A11 : G-G Ww/O2P pairing -A10-A15 : A-C O2'/Bh pairing -A10-A17 : A-G Bs/Ss pairing parallel trans one_hbond -A11-A13 : G-A O2P/Bh O2P/Hh pairing -A11-A34 : G-G Bs/O2' Ss/O2' pairing -A11-A35 : G-C O2'/Bh upward pairing -A12-A34 : A-G O2'/Bs Hh/O2' upward pairing -A14-A34 : A-G O2P/Ww pairing -A17-A34 : G-G Ww/Hw pairing parallel cis one_hbond -A18-A33 : U-A Ww/Ww pairing antiparallel cis XX -Residue conformations ------------------------------------------- -A6 : G O4p_endo anti -A7 : G O4p_endo anti -A8 : G C2p_exo anti -A9 : A C2p_exo anti -A10 : A C2p_exo anti -A11 : G O4p_endo anti -A12 : A O4p_endo anti -A13 : A O4p_endo anti -A14 : A O4p_endo anti -A15 : C C3p_endo anti -A16 : U C3p_endo anti -A17 : G C2p_exo anti -A18 : U C3p_endo anti -A33 : A C2p_exo anti -A34 : G C2p_endo syn -A35 : C C2p_exo anti -A41 : AMP -Adjacent stackings ---------------------------------------------- -A6-A7 : adjacent_5p inward pairing -A7-A8 : adjacent_5p outward pairing -A9-A10 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A33-A34 : adjacent_5p inward -Non-Adjacent stackings ------------------------------------------ -A11-A35 : upward pairing -A12-A34 : upward pairing -Number of stackings = 10 -Number of adjacent stackings = 8 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A6-A7 : G-G O2'/Hh adjacent_5p inward pairing -A6-A35 : G-C Ww/Ww pairing antiparallel cis XIX -A7-A8 : G-G O2'/Hh adjacent_5p outward pairing -A9-A14 : A-A O2'/Bh pairing -A11-A34 : G-G Bs/O2' pairing -A11-A35 : G-C O2'/Bh upward pairing -A12-A34 : A-G O2'/Bs Hh/O2' upward pairing -A17-A34 : G-G Ww/Hw pairing parallel cis one_hbond -A18-A33 : U-A Ww/Ww pairing antiparallel cis XX -Residue conformations ------------------------------------------- -A6 : G C4p_exo anti -A7 : G O4p_endo anti -A8 : G C2p_exo anti -A9 : A C2p_endo anti -A10 : A C4p_exo anti -A11 : G O4p_endo anti -A12 : A O4p_endo anti -A13 : A O4p_endo anti -A14 : A C4p_exo anti -A15 : C C2p_endo anti -A16 : U C3p_endo anti -A17 : G C3p_endo anti -A18 : U C3p_endo anti -A33 : A C2p_exo anti -A34 : G C1p_exo syn -A35 : C C2p_exo anti -A41 : AMP -Adjacent stackings ---------------------------------------------- -A6-A7 : adjacent_5p inward -A7-A8 : adjacent_5p outward pairing -A9-A10 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A33-A34 : adjacent_5p inward -Non-Adjacent stackings ------------------------------------------ -A11-A35 : upward -A12-A34 : upward pairing -Number of stackings = 11 -Number of adjacent stackings = 9 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A6-A35 : G-C Ww/Ww pairing antiparallel cis XIX -A7-A8 : G-G O2'/Hh adjacent_5p outward pairing -A8-A9 : G-A Ww/O2' Ss/O2' adjacent_5p pairing -A8-A11 : G-G Ww/O2P pairing -A10-A14 : A-A O2P/Bh pairing -A10-A17 : A-G Bs/Ss pairing parallel trans one_hbond -A11-A13 : G-A O2P/Hh pairing -A11-A34 : G-G Bs/O2' Ss/O2' pairing -A12-A34 : A-G O2'/Bs Bh/O2' Hh/O2' upward pairing -A17-A34 : G-G Ww/Hh pairing parallel cis one_hbond -A18-A33 : U-A Ww/Ww pairing antiparallel cis XX -Residue conformations ------------------------------------------- -A6 : G C2p_endo anti -A7 : G O4p_endo anti -A8 : G O4p_endo anti -A9 : A C2p_endo anti -A10 : A O4p_endo anti -A11 : G O4p_endo anti -A12 : A O4p_endo anti -A13 : A C2p_exo anti -A14 : A C2p_exo anti -A15 : C C4p_exo anti -A16 : U O4p_endo anti -A17 : G C3p_endo anti -A18 : U C2p_exo anti -A33 : A C2p_exo anti -A34 : G C3p_exo syn -A35 : C C2p_exo anti -A41 : AMP -Adjacent stackings ---------------------------------------------- -A6-A7 : adjacent_5p upward pairing -A7-A8 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A33-A34 : adjacent_5p inward -Non-Adjacent stackings ------------------------------------------ -A11-A35 : upward pairing -A12-A34 : upward pairing -Number of stackings = 7 -Number of adjacent stackings = 5 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A6-A7 : G-G O2'/C8 adjacent_5p upward pairing -A6-A35 : G-C Ww/Ww pairing antiparallel cis XIX -A7-A11 : G-G Ww/Hh pairing antiparallel trans VII -A8-A10 : G-A C8/O2P pairing -A8-A11 : G-G Ww/O2P pairing -A9-A10 : A-A O2'/Hh O2'/C8 C8/O2P adjacent_5p pairing -A9-A16 : A-U Ww/O2' pairing -A10-A17 : A-G Ww/O2' Bh/O2' pairing -A11-A12 : G-A Ss/Hw O2'/Hh adjacent_5p pairing antiparallel cis one_hbond -A11-A34 : G-G Bs/O2' Ss/O2' pairing -A11-A35 : G-C O2'/Bh upward pairing -A12-A34 : A-G O2'/Ww O2'/Bs upward pairing -A13-A14 : A-A O2P/Hh adjacent_5p pairing -A14-A17 : A-G Wh/Wh pairing parallel cis one_hbond 66 -A14-A34 : A-G Wh/Wh pairing parallel cis one_hbond 66 -A16-A17 : U-G O2P/Hh adjacent_5p pairing -A17-A34 : G-G Ww/Hh pairing parallel cis VI -A18-A33 : U-A Ww/Ww pairing antiparallel cis XX -Residue conformations ------------------------------------------- -A6 : G O4p_endo anti -A7 : G O4p_endo anti -A8 : G C3p_endo anti -A9 : A C3p_exo anti -A10 : A C4p_exo anti -A11 : G O4p_endo anti -A12 : A O4p_endo anti -A13 : A C4p_endo anti -A14 : A O4p_endo anti -A15 : C C1p_exo anti -A16 : U C3p_endo anti -A17 : G C2p_exo anti -A18 : U C2p_exo anti -A33 : A C2p_exo anti -A34 : G C3p_exo syn -A35 : C C2p_exo anti -A41 : AMP -Adjacent stackings ---------------------------------------------- -A6-A7 : adjacent_5p upward pairing -A7-A8 : adjacent_5p upward -A9-A10 : adjacent_5p outward pairing -A13-A14 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A33-A34 : adjacent_5p inward -Non-Adjacent stackings ------------------------------------------ -A11-A35 : upward pairing -A12-A34 : upward pairing -Number of stackings = 9 -Number of adjacent stackings = 7 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A6-A7 : G-G O2'/C8 adjacent_5p upward pairing -A6-A35 : G-C Ww/Ww pairing antiparallel cis XIX -A7-A11 : G-G Ww/Hh pairing antiparallel trans -A8-A10 : G-A Hh/O2P pairing -A8-A11 : G-G Ww/O2P pairing -A9-A10 : A-A O2'/Hh adjacent_5p outward pairing -A9-A15 : A-C Hw/Ww pairing parallel trans one_hbond -A10-A17 : A-G Ww/O2' pairing -A11-A12 : G-A Ss/Hw O2'/Hh adjacent_5p pairing parallel cis one_hbond -A11-A34 : G-G Bs/O2' Ss/O2' pairing -A11-A35 : G-C O2'/Bh upward pairing -A12-A13 : A-A O2'/Hh adjacent_5p pairing -A12-A34 : A-G O2'/Bs upward pairing -A14-A15 : A-C O2'/Hh adjacent_5p pairing -A17-A34 : G-G Ww/Hh pairing parallel cis VI -A18-A33 : U-A Ww/Ww pairing antiparallel cis XX diff --git a/MCdata/1anr_MC b/MCdata/1anr_MC deleted file mode 100644 index c2793fad630eade6c26a77d8e1bf6b492e555dea..0000000000000000000000000000000000000000 --- a/MCdata/1anr_MC +++ /dev/null @@ -1,1200 +0,0 @@ -Residue conformations ------------------------------------------- -A17 : G C2p_exo anti -A18 : G C3p_endo anti -A19 : C C3p_endo anti -A20 : A C3p_endo anti -A21 : G C3p_endo anti -A22 : A C3p_endo anti -A23 : U C3p_endo anti -A24 : C C2p_endo anti -A25 : U C3p_endo anti -A26 : G C3p_endo anti -A27 : A O4p_endo anti -A28 : G O4p_endo anti -A29 : C C2p_exo anti -A30 : C C4p_endo syn -A31 : U C3p_endo anti -A32 : G C3p_endo anti -A33 : G C3p_exo anti -A34 : G C2p_exo anti -A35 : A C3p_exo anti -A36 : G C3p_endo anti -A37 : C C2p_exo anti -A38 : U C2p_exo anti -A39 : C C3p_endo anti -A40 : U C2p_exo anti -A41 : C C3p_endo anti -A42 : U C3p_endo anti -A43 : G C3p_endo anti -A44 : C C2p_exo anti -A45 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A22-A23 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A28-A29 : adjacent_5p upward -A36-A37 : adjacent_5p upward -A38-A39 : adjacent_5p upward -A41-A42 : adjacent_5p upward -A43-A44 : adjacent_5p upward -A44-A45 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A20-A43 : outward -A28-A38 : outward -Number of stackings = 16 -Number of adjacent stackings = 14 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A17-A44 : G-C Wh/Wh pairing antiparallel cis one_hbond -A19-A43 : C-G Ww/Ww pairing antiparallel cis XIX -A20-A42 : A-U Ww/Ww pairing antiparallel cis XX -A21-A41 : G-C Ww/Ww pairing antiparallel cis XIX -A22-A40 : A-U Bs/Ws pairing antiparallel cis one_hbond -A26-A39 : G-C Ww/Ww pairing antiparallel cis XIX -A27-A38 : A-U Ww/Ww pairing antiparallel cis XX -A28-A37 : G-C Ww/Ww pairing antiparallel cis -A29-A36 : C-G Ww/Wh pairing antiparallel cis one_hbond -A31-A33 : U-G O2P/Hh pairing -A32-A34 : G-G O2'/Bs pairing -Residue conformations ------------------------------------------- -A17 : G C2p_exo anti -A18 : G C4p_exo anti -A19 : C C2p_exo anti -A20 : A C3p_endo anti -A21 : G C2p_exo anti -A22 : A C3p_endo anti -A23 : U C2p_exo anti -A24 : C C3p_endo anti -A25 : U C2p_exo anti -A26 : G C3p_endo anti -A27 : A C3p_endo anti -A28 : G C3p_endo anti -A29 : C C3p_endo anti -A30 : C C2p_exo anti -A31 : U C3p_endo anti -A32 : G C3p_endo anti -A33 : G C2p_exo anti -A34 : G C3p_endo syn -A35 : A C3p_exo anti -A36 : G C3p_endo anti -A37 : C C2p_exo anti -A38 : U C2p_exo anti -A39 : C C3p_endo anti -A40 : U C3p_endo anti -A41 : C C3p_endo anti -A42 : U C3p_endo anti -A43 : G C3p_endo anti -A44 : C C3p_endo anti -A45 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A22-A23 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A28-A29 : adjacent_5p upward -A36-A37 : adjacent_5p upward -A43-A44 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A18-A45 : outward -A20-A43 : outward -A22-A41 : outward -A27-A39 : outward -Number of stackings = 16 -Number of adjacent stackings = 12 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A17-A45 : G-C Ww/Ww pairing antiparallel cis XIX -A18-A44 : G-C Ww/Ww pairing antiparallel cis XIX -A19-A43 : C-G Ww/Ww pairing antiparallel cis XIX -A20-A42 : A-U Ww/Ww pairing antiparallel cis XX -A21-A41 : G-C Ww/Ww pairing antiparallel cis XIX -A22-A24 : A-C O2P/Bh pairing -A22-A40 : A-U Ww/Ws pairing antiparallel cis -A26-A39 : G-C Ww/Ww pairing antiparallel cis XIX -A27-A38 : A-U Ww/Ww pairing antiparallel cis XX -A28-A37 : G-C Ww/Ws pairing antiparallel cis one_hbond 130 -A29-A36 : C-G Ww/Ww pairing antiparallel cis XIX -A30-A34 : C-G Ws/Sw pairing antiparallel cis one_hbond 128 -A33-A34 : G-G O2'/Ss O2'/C8 adjacent_5p pairing -A34-A35 : G-A O2'/Hh adjacent_5p pairing -Residue conformations ------------------------------------------- -A17 : G C3p_endo anti -A18 : G C3p_endo anti -A19 : C C2p_exo anti -A20 : A C2p_exo anti -A21 : G C3p_endo anti -A22 : A C2p_exo anti -A23 : U C2p_exo anti -A24 : C C3p_exo anti -A25 : U O4p_endo syn -A26 : G C3p_endo anti -A27 : A C3p_endo anti -A28 : G C3p_endo anti -A29 : C C3p_endo anti -A30 : C C2p_exo anti -A31 : U C3p_endo anti -A32 : G O4p_endo anti -A33 : G C3p_exo anti -A34 : G C3p_endo syn -A35 : A O4p_endo anti -A36 : G C3p_endo anti -A37 : C C3p_endo anti -A38 : U C3p_endo anti -A39 : C C3p_endo anti -A40 : U C2p_exo anti -A41 : C C3p_endo anti -A42 : U C3p_endo anti -A43 : G C3p_endo anti -A44 : C C3p_endo anti -A45 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A18-A19 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A28-A29 : adjacent_5p upward -A36-A37 : adjacent_5p upward -A43-A44 : adjacent_5p upward -A44-A45 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A20-A43 : outward -A27-A39 : outward -Number of stackings = 11 -Number of adjacent stackings = 9 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A17-A45 : G-C Ww/Ww pairing antiparallel cis one_hbond -A18-A44 : G-C Ww/Ww pairing antiparallel cis XIX -A19-A43 : C-G Ww/Ww pairing antiparallel cis XIX -A20-A42 : A-U Ww/Ww pairing antiparallel cis XX -A21-A41 : G-C Ww/Ww pairing antiparallel cis XIX -A26-A39 : G-C Ww/Ww pairing antiparallel cis XIX -A27-A38 : A-U Ww/Ww pairing antiparallel cis XX -A28-A37 : G-C Ww/Ww pairing antiparallel cis XIX -A29-A36 : C-G Ww/Ww pairing antiparallel cis XIX -A32-A33 : G-G Sw/Hw adjacent_5p pairing parallel cis one_hbond -A33-A34 : G-G O2P/Bs adjacent_5p pairing -A34-A35 : G-A O2'/C8 adjacent_5p pairing -Residue conformations ------------------------------------------- -A17 : G C4p_exo anti -A18 : G C3p_endo anti -A19 : C C2p_exo anti -A20 : A C2p_exo anti -A21 : G C3p_endo anti -A22 : A C2p_exo anti -A23 : U C3p_endo anti -A24 : C C2p_endo anti -A25 : U C2p_exo anti -A26 : G C3p_endo anti -A27 : A C3p_endo anti -A28 : G C3p_endo anti -A29 : C C3p_endo anti -A30 : C C2p_exo anti -A31 : U C4p_exo anti -A32 : G C1p_endo anti -A33 : G C2p_endo anti -A34 : G C3p_endo anti -A35 : A O4p_endo anti -A36 : G C2p_exo anti -A37 : C C2p_exo anti -A38 : U O4p_endo anti -A39 : C C4p_exo anti -A40 : U C2p_exo anti -A41 : C C3p_endo anti -A42 : U C2p_exo anti -A43 : G C3p_endo anti -A44 : C C2p_exo anti -A45 : C C2p_exo anti -Adjacent stackings ---------------------------------------------- -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A22-A23 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A29-A30 : adjacent_5p upward -A34-A35 : adjacent_5p upward -A36-A37 : adjacent_5p upward -A40-A41 : adjacent_5p upward -A41-A42 : adjacent_5p upward -A42-A43 : adjacent_5p upward -A43-A44 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A18-A45 : outward -A20-A43 : outward -A34-A36 : upward -Number of stackings = 18 -Number of adjacent stackings = 15 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -A17-A45 : G-C Ww/Ww pairing antiparallel cis XIX -A18-A44 : G-C Ww/Ww pairing antiparallel cis XIX -A19-A43 : C-G Ww/Ww pairing antiparallel cis XIX -A20-A42 : A-U Ww/Ww pairing antiparallel cis XX -A21-A41 : G-C Ww/Ww pairing antiparallel cis XIX -A22-A24 : A-C O2P/Bh pairing -A22-A40 : A-U Ww/Ww pairing antiparallel cis XX -A26-A39 : G-C Ww/Ww pairing antiparallel cis -A29-A36 : C-G Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -A17 : G C3p_endo anti -A18 : G C3p_endo anti -A19 : C C2p_exo anti -A20 : A C2p_exo anti -A21 : G C2p_exo anti -A22 : A C1p_exo anti -A23 : U C3p_exo syn -A24 : C C3p_exo anti -A25 : U C2p_endo anti -A26 : G C2p_exo anti -A27 : A C2p_exo anti -A28 : G C3p_endo anti -A29 : C C2p_exo anti -A30 : C C2p_exo anti -A31 : U C3p_endo anti -A32 : G C3p_endo anti -A33 : G C3p_endo anti -A34 : G C3p_endo syn -A35 : A C3p_exo anti -A36 : G C2p_exo anti -A37 : C C2p_exo anti -A38 : U C3p_endo anti -A39 : C C3p_endo anti -A40 : U C2p_exo anti -A41 : C C2p_exo anti -A42 : U C3p_endo anti -A43 : G C3p_endo anti -A44 : C C3p_endo anti -A45 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A18-A19 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A28-A29 : adjacent_5p upward -A36-A37 : adjacent_5p upward -A39-A40 : adjacent_5p upward -A43-A44 : adjacent_5p upward -A44-A45 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A18-A45 : outward -A20-A43 : outward -A21-A42 : outward -A22-A24 : upward -A22-A41 : outward -Number of stackings = 15 -Number of adjacent stackings = 10 -Number of non adjacent stackings = 5 -Base-pairs ------------------------------------------------------ -A17-A45 : G-C Ww/Ww pairing antiparallel cis XIX -A18-A44 : G-C Ww/Ww pairing antiparallel cis XIX -A19-A43 : C-G Ww/Ww pairing antiparallel cis XIX -A20-A42 : A-U Ww/Ww pairing antiparallel cis XX -A21-A41 : G-C Ww/Ww pairing antiparallel cis XIX -A23-A24 : U-C O2'/Hh adjacent_5p pairing -A23-A41 : U-C Ww/O2' pairing -A24-A40 : C-U Ws/Ww pairing antiparallel cis one_hbond 106 -A26-A39 : G-C Ww/Ww pairing antiparallel cis XIX -A27-A38 : A-U Ww/Ww pairing antiparallel cis XX -A28-A37 : G-C Ww/Ww pairing antiparallel cis one_hbond 130 -A29-A36 : C-G Ww/Ww pairing antiparallel cis XIX -A30-A34 : C-G Ws/Ww pairing antiparallel cis one_hbond 130 -A33-A34 : G-G O2'/Ss adjacent_5p pairing -A34-A35 : G-A O2'/Hh O2'/C8 adjacent_5p pairing -Residue conformations ------------------------------------------- -A17 : G C4p_exo anti -A18 : G C3p_endo anti -A19 : C C2p_exo anti -A20 : A C3p_endo anti -A21 : G C3p_endo anti -A22 : A C2p_exo anti -A23 : U C3p_exo anti -A24 : C C3p_endo anti -A25 : U C2p_endo anti -A26 : G C3p_endo anti -A27 : A C3p_endo anti -A28 : G C3p_endo anti -A29 : C O4p_endo anti -A30 : C O4p_endo anti -A31 : U O4p_endo anti -A32 : G C3p_endo anti -A33 : G C3p_exo anti -A34 : G C1p_endo syn -A35 : A C2p_exo anti -A36 : G C2p_exo anti -A37 : C C2p_exo anti -A38 : U C2p_exo anti -A39 : C C2p_exo anti -A40 : U C3p_endo anti -A41 : C C4p_exo anti -A42 : U C3p_endo anti -A43 : G C3p_endo anti -A44 : C C2p_exo anti -A45 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A22-A23 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A28-A29 : adjacent_5p upward -A29-A30 : adjacent_5p upward -A32-A33 : adjacent_5p upward -A41-A42 : adjacent_5p upward -A43-A44 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A20-A43 : outward -Number of stackings = 13 -Number of adjacent stackings = 12 -Number of non adjacent stackings = 1 -Base-pairs ------------------------------------------------------ -A17-A45 : G-C Ww/Ww pairing antiparallel cis XIX -A18-A44 : G-C Ww/Ww pairing antiparallel cis XIX -A19-A43 : C-G Ww/Ww pairing antiparallel cis XIX -A20-A42 : A-U Ww/Ww pairing antiparallel cis XX -A26-A39 : G-C Ww/Ww pairing antiparallel cis -A26-A41 : G-C Ww/O2P pairing -A27-A38 : A-U Ww/Ww pairing antiparallel cis XX -A28-A37 : G-C Ww/Ww pairing antiparallel cis XIX -A29-A36 : C-G Ww/Ww pairing antiparallel cis XIX -A31-A32 : U-G O2'/C8 adjacent_5p pairing -A32-A34 : G-G O2'/Bs O2'/Ss pairing -A34-A35 : G-A O2'/Hh adjacent_5p pairing -Residue conformations ------------------------------------------- -A17 : G C2p_exo anti -A18 : G C2p_exo anti -A19 : C C3p_endo anti -A20 : A C3p_endo anti -A21 : G C2p_exo anti -A22 : A C2p_exo anti -A23 : U C2p_exo anti -A24 : C C2p_endo anti -A25 : U C3p_endo anti -A26 : G C4p_exo anti -A27 : A C4p_exo anti -A28 : G C4p_exo anti -A29 : C C4p_exo anti -A30 : C C3p_endo anti -A31 : U C3p_endo anti -A32 : G C2p_exo anti -A33 : G C3p_endo anti -A34 : G C3p_endo anti -A35 : A C3p_exo anti -A36 : G C2p_exo anti -A37 : C C3p_endo anti -A38 : U C3p_endo anti -A39 : C C3p_endo anti -A40 : U C3p_endo anti -A41 : C C3p_endo anti -A42 : U C2p_exo anti -A43 : G C3p_endo anti -A44 : C C3p_endo anti -A45 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A18-A19 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A22-A23 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A28-A29 : adjacent_5p upward -A36-A37 : adjacent_5p upward -A38-A39 : adjacent_5p upward -A43-A44 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A20-A43 : outward -A21-A42 : outward -A34-A36 : upward -Number of stackings = 13 -Number of adjacent stackings = 10 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -A18-A44 : G-C Ww/Ww pairing antiparallel cis XIX -A19-A43 : C-G Ww/Ww pairing antiparallel cis XIX -A20-A42 : A-U Ww/Ww pairing antiparallel cis XX -A25-A27 : U-A Ws/Hw pairing parallel cis one_hbond 47 -A26-A39 : G-C Ww/Ww pairing antiparallel cis one_hbond 130 -A27-A38 : A-U Ww/Ww pairing antiparallel cis XX -A30-A33 : C-G Ww/Sw pairing antiparallel cis one_hbond 125 -A32-A33 : G-G O2'/C8 adjacent_5p pairing -A34-A35 : G-A O2'/Hh O2'/C8 adjacent_5p pairing -Residue conformations ------------------------------------------- -A17 : G C3p_endo anti -A18 : G C3p_endo anti -A19 : C C2p_exo anti -A20 : A C3p_endo anti -A21 : G C2p_exo anti -A22 : A C2p_exo anti -A23 : U C3p_endo anti -A24 : C C3p_endo anti -A25 : U C4p_exo syn -A26 : G C3p_endo anti -A27 : A C3p_endo anti -A28 : G C4p_exo anti -A29 : C O4p_endo anti -A30 : C O4p_endo anti -A31 : U C3p_endo anti -A32 : G C3p_exo anti -A33 : G C3p_endo anti -A34 : G C2p_exo syn -A35 : A C3p_exo anti -A36 : G C2p_exo anti -A37 : C C3p_endo anti -A38 : U C3p_endo anti -A39 : C O4p_endo anti -A40 : U C2p_exo anti -A41 : C C3p_endo anti -A42 : U C4p_exo anti -A43 : G C3p_endo anti -A44 : C C3p_endo anti -A45 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A18-A19 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A22-A23 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A28-A29 : adjacent_5p upward -A36-A37 : adjacent_5p upward -A41-A42 : adjacent_5p upward -A43-A44 : adjacent_5p upward -A44-A45 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A20-A43 : outward -A22-A41 : outward -A28-A38 : outward -Number of stackings = 16 -Number of adjacent stackings = 13 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -A18-A44 : G-C Wh/Wh pairing antiparallel cis one_hbond -A19-A43 : C-G Ww/Ww pairing antiparallel cis XIX -A20-A42 : A-U Ww/Ww pairing antiparallel cis XX -A21-A41 : G-C Ww/Ww pairing antiparallel cis XIX -A22-A40 : A-U Ww/Ww pairing antiparallel cis one_hbond -A27-A38 : A-U Ww/Ww pairing antiparallel cis XX -A31-A32 : U-G O2'/Ss adjacent_5p pairing -A32-A33 : G-G Sw/Hh adjacent_5p pairing parallel cis one_hbond 109 -A33-A34 : G-G O2'/Ss O2'/C8 adjacent_5p pairing -Residue conformations ------------------------------------------- -A17 : G C3p_endo anti -A18 : G C2p_exo anti -A19 : C C2p_exo anti -A20 : A C2p_exo anti -A21 : G C3p_endo anti -A22 : A C3p_endo anti -A23 : U C2p_exo anti -A24 : C C2p_endo anti -A25 : U C2p_endo syn -A26 : G C2p_exo anti -A27 : A C4p_exo anti -A28 : G C4p_exo anti -A29 : C C2p_exo anti -A30 : C C3p_endo anti -A31 : U C3p_endo anti -A32 : G C2p_exo anti -A33 : G C2p_exo anti -A34 : G C2p_exo syn -A35 : A C3p_exo anti -A36 : G C3p_endo anti -A37 : C C3p_endo anti -A38 : U C3p_endo anti -A39 : C C3p_endo anti -A40 : U C3p_endo anti -A41 : C C3p_endo anti -A42 : U C2p_exo anti -A43 : G C2p_exo anti -A44 : C C2p_exo anti -A45 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A22-A23 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A28-A29 : adjacent_5p upward -A29-A30 : adjacent_5p upward -A40-A41 : adjacent_5p upward -A43-A44 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A20-A43 : outward -A21-A42 : outward -Number of stackings = 13 -Number of adjacent stackings = 11 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A17-A45 : G-C Ww/Ww pairing antiparallel cis XIX -A18-A44 : G-C Ww/Ww pairing antiparallel cis -A19-A43 : C-G Ww/Ww pairing antiparallel cis XIX -A20-A42 : A-U Ww/Ww pairing antiparallel cis XX -A21-A41 : G-C Ww/Ww pairing antiparallel cis -A22-A40 : A-U Bs/Ws pairing antiparallel cis one_hbond -A27-A38 : A-U Ww/Ww pairing antiparallel cis XX -A28-A37 : G-C Ww/Ww pairing antiparallel cis XIX -A29-A36 : C-G Ww/Ww pairing antiparallel cis XIX -A33-A34 : G-G O2P/Bs adjacent_5p pairing -Residue conformations ------------------------------------------- -A17 : G C2p_exo anti -A18 : G C3p_endo anti -A19 : C C2p_exo anti -A20 : A C3p_endo anti -A21 : G C2p_exo anti -A22 : A C2p_exo anti -A23 : U C3p_exo anti -A24 : C C3p_endo anti -A25 : U C2p_endo anti -A26 : G C3p_endo anti -A27 : A O4p_endo anti -A28 : G O4p_endo anti -A29 : C C2p_exo anti -A30 : C C3p_endo anti -A31 : U C3p_endo anti -A32 : G C3p_exo anti -A33 : G C2p_endo anti -A34 : G C2p_exo syn -A35 : A C3p_exo anti -A36 : G C2p_exo anti -A37 : C C3p_endo anti -A38 : U C2p_exo anti -A39 : C O4p_endo anti -A40 : U C3p_endo anti -A41 : C C3p_endo anti -A42 : U C2p_exo anti -A43 : G C3p_endo anti -A44 : C C3p_endo anti -A45 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A22-A23 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A28-A29 : adjacent_5p upward -A29-A30 : adjacent_5p upward -A30-A31 : adjacent_5p upward -A36-A37 : adjacent_5p upward -A38-A39 : adjacent_5p upward -A40-A41 : adjacent_5p upward -A43-A44 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A20-A43 : outward -A21-A42 : outward -A28-A38 : outward -Number of stackings = 17 -Number of adjacent stackings = 14 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -A18-A44 : G-C Ww/Ww pairing antiparallel cis XIX -A19-A43 : C-G Ww/Ww pairing antiparallel cis XIX -A20-A42 : A-U Ww/Ww pairing antiparallel cis XX -A21-A41 : G-C Ww/Ww pairing antiparallel cis XIX -A26-A39 : G-C Ww/Ww pairing antiparallel cis 130 -A27-A38 : A-U Ww/Ww pairing antiparallel cis XX -A29-A36 : C-G Ww/Ww pairing antiparallel cis -A34-A35 : G-A O2'/Hh O2'/C8 adjacent_5p pairing -Residue conformations ------------------------------------------- -A17 : G C3p_endo anti -A18 : G C2p_exo anti -A19 : C C2p_exo anti -A20 : A C3p_endo anti -A21 : G C2p_exo anti -A22 : A C1p_endo syn -A23 : U C2p_exo anti -A24 : C C2p_exo anti -A25 : U C2p_endo anti -A26 : G C3p_endo anti -A27 : A C4p_exo anti -A28 : G C3p_endo anti -A29 : C C4p_exo anti -A30 : C C3p_endo anti -A31 : U C3p_endo anti -A32 : G C3p_exo anti -A33 : G C2p_exo anti -A34 : G C2p_exo anti -A35 : A C2p_endo anti -A36 : G C3p_endo anti -A37 : C C3p_endo anti -A38 : U C2p_exo anti -A39 : C O4p_endo anti -A40 : U C2p_exo anti -A41 : C C3p_endo anti -A42 : U C3p_endo anti -A43 : G C3p_endo anti -A44 : C C4p_exo anti -A45 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A18-A19 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A28-A29 : adjacent_5p upward -A29-A30 : adjacent_5p upward -A36-A37 : adjacent_5p upward -A43-A44 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A18-A45 : outward -A20-A43 : outward -A21-A42 : outward -Number of stackings = 12 -Number of adjacent stackings = 9 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -A18-A44 : G-C Ww/Ww pairing antiparallel cis -A19-A43 : C-G Ww/Ww pairing antiparallel cis XIX -A20-A42 : A-U Ww/Ww pairing antiparallel cis XX -A21-A41 : G-C Ww/Ww pairing antiparallel cis -A26-A39 : G-C Ww/Ww pairing antiparallel cis -A27-A38 : A-U Ww/Ww pairing antiparallel cis XX -A30-A34 : C-G O2'/Bs pairing -A33-A34 : G-G O2'/Hh O2'/C8 adjacent_5p pairing -Residue conformations ------------------------------------------- -A17 : G C2p_exo anti -A18 : G C2p_exo anti -A19 : C C3p_endo anti -A20 : A C2p_exo anti -A21 : G C3p_endo anti -A22 : A C3p_endo anti -A23 : U C3p_endo anti -A24 : C C2p_endo anti -A25 : U C3p_endo anti -A26 : G C2p_exo anti -A27 : A C4p_exo anti -A28 : G C3p_endo anti -A29 : C C3p_endo anti -A30 : C C2p_exo anti -A31 : U C3p_endo anti -A32 : G C3p_endo anti -A33 : G C3p_endo anti -A34 : G C1p_endo anti -A35 : A C3p_exo anti -A36 : G C2p_exo anti -A37 : C C3p_endo anti -A38 : U C2p_exo anti -A39 : C O4p_endo anti -A40 : U C2p_exo anti -A41 : C C3p_endo anti -A42 : U C3p_endo anti -A43 : G C3p_endo anti -A44 : C C3p_endo anti -A45 : C C2p_exo anti -Adjacent stackings ---------------------------------------------- -A18-A19 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A22-A23 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A28-A29 : adjacent_5p upward -A29-A30 : adjacent_5p upward -A36-A37 : adjacent_5p upward -A37-A38 : adjacent_5p upward -A41-A42 : adjacent_5p upward -A43-A44 : adjacent_5p upward -A44-A45 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A20-A43 : outward -A34-A36 : upward -Number of stackings = 15 -Number of adjacent stackings = 13 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A18-A44 : G-C Ww/Ww pairing antiparallel cis -A19-A43 : C-G Ww/Ww pairing antiparallel cis XIX -A20-A42 : A-U Ww/Ww pairing antiparallel cis one_hbond -A21-A41 : G-C Ww/Ww pairing antiparallel cis XIX -A27-A38 : A-U Ww/Ww pairing antiparallel cis XX -A30-A34 : C-G O2'/Ww pairing -A33-A34 : G-G O2'/Ss O2'/C8 adjacent_5p pairing -A34-A35 : G-A O2'/Hh O2'/C8 adjacent_5p pairing -Residue conformations ------------------------------------------- -A17 : G C2p_exo anti -A18 : G C3p_endo anti -A19 : C C3p_endo anti -A20 : A C2p_exo anti -A21 : G C2p_exo anti -A22 : A O4p_endo syn -A23 : U C4p_endo anti -A24 : C C3p_endo anti -A25 : U C3p_endo syn -A26 : G C3p_endo anti -A27 : A C2p_exo anti -A28 : G C4p_exo anti -A29 : C C2p_exo anti -A30 : C C3p_endo syn -A31 : U C3p_endo anti -A32 : G C3p_endo anti -A33 : G C3p_exo anti -A34 : G C3p_endo anti -A35 : A C2p_endo anti -A36 : G C2p_exo anti -A37 : C C3p_endo anti -A38 : U C4p_exo anti -A39 : C O4p_endo anti -A40 : U C2p_exo anti -A41 : C C4p_exo anti -A42 : U C4p_exo anti -A43 : G C3p_endo anti -A44 : C C2p_exo anti -A45 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A28-A29 : adjacent_5p upward -A37-A38 : adjacent_5p upward -A43-A44 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A20-A43 : outward -A21-A42 : outward -A27-A39 : outward -Number of stackings = 12 -Number of adjacent stackings = 9 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -A18-A44 : G-C Ww/Ww pairing antiparallel cis XIX -A19-A43 : C-G Ww/Ww pairing antiparallel cis XIX -A20-A42 : A-U Ww/Ww pairing antiparallel cis XX -A22-A41 : A-C Bh/O2' pairing -A23-A40 : U-U Ww/Wh pairing antiparallel cis one_hbond -A23-A41 : U-C Hw/Wh pairing antiparallel cis one_hbond 102 -A25-A26 : U-G O2'/Hh adjacent_5p pairing -A26-A39 : G-C Ww/Ww pairing antiparallel cis 130 -A27-A38 : A-U Ww/Ww pairing antiparallel cis XX -A28-A37 : G-C Ww/Ww pairing antiparallel cis one_hbond -A29-A30 : C-C Ss/Hh adjacent_5p pairing antiparallel trans one_hbond -A29-A36 : C-G Ww/Ww pairing antiparallel cis -Residue conformations ------------------------------------------- -A17 : G C3p_endo anti -A18 : G C2p_exo anti -A19 : C C3p_endo anti -A20 : A C3p_endo anti -A21 : G C3p_endo anti -A22 : A C2p_exo anti -A23 : U C2p_exo anti -A24 : C C3p_endo anti -A25 : U C3p_endo anti -A26 : G C3p_endo anti -A27 : A C4p_exo anti -A28 : G C3p_endo anti -A29 : C C4p_exo anti -A30 : C C1p_exo anti -A31 : U O4p_endo anti -A32 : G C2p_exo anti -A33 : G C2p_endo anti -A34 : G C2p_exo syn -A35 : A C3p_exo anti -A36 : G C2p_exo anti -A37 : C C3p_endo anti -A38 : U O4p_endo anti -A39 : C C4p_exo anti -A40 : U C3p_endo anti -A41 : C C3p_endo anti -A42 : U C3p_endo anti -A43 : G C3p_endo anti -A44 : C C2p_exo anti -A45 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A18-A19 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A22-A23 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A28-A29 : adjacent_5p upward -A29-A30 : adjacent_5p upward pairing -A32-A33 : adjacent_5p upward -A36-A37 : adjacent_5p upward -A43-A44 : adjacent_5p upward -A44-A45 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A20-A43 : outward -A21-A42 : outward -Number of stackings = 16 -Number of adjacent stackings = 14 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A19-A43 : C-G Ww/Ww pairing antiparallel cis -A20-A42 : A-U Ww/Ww pairing antiparallel cis XX -A21-A41 : G-C Ww/Ww pairing antiparallel cis -A22-A24 : A-C O2P/Bh pairing -A27-A38 : A-U Ww/Ww pairing antiparallel cis XX -A29-A30 : C-C O2P/Bh adjacent_5p upward pairing -A29-A36 : C-G Wh/Wh pairing antiparallel cis one_hbond -A34-A35 : G-A O2'/Hh adjacent_5p pairing -Residue conformations ------------------------------------------- -A17 : G O4p_endo anti -A18 : G C2p_exo anti -A19 : C C4p_exo anti -A20 : A C4p_exo anti -A21 : G C3p_endo anti -A22 : A C2p_exo anti -A23 : U C3p_endo anti -A24 : C C3p_endo anti -A25 : U C3p_endo syn -A26 : G C2p_exo anti -A27 : A C4p_exo anti -A28 : G C4p_exo anti -A29 : C O4p_endo anti -A30 : C C3p_endo anti -A31 : U O4p_endo anti -A32 : G C3p_endo anti -A33 : G C2p_endo anti -A34 : G C1p_endo anti -A35 : A C3p_exo anti -A36 : G C2p_exo anti -A37 : C C3p_endo anti -A38 : U C2p_exo anti -A39 : C O4p_endo anti -A40 : U C3p_endo anti -A41 : C C3p_endo anti -A42 : U C2p_exo anti -A43 : G C2p_exo anti -A44 : C C2p_exo anti -A45 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A22-A23 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A28-A29 : adjacent_5p upward -A36-A37 : adjacent_5p upward -A43-A44 : adjacent_5p upward -A44-A45 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A20-A43 : outward -A21-A42 : outward -Number of stackings = 14 -Number of adjacent stackings = 12 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A19-A43 : C-G Ww/Ww pairing antiparallel cis XIX -A20-A42 : A-U Ww/Ww pairing antiparallel cis XX -A21-A41 : G-C Ww/Ww pairing antiparallel cis XIX -A26-A39 : G-C Ww/Ww pairing antiparallel cis XIX -A27-A38 : A-U Ww/Ww pairing antiparallel cis XX -A30-A34 : C-G O2'/Bs pairing -A33-A34 : G-G O2P/Bs adjacent_5p pairing -Residue conformations ------------------------------------------- -A17 : G C2p_exo anti -A18 : G C2p_exo anti -A19 : C C3p_endo anti -A20 : A C2p_exo anti -A21 : G C2p_exo anti -A22 : A C3p_endo anti -A23 : U C3p_exo anti -A24 : C C3p_endo anti -A25 : U C2p_endo anti -A26 : G C3p_endo anti -A27 : A C3p_endo anti -A28 : G C3p_endo anti -A29 : C C3p_endo anti -A30 : C C3p_endo anti -A31 : U C3p_endo anti -A32 : G C2p_exo anti -A33 : G C2p_exo anti -A34 : G C2p_exo syn -A35 : A C3p_exo anti -A36 : G C3p_endo anti -A37 : C C3p_endo anti -A38 : U O4p_endo anti -A39 : C C3p_endo anti -A40 : U C2p_exo anti -A41 : C C3p_endo anti -A42 : U O4p_endo anti -A43 : G C2p_exo anti -A44 : C C3p_endo anti -A45 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A28-A29 : adjacent_5p upward -A29-A30 : adjacent_5p upward -A36-A37 : adjacent_5p upward -A43-A44 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A20-A43 : outward -Number of stackings = 10 -Number of adjacent stackings = 9 -Number of non adjacent stackings = 1 -Base-pairs ------------------------------------------------------ -A17-A45 : G-C Ww/Ww pairing antiparallel cis XIX -A18-A44 : G-C Ww/Ww pairing antiparallel cis one_hbond -A19-A43 : C-G Ww/Ww pairing antiparallel cis XIX -A20-A42 : A-U Ww/Ww pairing antiparallel cis XX -A21-A41 : G-C Ww/Ww pairing antiparallel cis -A22-A23 : A-U Ss/Hh adjacent_5p pairing antiparallel trans one_hbond -A22-A24 : A-C O2P/Bh pairing -A27-A38 : A-U Ww/Ww pairing antiparallel cis XX -A29-A36 : C-G Ww/Ww pairing antiparallel cis -Residue conformations ------------------------------------------- -A17 : G C4p_exo anti -A18 : G C3p_endo anti -A19 : C C3p_endo anti -A20 : A C3p_endo anti -A21 : G C2p_exo anti -A22 : A C4p_exo anti -A23 : U C2p_exo anti -A24 : C C3p_endo anti -A25 : U C2p_endo anti -A26 : G C2p_exo anti -A27 : A O4p_endo anti -A28 : G O4p_endo anti -A29 : C C2p_exo anti -A30 : C C2p_exo anti -A31 : U C4p_endo anti -A32 : G C2p_exo anti -A33 : G C3p_endo anti -A34 : G O4p_exo anti -A35 : A C1p_exo anti -A36 : G C2p_exo anti -A37 : C C3p_endo anti -A38 : U O4p_endo anti -A39 : C O4p_endo anti -A40 : U C3p_endo anti -A41 : C C3p_endo anti -A42 : U C3p_endo anti -A43 : G C3p_endo anti -A44 : C C4p_exo anti -A45 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A22-A23 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A28-A29 : adjacent_5p upward -A29-A30 : adjacent_5p upward -A36-A37 : adjacent_5p upward -A43-A44 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A20-A43 : outward -A22-A41 : outward -Number of stackings = 13 -Number of adjacent stackings = 11 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A17-A45 : G-C Ww/Ww pairing antiparallel cis -A18-A44 : G-C Ww/Ww pairing antiparallel cis XIX -A19-A43 : C-G Ww/Ww pairing antiparallel cis XIX -A20-A42 : A-U Ww/Ww pairing antiparallel cis XX -A21-A41 : G-C Ww/Ww pairing antiparallel cis XIX -A26-A39 : G-C Ww/Ww pairing antiparallel cis -A27-A38 : A-U Ww/Ww pairing antiparallel cis XX -A28-A37 : G-C Ws/Ws pairing antiparallel cis one_hbond -A28-A38 : G-U Bs/O2' pairing -A29-A36 : C-G Ww/Ww pairing antiparallel cis XIX -A30-A33 : C-G O2'/Ss O2'/C8 pairing -A31-A32 : U-G O2P/Hh adjacent_5p pairing -A31-A33 : U-G O2P/Hh pairing -A33-A34 : G-G O2'/Ss O2'/C8 adjacent_5p pairing -Residue conformations ------------------------------------------- -A17 : G C3p_endo anti -A18 : G C3p_endo anti -A19 : C C2p_exo anti -A20 : A C2p_exo anti -A21 : G C2p_exo anti -A22 : A C1p_endo syn -A23 : U C2p_exo anti -A24 : C C1p_exo anti -A25 : U C3p_endo syn -A26 : G C3p_endo anti -A27 : A C4p_exo anti -A28 : G C4p_exo anti -A29 : C C2p_exo anti -A30 : C C3p_endo anti -A31 : U C3p_endo anti -A32 : G C2p_exo anti -A33 : G C2p_endo anti -A34 : G C2p_exo syn -A35 : A C3p_exo anti -A36 : G C2p_exo anti -A37 : C C3p_endo anti -A38 : U O4p_endo anti -A39 : C C4p_exo anti -A40 : U C2p_exo anti -A41 : C C3p_endo anti -A42 : U C4p_exo anti -A43 : G C3p_endo anti -A44 : C C3p_endo anti -A45 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A18-A19 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A28-A29 : adjacent_5p upward -A36-A37 : adjacent_5p upward -A37-A38 : adjacent_5p upward -A43-A44 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A18-A45 : outward -A20-A43 : outward -A21-A42 : outward -Number of stackings = 11 -Number of adjacent stackings = 8 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -A18-A44 : G-C Ww/Ww pairing antiparallel cis one_hbond -A19-A43 : C-G Ww/Ww pairing antiparallel cis XIX -A20-A42 : A-U Ww/Ww pairing antiparallel cis XX -A27-A38 : A-U Ww/Ww pairing antiparallel cis XX -A29-A36 : C-G Ww/Ww pairing antiparallel cis one_hbond -A31-A33 : U-G Ww/O2P pairing -A33-A34 : G-G O2P/Bs adjacent_5p pairing -A34-A35 : G-A O2'/Hh O2'/C8 adjacent_5p pairing -Residue conformations ------------------------------------------- -A17 : G C3p_endo anti -A18 : G C3p_endo anti -A19 : C C3p_endo anti -A20 : A C3p_endo anti -A21 : G C3p_endo anti -A22 : A C2p_exo anti -A23 : U C2p_exo anti -A24 : C C3p_endo anti -A25 : U C3p_endo syn -A26 : G C3p_endo anti -A27 : A C4p_exo anti -A28 : G O4p_endo anti -A29 : C C2p_exo anti -A30 : C O4p_endo anti -A31 : U C3p_endo anti -A32 : G C3p_endo anti -A33 : G C3p_exo anti -A34 : G C3p_endo anti -A35 : A C2p_endo anti -A36 : G C2p_exo anti -A37 : C C3p_endo anti -A38 : U C3p_endo anti -A39 : C C3p_endo anti -A40 : U C2p_exo anti -A41 : C C3p_endo anti -A42 : U C3p_endo anti -A43 : G C3p_endo anti -A44 : C C2p_exo anti -A45 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A18-A19 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A37-A38 : adjacent_5p upward -A43-A44 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A18-A45 : outward -A20-A43 : outward -A27-A39 : outward -Number of stackings = 12 -Number of adjacent stackings = 9 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -A17-A45 : G-C Ww/Ww pairing antiparallel cis -A18-A44 : G-C Ww/Ww pairing antiparallel cis XIX -A19-A43 : C-G Ww/Ww pairing antiparallel cis XIX -A20-A42 : A-U Ww/Ww pairing antiparallel cis XX -A21-A41 : G-C Ww/Ww pairing antiparallel cis XIX -A22-A40 : A-U Bs/Ws pairing antiparallel cis one_hbond -A26-A39 : G-C Ww/Ww pairing antiparallel cis XIX -A27-A38 : A-U Ww/Ww pairing antiparallel cis XX -A28-A37 : G-C Ww/Ww pairing antiparallel cis XIX -A29-A36 : C-G Ws/Ww pairing antiparallel cis one_hbond -A31-A32 : U-G Ww/Hw adjacent_5p pairing parallel cis one_hbond -Residue conformations ------------------------------------------- -A17 : G C3p_endo anti -A18 : G C2p_exo anti -A19 : C C3p_endo anti -A20 : A C3p_endo anti -A21 : G C2p_exo anti -A22 : A C3p_endo anti -A23 : U C3p_exo anti -A24 : C C3p_endo anti -A25 : U C1p_exo syn -A26 : G C3p_endo anti -A27 : A O4p_endo anti -A28 : G O4p_endo anti -A29 : C C2p_exo anti -A30 : C C2p_exo anti -A31 : U C3p_endo anti -A32 : G C3p_endo anti -A33 : G C2p_endo anti -A34 : G C2p_exo anti -A35 : A C4p_endo anti -A36 : G C2p_exo anti -A37 : C C3p_endo anti -A38 : U C2p_exo anti -A39 : C C3p_endo anti -A40 : U C3p_endo anti -A41 : C C3p_endo anti -A42 : U C2p_exo anti -A43 : G C3p_endo anti -A44 : C C2p_exo anti -A45 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A22-A23 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A36-A37 : adjacent_5p upward -A39-A40 : adjacent_5p upward -A43-A44 : adjacent_5p upward -A44-A45 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A20-A43 : outward -A21-A42 : outward -A22-A41 : outward -Number of stackings = 15 -Number of adjacent stackings = 12 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -A17-A45 : G-C Ww/Ww pairing antiparallel cis -A19-A43 : C-G Ww/Ww pairing antiparallel cis XIX -A20-A42 : A-U Ww/Ww pairing antiparallel cis XX -A21-A41 : G-C Ww/Ww pairing antiparallel cis -A26-A39 : G-C Ww/Ww pairing antiparallel cis XIX -A27-A38 : A-U Ww/Ww pairing antiparallel cis XX -A29-A36 : C-G Ww/Ww pairing antiparallel cis XIX -A34-A35 : G-A O2'/Hh O2'/C8 adjacent_5p pairing diff --git a/MCdata/1aq3_MC b/MCdata/1aq3_MC deleted file mode 100644 index 8e8cff28621cbc0b713dd54b5230368c68112f47..0000000000000000000000000000000000000000 --- a/MCdata/1aq3_MC +++ /dev/null @@ -1,663 +0,0 @@ -Residue conformations ------------------------------------------- -R3 : A C3p_endo anti -R4 : U C3p_endo anti -R5 : G C3p_endo anti -R6 : A C2p_exo syn -R7 : G C3p_endo anti -R8 : G C3p_endo anti -R9 : A C3p_endo anti -R10 : U C2p_endo anti -R11 : U C2p_endo anti -R12 : A C2p_endo anti -R13 : C C3p_endo anti -R14 : C C3p_endo anti -R15 : C C3p_endo anti -R16 : A C3p_endo anti -R17 : U C3p_endo anti -R18 : G C4p_exo anti -S4 : U C3p_endo anti -S5 : G C3p_endo anti -S6 : A C2p_exo syn -S7 : G C3p_endo anti -S8 : G C3p_endo anti -S9 : A C3p_endo anti -S10 : U C1p_exo anti -S11 : U C2p_endo anti -S12 : A C2p_endo anti -S13 : C C3p_endo anti -S14 : C C3p_endo anti -S15 : C C3p_endo anti -A1 : ALA -A2 : SER -A3 : ASN -A4 : PHE -A5 : THR -A6 : GLN -A7 : PHE -A8 : VAL -A9 : LEU -A10 : VAL -A11 : ASP -A12 : ASN -A13 : GLY -A14 : GLY -A15 : THR -A16 : GLY -A17 : ASP -A18 : VAL -A19 : THR -A20 : VAL -A21 : ALA -A22 : PRO -A23 : SER -A24 : ASN -A25 : PHE -A26 : ALA -A27 : ASN -A28 : GLY -A29 : VAL -A30 : ALA -A31 : GLU -A32 : TRP -A33 : ILE -A34 : SER -A35 : SER -A36 : ASN -A37 : SER -A38 : ARG -A39 : SER -A40 : GLN -A41 : ALA -A42 : TYR -A43 : LYS -A44 : VAL -A45 : THR -A46 : CYS -A47 : SER -A48 : VAL -A49 : ARG -A50 : GLN -A51 : SER -A52 : SER -A53 : ALA -A54 : GLN -A55 : ASN -A56 : ARG -A57 : LYS -A58 : TYR -A59 : SER -A60 : ILE -A61 : LYS -A62 : VAL -A63 : GLU -A64 : VAL -A65 : PRO -A66 : LYS -A67 : VAL -A68 : ALA -A69 : THR -A70 : GLN -A71 : THR -A72 : VAL -A73 : GLY -A74 : GLY -A75 : VAL -A76 : GLU -A77 : LEU -A78 : PRO -A79 : VAL -A80 : ALA -A81 : ALA -A82 : TRP -A83 : ARG -A84 : SER -A85 : TYR -A86 : LEU -A87 : ASN -A88 : MET -A89 : GLU -A90 : LEU -A91 : THR -A92 : ILE -A93 : PRO -A94 : ILE -A95 : PHE -A96 : ALA -A97 : THR -A98 : ASN -A99 : SER -A100 : ASP -A101 : CYS -A102 : GLU -A103 : LEU -A104 : ILE -A105 : VAL -A106 : LYS -A107 : ALA -A108 : MET -A109 : GLN -A110 : GLY -A111 : LEU -A112 : LEU -A113 : LYS -A114 : ASP -A115 : GLY -A116 : ASN -A117 : PRO -A118 : ILE -A119 : PRO -A120 : SER -A121 : ALA -A122 : ILE -A123 : ALA -A124 : ALA -A125 : ASN -A126 : SER -A127 : GLY -A128 : ILE -A129 : TYR -B1 : ALA -B2 : SER -B3 : ASN -B4 : PHE -B5 : THR -B6 : GLN -B7 : PHE -B8 : VAL -B9 : LEU -B10 : VAL -B11 : ASP -B12 : ASN -B13 : GLY -B14 : GLY -B15 : THR -B16 : GLY -B17 : ASP -B18 : VAL -B19 : THR -B20 : VAL -B21 : ALA -B22 : PRO -B23 : SER -B24 : ASN -B25 : PHE -B26 : ALA -B27 : ASN -B28 : GLY -B29 : VAL -B30 : ALA -B31 : GLU -B32 : TRP -B33 : ILE -B34 : SER -B35 : SER -B36 : ASN -B37 : SER -B38 : ARG -B39 : SER -B40 : GLN -B41 : ALA -B42 : TYR -B43 : LYS -B44 : VAL -B45 : THR -B46 : CYS -B47 : SER -B48 : VAL -B49 : ARG -B50 : GLN -B51 : SER -B52 : SER -B53 : ALA -B54 : GLN -B55 : ASN -B56 : ARG -B57 : LYS -B58 : TYR -B59 : SER -B60 : ILE -B61 : LYS -B62 : VAL -B63 : GLU -B64 : VAL -B65 : PRO -B66 : LYS -B67 : VAL -B68 : ALA -B69 : THR -B70 : GLN -B71 : THR -B72 : VAL -B73 : GLY -B74 : GLY -B75 : VAL -B76 : GLU -B77 : LEU -B78 : PRO -B79 : VAL -B80 : ALA -B81 : ALA -B82 : TRP -B83 : ARG -B84 : SER -B85 : TYR -B86 : LEU -B87 : ASN -B88 : MET -B89 : GLU -B90 : LEU -B91 : THR -B92 : ILE -B93 : PRO -B94 : ILE -B95 : PHE -B96 : ALA -B97 : THR -B98 : ASN -B99 : SER -B100 : ASP -B101 : CYS -B102 : GLU -B103 : LEU -B104 : ILE -B105 : VAL -B106 : LYS -B107 : ALA -B108 : MET -B109 : GLN -B110 : GLY -B111 : LEU -B112 : LEU -B113 : LYS -B114 : ASP -B115 : GLY -B116 : ASN -B117 : PRO -B118 : ILE -B119 : PRO -B120 : SER -B121 : ALA -B122 : ILE -B123 : ALA -B124 : ALA -B125 : ASN -B126 : SER -B127 : GLY -B128 : ILE -B129 : TYR -C1 : ALA -C2 : SER -C3 : ASN -C4 : PHE -C5 : THR -C6 : GLN -C7 : PHE -C8 : VAL -C9 : LEU -C10 : VAL -C11 : ASP -C12 : ASN -C13 : GLY -C14 : GLY -C15 : THR -C16 : GLY -C17 : ASP -C18 : VAL -C19 : THR -C20 : VAL -C21 : ALA -C22 : PRO -C23 : SER -C24 : ASN -C25 : PHE -C26 : ALA -C27 : ASN -C28 : GLY -C29 : VAL -C30 : ALA -C31 : GLU -C32 : TRP -C33 : ILE -C34 : SER -C35 : SER -C36 : ASN -C37 : SER -C38 : ARG -C39 : SER -C40 : GLN -C41 : ALA -C42 : TYR -C43 : LYS -C44 : VAL -C45 : THR -C46 : CYS -C47 : SER -C48 : VAL -C49 : ARG -C50 : GLN -C51 : SER -C52 : SER -C53 : ALA -C54 : GLN -C55 : ASN -C56 : ARG -C57 : LYS -C58 : TYR -C59 : SER -C60 : ILE -C61 : LYS -C62 : VAL -C63 : GLU -C64 : VAL -C65 : PRO -C66 : LYS -C67 : VAL -C68 : ALA -C69 : THR -C70 : GLN -C71 : THR -C72 : VAL -C73 : GLY -C74 : GLY -C75 : VAL -C76 : GLU -C77 : LEU -C78 : PRO -C79 : VAL -C80 : ALA -C81 : ALA -C82 : TRP -C83 : ARG -C84 : SER -C85 : TYR -C86 : LEU -C87 : ASN -C88 : MET -C89 : GLU -C90 : LEU -C91 : THR -C92 : ILE -C93 : PRO -C94 : ILE -C95 : PHE -C96 : ALA -C97 : THR -C98 : ASN -C99 : SER -C100 : ASP -C101 : CYS -C102 : GLU -C103 : LEU -C104 : ILE -C105 : VAL -C106 : LYS -C107 : ALA -C108 : MET -C109 : GLN -C110 : GLY -C111 : LEU -C112 : LEU -C113 : LYS -C114 : ASP -C115 : GLY -C116 : ASN -C117 : PRO -C118 : ILE -C119 : PRO -C120 : SER -C121 : ALA -C122 : ILE -C123 : ALA -C124 : ALA -C125 : ASN -C126 : SER -C127 : GLY -C128 : ILE -C129 : TYR -R60 : HOH -R214 : HOH -R2059 : HOH -S169 : HOH -A130 : HOH -A131 : HOH -A132 : HOH -A133 : HOH -A134 : HOH -A135 : HOH -A136 : HOH -A137 : HOH -A138 : HOH -A139 : HOH -A140 : HOH -A141 : HOH -A142 : HOH -A143 : HOH -A144 : HOH -A145 : HOH -A146 : HOH -A147 : HOH -A148 : HOH -A149 : HOH -A150 : HOH -A151 : HOH -A152 : HOH -A153 : HOH -A154 : HOH -A155 : HOH -A156 : HOH -A157 : HOH -A158 : HOH -A159 : HOH -A160 : HOH -A161 : HOH -A162 : HOH -A163 : HOH -A164 : HOH -A165 : HOH -A166 : HOH -A167 : HOH -A168 : HOH -A169 : HOH -A170 : HOH -A171 : HOH -A172 : HOH -A173 : HOH -A174 : HOH -A175 : HOH -A176 : HOH -A177 : HOH -A178 : HOH -A179 : HOH -A180 : HOH -A181 : HOH -A182 : HOH -A183 : HOH -A184 : HOH -A185 : HOH -A186 : HOH -A187 : HOH -A188 : HOH -A189 : HOH -A190 : HOH -A191 : HOH -A192 : HOH -A193 : HOH -A194 : HOH -A195 : HOH -A196 : HOH -A197 : HOH -A198 : HOH -A199 : HOH -A200 : HOH -A201 : HOH -A202 : HOH -A203 : HOH -B130 : HOH -B131 : HOH -B132 : HOH -B133 : HOH -B134 : HOH -B135 : HOH -B136 : HOH -B137 : HOH -B138 : HOH -B139 : HOH -B140 : HOH -B141 : HOH -B142 : HOH -B143 : HOH -B144 : HOH -B145 : HOH -B146 : HOH -B147 : HOH -B148 : HOH -B149 : HOH -B150 : HOH -B151 : HOH -B152 : HOH -B153 : HOH -B154 : HOH -B155 : HOH -B156 : HOH -B157 : HOH -B158 : HOH -B159 : HOH -B160 : HOH -B161 : HOH -B162 : HOH -B163 : HOH -B164 : HOH -B165 : HOH -B166 : HOH -B167 : HOH -B168 : HOH -B169 : HOH -B170 : HOH -B171 : HOH -B172 : HOH -B173 : HOH -B174 : HOH -B175 : HOH -B176 : HOH -B177 : HOH -B178 : HOH -B179 : HOH -B180 : HOH -B181 : HOH -B182 : HOH -B183 : HOH -B184 : HOH -B185 : HOH -B186 : HOH -B187 : HOH -B188 : HOH -B189 : HOH -B190 : HOH -B191 : HOH -B192 : HOH -B193 : HOH -B194 : HOH -B195 : HOH -B196 : HOH -C130 : HOH -C131 : HOH -C132 : HOH -C133 : HOH -C134 : HOH -C135 : HOH -C136 : HOH -C137 : HOH -C138 : HOH -C139 : HOH -C140 : HOH -C141 : HOH -C142 : HOH -C143 : HOH -C144 : HOH -C145 : HOH -C146 : HOH -C147 : HOH -C148 : HOH -C149 : HOH -C150 : HOH -C151 : HOH -C152 : HOH -C153 : HOH -C154 : HOH -C155 : HOH -C156 : HOH -C157 : HOH -C158 : HOH -C159 : HOH -C160 : HOH -C161 : HOH -C162 : HOH -C163 : HOH -C164 : HOH -C165 : HOH -C166 : HOH -C167 : HOH -C168 : HOH -C169 : HOH -C170 : HOH -C171 : HOH -C172 : HOH -C173 : HOH -C174 : HOH -C175 : HOH -C176 : HOH -C177 : HOH -C178 : HOH -C179 : HOH -C180 : HOH -C181 : HOH -C182 : HOH -C183 : HOH -C184 : HOH -C185 : HOH -C186 : HOH -C187 : HOH -C188 : HOH -C189 : HOH -C190 : HOH -C191 : HOH -C192 : HOH -C193 : HOH -C194 : HOH -C195 : HOH -C196 : HOH -C197 : HOH -C198 : HOH -C199 : HOH -C200 : HOH -Adjacent stackings ---------------------------------------------- -R3-R4 : adjacent_5p upward -R7-R8 : adjacent_5p upward -R8-R9 : adjacent_5p upward -R15-R16 : adjacent_5p upward -R16-R17 : adjacent_5p upward -S4-S5 : adjacent_5p upward -S7-S8 : adjacent_5p upward -S8-S9 : adjacent_5p upward -S13-S14 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -R3-R18 : outward -R5-R7 : upward -R5-R16 : outward -R9-R11 : upward -S5-S7 : upward -S7-S15 : outward -S9-S11 : upward -S9-S13 : outward -Number of stackings = 17 -Number of adjacent stackings = 9 -Number of non adjacent stackings = 8 -Base-pairs ------------------------------------------------------ -R3-R17 : A-U Ww/Ww pairing antiparallel cis XX -R4-R16 : U-A Ww/Ww pairing antiparallel cis XX -R5-R15 : G-C Ww/Ww pairing antiparallel cis XIX -R7-R14 : G-C Ww/Ww pairing antiparallel cis XIX -R8-R13 : G-C Ww/Ww pairing antiparallel cis XIX -S5-S15 : G-C Ww/Ww pairing antiparallel cis XIX -S7-S14 : G-C Ww/Ww pairing antiparallel cis XIX -S8-S13 : G-C Ww/Ww pairing antiparallel cis XIX diff --git a/MCdata/1aq4_MC b/MCdata/1aq4_MC deleted file mode 100644 index 593c7ef682b595ef93568d0987489a229caf506c..0000000000000000000000000000000000000000 --- a/MCdata/1aq4_MC +++ /dev/null @@ -1,667 +0,0 @@ -Residue conformations ------------------------------------------- -R3 : A C3p_endo anti -R4 : U C3p_endo anti -R5 : G C3p_endo anti -R6 : A C2p_exo syn -R7 : G C3p_endo anti -R8 : G C3p_endo anti -R9 : A C3p_endo anti -R10 : U C2p_endo anti -R11 : U C2p_endo anti -R12 : A C2p_endo anti -R13 : C C3p_endo anti -R14 : C C3p_endo anti -R15 : C C3p_endo anti -R16 : A C3p_endo anti -R17 : U C3p_endo anti -R18 : G C4p_exo anti -S3 : A C3p_endo anti -S4 : U C3p_endo anti -S5 : G C3p_endo anti -S6 : A C2p_exo syn -S7 : G C3p_endo anti -S8 : G C3p_endo anti -S9 : A C3p_endo anti -S10 : U C2p_endo anti -S11 : U C2p_endo anti -S12 : A C2p_endo anti -S13 : C C3p_endo anti -S14 : C C3p_endo anti -S15 : C C3p_endo anti -S16 : A C3p_endo anti -A1 : ALA -A2 : SER -A3 : ASN -A4 : PHE -A5 : THR -A6 : GLN -A7 : PHE -A8 : VAL -A9 : LEU -A10 : VAL -A11 : ASP -A12 : ASN -A13 : GLY -A14 : GLY -A15 : THR -A16 : GLY -A17 : ASP -A18 : VAL -A19 : THR -A20 : VAL -A21 : ALA -A22 : PRO -A23 : SER -A24 : ASN -A25 : PHE -A26 : ALA -A27 : ASN -A28 : GLY -A29 : VAL -A30 : ALA -A31 : GLU -A32 : TRP -A33 : ILE -A34 : SER -A35 : SER -A36 : ASN -A37 : SER -A38 : ARG -A39 : SER -A40 : GLN -A41 : ALA -A42 : TYR -A43 : LYS -A44 : VAL -A45 : ALA -A46 : CYS -A47 : SER -A48 : VAL -A49 : ARG -A50 : GLN -A51 : SER -A52 : SER -A53 : ALA -A54 : GLN -A55 : ASN -A56 : ARG -A57 : LYS -A58 : TYR -A59 : THR -A60 : ILE -A61 : LYS -A62 : VAL -A63 : GLU -A64 : VAL -A65 : PRO -A66 : LYS -A67 : VAL -A68 : ALA -A69 : THR -A70 : GLN -A71 : THR -A72 : VAL -A73 : GLY -A74 : GLY -A75 : VAL -A76 : GLU -A77 : LEU -A78 : PRO -A79 : VAL -A80 : ALA -A81 : ALA -A82 : TRP -A83 : ARG -A84 : SER -A85 : TYR -A86 : LEU -A87 : ASN -A88 : MET -A89 : GLU -A90 : LEU -A91 : THR -A92 : ILE -A93 : PRO -A94 : ILE -A95 : PHE -A96 : ALA -A97 : THR -A98 : ASN -A99 : SER -A100 : ASP -A101 : CYS -A102 : GLU -A103 : LEU -A104 : ILE -A105 : VAL -A106 : LYS -A107 : ALA -A108 : MET -A109 : GLN -A110 : GLY -A111 : LEU -A112 : LEU -A113 : LYS -A114 : ASP -A115 : GLY -A116 : ASN -A117 : PRO -A118 : ILE -A119 : PRO -A120 : SER -A121 : ALA -A122 : ILE -A123 : ALA -A124 : ALA -A125 : ASN -A126 : SER -A127 : GLY -A128 : ILE -A129 : TYR -B1 : ALA -B2 : SER -B3 : ASN -B4 : PHE -B5 : THR -B6 : GLN -B7 : PHE -B8 : VAL -B9 : LEU -B10 : VAL -B11 : ASP -B12 : ASN -B13 : GLY -B14 : GLY -B15 : THR -B16 : GLY -B17 : ASP -B18 : VAL -B19 : THR -B20 : VAL -B21 : ALA -B22 : PRO -B23 : SER -B24 : ASN -B25 : PHE -B26 : ALA -B27 : ASN -B28 : GLY -B29 : VAL -B30 : ALA -B31 : GLU -B32 : TRP -B33 : ILE -B34 : SER -B35 : SER -B36 : ASN -B37 : SER -B38 : ARG -B39 : SER -B40 : GLN -B41 : ALA -B42 : TYR -B43 : LYS -B44 : VAL -B45 : ALA -B46 : CYS -B47 : SER -B48 : VAL -B49 : ARG -B50 : GLN -B51 : SER -B52 : SER -B53 : ALA -B54 : GLN -B55 : ASN -B56 : ARG -B57 : LYS -B58 : TYR -B59 : THR -B60 : ILE -B61 : LYS -B62 : VAL -B63 : GLU -B64 : VAL -B65 : PRO -B66 : LYS -B67 : VAL -B68 : ALA -B69 : THR -B70 : GLN -B71 : THR -B72 : VAL -B73 : GLY -B74 : GLY -B75 : VAL -B76 : GLU -B77 : LEU -B78 : PRO -B79 : VAL -B80 : ALA -B81 : ALA -B82 : TRP -B83 : ARG -B84 : SER -B85 : TYR -B86 : LEU -B87 : ASN -B88 : MET -B89 : GLU -B90 : LEU -B91 : THR -B92 : ILE -B93 : PRO -B94 : ILE -B95 : PHE -B96 : ALA -B97 : THR -B98 : ASN -B99 : SER -B100 : ASP -B101 : CYS -B102 : GLU -B103 : LEU -B104 : ILE -B105 : VAL -B106 : LYS -B107 : ALA -B108 : MET -B109 : GLN -B110 : GLY -B111 : LEU -B112 : LEU -B113 : LYS -B114 : ASP -B115 : GLY -B116 : ASN -B117 : PRO -B118 : ILE -B119 : PRO -B120 : SER -B121 : ALA -B122 : ILE -B123 : ALA -B124 : ALA -B125 : ASN -B126 : SER -B127 : GLY -B128 : ILE -B129 : TYR -C1 : ALA -C2 : SER -C3 : ASN -C4 : PHE -C5 : THR -C6 : GLN -C7 : PHE -C8 : VAL -C9 : LEU -C10 : VAL -C11 : ASP -C12 : ASN -C13 : GLY -C14 : GLY -C15 : THR -C16 : GLY -C17 : ASP -C18 : VAL -C19 : THR -C20 : VAL -C21 : ALA -C22 : PRO -C23 : SER -C24 : ASN -C25 : PHE -C26 : ALA -C27 : ASN -C28 : GLY -C29 : VAL -C30 : ALA -C31 : GLU -C32 : TRP -C33 : ILE -C34 : SER -C35 : SER -C36 : ASN -C37 : SER -C38 : ARG -C39 : SER -C40 : GLN -C41 : ALA -C42 : TYR -C43 : LYS -C44 : VAL -C45 : ALA -C46 : CYS -C47 : SER -C48 : VAL -C49 : ARG -C50 : GLN -C51 : SER -C52 : SER -C53 : ALA -C54 : GLN -C55 : ASN -C56 : ARG -C57 : LYS -C58 : TYR -C59 : THR -C60 : ILE -C61 : LYS -C62 : VAL -C63 : GLU -C64 : VAL -C65 : PRO -C66 : LYS -C67 : VAL -C68 : ALA -C69 : THR -C70 : GLN -C71 : THR -C72 : VAL -C73 : GLY -C74 : GLY -C75 : VAL -C76 : GLU -C77 : LEU -C78 : PRO -C79 : VAL -C80 : ALA -C81 : ALA -C82 : TRP -C83 : ARG -C84 : SER -C85 : TYR -C86 : LEU -C87 : ASN -C88 : MET -C89 : GLU -C90 : LEU -C91 : THR -C92 : ILE -C93 : PRO -C94 : ILE -C95 : PHE -C96 : ALA -C97 : THR -C98 : ASN -C99 : SER -C100 : ASP -C101 : CYS -C102 : GLU -C103 : LEU -C104 : ILE -C105 : VAL -C106 : LYS -C107 : ALA -C108 : MET -C109 : GLN -C110 : GLY -C111 : LEU -C112 : LEU -C113 : LYS -C114 : ASP -C115 : GLY -C116 : ASN -C117 : PRO -C118 : ILE -C119 : PRO -C120 : SER -C121 : ALA -C122 : ILE -C123 : ALA -C124 : ALA -C125 : ASN -C126 : SER -C127 : GLY -C128 : ILE -C129 : TYR -R214 : HOH -R2059 : HOH -S166 : HOH -S169 : HOH -A130 : HOH -A131 : HOH -A132 : HOH -A133 : HOH -A134 : HOH -A135 : HOH -A136 : HOH -A137 : HOH -A138 : HOH -A139 : HOH -A140 : HOH -A141 : HOH -A142 : HOH -A143 : HOH -A144 : HOH -A145 : HOH -A146 : HOH -A147 : HOH -A148 : HOH -A149 : HOH -A150 : HOH -A151 : HOH -A152 : HOH -A153 : HOH -A154 : HOH -A155 : HOH -A156 : HOH -A157 : HOH -A158 : HOH -A159 : HOH -A160 : HOH -A161 : HOH -A162 : HOH -A163 : HOH -A164 : HOH -A165 : HOH -A166 : HOH -A167 : HOH -A168 : HOH -A169 : HOH -A170 : HOH -A171 : HOH -A172 : HOH -A173 : HOH -A174 : HOH -A175 : HOH -A176 : HOH -A177 : HOH -A178 : HOH -A179 : HOH -A180 : HOH -A181 : HOH -A182 : HOH -A183 : HOH -A184 : HOH -A185 : HOH -A186 : HOH -A187 : HOH -A188 : HOH -A189 : HOH -A190 : HOH -A191 : HOH -A192 : HOH -A193 : HOH -A194 : HOH -A195 : HOH -A196 : HOH -A197 : HOH -A198 : HOH -A199 : HOH -A200 : HOH -A201 : HOH -B130 : HOH -B131 : HOH -B132 : HOH -B133 : HOH -B134 : HOH -B135 : HOH -B136 : HOH -B137 : HOH -B138 : HOH -B139 : HOH -B140 : HOH -B141 : HOH -B142 : HOH -B143 : HOH -B144 : HOH -B145 : HOH -B146 : HOH -B147 : HOH -B148 : HOH -B149 : HOH -B150 : HOH -B151 : HOH -B152 : HOH -B153 : HOH -B154 : HOH -B155 : HOH -B156 : HOH -B157 : HOH -B158 : HOH -B159 : HOH -B160 : HOH -B161 : HOH -B162 : HOH -B163 : HOH -B164 : HOH -B165 : HOH -B166 : HOH -B167 : HOH -B168 : HOH -B169 : HOH -B170 : HOH -B171 : HOH -B172 : HOH -B173 : HOH -B174 : HOH -B175 : HOH -B176 : HOH -B177 : HOH -B178 : HOH -B179 : HOH -B180 : HOH -B181 : HOH -B182 : HOH -B183 : HOH -B184 : HOH -B185 : HOH -B186 : HOH -B187 : HOH -B188 : HOH -B189 : HOH -B190 : HOH -B191 : HOH -B192 : HOH -B193 : HOH -B194 : HOH -B195 : HOH -B196 : HOH -C130 : HOH -C131 : HOH -C132 : HOH -C133 : HOH -C134 : HOH -C135 : HOH -C136 : HOH -C137 : HOH -C138 : HOH -C139 : HOH -C140 : HOH -C141 : HOH -C142 : HOH -C143 : HOH -C144 : HOH -C145 : HOH -C146 : HOH -C147 : HOH -C148 : HOH -C149 : HOH -C150 : HOH -C151 : HOH -C152 : HOH -C153 : HOH -C154 : HOH -C155 : HOH -C156 : HOH -C157 : HOH -C158 : HOH -C159 : HOH -C160 : HOH -C161 : HOH -C162 : HOH -C163 : HOH -C164 : HOH -C165 : HOH -C166 : HOH -C167 : HOH -C168 : HOH -C169 : HOH -C170 : HOH -C171 : HOH -C172 : HOH -C173 : HOH -C174 : HOH -C175 : HOH -C176 : HOH -C177 : HOH -C178 : HOH -C179 : HOH -C180 : HOH -C181 : HOH -C182 : HOH -C183 : HOH -C184 : HOH -C185 : HOH -C186 : HOH -C187 : HOH -C188 : HOH -C189 : HOH -C190 : HOH -C191 : HOH -C192 : HOH -C193 : HOH -C194 : HOH -C195 : HOH -C196 : HOH -C197 : HOH -C198 : HOH -C199 : HOH -C200 : HOH -Adjacent stackings ---------------------------------------------- -R3-R4 : adjacent_5p upward -R4-R5 : adjacent_5p upward -R7-R8 : adjacent_5p upward -R8-R9 : adjacent_5p upward -R15-R16 : adjacent_5p upward -R16-R17 : adjacent_5p upward -S3-S4 : adjacent_5p upward -S4-S5 : adjacent_5p upward -S7-S8 : adjacent_5p upward -S8-S9 : adjacent_5p upward -S13-S14 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -R3-R18 : outward -R5-R7 : upward -R5-R16 : outward -R9-R11 : upward -S5-S7 : upward -S5-S16 : outward -S7-S15 : outward -S9-S11 : upward -S9-S13 : outward -Number of stackings = 20 -Number of adjacent stackings = 11 -Number of non adjacent stackings = 9 -Base-pairs ------------------------------------------------------ -R3-R17 : A-U Ww/Ww pairing antiparallel cis XX -R4-R16 : U-A Ww/Ww pairing antiparallel cis XX -R5-R15 : G-C Ww/Ww pairing antiparallel cis XIX -R7-R14 : G-C Ww/Ww pairing antiparallel cis XIX -R8-R13 : G-C Ww/Ww pairing antiparallel cis XIX -S4-S16 : U-A Ww/Ww pairing antiparallel cis XX -S5-S15 : G-C Ww/Ww pairing antiparallel cis XIX -S7-S14 : G-C Ww/Ww pairing antiparallel cis XIX -S8-S13 : G-C Ww/Ww pairing antiparallel cis XIX diff --git a/MCdata/1aqo_MC b/MCdata/1aqo_MC deleted file mode 100644 index f1d883911d9b14939e929f52031e8760804ca4af..0000000000000000000000000000000000000000 --- a/MCdata/1aqo_MC +++ /dev/null @@ -1,1014 +0,0 @@ -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : A C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : G C2p_endo anti -A7 : C C2p_endo anti -A8 : U C3p_endo anti -A9 : U C3p_endo anti -A10 : C C3p_endo anti -A11 : A C3p_endo anti -A12 : A C3p_endo anti -A13 : C C3p_endo anti -A14 : A C3p_endo anti -A15 : G C3p_exo syn -A16 : U C2p_endo anti -A17 : G C2p_endo anti -A18 : C C2p_endo anti -A19 : U C3p_endo anti -A20 : U C3p_endo anti -A21 : G C3p_endo anti -A22 : G C3p_endo anti -A23 : A C3p_endo anti -A24 : C C3p_endo anti -A25 : G C3p_endo anti -A26 : C C3p_endo anti -A27 : U C3p_endo anti -A28 : C C3p_endo anti -A29 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A22-A23 : adjacent_5p upward -A23-A24 : adjacent_5p upward pairing -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A3-A28 : outward -A6-A25 : outward -A14-A17 : outward -A17-A19 : upward -Number of stackings = 18 -Number of adjacent stackings = 14 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A1-A29 : G-C Ww/Ww pairing antiparallel cis -A2-A28 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A27 : A-U Ww/Ww pairing antiparallel cis XX -A4-A26 : G-C Ww/Ww pairing antiparallel cis -A5-A25 : U-G Ww/Wh pairing antiparallel cis one_hbond -A6-A24 : G-C Ww/Ww pairing antiparallel cis XIX -A9-A22 : U-G Ws/Ww pairing antiparallel cis XXVIII -A11-A20 : A-U Ww/Ww pairing antiparallel cis XX -A12-A19 : A-U Ww/Ww pairing antiparallel cis XX -A13-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A23-A24 : A-C O2P/Bh adjacent_5p upward pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : A C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : G C2p_endo anti -A7 : C C2p_endo anti -A8 : U C3p_endo anti -A9 : U C4p_exo anti -A10 : C C3p_endo anti -A11 : A C3p_endo anti -A12 : A C3p_endo anti -A13 : C C3p_endo anti -A14 : A C3p_endo anti -A15 : G C3p_exo syn -A16 : U C3p_exo anti -A17 : G C3p_exo syn -A18 : C C2p_endo anti -A19 : U C4p_exo anti -A20 : U C3p_endo anti -A21 : G C3p_endo anti -A22 : G C3p_endo anti -A23 : A C3p_endo anti -A24 : C C3p_endo anti -A25 : G C3p_endo anti -A26 : C C3p_endo anti -A27 : U C3p_endo anti -A28 : C C3p_endo anti -A29 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A22-A23 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A27-A28 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A27 : outward -A6-A25 : outward -A11-A21 : outward -A14-A17 : outward -Number of stackings = 17 -Number of adjacent stackings = 13 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A1-A29 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A28 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A27 : A-U Ww/Ww pairing antiparallel cis XX -A4-A26 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A25 : U-G Ww/Wh pairing antiparallel cis one_hbond -A7-A9 : C-U Ws/Hh pairing parallel cis one_hbond -A7-A17 : C-G Hw/Hh pairing antiparallel cis one_hbond 116 -A8-A23 : U-A Ww/Ww pairing antiparallel cis XX -A9-A22 : U-G Ws/Ww pairing antiparallel cis XXVIII -A10-A21 : C-G Ww/Ww pairing antiparallel cis XIX -A11-A20 : A-U Ww/Ww pairing antiparallel cis XX -A16-A17 : U-G O2'/Hh adjacent_5p pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : A C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : G C2p_endo anti -A7 : C C2p_endo anti -A8 : U C3p_endo anti -A9 : U C4p_exo anti -A10 : C C3p_endo anti -A11 : A C3p_endo anti -A12 : A C3p_endo anti -A13 : C C3p_endo anti -A14 : A C3p_endo anti -A15 : G C3p_exo syn -A16 : U C2p_endo anti -A17 : G C3p_exo anti -A18 : C C2p_endo anti -A19 : U C4p_exo anti -A20 : U C3p_endo anti -A21 : G C3p_endo anti -A22 : G C3p_endo anti -A23 : A C3p_endo anti -A24 : C C3p_endo anti -A25 : G C3p_endo anti -A26 : C C3p_endo anti -A27 : U C3p_endo anti -A28 : C C3p_endo anti -A29 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A22-A23 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A24-A25 : adjacent_5p upward -A25-A26 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A11-A21 : outward -A12-A20 : outward -A14-A17 : outward -A17-A19 : upward -Number of stackings = 17 -Number of adjacent stackings = 13 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A1-A29 : G-C Ww/Ww pairing antiparallel cis 128 -A2-A28 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A27 : A-U Ww/Ww pairing antiparallel cis XX -A4-A26 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A25 : U-G Ww/Wh pairing antiparallel cis one_hbond -A6-A7 : G-C O2'/Hh adjacent_5p pairing -A6-A24 : G-C Ww/Ww pairing antiparallel cis XIX -A7-A8 : C-U Ss/Hh adjacent_5p pairing parallel cis one_hbond -A8-A23 : U-A Ww/Ww pairing antiparallel cis XX -A9-A22 : U-G Ws/Ww pairing antiparallel cis XXVIII -A10-A21 : C-G Ww/Ww pairing antiparallel cis XIX -A11-A20 : A-U Ww/Ww pairing antiparallel cis XX -A12-A19 : A-U Ww/Ww pairing antiparallel cis XX -A13-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A14-A16 : A-U Ss/O2P pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : A C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : G C2p_endo anti -A7 : C C2p_endo anti -A8 : U C3p_endo anti -A9 : U C3p_endo anti -A10 : C C3p_endo anti -A11 : A C3p_endo anti -A12 : A C3p_endo anti -A13 : C C3p_endo anti -A14 : A C3p_endo anti -A15 : G C3p_exo syn -A16 : U C2p_endo anti -A17 : G C3p_exo syn -A18 : C C2p_endo anti -A19 : U C4p_exo anti -A20 : U C3p_endo anti -A21 : G C3p_endo anti -A22 : G C3p_endo anti -A23 : A C3p_endo anti -A24 : C C3p_endo anti -A25 : G C3p_endo anti -A26 : C C3p_endo anti -A27 : U C3p_endo anti -A28 : C C3p_endo anti -A29 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A22-A23 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A27-A28 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A6-A25 : outward -A11-A21 : outward -A14-A17 : outward -A17-A19 : upward -Number of stackings = 19 -Number of adjacent stackings = 15 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A1-A29 : G-C Ww/Ww pairing antiparallel cis -A2-A28 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A27 : A-U Ww/Ww pairing antiparallel cis XX -A4-A26 : G-C Ww/Ww pairing antiparallel cis -A5-A25 : U-G Ww/Wh pairing antiparallel cis one_hbond -A7-A8 : C-U Ss/Hh adjacent_5p pairing parallel cis one_hbond -A9-A22 : U-G Ws/Ww pairing antiparallel cis XXVIII -A10-A21 : C-G Ww/Ww pairing antiparallel cis XIX -A11-A20 : A-U Ww/Ww pairing antiparallel cis XX -A12-A19 : A-U Ww/Ww pairing antiparallel cis XX -A13-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A24-A26 : C-C O2P/Bh pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : A C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : G C2p_endo anti -A7 : C C2p_endo syn -A8 : U C3p_endo anti -A9 : U C3p_endo anti -A10 : C C3p_endo anti -A11 : A C3p_endo anti -A12 : A C3p_endo anti -A13 : C C3p_endo anti -A14 : A C3p_endo anti -A15 : G C3p_exo syn -A16 : U C2p_endo anti -A17 : G C2p_endo anti -A18 : C C2p_endo anti -A19 : U C4p_exo anti -A20 : U C3p_endo anti -A21 : G C3p_endo anti -A22 : G C3p_endo anti -A23 : A C3p_endo anti -A24 : C C3p_endo anti -A25 : G C3p_endo anti -A26 : C C3p_endo anti -A27 : U C3p_endo anti -A28 : C C3p_endo anti -A29 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A22-A23 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A25-A26 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A3-A28 : outward -A4-A27 : outward -A6-A25 : outward -A11-A21 : outward -A14-A16 : upward -A14-A17 : outward -A17-A19 : upward -Number of stackings = 20 -Number of adjacent stackings = 13 -Number of non adjacent stackings = 7 -Base-pairs ------------------------------------------------------ -A2-A28 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A27 : A-U Ww/Ww pairing antiparallel cis XX -A4-A26 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A25 : U-G Ww/Wh pairing antiparallel cis one_hbond -A6-A24 : G-C Ww/Ww pairing antiparallel cis XIX -A8-A23 : U-A Ww/Ww pairing antiparallel cis XX -A9-A22 : U-G Ws/Ww pairing antiparallel cis XXVIII -A10-A21 : C-G Ww/Ww pairing antiparallel cis XIX -A11-A20 : A-U Ww/Ww pairing antiparallel cis XX -A12-A19 : A-U Ww/Ww pairing antiparallel cis XX -A13-A17 : C-G Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : A C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : G C3p_exo anti -A7 : C C3p_exo syn -A8 : U C3p_endo anti -A9 : U C3p_endo anti -A10 : C C3p_endo anti -A11 : A C3p_endo anti -A12 : A C3p_endo anti -A13 : C C3p_endo anti -A14 : A C3p_endo anti -A15 : G C3p_exo syn -A16 : U C2p_endo anti -A17 : G C3p_exo syn -A18 : C C2p_endo anti -A19 : U C4p_exo anti -A20 : U C3p_endo anti -A21 : G C3p_endo anti -A22 : G C3p_endo anti -A23 : A C3p_endo anti -A24 : C C3p_endo anti -A25 : G C3p_endo anti -A26 : C C3p_endo anti -A27 : U C3p_endo anti -A28 : C C3p_endo anti -A29 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A22-A23 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A27-A28 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A6-A25 : outward -A11-A21 : outward -A14-A17 : outward -A17-A19 : upward -Number of stackings = 19 -Number of adjacent stackings = 15 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A1-A29 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A28 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A27 : A-U Ww/Ww pairing antiparallel cis XX -A4-A26 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A25 : U-G Ws/Ww pairing antiparallel cis XXVIII -A6-A24 : G-C Ww/Ww pairing antiparallel cis XIX -A8-A23 : U-A Ww/Ww pairing antiparallel cis XX -A9-A22 : U-G Ws/Ww pairing antiparallel cis XXVIII -A10-A21 : C-G Ww/Ww pairing antiparallel cis -A11-A20 : A-U Ww/Ww pairing antiparallel cis XX -A12-A19 : A-U Ww/Ww pairing antiparallel cis XX -A13-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A14-A18 : A-C O2'/Bh pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : A C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : G C2p_endo anti -A7 : C C2p_endo anti -A8 : U C3p_endo anti -A9 : U C3p_endo anti -A10 : C C3p_endo anti -A11 : A C3p_endo anti -A12 : A C4p_exo anti -A13 : C C3p_endo anti -A14 : A C3p_endo anti -A15 : G C3p_exo syn -A16 : U C3p_exo anti -A17 : G C3p_exo syn -A18 : C C2p_endo anti -A19 : U C4p_exo anti -A20 : U C3p_endo anti -A21 : G C3p_endo anti -A22 : G C3p_endo anti -A23 : A C3p_endo anti -A24 : C C3p_endo anti -A25 : G C3p_endo anti -A26 : C C3p_endo anti -A27 : U C3p_endo anti -A28 : C C3p_endo anti -A29 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A22-A23 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A28-A29 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A6-A25 : outward -A11-A21 : outward -A14-A17 : outward -A17-A19 : upward -Number of stackings = 19 -Number of adjacent stackings = 15 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A1-A29 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A28 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A27 : A-U Ww/Ww pairing antiparallel cis XX -A4-A26 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A25 : U-G Ww/Wh pairing antiparallel cis one_hbond -A6-A24 : G-C Ww/Ww pairing antiparallel cis XIX -A7-A9 : C-U Ws/Hh pairing parallel cis one_hbond -A8-A23 : U-A Ww/Ww pairing antiparallel cis XX -A9-A22 : U-G Ws/Ww pairing antiparallel cis XXVIII -A10-A21 : C-G Ww/Ww pairing antiparallel cis XIX -A11-A20 : A-U Ww/Ww pairing antiparallel cis XX -A12-A19 : A-U Ww/Ww pairing antiparallel cis XX -A13-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A14-A18 : A-C O2'/Bh pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : A C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : G C2p_endo anti -A7 : C C2p_endo anti -A8 : U C3p_endo anti -A9 : U C3p_endo anti -A10 : C C3p_endo anti -A11 : A C3p_endo anti -A12 : A C3p_endo anti -A13 : C C3p_endo anti -A14 : A C3p_endo anti -A15 : G C3p_exo syn -A16 : U C2p_endo anti -A17 : G C3p_exo anti -A18 : C C2p_endo anti -A19 : U C3p_endo anti -A20 : U C3p_endo anti -A21 : G C3p_endo anti -A22 : G C3p_endo anti -A23 : A C3p_endo anti -A24 : C C3p_endo anti -A25 : G C3p_endo anti -A26 : C C3p_endo anti -A27 : U C3p_endo anti -A28 : C C3p_endo anti -A29 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A22-A23 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A28-A29 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A6-A25 : outward -A11-A21 : outward -A14-A17 : outward -A17-A19 : upward -Number of stackings = 19 -Number of adjacent stackings = 15 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A1-A29 : G-C Ww/Ww pairing antiparallel cis 128 -A2-A28 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A27 : A-U Ww/Ww pairing antiparallel cis XX -A4-A26 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A25 : U-G Ws/Ww pairing antiparallel cis XXVIII -A6-A24 : G-C Ww/Ww pairing antiparallel cis XIX -A8-A23 : U-A Ww/Ww pairing antiparallel cis XX -A9-A22 : U-G Ws/Ww pairing antiparallel cis XXVIII -A10-A21 : C-G Ww/Ww pairing antiparallel cis XIX -A11-A20 : A-U Ww/Ww pairing antiparallel cis XX -A12-A19 : A-U Ww/Ww pairing antiparallel cis XX -A13-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A14-A16 : A-U O2'/Ww Ss/O2' pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : A C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : G C2p_endo anti -A7 : C C2p_endo anti -A8 : U C3p_endo anti -A9 : U C3p_endo anti -A10 : C C4p_exo anti -A11 : A C3p_endo anti -A12 : A C4p_exo anti -A13 : C C3p_endo anti -A14 : A C3p_endo anti -A15 : G C3p_exo syn -A16 : U C3p_exo anti -A17 : G C2p_endo anti -A18 : C C2p_endo anti -A19 : U C3p_endo anti -A20 : U C3p_endo anti -A21 : G C3p_endo anti -A22 : G C3p_endo anti -A23 : A C3p_endo anti -A24 : C C3p_endo anti -A25 : G C3p_endo anti -A26 : C C3p_endo anti -A27 : U C3p_endo anti -A28 : C C3p_endo anti -A29 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A22-A23 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A27-A28 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A6-A25 : outward -A11-A21 : outward -A12-A20 : outward -A14-A17 : outward -A17-A19 : upward -Number of stackings = 19 -Number of adjacent stackings = 14 -Number of non adjacent stackings = 5 -Base-pairs ------------------------------------------------------ -A1-A29 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A28 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A27 : A-U Ww/Ww pairing antiparallel cis XX -A4-A26 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A25 : U-G Ww/Wh pairing antiparallel cis one_hbond -A6-A24 : G-C Ww/Ww pairing antiparallel cis XIX -A9-A22 : U-G Ws/Ww pairing antiparallel cis XXVIII -A11-A20 : A-U Ww/Ww pairing antiparallel cis XX -A12-A19 : A-U Ww/Ww pairing antiparallel cis XX -A13-A17 : C-G Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : A C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : G C2p_endo anti -A7 : C C2p_endo anti -A8 : U C3p_endo anti -A9 : U C3p_endo anti -A10 : C C3p_endo anti -A11 : A C3p_endo anti -A12 : A C3p_endo anti -A13 : C C3p_endo anti -A14 : A C3p_endo anti -A15 : G C2p_endo syn -A16 : U C2p_endo anti -A17 : G C3p_exo syn -A18 : C C2p_endo anti -A19 : U C4p_exo anti -A20 : U C3p_endo anti -A21 : G C3p_endo anti -A22 : G C3p_endo anti -A23 : A C4p_exo anti -A24 : C C3p_endo anti -A25 : G C3p_endo anti -A26 : C C3p_endo anti -A27 : U C3p_endo anti -A28 : C C3p_endo anti -A29 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A22-A23 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A28-A29 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A6-A25 : outward -A11-A21 : outward -A14-A17 : outward -A17-A19 : upward -Number of stackings = 20 -Number of adjacent stackings = 16 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A1-A29 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A28 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A27 : A-U Ww/Ww pairing antiparallel cis XX -A4-A26 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A25 : U-G Ws/Wh pairing antiparallel cis one_hbond -A8-A23 : U-A Ww/Ww pairing antiparallel cis XX -A9-A22 : U-G Ws/Wh pairing antiparallel cis one_hbond -A10-A21 : C-G Ww/Ww pairing antiparallel cis XIX -A11-A20 : A-U Ww/Ww pairing antiparallel cis XX -A13-A15 : C-G O2P/Ww O2P/Bs pairing -A13-A17 : C-G Ww/Ww pairing antiparallel cis one_hbond -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : A C3p_endo anti -A4 : G C3p_endo anti -A5 : U C4p_exo anti -A6 : G C2p_endo syn -A7 : C C2p_endo anti -A8 : U C4p_exo anti -A9 : U C3p_endo anti -A10 : C C3p_endo anti -A11 : A C3p_endo anti -A12 : A C3p_endo anti -A13 : C C3p_endo anti -A14 : A C3p_endo anti -A15 : G C3p_exo syn -A16 : U C2p_endo anti -A17 : G C2p_endo anti -A18 : C C2p_endo anti -A19 : U C4p_exo anti -A20 : U C3p_endo anti -A21 : G C3p_endo anti -A22 : G C3p_endo anti -A23 : A C3p_endo anti -A24 : C C3p_endo anti -A25 : G C3p_endo anti -A26 : C C3p_endo anti -A27 : U C3p_endo anti -A28 : C C3p_endo anti -A29 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A22-A23 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A27-A28 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A2-A29 : outward -A3-A28 : outward -A6-A25 : outward -A10-A22 : outward -A11-A21 : outward -A14-A17 : outward -A17-A19 : upward -Number of stackings = 21 -Number of adjacent stackings = 14 -Number of non adjacent stackings = 7 -Base-pairs ------------------------------------------------------ -A1-A29 : G-C Ww/Ww pairing antiparallel cis -A2-A28 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A27 : A-U Ww/Ww pairing antiparallel cis XX -A4-A26 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A25 : U-G Ww/Wh pairing antiparallel cis one_hbond -A6-A24 : G-C Ww/Ww pairing antiparallel cis XIX -A7-A8 : C-U Ss/Hh adjacent_5p pairing parallel cis one_hbond -A8-A23 : U-A Ww/Ww pairing antiparallel cis XX -A9-A22 : U-G Ws/Ww pairing antiparallel cis XXVIII -A10-A21 : C-G Ww/Ww pairing antiparallel cis XIX -A11-A20 : A-U Ww/Ww pairing antiparallel cis XX -A12-A19 : A-U Ww/Ww pairing antiparallel cis XX -A13-A17 : C-G Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : A C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : G C3p_exo anti -A7 : C C2p_endo anti -A8 : U C3p_endo anti -A9 : U C3p_endo anti -A10 : C C3p_endo anti -A11 : A C3p_endo anti -A12 : A C3p_endo anti -A13 : C C3p_endo anti -A14 : A C3p_endo anti -A15 : G C3p_exo syn -A16 : U C2p_endo anti -A17 : G C2p_endo anti -A18 : C C2p_endo anti -A19 : U C3p_endo anti -A20 : U C3p_endo anti -A21 : G C3p_endo anti -A22 : G C3p_endo anti -A23 : A C3p_endo anti -A24 : C C3p_endo anti -A25 : G C3p_endo anti -A26 : C C3p_endo anti -A27 : U C3p_endo anti -A28 : C C3p_endo anti -A29 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A22-A23 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A27-A28 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A6-A25 : outward -A11-A21 : outward -A14-A17 : outward -A17-A19 : upward -Number of stackings = 21 -Number of adjacent stackings = 17 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A2-A28 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A27 : A-U Ww/Ww pairing antiparallel cis XX -A4-A26 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A25 : U-G Ws/Ww pairing antiparallel cis XXVIII -A6-A24 : G-C Ww/Ww pairing antiparallel cis XIX -A8-A23 : U-A Ww/Ww pairing antiparallel cis one_hbond -A9-A22 : U-G Ws/Ww pairing antiparallel cis XXVIII -A10-A21 : C-G Ww/Ww pairing antiparallel cis XIX -A11-A20 : A-U Ww/Ww pairing antiparallel cis XX -A12-A19 : A-U Ww/Ww pairing antiparallel cis XX -A13-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A14-A16 : A-U Ss/O2P pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : A C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : G C2p_endo anti -A7 : C C2p_endo anti -A8 : U C3p_endo anti -A9 : U C3p_endo anti -A10 : C C3p_endo anti -A11 : A C3p_endo anti -A12 : A C3p_endo anti -A13 : C C3p_endo anti -A14 : A C3p_endo anti -A15 : G C3p_exo syn -A16 : U C2p_endo anti -A17 : G C2p_endo syn -A18 : C C2p_endo anti -A19 : U C4p_exo anti -A20 : U C3p_endo anti -A21 : G C3p_endo anti -A22 : G C3p_endo anti -A23 : A C3p_endo anti -A24 : C C3p_endo anti -A25 : G C3p_endo anti -A26 : C C3p_endo anti -A27 : U C3p_endo anti -A28 : C C3p_endo anti -A29 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A22-A23 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A24-A25 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A28-A29 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A10-A22 : outward -A11-A21 : outward -A14-A17 : outward -A17-A19 : upward -Number of stackings = 19 -Number of adjacent stackings = 15 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A1-A29 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A28 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A27 : A-U Ww/Ww pairing antiparallel cis XX -A4-A26 : G-C Ww/Ww pairing antiparallel cis -A5-A25 : U-G Ww/Wh pairing antiparallel cis one_hbond -A6-A7 : G-C O2'/Hh adjacent_5p pairing -A6-A24 : G-C Ww/Ww pairing antiparallel cis XIX -A8-A23 : U-A Ww/Ww pairing antiparallel cis XX -A9-A22 : U-G Ws/Ww pairing antiparallel cis XXVIII -A10-A21 : C-G Wh/Wh pairing antiparallel cis one_hbond -A11-A20 : A-U Ww/Ww pairing antiparallel cis XX -A12-A19 : A-U Ww/Ww pairing antiparallel cis XX -A13-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A16-A18 : U-C O2P/Bh pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : A C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : G C2p_endo anti -A7 : C C2p_endo anti -A8 : U C3p_endo anti -A9 : U C3p_endo anti -A10 : C C3p_endo anti -A11 : A C3p_endo anti -A12 : A C3p_endo anti -A13 : C C3p_endo anti -A14 : A C3p_endo anti -A15 : G C2p_endo syn -A16 : U C2p_endo anti -A17 : G C2p_endo syn -A18 : C C2p_endo anti -A19 : U C3p_endo anti -A20 : U C3p_endo anti -A21 : G C3p_endo anti -A22 : G C3p_endo anti -A23 : A C3p_endo anti -A24 : C C3p_endo anti -A25 : G C3p_endo anti -A26 : C C3p_endo anti -A27 : U C3p_endo anti -A28 : C C3p_endo anti -A29 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A22-A23 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A28-A29 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A6-A25 : outward -A10-A22 : outward -A11-A21 : outward -A12-A20 : outward -A14-A17 : outward -A17-A19 : upward -Number of stackings = 22 -Number of adjacent stackings = 16 -Number of non adjacent stackings = 6 -Base-pairs ------------------------------------------------------ -A1-A29 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A28 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A27 : A-U Ww/Ww pairing antiparallel cis XX -A4-A26 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A25 : U-G Ww/Wh pairing antiparallel cis one_hbond -A6-A24 : G-C Ww/Ww pairing antiparallel cis -A8-A23 : U-A Ww/Ww pairing antiparallel cis XX -A9-A22 : U-G Ws/Ww pairing antiparallel cis XXVIII -A10-A21 : C-G Ww/Ww pairing antiparallel cis XIX -A11-A20 : A-U Ww/Ww pairing antiparallel cis XX -A12-A19 : A-U Ww/Ww pairing antiparallel cis XX -A13-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A14-A15 : A-G O2P/Bs adjacent_5p pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : A C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : G C2p_endo anti -A7 : C C2p_endo anti -A8 : U C3p_endo anti -A9 : U C3p_endo anti -A10 : C C3p_endo anti -A11 : A C3p_endo anti -A12 : A C3p_endo anti -A13 : C C3p_endo anti -A14 : A C3p_endo anti -A15 : G C3p_exo syn -A16 : U C2p_endo anti -A17 : G C3p_exo syn -A18 : C C2p_endo anti -A19 : U C4p_exo anti -A20 : U C3p_endo anti -A21 : G C3p_endo anti -A22 : G C3p_endo anti -A23 : A C3p_endo anti -A24 : C C3p_endo anti -A25 : G C3p_endo anti -A26 : C C3p_endo anti -A27 : U C3p_endo anti -A28 : C C3p_endo anti -A29 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A22-A23 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A27-A28 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A2-A29 : outward -A4-A27 : outward -A6-A25 : outward -A14-A17 : outward -A17-A19 : upward -Number of stackings = 18 -Number of adjacent stackings = 13 -Number of non adjacent stackings = 5 -Base-pairs ------------------------------------------------------ -A1-A29 : G-C Ww/Ww pairing antiparallel cis -A2-A28 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A27 : A-U Ww/Ww pairing antiparallel cis XX -A4-A26 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A25 : U-G Ww/Wh pairing antiparallel cis one_hbond -A6-A24 : G-C Ww/Ww pairing antiparallel cis XIX -A7-A8 : C-U Ss/Hh adjacent_5p pairing parallel cis one_hbond -A8-A23 : U-A Ww/Ww pairing antiparallel cis XX -A9-A22 : U-G Ws/Ww pairing antiparallel cis XXVIII -A11-A20 : A-U Ww/Ww pairing antiparallel cis XX -A12-A19 : A-U Ww/Ww pairing antiparallel cis XX -A13-A17 : C-G Ww/Ww pairing antiparallel cis XIX diff --git a/MCdata/1arj_MC b/MCdata/1arj_MC deleted file mode 100644 index 9073104b196da9364b70a6696f2c5fb1ce9cc855..0000000000000000000000000000000000000000 --- a/MCdata/1arj_MC +++ /dev/null @@ -1,1319 +0,0 @@ -Residue conformations ------------------------------------------- -N17 : G C2p_exo anti -N18 : G C1p_exo anti -N19 : C C3p_endo anti -N20 : A C2p_exo anti -N21 : G C3p_endo anti -N22 : A C2p_exo anti -N23 : U C3p_endo anti -N24 : C C2p_exo anti -N25 : U C3p_endo anti -N26 : G C4p_exo anti -N27 : A C4p_exo anti -N28 : G C3p_endo anti -N29 : C C3p_endo anti -N30 : C C2p_exo anti -N31 : U C3p_endo anti -N32 : G C2p_exo anti -N33 : G C2p_exo anti -N34 : G C2p_exo syn -N35 : A C2p_exo anti -N36 : G C3p_endo anti -N37 : C C2p_exo anti -N38 : U C3p_endo anti -N39 : C C3p_endo anti -N40 : U C2p_exo anti -N41 : C C3p_endo anti -N42 : U C3p_endo anti -N43 : G C3p_endo anti -N44 : C C3p_endo anti -N45 : C C3p_endo anti -N1 : ARG -Adjacent stackings ---------------------------------------------- -N18-N19 : adjacent_5p outward pairing -N19-N20 : adjacent_5p upward -N20-N21 : adjacent_5p upward -N21-N22 : adjacent_5p upward -N26-N27 : adjacent_5p upward -N27-N28 : adjacent_5p upward -N28-N29 : adjacent_5p upward -N36-N37 : adjacent_5p upward -N37-N38 : adjacent_5p upward -N38-N39 : adjacent_5p upward -N39-N40 : adjacent_5p upward -N40-N41 : adjacent_5p upward -N41-N42 : adjacent_5p upward -N43-N44 : adjacent_5p inward -Non-Adjacent stackings ------------------------------------------ -N18-N45 : inward -Number of stackings = 15 -Number of adjacent stackings = 14 -Number of non adjacent stackings = 1 -Base-pairs ------------------------------------------------------ -N18-N19 : G-C O2'/Hh adjacent_5p outward pairing -N18-N43 : G-G Ws/Wh pairing parallel trans one_hbond -N18-N44 : G-C Ww/Ws pairing antiparallel cis one_hbond 130 -N19-N43 : C-G Ww/Ww pairing antiparallel cis XIX -N20-N42 : A-U Ww/Ww pairing antiparallel cis XX -N21-N41 : G-C Ww/Ww pairing antiparallel cis XIX -N22-N40 : A-U Ww/Ww pairing antiparallel cis XX -N26-N39 : G-C Ww/Ww pairing antiparallel cis XIX -N27-N38 : A-U Ww/Ww pairing antiparallel cis XX -N28-N37 : G-C Ww/Ww pairing antiparallel cis XIX -N29-N36 : C-G Ww/Ww pairing antiparallel cis XIX -N30-N34 : C-G Ss/Ws pairing antiparallel cis one_hbond 127 -N33-N34 : G-G O2P/Bs adjacent_5p pairing -N34-N35 : G-A O2'/Hh adjacent_5p pairing -N43-N45 : G-C Hh/O2P pairing -N44-N45 : C-C Ss/Hh adjacent_5p pairing parallel cis one_hbond -Residue conformations ------------------------------------------- -N17 : G C3p_endo anti -N18 : G C2p_exo anti -N19 : C C3p_endo anti -N20 : A C2p_exo anti -N21 : G C3p_endo anti -N22 : A C2p_exo anti -N23 : U C3p_endo anti -N24 : C C2p_exo anti -N25 : U C1p_exo anti -N26 : G C4p_exo anti -N27 : A C3p_endo anti -N28 : G C3p_endo anti -N29 : C C3p_endo anti -N30 : C C2p_exo anti -N31 : U C4p_endo anti -N32 : G C3p_endo anti -N33 : G C2p_endo anti -N34 : G C2p_exo anti -N35 : A C2p_endo anti -N36 : G C3p_endo anti -N37 : C C2p_exo anti -N38 : U C3p_endo anti -N39 : C C3p_endo anti -N40 : U C3p_endo anti -N41 : C C3p_endo anti -N42 : U C3p_endo anti -N43 : G C4p_exo anti -N44 : C C2p_exo anti -N45 : C C3p_endo anti -N1 : ARG -Adjacent stackings ---------------------------------------------- -N17-N18 : adjacent_5p upward -N18-N19 : adjacent_5p upward -N19-N20 : adjacent_5p upward -N20-N21 : adjacent_5p upward -N21-N22 : adjacent_5p upward -N26-N27 : adjacent_5p upward -N27-N28 : adjacent_5p upward -N28-N29 : adjacent_5p upward -N29-N30 : adjacent_5p upward pairing -N38-N39 : adjacent_5p upward -N40-N41 : adjacent_5p upward -N41-N42 : adjacent_5p upward -N42-N43 : adjacent_5p upward -N43-N44 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -N20-N43 : outward -Number of stackings = 15 -Number of adjacent stackings = 14 -Number of non adjacent stackings = 1 -Base-pairs ------------------------------------------------------ -N17-N44 : G-C Bh/Wh pairing antiparallel cis one_hbond -N17-N45 : G-C Ww/Ww pairing antiparallel cis -N19-N43 : C-G Ww/Ww pairing antiparallel cis XIX -N20-N42 : A-U Ww/Ww pairing antiparallel cis XX -N21-N41 : G-C Ww/Ww pairing antiparallel cis XIX -N26-N39 : G-C Ww/Ww pairing antiparallel cis XIX -N27-N38 : A-U Ww/Ww pairing antiparallel cis XX -N28-N37 : G-C Ww/Ww pairing antiparallel cis XIX -N29-N30 : C-C O2P/Bh adjacent_5p upward pairing -N29-N36 : C-G Wh/Wh pairing antiparallel cis one_hbond -N33-N34 : G-G O2P/Bs adjacent_5p pairing -Residue conformations ------------------------------------------- -N17 : G C3p_endo anti -N18 : G C3p_endo anti -N19 : C C2p_exo anti -N20 : A C3p_endo anti -N21 : G C3p_endo anti -N22 : A C2p_exo anti -N23 : U C3p_endo anti -N24 : C C3p_endo anti -N25 : U C2p_endo syn -N26 : G C3p_endo anti -N27 : A C4p_exo anti -N28 : G C4p_exo anti -N29 : C C3p_endo anti -N30 : C C2p_exo anti -N31 : U C2p_exo anti -N32 : G C3p_exo anti -N33 : G C2p_exo anti -N34 : G C3p_endo syn -N35 : A C1p_endo anti -N36 : G C2p_exo anti -N37 : C C2p_exo anti -N38 : U C3p_endo anti -N39 : C C2p_exo anti -N40 : U C3p_endo anti -N41 : C C4p_exo anti -N42 : U C3p_endo anti -N43 : G C3p_endo anti -N44 : C C4p_exo anti -N45 : C C2p_exo anti -N1 : ARG -Adjacent stackings ---------------------------------------------- -N18-N19 : adjacent_5p upward -N19-N20 : adjacent_5p upward -N20-N21 : adjacent_5p upward -N21-N22 : adjacent_5p upward -N26-N27 : adjacent_5p upward -N27-N28 : adjacent_5p upward -N28-N29 : adjacent_5p upward -N29-N30 : adjacent_5p upward -N36-N37 : adjacent_5p upward -N38-N39 : adjacent_5p upward -N39-N40 : adjacent_5p upward -N40-N41 : adjacent_5p upward -N41-N42 : adjacent_5p upward -N43-N44 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -N20-N43 : outward -Number of stackings = 15 -Number of adjacent stackings = 14 -Number of non adjacent stackings = 1 -Base-pairs ------------------------------------------------------ -N17-N45 : G-C Ww/Ww pairing antiparallel cis XIX -N18-N44 : G-C Ww/Ww pairing antiparallel cis XIX -N19-N43 : C-G Ww/Ww pairing antiparallel cis XIX -N20-N42 : A-U Ww/Ww pairing antiparallel cis XX -N21-N41 : G-C Ww/Ww pairing antiparallel cis XIX -N22-N26 : A-G Wh/Hw pairing parallel cis one_hbond -N22-N40 : A-U Ww/Ww pairing antiparallel cis one_hbond -N26-N39 : G-C Ww/Ww pairing antiparallel cis XIX -N27-N38 : A-U Ww/Ww pairing antiparallel cis XX -N28-N37 : G-C Ww/Ww pairing antiparallel cis -N29-N36 : C-G Ww/Ww pairing antiparallel cis -N30-N34 : C-G Ss/Ws O2'/Bs pairing antiparallel cis one_hbond 127 -N34-N35 : G-A O2'/Hh adjacent_5p pairing -N35-N36 : A-G Ww/O2' adjacent_5p pairing -Residue conformations ------------------------------------------- -N17 : G C3p_endo anti -N18 : G C2p_exo anti -N19 : C C2p_exo anti -N20 : A C2p_exo anti -N21 : G C2p_exo anti -N22 : A C3p_endo anti -N23 : U C2p_exo anti -N24 : C C3p_endo anti -N25 : U C1p_exo anti -N26 : G C4p_exo anti -N27 : A C4p_exo anti -N28 : G C4p_exo anti -N29 : C C2p_exo anti -N30 : C C3p_endo anti -N31 : U C3p_exo anti -N32 : G O4p_endo anti -N33 : G C2p_exo anti -N34 : G C3p_endo syn -N35 : A C3p_endo anti -N36 : G C2p_exo anti -N37 : C C2p_exo anti -N38 : U C3p_endo anti -N39 : C C2p_exo anti -N40 : U C3p_endo anti -N41 : C C4p_exo anti -N42 : U C2p_exo anti -N43 : G C2p_exo anti -N44 : C C3p_endo anti -N45 : C C3p_endo anti -N1 : ARG -Adjacent stackings ---------------------------------------------- -N18-N19 : adjacent_5p upward -N20-N21 : adjacent_5p upward -N21-N22 : adjacent_5p upward -N26-N27 : adjacent_5p upward -N27-N28 : adjacent_5p upward -N28-N29 : adjacent_5p upward -N29-N30 : adjacent_5p upward -N37-N38 : adjacent_5p upward -N38-N39 : adjacent_5p upward -N39-N40 : adjacent_5p upward -N40-N41 : adjacent_5p upward -N42-N43 : adjacent_5p upward -N43-N44 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -N20-N43 : outward -Number of stackings = 14 -Number of adjacent stackings = 13 -Number of non adjacent stackings = 1 -Base-pairs ------------------------------------------------------ -N17-N45 : G-C Ww/Ww pairing antiparallel cis XIX -N18-N44 : G-C Ww/Ww pairing antiparallel cis XIX -N19-N43 : C-G Ww/Ww pairing antiparallel cis XIX -N21-N41 : G-C Ww/Ww pairing antiparallel cis XIX -N22-N40 : A-U Ww/Ww pairing antiparallel cis one_hbond -N26-N39 : G-C Ww/Ww pairing antiparallel cis XIX -N27-N38 : A-U Ww/Ww pairing antiparallel cis XX -N28-N37 : G-C Ww/Ww pairing antiparallel cis XIX -N29-N36 : C-G Ww/Ww pairing antiparallel cis XIX -N33-N34 : G-G O2'/Ss adjacent_5p pairing -Residue conformations ------------------------------------------- -N17 : G C3p_endo anti -N18 : G C2p_exo anti -N19 : C C2p_exo anti -N20 : A C3p_endo anti -N21 : G C4p_exo anti -N22 : A C2p_exo anti -N23 : U C2p_exo anti -N24 : C C2p_exo anti -N25 : U C2p_exo syn -N26 : G C3p_endo anti -N27 : A C2p_exo anti -N28 : G C4p_exo anti -N29 : C C3p_endo anti -N30 : C C3p_endo anti -N31 : U C3p_endo anti -N32 : G C3p_endo anti -N33 : G C3p_exo anti -N34 : G C2p_exo syn -N35 : A C3p_exo anti -N36 : G C3p_endo anti -N37 : C C2p_exo anti -N38 : U C3p_endo anti -N39 : C C3p_endo anti -N40 : U C3p_endo anti -N41 : C C4p_exo anti -N42 : U C2p_exo anti -N43 : G C2p_exo anti -N44 : C C3p_endo anti -N45 : C C3p_endo anti -N1 : ARG -Adjacent stackings ---------------------------------------------- -N17-N18 : adjacent_5p upward -N18-N19 : adjacent_5p upward -N19-N20 : adjacent_5p upward -N20-N21 : adjacent_5p upward -N21-N22 : adjacent_5p upward -N26-N27 : adjacent_5p upward -N27-N28 : adjacent_5p upward -N28-N29 : adjacent_5p upward -N38-N39 : adjacent_5p upward -N39-N40 : adjacent_5p upward -N40-N41 : adjacent_5p upward -N41-N42 : adjacent_5p upward -N43-N44 : adjacent_5p upward -N44-N45 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -N18-N45 : outward -N20-N43 : outward -Number of stackings = 16 -Number of adjacent stackings = 14 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -N17-N45 : G-C Ww/Ww pairing antiparallel cis XIX -N18-N44 : G-C Ww/Ww pairing antiparallel cis XIX -N19-N43 : C-G Ww/Ww pairing antiparallel cis XIX -N20-N42 : A-U Ww/Ww pairing antiparallel cis XX -N21-N41 : G-C Ww/Ww pairing antiparallel cis XIX -N22-N25 : A-U Ss/Hh pairing antiparallel trans one_hbond -N22-N26 : A-G Wh/Hw pairing parallel cis one_hbond -N27-N38 : A-U Ww/Ww pairing antiparallel cis XX -N28-N37 : G-C Ww/Ww pairing antiparallel cis XIX -N29-N36 : C-G Ww/Ww pairing antiparallel cis -N32-N33 : G-G O2'/Hh adjacent_5p pairing -N34-N35 : G-A O2'/C8 adjacent_5p pairing -Residue conformations ------------------------------------------- -N17 : G C2p_exo syn -N18 : G C1p_exo anti -N19 : C C2p_exo anti -N20 : A C3p_endo anti -N21 : G C3p_endo anti -N22 : A C2p_exo anti -N23 : U C3p_endo anti -N24 : C C2p_exo anti -N25 : U C3p_endo syn -N26 : G C3p_endo anti -N27 : A C2p_exo anti -N28 : G C4p_exo anti -N29 : C C2p_exo anti -N30 : C C3p_endo anti -N31 : U C2p_endo anti -N32 : G C3p_exo anti -N33 : G C2p_endo anti -N34 : G C2p_exo anti -N35 : A C2p_exo anti -N36 : G C2p_exo anti -N37 : C C2p_exo anti -N38 : U C3p_endo anti -N39 : C C3p_endo anti -N40 : U C3p_endo anti -N41 : C C4p_exo anti -N42 : U C2p_exo anti -N43 : G C3p_endo anti -N44 : C C1p_endo anti -N45 : C O4p_endo anti -N1 : ARG -Adjacent stackings ---------------------------------------------- -N17-N18 : adjacent_5p downward -N18-N19 : adjacent_5p outward pairing -N19-N20 : adjacent_5p upward -N20-N21 : adjacent_5p upward -N21-N22 : adjacent_5p upward -N26-N27 : adjacent_5p upward -N27-N28 : adjacent_5p upward -N28-N29 : adjacent_5p upward -N29-N30 : adjacent_5p upward -N38-N39 : adjacent_5p upward -N39-N40 : adjacent_5p upward -N40-N41 : adjacent_5p upward -N41-N42 : adjacent_5p upward -N42-N43 : adjacent_5p upward -N43-N44 : adjacent_5p inward -Non-Adjacent stackings ------------------------------------------ -N34-N36 : upward -Number of stackings = 16 -Number of adjacent stackings = 15 -Number of non adjacent stackings = 1 -Base-pairs ------------------------------------------------------ -N18-N19 : G-C O2'/Hh adjacent_5p outward pairing -N18-N44 : G-C Ww/Ww pairing antiparallel cis -N18-N45 : G-C Bs/O2' pairing -N19-N43 : C-G Ww/Ww pairing antiparallel cis XIX -N20-N42 : A-U Ww/Ww pairing antiparallel cis one_hbond -N21-N41 : G-C Ww/Ww pairing antiparallel cis -N22-N40 : A-U Ww/Ww pairing antiparallel cis one_hbond -N26-N39 : G-C Ww/Ws pairing antiparallel cis one_hbond 130 -N27-N38 : A-U Ww/Ww pairing antiparallel cis XX -N28-N37 : G-C Ww/Ww pairing antiparallel cis XIX -N29-N36 : C-G Ww/Ww pairing antiparallel cis -N30-N34 : C-G Bs/Ww O2'/Bs pairing antiparallel cis one_hbond 127 -N34-N35 : G-A O2'/Hh adjacent_5p pairing -N35-N36 : A-G Ww/O2' adjacent_5p pairing -N43-N45 : G-C Hh/O2P pairing -N44-N45 : C-C Ss/Hh adjacent_5p pairing parallel cis one_hbond -Residue conformations ------------------------------------------- -N17 : G C3p_endo anti -N18 : G C3p_endo anti -N19 : C C2p_exo anti -N20 : A C3p_endo anti -N21 : G C2p_exo anti -N22 : A C2p_exo anti -N23 : U C2p_exo anti -N24 : C C2p_exo anti -N25 : U C1p_exo syn -N26 : G C3p_endo anti -N27 : A C2p_exo anti -N28 : G C4p_exo anti -N29 : C C2p_exo anti -N30 : C C3p_endo anti -N31 : U C2p_exo anti -N32 : G C2p_exo anti -N33 : G C2p_endo anti -N34 : G C1p_endo anti -N35 : A C3p_exo anti -N36 : G C2p_exo anti -N37 : C C3p_endo anti -N38 : U C3p_endo anti -N39 : C C2p_exo anti -N40 : U C3p_endo anti -N41 : C C4p_exo anti -N42 : U C3p_endo anti -N43 : G C2p_exo anti -N44 : C C3p_endo anti -N45 : C C3p_endo anti -N1 : ARG -Adjacent stackings ---------------------------------------------- -N17-N18 : adjacent_5p upward -N18-N19 : adjacent_5p upward -N19-N20 : adjacent_5p upward -N20-N21 : adjacent_5p upward -N21-N22 : adjacent_5p upward -N26-N27 : adjacent_5p upward -N27-N28 : adjacent_5p upward -N28-N29 : adjacent_5p upward -N36-N37 : adjacent_5p upward -N37-N38 : adjacent_5p upward -N38-N39 : adjacent_5p upward -N39-N40 : adjacent_5p upward -N41-N42 : adjacent_5p upward -N43-N44 : adjacent_5p upward -N44-N45 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 15 -Number of adjacent stackings = 15 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -N17-N45 : G-C Ww/Ww pairing antiparallel cis XIX -N18-N44 : G-C Ww/Ww pairing antiparallel cis XIX -N19-N43 : C-G Ww/Ww pairing antiparallel cis XIX -N20-N42 : A-U Ww/Ww pairing antiparallel cis XX -N21-N41 : G-C Ww/Ww pairing antiparallel cis XIX -N22-N40 : A-U Ww/Ww pairing antiparallel cis XX -N26-N39 : G-C Ww/Ww pairing antiparallel cis -N27-N38 : A-U Ww/Ww pairing antiparallel cis XX -N28-N37 : G-C Ww/Ww pairing antiparallel cis XIX -N29-N36 : C-G Ww/Ww pairing antiparallel cis XIX -N30-N31 : C-U O2'/Hh adjacent_5p pairing -N32-N33 : G-G O2'/Hh adjacent_5p pairing -Residue conformations ------------------------------------------- -N17 : G C2p_exo anti -N18 : G C2p_exo anti -N19 : C C3p_endo anti -N20 : A C3p_endo anti -N21 : G C3p_endo anti -N22 : A C2p_exo anti -N23 : U C2p_exo anti -N24 : C C2p_exo anti -N25 : U C2p_endo syn -N26 : G C3p_endo anti -N27 : A C3p_endo anti -N28 : G C4p_exo anti -N29 : C C3p_endo anti -N30 : C C2p_exo anti -N31 : U O4p_endo anti -N32 : G C3p_exo anti -N33 : G C3p_endo anti -N34 : G C2p_exo anti -N35 : A C2p_endo anti -N36 : G C2p_exo anti -N37 : C C4p_exo anti -N38 : U C3p_endo anti -N39 : C C2p_exo anti -N40 : U C3p_endo anti -N41 : C C4p_exo anti -N42 : U C3p_endo anti -N43 : G C3p_endo anti -N44 : C C2p_exo anti -N45 : C C3p_endo anti -N1 : ARG -Adjacent stackings ---------------------------------------------- -N17-N18 : adjacent_5p upward -N18-N19 : adjacent_5p upward -N19-N20 : adjacent_5p upward -N20-N21 : adjacent_5p upward -N21-N22 : adjacent_5p upward -N26-N27 : adjacent_5p upward -N27-N28 : adjacent_5p upward -N28-N29 : adjacent_5p upward -N29-N30 : adjacent_5p upward -N38-N39 : adjacent_5p upward -N40-N41 : adjacent_5p upward -N41-N42 : adjacent_5p upward -N42-N43 : adjacent_5p upward -N43-N44 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -N20-N43 : outward -Number of stackings = 15 -Number of adjacent stackings = 14 -Number of non adjacent stackings = 1 -Base-pairs ------------------------------------------------------ -N17-N45 : G-C Ww/Ww pairing antiparallel cis XIX -N18-N44 : G-C Ww/Ww pairing antiparallel cis 130 -N19-N43 : C-G Ww/Ww pairing antiparallel cis XIX -N20-N42 : A-U Ww/Ww pairing antiparallel cis XX -N21-N41 : G-C Ww/Ww pairing antiparallel cis XIX -N22-N40 : A-U Ww/Ww pairing antiparallel cis XX -N26-N39 : G-C Ww/Ww pairing antiparallel cis XIX -N27-N38 : A-U Ww/Ww pairing antiparallel cis XX -N28-N37 : G-C Ww/Ww pairing antiparallel cis -N29-N36 : C-G Ww/Ww pairing antiparallel cis -N30-N34 : C-G O2'/Bs pairing -N31-N36 : U-G Hw/Sw pairing parallel trans one_hbond 89 -N32-N33 : G-G O2P/Ss adjacent_5p pairing -Residue conformations ------------------------------------------- -N17 : G C3p_endo syn -N18 : G C1p_exo anti -N19 : C C2p_exo anti -N20 : A C2p_exo anti -N21 : G C3p_endo anti -N22 : A C2p_exo anti -N23 : U C2p_exo anti -N24 : C C2p_exo anti -N25 : U C2p_endo syn -N26 : G C3p_endo anti -N27 : A C2p_exo anti -N28 : G C4p_exo anti -N29 : C C2p_exo anti -N30 : C C3p_endo anti -N31 : U C1p_exo anti -N32 : G C4p_exo anti -N33 : G C3p_exo anti -N34 : G C1p_endo anti -N35 : A C2p_exo anti -N36 : G C2p_exo anti -N37 : C C3p_endo anti -N38 : U C3p_endo anti -N39 : C C3p_endo anti -N40 : U C2p_exo anti -N41 : C O4p_endo anti -N42 : U C4p_exo anti -N43 : G C2p_exo anti -N44 : C C2p_exo anti -N45 : C C4p_exo anti -N1 : ARG -Adjacent stackings ---------------------------------------------- -N17-N18 : adjacent_5p downward -N18-N19 : adjacent_5p outward pairing -N19-N20 : adjacent_5p upward -N20-N21 : adjacent_5p upward -N21-N22 : adjacent_5p upward -N26-N27 : adjacent_5p upward -N27-N28 : adjacent_5p upward -N28-N29 : adjacent_5p upward -N29-N30 : adjacent_5p upward -N37-N38 : adjacent_5p upward -N38-N39 : adjacent_5p upward -N39-N40 : adjacent_5p upward -N40-N41 : adjacent_5p upward -N41-N42 : adjacent_5p upward -N42-N43 : adjacent_5p upward -N43-N44 : adjacent_5p inward -Non-Adjacent stackings ------------------------------------------ -N34-N36 : upward -Number of stackings = 17 -Number of adjacent stackings = 16 -Number of non adjacent stackings = 1 -Base-pairs ------------------------------------------------------ -N18-N19 : G-C O2'/Hh adjacent_5p outward pairing -N18-N44 : G-C Ww/Ww pairing antiparallel cis -N18-N45 : G-C Bs/O2' Ss/O2' pairing -N19-N43 : C-G Ww/Ww pairing antiparallel cis XIX -N20-N42 : A-U Ww/Ww pairing antiparallel cis XX -N21-N41 : G-C Ww/Ww pairing antiparallel cis XIX -N22-N40 : A-U Ww/Ww pairing antiparallel cis XX -N26-N39 : G-C Ww/Ww pairing antiparallel cis XIX -N27-N38 : A-U Ww/Ww pairing antiparallel cis XX -N28-N37 : G-C Ww/Ww pairing antiparallel cis XIX -N29-N36 : C-G Ww/Ww pairing antiparallel cis XIX -N33-N34 : G-G O2P/Ss adjacent_5p pairing -N34-N35 : G-A O2'/Hh adjacent_5p pairing -N43-N45 : G-C Hh/O2P pairing -N44-N45 : C-C Ss/Hh adjacent_5p pairing parallel cis one_hbond -Residue conformations ------------------------------------------- -N17 : G C3p_endo anti -N18 : G C2p_exo anti -N19 : C C3p_endo anti -N20 : A C2p_exo anti -N21 : G C3p_endo anti -N22 : A C2p_exo anti -N23 : U C2p_exo anti -N24 : C C3p_endo anti -N25 : U C1p_exo anti -N26 : G C4p_exo anti -N27 : A C2p_exo anti -N28 : G C3p_endo anti -N29 : C C2p_exo anti -N30 : C C2p_exo anti -N31 : U C3p_exo anti -N32 : G C2p_exo anti -N33 : G C3p_exo anti -N34 : G C1p_endo syn -N35 : A C3p_exo anti -N36 : G C2p_exo anti -N37 : C C2p_exo anti -N38 : U C3p_endo anti -N39 : C C3p_endo anti -N40 : U C2p_exo anti -N41 : C C4p_exo anti -N42 : U C3p_endo anti -N43 : G C2p_exo anti -N44 : C C3p_endo anti -N45 : C C3p_endo anti -N1 : ARG -Adjacent stackings ---------------------------------------------- -N18-N19 : adjacent_5p upward -N19-N20 : adjacent_5p upward -N20-N21 : adjacent_5p upward -N26-N27 : adjacent_5p upward -N27-N28 : adjacent_5p upward -N29-N30 : adjacent_5p upward -N36-N37 : adjacent_5p upward -N37-N38 : adjacent_5p upward -N38-N39 : adjacent_5p upward -N39-N40 : adjacent_5p upward -N40-N41 : adjacent_5p upward -N41-N42 : adjacent_5p upward -N43-N44 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -N20-N43 : outward -Number of stackings = 14 -Number of adjacent stackings = 13 -Number of non adjacent stackings = 1 -Base-pairs ------------------------------------------------------ -N17-N45 : G-C Ww/Ww pairing antiparallel cis XIX -N18-N44 : G-C Ww/Ww pairing antiparallel cis -N19-N43 : C-G Ww/Ww pairing antiparallel cis XIX -N20-N42 : A-U Ww/Ww pairing antiparallel cis XX -N21-N41 : G-C Ww/Ww pairing antiparallel cis one_hbond 130 -N22-N40 : A-U Ww/Ww pairing antiparallel cis XX -N26-N39 : G-C Ww/Ww pairing antiparallel cis XIX -N27-N38 : A-U Ww/Ww pairing antiparallel cis XX -N28-N37 : G-C Ww/Ww pairing antiparallel cis one_hbond 130 -N31-N32 : U-G O2'/Hh adjacent_5p pairing -N34-N35 : G-A O2'/C8 adjacent_5p pairing -N34-N37 : G-C Hh/O2P pairing -Residue conformations ------------------------------------------- -N17 : G C2p_exo anti -N18 : G C3p_endo anti -N19 : C C2p_exo anti -N20 : A C2p_exo anti -N21 : G C4p_exo anti -N22 : A C2p_exo anti -N23 : U C2p_exo anti -N24 : C C2p_exo anti -N25 : U C1p_exo syn -N26 : G C3p_endo anti -N27 : A C2p_exo anti -N28 : G C4p_exo anti -N29 : C C2p_exo anti -N30 : C C3p_endo anti -N31 : U C2p_exo anti -N32 : G C1p_exo anti -N33 : G C3p_endo anti -N34 : G C2p_exo anti -N35 : A C2p_exo anti -N36 : G C2p_exo anti -N37 : C C3p_endo anti -N38 : U C3p_endo anti -N39 : C C3p_endo anti -N40 : U C3p_endo anti -N41 : C C4p_exo anti -N42 : U C3p_endo anti -N43 : G C2p_exo anti -N44 : C C2p_exo anti -N45 : C C3p_endo anti -N1 : ARG -Adjacent stackings ---------------------------------------------- -N17-N18 : adjacent_5p upward -N18-N19 : adjacent_5p upward -N19-N20 : adjacent_5p upward -N20-N21 : adjacent_5p upward -N21-N22 : adjacent_5p upward -N26-N27 : adjacent_5p upward -N27-N28 : adjacent_5p upward -N28-N29 : adjacent_5p upward -N36-N37 : adjacent_5p upward -N38-N39 : adjacent_5p upward -N39-N40 : adjacent_5p upward -N40-N41 : adjacent_5p upward -N41-N42 : adjacent_5p upward -N42-N43 : adjacent_5p upward -N43-N44 : adjacent_5p upward -N44-N45 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -N20-N43 : outward -N34-N36 : upward -Number of stackings = 18 -Number of adjacent stackings = 16 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -N17-N45 : G-C Ww/Ww pairing antiparallel cis XIX -N18-N44 : G-C Ww/Ww pairing antiparallel cis XIX -N19-N43 : C-G Ww/Ww pairing antiparallel cis XIX -N20-N42 : A-U Ww/Ww pairing antiparallel cis XX -N21-N41 : G-C Ww/Ww pairing antiparallel cis XIX -N22-N26 : A-G Wh/Hw pairing parallel cis one_hbond -N27-N38 : A-U Ww/Ww pairing antiparallel cis XX -N28-N37 : G-C Ww/Ww pairing antiparallel cis XIX -N29-N36 : C-G Ww/Ww pairing antiparallel cis XIX -N31-N32 : U-G O2'/C8 adjacent_5p pairing -N33-N34 : G-G Sw/Wh O2'/C8 adjacent_5p pairing antiparallel cis one_hbond -N34-N35 : G-A O2'/Hh adjacent_5p pairing -Residue conformations ------------------------------------------- -N17 : G C2p_exo anti -N18 : G C1p_exo anti -N19 : C C2p_exo anti -N20 : A C3p_endo anti -N21 : G C3p_endo anti -N22 : A C2p_exo anti -N23 : U C2p_exo anti -N24 : C C3p_endo anti -N25 : U C2p_endo syn -N26 : G C3p_endo anti -N27 : A C3p_endo anti -N28 : G C4p_exo anti -N29 : C C3p_endo anti -N30 : C C2p_exo anti -N31 : U C4p_endo anti -N32 : G C3p_exo anti -N33 : G C2p_exo anti -N34 : G C3p_endo syn -N35 : A C2p_endo anti -N36 : G C3p_endo anti -N37 : C C2p_exo anti -N38 : U C3p_endo anti -N39 : C C3p_endo anti -N40 : U C3p_endo anti -N41 : C C4p_exo anti -N42 : U C2p_exo anti -N43 : G C3p_endo anti -N44 : C C2p_exo anti -N45 : C O4p_endo anti -N1 : ARG -Adjacent stackings ---------------------------------------------- -N19-N20 : adjacent_5p upward -N20-N21 : adjacent_5p upward -N21-N22 : adjacent_5p upward -N26-N27 : adjacent_5p upward -N27-N28 : adjacent_5p upward -N28-N29 : adjacent_5p upward -N29-N30 : adjacent_5p upward -N37-N38 : adjacent_5p upward -N38-N39 : adjacent_5p upward -N39-N40 : adjacent_5p upward -N40-N41 : adjacent_5p upward -N41-N42 : adjacent_5p upward -N42-N43 : adjacent_5p upward -N43-N44 : adjacent_5p inward -Non-Adjacent stackings ------------------------------------------ -N20-N43 : outward -Number of stackings = 15 -Number of adjacent stackings = 14 -Number of non adjacent stackings = 1 -Base-pairs ------------------------------------------------------ -N17-N45 : G-C Ww/Ww pairing antiparallel cis -N18-N19 : G-C O2'/Hh adjacent_5p pairing -N18-N44 : G-C Ww/Ww pairing antiparallel cis -N18-N45 : G-C Bs/O2' pairing -N20-N42 : A-U Ww/Ww pairing antiparallel cis XX -N21-N41 : G-C Ww/Ww pairing antiparallel cis XIX -N22-N25 : A-U O2'/Hh O2'/Ww pairing -N22-N40 : A-U Ww/Ww pairing antiparallel cis XX -N26-N39 : G-C Ww/Ww pairing antiparallel cis XIX -N27-N38 : A-U Ww/Ww pairing antiparallel cis XX -N28-N37 : G-C Ww/Ww pairing antiparallel cis XIX -N29-N36 : C-G Wh/Wh pairing antiparallel cis one_hbond -N33-N34 : G-G O2'/C8 adjacent_5p pairing -N43-N45 : G-C Hh/O2P pairing -N44-N45 : C-C Ss/Hh adjacent_5p pairing parallel cis one_hbond -Residue conformations ------------------------------------------- -N17 : G C3p_endo anti -N18 : G C3p_endo anti -N19 : C C2p_exo anti -N20 : A C2p_exo anti -N21 : G C3p_endo anti -N22 : A C2p_exo anti -N23 : U C2p_exo anti -N24 : C C2p_exo anti -N25 : U C3p_endo syn -N26 : G C3p_endo anti -N27 : A C2p_exo anti -N28 : G C4p_exo anti -N29 : C C2p_exo anti -N30 : C C2p_exo anti -N31 : U C3p_endo anti -N32 : G C1p_endo syn -N33 : G C2p_endo anti -N34 : G C1p_endo syn -N35 : A C3p_exo anti -N36 : G C2p_exo anti -N37 : C C3p_endo anti -N38 : U C3p_endo anti -N39 : C C2p_exo anti -N40 : U C3p_endo anti -N41 : C C4p_exo anti -N42 : U C3p_endo anti -N43 : G C2p_exo anti -N44 : C C2p_exo anti -N45 : C C3p_endo anti -N1 : ARG -Adjacent stackings ---------------------------------------------- -N18-N19 : adjacent_5p upward -N19-N20 : adjacent_5p upward -N20-N21 : adjacent_5p upward -N21-N22 : adjacent_5p upward -N26-N27 : adjacent_5p upward -N27-N28 : adjacent_5p upward -N28-N29 : adjacent_5p upward -N29-N30 : adjacent_5p upward -N37-N38 : adjacent_5p upward -N38-N39 : adjacent_5p upward -N39-N40 : adjacent_5p upward -N40-N41 : adjacent_5p upward -N43-N44 : adjacent_5p upward -N44-N45 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -N20-N43 : outward -Number of stackings = 15 -Number of adjacent stackings = 14 -Number of non adjacent stackings = 1 -Base-pairs ------------------------------------------------------ -N17-N45 : G-C Ww/Ww pairing antiparallel cis one_hbond -N19-N43 : C-G Ww/Ww pairing antiparallel cis XIX -N20-N42 : A-U Ww/Ww pairing antiparallel cis XX -N21-N41 : G-C Ww/Ww pairing antiparallel cis XIX -N22-N40 : A-U Ww/Ww pairing antiparallel cis XX -N23-N34 : U-G Ww/Hw pairing antiparallel trans one_hbond -N26-N39 : G-C Ww/Ws pairing antiparallel cis one_hbond 130 -N27-N38 : A-U Ww/Ww pairing antiparallel cis XX -N28-N37 : G-C Ww/Ww pairing antiparallel cis XIX -N29-N36 : C-G Ww/Ww pairing antiparallel cis XIX -N33-N35 : G-A O2P/Bh pairing -N34-N35 : G-A O2'/Hh O2'/C8 adjacent_5p pairing -Residue conformations ------------------------------------------- -N17 : G C2p_exo anti -N18 : G C2p_exo anti -N19 : C C3p_endo anti -N20 : A C3p_endo anti -N21 : G C4p_exo anti -N22 : A C2p_exo anti -N23 : U C2p_exo anti -N24 : C C3p_endo anti -N25 : U O4p_endo anti -N26 : G C3p_endo anti -N27 : A C2p_exo anti -N28 : G O4p_endo anti -N29 : C C2p_exo anti -N30 : C C2p_exo anti -N31 : U C3p_endo anti -N32 : G C3p_endo anti -N33 : G C2p_endo anti -N34 : G C2p_exo anti -N35 : A C3p_exo anti -N36 : G C2p_exo anti -N37 : C C3p_endo anti -N38 : U C3p_endo anti -N39 : C C3p_endo anti -N40 : U C2p_exo anti -N41 : C C4p_exo anti -N42 : U C3p_endo anti -N43 : G C2p_exo anti -N44 : C C3p_endo anti -N45 : C C3p_endo anti -N1 : ARG -Adjacent stackings ---------------------------------------------- -N17-N18 : adjacent_5p upward -N18-N19 : adjacent_5p upward -N19-N20 : adjacent_5p upward -N20-N21 : adjacent_5p upward -N21-N22 : adjacent_5p upward -N26-N27 : adjacent_5p upward -N27-N28 : adjacent_5p upward -N28-N29 : adjacent_5p upward -N29-N30 : adjacent_5p upward -N36-N37 : adjacent_5p upward -N37-N38 : adjacent_5p upward -N39-N40 : adjacent_5p upward -N40-N41 : adjacent_5p upward -N41-N42 : adjacent_5p upward -N43-N44 : adjacent_5p upward -N44-N45 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 16 -Number of adjacent stackings = 16 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -N17-N45 : G-C Ww/Ww pairing antiparallel cis XIX -N18-N44 : G-C Ww/Ww pairing antiparallel cis XIX -N19-N43 : C-G Ww/Ww pairing antiparallel cis XIX -N20-N42 : A-U Ww/Ww pairing antiparallel cis XX -N21-N41 : G-C Ww/Ww pairing antiparallel cis XIX -N22-N40 : A-U Ww/Ww pairing antiparallel cis XX -N26-N39 : G-C Ww/Ww pairing antiparallel cis XIX -N27-N38 : A-U Ww/Ww pairing antiparallel cis XX -N28-N37 : G-C Ww/Ww pairing antiparallel cis XIX -N29-N36 : C-G Ww/Ww pairing antiparallel cis XIX -N30-N34 : C-G Bs/Ww pairing antiparallel cis 127 -N34-N35 : G-A O2'/Hh adjacent_5p pairing -Residue conformations ------------------------------------------- -N17 : G C2p_exo anti -N18 : G C1p_exo anti -N19 : C C2p_exo anti -N20 : A C3p_endo anti -N21 : G C4p_exo anti -N22 : A C2p_exo anti -N23 : U C2p_exo anti -N24 : C C3p_endo anti -N25 : U C3p_exo syn -N26 : G C4p_exo anti -N27 : A C2p_exo anti -N28 : G C3p_endo anti -N29 : C C2p_exo anti -N30 : C C2p_endo anti -N31 : U C2p_exo anti -N32 : G C3p_exo anti -N33 : G C3p_exo syn -N34 : G C2p_exo syn -N35 : A C3p_endo anti -N36 : G C2p_exo anti -N37 : C C3p_endo anti -N38 : U C3p_endo anti -N39 : C C3p_endo anti -N40 : U C3p_endo anti -N41 : C C4p_exo anti -N42 : U C3p_endo anti -N43 : G C3p_endo anti -N44 : C C1p_endo anti -N45 : C C4p_exo anti -N1 : ARG -Adjacent stackings ---------------------------------------------- -N19-N20 : adjacent_5p upward -N20-N21 : adjacent_5p upward -N21-N22 : adjacent_5p upward -N26-N27 : adjacent_5p upward -N27-N28 : adjacent_5p upward -N28-N29 : adjacent_5p upward -N29-N30 : adjacent_5p upward -N36-N37 : adjacent_5p upward -N37-N38 : adjacent_5p upward -N39-N40 : adjacent_5p upward -N40-N41 : adjacent_5p upward -N41-N42 : adjacent_5p upward -N42-N43 : adjacent_5p upward -N43-N44 : adjacent_5p inward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 14 -Number of adjacent stackings = 14 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -N17-N45 : G-C Ww/Ww pairing antiparallel cis one_hbond -N18-N19 : G-C O2'/Hh adjacent_5p pairing -N18-N44 : G-C Ww/Ww pairing antiparallel cis -N18-N45 : G-C Bs/O2' pairing -N19-N43 : C-G Ww/Ww pairing antiparallel cis XIX -N20-N42 : A-U Ww/Ww pairing antiparallel cis XX -N21-N41 : G-C Ww/Ww pairing antiparallel cis XIX -N22-N40 : A-U Ww/Ww pairing antiparallel cis XX -N26-N39 : G-C Ww/Ww pairing antiparallel cis XIX -N27-N38 : A-U Ww/Ww pairing antiparallel cis XX -N28-N37 : G-C Ww/Ww pairing antiparallel cis XIX -N29-N34 : C-G Wh/Wh pairing antiparallel cis one_hbond -N29-N36 : C-G Ww/Ww pairing antiparallel cis XIX -N30-N34 : C-G Bs/Ww pairing antiparallel cis 127 -N31-N32 : U-G O2'/Ss adjacent_5p pairing -N32-N33 : G-G Sw/Wh adjacent_5p pairing parallel cis one_hbond 114 -N43-N45 : G-C Hh/O2P pairing -N44-N45 : C-C Ss/Hh adjacent_5p pairing parallel cis one_hbond -Residue conformations ------------------------------------------- -N17 : G C2p_exo anti -N18 : G C3p_endo anti -N19 : C C2p_exo anti -N20 : A C3p_endo anti -N21 : G C3p_endo anti -N22 : A C2p_exo anti -N23 : U C2p_exo anti -N24 : C C2p_exo anti -N25 : U C2p_endo anti -N26 : G C3p_endo anti -N27 : A C3p_endo anti -N28 : G C4p_exo anti -N29 : C C2p_exo anti -N30 : C C3p_endo anti -N31 : U C3p_endo anti -N32 : G C3p_endo anti -N33 : G C2p_exo anti -N34 : G C1p_endo syn -N35 : A C2p_exo anti -N36 : G C2p_exo anti -N37 : C C3p_endo anti -N38 : U C3p_endo anti -N39 : C C2p_exo anti -N40 : U C3p_endo anti -N41 : C C3p_endo anti -N42 : U C3p_endo anti -N43 : G C3p_endo anti -N44 : C C3p_endo anti -N45 : C C3p_endo anti -N1 : ARG -Adjacent stackings ---------------------------------------------- -N17-N18 : adjacent_5p upward -N18-N19 : adjacent_5p upward -N19-N20 : adjacent_5p upward -N20-N21 : adjacent_5p upward -N21-N22 : adjacent_5p upward -N26-N27 : adjacent_5p upward -N27-N28 : adjacent_5p upward -N28-N29 : adjacent_5p upward -N29-N30 : adjacent_5p upward -N36-N37 : adjacent_5p upward -N38-N39 : adjacent_5p upward -N39-N40 : adjacent_5p upward -N40-N41 : adjacent_5p upward -N41-N42 : adjacent_5p upward -N42-N43 : adjacent_5p upward -N43-N44 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 16 -Number of adjacent stackings = 16 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -N17-N45 : G-C Ww/Ww pairing antiparallel cis 130 -N18-N44 : G-C Ww/Ww pairing antiparallel cis XIX -N19-N43 : C-G Ww/Ww pairing antiparallel cis XIX -N20-N42 : A-U Ww/Ww pairing antiparallel cis XX -N21-N41 : G-C Ww/Ww pairing antiparallel cis XIX -N26-N39 : G-C Ww/Ww pairing antiparallel cis XIX -N27-N38 : A-U Ww/Ww pairing antiparallel cis XX -N28-N37 : G-C Ww/Ww pairing antiparallel cis XIX -N29-N36 : C-G Ww/Ww pairing antiparallel cis XIX -N30-N34 : C-G Ww/Ww pairing antiparallel cis one_hbond -N33-N34 : G-G O2P/Bs adjacent_5p pairing -N34-N35 : G-A O2'/Hh adjacent_5p pairing -Residue conformations ------------------------------------------- -N17 : G C2p_exo anti -N18 : G C1p_exo anti -N19 : C C2p_exo anti -N20 : A C2p_exo anti -N21 : G C3p_endo anti -N22 : A C2p_exo anti -N23 : U C3p_endo anti -N24 : C C3p_endo anti -N25 : U C3p_endo anti -N26 : G C3p_endo anti -N27 : A C2p_exo anti -N28 : G C4p_exo anti -N29 : C C3p_endo anti -N30 : C C2p_exo anti -N31 : U C3p_exo anti -N32 : G C2p_exo anti -N33 : G C3p_exo anti -N34 : G C2p_exo syn -N35 : A C2p_exo anti -N36 : G C2p_exo anti -N37 : C C3p_endo anti -N38 : U C3p_endo anti -N39 : C C3p_endo anti -N40 : U C2p_exo anti -N41 : C C4p_exo anti -N42 : U C2p_exo anti -N43 : G C3p_endo anti -N44 : C C1p_endo anti -N45 : C C4p_exo anti -N1 : ARG -Adjacent stackings ---------------------------------------------- -N18-N19 : adjacent_5p outward pairing -N19-N20 : adjacent_5p upward -N20-N21 : adjacent_5p upward -N21-N22 : adjacent_5p upward -N26-N27 : adjacent_5p upward -N27-N28 : adjacent_5p upward -N28-N29 : adjacent_5p upward -N36-N37 : adjacent_5p upward -N37-N38 : adjacent_5p upward -N39-N40 : adjacent_5p upward -N40-N41 : adjacent_5p upward -N41-N42 : adjacent_5p upward -N43-N44 : adjacent_5p inward -Non-Adjacent stackings ------------------------------------------ -N20-N43 : outward -Number of stackings = 14 -Number of adjacent stackings = 13 -Number of non adjacent stackings = 1 -Base-pairs ------------------------------------------------------ -N17-N45 : G-C Ww/Ww pairing antiparallel cis XIX -N18-N19 : G-C O2'/Hh adjacent_5p outward pairing -N18-N44 : G-C Ww/Ww pairing antiparallel cis -N18-N45 : G-C Bs/O2' pairing -N19-N43 : C-G Ww/Ww pairing antiparallel cis XIX -N21-N41 : G-C Ww/Ww pairing antiparallel cis -N22-N26 : A-G Wh/Hw pairing parallel cis one_hbond -N25-N26 : U-G O2'/C8 adjacent_5p pairing -N26-N39 : G-C Ww/Ww pairing antiparallel cis -N27-N38 : A-U Ww/Ww pairing antiparallel cis XX -N28-N37 : G-C Ww/Ww pairing antiparallel cis XIX -N29-N36 : C-G Ww/Ww pairing antiparallel cis XIX -N34-N35 : G-A O2'/Hh adjacent_5p pairing -N34-N36 : G-G Hh/O2P pairing -N43-N45 : G-C Hh/O2P pairing -N44-N45 : C-C Ss/Hh adjacent_5p pairing parallel cis one_hbond -Residue conformations ------------------------------------------- -N17 : G C2p_exo anti -N18 : G C3p_endo anti -N19 : C C2p_exo anti -N20 : A C3p_endo anti -N21 : G C2p_exo anti -N22 : A C2p_exo anti -N23 : U C3p_endo anti -N24 : C C2p_exo anti -N25 : U C1p_endo anti -N26 : G C3p_endo anti -N27 : A C3p_endo anti -N28 : G C3p_endo anti -N29 : C C3p_endo anti -N30 : C C3p_endo anti -N31 : U C3p_exo anti -N32 : G C2p_exo anti -N33 : G C2p_endo anti -N34 : G C2p_exo syn -N35 : A C3p_exo anti -N36 : G C2p_exo anti -N37 : C C3p_endo anti -N38 : U C3p_endo anti -N39 : C C3p_endo anti -N40 : U C2p_exo anti -N41 : C C4p_exo anti -N42 : U C3p_endo anti -N43 : G C3p_endo anti -N44 : C C2p_exo anti -N45 : C C3p_endo anti -N1 : ARG -Adjacent stackings ---------------------------------------------- -N17-N18 : adjacent_5p upward -N18-N19 : adjacent_5p upward -N19-N20 : adjacent_5p upward -N20-N21 : adjacent_5p upward -N21-N22 : adjacent_5p upward -N26-N27 : adjacent_5p upward -N27-N28 : adjacent_5p upward -N28-N29 : adjacent_5p upward -N29-N30 : adjacent_5p upward pairing -N30-N31 : adjacent_5p upward -N37-N38 : adjacent_5p upward -N38-N39 : adjacent_5p upward -N39-N40 : adjacent_5p upward -N40-N41 : adjacent_5p upward -N41-N42 : adjacent_5p upward -N43-N44 : adjacent_5p upward -N44-N45 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -N20-N43 : outward -Number of stackings = 18 -Number of adjacent stackings = 17 -Number of non adjacent stackings = 1 -Base-pairs ------------------------------------------------------ -N1-N22 : ARG-A pairing one_hbond -N17-N45 : G-C Ww/Ww pairing antiparallel cis XIX -N18-N44 : G-C Ww/Ww pairing antiparallel cis XIX -N19-N43 : C-G Ww/Ww pairing antiparallel cis XIX -N20-N42 : A-U Ww/Ww pairing antiparallel cis XX -N21-N41 : G-C Ww/Ww pairing antiparallel cis XIX -N25-N41 : U-C Ww/O2' pairing -N26-N39 : G-C Ww/Ww pairing antiparallel cis XIX -N27-N38 : A-U Ww/Ww pairing antiparallel cis XX -N28-N37 : G-C Ww/Ww pairing antiparallel cis XIX -N29-N30 : C-C O2P/Bh adjacent_5p upward pairing -N29-N36 : C-G Ww/Ww pairing antiparallel cis XIX -N30-N34 : C-G O2'/Bs pairing -N33-N34 : G-G O2P/Bs adjacent_5p pairing -Residue conformations ------------------------------------------- -N17 : G C3p_endo anti -N18 : G C1p_exo anti -N19 : C C2p_exo anti -N20 : A C2p_exo anti -N21 : G C3p_endo anti -N22 : A C2p_exo anti -N23 : U C2p_exo anti -N24 : C C3p_endo anti -N25 : U C3p_exo syn -N26 : G C4p_exo anti -N27 : A C4p_exo anti -N28 : G C4p_exo anti -N29 : C C3p_endo anti -N30 : C C3p_endo anti -N31 : U O4p_endo anti -N32 : G C2p_exo anti -N33 : G C2p_exo anti -N34 : G C3p_endo anti -N35 : A C2p_exo anti -N36 : G C2p_exo anti -N37 : C C3p_endo anti -N38 : U C4p_exo anti -N39 : C C2p_exo anti -N40 : U C3p_endo anti -N41 : C C3p_endo anti -N42 : U C2p_exo anti -N43 : G C2p_exo anti -N44 : C C3p_endo anti -N45 : C O4p_endo anti -N1 : ARG -Adjacent stackings ---------------------------------------------- -N17-N18 : adjacent_5p downward -N18-N19 : adjacent_5p outward pairing -N20-N21 : adjacent_5p upward -N21-N22 : adjacent_5p upward -N26-N27 : adjacent_5p upward -N27-N28 : adjacent_5p upward -N28-N29 : adjacent_5p upward -N29-N30 : adjacent_5p upward pairing -N39-N40 : adjacent_5p upward -N40-N41 : adjacent_5p upward -N41-N42 : adjacent_5p upward -N43-N44 : adjacent_5p inward -Non-Adjacent stackings ------------------------------------------ -N27-N39 : outward -Number of stackings = 13 -Number of adjacent stackings = 12 -Number of non adjacent stackings = 1 -Base-pairs ------------------------------------------------------ -N18-N19 : G-C O2'/Hh adjacent_5p outward pairing -N18-N44 : G-C Ww/Ww pairing antiparallel cis -N18-N45 : G-C Bs/O2' pairing -N19-N43 : C-G Ww/Ww pairing antiparallel cis XIX -N20-N42 : A-U Ww/Ww pairing antiparallel cis XX -N21-N41 : G-C Ww/Ww pairing antiparallel cis XIX -N22-N40 : A-U Ww/Ww pairing antiparallel cis XX -N23-N33 : U-G O2P/Bs pairing -N26-N39 : G-C Ww/Ww pairing antiparallel cis XIX -N27-N38 : A-U Ww/Ww pairing antiparallel cis XX -N28-N37 : G-C Ww/Ww pairing antiparallel cis XIX -N29-N30 : C-C O2P/Bh adjacent_5p upward pairing -N29-N31 : C-U O2P/Ww pairing -N29-N36 : C-G Ww/Ww pairing antiparallel cis -N30-N34 : C-G Ws/Ws pairing antiparallel cis one_hbond -N33-N34 : G-G O2'/C8 adjacent_5p pairing -N34-N35 : G-A O2'/Hh adjacent_5p pairing -N35-N36 : A-G Ww/O2' adjacent_5p pairing -N43-N45 : G-C Hh/O2P pairing -N44-N45 : C-C Ss/Hh adjacent_5p pairing parallel cis one_hbond -Residue conformations ------------------------------------------- -N17 : G C2p_exo anti -N18 : G C3p_endo anti -N19 : C C2p_exo anti -N20 : A C3p_endo anti -N21 : G C2p_exo anti -N22 : A C2p_exo anti -N23 : U C2p_exo anti -N24 : C C3p_endo anti -N25 : U C2p_endo syn -N26 : G C4p_exo anti -N27 : A C4p_exo anti -N28 : G C3p_endo anti -N29 : C C2p_exo anti -N30 : C C2p_exo anti -N31 : U C2p_endo anti -N32 : G C2p_exo anti -N33 : G C2p_exo anti -N34 : G C2p_exo syn -N35 : A C3p_exo anti -N36 : G C2p_exo anti -N37 : C C3p_endo anti -N38 : U C3p_endo anti -N39 : C C3p_endo anti -N40 : U C2p_exo anti -N41 : C C3p_endo anti -N42 : U C3p_endo anti -N43 : G C3p_endo anti -N44 : C C2p_exo anti -N45 : C C3p_endo anti -N1 : ARG -Adjacent stackings ---------------------------------------------- -N17-N18 : adjacent_5p upward -N18-N19 : adjacent_5p upward -N19-N20 : adjacent_5p upward -N20-N21 : adjacent_5p upward -N21-N22 : adjacent_5p upward -N26-N27 : adjacent_5p upward -N27-N28 : adjacent_5p upward -N29-N30 : adjacent_5p upward -N36-N37 : adjacent_5p upward -N40-N41 : adjacent_5p upward -N41-N42 : adjacent_5p upward -N42-N43 : adjacent_5p upward -N43-N44 : adjacent_5p upward -N44-N45 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -N34-N36 : upward -Number of stackings = 15 -Number of adjacent stackings = 14 -Number of non adjacent stackings = 1 -Base-pairs ------------------------------------------------------ -N17-N45 : G-C Ww/Ws pairing antiparallel cis one_hbond 130 -N18-N44 : G-C Ww/Ww pairing antiparallel cis -N19-N43 : C-G Ww/Ww pairing antiparallel cis XIX -N20-N42 : A-U Ww/Ww pairing antiparallel cis XX -N21-N41 : G-C Ww/Ww pairing antiparallel cis -N22-N40 : A-U Ww/Ww pairing antiparallel cis one_hbond -N26-N39 : G-C Ww/Ww pairing antiparallel cis XIX -N27-N38 : A-U Ww/Ww pairing antiparallel cis XX -N29-N34 : C-G Ww/Ww pairing antiparallel cis XIX -N30-N33 : C-G O2'/Ss O2'/C8 pairing -N33-N34 : G-G O2'/Ss adjacent_5p pairing diff --git a/MCdata/1asy_MC b/MCdata/1asy_MC deleted file mode 100644 index 79a57ae95ff6d5dfde791a33930065a1efee6e56..0000000000000000000000000000000000000000 --- a/MCdata/1asy_MC +++ /dev/null @@ -1,1305 +0,0 @@ -Residue conformations ------------------------------------------- -R601 : U C3p_endo anti -R602 : C C3p_endo anti -R603 : C C3p_endo anti -R604 : G C3p_endo anti -R605 : U C3p_endo anti -R606 : G C3p_endo anti -R607 : A C2p_endo anti -R608 : U C3p_endo anti -R609 : A C2p_endo anti -R610 : G C3p_endo anti -R611 : U C3p_endo anti -R612 : U C3p_endo anti -R613 : PSU -R614 : A C3p_endo anti -R615 : A C3p_endo anti -R616 : H2U -R617 : G C2p_endo anti -R618 : G C2p_endo syn -R619 : H2U -R620 : C C3p_endo anti -R621 : A C3p_endo anti -R622 : G C3p_endo anti -R623 : A C3p_endo anti -R624 : A C3p_endo anti -R625 : U C3p_endo anti -R626 : G C3p_endo anti -R627 : G C3p_endo anti -R628 : G C3p_endo anti -R629 : C C3p_endo anti -R630 : G C3p_endo anti -R631 : C C3p_endo anti -R632 : PSU -R633 : U C3p_endo anti -R634 : G C3p_endo anti -R635 : U C3p_endo anti -R636 : C C3p_endo anti -R637 : 1MG -R638 : C C3p_endo anti -R639 : G C3p_endo anti -R640 : U C3p_endo anti -R641 : G C3p_endo anti -R642 : C C3p_endo anti -R643 : C C3p_endo anti -R644 : A C3p_endo anti -R645 : G C3p_endo anti -R646 : A C3p_endo anti -R648 : U C2p_endo anti -R649 : 5MC -R650 : G C3p_endo anti -R651 : G C3p_endo anti -R652 : G C3p_endo anti -R653 : G C3p_endo anti -R654 : 5MU -R655 : PSU -R656 : C C3p_endo anti -R657 : A C3p_endo anti -R658 : A C2p_endo syn -R659 : U C3p_endo anti -R660 : U C2p_endo syn -R661 : C C3p_endo anti -R662 : C C3p_endo anti -R663 : C C3p_endo anti -R664 : C C3p_endo anti -R665 : G C3p_endo anti -R666 : U C3p_endo anti -R667 : C C3p_endo anti -R668 : G C3p_endo anti -R669 : C C3p_endo anti -R670 : G C3p_endo anti -R671 : G C3p_endo anti -R672 : A C3p_endo anti -R673 : G C3p_endo anti -R674 : C C3p_endo anti -R675 : C C3p_endo anti -R676 : A C2p_endo anti -S601 : U C3p_endo anti -S602 : C C3p_endo anti -S603 : C C3p_endo anti -S604 : G C3p_endo anti -S605 : U C3p_endo anti -S606 : G C3p_endo anti -S607 : A C2p_endo anti -S608 : U C3p_endo anti -S609 : A C2p_endo anti -S610 : G C3p_endo anti -S611 : U C3p_endo anti -S612 : U C3p_endo anti -S613 : PSU -S614 : A C3p_endo anti -S615 : A C3p_endo anti -S616 : H2U -S617 : G C2p_endo anti -S618 : G C2p_endo anti -S619 : H2U -S620 : C C3p_endo anti -S621 : A C3p_endo anti -S622 : G C3p_endo anti -S623 : A C3p_endo anti -S624 : A C3p_endo anti -S625 : U C3p_endo anti -S626 : G C3p_endo anti -S627 : G C3p_endo anti -S628 : G C3p_endo anti -S629 : C C3p_endo anti -S630 : G C3p_endo anti -S631 : C C3p_endo anti -S632 : PSU -S633 : U C3p_endo anti -S634 : G C3p_endo anti -S635 : U C3p_endo anti -S636 : C C3p_endo anti -S637 : 1MG -S638 : C C3p_endo anti -S639 : G C3p_endo anti -S640 : U C3p_endo anti -S641 : G C3p_endo anti -S642 : C C3p_endo anti -S643 : C C3p_endo anti -S644 : A C3p_endo anti -S645 : G C3p_endo anti -S646 : A C3p_endo anti -S648 : U C2p_endo anti -S649 : 5MC -S650 : G C3p_endo anti -S651 : G C3p_endo anti -S652 : G C3p_endo anti -S653 : G C3p_endo anti -S654 : 5MU -S655 : PSU -S656 : C C3p_endo anti -S657 : A C3p_endo anti -S658 : A C2p_endo syn -S659 : U C3p_endo anti -S660 : U C2p_endo anti -S661 : C C3p_endo anti -S662 : C C3p_endo anti -S663 : C C3p_endo anti -S664 : C C3p_endo anti -S665 : G C3p_endo anti -S666 : U C3p_endo anti -S667 : C C3p_endo anti -S668 : G C3p_endo anti -S669 : C C3p_endo anti -S670 : G C3p_endo anti -S671 : G C3p_endo anti -S672 : A C3p_endo anti -S673 : G C3p_endo anti -S674 : C C3p_endo anti -S675 : C C3p_endo anti -S676 : A C2p_endo anti -A68 : GLU -A69 : ASP -A70 : THR -A71 : ALA -A72 : LYS -A73 : ASP -A74 : ASN -A75 : TYR -A76 : GLY -A77 : LYS -A78 : LEU -A79 : PRO -A80 : LEU -A81 : ILE -A82 : GLN -A83 : SER -A84 : ARG -A85 : ASP -A86 : SER -A87 : ASP -A88 : ARG -A89 : THR -A90 : GLY -A91 : GLN -A92 : LYS -A93 : ARG -A94 : VAL -A95 : LYS -A96 : PHE -A97 : VAL -A98 : ASP -A99 : LEU -A100 : ASP -A101 : GLU -A102 : ALA -A103 : LYS -A104 : ASP -A105 : SER -A106 : ASP -A107 : LYS -A108 : GLU -A109 : VAL -A110 : LEU -A111 : PHE -A112 : ARG -A113 : ALA -A114 : ARG -A115 : VAL -A116 : HIS -A117 : ASN -A118 : THR -A119 : ARG -A120 : GLN -A121 : GLN -A122 : GLY -A123 : ALA -A124 : THR -A125 : LEU -A126 : ALA -A127 : PHE -A128 : LEU -A129 : THR -A130 : LEU -A131 : ARG -A132 : GLN -A133 : GLN -A134 : ALA -A135 : SER -A136 : LEU -A137 : ILE -A138 : GLN -A139 : GLY -A140 : LEU -A141 : VAL -A142 : LYS -A143 : ALA -A144 : ASN -A145 : LYS -A146 : GLU -A147 : GLY -A148 : THR -A149 : ILE -A150 : SER -A151 : LYS -A152 : ASN -A153 : MET -A154 : VAL -A155 : LYS -A156 : TRP -A157 : ALA -A158 : GLY -A159 : SER -A160 : LEU -A161 : ASN -A162 : LEU -A163 : GLU -A164 : SER -A165 : ILE -A166 : VAL -A167 : LEU -A168 : VAL -A169 : ARG -A170 : GLY -A171 : ILE -A172 : VAL -A173 : LYS -A174 : LYS -A175 : VAL -A176 : ASP -A177 : GLU -A178 : PRO -A179 : ILE -A180 : LYS -A181 : SER -A182 : ALA -A183 : THR -A184 : VAL -A185 : GLN -A186 : ASN -A187 : LEU -A188 : GLU -A189 : ILE -A190 : HIS -A191 : ILE -A192 : THR -A193 : LYS -A194 : ILE -A195 : TYR -A196 : THR -A197 : ILE -A198 : SER -A199 : GLU -A200 : THR -A201 : PRO -A202 : GLU -A203 : ALA -A204 : LEU -A205 : PRO -A206 : ILE -A207 : LEU -A208 : LEU -A209 : GLU -A210 : ASP -A211 : ALA -A212 : SER -A213 : ARG -A214 : SER -A215 : GLU -A216 : ALA -A217 : GLU -A218 : ALA -A219 : GLU -A220 : ALA -A221 : ALA -A222 : GLY -A223 : LEU -A224 : PRO -A225 : VAL -A226 : VAL -A227 : ASN -A228 : LEU -A229 : ASP -A230 : THR -A231 : ARG -A232 : LEU -A233 : ASP -A234 : TYR -A235 : ARG -A236 : VAL -A237 : ILE -A238 : ASP -A239 : LEU -A240 : ARG -A241 : THR -A242 : VAL -A243 : THR -A244 : ASN -A245 : GLN -A246 : ALA -A247 : ILE -A248 : PHE -A249 : ARG -A250 : ILE -A251 : GLN -A252 : ALA -A253 : GLY -A254 : VAL -A255 : CYS -A256 : GLU -A257 : LEU -A258 : PHE -A259 : ARG -A260 : GLU -A261 : TYR -A262 : LEU -A263 : ALA -A264 : THR -A265 : LYS -A266 : LYS -A267 : PHE -A268 : THR -A269 : GLU -A270 : VAL -A271 : HIS -A272 : THR -A273 : PRO -A274 : LYS -A275 : LEU -A276 : LEU -A277 : GLY -A278 : ALA -A279 : PRO -A280 : SER -A281 : GLU -A282 : GLY -A283 : GLY -A284 : SER -A285 : SER -A286 : VAL -A287 : PHE -A288 : GLU -A289 : VAL -A290 : THR -A291 : TYR -A292 : PHE -A293 : LYS -A294 : GLY -A295 : LYS -A296 : ALA -A297 : TYR -A298 : LEU -A299 : ALA -A300 : GLN -A301 : SER -A302 : PRO -A303 : GLN -A304 : PHE -A305 : ASN -A306 : LYS -A307 : GLN -A308 : GLN -A309 : LEU -A310 : ILE -A311 : VAL -A312 : ALA -A313 : ASP -A314 : PHE -A315 : GLU -A316 : ARG -A317 : VAL -A318 : TYR -A319 : GLU -A320 : ILE -A321 : GLY -A322 : PRO -A323 : VAL -A324 : PHE -A325 : ARG -A326 : ALA -A327 : GLU -A328 : ASN -A329 : SER -A330 : ASN -A331 : THR -A332 : HIS -A333 : ARG -A334 : HIS -A335 : MET -A336 : THR -A337 : GLU -A338 : PHE -A339 : THR -A340 : GLY -A341 : LEU -A342 : ASP -A343 : MET -A344 : GLU -A345 : MET -A346 : ALA -A347 : PHE -A348 : GLU -A349 : GLU -A350 : HIS -A351 : TYR -A352 : HIS -A353 : GLU -A354 : VAL -A355 : LEU -A356 : ASP -A357 : THR -A358 : LEU -A359 : SER -A360 : GLU -A361 : LEU -A362 : PHE -A363 : VAL -A364 : PHE -A365 : ILE -A366 : PHE -A367 : SER -A368 : GLU -A369 : LEU -A370 : PRO -A371 : LYS -A372 : ARG -A373 : PHE -A374 : ALA -A375 : HIS -A376 : GLU -A377 : ILE -A378 : GLU -A379 : LEU -A380 : VAL -A381 : ARG -A382 : LYS -A383 : GLN -A384 : TYR -A385 : PRO -A386 : VAL -A387 : GLU -A388 : GLU -A389 : PHE -A390 : LYS -A391 : LEU -A392 : PRO -A393 : LYS -A394 : ASP -A395 : GLY -A396 : LYS -A397 : MET -A398 : VAL -A399 : ARG -A400 : LEU -A401 : THR -A402 : TYR -A403 : LYS -A404 : GLU -A405 : GLY -A406 : ILE -A407 : GLU -A408 : MET -A409 : LEU -A410 : ARG -A411 : ALA -A412 : ALA -A413 : GLY -A414 : LYS -A415 : GLU -A416 : ILE -A417 : GLY -A418 : ASP -A419 : PHE -A420 : GLU -A421 : ASP -A422 : LEU -A423 : SER -A424 : THR -A425 : GLU -A426 : ASN -A427 : GLU -A428 : LYS -A429 : PHE -A430 : LEU -A431 : GLY -A432 : LYS -A433 : LEU -A434 : VAL -A435 : ARG -A436 : ASP -A437 : LYS -A438 : TYR -A439 : ASP -A440 : THR -A441 : ASP -A442 : PHE -A443 : TYR -A444 : ILE -A445 : LEU -A446 : ASP -A447 : LYS -A448 : PHE -A449 : PRO -A450 : LEU -A451 : GLU -A452 : ILE -A453 : ARG -A454 : PRO -A455 : PHE -A456 : TYR -A457 : THR -A458 : MET -A459 : PRO -A460 : ASP -A461 : PRO -A462 : ALA -A463 : ASN -A464 : PRO -A465 : LYS -A466 : TYR -A467 : SER -A468 : ASN -A469 : SER -A470 : TYR -A471 : ASP -A472 : PHE -A473 : PHE -A474 : MET -A475 : ARG -A476 : GLY -A477 : GLU -A478 : GLU -A479 : ILE -A480 : LEU -A481 : SER -A482 : GLY -A483 : ALA -A484 : GLN -A485 : ARG -A486 : ILE -A487 : HIS -A488 : ASP -A489 : HIS -A490 : ALA -A491 : LEU -A492 : LEU -A493 : GLN -A494 : GLU -A495 : ARG -A496 : MET -A497 : LYS -A498 : ALA -A499 : HIS -A500 : GLY -A501 : LEU -A502 : SER -A503 : PRO -A504 : GLU -A505 : ASP -A506 : PRO -A507 : GLY -A508 : LEU -A509 : LYS -A510 : ASP -A511 : TYR -A512 : CYS -A513 : ASP -A514 : GLY -A515 : PHE -A516 : SER -A517 : TYR -A518 : GLY -A519 : CYS -A520 : PRO -A521 : PRO -A522 : HIS -A523 : ALA -A524 : GLY -A525 : GLY -A526 : GLY -A527 : ILE -A528 : GLY -A529 : LEU -A530 : GLU -A531 : ARG -A532 : VAL -A533 : VAL -A534 : MET -A535 : PHE -A536 : TYR -A537 : LEU -A538 : ASP -A539 : LEU -A540 : LYS -A541 : ASN -A542 : ILE -A543 : ARG -A544 : ARG -A545 : ALA -A546 : SER -A547 : LEU -A548 : PHE -A549 : PRO -A550 : ARG -A551 : ASP -A552 : PRO -A553 : LYS -A554 : ARG -A555 : LEU -A556 : ARG -A557 : PRO -B68 : GLU -B69 : ASP -B70 : THR -B71 : ALA -B72 : LYS -B73 : ASP -B74 : ASN -B75 : TYR -B76 : GLY -B77 : LYS -B78 : LEU -B79 : PRO -B80 : LEU -B81 : ILE -B82 : GLN -B83 : SER -B84 : ARG -B85 : ASP -B86 : SER -B87 : ASP -B88 : ARG -B89 : THR -B90 : GLY -B91 : GLN -B92 : LYS -B93 : ARG -B94 : VAL -B95 : LYS -B96 : PHE -B97 : VAL -B98 : ASP -B99 : LEU -B100 : ASP -B101 : GLU -B102 : ALA -B103 : LYS -B104 : ASP -B105 : SER -B106 : ASP -B107 : LYS -B108 : GLU -B109 : VAL -B110 : LEU -B111 : PHE -B112 : ARG -B113 : ALA -B114 : ARG -B115 : VAL -B116 : HIS -B117 : ASN -B118 : THR -B119 : ARG -B120 : GLN -B121 : GLN -B122 : GLY -B123 : ALA -B124 : THR -B125 : LEU -B126 : ALA -B127 : PHE -B128 : LEU -B129 : THR -B130 : LEU -B131 : ARG -B132 : GLN -B133 : GLN -B134 : ALA -B135 : SER -B136 : LEU -B137 : ILE -B138 : GLN -B139 : GLY -B140 : LEU -B141 : VAL -B142 : LYS -B143 : ALA -B144 : ASN -B145 : LYS -B146 : GLU -B147 : GLY -B148 : THR -B149 : ILE -B150 : SER -B151 : LYS -B152 : ASN -B153 : MET -B154 : VAL -B155 : LYS -B156 : TRP -B157 : ALA -B158 : GLY -B159 : SER -B160 : LEU -B161 : ASN -B162 : LEU -B163 : GLU -B164 : SER -B165 : ILE -B166 : VAL -B167 : LEU -B168 : VAL -B169 : ARG -B170 : GLY -B171 : ILE -B172 : VAL -B173 : LYS -B174 : LYS -B175 : VAL -B176 : ASP -B177 : GLU -B178 : PRO -B179 : ILE -B180 : LYS -B181 : SER -B182 : ALA -B183 : THR -B184 : VAL -B185 : GLN -B186 : ASN -B187 : LEU -B188 : GLU -B189 : ILE -B190 : HIS -B191 : ILE -B192 : THR -B193 : LYS -B194 : ILE -B195 : TYR -B196 : THR -B197 : ILE -B198 : SER -B199 : GLU -B200 : THR -B201 : PRO -B202 : GLU -B203 : ALA -B204 : LEU -B205 : PRO -B206 : ILE -B207 : LEU -B208 : LEU -B209 : GLU -B210 : ASP -B211 : ALA -B212 : SER -B213 : ARG -B214 : SER -B215 : GLU -B216 : ALA -B217 : GLU -B218 : ALA -B219 : GLU -B220 : ALA -B221 : ALA -B222 : GLY -B223 : LEU -B224 : PRO -B225 : VAL -B226 : VAL -B227 : ASN -B228 : LEU -B229 : ASP -B230 : THR -B231 : ARG -B232 : LEU -B233 : ASP -B234 : TYR -B235 : ARG -B236 : VAL -B237 : ILE -B238 : ASP -B239 : LEU -B240 : ARG -B241 : THR -B242 : VAL -B243 : THR -B244 : ASN -B245 : GLN -B246 : ALA -B247 : ILE -B248 : PHE -B249 : ARG -B250 : ILE -B251 : GLN -B252 : ALA -B253 : GLY -B254 : VAL -B255 : CYS -B256 : GLU -B257 : LEU -B258 : PHE -B259 : ARG -B260 : GLU -B261 : TYR -B262 : LEU -B263 : ALA -B264 : THR -B265 : LYS -B266 : LYS -B267 : PHE -B268 : THR -B269 : GLU -B270 : VAL -B271 : HIS -B272 : THR -B273 : PRO -B274 : LYS -B275 : LEU -B276 : LEU -B277 : GLY -B278 : ALA -B279 : PRO -B280 : SER -B281 : GLU -B282 : GLY -B283 : GLY -B284 : SER -B285 : SER -B286 : VAL -B287 : PHE -B288 : GLU -B289 : VAL -B290 : THR -B291 : TYR -B292 : PHE -B293 : LYS -B294 : GLY -B295 : LYS -B296 : ALA -B297 : TYR -B298 : LEU -B299 : ALA -B300 : GLN -B301 : SER -B302 : PRO -B303 : GLN -B304 : PHE -B305 : ASN -B306 : LYS -B307 : GLN -B308 : GLN -B309 : LEU -B310 : ILE -B311 : VAL -B312 : ALA -B313 : ASP -B314 : PHE -B315 : GLU -B316 : ARG -B317 : VAL -B318 : TYR -B319 : GLU -B320 : ILE -B321 : GLY -B322 : PRO -B323 : VAL -B324 : PHE -B325 : ARG -B326 : ALA -B327 : GLU -B328 : ASN -B329 : SER -B330 : ASN -B331 : THR -B332 : HIS -B333 : ARG -B334 : HIS -B335 : MET -B336 : THR -B337 : GLU -B338 : PHE -B339 : THR -B340 : GLY -B341 : LEU -B342 : ASP -B343 : MET -B344 : GLU -B345 : MET -B346 : ALA -B347 : PHE -B348 : GLU -B349 : GLU -B350 : HIS -B351 : TYR -B352 : HIS -B353 : GLU -B354 : VAL -B355 : LEU -B356 : ASP -B357 : THR -B358 : LEU -B359 : SER -B360 : GLU -B361 : LEU -B362 : PHE -B363 : VAL -B364 : PHE -B365 : ILE -B366 : PHE -B367 : SER -B368 : GLU -B369 : LEU -B370 : PRO -B371 : LYS -B372 : ARG -B373 : PHE -B374 : ALA -B375 : HIS -B376 : GLU -B377 : ILE -B378 : GLU -B379 : LEU -B380 : VAL -B381 : ARG -B382 : LYS -B383 : GLN -B384 : TYR -B385 : PRO -B386 : VAL -B387 : GLU -B388 : GLU -B389 : PHE -B390 : LYS -B391 : LEU -B392 : PRO -B393 : LYS -B394 : ASP -B395 : GLY -B396 : LYS -B397 : MET -B398 : VAL -B399 : ARG -B400 : LEU -B401 : THR -B402 : TYR -B403 : LYS -B404 : GLU -B405 : GLY -B406 : ILE -B407 : GLU -B408 : MET -B409 : LEU -B410 : ARG -B411 : ALA -B412 : ALA -B413 : GLY -B414 : LYS -B415 : GLU -B416 : ILE -B417 : GLY -B418 : ASP -B419 : PHE -B420 : GLU -B421 : ASP -B422 : LEU -B423 : SER -B424 : THR -B425 : GLU -B426 : ASN -B427 : GLU -B428 : LYS -B429 : PHE -B430 : LEU -B431 : GLY -B432 : LYS -B433 : LEU -B434 : VAL -B435 : ARG -B436 : ASP -B437 : LYS -B438 : TYR -B439 : ASP -B440 : THR -B441 : ASP -B442 : PHE -B443 : TYR -B444 : ILE -B445 : LEU -B446 : ASP -B447 : LYS -B448 : PHE -B449 : PRO -B450 : LEU -B451 : GLU -B452 : ILE -B453 : ARG -B454 : PRO -B455 : PHE -B456 : TYR -B457 : THR -B458 : MET -B459 : PRO -B460 : ASP -B461 : PRO -B462 : ALA -B463 : ASN -B464 : PRO -B465 : LYS -B466 : TYR -B467 : SER -B468 : ASN -B469 : SER -B470 : TYR -B471 : ASP -B472 : PHE -B473 : PHE -B474 : MET -B475 : ARG -B476 : GLY -B477 : GLU -B478 : GLU -B479 : ILE -B480 : LEU -B481 : SER -B482 : GLY -B483 : ALA -B484 : GLN -B485 : ARG -B486 : ILE -B487 : HIS -B488 : ASP -B489 : HIS -B490 : ALA -B491 : LEU -B492 : LEU -B493 : GLN -B494 : GLU -B495 : ARG -B496 : MET -B497 : LYS -B498 : ALA -B499 : HIS -B500 : GLY -B501 : LEU -B502 : SER -B503 : PRO -B504 : GLU -B505 : ASP -B506 : PRO -B507 : GLY -B508 : LEU -B509 : LYS -B510 : ASP -B511 : TYR -B512 : CYS -B513 : ASP -B514 : GLY -B515 : PHE -B516 : SER -B517 : TYR -B518 : GLY -B519 : CYS -B520 : PRO -B521 : PRO -B522 : HIS -B523 : ALA -B524 : GLY -B525 : GLY -B526 : GLY -B527 : ILE -B528 : GLY -B529 : LEU -B530 : GLU -B531 : ARG -B532 : VAL -B533 : VAL -B534 : MET -B535 : PHE -B536 : TYR -B537 : LEU -B538 : ASP -B539 : LEU -B540 : LYS -B541 : ASN -B542 : ILE -B543 : ARG -B544 : ARG -B545 : ALA -B546 : SER -B547 : LEU -B548 : PHE -B549 : PRO -B550 : ARG -B551 : ASP -B552 : PRO -B553 : LYS -B554 : ARG -B555 : LEU -B556 : ARG -B557 : PRO -Adjacent stackings ---------------------------------------------- -R602-R603 : adjacent_5p upward -R603-R604 : adjacent_5p upward -R604-R605 : adjacent_5p upward -R605-R606 : adjacent_5p upward -R606-R607 : adjacent_5p upward -R610-R611 : adjacent_5p upward -R611-R612 : adjacent_5p upward -R614-R615 : adjacent_5p upward -R622-R623 : adjacent_5p upward -R623-R624 : adjacent_5p upward -R624-R625 : adjacent_5p upward -R625-R626 : adjacent_5p upward -R626-R627 : adjacent_5p upward -R627-R628 : adjacent_5p upward -R628-R629 : adjacent_5p upward -R630-R631 : adjacent_5p upward -R639-R640 : adjacent_5p upward -R641-R642 : adjacent_5p upward -R643-R644 : adjacent_5p upward -R650-R651 : adjacent_5p upward -R651-R652 : adjacent_5p upward -R652-R653 : adjacent_5p upward -R656-R657 : adjacent_5p upward -R662-R663 : adjacent_5p upward -R663-R664 : adjacent_5p upward -R664-R665 : adjacent_5p upward -R665-R666 : adjacent_5p upward -R666-R667 : adjacent_5p upward -R668-R669 : adjacent_5p upward -R669-R670 : adjacent_5p upward -R670-R671 : adjacent_5p upward -R671-R672 : adjacent_5p upward -R672-R673 : adjacent_5p upward -R673-R674 : adjacent_5p upward -R674-R675 : adjacent_5p upward -S602-S603 : adjacent_5p upward -S603-S604 : adjacent_5p upward -S604-S605 : adjacent_5p upward -S606-S607 : adjacent_5p upward -S610-S611 : adjacent_5p upward -S614-S615 : adjacent_5p upward -S622-S623 : adjacent_5p upward -S623-S624 : adjacent_5p upward -S624-S625 : adjacent_5p upward -S626-S627 : adjacent_5p upward -S627-S628 : adjacent_5p upward -S628-S629 : adjacent_5p upward -S630-S631 : adjacent_5p upward -S635-S636 : adjacent_5p upward -S639-S640 : adjacent_5p upward -S641-S642 : adjacent_5p upward -S642-S643 : adjacent_5p upward -S644-S645 : adjacent_5p upward -S650-S651 : adjacent_5p upward -S651-S652 : adjacent_5p upward -S652-S653 : adjacent_5p upward -S656-S657 : adjacent_5p upward -S659-S660 : adjacent_5p upward -S662-S663 : adjacent_5p upward -S663-S664 : adjacent_5p upward -S664-S665 : adjacent_5p upward -S665-S666 : adjacent_5p upward -S666-S667 : adjacent_5p upward -S668-S669 : adjacent_5p upward -S669-S670 : adjacent_5p upward -S670-S671 : adjacent_5p upward -S671-S672 : adjacent_5p upward -S672-S673 : adjacent_5p upward -S673-S674 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -R604-R670 : outward -R606-R668 : outward -R609-R645 : inward -R609-R646 : outward -R614-R622 : outward -R617-R657 : inward -R617-R658 : outward pairing -R618-R657 : outward -R621-R646 : inward -R621-R648 : outward -R627-R644 : outward -R630-R641 : outward -R650-R665 : outward -R658-R661 : upward -S604-S670 : outward -S606-S668 : outward -S609-S645 : inward pairing -S609-S646 : outward -S614-S622 : outward -S617-S657 : inward pairing -S617-S658 : outward pairing -S618-S657 : outward -S621-S646 : inward -S621-S648 : outward pairing -S627-S644 : outward -S630-S641 : outward -S648-S659 : upward -S650-S665 : outward -S658-S661 : upward -Number of stackings = 98 -Number of adjacent stackings = 69 -Number of non adjacent stackings = 29 -Base-pairs ------------------------------------------------------ -R601-R672 : U-A Ww/Ww pairing antiparallel cis XX -R602-R671 : C-G Ww/Ww pairing antiparallel cis XIX -R603-R670 : C-G Ww/Ww pairing antiparallel cis XIX -R604-R669 : G-C Ww/Ww pairing antiparallel cis XIX -R605-R668 : U-G Ws/Ww pairing antiparallel cis XXVIII -R606-R667 : G-C Ww/Ww pairing antiparallel cis XIX -R607-R666 : A-U Ww/Ww pairing antiparallel cis XX -R608-R614 : U-A Ws/Hh pairing antiparallel trans XXIV -R608-R621 : U-A Ss/Bs pairing parallel trans one_hbond -R609-R610 : A-G O2'/Hh adjacent_5p pairing -R609-R623 : A-A Hh/Hh pairing parallel trans II -R610-R625 : G-U Ww/Ws pairing antiparallel cis XXVIII -R610-R645 : G-G Hw/Bs pairing parallel cis one_hbond 113 -R611-R624 : U-A Ww/Ww pairing antiparallel cis XX -R612-R623 : U-A Ww/Ww pairing antiparallel cis XX -R614-R621 : A-A Wh/Ss pairing antiparallel cis one_hbond 40 -R615-R648 : A-U Ww/Ws pairing parallel trans XXI -R617-R658 : G-A Bs/O2P outward pairing -R618-R656 : G-C Ww/Ww pairing antiparallel cis XIX -R622-R646 : G-A Hh/Wh pairing antiparallel trans one_hbond 60 -R626-R644 : G-A Ww/Ww pairing antiparallel cis VIII -R627-R643 : G-C Ww/Ww pairing antiparallel cis XIX -R628-R642 : G-C Ww/Ww pairing antiparallel cis XIX -R629-R641 : C-G Ww/Ww pairing antiparallel cis one_hbond -R630-R640 : G-U Ww/Ws pairing antiparallel cis XXVIII -R631-R639 : C-G Ww/Ww pairing antiparallel cis XIX -R634-R635 : G-U O2'/Hh adjacent_5p pairing -R650-R664 : G-C Ww/Ww pairing antiparallel cis XIX -R651-R663 : G-C Ww/Ww pairing antiparallel cis XIX -R652-R662 : G-C Ww/Ww pairing antiparallel cis XIX -R653-R661 : G-C Ww/Ww pairing antiparallel cis XIX -R658-R660 : A-U Ss/Hh pairing antiparallel trans one_hbond -R660-R661 : U-C O2P/Bh O2P/Bh adjacent_5p pairing -R675-R676 : C-A O2'/Hh adjacent_5p pairing -S601-S672 : U-A Ww/Ww pairing antiparallel cis XX -S602-S671 : C-G Ww/Ww pairing antiparallel cis XIX -S603-S670 : C-G Ww/Ww pairing antiparallel cis XIX -S604-S669 : G-C Ww/Ww pairing antiparallel cis XIX -S605-S668 : U-G Ws/Ww pairing antiparallel cis XXVIII -S606-S667 : G-C Ww/Ww pairing antiparallel cis XIX -S607-S666 : A-U Ww/Ww pairing antiparallel cis XX -S608-S614 : U-A Ws/Hh pairing antiparallel trans XXIV -S608-S621 : U-A Ss/Bs O2'/Ww pairing parallel trans one_hbond -S609-S610 : A-G O2'/Hh adjacent_5p pairing -S609-S623 : A-A Hh/Hh pairing parallel trans II -S609-S645 : A-G O2'/Ss inward pairing -S610-S625 : G-U Ww/Ws pairing antiparallel cis XXVIII -S610-S645 : G-G Hw/Bs pairing parallel cis one_hbond 113 -S611-S624 : U-A Ww/Ww pairing antiparallel cis XX -S612-S623 : U-A Ww/Ww pairing antiparallel cis XX -S614-S621 : A-A Wh/Ss pairing antiparallel cis one_hbond 40 -S615-S648 : A-U Ww/Ww pairing parallel trans XXI -S617-S657 : G-A O2'/Ww inward pairing -S617-S658 : G-A Bs/O2P outward pairing -S618-S656 : G-C Ww/Ww pairing antiparallel cis XIX -S621-S648 : A-U Bh/O2P outward pairing -S622-S646 : G-A Hh/Ww pairing antiparallel trans one_hbond 60 -S625-S645 : U-G Wh/Ws pairing antiparallel cis one_hbond 94 -S626-S644 : G-A Ww/Ww pairing antiparallel cis VIII -S627-S643 : G-C Ww/Ww pairing antiparallel cis XIX -S628-S642 : G-C Ww/Ww pairing antiparallel cis XIX -S629-S641 : C-G Ww/Ww pairing antiparallel cis XIX -S630-S640 : G-U Ww/Ws pairing antiparallel cis XXVIII -S631-S639 : C-G Ww/Ww pairing antiparallel cis XIX -S650-S664 : G-C Ww/Ww pairing antiparallel cis XIX -S651-S663 : G-C Ww/Ww pairing antiparallel cis XIX -S652-S662 : G-C Ww/Ww pairing antiparallel cis XIX -S653-S661 : G-C Ww/Ww pairing antiparallel cis XIX -S660-S661 : U-C O2P/Bh O2P/Bh adjacent_5p pairing -S674-S675 : C-C O2P/Bh adjacent_5p pairing diff --git a/MCdata/1asz_MC b/MCdata/1asz_MC deleted file mode 100644 index f685af24dfd57d7051f26d29b4b19b26699ecd1f..0000000000000000000000000000000000000000 --- a/MCdata/1asz_MC +++ /dev/null @@ -1,1306 +0,0 @@ -Residue conformations ------------------------------------------- -R601 : U C3p_endo anti -R602 : C C3p_endo anti -R603 : C C3p_endo anti -R604 : G C3p_endo anti -R605 : U C3p_endo anti -R606 : G C3p_endo anti -R607 : A C2p_endo anti -R608 : U C3p_endo anti -R609 : A C2p_endo anti -R610 : G C3p_endo anti -R611 : U C3p_endo anti -R612 : U C3p_endo anti -R613 : PSU -R614 : A C3p_endo anti -R615 : A C3p_endo anti -R616 : H2U -R617 : G C2p_endo anti -R618 : G C2p_endo syn -R619 : H2U -R620 : C C3p_endo anti -R621 : A C3p_endo anti -R622 : G C3p_endo anti -R623 : A C3p_endo anti -R624 : A C3p_endo anti -R625 : U C3p_endo anti -R626 : G C3p_endo anti -R627 : G C3p_endo anti -R628 : G C3p_endo anti -R629 : C C3p_endo anti -R630 : G C3p_endo anti -R631 : C C3p_endo anti -R632 : PSU -R633 : U C3p_endo anti -R634 : G C3p_endo anti -R635 : U C3p_endo anti -R636 : C C3p_endo anti -R637 : 1MG -R638 : C C3p_endo anti -R639 : G C3p_endo anti -R640 : U C3p_endo anti -R641 : G C3p_endo anti -R642 : C C3p_endo anti -R643 : C C3p_endo anti -R644 : A C3p_endo anti -R645 : G C3p_endo anti -R646 : A C3p_endo anti -R648 : U C2p_endo anti -R649 : 5MC -R650 : G C3p_endo anti -R651 : G C3p_endo anti -R652 : G C3p_endo anti -R653 : G C3p_endo anti -R654 : 5MU -R655 : PSU -R656 : C C3p_endo anti -R657 : A C3p_endo anti -R658 : A C2p_endo syn -R659 : U C3p_endo anti -R660 : U C2p_endo syn -R661 : C C3p_endo anti -R662 : C C3p_endo anti -R663 : C C3p_endo anti -R664 : C C3p_endo anti -R665 : G C3p_endo anti -R666 : U C3p_endo anti -R667 : C C3p_endo anti -R668 : G C3p_endo anti -R669 : C C3p_endo anti -R670 : G C3p_endo anti -R671 : G C3p_endo anti -R672 : A C3p_endo anti -R673 : G C3p_endo anti -R674 : C C3p_endo anti -R675 : C C3p_endo anti -R676 : A C2p_endo anti -S601 : U C3p_endo anti -S602 : C C3p_endo anti -S603 : C C3p_endo anti -S604 : G C3p_endo anti -S605 : U C3p_endo anti -S606 : G C3p_endo anti -S607 : A C2p_endo anti -S608 : U C3p_endo anti -S609 : A C2p_endo anti -S610 : G C3p_endo anti -S611 : U C3p_endo anti -S612 : U C3p_endo anti -S613 : PSU -S614 : A C3p_endo anti -S615 : A C3p_endo anti -S616 : H2U -S617 : G C2p_endo anti -S618 : G C2p_endo syn -S619 : H2U -S620 : C C3p_endo anti -S621 : A C3p_endo anti -S622 : G C3p_endo anti -S623 : A C3p_endo anti -S624 : A C3p_endo anti -S625 : U C3p_endo anti -S626 : G C3p_endo anti -S627 : G C3p_endo anti -S628 : G C3p_endo anti -S629 : C C3p_endo anti -S630 : G C3p_endo anti -S631 : C C3p_endo anti -S632 : PSU -S633 : U C3p_endo anti -S634 : G C3p_endo anti -S635 : U C3p_endo anti -S636 : C C3p_endo anti -S637 : 1MG -S638 : C C3p_endo anti -S639 : G C3p_endo anti -S640 : U C3p_endo anti -S641 : G C3p_endo anti -S642 : C C3p_endo anti -S643 : C C3p_endo anti -S644 : A C3p_endo anti -S645 : G C3p_endo anti -S646 : A C3p_endo anti -S648 : U C2p_endo anti -S649 : 5MC -S650 : G C3p_endo anti -S651 : G C3p_endo anti -S652 : G C3p_endo anti -S653 : G C3p_endo anti -S654 : 5MU -S655 : PSU -S656 : C C3p_endo anti -S657 : A C3p_endo anti -S658 : A C2p_endo syn -S659 : U C3p_endo anti -S660 : U C2p_endo anti -S661 : C C3p_endo anti -S662 : C C3p_endo anti -S663 : C C3p_endo anti -S664 : C C3p_endo anti -S665 : G C3p_endo anti -S666 : U C3p_endo anti -S667 : C C3p_endo anti -S668 : G C3p_endo anti -S669 : C C3p_endo anti -S670 : G C3p_endo anti -S671 : G C3p_endo anti -S672 : A C3p_endo anti -S673 : G C3p_endo anti -S674 : C C3p_endo anti -S675 : C C3p_endo anti -S676 : A C2p_endo anti -A68 : GLU -A69 : ASP -A70 : THR -A71 : ALA -A72 : LYS -A73 : ASP -A74 : ASN -A75 : TYR -A76 : GLY -A77 : LYS -A78 : LEU -A79 : PRO -A80 : LEU -A81 : ILE -A82 : GLN -A83 : SER -A84 : ARG -A85 : ASP -A86 : SER -A87 : ASP -A88 : ARG -A89 : THR -A90 : GLY -A91 : GLN -A92 : LYS -A93 : ARG -A94 : VAL -A95 : LYS -A96 : PHE -A97 : VAL -A98 : ASP -A99 : LEU -A100 : ASP -A101 : GLU -A102 : ALA -A103 : LYS -A104 : ASP -A105 : SER -A106 : ASP -A107 : LYS -A108 : GLU -A109 : VAL -A110 : LEU -A111 : PHE -A112 : ARG -A113 : ALA -A114 : ARG -A115 : VAL -A116 : HIS -A117 : ASN -A118 : THR -A119 : ARG -A120 : GLN -A121 : GLN -A122 : GLY -A123 : ALA -A124 : THR -A125 : LEU -A126 : ALA -A127 : PHE -A128 : LEU -A129 : THR -A130 : LEU -A131 : ARG -A132 : GLN -A133 : GLN -A134 : ALA -A135 : SER -A136 : LEU -A137 : ILE -A138 : GLN -A139 : GLY -A140 : LEU -A141 : VAL -A142 : LYS -A143 : ALA -A144 : ASN -A145 : LYS -A146 : GLU -A147 : GLY -A148 : THR -A149 : ILE -A150 : SER -A151 : LYS -A152 : ASN -A153 : MET -A154 : VAL -A155 : LYS -A156 : TRP -A157 : ALA -A158 : GLY -A159 : SER -A160 : LEU -A161 : ASN -A162 : LEU -A163 : GLU -A164 : SER -A165 : ILE -A166 : VAL -A167 : LEU -A168 : VAL -A169 : ARG -A170 : GLY -A171 : ILE -A172 : VAL -A173 : LYS -A174 : LYS -A175 : VAL -A176 : ASP -A177 : GLU -A178 : PRO -A179 : ILE -A180 : LYS -A181 : SER -A182 : ALA -A183 : THR -A184 : VAL -A185 : GLN -A186 : ASN -A187 : LEU -A188 : GLU -A189 : ILE -A190 : HIS -A191 : ILE -A192 : THR -A193 : LYS -A194 : ILE -A195 : TYR -A196 : THR -A197 : ILE -A198 : SER -A199 : GLU -A200 : THR -A201 : PRO -A202 : GLU -A203 : ALA -A204 : LEU -A205 : PRO -A206 : ILE -A207 : LEU -A208 : LEU -A209 : GLU -A210 : ASP -A211 : ALA -A212 : SER -A213 : ARG -A214 : SER -A215 : GLU -A216 : ALA -A217 : GLU -A218 : ALA -A219 : GLU -A220 : ALA -A221 : ALA -A222 : GLY -A223 : LEU -A224 : PRO -A225 : VAL -A226 : VAL -A227 : ASN -A228 : LEU -A229 : ASP -A230 : THR -A231 : ARG -A232 : LEU -A233 : ASP -A234 : TYR -A235 : ARG -A236 : VAL -A237 : ILE -A238 : ASP -A239 : LEU -A240 : ARG -A241 : THR -A242 : VAL -A243 : THR -A244 : ASN -A245 : GLN -A246 : ALA -A247 : ILE -A248 : PHE -A249 : ARG -A250 : ILE -A251 : GLN -A252 : ALA -A253 : GLY -A254 : VAL -A255 : CYS -A256 : GLU -A257 : LEU -A258 : PHE -A259 : ARG -A260 : GLU -A261 : TYR -A262 : LEU -A263 : ALA -A264 : THR -A265 : LYS -A266 : LYS -A267 : PHE -A268 : THR -A269 : GLU -A270 : VAL -A271 : HIS -A272 : THR -A273 : PRO -A274 : LYS -A275 : LEU -A276 : LEU -A277 : GLY -A278 : ALA -A279 : PRO -A280 : SER -A281 : GLU -A282 : GLY -A283 : GLY -A284 : SER -A285 : SER -A286 : VAL -A287 : PHE -A288 : GLU -A289 : VAL -A290 : THR -A291 : TYR -A292 : PHE -A293 : LYS -A294 : GLY -A295 : LYS -A296 : ALA -A297 : TYR -A298 : LEU -A299 : ALA -A300 : GLN -A301 : SER -A302 : PRO -A303 : GLN -A304 : PHE -A305 : ASN -A306 : LYS -A307 : GLN -A308 : GLN -A309 : LEU -A310 : ILE -A311 : VAL -A312 : ALA -A313 : ASP -A314 : PHE -A315 : GLU -A316 : ARG -A317 : VAL -A318 : TYR -A319 : GLU -A320 : ILE -A321 : GLY -A322 : PRO -A323 : VAL -A324 : PHE -A325 : ARG -A326 : ALA -A327 : GLU -A328 : ASN -A329 : SER -A330 : ASN -A331 : THR -A332 : HIS -A333 : ARG -A334 : HIS -A335 : MET -A336 : THR -A337 : GLU -A338 : PHE -A339 : THR -A340 : GLY -A341 : LEU -A342 : ASP -A343 : MET -A344 : GLU -A345 : MET -A346 : ALA -A347 : PHE -A348 : GLU -A349 : GLU -A350 : HIS -A351 : TYR -A352 : HIS -A353 : GLU -A354 : VAL -A355 : LEU -A356 : ASP -A357 : THR -A358 : LEU -A359 : SER -A360 : GLU -A361 : LEU -A362 : PHE -A363 : VAL -A364 : PHE -A365 : ILE -A366 : PHE -A367 : SER -A368 : GLU -A369 : LEU -A370 : PRO -A371 : LYS -A372 : ARG -A373 : PHE -A374 : ALA -A375 : HIS -A376 : GLU -A377 : ILE -A378 : GLU -A379 : LEU -A380 : VAL -A381 : ARG -A382 : LYS -A383 : GLN -A384 : TYR -A385 : PRO -A386 : VAL -A387 : GLU -A388 : GLU -A389 : PHE -A390 : LYS -A391 : LEU -A392 : PRO -A393 : LYS -A394 : ASP -A395 : GLY -A396 : LYS -A397 : MET -A398 : VAL -A399 : ARG -A400 : LEU -A401 : THR -A402 : TYR -A403 : LYS -A404 : GLU -A405 : GLY -A406 : ILE -A407 : GLU -A408 : MET -A409 : LEU -A410 : ARG -A411 : ALA -A412 : ALA -A413 : GLY -A414 : LYS -A415 : GLU -A416 : ILE -A417 : GLY -A418 : ASP -A419 : PHE -A420 : GLU -A421 : ASP -A422 : LEU -A423 : SER -A424 : THR -A425 : GLU -A426 : ASN -A427 : GLU -A428 : LYS -A429 : PHE -A430 : LEU -A431 : GLY -A432 : LYS -A433 : LEU -A434 : VAL -A435 : ARG -A436 : ASP -A437 : LYS -A438 : TYR -A439 : ASP -A440 : THR -A441 : ASP -A442 : PHE -A443 : TYR -A444 : ILE -A445 : LEU -A446 : ASP -A447 : LYS -A448 : PHE -A449 : PRO -A450 : LEU -A451 : GLU -A452 : ILE -A453 : ARG -A454 : PRO -A455 : PHE -A456 : TYR -A457 : THR -A458 : MET -A459 : PRO -A460 : ASP -A461 : PRO -A462 : ALA -A463 : ASN -A464 : PRO -A465 : LYS -A466 : TYR -A467 : SER -A468 : ASN -A469 : SER -A470 : TYR -A471 : ASP -A472 : PHE -A473 : PHE -A474 : MET -A475 : ARG -A476 : GLY -A477 : GLU -A478 : GLU -A479 : ILE -A480 : LEU -A481 : SER -A482 : GLY -A483 : ALA -A484 : GLN -A485 : ARG -A486 : ILE -A487 : HIS -A488 : ASP -A489 : HIS -A490 : ALA -A491 : LEU -A492 : LEU -A493 : GLN -A494 : GLU -A495 : ARG -A496 : MET -A497 : LYS -A498 : ALA -A499 : HIS -A500 : GLY -A501 : LEU -A502 : SER -A503 : PRO -A504 : GLU -A505 : ASP -A506 : PRO -A507 : GLY -A508 : LEU -A509 : LYS -A510 : ASP -A511 : TYR -A512 : CYS -A513 : ASP -A514 : GLY -A515 : PHE -A516 : SER -A517 : TYR -A518 : GLY -A519 : CYS -A520 : PRO -A521 : PRO -A522 : HIS -A523 : ALA -A524 : GLY -A525 : GLY -A526 : GLY -A527 : ILE -A528 : GLY -A529 : LEU -A530 : GLU -A531 : ARG -A532 : VAL -A533 : VAL -A534 : MET -A535 : PHE -A536 : TYR -A537 : LEU -A538 : ASP -A539 : LEU -A540 : LYS -A541 : ASN -A542 : ILE -A543 : ARG -A544 : ARG -A545 : ALA -A546 : SER -A547 : LEU -A548 : PHE -A549 : PRO -A550 : ARG -A551 : ASP -A552 : PRO -A553 : LYS -A554 : ARG -A555 : LEU -A556 : ARG -A557 : PRO -B68 : GLU -B69 : ASP -B70 : THR -B71 : ALA -B72 : LYS -B73 : ASP -B74 : ASN -B75 : TYR -B76 : GLY -B77 : LYS -B78 : LEU -B79 : PRO -B80 : LEU -B81 : ILE -B82 : GLN -B83 : SER -B84 : ARG -B85 : ASP -B86 : SER -B87 : ASP -B88 : ARG -B89 : THR -B90 : GLY -B91 : GLN -B92 : LYS -B93 : ARG -B94 : VAL -B95 : LYS -B96 : PHE -B97 : VAL -B98 : ASP -B99 : LEU -B100 : ASP -B101 : GLU -B102 : ALA -B103 : LYS -B104 : ASP -B105 : SER -B106 : ASP -B107 : LYS -B108 : GLU -B109 : VAL -B110 : LEU -B111 : PHE -B112 : ARG -B113 : ALA -B114 : ARG -B115 : VAL -B116 : HIS -B117 : ASN -B118 : THR -B119 : ARG -B120 : GLN -B121 : GLN -B122 : GLY -B123 : ALA -B124 : THR -B125 : LEU -B126 : ALA -B127 : PHE -B128 : LEU -B129 : THR -B130 : LEU -B131 : ARG -B132 : GLN -B133 : GLN -B134 : ALA -B135 : SER -B136 : LEU -B137 : ILE -B138 : GLN -B139 : GLY -B140 : LEU -B141 : VAL -B142 : LYS -B143 : ALA -B144 : ASN -B145 : LYS -B146 : GLU -B147 : GLY -B148 : THR -B149 : ILE -B150 : SER -B151 : LYS -B152 : ASN -B153 : MET -B154 : VAL -B155 : LYS -B156 : TRP -B157 : ALA -B158 : GLY -B159 : SER -B160 : LEU -B161 : ASN -B162 : LEU -B163 : GLU -B164 : SER -B165 : ILE -B166 : VAL -B167 : LEU -B168 : VAL -B169 : ARG -B170 : GLY -B171 : ILE -B172 : VAL -B173 : LYS -B174 : LYS -B175 : VAL -B176 : ASP -B177 : GLU -B178 : PRO -B179 : ILE -B180 : LYS -B181 : SER -B182 : ALA -B183 : THR -B184 : VAL -B185 : GLN -B186 : ASN -B187 : LEU -B188 : GLU -B189 : ILE -B190 : HIS -B191 : ILE -B192 : THR -B193 : LYS -B194 : ILE -B195 : TYR -B196 : THR -B197 : ILE -B198 : SER -B199 : GLU -B200 : THR -B201 : PRO -B202 : GLU -B203 : ALA -B204 : LEU -B205 : PRO -B206 : ILE -B207 : LEU -B208 : LEU -B209 : GLU -B210 : ASP -B211 : ALA -B212 : SER -B213 : ARG -B214 : SER -B215 : GLU -B216 : ALA -B217 : GLU -B218 : ALA -B219 : GLU -B220 : ALA -B221 : ALA -B222 : GLY -B223 : LEU -B224 : PRO -B225 : VAL -B226 : VAL -B227 : ASN -B228 : LEU -B229 : ASP -B230 : THR -B231 : ARG -B232 : LEU -B233 : ASP -B234 : TYR -B235 : ARG -B236 : VAL -B237 : ILE -B238 : ASP -B239 : LEU -B240 : ARG -B241 : THR -B242 : VAL -B243 : THR -B244 : ASN -B245 : GLN -B246 : ALA -B247 : ILE -B248 : PHE -B249 : ARG -B250 : ILE -B251 : GLN -B252 : ALA -B253 : GLY -B254 : VAL -B255 : CYS -B256 : GLU -B257 : LEU -B258 : PHE -B259 : ARG -B260 : GLU -B261 : TYR -B262 : LEU -B263 : ALA -B264 : THR -B265 : LYS -B266 : LYS -B267 : PHE -B268 : THR -B269 : GLU -B270 : VAL -B271 : HIS -B272 : THR -B273 : PRO -B274 : LYS -B275 : LEU -B276 : LEU -B277 : GLY -B278 : ALA -B279 : PRO -B280 : SER -B281 : GLU -B282 : GLY -B283 : GLY -B284 : SER -B285 : SER -B286 : VAL -B287 : PHE -B288 : GLU -B289 : VAL -B290 : THR -B291 : TYR -B292 : PHE -B293 : LYS -B294 : GLY -B295 : LYS -B296 : ALA -B297 : TYR -B298 : LEU -B299 : ALA -B300 : GLN -B301 : SER -B302 : PRO -B303 : GLN -B304 : PHE -B305 : ASN -B306 : LYS -B307 : GLN -B308 : GLN -B309 : LEU -B310 : ILE -B311 : VAL -B312 : ALA -B313 : ASP -B314 : PHE -B315 : GLU -B316 : ARG -B317 : VAL -B318 : TYR -B319 : GLU -B320 : ILE -B321 : GLY -B322 : PRO -B323 : VAL -B324 : PHE -B325 : ARG -B326 : ALA -B327 : GLU -B328 : ASN -B329 : SER -B330 : ASN -B331 : THR -B332 : HIS -B333 : ARG -B334 : HIS -B335 : MET -B336 : THR -B337 : GLU -B338 : PHE -B339 : THR -B340 : GLY -B341 : LEU -B342 : ASP -B343 : MET -B344 : GLU -B345 : MET -B346 : ALA -B347 : PHE -B348 : GLU -B349 : GLU -B350 : HIS -B351 : TYR -B352 : HIS -B353 : GLU -B354 : VAL -B355 : LEU -B356 : ASP -B357 : THR -B358 : LEU -B359 : SER -B360 : GLU -B361 : LEU -B362 : PHE -B363 : VAL -B364 : PHE -B365 : ILE -B366 : PHE -B367 : SER -B368 : GLU -B369 : LEU -B370 : PRO -B371 : LYS -B372 : ARG -B373 : PHE -B374 : ALA -B375 : HIS -B376 : GLU -B377 : ILE -B378 : GLU -B379 : LEU -B380 : VAL -B381 : ARG -B382 : LYS -B383 : GLN -B384 : TYR -B385 : PRO -B386 : VAL -B387 : GLU -B388 : GLU -B389 : PHE -B390 : LYS -B391 : LEU -B392 : PRO -B393 : LYS -B394 : ASP -B395 : GLY -B396 : LYS -B397 : MET -B398 : VAL -B399 : ARG -B400 : LEU -B401 : THR -B402 : TYR -B403 : LYS -B404 : GLU -B405 : GLY -B406 : ILE -B407 : GLU -B408 : MET -B409 : LEU -B410 : ARG -B411 : ALA -B412 : ALA -B413 : GLY -B414 : LYS -B415 : GLU -B416 : ILE -B417 : GLY -B418 : ASP -B419 : PHE -B420 : GLU -B421 : ASP -B422 : LEU -B423 : SER -B424 : THR -B425 : GLU -B426 : ASN -B427 : GLU -B428 : LYS -B429 : PHE -B430 : LEU -B431 : GLY -B432 : LYS -B433 : LEU -B434 : VAL -B435 : ARG -B436 : ASP -B437 : LYS -B438 : TYR -B439 : ASP -B440 : THR -B441 : ASP -B442 : PHE -B443 : TYR -B444 : ILE -B445 : LEU -B446 : ASP -B447 : LYS -B448 : PHE -B449 : PRO -B450 : LEU -B451 : GLU -B452 : ILE -B453 : ARG -B454 : PRO -B455 : PHE -B456 : TYR -B457 : THR -B458 : MET -B459 : PRO -B460 : ASP -B461 : PRO -B462 : ALA -B463 : ASN -B464 : PRO -B465 : LYS -B466 : TYR -B467 : SER -B468 : ASN -B469 : SER -B470 : TYR -B471 : ASP -B472 : PHE -B473 : PHE -B474 : MET -B475 : ARG -B476 : GLY -B477 : GLU -B478 : GLU -B479 : ILE -B480 : LEU -B481 : SER -B482 : GLY -B483 : ALA -B484 : GLN -B485 : ARG -B486 : ILE -B487 : HIS -B488 : ASP -B489 : HIS -B490 : ALA -B491 : LEU -B492 : LEU -B493 : GLN -B494 : GLU -B495 : ARG -B496 : MET -B497 : LYS -B498 : ALA -B499 : HIS -B500 : GLY -B501 : LEU -B502 : SER -B503 : PRO -B504 : GLU -B505 : ASP -B506 : PRO -B507 : GLY -B508 : LEU -B509 : LYS -B510 : ASP -B511 : TYR -B512 : CYS -B513 : ASP -B514 : GLY -B515 : PHE -B516 : SER -B517 : TYR -B518 : GLY -B519 : CYS -B520 : PRO -B521 : PRO -B522 : HIS -B523 : ALA -B524 : GLY -B525 : GLY -B526 : GLY -B527 : ILE -B528 : GLY -B529 : LEU -B530 : GLU -B531 : ARG -B532 : VAL -B533 : VAL -B534 : MET -B535 : PHE -B536 : TYR -B537 : LEU -B538 : ASP -B539 : LEU -B540 : LYS -B541 : ASN -B542 : ILE -B543 : ARG -B544 : ARG -B545 : ALA -B546 : SER -B547 : LEU -B548 : PHE -B549 : PRO -B550 : ARG -B551 : ASP -B552 : PRO -B553 : LYS -B554 : ARG -B555 : LEU -B556 : ARG -B557 : PRO -A701 : ATP -B701 : ATP -Adjacent stackings ---------------------------------------------- -R602-R603 : adjacent_5p upward -R603-R604 : adjacent_5p upward -R604-R605 : adjacent_5p upward -R606-R607 : adjacent_5p upward -R610-R611 : adjacent_5p upward -R611-R612 : adjacent_5p upward -R614-R615 : adjacent_5p upward -R622-R623 : adjacent_5p upward -R623-R624 : adjacent_5p upward -R624-R625 : adjacent_5p upward -R625-R626 : adjacent_5p upward -R626-R627 : adjacent_5p upward -R627-R628 : adjacent_5p upward -R628-R629 : adjacent_5p upward -R630-R631 : adjacent_5p upward -R635-R636 : adjacent_5p upward -R639-R640 : adjacent_5p upward -R641-R642 : adjacent_5p upward -R642-R643 : adjacent_5p upward -R644-R645 : adjacent_5p upward -R650-R651 : adjacent_5p upward -R651-R652 : adjacent_5p upward -R652-R653 : adjacent_5p upward -R656-R657 : adjacent_5p upward -R663-R664 : adjacent_5p upward -R664-R665 : adjacent_5p upward -R665-R666 : adjacent_5p upward -R666-R667 : adjacent_5p upward -R668-R669 : adjacent_5p upward -R669-R670 : adjacent_5p upward -R670-R671 : adjacent_5p upward -R671-R672 : adjacent_5p upward -R672-R673 : adjacent_5p upward -R673-R674 : adjacent_5p upward -R674-R675 : adjacent_5p upward pairing -S601-S602 : adjacent_5p upward -S602-S603 : adjacent_5p upward -S603-S604 : adjacent_5p upward -S604-S605 : adjacent_5p upward -S605-S606 : adjacent_5p upward -S606-S607 : adjacent_5p upward -S610-S611 : adjacent_5p upward -S614-S615 : adjacent_5p upward -S622-S623 : adjacent_5p upward -S623-S624 : adjacent_5p upward -S624-S625 : adjacent_5p upward -S625-S626 : adjacent_5p upward -S626-S627 : adjacent_5p upward -S627-S628 : adjacent_5p upward -S628-S629 : adjacent_5p upward -S630-S631 : adjacent_5p upward -S638-S639 : adjacent_5p upward -S639-S640 : adjacent_5p upward -S641-S642 : adjacent_5p upward -S644-S645 : adjacent_5p upward -S650-S651 : adjacent_5p upward -S651-S652 : adjacent_5p upward -S652-S653 : adjacent_5p upward -S656-S657 : adjacent_5p upward -S659-S660 : adjacent_5p upward -S661-S662 : adjacent_5p upward -S662-S663 : adjacent_5p upward -S663-S664 : adjacent_5p upward -S664-S665 : adjacent_5p upward -S665-S666 : adjacent_5p upward -S666-S667 : adjacent_5p upward -S668-S669 : adjacent_5p upward -S669-S670 : adjacent_5p upward -S670-S671 : adjacent_5p upward -S671-S672 : adjacent_5p upward -S672-S673 : adjacent_5p upward -S673-S674 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -R604-R670 : outward -R606-R668 : outward -R609-R645 : inward -R609-R646 : outward -R614-R622 : outward -R617-R657 : inward -R617-R658 : outward -R618-R657 : outward -R621-R646 : inward -R621-R648 : outward pairing -R627-R644 : outward -R630-R641 : outward -R648-R659 : upward -R650-R665 : outward -R658-R661 : upward -S604-S670 : outward -S606-S668 : outward -S609-S645 : inward -S609-S646 : outward -S614-S622 : outward -S617-S657 : inward pairing -S617-S658 : outward -S618-S657 : outward -S621-S646 : inward -S621-S648 : outward -S627-S644 : outward -S630-S641 : outward -S648-S659 : upward -S650-S665 : outward -S658-S661 : upward -Number of stackings = 102 -Number of adjacent stackings = 72 -Number of non adjacent stackings = 30 -Base-pairs ------------------------------------------------------ -R601-R672 : U-A Ww/Ww pairing antiparallel cis XX -R602-R671 : C-G Ww/Ww pairing antiparallel cis XIX -R603-R670 : C-G Ww/Ww pairing antiparallel cis XIX -R604-R669 : G-C Ww/Ww pairing antiparallel cis XIX -R605-R668 : U-G Ws/Ww pairing antiparallel cis XXVIII -R606-R667 : G-C Ww/Ww pairing antiparallel cis XIX -R607-R666 : A-U Ww/Ww pairing antiparallel cis XX -R608-R614 : U-A Ws/Hh pairing antiparallel trans XXIV -R608-R621 : U-A Ss/Bs pairing parallel trans one_hbond -R609-R610 : A-G O2'/Hh adjacent_5p pairing -R609-R623 : A-A Hh/Hh pairing parallel trans II -R610-R625 : G-U Ww/Ws pairing antiparallel cis XXVIII -R610-R645 : G-G Hw/Bs pairing parallel cis one_hbond 113 -R611-R624 : U-A Ww/Ww pairing antiparallel cis XX -R612-R623 : U-A Ww/Ww pairing antiparallel cis XX -R614-R621 : A-A Wh/Ss Ww/O2' pairing antiparallel cis one_hbond 40 -R615-R648 : A-U Ww/Ws pairing parallel trans XXI -R618-R656 : G-C Ww/Ww pairing antiparallel cis XIX -R621-R648 : A-U Bh/O2P outward pairing -R622-R646 : G-A Hh/Wh pairing antiparallel trans one_hbond 60 -R626-R644 : G-A Wh/Wh pairing antiparallel cis one_hbond -R627-R643 : G-C Ww/Ww pairing antiparallel cis XIX -R628-R642 : G-C Ww/Ww pairing antiparallel cis XIX -R629-R641 : C-G Ww/Ww pairing antiparallel cis -R630-R640 : G-U Ww/Ws pairing antiparallel cis XXVIII -R631-R639 : C-G Ww/Ww pairing antiparallel cis XIX -R650-R664 : G-C Ww/Ww pairing antiparallel cis XIX -R651-R663 : G-C Ww/Ww pairing antiparallel cis XIX -R652-R662 : G-C Ww/Ww pairing antiparallel cis XIX -R653-R661 : G-C Ww/Ww pairing antiparallel cis XIX -R658-R660 : A-U Ss/Hh pairing antiparallel trans one_hbond -R660-R661 : U-C O2P/Bh O2P/Bh adjacent_5p pairing -R674-R675 : C-C O2P/Bh adjacent_5p upward pairing -S601-S672 : U-A Ww/Ww pairing antiparallel cis XX -S602-S671 : C-G Ww/Ww pairing antiparallel cis XIX -S603-S670 : C-G Ww/Ww pairing antiparallel cis XIX -S604-S669 : G-C Ww/Ww pairing antiparallel cis XIX -S605-S668 : U-G Ws/Ww pairing antiparallel cis XXVIII -S606-S667 : G-C Ww/Ww pairing antiparallel cis XIX -S607-S666 : A-U Ww/Ww pairing antiparallel cis XX -S608-S614 : U-A Ws/Hh pairing antiparallel trans XXIV -S608-S621 : U-A O2'/Ww pairing -S608-S646 : U-A O2'/Ss pairing -S609-S610 : A-G O2'/Hh adjacent_5p pairing -S609-S623 : A-A Hh/Hh pairing parallel trans II -S610-S625 : G-U Ww/Ws pairing antiparallel cis XXVIII -S610-S645 : G-G Hw/Bs pairing parallel cis one_hbond 113 -S611-S624 : U-A Ww/Ww pairing antiparallel cis XX -S612-S623 : U-A Ww/Ww pairing antiparallel cis XX -S614-S621 : A-A Wh/Ss Ww/O2' pairing antiparallel cis one_hbond 40 -S615-S648 : A-U Ww/Ws pairing parallel trans XXI -S617-S657 : G-A O2'/Ww inward pairing -S618-S656 : G-C Ww/Ww pairing antiparallel cis XIX -S622-S646 : G-A Hh/Ww pairing antiparallel trans 60 -S626-S644 : G-A Ww/Ww pairing antiparallel cis VIII -S627-S643 : G-C Ww/Ww pairing antiparallel cis XIX -S628-S642 : G-C Ww/Ww pairing antiparallel cis XIX -S629-S641 : C-G Ww/Ww pairing antiparallel cis XIX -S630-S640 : G-U Ww/Ws pairing antiparallel cis XXVIII -S631-S639 : C-G Ww/Ww pairing antiparallel cis XIX -S650-S664 : G-C Ww/Ww pairing antiparallel cis XIX -S651-S663 : G-C Ww/Ww pairing antiparallel cis XIX -S652-S662 : G-C Ww/Ww pairing antiparallel cis XIX -S653-S661 : G-C Ww/Ww pairing antiparallel cis XIX -S660-S661 : U-C O2P/Bh O2P/Bh adjacent_5p pairing diff --git a/MCdata/1ato_MC b/MCdata/1ato_MC deleted file mode 100644 index 2484919739ca2be953540983b1b42f8fce111dce..0000000000000000000000000000000000000000 --- a/MCdata/1ato_MC +++ /dev/null @@ -1,457 +0,0 @@ -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : A C3p_endo anti -A5 : C C3p_endo anti -A6 : C C3p_endo anti -A7 : U C3p_endo anti -A8 : C C3p_endo anti -A9 : C C2p_exo anti -A10 : U C3p_exo anti -A11 : C C1p_endo anti -A12 : G C1p_endo anti -A13 : C C3p_endo anti -A14 : G C3p_endo anti -A15 : G C3p_endo anti -A16 : U C3p_endo anti -A17 : G C3p_endo anti -A18 : C C3p_endo anti -A19 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward pairing -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A17 : outward -Number of stackings = 14 -Number of adjacent stackings = 13 -Number of non adjacent stackings = 1 -Base-pairs ------------------------------------------------------ -A1-A19 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A18 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A16 : A-U Ww/Ww pairing antiparallel cis XX -A5-A15 : C-G Ww/Ww pairing antiparallel cis XIX -A6-A14 : C-G Ww/Ww pairing antiparallel cis XIX -A7-A13 : U-C Ws/Bh pairing antiparallel cis one_hbond 100 -A8-A9 : C-C O2P/Bh adjacent_5p upward pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : A C3p_endo anti -A5 : C C3p_endo anti -A6 : C C3p_endo anti -A7 : U C3p_endo anti -A8 : C C3p_endo anti -A9 : C C3p_endo anti -A10 : U C2p_endo anti -A11 : C C1p_endo anti -A12 : G C4p_exo anti -A13 : C C3p_endo anti -A14 : G C3p_endo anti -A15 : G C3p_endo anti -A16 : U C3p_endo anti -A17 : G C3p_endo anti -A18 : C C3p_endo anti -A19 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A17 : outward -Number of stackings = 14 -Number of adjacent stackings = 13 -Number of non adjacent stackings = 1 -Base-pairs ------------------------------------------------------ -A1-A19 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A18 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A16 : A-U Ww/Ww pairing antiparallel cis XX -A5-A15 : C-G Ww/Ww pairing antiparallel cis XIX -A6-A14 : C-G Ww/Ww pairing antiparallel cis XIX -A7-A13 : U-C Ws/Wh pairing antiparallel cis one_hbond 100 -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : A C3p_endo anti -A5 : C C3p_endo anti -A6 : C C3p_endo anti -A7 : U C3p_endo anti -A8 : C C3p_endo anti -A9 : C C3p_endo anti -A10 : U C2p_endo anti -A11 : C C1p_endo anti -A12 : G C1p_endo anti -A13 : C C3p_endo anti -A14 : G C3p_endo anti -A15 : G C3p_endo anti -A16 : U C3p_endo anti -A17 : G C3p_endo anti -A18 : C C3p_endo anti -A19 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A17 : outward -Number of stackings = 14 -Number of adjacent stackings = 13 -Number of non adjacent stackings = 1 -Base-pairs ------------------------------------------------------ -A1-A19 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A18 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A16 : A-U Ww/Ww pairing antiparallel cis XX -A5-A15 : C-G Ww/Ww pairing antiparallel cis XIX -A6-A14 : C-G Ww/Ww pairing antiparallel cis XIX -A7-A13 : U-C Ws/Hw pairing antiparallel trans one_hbond -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : A C3p_endo anti -A5 : C C3p_endo anti -A6 : C C3p_endo anti -A7 : U C3p_endo anti -A8 : C C3p_endo anti -A9 : C C3p_endo anti -A10 : U C2p_endo anti -A11 : C O4p_exo anti -A12 : G O4p_exo anti -A13 : C C3p_endo anti -A14 : G C3p_endo anti -A15 : G C3p_endo anti -A16 : U C3p_endo anti -A17 : G C3p_endo anti -A18 : C C3p_endo anti -A19 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 11 -Number of adjacent stackings = 11 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-A19 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A18 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A16 : A-U Ww/Ww pairing antiparallel cis XX -A5-A15 : C-G Ww/Ww pairing antiparallel cis XIX -A6-A14 : C-G Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : A C3p_endo anti -A5 : C C3p_endo anti -A6 : C C3p_endo anti -A7 : U C3p_endo anti -A8 : C C3p_endo anti -A9 : C C2p_exo anti -A10 : U C2p_endo anti -A11 : C C1p_endo anti -A12 : G C3p_endo anti -A13 : C C3p_endo anti -A14 : G C3p_endo anti -A15 : G C3p_endo anti -A16 : U C3p_endo anti -A17 : G C3p_endo anti -A18 : C C3p_endo anti -A19 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A17 : outward -Number of stackings = 13 -Number of adjacent stackings = 12 -Number of non adjacent stackings = 1 -Base-pairs ------------------------------------------------------ -A1-A19 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A18 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A16 : A-U Ww/Ww pairing antiparallel cis XX -A5-A15 : C-G Ww/Ww pairing antiparallel cis XIX -A6-A14 : C-G Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : A C3p_endo anti -A5 : C C3p_endo anti -A6 : C C3p_endo anti -A7 : U C3p_endo anti -A8 : C C3p_endo anti -A9 : C C2p_exo anti -A10 : U C2p_endo anti -A11 : C C1p_endo anti -A12 : G C2p_exo anti -A13 : C C3p_endo anti -A14 : G C3p_endo anti -A15 : G C2p_exo anti -A16 : U C3p_endo anti -A17 : G C3p_endo anti -A18 : C C3p_endo anti -A19 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A17 : outward -Number of stackings = 13 -Number of adjacent stackings = 12 -Number of non adjacent stackings = 1 -Base-pairs ------------------------------------------------------ -A1-A19 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A18 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A16 : A-U Ww/Ww pairing antiparallel cis XX -A5-A15 : C-G Ww/Ww pairing antiparallel cis XIX -A6-A14 : C-G Ww/Ww pairing antiparallel cis XIX -A7-A13 : U-C Ws/Wh pairing antiparallel cis one_hbond 100 -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : A C3p_endo anti -A5 : C C3p_endo anti -A6 : C C3p_endo anti -A7 : U C3p_endo anti -A8 : C C3p_endo anti -A9 : C C2p_exo anti -A10 : U C2p_endo anti -A11 : C C1p_endo anti -A12 : G O4p_exo anti -A13 : C C3p_endo anti -A14 : G C3p_endo anti -A15 : G C3p_endo anti -A16 : U C3p_endo anti -A17 : G C3p_endo anti -A18 : C C3p_endo anti -A19 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A17 : outward -Number of stackings = 13 -Number of adjacent stackings = 12 -Number of non adjacent stackings = 1 -Base-pairs ------------------------------------------------------ -A1-A19 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A18 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A16 : A-U Ww/Ww pairing antiparallel cis XX -A5-A15 : C-G Ww/Ww pairing antiparallel cis XIX -A6-A14 : C-G Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : A C3p_endo anti -A5 : C C3p_endo anti -A6 : C C3p_endo anti -A7 : U C3p_endo anti -A8 : C C3p_endo anti -A9 : C C2p_exo anti -A10 : U C2p_endo anti -A11 : C C1p_endo anti -A12 : G C1p_endo anti -A13 : C C3p_endo anti -A14 : G C3p_endo anti -A15 : G C3p_endo anti -A16 : U C3p_endo anti -A17 : G C3p_endo anti -A18 : C C3p_endo anti -A19 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A17 : outward -Number of stackings = 12 -Number of adjacent stackings = 11 -Number of non adjacent stackings = 1 -Base-pairs ------------------------------------------------------ -A1-A19 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A18 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A16 : A-U Ww/Ww pairing antiparallel cis XX -A5-A15 : C-G Ww/Ww pairing antiparallel cis XIX -A6-A14 : C-G Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : A C3p_endo anti -A5 : C C3p_endo anti -A6 : C C3p_endo anti -A7 : U C3p_endo anti -A8 : C C3p_endo anti -A9 : C C2p_exo anti -A10 : U C3p_exo anti -A11 : C O4p_exo anti -A12 : G C2p_exo anti -A13 : C C3p_endo anti -A14 : G C3p_endo anti -A15 : G C3p_endo anti -A16 : U C3p_endo anti -A17 : G C3p_endo anti -A18 : C C3p_endo anti -A19 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A17 : outward -Number of stackings = 13 -Number of adjacent stackings = 12 -Number of non adjacent stackings = 1 -Base-pairs ------------------------------------------------------ -A1-A19 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A18 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A16 : A-U Ww/Ww pairing antiparallel cis XX -A5-A15 : C-G Ww/Ww pairing antiparallel cis XIX -A6-A14 : C-G Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : A C3p_endo anti -A5 : C C3p_endo anti -A6 : C C3p_endo anti -A7 : U C3p_endo anti -A8 : C C3p_endo anti -A9 : C C3p_endo anti -A10 : U C2p_endo anti -A11 : C O4p_exo anti -A12 : G O4p_endo anti -A13 : C C3p_endo anti -A14 : G C3p_endo anti -A15 : G C3p_endo anti -A16 : U C3p_endo anti -A17 : G C3p_endo anti -A18 : C C3p_endo anti -A19 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A17 : outward -Number of stackings = 14 -Number of adjacent stackings = 13 -Number of non adjacent stackings = 1 -Base-pairs ------------------------------------------------------ -A1-A19 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A18 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A16 : A-U Ww/Ww pairing antiparallel cis XX -A5-A15 : C-G Ww/Ww pairing antiparallel cis XIX -A6-A14 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A9 : C-C O2P/Bh adjacent_5p pairing diff --git a/MCdata/1atv_MC b/MCdata/1atv_MC deleted file mode 100644 index 5c11e768975422e4105bd17fba105e763fcc6f79..0000000000000000000000000000000000000000 --- a/MCdata/1atv_MC +++ /dev/null @@ -1,186 +0,0 @@ -Residue conformations ------------------------------------------- -A1 : G C4p_exo anti -A2 : G C3p_endo anti -A3 : G C3p_endo anti -A4 : A C3p_endo anti -A5 : C C3p_endo anti -A6 : C C3p_endo anti -A7 : A C3p_endo anti -A8 : G C4p_exo anti -A9 : A C3p_endo syn -A10 : A C4p_exo anti -A11 : G C3p_endo anti -A12 : G C3p_endo anti -A13 : U C3p_endo anti -A14 : C C3p_endo anti -A15 : C C3p_endo anti -A16 : C C3p_endo anti -A17 : G C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward pairing -A11-A12 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p inward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 12 -Number of adjacent stackings = 12 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-A16 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A15 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A14 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A13 : A-U Ww/Ww pairing antiparallel cis XX -A5-A7 : C-A O2P/Bh pairing -A5-A12 : C-G Ww/Ww pairing antiparallel cis XIX -A6-A7 : C-A O2P/Hh adjacent_5p pairing -A6-A11 : C-G Ww/Ww pairing antiparallel cis XIX -A7-A10 : A-A Ss/Wh pairing antiparallel cis one_hbond 40 -A8-A9 : G-A Ww/O2' Ss/O2' adjacent_5p pairing -A10-A11 : A-G O2'/C8 adjacent_5p upward pairing -Residue conformations ------------------------------------------- -A1 : G C4p_exo anti -A2 : G C3p_endo anti -A3 : G C3p_endo anti -A4 : A C3p_endo anti -A5 : C C3p_endo anti -A6 : C C3p_endo anti -A7 : A C3p_endo anti -A8 : G C4p_exo anti -A9 : A C3p_endo syn -A10 : A C4p_exo anti -A11 : G C3p_endo anti -A12 : G C3p_endo anti -A13 : U C3p_endo anti -A14 : C C3p_endo anti -A15 : C C3p_endo anti -A16 : C C3p_endo anti -A17 : G C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A6-A7 : adjacent_5p upward pairing -A10-A11 : adjacent_5p upward pairing -A11-A12 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A1-A17 : outward -Number of stackings = 13 -Number of adjacent stackings = 12 -Number of non adjacent stackings = 1 -Base-pairs ------------------------------------------------------ -A1-A16 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A15 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A14 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A13 : A-U Ww/Ww pairing antiparallel cis XX -A5-A7 : C-A O2P/Bh pairing -A5-A12 : C-G Ww/Ww pairing antiparallel cis XIX -A6-A7 : C-A O2P/Hh adjacent_5p upward pairing -A6-A11 : C-G Ww/Ww pairing antiparallel cis XIX -A7-A10 : A-A Ss/Wh O2'/Ww pairing antiparallel trans one_hbond 40 -A10-A11 : A-G O2'/C8 adjacent_5p upward pairing -Residue conformations ------------------------------------------- -A1 : G C4p_exo anti -A2 : G C3p_endo anti -A3 : G C3p_endo anti -A4 : A C3p_endo anti -A5 : C C3p_endo anti -A6 : C C3p_endo anti -A7 : A C3p_endo anti -A8 : G C4p_exo anti -A9 : A C3p_exo anti -A10 : A C4p_exo anti -A11 : G C3p_endo anti -A12 : G C3p_endo anti -A13 : U C3p_endo anti -A14 : C C3p_endo anti -A15 : C C3p_endo anti -A16 : C C3p_endo anti -A17 : G C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 12 -Number of adjacent stackings = 12 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-A16 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A15 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A14 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A13 : A-U Ww/Ww pairing antiparallel cis XX -A5-A12 : C-G Ww/Ww pairing antiparallel cis XIX -A6-A8 : C-G O2P/Bs pairing -A6-A11 : C-G Ww/Ww pairing antiparallel cis XIX -A7-A8 : A-G Hh/Sw Ss/O2' adjacent_5p pairing antiparallel cis one_hbond -A7-A9 : A-A O2'/Bh pairing -Residue conformations ------------------------------------------- -A1 : G C4p_exo anti -A2 : G C3p_endo anti -A3 : G C3p_endo anti -A4 : A C3p_endo anti -A5 : C C3p_endo anti -A6 : C C3p_endo anti -A7 : A C3p_endo anti -A8 : G C4p_exo anti -A9 : A C3p_endo syn -A10 : A C4p_exo anti -A11 : G C3p_endo anti -A12 : G C3p_endo anti -A13 : U C3p_endo anti -A14 : C C3p_endo anti -A15 : C C3p_endo anti -A16 : C C3p_endo anti -A17 : G C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward pairing -A11-A12 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p inward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 12 -Number of adjacent stackings = 12 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-A16 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A15 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A14 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A13 : A-U Ww/Ww pairing antiparallel cis XX -A5-A7 : C-A O2P/Bh pairing -A5-A12 : C-G Ww/Ww pairing antiparallel cis XIX -A6-A7 : C-A O2P/Hh adjacent_5p pairing -A6-A11 : C-G Ww/Ww pairing antiparallel cis XIX -A7-A10 : A-A Ss/Wh pairing antiparallel cis one_hbond 40 -A8-A9 : G-A Ww/O2' Ss/O2' adjacent_5p pairing -A10-A11 : A-G O2'/C8 adjacent_5p upward pairing diff --git a/MCdata/1atw_MC b/MCdata/1atw_MC deleted file mode 100644 index f31fce87e0bbe2180bed782cfbe487f2d99279b1..0000000000000000000000000000000000000000 --- a/MCdata/1atw_MC +++ /dev/null @@ -1,114 +0,0 @@ -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : C C3p_endo anti -A3 : U C3p_endo anti -A4 : C C3p_endo anti -A5 : C C3p_endo anti -A6 : A C4p_exo anti -A7 : G C3p_exo anti -A8 : A C3p_endo anti -A9 : U C3p_endo anti -A10 : G C3p_endo anti -A11 : G C3p_endo anti -A12 : A C3p_endo anti -A13 : G C3p_endo anti -A14 : C C3p_endo anti -A15 : G C4p_exo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A1-A15 : outward -Number of stackings = 10 -Number of adjacent stackings = 9 -Number of non adjacent stackings = 1 -Base-pairs ------------------------------------------------------ -A1-A14 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A13 : C-G Ww/Ww pairing antiparallel cis XIX -A3-A12 : U-A Ww/Ww pairing antiparallel cis XX -A4-A11 : C-G Ww/Ww pairing antiparallel cis XIX -A5-A6 : C-A O2P/Ss O2P/C8 adjacent_5p pairing -A5-A10 : C-G Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : C C3p_endo anti -A3 : U C3p_endo anti -A4 : C C3p_endo anti -A5 : C C3p_endo anti -A6 : A C3p_endo anti -A7 : G C2p_endo anti -A8 : A C3p_endo anti -A9 : U C3p_endo anti -A10 : G C3p_endo anti -A11 : G C3p_endo anti -A12 : A C3p_endo anti -A13 : G C3p_endo anti -A14 : C C3p_endo anti -A15 : G C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 8 -Number of adjacent stackings = 8 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-A14 : G-C Ww/Ww pairing antiparallel cis XIX -A1-A15 : G-G O2'/Bs pairing -A2-A13 : C-G Ww/Ww pairing antiparallel cis XIX -A3-A12 : U-A Ww/Ww pairing antiparallel cis XX -A4-A11 : C-G Ww/Ww pairing antiparallel cis XIX -A5-A10 : C-G Ww/Ww pairing antiparallel cis XIX -A7-A10 : G-G Sw/Ss O2'/Bs Bs/O2' pairing parallel cis one_hbond -Residue conformations ------------------------------------------- -A1 : G C4p_exo anti -A2 : C C3p_endo anti -A3 : U C3p_endo anti -A4 : C C3p_endo anti -A5 : C C3p_endo anti -A6 : A C3p_endo anti -A7 : G C2p_endo anti -A8 : A C3p_endo anti -A9 : U C3p_endo anti -A10 : G C3p_endo anti -A11 : G C3p_endo anti -A12 : A C3p_endo anti -A13 : G C3p_endo anti -A14 : C C3p_endo anti -A15 : G C4p_exo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 9 -Number of adjacent stackings = 9 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-A14 : G-C Ww/Ww pairing antiparallel cis XIX -A1-A15 : G-G Bs/Hh pairing antiparallel trans 34 -A2-A13 : C-G Ww/Ww pairing antiparallel cis XIX -A3-A12 : U-A Ww/Ww pairing antiparallel cis XX -A4-A11 : C-G Ww/Ww pairing antiparallel cis XIX -A5-A6 : C-A O2P/Hh O2P/Ss adjacent_5p pairing -A5-A10 : C-G Ww/Ww pairing antiparallel cis XIX -A9-A10 : U-G O2P/Hh adjacent_5p pairing diff --git a/MCdata/1aud_MC b/MCdata/1aud_MC deleted file mode 100644 index faaf17f258310c4c694b5b7d0f7304148c6eacae..0000000000000000000000000000000000000000 --- a/MCdata/1aud_MC +++ /dev/null @@ -1,4858 +0,0 @@ -Residue conformations ------------------------------------------- -B19 : G C3p_endo anti -B20 : G C3p_endo anti -B21 : C C3p_endo anti -B22 : A C3p_endo anti -B23 : G C3p_endo anti -B24 : A C4p_exo anti -B25 : G O4p_endo anti -B26 : U C3p_endo anti -B27 : C C4p_exo anti -B28 : C C3p_endo anti -B29 : U C3p_endo anti -B30 : U C3p_exo anti -B33 : C C3p_exo anti -B34 : G C3p_endo syn -B35 : G C3p_endo anti -B36 : G C4p_exo anti -B37 : A C3p_endo anti -B38 : C C3p_endo anti -B39 : A C3p_endo anti -B40 : U C3p_endo anti -B41 : U C2p_endo anti -B42 : G C3p_endo anti -B43 : C C2p_endo anti -B44 : A C2p_exo anti -B45 : C C3p_endo anti -B46 : C C3p_endo anti -B47 : U C3p_endo anti -B48 : G C3p_endo anti -B49 : C C3p_endo anti -B50 : C C3p_endo anti -A1 : ALA -A2 : VAL -A3 : PRO -A4 : GLU -A5 : THR -A6 : ARG -A7 : PRO -A8 : ASN -A9 : HIS -A10 : THR -A11 : ILE -A12 : TYR -A13 : ILE -A14 : ASN -A15 : ASN -A16 : LEU -A17 : ASN -A18 : GLU -A19 : LYS -A20 : ILE -A21 : LYS -A22 : LYS -A23 : ASP -A24 : GLU -A25 : LEU -A26 : LYS -A27 : LYS -A28 : SER -A29 : LEU -A30 : HIS -A31 : ALA -A32 : ILE -A33 : PHE -A34 : SER -A35 : ARG -A36 : PHE -A37 : GLY -A38 : GLN -A39 : ILE -A40 : LEU -A41 : ASP -A42 : ILE -A43 : LEU -A44 : VAL -A45 : SER -A46 : ARG -A47 : SER -A48 : LEU -A49 : LYS -A50 : MET -A51 : ARG -A52 : GLY -A53 : GLN -A54 : ALA -A55 : PHE -A56 : VAL -A57 : ILE -A58 : PHE -A59 : LYS -A60 : GLU -A61 : VAL -A62 : SER -A63 : SER -A64 : ALA -A65 : THR -A66 : ASN -A67 : ALA -A68 : LEU -A69 : ARG -A70 : SER -A71 : MET -A72 : GLN -A73 : GLY -A74 : PHE -A75 : PRO -A76 : PHE -A77 : TYR -A78 : ASP -A79 : LYS -A80 : PRO -A81 : MET -A82 : ARG -A83 : ILE -A84 : GLN -A85 : TYR -A86 : ALA -A87 : LYS -A88 : THR -A89 : ASP -A90 : SER -A91 : ASP -A92 : ILE -A93 : ILE -A94 : ALA -A95 : LYS -A96 : MET -A97 : LYS -A98 : GLY -A99 : THR -A100 : PHE -A101 : VAL -Adjacent stackings ---------------------------------------------- -B20-B21 : adjacent_5p upward -B22-B23 : adjacent_5p upward -B23-B24 : adjacent_5p upward -B26-B27 : adjacent_5p upward -B28-B29 : adjacent_5p upward -B34-B35 : adjacent_5p outward -B35-B36 : adjacent_5p upward -B37-B38 : adjacent_5p upward -B39-B40 : adjacent_5p upward -B44-B45 : adjacent_5p upward -B49-B50 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 11 -Number of adjacent stackings = 11 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -B21-B48 : C-G Ww/Ww pairing antiparallel cis XIX -B22-B47 : A-U Ww/Ww pairing antiparallel cis XX -B23-B46 : G-C Ww/Ww pairing antiparallel cis one_hbond -B25-B38 : G-C Ww/Ww pairing antiparallel cis one_hbond -B26-B37 : U-A Ww/Ww pairing antiparallel cis XX -B28-B35 : C-G Ww/Ww pairing antiparallel cis XIX -B30-B34 : U-G O2'/Hh pairing -Residue conformations ------------------------------------------- -B19 : G C3p_endo anti -B20 : G C3p_endo anti -B21 : C C3p_endo anti -B22 : A C3p_endo anti -B23 : G C3p_endo anti -B24 : A C3p_endo anti -B25 : G C4p_exo anti -B26 : U C3p_endo anti -B27 : C C4p_exo anti -B28 : C C3p_endo anti -B29 : U C3p_endo anti -B30 : U C3p_exo anti -B33 : C C3p_exo anti -B34 : G C4p_exo syn -B35 : G C3p_endo anti -B36 : G C3p_endo anti -B37 : A C4p_exo anti -B38 : C C3p_endo anti -B39 : A C3p_endo anti -B40 : U C3p_endo anti -B41 : U C2p_endo anti -B42 : G C3p_endo anti -B43 : C C3p_exo anti -B44 : A C3p_endo anti -B45 : C C4p_exo anti -B46 : C C3p_endo anti -B47 : U C3p_endo anti -B48 : G C3p_endo anti -B49 : C C3p_endo anti -B50 : C C3p_endo anti -A1 : ALA -A2 : VAL -A3 : PRO -A4 : GLU -A5 : THR -A6 : ARG -A7 : PRO -A8 : ASN -A9 : HIS -A10 : THR -A11 : ILE -A12 : TYR -A13 : ILE -A14 : ASN -A15 : ASN -A16 : LEU -A17 : ASN -A18 : GLU -A19 : LYS -A20 : ILE -A21 : LYS -A22 : LYS -A23 : ASP -A24 : GLU -A25 : LEU -A26 : LYS -A27 : LYS -A28 : SER -A29 : LEU -A30 : HIS -A31 : ALA -A32 : ILE -A33 : PHE -A34 : SER -A35 : ARG -A36 : PHE -A37 : GLY -A38 : GLN -A39 : ILE -A40 : LEU -A41 : ASP -A42 : ILE -A43 : LEU -A44 : VAL -A45 : SER -A46 : ARG -A47 : SER -A48 : LEU -A49 : LYS -A50 : MET -A51 : ARG -A52 : GLY -A53 : GLN -A54 : ALA -A55 : PHE -A56 : VAL -A57 : ILE -A58 : PHE -A59 : LYS -A60 : GLU -A61 : VAL -A62 : SER -A63 : SER -A64 : ALA -A65 : THR -A66 : ASN -A67 : ALA -A68 : LEU -A69 : ARG -A70 : SER -A71 : MET -A72 : GLN -A73 : GLY -A74 : PHE -A75 : PRO -A76 : PHE -A77 : TYR -A78 : ASP -A79 : LYS -A80 : PRO -A81 : MET -A82 : ARG -A83 : ILE -A84 : GLN -A85 : TYR -A86 : ALA -A87 : LYS -A88 : THR -A89 : ASP -A90 : SER -A91 : ASP -A92 : ILE -A93 : ILE -A94 : ALA -A95 : LYS -A96 : MET -A97 : LYS -A98 : GLY -A99 : THR -A100 : PHE -A101 : VAL -Adjacent stackings ---------------------------------------------- -B20-B21 : adjacent_5p upward -B22-B23 : adjacent_5p upward -B23-B24 : adjacent_5p upward -B26-B27 : adjacent_5p upward -B36-B37 : adjacent_5p upward -B37-B38 : adjacent_5p upward -B38-B39 : adjacent_5p upward -B39-B40 : adjacent_5p upward -B44-B45 : adjacent_5p upward -B47-B48 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 10 -Number of adjacent stackings = 10 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -B19-B50 : G-C Ww/Ww pairing antiparallel cis one_hbond -B21-B48 : C-G Ww/Ww pairing antiparallel cis XIX -B22-B47 : A-U Ww/Ww pairing antiparallel cis XX -B23-B46 : G-C Ww/Ww pairing antiparallel cis 130 -B25-B38 : G-C Wh/Ww pairing antiparallel cis one_hbond -B26-B37 : U-A Ww/Ww pairing antiparallel cis one_hbond -B27-B36 : C-G Ww/Ww pairing antiparallel cis one_hbond -B30-B34 : U-G O2'/Hh pairing -Residue conformations ------------------------------------------- -B19 : G C4p_exo anti -B20 : G C3p_endo anti -B21 : C C3p_endo anti -B22 : A C3p_endo anti -B23 : G C2p_exo anti -B24 : A C3p_endo anti -B25 : G O4p_endo anti -B26 : U C3p_endo anti -B27 : C C3p_endo anti -B28 : C C3p_endo anti -B29 : U C3p_endo anti -B30 : U C3p_exo anti -B33 : C C3p_exo anti -B34 : G C4p_exo syn -B35 : G C3p_endo anti -B36 : G C4p_exo anti -B37 : A C3p_endo anti -B38 : C C3p_endo anti -B39 : A C3p_endo anti -B40 : U C3p_endo anti -B41 : U C2p_endo anti -B42 : G C3p_endo anti -B43 : C C2p_endo anti -B44 : A C3p_endo anti -B45 : C C3p_endo anti -B46 : C C3p_endo anti -B47 : U C3p_endo anti -B48 : G C3p_endo anti -B49 : C C3p_endo anti -B50 : C C3p_endo anti -A1 : ALA -A2 : VAL -A3 : PRO -A4 : GLU -A5 : THR -A6 : ARG -A7 : PRO -A8 : ASN -A9 : HIS -A10 : THR -A11 : ILE -A12 : TYR -A13 : ILE -A14 : ASN -A15 : ASN -A16 : LEU -A17 : ASN -A18 : GLU -A19 : LYS -A20 : ILE -A21 : LYS -A22 : LYS -A23 : ASP -A24 : GLU -A25 : LEU -A26 : LYS -A27 : LYS -A28 : SER -A29 : LEU -A30 : HIS -A31 : ALA -A32 : ILE -A33 : PHE -A34 : SER -A35 : ARG -A36 : PHE -A37 : GLY -A38 : GLN -A39 : ILE -A40 : LEU -A41 : ASP -A42 : ILE -A43 : LEU -A44 : VAL -A45 : SER -A46 : ARG -A47 : SER -A48 : LEU -A49 : LYS -A50 : MET -A51 : ARG -A52 : GLY -A53 : GLN -A54 : ALA -A55 : PHE -A56 : VAL -A57 : ILE -A58 : PHE -A59 : LYS -A60 : GLU -A61 : VAL -A62 : SER -A63 : SER -A64 : ALA -A65 : THR -A66 : ASN -A67 : ALA -A68 : LEU -A69 : ARG -A70 : SER -A71 : MET -A72 : GLN -A73 : GLY -A74 : PHE -A75 : PRO -A76 : PHE -A77 : TYR -A78 : ASP -A79 : LYS -A80 : PRO -A81 : MET -A82 : ARG -A83 : ILE -A84 : GLN -A85 : TYR -A86 : ALA -A87 : LYS -A88 : THR -A89 : ASP -A90 : SER -A91 : ASP -A92 : ILE -A93 : ILE -A94 : ALA -A95 : LYS -A96 : MET -A97 : LYS -A98 : GLY -A99 : THR -A100 : PHE -A101 : VAL -Adjacent stackings ---------------------------------------------- -B20-B21 : adjacent_5p upward -B22-B23 : adjacent_5p upward -B23-B24 : adjacent_5p upward -B26-B27 : adjacent_5p upward -B28-B29 : adjacent_5p upward -B34-B35 : adjacent_5p outward -B35-B36 : adjacent_5p upward -B37-B38 : adjacent_5p upward -B39-B40 : adjacent_5p upward -B44-B45 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -B22-B48 : outward -B25-B39 : outward -Number of stackings = 12 -Number of adjacent stackings = 10 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -B20-B49 : G-C Wh/Wh pairing antiparallel cis one_hbond -B21-B48 : C-G Ww/Ww pairing antiparallel cis XIX -B22-B47 : A-U Ww/Ww pairing antiparallel cis one_hbond -B23-B46 : G-C Wh/Ww pairing antiparallel cis one_hbond -B26-B37 : U-A Ww/Ww pairing antiparallel cis XX -B27-B36 : C-G Ww/Ww pairing antiparallel cis -B28-B35 : C-G Ww/Ww pairing antiparallel cis XIX -B30-B34 : U-G O2'/Hh pairing -B40-B42 : U-G Ss/Ws O2'/Bs pairing antiparallel cis one_hbond 84 -Residue conformations ------------------------------------------- -B19 : G C3p_endo anti -B20 : G C3p_endo anti -B21 : C C4p_exo anti -B22 : A C3p_endo anti -B23 : G C3p_endo anti -B24 : A C4p_exo anti -B25 : G C4p_exo anti -B26 : U C3p_endo anti -B27 : C C4p_exo anti -B28 : C C3p_endo anti -B29 : U C3p_endo anti -B30 : U C3p_exo anti -B33 : C C3p_exo anti -B34 : G C4p_exo syn -B35 : G C3p_endo anti -B36 : G C3p_endo anti -B37 : A C4p_exo anti -B38 : C C3p_endo anti -B39 : A C3p_endo anti -B40 : U C3p_endo anti -B41 : U C2p_endo anti -B42 : G C3p_endo anti -B43 : C C2p_endo anti -B44 : A C3p_endo anti -B45 : C C4p_exo anti -B46 : C C3p_endo anti -B47 : U C3p_endo anti -B48 : G C3p_endo anti -B49 : C C3p_endo anti -B50 : C C3p_endo anti -A1 : ALA -A2 : VAL -A3 : PRO -A4 : GLU -A5 : THR -A6 : ARG -A7 : PRO -A8 : ASN -A9 : HIS -A10 : THR -A11 : ILE -A12 : TYR -A13 : ILE -A14 : ASN -A15 : ASN -A16 : LEU -A17 : ASN -A18 : GLU -A19 : LYS -A20 : ILE -A21 : LYS -A22 : LYS -A23 : ASP -A24 : GLU -A25 : LEU -A26 : LYS -A27 : LYS -A28 : SER -A29 : LEU -A30 : HIS -A31 : ALA -A32 : ILE -A33 : PHE -A34 : SER -A35 : ARG -A36 : PHE -A37 : GLY -A38 : GLN -A39 : ILE -A40 : LEU -A41 : ASP -A42 : ILE -A43 : LEU -A44 : VAL -A45 : SER -A46 : ARG -A47 : SER -A48 : LEU -A49 : LYS -A50 : MET -A51 : ARG -A52 : GLY -A53 : GLN -A54 : ALA -A55 : PHE -A56 : VAL -A57 : ILE -A58 : PHE -A59 : LYS -A60 : GLU -A61 : VAL -A62 : SER -A63 : SER -A64 : ALA -A65 : THR -A66 : ASN -A67 : ALA -A68 : LEU -A69 : ARG -A70 : SER -A71 : MET -A72 : GLN -A73 : GLY -A74 : PHE -A75 : PRO -A76 : PHE -A77 : TYR -A78 : ASP -A79 : LYS -A80 : PRO -A81 : MET -A82 : ARG -A83 : ILE -A84 : GLN -A85 : TYR -A86 : ALA -A87 : LYS -A88 : THR -A89 : ASP -A90 : SER -A91 : ASP -A92 : ILE -A93 : ILE -A94 : ALA -A95 : LYS -A96 : MET -A97 : LYS -A98 : GLY -A99 : THR -A100 : PHE -A101 : VAL -Adjacent stackings ---------------------------------------------- -B20-B21 : adjacent_5p upward -B22-B23 : adjacent_5p upward -B23-B24 : adjacent_5p upward -B25-B26 : adjacent_5p upward -B26-B27 : adjacent_5p upward -B28-B29 : adjacent_5p upward -B34-B35 : adjacent_5p outward -B35-B36 : adjacent_5p upward -B36-B37 : adjacent_5p upward -B38-B39 : adjacent_5p upward -B39-B40 : adjacent_5p upward -B44-B45 : adjacent_5p upward -B48-B49 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 13 -Number of adjacent stackings = 13 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -B21-B48 : C-G Ww/Ww pairing antiparallel cis XIX -B22-B47 : A-U Ww/Ww pairing antiparallel cis XX -B23-B46 : G-C Ww/Ww pairing antiparallel cis one_hbond -B26-B37 : U-A Ww/Ww pairing antiparallel cis XX -B28-B35 : C-G Ws/Ws pairing antiparallel cis one_hbond -B30-B34 : U-G O2'/Hh pairing -B40-B42 : U-G O2'/Bs pairing -B41-B42 : U-G O2P/Bs O2P/Ss adjacent_5p pairing -Residue conformations ------------------------------------------- -B19 : G C3p_endo anti -B20 : G C3p_endo anti -B21 : C C3p_endo anti -B22 : A C3p_endo anti -B23 : G C3p_endo anti -B24 : A C3p_endo anti -B25 : G O4p_endo anti -B26 : U C3p_endo anti -B27 : C C3p_endo anti -B28 : C C3p_endo anti -B29 : U C3p_endo anti -B30 : U C3p_exo anti -B33 : C C3p_exo anti -B34 : G C3p_endo syn -B35 : G C3p_endo anti -B36 : G C3p_endo anti -B37 : A C3p_endo anti -B38 : C C3p_endo anti -B39 : A C2p_exo anti -B40 : U C3p_endo anti -B41 : U C3p_exo anti -B42 : G C3p_endo anti -B43 : C C2p_endo anti -B44 : A C3p_endo anti -B45 : C C4p_exo anti -B46 : C C3p_endo anti -B47 : U C3p_endo anti -B48 : G C3p_endo anti -B49 : C C3p_endo anti -B50 : C C3p_endo anti -A1 : ALA -A2 : VAL -A3 : PRO -A4 : GLU -A5 : THR -A6 : ARG -A7 : PRO -A8 : ASN -A9 : HIS -A10 : THR -A11 : ILE -A12 : TYR -A13 : ILE -A14 : ASN -A15 : ASN -A16 : LEU -A17 : ASN -A18 : GLU -A19 : LYS -A20 : ILE -A21 : LYS -A22 : LYS -A23 : ASP -A24 : GLU -A25 : LEU -A26 : LYS -A27 : LYS -A28 : SER -A29 : LEU -A30 : HIS -A31 : ALA -A32 : ILE -A33 : PHE -A34 : SER -A35 : ARG -A36 : PHE -A37 : GLY -A38 : GLN -A39 : ILE -A40 : LEU -A41 : ASP -A42 : ILE -A43 : LEU -A44 : VAL -A45 : SER -A46 : ARG -A47 : SER -A48 : LEU -A49 : LYS -A50 : MET -A51 : ARG -A52 : GLY -A53 : GLN -A54 : ALA -A55 : PHE -A56 : VAL -A57 : ILE -A58 : PHE -A59 : LYS -A60 : GLU -A61 : VAL -A62 : SER -A63 : SER -A64 : ALA -A65 : THR -A66 : ASN -A67 : ALA -A68 : LEU -A69 : ARG -A70 : SER -A71 : MET -A72 : GLN -A73 : GLY -A74 : PHE -A75 : PRO -A76 : PHE -A77 : TYR -A78 : ASP -A79 : LYS -A80 : PRO -A81 : MET -A82 : ARG -A83 : ILE -A84 : GLN -A85 : TYR -A86 : ALA -A87 : LYS -A88 : THR -A89 : ASP -A90 : SER -A91 : ASP -A92 : ILE -A93 : ILE -A94 : ALA -A95 : LYS -A96 : MET -A97 : LYS -A98 : GLY -A99 : THR -A100 : PHE -A101 : VAL -Adjacent stackings ---------------------------------------------- -B20-B21 : adjacent_5p upward -B22-B23 : adjacent_5p upward -B23-B24 : adjacent_5p upward -B26-B27 : adjacent_5p upward -B28-B29 : adjacent_5p upward -B34-B35 : adjacent_5p outward -B35-B36 : adjacent_5p upward -B37-B38 : adjacent_5p upward -B39-B40 : adjacent_5p upward -B44-B45 : adjacent_5p upward -B49-B50 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 11 -Number of adjacent stackings = 11 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -B19-B50 : G-C Ww/Ww pairing antiparallel cis one_hbond -B21-B48 : C-G Ww/Ww pairing antiparallel cis XIX -B22-B47 : A-U Ww/Ww pairing antiparallel cis XX -B23-B46 : G-C Ww/Ww pairing antiparallel cis -B25-B38 : G-C Ww/Ws pairing antiparallel cis one_hbond -B26-B37 : U-A Ww/Ww pairing antiparallel cis XX -B28-B35 : C-G Ww/Wh pairing antiparallel cis one_hbond -B30-B34 : U-G O2'/Hh pairing -Residue conformations ------------------------------------------- -B19 : G C3p_endo anti -B20 : G C3p_endo anti -B21 : C C4p_exo anti -B22 : A C3p_endo anti -B23 : G C3p_endo anti -B24 : A C4p_exo anti -B25 : G O4p_endo anti -B26 : U C3p_endo anti -B27 : C C4p_exo anti -B28 : C C3p_endo anti -B29 : U C3p_endo anti -B30 : U C3p_exo anti -B33 : C C3p_exo anti -B34 : G C4p_exo syn -B35 : G C3p_endo anti -B36 : G C4p_exo anti -B37 : A C3p_endo anti -B38 : C C3p_endo anti -B39 : A C3p_endo anti -B40 : U C3p_endo anti -B41 : U C2p_endo anti -B42 : G C3p_endo anti -B43 : C C2p_endo anti -B44 : A C3p_endo anti -B45 : C C3p_endo anti -B46 : C C3p_endo anti -B47 : U C3p_endo anti -B48 : G C3p_endo anti -B49 : C C3p_endo anti -B50 : C C3p_endo anti -A1 : ALA -A2 : VAL -A3 : PRO -A4 : GLU -A5 : THR -A6 : ARG -A7 : PRO -A8 : ASN -A9 : HIS -A10 : THR -A11 : ILE -A12 : TYR -A13 : ILE -A14 : ASN -A15 : ASN -A16 : LEU -A17 : ASN -A18 : GLU -A19 : LYS -A20 : ILE -A21 : LYS -A22 : LYS -A23 : ASP -A24 : GLU -A25 : LEU -A26 : LYS -A27 : LYS -A28 : SER -A29 : LEU -A30 : HIS -A31 : ALA -A32 : ILE -A33 : PHE -A34 : SER -A35 : ARG -A36 : PHE -A37 : GLY -A38 : GLN -A39 : ILE -A40 : LEU -A41 : ASP -A42 : ILE -A43 : LEU -A44 : VAL -A45 : SER -A46 : ARG -A47 : SER -A48 : LEU -A49 : LYS -A50 : MET -A51 : ARG -A52 : GLY -A53 : GLN -A54 : ALA -A55 : PHE -A56 : VAL -A57 : ILE -A58 : PHE -A59 : LYS -A60 : GLU -A61 : VAL -A62 : SER -A63 : SER -A64 : ALA -A65 : THR -A66 : ASN -A67 : ALA -A68 : LEU -A69 : ARG -A70 : SER -A71 : MET -A72 : GLN -A73 : GLY -A74 : PHE -A75 : PRO -A76 : PHE -A77 : TYR -A78 : ASP -A79 : LYS -A80 : PRO -A81 : MET -A82 : ARG -A83 : ILE -A84 : GLN -A85 : TYR -A86 : ALA -A87 : LYS -A88 : THR -A89 : ASP -A90 : SER -A91 : ASP -A92 : ILE -A93 : ILE -A94 : ALA -A95 : LYS -A96 : MET -A97 : LYS -A98 : GLY -A99 : THR -A100 : PHE -A101 : VAL -Adjacent stackings ---------------------------------------------- -B20-B21 : adjacent_5p upward -B22-B23 : adjacent_5p upward -B23-B24 : adjacent_5p upward -B25-B26 : adjacent_5p upward -B26-B27 : adjacent_5p upward -B28-B29 : adjacent_5p upward -B35-B36 : adjacent_5p upward -B36-B37 : adjacent_5p upward -B39-B40 : adjacent_5p upward -B44-B45 : adjacent_5p upward -B48-B49 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -B22-B48 : outward -Number of stackings = 12 -Number of adjacent stackings = 11 -Number of non adjacent stackings = 1 -Base-pairs ------------------------------------------------------ -B19-B50 : G-C Ww/Ww pairing antiparallel cis one_hbond -B21-B48 : C-G Ww/Ww pairing antiparallel cis -B23-B46 : G-C Ww/Ww pairing antiparallel cis one_hbond -B26-B37 : U-A Ww/Ww pairing antiparallel cis XX -B27-B36 : C-G Ww/Ww pairing antiparallel cis one_hbond -B28-B35 : C-G Ww/Ww pairing antiparallel cis XIX -B30-B34 : U-G O2'/Hh pairing -Residue conformations ------------------------------------------- -B19 : G C3p_endo anti -B20 : G C3p_endo anti -B21 : C C3p_endo anti -B22 : A C3p_endo anti -B23 : G C3p_endo anti -B24 : A C3p_endo anti -B25 : G O4p_endo anti -B26 : U C4p_exo anti -B27 : C C3p_endo anti -B28 : C C4p_exo anti -B29 : U C4p_exo anti -B30 : U C3p_exo anti -B33 : C C3p_exo anti -B34 : G C4p_exo syn -B35 : G C3p_endo anti -B36 : G C3p_endo anti -B37 : A C4p_exo anti -B38 : C C3p_endo anti -B39 : A C3p_endo anti -B40 : U C3p_endo anti -B41 : U C2p_endo anti -B42 : G C1p_endo anti -B43 : C C2p_endo anti -B44 : A C2p_exo anti -B45 : C C3p_endo anti -B46 : C C3p_endo anti -B47 : U C3p_endo anti -B48 : G C3p_endo anti -B49 : C C3p_endo anti -B50 : C C3p_endo anti -A1 : ALA -A2 : VAL -A3 : PRO -A4 : GLU -A5 : THR -A6 : ARG -A7 : PRO -A8 : ASN -A9 : HIS -A10 : THR -A11 : ILE -A12 : TYR -A13 : ILE -A14 : ASN -A15 : ASN -A16 : LEU -A17 : ASN -A18 : GLU -A19 : LYS -A20 : ILE -A21 : LYS -A22 : LYS -A23 : ASP -A24 : GLU -A25 : LEU -A26 : LYS -A27 : LYS -A28 : SER -A29 : LEU -A30 : HIS -A31 : ALA -A32 : ILE -A33 : PHE -A34 : SER -A35 : ARG -A36 : PHE -A37 : GLY -A38 : GLN -A39 : ILE -A40 : LEU -A41 : ASP -A42 : ILE -A43 : LEU -A44 : VAL -A45 : SER -A46 : ARG -A47 : SER -A48 : LEU -A49 : LYS -A50 : MET -A51 : ARG -A52 : GLY -A53 : GLN -A54 : ALA -A55 : PHE -A56 : VAL -A57 : ILE -A58 : PHE -A59 : LYS -A60 : GLU -A61 : VAL -A62 : SER -A63 : SER -A64 : ALA -A65 : THR -A66 : ASN -A67 : ALA -A68 : LEU -A69 : ARG -A70 : SER -A71 : MET -A72 : GLN -A73 : GLY -A74 : PHE -A75 : PRO -A76 : PHE -A77 : TYR -A78 : ASP -A79 : LYS -A80 : PRO -A81 : MET -A82 : ARG -A83 : ILE -A84 : GLN -A85 : TYR -A86 : ALA -A87 : LYS -A88 : THR -A89 : ASP -A90 : SER -A91 : ASP -A92 : ILE -A93 : ILE -A94 : ALA -A95 : LYS -A96 : MET -A97 : LYS -A98 : GLY -A99 : THR -A100 : PHE -A101 : VAL -Adjacent stackings ---------------------------------------------- -B20-B21 : adjacent_5p upward -B22-B23 : adjacent_5p upward -B23-B24 : adjacent_5p upward -B25-B26 : adjacent_5p upward -B26-B27 : adjacent_5p upward -B35-B36 : adjacent_5p upward -B36-B37 : adjacent_5p upward -B37-B38 : adjacent_5p upward -B39-B40 : adjacent_5p upward -B44-B45 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 10 -Number of adjacent stackings = 10 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -B19-B50 : G-C Ww/Ww pairing antiparallel cis -B21-B48 : C-G Ww/Ww pairing antiparallel cis XIX -B22-B47 : A-U Ww/Ww pairing antiparallel cis XX -B24-B46 : A-C Ss/Wh pairing antiparallel cis one_hbond 74 -B27-B36 : C-G Ww/Ww pairing antiparallel cis XIX -B28-B35 : C-G Ws/Ws pairing antiparallel cis one_hbond -B30-B33 : U-C O2P/Bh adjacent_5p pairing -Residue conformations ------------------------------------------- -B19 : G C2p_exo anti -B20 : G C3p_endo anti -B21 : C C3p_endo anti -B22 : A C3p_endo anti -B23 : G C3p_endo anti -B24 : A C3p_endo anti -B25 : G C4p_exo anti -B26 : U C3p_endo anti -B27 : C C4p_exo anti -B28 : C C3p_endo anti -B29 : U C3p_endo anti -B30 : U C3p_exo anti -B33 : C C3p_exo anti -B34 : G C4p_exo syn -B35 : G C3p_endo anti -B36 : G C4p_exo anti -B37 : A C3p_endo anti -B38 : C C3p_endo anti -B39 : A C2p_exo anti -B40 : U C3p_endo anti -B41 : U C2p_endo anti -B42 : G C3p_endo anti -B43 : C C2p_endo anti -B44 : A C2p_exo anti -B45 : C C4p_exo anti -B46 : C C3p_endo anti -B47 : U C3p_endo anti -B48 : G C3p_endo anti -B49 : C C3p_endo anti -B50 : C C3p_endo anti -A1 : ALA -A2 : VAL -A3 : PRO -A4 : GLU -A5 : THR -A6 : ARG -A7 : PRO -A8 : ASN -A9 : HIS -A10 : THR -A11 : ILE -A12 : TYR -A13 : ILE -A14 : ASN -A15 : ASN -A16 : LEU -A17 : ASN -A18 : GLU -A19 : LYS -A20 : ILE -A21 : LYS -A22 : LYS -A23 : ASP -A24 : GLU -A25 : LEU -A26 : LYS -A27 : LYS -A28 : SER -A29 : LEU -A30 : HIS -A31 : ALA -A32 : ILE -A33 : PHE -A34 : SER -A35 : ARG -A36 : PHE -A37 : GLY -A38 : GLN -A39 : ILE -A40 : LEU -A41 : ASP -A42 : ILE -A43 : LEU -A44 : VAL -A45 : SER -A46 : ARG -A47 : SER -A48 : LEU -A49 : LYS -A50 : MET -A51 : ARG -A52 : GLY -A53 : GLN -A54 : ALA -A55 : PHE -A56 : VAL -A57 : ILE -A58 : PHE -A59 : LYS -A60 : GLU -A61 : VAL -A62 : SER -A63 : SER -A64 : ALA -A65 : THR -A66 : ASN -A67 : ALA -A68 : LEU -A69 : ARG -A70 : SER -A71 : MET -A72 : GLN -A73 : GLY -A74 : PHE -A75 : PRO -A76 : PHE -A77 : TYR -A78 : ASP -A79 : LYS -A80 : PRO -A81 : MET -A82 : ARG -A83 : ILE -A84 : GLN -A85 : TYR -A86 : ALA -A87 : LYS -A88 : THR -A89 : ASP -A90 : SER -A91 : ASP -A92 : ILE -A93 : ILE -A94 : ALA -A95 : LYS -A96 : MET -A97 : LYS -A98 : GLY -A99 : THR -A100 : PHE -A101 : VAL -Adjacent stackings ---------------------------------------------- -B19-B20 : adjacent_5p upward -B20-B21 : adjacent_5p upward -B22-B23 : adjacent_5p upward -B23-B24 : adjacent_5p upward -B26-B27 : adjacent_5p upward -B28-B29 : adjacent_5p upward -B35-B36 : adjacent_5p upward -B39-B40 : adjacent_5p upward -B44-B45 : adjacent_5p upward -B48-B49 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 10 -Number of adjacent stackings = 10 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -B20-B49 : G-C Ww/Ww pairing antiparallel cis one_hbond -B22-B47 : A-U Ww/Ww pairing antiparallel cis XX -B23-B46 : G-C Ww/Ww pairing antiparallel cis -B25-B38 : G-C Wh/Wh pairing antiparallel cis one_hbond -B26-B37 : U-A Ww/Ww pairing antiparallel cis XX -B27-B36 : C-G Ww/Ww pairing antiparallel cis one_hbond -B28-B35 : C-G Ww/Ww pairing antiparallel cis XIX -B30-B34 : U-G O2'/Hh pairing -B40-B42 : U-G Ss/Ws O2'/Bs pairing antiparallel cis one_hbond 84 -Residue conformations ------------------------------------------- -B19 : G C3p_endo anti -B20 : G C3p_endo anti -B21 : C C3p_endo anti -B22 : A C3p_endo anti -B23 : G C3p_endo anti -B24 : A C4p_exo anti -B25 : G C4p_exo anti -B26 : U C3p_endo anti -B27 : C C3p_endo anti -B28 : C C3p_endo anti -B29 : U C4p_exo anti -B30 : U C3p_exo anti -B33 : C C3p_exo anti -B34 : G C4p_exo syn -B35 : G C3p_endo anti -B36 : G C3p_endo anti -B37 : A C4p_exo anti -B38 : C C3p_endo anti -B39 : A C3p_endo anti -B40 : U C3p_endo anti -B41 : U C2p_endo anti -B42 : G C3p_endo anti -B43 : C C2p_endo anti -B44 : A C3p_endo anti -B45 : C C3p_endo anti -B46 : C C3p_endo anti -B47 : U C3p_endo anti -B48 : G C3p_endo anti -B49 : C C3p_endo anti -B50 : C C3p_endo anti -A1 : ALA -A2 : VAL -A3 : PRO -A4 : GLU -A5 : THR -A6 : ARG -A7 : PRO -A8 : ASN -A9 : HIS -A10 : THR -A11 : ILE -A12 : TYR -A13 : ILE -A14 : ASN -A15 : ASN -A16 : LEU -A17 : ASN -A18 : GLU -A19 : LYS -A20 : ILE -A21 : LYS -A22 : LYS -A23 : ASP -A24 : GLU -A25 : LEU -A26 : LYS -A27 : LYS -A28 : SER -A29 : LEU -A30 : HIS -A31 : ALA -A32 : ILE -A33 : PHE -A34 : SER -A35 : ARG -A36 : PHE -A37 : GLY -A38 : GLN -A39 : ILE -A40 : LEU -A41 : ASP -A42 : ILE -A43 : LEU -A44 : VAL -A45 : SER -A46 : ARG -A47 : SER -A48 : LEU -A49 : LYS -A50 : MET -A51 : ARG -A52 : GLY -A53 : GLN -A54 : ALA -A55 : PHE -A56 : VAL -A57 : ILE -A58 : PHE -A59 : LYS -A60 : GLU -A61 : VAL -A62 : SER -A63 : SER -A64 : ALA -A65 : THR -A66 : ASN -A67 : ALA -A68 : LEU -A69 : ARG -A70 : SER -A71 : MET -A72 : GLN -A73 : GLY -A74 : PHE -A75 : PRO -A76 : PHE -A77 : TYR -A78 : ASP -A79 : LYS -A80 : PRO -A81 : MET -A82 : ARG -A83 : ILE -A84 : GLN -A85 : TYR -A86 : ALA -A87 : LYS -A88 : THR -A89 : ASP -A90 : SER -A91 : ASP -A92 : ILE -A93 : ILE -A94 : ALA -A95 : LYS -A96 : MET -A97 : LYS -A98 : GLY -A99 : THR -A100 : PHE -A101 : VAL -Adjacent stackings ---------------------------------------------- -B19-B20 : adjacent_5p upward -B20-B21 : adjacent_5p upward -B22-B23 : adjacent_5p upward -B23-B24 : adjacent_5p upward -B25-B26 : adjacent_5p upward -B26-B27 : adjacent_5p upward -B35-B36 : adjacent_5p upward -B36-B37 : adjacent_5p upward -B38-B39 : adjacent_5p upward -B39-B40 : adjacent_5p upward -B44-B45 : adjacent_5p upward -B47-B48 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 12 -Number of adjacent stackings = 12 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -B21-B48 : C-G Ww/Ww pairing antiparallel cis XIX -B22-B47 : A-U Ww/Ww pairing antiparallel cis XX -B23-B46 : G-C Ww/Ww pairing antiparallel cis XIX -B30-B33 : U-C O2P/Bh adjacent_5p pairing -B40-B42 : U-G O2'/Bs pairing -Residue conformations ------------------------------------------- -B19 : G C3p_exo anti -B20 : G C3p_endo anti -B21 : C C3p_endo anti -B22 : A C3p_endo anti -B23 : G C3p_endo anti -B24 : A C3p_endo anti -B25 : G O4p_endo anti -B26 : U C3p_endo anti -B27 : C C3p_endo anti -B28 : C C3p_endo anti -B29 : U C3p_endo anti -B30 : U C3p_exo anti -B33 : C C3p_exo anti -B34 : G C4p_exo syn -B35 : G C3p_endo anti -B36 : G C3p_endo anti -B37 : A C3p_endo anti -B38 : C C3p_endo anti -B39 : A C3p_endo anti -B40 : U C3p_endo anti -B41 : U C2p_endo anti -B42 : G C3p_endo anti -B43 : C C2p_endo anti -B44 : A C3p_endo anti -B45 : C C3p_endo anti -B46 : C C3p_endo anti -B47 : U C3p_endo anti -B48 : G C3p_endo anti -B49 : C C3p_endo anti -B50 : C C3p_endo anti -A1 : ALA -A2 : VAL -A3 : PRO -A4 : GLU -A5 : THR -A6 : ARG -A7 : PRO -A8 : ASN -A9 : HIS -A10 : THR -A11 : ILE -A12 : TYR -A13 : ILE -A14 : ASN -A15 : ASN -A16 : LEU -A17 : ASN -A18 : GLU -A19 : LYS -A20 : ILE -A21 : LYS -A22 : LYS -A23 : ASP -A24 : GLU -A25 : LEU -A26 : LYS -A27 : LYS -A28 : SER -A29 : LEU -A30 : HIS -A31 : ALA -A32 : ILE -A33 : PHE -A34 : SER -A35 : ARG -A36 : PHE -A37 : GLY -A38 : GLN -A39 : ILE -A40 : LEU -A41 : ASP -A42 : ILE -A43 : LEU -A44 : VAL -A45 : SER -A46 : ARG -A47 : SER -A48 : LEU -A49 : LYS -A50 : MET -A51 : ARG -A52 : GLY -A53 : GLN -A54 : ALA -A55 : PHE -A56 : VAL -A57 : ILE -A58 : PHE -A59 : LYS -A60 : GLU -A61 : VAL -A62 : SER -A63 : SER -A64 : ALA -A65 : THR -A66 : ASN -A67 : ALA -A68 : LEU -A69 : ARG -A70 : SER -A71 : MET -A72 : GLN -A73 : GLY -A74 : PHE -A75 : PRO -A76 : PHE -A77 : TYR -A78 : ASP -A79 : LYS -A80 : PRO -A81 : MET -A82 : ARG -A83 : ILE -A84 : GLN -A85 : TYR -A86 : ALA -A87 : LYS -A88 : THR -A89 : ASP -A90 : SER -A91 : ASP -A92 : ILE -A93 : ILE -A94 : ALA -A95 : LYS -A96 : MET -A97 : LYS -A98 : GLY -A99 : THR -A100 : PHE -A101 : VAL -Adjacent stackings ---------------------------------------------- -B20-B21 : adjacent_5p upward -B22-B23 : adjacent_5p upward -B23-B24 : adjacent_5p upward -B26-B27 : adjacent_5p upward -B35-B36 : adjacent_5p upward -B36-B37 : adjacent_5p upward -B38-B39 : adjacent_5p upward -B39-B40 : adjacent_5p upward -B44-B45 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 9 -Number of adjacent stackings = 9 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -B22-B47 : A-U Wh/Ww pairing antiparallel cis one_hbond -B23-B46 : G-C Ww/Ww pairing antiparallel cis -B27-B36 : C-G Ww/Ww pairing antiparallel cis -B28-B35 : C-G Ws/Ww pairing antiparallel cis one_hbond -B30-B34 : U-G O2'/Hh pairing -B40-B42 : U-G O2'/Bs pairing -Residue conformations ------------------------------------------- -B19 : G C3p_endo anti -B20 : G C3p_endo anti -B21 : C C3p_endo anti -B22 : A C3p_endo anti -B23 : G C3p_endo anti -B24 : A C3p_endo anti -B25 : G C4p_exo anti -B26 : U C3p_endo anti -B27 : C C4p_exo anti -B28 : C C3p_endo anti -B29 : U C3p_endo anti -B30 : U C3p_exo anti -B33 : C C3p_exo anti -B34 : G C3p_endo syn -B35 : G C3p_endo anti -B36 : G C4p_exo anti -B37 : A C3p_endo anti -B38 : C C3p_endo anti -B39 : A C3p_endo anti -B40 : U C3p_endo anti -B41 : U C2p_endo anti -B42 : G C3p_endo anti -B43 : C C3p_exo anti -B44 : A C2p_exo anti -B45 : C C3p_endo anti -B46 : C C3p_endo anti -B47 : U C3p_endo anti -B48 : G C3p_endo anti -B49 : C C3p_endo anti -B50 : C C3p_endo anti -A1 : ALA -A2 : VAL -A3 : PRO -A4 : GLU -A5 : THR -A6 : ARG -A7 : PRO -A8 : ASN -A9 : HIS -A10 : THR -A11 : ILE -A12 : TYR -A13 : ILE -A14 : ASN -A15 : ASN -A16 : LEU -A17 : ASN -A18 : GLU -A19 : LYS -A20 : ILE -A21 : LYS -A22 : LYS -A23 : ASP -A24 : GLU -A25 : LEU -A26 : LYS -A27 : LYS -A28 : SER -A29 : LEU -A30 : HIS -A31 : ALA -A32 : ILE -A33 : PHE -A34 : SER -A35 : ARG -A36 : PHE -A37 : GLY -A38 : GLN -A39 : ILE -A40 : LEU -A41 : ASP -A42 : ILE -A43 : LEU -A44 : VAL -A45 : SER -A46 : ARG -A47 : SER -A48 : LEU -A49 : LYS -A50 : MET -A51 : ARG -A52 : GLY -A53 : GLN -A54 : ALA -A55 : PHE -A56 : VAL -A57 : ILE -A58 : PHE -A59 : LYS -A60 : GLU -A61 : VAL -A62 : SER -A63 : SER -A64 : ALA -A65 : THR -A66 : ASN -A67 : ALA -A68 : LEU -A69 : ARG -A70 : SER -A71 : MET -A72 : GLN -A73 : GLY -A74 : PHE -A75 : PRO -A76 : PHE -A77 : TYR -A78 : ASP -A79 : LYS -A80 : PRO -A81 : MET -A82 : ARG -A83 : ILE -A84 : GLN -A85 : TYR -A86 : ALA -A87 : LYS -A88 : THR -A89 : ASP -A90 : SER -A91 : ASP -A92 : ILE -A93 : ILE -A94 : ALA -A95 : LYS -A96 : MET -A97 : LYS -A98 : GLY -A99 : THR -A100 : PHE -A101 : VAL -Adjacent stackings ---------------------------------------------- -B20-B21 : adjacent_5p upward -B22-B23 : adjacent_5p upward -B23-B24 : adjacent_5p upward -B25-B26 : adjacent_5p upward -B26-B27 : adjacent_5p upward -B28-B29 : adjacent_5p upward -B34-B35 : adjacent_5p outward -B35-B36 : adjacent_5p upward -B37-B38 : adjacent_5p upward -B39-B40 : adjacent_5p upward -B44-B45 : adjacent_5p upward -B47-B48 : adjacent_5p upward -B49-B50 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 13 -Number of adjacent stackings = 13 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -B19-B50 : G-C Ww/Ww pairing antiparallel cis one_hbond -B21-B48 : C-G Ww/Ww pairing antiparallel cis XIX -B22-B47 : A-U Ww/Ww pairing antiparallel cis XX -B23-B46 : G-C Ww/Ww pairing antiparallel cis -B26-B37 : U-A Ww/Ww pairing antiparallel cis XX -B27-B36 : C-G Ww/Ww pairing antiparallel cis one_hbond -B28-B35 : C-G Ww/Ww pairing antiparallel cis XIX -B30-B34 : U-G O2'/Hh pairing -B40-B42 : U-G O2'/Bs pairing -Residue conformations ------------------------------------------- -B19 : G O4p_endo anti -B20 : G C3p_endo anti -B21 : C C3p_endo anti -B22 : A C3p_endo anti -B23 : G C2p_exo anti -B24 : A C4p_exo anti -B25 : G C4p_exo anti -B26 : U C3p_endo anti -B27 : C C3p_endo anti -B28 : C C3p_endo anti -B29 : U C4p_exo anti -B30 : U C3p_exo anti -B33 : C C3p_exo anti -B34 : G C4p_exo syn -B35 : G C3p_endo anti -B36 : G C3p_endo anti -B37 : A C4p_exo anti -B38 : C C3p_endo anti -B39 : A C3p_endo anti -B40 : U C2p_exo anti -B41 : U C3p_exo anti -B42 : G C3p_endo anti -B43 : C C2p_endo anti -B44 : A C3p_endo anti -B45 : C C3p_endo anti -B46 : C C3p_endo anti -B47 : U C3p_endo anti -B48 : G C3p_endo anti -B49 : C C3p_endo anti -B50 : C C3p_endo anti -A1 : ALA -A2 : VAL -A3 : PRO -A4 : GLU -A5 : THR -A6 : ARG -A7 : PRO -A8 : ASN -A9 : HIS -A10 : THR -A11 : ILE -A12 : TYR -A13 : ILE -A14 : ASN -A15 : ASN -A16 : LEU -A17 : ASN -A18 : GLU -A19 : LYS -A20 : ILE -A21 : LYS -A22 : LYS -A23 : ASP -A24 : GLU -A25 : LEU -A26 : LYS -A27 : LYS -A28 : SER -A29 : LEU -A30 : HIS -A31 : ALA -A32 : ILE -A33 : PHE -A34 : SER -A35 : ARG -A36 : PHE -A37 : GLY -A38 : GLN -A39 : ILE -A40 : LEU -A41 : ASP -A42 : ILE -A43 : LEU -A44 : VAL -A45 : SER -A46 : ARG -A47 : SER -A48 : LEU -A49 : LYS -A50 : MET -A51 : ARG -A52 : GLY -A53 : GLN -A54 : ALA -A55 : PHE -A56 : VAL -A57 : ILE -A58 : PHE -A59 : LYS -A60 : GLU -A61 : VAL -A62 : SER -A63 : SER -A64 : ALA -A65 : THR -A66 : ASN -A67 : ALA -A68 : LEU -A69 : ARG -A70 : SER -A71 : MET -A72 : GLN -A73 : GLY -A74 : PHE -A75 : PRO -A76 : PHE -A77 : TYR -A78 : ASP -A79 : LYS -A80 : PRO -A81 : MET -A82 : ARG -A83 : ILE -A84 : GLN -A85 : TYR -A86 : ALA -A87 : LYS -A88 : THR -A89 : ASP -A90 : SER -A91 : ASP -A92 : ILE -A93 : ILE -A94 : ALA -A95 : LYS -A96 : MET -A97 : LYS -A98 : GLY -A99 : THR -A100 : PHE -A101 : VAL -Adjacent stackings ---------------------------------------------- -B20-B21 : adjacent_5p upward -B23-B24 : adjacent_5p upward -B25-B26 : adjacent_5p upward -B35-B36 : adjacent_5p upward -B36-B37 : adjacent_5p upward -B37-B38 : adjacent_5p upward -B39-B40 : adjacent_5p upward -B44-B45 : adjacent_5p upward -B46-B47 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -B25-B39 : outward -Number of stackings = 10 -Number of adjacent stackings = 9 -Number of non adjacent stackings = 1 -Base-pairs ------------------------------------------------------ -B20-B49 : G-C Wh/Wh pairing antiparallel cis one_hbond -B21-B48 : C-G Ww/Ww pairing antiparallel cis XIX -B22-B47 : A-U Ww/Ww pairing antiparallel cis XX -B23-B46 : G-C Ws/Ws pairing antiparallel cis one_hbond -B25-B38 : G-C Ws/Ww pairing antiparallel cis one_hbond -B26-B37 : U-A Ww/Ww pairing antiparallel cis one_hbond -B27-B36 : C-G Ww/Ww pairing antiparallel cis 130 -B28-B35 : C-G Ws/Ws pairing antiparallel cis one_hbond -B30-B33 : U-C O2P/Bh adjacent_5p pairing -Residue conformations ------------------------------------------- -B19 : G C3p_endo anti -B20 : G C3p_endo anti -B21 : C C3p_endo anti -B22 : A C3p_endo anti -B23 : G C3p_endo anti -B24 : A C3p_endo anti -B25 : G O4p_endo anti -B26 : U C3p_endo anti -B27 : C C4p_exo anti -B28 : C C3p_endo anti -B29 : U C3p_endo anti -B30 : U C3p_exo anti -B33 : C C3p_exo anti -B34 : G C3p_endo syn -B35 : G C3p_endo anti -B36 : G C4p_exo anti -B37 : A C3p_endo anti -B38 : C C3p_endo anti -B39 : A C3p_endo anti -B40 : U C3p_endo anti -B41 : U C2p_endo anti -B42 : G C3p_endo anti -B43 : C C2p_endo anti -B44 : A C2p_exo anti -B45 : C C3p_endo anti -B46 : C C4p_exo anti -B47 : U C3p_endo anti -B48 : G C3p_endo anti -B49 : C C3p_endo anti -B50 : C C3p_endo anti -A1 : ALA -A2 : VAL -A3 : PRO -A4 : GLU -A5 : THR -A6 : ARG -A7 : PRO -A8 : ASN -A9 : HIS -A10 : THR -A11 : ILE -A12 : TYR -A13 : ILE -A14 : ASN -A15 : ASN -A16 : LEU -A17 : ASN -A18 : GLU -A19 : LYS -A20 : ILE -A21 : LYS -A22 : LYS -A23 : ASP -A24 : GLU -A25 : LEU -A26 : LYS -A27 : LYS -A28 : SER -A29 : LEU -A30 : HIS -A31 : ALA -A32 : ILE -A33 : PHE -A34 : SER -A35 : ARG -A36 : PHE -A37 : GLY -A38 : GLN -A39 : ILE -A40 : LEU -A41 : ASP -A42 : ILE -A43 : LEU -A44 : VAL -A45 : SER -A46 : ARG -A47 : SER -A48 : LEU -A49 : LYS -A50 : MET -A51 : ARG -A52 : GLY -A53 : GLN -A54 : ALA -A55 : PHE -A56 : VAL -A57 : ILE -A58 : PHE -A59 : LYS -A60 : GLU -A61 : VAL -A62 : SER -A63 : SER -A64 : ALA -A65 : THR -A66 : ASN -A67 : ALA -A68 : LEU -A69 : ARG -A70 : SER -A71 : MET -A72 : GLN -A73 : GLY -A74 : PHE -A75 : PRO -A76 : PHE -A77 : TYR -A78 : ASP -A79 : LYS -A80 : PRO -A81 : MET -A82 : ARG -A83 : ILE -A84 : GLN -A85 : TYR -A86 : ALA -A87 : LYS -A88 : THR -A89 : ASP -A90 : SER -A91 : ASP -A92 : ILE -A93 : ILE -A94 : ALA -A95 : LYS -A96 : MET -A97 : LYS -A98 : GLY -A99 : THR -A100 : PHE -A101 : VAL -Adjacent stackings ---------------------------------------------- -B20-B21 : adjacent_5p upward -B21-B22 : adjacent_5p upward -B22-B23 : adjacent_5p upward -B23-B24 : adjacent_5p upward -B26-B27 : adjacent_5p upward -B28-B29 : adjacent_5p upward -B34-B35 : adjacent_5p outward -B35-B36 : adjacent_5p upward -B38-B39 : adjacent_5p upward -B39-B40 : adjacent_5p upward -B41-B42 : adjacent_5p outward -B44-B45 : adjacent_5p upward -B47-B48 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 13 -Number of adjacent stackings = 13 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -B21-B48 : C-G Ww/Ww pairing antiparallel cis XIX -B22-B47 : A-U Ww/Ww pairing antiparallel cis XX -B23-B46 : G-C Ww/Ww pairing antiparallel cis XIX -B25-B38 : G-C Wh/Wh pairing antiparallel cis one_hbond -B26-B37 : U-A Ww/Ww pairing antiparallel cis XX -B28-B35 : C-G Ww/Ww pairing antiparallel cis XIX -B30-B34 : U-G O2'/Hh pairing -B40-B42 : U-G O2'/Bs pairing -Residue conformations ------------------------------------------- -B19 : G C3p_endo anti -B20 : G C3p_endo anti -B21 : C C3p_endo anti -B22 : A C3p_endo anti -B23 : G C3p_endo anti -B24 : A C4p_exo anti -B25 : G C4p_exo anti -B26 : U C3p_endo anti -B27 : C C4p_exo anti -B28 : C C3p_endo anti -B29 : U C3p_endo anti -B30 : U C3p_exo anti -B33 : C C3p_exo anti -B34 : G C3p_endo syn -B35 : G C3p_endo anti -B36 : G C3p_endo anti -B37 : A C3p_endo anti -B38 : C C3p_endo anti -B39 : A C3p_endo anti -B40 : U C3p_endo anti -B41 : U C2p_endo anti -B42 : G C3p_endo anti -B43 : C C1p_exo anti -B44 : A C3p_endo anti -B45 : C C4p_exo anti -B46 : C C3p_endo anti -B47 : U C3p_endo anti -B48 : G C3p_endo anti -B49 : C C3p_endo anti -B50 : C C3p_endo anti -A1 : ALA -A2 : VAL -A3 : PRO -A4 : GLU -A5 : THR -A6 : ARG -A7 : PRO -A8 : ASN -A9 : HIS -A10 : THR -A11 : ILE -A12 : TYR -A13 : ILE -A14 : ASN -A15 : ASN -A16 : LEU -A17 : ASN -A18 : GLU -A19 : LYS -A20 : ILE -A21 : LYS -A22 : LYS -A23 : ASP -A24 : GLU -A25 : LEU -A26 : LYS -A27 : LYS -A28 : SER -A29 : LEU -A30 : HIS -A31 : ALA -A32 : ILE -A33 : PHE -A34 : SER -A35 : ARG -A36 : PHE -A37 : GLY -A38 : GLN -A39 : ILE -A40 : LEU -A41 : ASP -A42 : ILE -A43 : LEU -A44 : VAL -A45 : SER -A46 : ARG -A47 : SER -A48 : LEU -A49 : LYS -A50 : MET -A51 : ARG -A52 : GLY -A53 : GLN -A54 : ALA -A55 : PHE -A56 : VAL -A57 : ILE -A58 : PHE -A59 : LYS -A60 : GLU -A61 : VAL -A62 : SER -A63 : SER -A64 : ALA -A65 : THR -A66 : ASN -A67 : ALA -A68 : LEU -A69 : ARG -A70 : SER -A71 : MET -A72 : GLN -A73 : GLY -A74 : PHE -A75 : PRO -A76 : PHE -A77 : TYR -A78 : ASP -A79 : LYS -A80 : PRO -A81 : MET -A82 : ARG -A83 : ILE -A84 : GLN -A85 : TYR -A86 : ALA -A87 : LYS -A88 : THR -A89 : ASP -A90 : SER -A91 : ASP -A92 : ILE -A93 : ILE -A94 : ALA -A95 : LYS -A96 : MET -A97 : LYS -A98 : GLY -A99 : THR -A100 : PHE -A101 : VAL -Adjacent stackings ---------------------------------------------- -B20-B21 : adjacent_5p upward -B22-B23 : adjacent_5p upward -B23-B24 : adjacent_5p upward -B26-B27 : adjacent_5p upward -B28-B29 : adjacent_5p upward -B35-B36 : adjacent_5p upward -B36-B37 : adjacent_5p upward -B37-B38 : adjacent_5p upward -B39-B40 : adjacent_5p upward -B44-B45 : adjacent_5p upward -B47-B48 : adjacent_5p upward -B49-B50 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 12 -Number of adjacent stackings = 12 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -B19-B50 : G-C Ww/Ww pairing antiparallel cis -B21-B48 : C-G Ww/Ww pairing antiparallel cis XIX -B22-B47 : A-U Ww/Ww pairing antiparallel cis XX -B23-B46 : G-C Ww/Ww pairing antiparallel cis XIX -B25-B38 : G-C Wh/Wh pairing antiparallel cis one_hbond -B26-B37 : U-A Ww/Ww pairing antiparallel cis one_hbond -B28-B35 : C-G Ws/Ww pairing antiparallel cis one_hbond -B30-B34 : U-G O2'/Hh pairing -B40-B42 : U-G O2'/Bs pairing -Residue conformations ------------------------------------------- -B19 : G C3p_endo anti -B20 : G C3p_endo anti -B21 : C C3p_endo anti -B22 : A C4p_exo anti -B23 : G C3p_endo anti -B24 : A C3p_endo anti -B25 : G O4p_endo anti -B26 : U C3p_endo anti -B27 : C C4p_exo anti -B28 : C C3p_endo anti -B29 : U C3p_endo anti -B30 : U C3p_exo anti -B33 : C C3p_exo anti -B34 : G C4p_exo syn -B35 : G C3p_endo anti -B36 : G C3p_endo anti -B37 : A C3p_endo anti -B38 : C C3p_endo anti -B39 : A C3p_endo anti -B40 : U C3p_endo anti -B41 : U C2p_endo anti -B42 : G C3p_endo anti -B43 : C C2p_endo anti -B44 : A C2p_exo anti -B45 : C C3p_endo anti -B46 : C C3p_endo anti -B47 : U C3p_endo anti -B48 : G C3p_endo anti -B49 : C C3p_endo anti -B50 : C C3p_endo anti -A1 : ALA -A2 : VAL -A3 : PRO -A4 : GLU -A5 : THR -A6 : ARG -A7 : PRO -A8 : ASN -A9 : HIS -A10 : THR -A11 : ILE -A12 : TYR -A13 : ILE -A14 : ASN -A15 : ASN -A16 : LEU -A17 : ASN -A18 : GLU -A19 : LYS -A20 : ILE -A21 : LYS -A22 : LYS -A23 : ASP -A24 : GLU -A25 : LEU -A26 : LYS -A27 : LYS -A28 : SER -A29 : LEU -A30 : HIS -A31 : ALA -A32 : ILE -A33 : PHE -A34 : SER -A35 : ARG -A36 : PHE -A37 : GLY -A38 : GLN -A39 : ILE -A40 : LEU -A41 : ASP -A42 : ILE -A43 : LEU -A44 : VAL -A45 : SER -A46 : ARG -A47 : SER -A48 : LEU -A49 : LYS -A50 : MET -A51 : ARG -A52 : GLY -A53 : GLN -A54 : ALA -A55 : PHE -A56 : VAL -A57 : ILE -A58 : PHE -A59 : LYS -A60 : GLU -A61 : VAL -A62 : SER -A63 : SER -A64 : ALA -A65 : THR -A66 : ASN -A67 : ALA -A68 : LEU -A69 : ARG -A70 : SER -A71 : MET -A72 : GLN -A73 : GLY -A74 : PHE -A75 : PRO -A76 : PHE -A77 : TYR -A78 : ASP -A79 : LYS -A80 : PRO -A81 : MET -A82 : ARG -A83 : ILE -A84 : GLN -A85 : TYR -A86 : ALA -A87 : LYS -A88 : THR -A89 : ASP -A90 : SER -A91 : ASP -A92 : ILE -A93 : ILE -A94 : ALA -A95 : LYS -A96 : MET -A97 : LYS -A98 : GLY -A99 : THR -A100 : PHE -A101 : VAL -Adjacent stackings ---------------------------------------------- -B20-B21 : adjacent_5p upward -B21-B22 : adjacent_5p upward -B23-B24 : adjacent_5p upward -B26-B27 : adjacent_5p upward -B35-B36 : adjacent_5p upward -B37-B38 : adjacent_5p upward -B39-B40 : adjacent_5p upward -B44-B45 : adjacent_5p upward -B46-B47 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -B22-B48 : outward -Number of stackings = 10 -Number of adjacent stackings = 9 -Number of non adjacent stackings = 1 -Base-pairs ------------------------------------------------------ -B22-B47 : A-U Ww/Ww pairing antiparallel cis one_hbond -B23-B46 : G-C Ws/Ws pairing antiparallel cis one_hbond -B26-B37 : U-A Ww/Ww pairing antiparallel cis XX -B27-B36 : C-G Ww/Ww pairing antiparallel cis one_hbond -B29-B34 : U-G Bs/Ww pairing parallel trans one_hbond -B30-B34 : U-G O2'/Hh pairing -Residue conformations ------------------------------------------- -B19 : G C4p_exo anti -B20 : G C3p_endo anti -B21 : C C3p_endo anti -B22 : A C3p_endo anti -B23 : G C3p_endo anti -B24 : A C4p_exo anti -B25 : G C4p_exo anti -B26 : U C3p_endo anti -B27 : C C4p_exo anti -B28 : C C3p_endo anti -B29 : U C3p_endo anti -B30 : U C3p_exo anti -B33 : C C3p_exo anti -B34 : G C4p_exo syn -B35 : G C3p_endo anti -B36 : G C3p_endo anti -B37 : A C3p_endo anti -B38 : C C3p_endo anti -B39 : A C2p_exo anti -B40 : U C3p_endo anti -B41 : U C2p_endo anti -B42 : G C3p_endo anti -B43 : C C2p_endo anti -B44 : A C2p_exo anti -B45 : C C3p_endo anti -B46 : C C3p_endo anti -B47 : U C3p_endo anti -B48 : G C3p_endo anti -B49 : C C3p_endo anti -B50 : C C3p_endo anti -A1 : ALA -A2 : VAL -A3 : PRO -A4 : GLU -A5 : THR -A6 : ARG -A7 : PRO -A8 : ASN -A9 : HIS -A10 : THR -A11 : ILE -A12 : TYR -A13 : ILE -A14 : ASN -A15 : ASN -A16 : LEU -A17 : ASN -A18 : GLU -A19 : LYS -A20 : ILE -A21 : LYS -A22 : LYS -A23 : ASP -A24 : GLU -A25 : LEU -A26 : LYS -A27 : LYS -A28 : SER -A29 : LEU -A30 : HIS -A31 : ALA -A32 : ILE -A33 : PHE -A34 : SER -A35 : ARG -A36 : PHE -A37 : GLY -A38 : GLN -A39 : ILE -A40 : LEU -A41 : ASP -A42 : ILE -A43 : LEU -A44 : VAL -A45 : SER -A46 : ARG -A47 : SER -A48 : LEU -A49 : LYS -A50 : MET -A51 : ARG -A52 : GLY -A53 : GLN -A54 : ALA -A55 : PHE -A56 : VAL -A57 : ILE -A58 : PHE -A59 : LYS -A60 : GLU -A61 : VAL -A62 : SER -A63 : SER -A64 : ALA -A65 : THR -A66 : ASN -A67 : ALA -A68 : LEU -A69 : ARG -A70 : SER -A71 : MET -A72 : GLN -A73 : GLY -A74 : PHE -A75 : PRO -A76 : PHE -A77 : TYR -A78 : ASP -A79 : LYS -A80 : PRO -A81 : MET -A82 : ARG -A83 : ILE -A84 : GLN -A85 : TYR -A86 : ALA -A87 : LYS -A88 : THR -A89 : ASP -A90 : SER -A91 : ASP -A92 : ILE -A93 : ILE -A94 : ALA -A95 : LYS -A96 : MET -A97 : LYS -A98 : GLY -A99 : THR -A100 : PHE -A101 : VAL -Adjacent stackings ---------------------------------------------- -B20-B21 : adjacent_5p upward -B22-B23 : adjacent_5p upward -B23-B24 : adjacent_5p upward -B26-B27 : adjacent_5p upward -B28-B29 : adjacent_5p upward -B36-B37 : adjacent_5p upward -B37-B38 : adjacent_5p upward -B39-B40 : adjacent_5p upward -B44-B45 : adjacent_5p upward -B47-B48 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 10 -Number of adjacent stackings = 10 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -B19-B50 : G-C Ww/Ww pairing antiparallel cis one_hbond -B20-B49 : G-C Ww/Ws pairing antiparallel cis one_hbond -B21-B48 : C-G Ww/Ww pairing antiparallel cis XIX -B22-B47 : A-U Ww/Ww pairing antiparallel cis XX -B23-B46 : G-C Ww/Ww pairing antiparallel cis 130 -B25-B38 : G-C Wh/Wh pairing antiparallel cis one_hbond -B28-B35 : C-G Ws/Ws pairing antiparallel cis one_hbond -B30-B34 : U-G O2'/Hh pairing -B40-B42 : U-G O2'/Bs pairing -Residue conformations ------------------------------------------- -B19 : G C3p_endo anti -B20 : G C3p_endo anti -B21 : C C3p_endo anti -B22 : A C3p_endo anti -B23 : G C3p_endo anti -B24 : A C3p_endo anti -B25 : G O4p_endo anti -B26 : U C3p_endo anti -B27 : C C4p_exo anti -B28 : C C3p_endo anti -B29 : U C3p_endo anti -B30 : U C3p_exo anti -B33 : C C3p_exo anti -B34 : G C4p_exo syn -B35 : G C3p_endo anti -B36 : G C4p_exo anti -B37 : A C3p_endo anti -B38 : C C3p_endo anti -B39 : A C2p_exo anti -B40 : U C3p_endo anti -B41 : U C3p_exo anti -B42 : G C1p_endo syn -B43 : C C1p_exo syn -B44 : A C3p_endo anti -B45 : C C3p_endo anti -B46 : C C3p_endo anti -B47 : U C3p_endo anti -B48 : G C3p_endo anti -B49 : C C3p_endo anti -B50 : C C3p_endo anti -A1 : ALA -A2 : VAL -A3 : PRO -A4 : GLU -A5 : THR -A6 : ARG -A7 : PRO -A8 : ASN -A9 : HIS -A10 : THR -A11 : ILE -A12 : TYR -A13 : ILE -A14 : ASN -A15 : ASN -A16 : LEU -A17 : ASN -A18 : GLU -A19 : LYS -A20 : ILE -A21 : LYS -A22 : LYS -A23 : ASP -A24 : GLU -A25 : LEU -A26 : LYS -A27 : LYS -A28 : SER -A29 : LEU -A30 : HIS -A31 : ALA -A32 : ILE -A33 : PHE -A34 : SER -A35 : ARG -A36 : PHE -A37 : GLY -A38 : GLN -A39 : ILE -A40 : LEU -A41 : ASP -A42 : ILE -A43 : LEU -A44 : VAL -A45 : SER -A46 : ARG -A47 : SER -A48 : LEU -A49 : LYS -A50 : MET -A51 : ARG -A52 : GLY -A53 : GLN -A54 : ALA -A55 : PHE -A56 : VAL -A57 : ILE -A58 : PHE -A59 : LYS -A60 : GLU -A61 : VAL -A62 : SER -A63 : SER -A64 : ALA -A65 : THR -A66 : ASN -A67 : ALA -A68 : LEU -A69 : ARG -A70 : SER -A71 : MET -A72 : GLN -A73 : GLY -A74 : PHE -A75 : PRO -A76 : PHE -A77 : TYR -A78 : ASP -A79 : LYS -A80 : PRO -A81 : MET -A82 : ARG -A83 : ILE -A84 : GLN -A85 : TYR -A86 : ALA -A87 : LYS -A88 : THR -A89 : ASP -A90 : SER -A91 : ASP -A92 : ILE -A93 : ILE -A94 : ALA -A95 : LYS -A96 : MET -A97 : LYS -A98 : GLY -A99 : THR -A100 : PHE -A101 : VAL -Adjacent stackings ---------------------------------------------- -B20-B21 : adjacent_5p upward -B22-B23 : adjacent_5p upward -B23-B24 : adjacent_5p upward -B26-B27 : adjacent_5p upward -B28-B29 : adjacent_5p upward -B35-B36 : adjacent_5p upward -B36-B37 : adjacent_5p upward -B37-B38 : adjacent_5p upward -B39-B40 : adjacent_5p upward -B41-B42 : adjacent_5p outward -B44-B45 : adjacent_5p upward -B47-B48 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 12 -Number of adjacent stackings = 12 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -B19-B50 : G-C Ww/Ww pairing antiparallel cis one_hbond -B21-B48 : C-G Ww/Ww pairing antiparallel cis XIX -B22-B47 : A-U Ww/Ww pairing antiparallel cis one_hbond -B23-B46 : G-C Ww/Ww pairing antiparallel cis XIX -B26-B37 : U-A Ww/Ww pairing antiparallel cis one_hbond -B28-B35 : C-G Ww/Ww pairing antiparallel cis one_hbond -B30-B34 : U-G O2'/Hh pairing -Residue conformations ------------------------------------------- -B19 : G C3p_endo anti -B20 : G C3p_endo anti -B21 : C C3p_endo anti -B22 : A C3p_endo anti -B23 : G C3p_endo anti -B24 : A C4p_exo anti -B25 : G O4p_endo anti -B26 : U C3p_endo anti -B27 : C C4p_exo anti -B28 : C C3p_endo anti -B29 : U C3p_endo anti -B30 : U C3p_exo anti -B33 : C C3p_exo anti -B34 : G C4p_exo syn -B35 : G C3p_endo anti -B36 : G C4p_exo anti -B37 : A C3p_endo anti -B38 : C C3p_endo anti -B39 : A C3p_endo anti -B40 : U C3p_endo anti -B41 : U C2p_endo anti -B42 : G C3p_endo anti -B43 : C C2p_endo syn -B44 : A C3p_endo anti -B45 : C C3p_endo anti -B46 : C C3p_endo anti -B47 : U C3p_endo anti -B48 : G C3p_endo anti -B49 : C C3p_endo anti -B50 : C C3p_endo anti -A1 : ALA -A2 : VAL -A3 : PRO -A4 : GLU -A5 : THR -A6 : ARG -A7 : PRO -A8 : ASN -A9 : HIS -A10 : THR -A11 : ILE -A12 : TYR -A13 : ILE -A14 : ASN -A15 : ASN -A16 : LEU -A17 : ASN -A18 : GLU -A19 : LYS -A20 : ILE -A21 : LYS -A22 : LYS -A23 : ASP -A24 : GLU -A25 : LEU -A26 : LYS -A27 : LYS -A28 : SER -A29 : LEU -A30 : HIS -A31 : ALA -A32 : ILE -A33 : PHE -A34 : SER -A35 : ARG -A36 : PHE -A37 : GLY -A38 : GLN -A39 : ILE -A40 : LEU -A41 : ASP -A42 : ILE -A43 : LEU -A44 : VAL -A45 : SER -A46 : ARG -A47 : SER -A48 : LEU -A49 : LYS -A50 : MET -A51 : ARG -A52 : GLY -A53 : GLN -A54 : ALA -A55 : PHE -A56 : VAL -A57 : ILE -A58 : PHE -A59 : LYS -A60 : GLU -A61 : VAL -A62 : SER -A63 : SER -A64 : ALA -A65 : THR -A66 : ASN -A67 : ALA -A68 : LEU -A69 : ARG -A70 : SER -A71 : MET -A72 : GLN -A73 : GLY -A74 : PHE -A75 : PRO -A76 : PHE -A77 : TYR -A78 : ASP -A79 : LYS -A80 : PRO -A81 : MET -A82 : ARG -A83 : ILE -A84 : GLN -A85 : TYR -A86 : ALA -A87 : LYS -A88 : THR -A89 : ASP -A90 : SER -A91 : ASP -A92 : ILE -A93 : ILE -A94 : ALA -A95 : LYS -A96 : MET -A97 : LYS -A98 : GLY -A99 : THR -A100 : PHE -A101 : VAL -Adjacent stackings ---------------------------------------------- -B20-B21 : adjacent_5p upward -B22-B23 : adjacent_5p upward -B23-B24 : adjacent_5p upward -B26-B27 : adjacent_5p upward -B28-B29 : adjacent_5p upward -B35-B36 : adjacent_5p upward -B37-B38 : adjacent_5p upward -B39-B40 : adjacent_5p upward -B41-B42 : adjacent_5p outward -B44-B45 : adjacent_5p upward -B47-B48 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 11 -Number of adjacent stackings = 11 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -B19-B50 : G-C Ww/Ww pairing antiparallel cis -B21-B48 : C-G Ww/Ww pairing antiparallel cis XIX -B22-B47 : A-U Ww/Ww pairing antiparallel cis XX -B23-B46 : G-C Ww/Ww pairing antiparallel cis XIX -B26-B37 : U-A Ww/Ww pairing antiparallel cis XX -B30-B34 : U-G O2'/Hh pairing -B40-B42 : U-G Ws/Ws pairing antiparallel cis one_hbond -Residue conformations ------------------------------------------- -B19 : G C3p_endo anti -B20 : G C3p_endo anti -B21 : C C4p_exo anti -B22 : A C3p_endo anti -B23 : G C3p_endo anti -B24 : A C3p_endo anti -B25 : G O4p_endo anti -B26 : U C3p_endo anti -B27 : C C3p_endo anti -B28 : C C3p_endo anti -B29 : U C4p_exo anti -B30 : U C3p_exo anti -B33 : C C3p_exo anti -B34 : G C4p_exo syn -B35 : G C3p_endo anti -B36 : G C3p_endo anti -B37 : A C4p_exo anti -B38 : C C3p_endo anti -B39 : A C3p_endo anti -B40 : U C3p_endo anti -B41 : U C3p_exo anti -B42 : G C3p_endo anti -B43 : C C1p_exo anti -B44 : A C2p_exo anti -B45 : C C3p_endo anti -B46 : C C3p_endo anti -B47 : U C3p_endo anti -B48 : G C3p_endo anti -B49 : C C3p_endo anti -B50 : C C3p_endo anti -A1 : ALA -A2 : VAL -A3 : PRO -A4 : GLU -A5 : THR -A6 : ARG -A7 : PRO -A8 : ASN -A9 : HIS -A10 : THR -A11 : ILE -A12 : TYR -A13 : ILE -A14 : ASN -A15 : ASN -A16 : LEU -A17 : ASN -A18 : GLU -A19 : LYS -A20 : ILE -A21 : LYS -A22 : LYS -A23 : ASP -A24 : GLU -A25 : LEU -A26 : LYS -A27 : LYS -A28 : SER -A29 : LEU -A30 : HIS -A31 : ALA -A32 : ILE -A33 : PHE -A34 : SER -A35 : ARG -A36 : PHE -A37 : GLY -A38 : GLN -A39 : ILE -A40 : LEU -A41 : ASP -A42 : ILE -A43 : LEU -A44 : VAL -A45 : SER -A46 : ARG -A47 : SER -A48 : LEU -A49 : LYS -A50 : MET -A51 : ARG -A52 : GLY -A53 : GLN -A54 : ALA -A55 : PHE -A56 : VAL -A57 : ILE -A58 : PHE -A59 : LYS -A60 : GLU -A61 : VAL -A62 : SER -A63 : SER -A64 : ALA -A65 : THR -A66 : ASN -A67 : ALA -A68 : LEU -A69 : ARG -A70 : SER -A71 : MET -A72 : GLN -A73 : GLY -A74 : PHE -A75 : PRO -A76 : PHE -A77 : TYR -A78 : ASP -A79 : LYS -A80 : PRO -A81 : MET -A82 : ARG -A83 : ILE -A84 : GLN -A85 : TYR -A86 : ALA -A87 : LYS -A88 : THR -A89 : ASP -A90 : SER -A91 : ASP -A92 : ILE -A93 : ILE -A94 : ALA -A95 : LYS -A96 : MET -A97 : LYS -A98 : GLY -A99 : THR -A100 : PHE -A101 : VAL -Adjacent stackings ---------------------------------------------- -B20-B21 : adjacent_5p upward -B21-B22 : adjacent_5p upward -B22-B23 : adjacent_5p upward -B23-B24 : adjacent_5p upward -B26-B27 : adjacent_5p upward -B35-B36 : adjacent_5p upward -B36-B37 : adjacent_5p upward -B38-B39 : adjacent_5p upward -B39-B40 : adjacent_5p upward -B41-B42 : adjacent_5p outward pairing -B44-B45 : adjacent_5p upward -B48-B49 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 12 -Number of adjacent stackings = 12 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -B20-B49 : G-C Ww/Ww pairing antiparallel cis one_hbond -B21-B48 : C-G Ww/Ww pairing antiparallel cis XIX -B22-B47 : A-U Ww/Ww pairing antiparallel cis XX -B26-B37 : U-A Ww/Ww pairing antiparallel cis one_hbond -B27-B36 : C-G Ww/Ww pairing antiparallel cis -B30-B33 : U-C O2P/Bh adjacent_5p pairing -B41-B42 : U-G O2P/Ss adjacent_5p outward pairing -Residue conformations ------------------------------------------- -B19 : G C3p_endo anti -B20 : G C3p_endo anti -B21 : C C3p_endo anti -B22 : A C3p_endo anti -B23 : G C3p_endo anti -B24 : A C3p_endo anti -B25 : G O4p_endo anti -B26 : U C3p_endo anti -B27 : C C3p_endo anti -B28 : C C3p_endo anti -B29 : U C4p_exo anti -B30 : U C3p_exo anti -B33 : C C3p_exo anti -B34 : G C4p_exo syn -B35 : G C3p_endo anti -B36 : G C3p_endo anti -B37 : A C3p_endo anti -B38 : C C3p_endo anti -B39 : A C3p_endo anti -B40 : U C3p_endo anti -B41 : U C2p_endo anti -B42 : G C3p_endo anti -B43 : C C2p_endo anti -B44 : A C2p_exo anti -B45 : C C3p_endo anti -B46 : C C3p_endo anti -B47 : U C3p_endo anti -B48 : G C3p_endo anti -B49 : C C3p_endo anti -B50 : C C3p_endo anti -A1 : ALA -A2 : VAL -A3 : PRO -A4 : GLU -A5 : THR -A6 : ARG -A7 : PRO -A8 : ASN -A9 : HIS -A10 : THR -A11 : ILE -A12 : TYR -A13 : ILE -A14 : ASN -A15 : ASN -A16 : LEU -A17 : ASN -A18 : GLU -A19 : LYS -A20 : ILE -A21 : LYS -A22 : LYS -A23 : ASP -A24 : GLU -A25 : LEU -A26 : LYS -A27 : LYS -A28 : SER -A29 : LEU -A30 : HIS -A31 : ALA -A32 : ILE -A33 : PHE -A34 : SER -A35 : ARG -A36 : PHE -A37 : GLY -A38 : GLN -A39 : ILE -A40 : LEU -A41 : ASP -A42 : ILE -A43 : LEU -A44 : VAL -A45 : SER -A46 : ARG -A47 : SER -A48 : LEU -A49 : LYS -A50 : MET -A51 : ARG -A52 : GLY -A53 : GLN -A54 : ALA -A55 : PHE -A56 : VAL -A57 : ILE -A58 : PHE -A59 : LYS -A60 : GLU -A61 : VAL -A62 : SER -A63 : SER -A64 : ALA -A65 : THR -A66 : ASN -A67 : ALA -A68 : LEU -A69 : ARG -A70 : SER -A71 : MET -A72 : GLN -A73 : GLY -A74 : PHE -A75 : PRO -A76 : PHE -A77 : TYR -A78 : ASP -A79 : LYS -A80 : PRO -A81 : MET -A82 : ARG -A83 : ILE -A84 : GLN -A85 : TYR -A86 : ALA -A87 : LYS -A88 : THR -A89 : ASP -A90 : SER -A91 : ASP -A92 : ILE -A93 : ILE -A94 : ALA -A95 : LYS -A96 : MET -A97 : LYS -A98 : GLY -A99 : THR -A100 : PHE -A101 : VAL -Adjacent stackings ---------------------------------------------- -B20-B21 : adjacent_5p upward -B21-B22 : adjacent_5p upward -B22-B23 : adjacent_5p upward -B23-B24 : adjacent_5p upward -B25-B26 : adjacent_5p upward -B26-B27 : adjacent_5p upward -B35-B36 : adjacent_5p upward -B36-B37 : adjacent_5p upward -B37-B38 : adjacent_5p upward -B39-B40 : adjacent_5p upward -B44-B45 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 11 -Number of adjacent stackings = 11 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -B21-B48 : C-G Ww/Ww pairing antiparallel cis XIX -B22-B47 : A-U Ww/Ww pairing antiparallel cis XX -B23-B46 : G-C Ww/Ww pairing antiparallel cis XIX -B26-B37 : U-A Ww/Ww pairing antiparallel cis XX -B29-B35 : U-G Hw/Sw pairing parallel trans one_hbond 89 -B30-B33 : U-C O2P/Bh adjacent_5p pairing -Residue conformations ------------------------------------------- -B19 : G C3p_endo anti -B20 : G C3p_endo anti -B21 : C C3p_endo anti -B22 : A C3p_endo anti -B23 : G C3p_endo anti -B24 : A C3p_endo anti -B25 : G O4p_endo anti -B26 : U C3p_endo anti -B27 : C C4p_exo anti -B28 : C C3p_endo anti -B29 : U C3p_endo anti -B30 : U C3p_exo anti -B33 : C C3p_exo anti -B34 : G C4p_exo syn -B35 : G C3p_endo anti -B36 : G C4p_exo anti -B37 : A C3p_endo anti -B38 : C C3p_endo anti -B39 : A C2p_exo anti -B40 : U C3p_endo anti -B41 : U C2p_endo anti -B42 : G C3p_endo anti -B43 : C C2p_endo anti -B44 : A C3p_endo anti -B45 : C C3p_endo anti -B46 : C C3p_endo anti -B47 : U C3p_endo anti -B48 : G C3p_endo anti -B49 : C C3p_endo anti -B50 : C C3p_endo anti -A1 : ALA -A2 : VAL -A3 : PRO -A4 : GLU -A5 : THR -A6 : ARG -A7 : PRO -A8 : ASN -A9 : HIS -A10 : THR -A11 : ILE -A12 : TYR -A13 : ILE -A14 : ASN -A15 : ASN -A16 : LEU -A17 : ASN -A18 : GLU -A19 : LYS -A20 : ILE -A21 : LYS -A22 : LYS -A23 : ASP -A24 : GLU -A25 : LEU -A26 : LYS -A27 : LYS -A28 : SER -A29 : LEU -A30 : HIS -A31 : ALA -A32 : ILE -A33 : PHE -A34 : SER -A35 : ARG -A36 : PHE -A37 : GLY -A38 : GLN -A39 : ILE -A40 : LEU -A41 : ASP -A42 : ILE -A43 : LEU -A44 : VAL -A45 : SER -A46 : ARG -A47 : SER -A48 : LEU -A49 : LYS -A50 : MET -A51 : ARG -A52 : GLY -A53 : GLN -A54 : ALA -A55 : PHE -A56 : VAL -A57 : ILE -A58 : PHE -A59 : LYS -A60 : GLU -A61 : VAL -A62 : SER -A63 : SER -A64 : ALA -A65 : THR -A66 : ASN -A67 : ALA -A68 : LEU -A69 : ARG -A70 : SER -A71 : MET -A72 : GLN -A73 : GLY -A74 : PHE -A75 : PRO -A76 : PHE -A77 : TYR -A78 : ASP -A79 : LYS -A80 : PRO -A81 : MET -A82 : ARG -A83 : ILE -A84 : GLN -A85 : TYR -A86 : ALA -A87 : LYS -A88 : THR -A89 : ASP -A90 : SER -A91 : ASP -A92 : ILE -A93 : ILE -A94 : ALA -A95 : LYS -A96 : MET -A97 : LYS -A98 : GLY -A99 : THR -A100 : PHE -A101 : VAL -Adjacent stackings ---------------------------------------------- -B20-B21 : adjacent_5p upward -B22-B23 : adjacent_5p upward -B23-B24 : adjacent_5p upward -B26-B27 : adjacent_5p upward -B34-B35 : adjacent_5p outward -B35-B36 : adjacent_5p upward -B37-B38 : adjacent_5p upward -B39-B40 : adjacent_5p upward -B44-B45 : adjacent_5p upward -B47-B48 : adjacent_5p upward -B49-B50 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -B25-B39 : outward -Number of stackings = 12 -Number of adjacent stackings = 11 -Number of non adjacent stackings = 1 -Base-pairs ------------------------------------------------------ -B19-B50 : G-C Ww/Ww pairing antiparallel cis one_hbond -B21-B48 : C-G Ww/Ww pairing antiparallel cis XIX -B22-B47 : A-U Ww/Ww pairing antiparallel cis XX -B23-B46 : G-C Ww/Ww pairing antiparallel cis one_hbond -B26-B37 : U-A Ww/Ww pairing antiparallel cis XX -B27-B36 : C-G Ws/Ws pairing antiparallel cis one_hbond -B28-B35 : C-G Ws/Ww pairing antiparallel cis one_hbond -B30-B34 : U-G O2'/Hh pairing -B40-B42 : U-G Bs/Bs O2'/Bs pairing antiparallel cis one_hbond -Residue conformations ------------------------------------------- -B19 : G C3p_endo anti -B20 : G C3p_endo anti -B21 : C C3p_endo anti -B22 : A C3p_endo anti -B23 : G C3p_endo anti -B24 : A C3p_endo anti -B25 : G O4p_endo anti -B26 : U C3p_endo anti -B27 : C C4p_exo anti -B28 : C C3p_endo anti -B29 : U C3p_endo anti -B30 : U C3p_exo anti -B33 : C C3p_exo anti -B34 : G C3p_endo syn -B35 : G C3p_endo anti -B36 : G C4p_exo anti -B37 : A C3p_endo anti -B38 : C C3p_endo anti -B39 : A C3p_endo anti -B40 : U C3p_endo anti -B41 : U C2p_endo anti -B42 : G C3p_endo anti -B43 : C C4p_endo syn -B44 : A C2p_exo anti -B45 : C C3p_endo anti -B46 : C C3p_endo anti -B47 : U C3p_endo anti -B48 : G C3p_endo anti -B49 : C C3p_endo anti -B50 : C C3p_endo anti -A1 : ALA -A2 : VAL -A3 : PRO -A4 : GLU -A5 : THR -A6 : ARG -A7 : PRO -A8 : ASN -A9 : HIS -A10 : THR -A11 : ILE -A12 : TYR -A13 : ILE -A14 : ASN -A15 : ASN -A16 : LEU -A17 : ASN -A18 : GLU -A19 : LYS -A20 : ILE -A21 : LYS -A22 : LYS -A23 : ASP -A24 : GLU -A25 : LEU -A26 : LYS -A27 : LYS -A28 : SER -A29 : LEU -A30 : HIS -A31 : ALA -A32 : ILE -A33 : PHE -A34 : SER -A35 : ARG -A36 : PHE -A37 : GLY -A38 : GLN -A39 : ILE -A40 : LEU -A41 : ASP -A42 : ILE -A43 : LEU -A44 : VAL -A45 : SER -A46 : ARG -A47 : SER -A48 : LEU -A49 : LYS -A50 : MET -A51 : ARG -A52 : GLY -A53 : GLN -A54 : ALA -A55 : PHE -A56 : VAL -A57 : ILE -A58 : PHE -A59 : LYS -A60 : GLU -A61 : VAL -A62 : SER -A63 : SER -A64 : ALA -A65 : THR -A66 : ASN -A67 : ALA -A68 : LEU -A69 : ARG -A70 : SER -A71 : MET -A72 : GLN -A73 : GLY -A74 : PHE -A75 : PRO -A76 : PHE -A77 : TYR -A78 : ASP -A79 : LYS -A80 : PRO -A81 : MET -A82 : ARG -A83 : ILE -A84 : GLN -A85 : TYR -A86 : ALA -A87 : LYS -A88 : THR -A89 : ASP -A90 : SER -A91 : ASP -A92 : ILE -A93 : ILE -A94 : ALA -A95 : LYS -A96 : MET -A97 : LYS -A98 : GLY -A99 : THR -A100 : PHE -A101 : VAL -Adjacent stackings ---------------------------------------------- -B19-B20 : adjacent_5p upward -B20-B21 : adjacent_5p upward -B22-B23 : adjacent_5p upward -B23-B24 : adjacent_5p upward -B26-B27 : adjacent_5p upward -B28-B29 : adjacent_5p upward -B35-B36 : adjacent_5p upward -B37-B38 : adjacent_5p upward -B39-B40 : adjacent_5p upward -B44-B45 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 10 -Number of adjacent stackings = 10 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -B21-B48 : C-G Ww/Ww pairing antiparallel cis XIX -B22-B47 : A-U Ww/Ww pairing antiparallel cis XX -B24-B46 : A-C Ss/Wh pairing antiparallel cis one_hbond 74 -B26-B37 : U-A Ww/Ww pairing antiparallel cis XX -B27-B36 : C-G Ws/Ww pairing antiparallel cis one_hbond -B28-B35 : C-G Ww/Ww pairing antiparallel cis -B30-B34 : U-G O2'/Hh pairing -B40-B42 : U-G Bs/Bs O2'/Bs pairing antiparallel cis one_hbond -Residue conformations ------------------------------------------- -B19 : G C4p_endo anti -B20 : G C3p_endo anti -B21 : C C3p_endo anti -B22 : A C3p_endo anti -B23 : G C3p_endo anti -B24 : A C3p_endo anti -B25 : G C4p_exo anti -B26 : U C3p_endo anti -B27 : C C4p_exo anti -B28 : C C3p_endo anti -B29 : U C3p_endo anti -B30 : U C3p_exo anti -B33 : C C3p_exo anti -B34 : G C4p_exo syn -B35 : G C3p_endo anti -B36 : G C4p_exo anti -B37 : A C3p_endo anti -B38 : C C3p_endo anti -B39 : A C3p_endo anti -B40 : U C3p_endo anti -B41 : U C2p_endo anti -B42 : G C3p_endo anti -B43 : C C2p_endo anti -B44 : A C3p_endo anti -B45 : C C3p_endo anti -B46 : C C3p_endo anti -B47 : U C3p_endo anti -B48 : G C3p_endo anti -B49 : C C3p_endo anti -B50 : C C3p_endo anti -A1 : ALA -A2 : VAL -A3 : PRO -A4 : GLU -A5 : THR -A6 : ARG -A7 : PRO -A8 : ASN -A9 : HIS -A10 : THR -A11 : ILE -A12 : TYR -A13 : ILE -A14 : ASN -A15 : ASN -A16 : LEU -A17 : ASN -A18 : GLU -A19 : LYS -A20 : ILE -A21 : LYS -A22 : LYS -A23 : ASP -A24 : GLU -A25 : LEU -A26 : LYS -A27 : LYS -A28 : SER -A29 : LEU -A30 : HIS -A31 : ALA -A32 : ILE -A33 : PHE -A34 : SER -A35 : ARG -A36 : PHE -A37 : GLY -A38 : GLN -A39 : ILE -A40 : LEU -A41 : ASP -A42 : ILE -A43 : LEU -A44 : VAL -A45 : SER -A46 : ARG -A47 : SER -A48 : LEU -A49 : LYS -A50 : MET -A51 : ARG -A52 : GLY -A53 : GLN -A54 : ALA -A55 : PHE -A56 : VAL -A57 : ILE -A58 : PHE -A59 : LYS -A60 : GLU -A61 : VAL -A62 : SER -A63 : SER -A64 : ALA -A65 : THR -A66 : ASN -A67 : ALA -A68 : LEU -A69 : ARG -A70 : SER -A71 : MET -A72 : GLN -A73 : GLY -A74 : PHE -A75 : PRO -A76 : PHE -A77 : TYR -A78 : ASP -A79 : LYS -A80 : PRO -A81 : MET -A82 : ARG -A83 : ILE -A84 : GLN -A85 : TYR -A86 : ALA -A87 : LYS -A88 : THR -A89 : ASP -A90 : SER -A91 : ASP -A92 : ILE -A93 : ILE -A94 : ALA -A95 : LYS -A96 : MET -A97 : LYS -A98 : GLY -A99 : THR -A100 : PHE -A101 : VAL -Adjacent stackings ---------------------------------------------- -B21-B22 : adjacent_5p upward -B22-B23 : adjacent_5p upward -B23-B24 : adjacent_5p upward -B26-B27 : adjacent_5p upward -B28-B29 : adjacent_5p upward -B34-B35 : adjacent_5p outward -B35-B36 : adjacent_5p upward -B39-B40 : adjacent_5p upward -B44-B45 : adjacent_5p upward -B48-B49 : adjacent_5p upward -B49-B50 : adjacent_5p inward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 11 -Number of adjacent stackings = 11 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -B19-B20 : G-G O2'/C8 adjacent_5p pairing -B20-B49 : G-C Ws/Ww pairing antiparallel cis one_hbond -B21-B48 : C-G Ww/Ww pairing antiparallel cis XIX -B22-B47 : A-U Wh/Wh pairing antiparallel cis one_hbond -B23-B46 : G-C Wh/Wh pairing antiparallel cis one_hbond -B26-B37 : U-A Ww/Ww pairing antiparallel cis XX -B28-B35 : C-G Ww/Wh pairing antiparallel cis one_hbond -B40-B42 : U-G Ss/Ws O2'/Bs pairing antiparallel cis one_hbond 84 -Residue conformations ------------------------------------------- -B19 : G C3p_endo anti -B20 : G C3p_endo anti -B21 : C C3p_endo anti -B22 : A C3p_endo anti -B23 : G C3p_endo anti -B24 : A C3p_endo anti -B25 : G O4p_endo anti -B26 : U C4p_exo anti -B27 : C C3p_endo anti -B28 : C C3p_endo anti -B29 : U C3p_endo anti -B30 : U C3p_exo anti -B33 : C C3p_exo anti -B34 : G C3p_endo syn -B35 : G C3p_endo anti -B36 : G C4p_exo anti -B37 : A C3p_endo anti -B38 : C C3p_endo anti -B39 : A C2p_exo anti -B40 : U C3p_endo anti -B41 : U C3p_exo anti -B42 : G C3p_endo anti -B43 : C C2p_endo anti -B44 : A C3p_endo anti -B45 : C C3p_endo anti -B46 : C C3p_endo anti -B47 : U C3p_endo anti -B48 : G C3p_endo anti -B49 : C C3p_endo anti -B50 : C C3p_endo anti -A1 : ALA -A2 : VAL -A3 : PRO -A4 : GLU -A5 : THR -A6 : ARG -A7 : PRO -A8 : ASN -A9 : HIS -A10 : THR -A11 : ILE -A12 : TYR -A13 : ILE -A14 : ASN -A15 : ASN -A16 : LEU -A17 : ASN -A18 : GLU -A19 : LYS -A20 : ILE -A21 : LYS -A22 : LYS -A23 : ASP -A24 : GLU -A25 : LEU -A26 : LYS -A27 : LYS -A28 : SER -A29 : LEU -A30 : HIS -A31 : ALA -A32 : ILE -A33 : PHE -A34 : SER -A35 : ARG -A36 : PHE -A37 : GLY -A38 : GLN -A39 : ILE -A40 : LEU -A41 : ASP -A42 : ILE -A43 : LEU -A44 : VAL -A45 : SER -A46 : ARG -A47 : SER -A48 : LEU -A49 : LYS -A50 : MET -A51 : ARG -A52 : GLY -A53 : GLN -A54 : ALA -A55 : PHE -A56 : VAL -A57 : ILE -A58 : PHE -A59 : LYS -A60 : GLU -A61 : VAL -A62 : SER -A63 : SER -A64 : ALA -A65 : THR -A66 : ASN -A67 : ALA -A68 : LEU -A69 : ARG -A70 : SER -A71 : MET -A72 : GLN -A73 : GLY -A74 : PHE -A75 : PRO -A76 : PHE -A77 : TYR -A78 : ASP -A79 : LYS -A80 : PRO -A81 : MET -A82 : ARG -A83 : ILE -A84 : GLN -A85 : TYR -A86 : ALA -A87 : LYS -A88 : THR -A89 : ASP -A90 : SER -A91 : ASP -A92 : ILE -A93 : ILE -A94 : ALA -A95 : LYS -A96 : MET -A97 : LYS -A98 : GLY -A99 : THR -A100 : PHE -A101 : VAL -Adjacent stackings ---------------------------------------------- -B20-B21 : adjacent_5p upward -B22-B23 : adjacent_5p upward -B23-B24 : adjacent_5p upward -B26-B27 : adjacent_5p upward -B28-B29 : adjacent_5p upward -B34-B35 : adjacent_5p outward -B35-B36 : adjacent_5p upward -B36-B37 : adjacent_5p upward -B38-B39 : adjacent_5p upward -B39-B40 : adjacent_5p upward -B44-B45 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 11 -Number of adjacent stackings = 11 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -B19-B50 : G-C Wh/Wh pairing antiparallel cis one_hbond -B21-B48 : C-G Ww/Ww pairing antiparallel cis XIX -B22-B47 : A-U Ww/Ww pairing antiparallel cis XX -B23-B46 : G-C Ww/Ww pairing antiparallel cis one_hbond -B24-B46 : A-C Ss/Wh pairing antiparallel cis one_hbond 74 -B26-B37 : U-A Wh/Wh pairing antiparallel cis one_hbond -B28-B35 : C-G Wh/Wh pairing antiparallel cis one_hbond -B30-B34 : U-G O2'/Hh pairing -B40-B42 : U-G O2'/Bs pairing -Residue conformations ------------------------------------------- -B19 : G C4p_exo anti -B20 : G C3p_endo anti -B21 : C C3p_endo anti -B22 : A C3p_endo anti -B23 : G C3p_endo anti -B24 : A C4p_exo anti -B25 : G O4p_endo anti -B26 : U C3p_endo anti -B27 : C C3p_endo anti -B28 : C C3p_endo anti -B29 : U C3p_endo anti -B30 : U C3p_exo anti -B33 : C C3p_exo anti -B34 : G C3p_endo syn -B35 : G C3p_endo anti -B36 : G C4p_exo anti -B37 : A C3p_endo anti -B38 : C C3p_endo anti -B39 : A C3p_endo anti -B40 : U C3p_endo anti -B41 : U C3p_exo anti -B42 : G C3p_endo anti -B43 : C C2p_endo anti -B44 : A C3p_endo anti -B45 : C C4p_exo anti -B46 : C C3p_endo anti -B47 : U C3p_endo anti -B48 : G C3p_endo anti -B49 : C C3p_endo anti -B50 : C C3p_endo anti -A1 : ALA -A2 : VAL -A3 : PRO -A4 : GLU -A5 : THR -A6 : ARG -A7 : PRO -A8 : ASN -A9 : HIS -A10 : THR -A11 : ILE -A12 : TYR -A13 : ILE -A14 : ASN -A15 : ASN -A16 : LEU -A17 : ASN -A18 : GLU -A19 : LYS -A20 : ILE -A21 : LYS -A22 : LYS -A23 : ASP -A24 : GLU -A25 : LEU -A26 : LYS -A27 : LYS -A28 : SER -A29 : LEU -A30 : HIS -A31 : ALA -A32 : ILE -A33 : PHE -A34 : SER -A35 : ARG -A36 : PHE -A37 : GLY -A38 : GLN -A39 : ILE -A40 : LEU -A41 : ASP -A42 : ILE -A43 : LEU -A44 : VAL -A45 : SER -A46 : ARG -A47 : SER -A48 : LEU -A49 : LYS -A50 : MET -A51 : ARG -A52 : GLY -A53 : GLN -A54 : ALA -A55 : PHE -A56 : VAL -A57 : ILE -A58 : PHE -A59 : LYS -A60 : GLU -A61 : VAL -A62 : SER -A63 : SER -A64 : ALA -A65 : THR -A66 : ASN -A67 : ALA -A68 : LEU -A69 : ARG -A70 : SER -A71 : MET -A72 : GLN -A73 : GLY -A74 : PHE -A75 : PRO -A76 : PHE -A77 : TYR -A78 : ASP -A79 : LYS -A80 : PRO -A81 : MET -A82 : ARG -A83 : ILE -A84 : GLN -A85 : TYR -A86 : ALA -A87 : LYS -A88 : THR -A89 : ASP -A90 : SER -A91 : ASP -A92 : ILE -A93 : ILE -A94 : ALA -A95 : LYS -A96 : MET -A97 : LYS -A98 : GLY -A99 : THR -A100 : PHE -A101 : VAL -Adjacent stackings ---------------------------------------------- -B20-B21 : adjacent_5p upward -B22-B23 : adjacent_5p upward -B23-B24 : adjacent_5p upward -B28-B29 : adjacent_5p upward -B34-B35 : adjacent_5p outward -B35-B36 : adjacent_5p upward -B38-B39 : adjacent_5p upward -B39-B40 : adjacent_5p upward -B41-B42 : adjacent_5p outward -B44-B45 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 10 -Number of adjacent stackings = 10 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -B21-B48 : C-G Ww/Ww pairing antiparallel cis XIX -B22-B47 : A-U Ww/Ww pairing antiparallel cis one_hbond -B23-B46 : G-C Ww/Ww pairing antiparallel cis XIX -B26-B37 : U-A Ww/Ww pairing antiparallel cis XX -B28-B35 : C-G Ww/Ww pairing antiparallel cis one_hbond -B30-B34 : U-G O2'/Hh pairing -Residue conformations ------------------------------------------- -B19 : G C3p_endo anti -B20 : G C3p_endo anti -B21 : C C3p_endo anti -B22 : A C3p_endo anti -B23 : G C3p_endo anti -B24 : A O4p_endo anti -B25 : G C4p_exo anti -B26 : U C3p_endo anti -B27 : C C3p_endo anti -B28 : C C3p_endo anti -B29 : U C3p_endo anti -B30 : U C3p_exo anti -B33 : C C3p_exo anti -B34 : G C4p_exo syn -B35 : G C3p_endo anti -B36 : G C3p_endo anti -B37 : A C3p_endo anti -B38 : C C3p_endo anti -B39 : A C3p_endo anti -B40 : U C3p_endo anti -B41 : U C3p_exo anti -B42 : G C3p_endo anti -B43 : C C2p_endo anti -B44 : A C3p_endo anti -B45 : C C3p_endo anti -B46 : C C3p_endo anti -B47 : U C3p_endo anti -B48 : G C3p_endo anti -B49 : C C3p_endo anti -B50 : C C3p_endo anti -A1 : ALA -A2 : VAL -A3 : PRO -A4 : GLU -A5 : THR -A6 : ARG -A7 : PRO -A8 : ASN -A9 : HIS -A10 : THR -A11 : ILE -A12 : TYR -A13 : ILE -A14 : ASN -A15 : ASN -A16 : LEU -A17 : ASN -A18 : GLU -A19 : LYS -A20 : ILE -A21 : LYS -A22 : LYS -A23 : ASP -A24 : GLU -A25 : LEU -A26 : LYS -A27 : LYS -A28 : SER -A29 : LEU -A30 : HIS -A31 : ALA -A32 : ILE -A33 : PHE -A34 : SER -A35 : ARG -A36 : PHE -A37 : GLY -A38 : GLN -A39 : ILE -A40 : LEU -A41 : ASP -A42 : ILE -A43 : LEU -A44 : VAL -A45 : SER -A46 : ARG -A47 : SER -A48 : LEU -A49 : LYS -A50 : MET -A51 : ARG -A52 : GLY -A53 : GLN -A54 : ALA -A55 : PHE -A56 : VAL -A57 : ILE -A58 : PHE -A59 : LYS -A60 : GLU -A61 : VAL -A62 : SER -A63 : SER -A64 : ALA -A65 : THR -A66 : ASN -A67 : ALA -A68 : LEU -A69 : ARG -A70 : SER -A71 : MET -A72 : GLN -A73 : GLY -A74 : PHE -A75 : PRO -A76 : PHE -A77 : TYR -A78 : ASP -A79 : LYS -A80 : PRO -A81 : MET -A82 : ARG -A83 : ILE -A84 : GLN -A85 : TYR -A86 : ALA -A87 : LYS -A88 : THR -A89 : ASP -A90 : SER -A91 : ASP -A92 : ILE -A93 : ILE -A94 : ALA -A95 : LYS -A96 : MET -A97 : LYS -A98 : GLY -A99 : THR -A100 : PHE -A101 : VAL -Adjacent stackings ---------------------------------------------- -B20-B21 : adjacent_5p upward -B21-B22 : adjacent_5p upward -B22-B23 : adjacent_5p upward -B23-B24 : adjacent_5p upward -B25-B26 : adjacent_5p upward pairing -B26-B27 : adjacent_5p upward -B36-B37 : adjacent_5p upward -B38-B39 : adjacent_5p upward -B39-B40 : adjacent_5p upward -B44-B45 : adjacent_5p upward -B49-B50 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 11 -Number of adjacent stackings = 11 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -B19-B50 : G-C Ww/Ww pairing antiparallel cis -B22-B47 : A-U Ww/Ww pairing antiparallel cis one_hbond -B23-B46 : G-C Ww/Ww pairing antiparallel cis XIX -B25-B26 : G-U O2'/Hh adjacent_5p upward pairing -B26-B37 : U-A Ww/Ww pairing antiparallel cis XX -B27-B36 : C-G Ww/Ww pairing antiparallel cis -B28-B35 : C-G Ws/Ws pairing antiparallel cis one_hbond -B30-B34 : U-G O2'/Hh pairing -Residue conformations ------------------------------------------- -B19 : G C3p_endo anti -B20 : G C3p_endo anti -B21 : C C4p_exo anti -B22 : A C3p_endo anti -B23 : G C2p_exo anti -B24 : A C3p_endo anti -B25 : G C4p_exo anti -B26 : U C3p_endo anti -B27 : C C4p_exo anti -B28 : C C3p_endo anti -B29 : U C3p_endo anti -B30 : U C3p_exo anti -B33 : C C3p_exo anti -B34 : G C3p_endo syn -B35 : G C3p_endo anti -B36 : G C4p_exo anti -B37 : A C3p_endo anti -B38 : C C3p_endo anti -B39 : A C3p_endo anti -B40 : U C3p_endo anti -B41 : U C2p_endo anti -B42 : G C1p_endo anti -B43 : C C2p_endo anti -B44 : A C2p_exo anti -B45 : C C3p_endo anti -B46 : C C3p_endo anti -B47 : U C3p_endo anti -B48 : G C3p_endo anti -B49 : C C3p_endo anti -B50 : C C3p_endo anti -A1 : ALA -A2 : VAL -A3 : PRO -A4 : GLU -A5 : THR -A6 : ARG -A7 : PRO -A8 : ASN -A9 : HIS -A10 : THR -A11 : ILE -A12 : TYR -A13 : ILE -A14 : ASN -A15 : ASN -A16 : LEU -A17 : ASN -A18 : GLU -A19 : LYS -A20 : ILE -A21 : LYS -A22 : LYS -A23 : ASP -A24 : GLU -A25 : LEU -A26 : LYS -A27 : LYS -A28 : SER -A29 : LEU -A30 : HIS -A31 : ALA -A32 : ILE -A33 : PHE -A34 : SER -A35 : ARG -A36 : PHE -A37 : GLY -A38 : GLN -A39 : ILE -A40 : LEU -A41 : ASP -A42 : ILE -A43 : LEU -A44 : VAL -A45 : SER -A46 : ARG -A47 : SER -A48 : LEU -A49 : LYS -A50 : MET -A51 : ARG -A52 : GLY -A53 : GLN -A54 : ALA -A55 : PHE -A56 : VAL -A57 : ILE -A58 : PHE -A59 : LYS -A60 : GLU -A61 : VAL -A62 : SER -A63 : SER -A64 : ALA -A65 : THR -A66 : ASN -A67 : ALA -A68 : LEU -A69 : ARG -A70 : SER -A71 : MET -A72 : GLN -A73 : GLY -A74 : PHE -A75 : PRO -A76 : PHE -A77 : TYR -A78 : ASP -A79 : LYS -A80 : PRO -A81 : MET -A82 : ARG -A83 : ILE -A84 : GLN -A85 : TYR -A86 : ALA -A87 : LYS -A88 : THR -A89 : ASP -A90 : SER -A91 : ASP -A92 : ILE -A93 : ILE -A94 : ALA -A95 : LYS -A96 : MET -A97 : LYS -A98 : GLY -A99 : THR -A100 : PHE -A101 : VAL -Adjacent stackings ---------------------------------------------- -B20-B21 : adjacent_5p upward -B22-B23 : adjacent_5p upward -B23-B24 : adjacent_5p upward -B26-B27 : adjacent_5p upward -B28-B29 : adjacent_5p upward -B34-B35 : adjacent_5p outward -B35-B36 : adjacent_5p upward -B37-B38 : adjacent_5p upward -B38-B39 : adjacent_5p upward -B39-B40 : adjacent_5p upward -B44-B45 : adjacent_5p upward -B47-B48 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 12 -Number of adjacent stackings = 12 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -B20-B49 : G-C Ww/Ww pairing antiparallel cis one_hbond -B21-B48 : C-G Ww/Ww pairing antiparallel cis XIX -B22-B47 : A-U Ww/Ww pairing antiparallel cis XX -B23-B46 : G-C Ww/Ww pairing antiparallel cis 130 -B25-B38 : G-C Ww/Ww pairing antiparallel cis one_hbond -B26-B37 : U-A Ww/Ww pairing antiparallel cis XX -B28-B35 : C-G Ww/Wh pairing antiparallel cis one_hbond -B30-B34 : U-G O2'/Hh pairing -B40-B42 : U-G O2'/Bs pairing -Residue conformations ------------------------------------------- -B19 : G C3p_exo anti -B20 : G C3p_endo anti -B21 : C C3p_endo anti -B22 : A C3p_endo anti -B23 : G C3p_endo anti -B24 : A C4p_exo anti -B25 : G C4p_exo anti -B26 : U C4p_exo anti -B27 : C C4p_exo anti -B28 : C C3p_endo anti -B29 : U C3p_endo anti -B30 : U C3p_exo anti -B33 : C C4p_endo syn -B34 : G C4p_exo syn -B35 : G C3p_endo anti -B36 : G C4p_exo anti -B37 : A C3p_endo anti -B38 : C C3p_endo anti -B39 : A C3p_endo anti -B40 : U C3p_endo anti -B41 : U C2p_endo anti -B42 : G C3p_endo anti -B43 : C C2p_endo anti -B44 : A C3p_endo anti -B45 : C C3p_endo anti -B46 : C C3p_endo anti -B47 : U C3p_endo anti -B48 : G C3p_endo anti -B49 : C C3p_endo anti -B50 : C C3p_endo anti -A1 : ALA -A2 : VAL -A3 : PRO -A4 : GLU -A5 : THR -A6 : ARG -A7 : PRO -A8 : ASN -A9 : HIS -A10 : THR -A11 : ILE -A12 : TYR -A13 : ILE -A14 : ASN -A15 : ASN -A16 : LEU -A17 : ASN -A18 : GLU -A19 : LYS -A20 : ILE -A21 : LYS -A22 : LYS -A23 : ASP -A24 : GLU -A25 : LEU -A26 : LYS -A27 : LYS -A28 : SER -A29 : LEU -A30 : HIS -A31 : ALA -A32 : ILE -A33 : PHE -A34 : SER -A35 : ARG -A36 : PHE -A37 : GLY -A38 : GLN -A39 : ILE -A40 : LEU -A41 : ASP -A42 : ILE -A43 : LEU -A44 : VAL -A45 : SER -A46 : ARG -A47 : SER -A48 : LEU -A49 : LYS -A50 : MET -A51 : ARG -A52 : GLY -A53 : GLN -A54 : ALA -A55 : PHE -A56 : VAL -A57 : ILE -A58 : PHE -A59 : LYS -A60 : GLU -A61 : VAL -A62 : SER -A63 : SER -A64 : ALA -A65 : THR -A66 : ASN -A67 : ALA -A68 : LEU -A69 : ARG -A70 : SER -A71 : MET -A72 : GLN -A73 : GLY -A74 : PHE -A75 : PRO -A76 : PHE -A77 : TYR -A78 : ASP -A79 : LYS -A80 : PRO -A81 : MET -A82 : ARG -A83 : ILE -A84 : GLN -A85 : TYR -A86 : ALA -A87 : LYS -A88 : THR -A89 : ASP -A90 : SER -A91 : ASP -A92 : ILE -A93 : ILE -A94 : ALA -A95 : LYS -A96 : MET -A97 : LYS -A98 : GLY -A99 : THR -A100 : PHE -A101 : VAL -Adjacent stackings ---------------------------------------------- -B20-B21 : adjacent_5p upward -B22-B23 : adjacent_5p upward -B23-B24 : adjacent_5p upward -B26-B27 : adjacent_5p upward -B28-B29 : adjacent_5p upward -B33-B34 : adjacent_5p inward -B35-B36 : adjacent_5p upward -B36-B37 : adjacent_5p upward -B38-B39 : adjacent_5p upward -B39-B40 : adjacent_5p upward -B44-B45 : adjacent_5p upward -B46-B47 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 12 -Number of adjacent stackings = 12 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -B19-B20 : G-G O2'/C8 adjacent_5p pairing -B21-B48 : C-G Ww/Ww pairing antiparallel cis XIX -B22-B47 : A-U Ww/Ww pairing antiparallel cis XX -B23-B46 : G-C Ws/Ws pairing antiparallel cis one_hbond -B25-B38 : G-C Ww/Ww pairing antiparallel cis one_hbond -B28-B35 : C-G Ww/Ww pairing antiparallel cis one_hbond -B30-B33 : U-C O2'/Ww O2'/Bh adjacent_5p pairing -B40-B42 : U-G O2'/Bs pairing -Residue conformations ------------------------------------------- -B19 : G C3p_endo anti -B20 : G C3p_endo anti -B21 : C C3p_endo anti -B22 : A C3p_endo anti -B23 : G C3p_endo anti -B24 : A C3p_endo anti -B25 : G O4p_endo anti -B26 : U C3p_endo anti -B27 : C C4p_exo anti -B28 : C C3p_endo anti -B29 : U C3p_endo anti -B30 : U C3p_exo anti -B33 : C C3p_exo anti -B34 : G C3p_endo syn -B35 : G C3p_endo anti -B36 : G C4p_exo anti -B37 : A C3p_endo anti -B38 : C C3p_endo anti -B39 : A C2p_exo anti -B40 : U C3p_endo anti -B41 : U C3p_exo anti -B42 : G C3p_endo anti -B43 : C C2p_endo anti -B44 : A C3p_endo anti -B45 : C C3p_endo anti -B46 : C C4p_exo anti -B47 : U C3p_endo anti -B48 : G C3p_endo anti -B49 : C C3p_endo anti -B50 : C C3p_endo anti -A1 : ALA -A2 : VAL -A3 : PRO -A4 : GLU -A5 : THR -A6 : ARG -A7 : PRO -A8 : ASN -A9 : HIS -A10 : THR -A11 : ILE -A12 : TYR -A13 : ILE -A14 : ASN -A15 : ASN -A16 : LEU -A17 : ASN -A18 : GLU -A19 : LYS -A20 : ILE -A21 : LYS -A22 : LYS -A23 : ASP -A24 : GLU -A25 : LEU -A26 : LYS -A27 : LYS -A28 : SER -A29 : LEU -A30 : HIS -A31 : ALA -A32 : ILE -A33 : PHE -A34 : SER -A35 : ARG -A36 : PHE -A37 : GLY -A38 : GLN -A39 : ILE -A40 : LEU -A41 : ASP -A42 : ILE -A43 : LEU -A44 : VAL -A45 : SER -A46 : ARG -A47 : SER -A48 : LEU -A49 : LYS -A50 : MET -A51 : ARG -A52 : GLY -A53 : GLN -A54 : ALA -A55 : PHE -A56 : VAL -A57 : ILE -A58 : PHE -A59 : LYS -A60 : GLU -A61 : VAL -A62 : SER -A63 : SER -A64 : ALA -A65 : THR -A66 : ASN -A67 : ALA -A68 : LEU -A69 : ARG -A70 : SER -A71 : MET -A72 : GLN -A73 : GLY -A74 : PHE -A75 : PRO -A76 : PHE -A77 : TYR -A78 : ASP -A79 : LYS -A80 : PRO -A81 : MET -A82 : ARG -A83 : ILE -A84 : GLN -A85 : TYR -A86 : ALA -A87 : LYS -A88 : THR -A89 : ASP -A90 : SER -A91 : ASP -A92 : ILE -A93 : ILE -A94 : ALA -A95 : LYS -A96 : MET -A97 : LYS -A98 : GLY -A99 : THR -A100 : PHE -A101 : VAL -Adjacent stackings ---------------------------------------------- -B20-B21 : adjacent_5p upward -B22-B23 : adjacent_5p upward -B23-B24 : adjacent_5p upward -B26-B27 : adjacent_5p upward -B28-B29 : adjacent_5p upward -B34-B35 : adjacent_5p outward -B35-B36 : adjacent_5p upward -B37-B38 : adjacent_5p upward -B39-B40 : adjacent_5p upward -B44-B45 : adjacent_5p upward -B49-B50 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 11 -Number of adjacent stackings = 11 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -B21-B48 : C-G Ww/Ww pairing antiparallel cis XIX -B22-B47 : A-U Ww/Ww pairing antiparallel cis XX -B24-B46 : A-C Ss/Wh pairing antiparallel cis one_hbond 74 -B26-B37 : U-A Ww/Ww pairing antiparallel cis XX -B28-B35 : C-G Ww/Ww pairing antiparallel cis -B40-B42 : U-G Bs/Ws pairing antiparallel cis one_hbond -Residue conformations ------------------------------------------- -B19 : G C4p_exo anti -B20 : G C3p_endo anti -B21 : C C3p_endo anti -B22 : A C3p_endo anti -B23 : G C3p_endo anti -B24 : A C3p_endo anti -B25 : G C4p_exo anti -B26 : U C3p_endo anti -B27 : C C4p_exo anti -B28 : C C3p_endo anti -B29 : U C3p_endo anti -B30 : U C3p_exo anti -B33 : C C3p_exo anti -B34 : G C3p_endo syn -B35 : G C3p_endo anti -B36 : G C4p_exo anti -B37 : A C3p_endo anti -B38 : C C3p_endo anti -B39 : A C3p_endo anti -B40 : U C3p_endo anti -B41 : U C3p_exo anti -B42 : G C3p_endo anti -B43 : C C2p_endo anti -B44 : A C2p_exo anti -B45 : C C3p_endo anti -B46 : C C3p_endo anti -B47 : U C3p_endo anti -B48 : G C3p_endo anti -B49 : C C3p_endo anti -B50 : C C3p_endo anti -A1 : ALA -A2 : VAL -A3 : PRO -A4 : GLU -A5 : THR -A6 : ARG -A7 : PRO -A8 : ASN -A9 : HIS -A10 : THR -A11 : ILE -A12 : TYR -A13 : ILE -A14 : ASN -A15 : ASN -A16 : LEU -A17 : ASN -A18 : GLU -A19 : LYS -A20 : ILE -A21 : LYS -A22 : LYS -A23 : ASP -A24 : GLU -A25 : LEU -A26 : LYS -A27 : LYS -A28 : SER -A29 : LEU -A30 : HIS -A31 : ALA -A32 : ILE -A33 : PHE -A34 : SER -A35 : ARG -A36 : PHE -A37 : GLY -A38 : GLN -A39 : ILE -A40 : LEU -A41 : ASP -A42 : ILE -A43 : LEU -A44 : VAL -A45 : SER -A46 : ARG -A47 : SER -A48 : LEU -A49 : LYS -A50 : MET -A51 : ARG -A52 : GLY -A53 : GLN -A54 : ALA -A55 : PHE -A56 : VAL -A57 : ILE -A58 : PHE -A59 : LYS -A60 : GLU -A61 : VAL -A62 : SER -A63 : SER -A64 : ALA -A65 : THR -A66 : ASN -A67 : ALA -A68 : LEU -A69 : ARG -A70 : SER -A71 : MET -A72 : GLN -A73 : GLY -A74 : PHE -A75 : PRO -A76 : PHE -A77 : TYR -A78 : ASP -A79 : LYS -A80 : PRO -A81 : MET -A82 : ARG -A83 : ILE -A84 : GLN -A85 : TYR -A86 : ALA -A87 : LYS -A88 : THR -A89 : ASP -A90 : SER -A91 : ASP -A92 : ILE -A93 : ILE -A94 : ALA -A95 : LYS -A96 : MET -A97 : LYS -A98 : GLY -A99 : THR -A100 : PHE -A101 : VAL -Adjacent stackings ---------------------------------------------- -B20-B21 : adjacent_5p upward -B22-B23 : adjacent_5p upward -B23-B24 : adjacent_5p upward -B26-B27 : adjacent_5p upward -B28-B29 : adjacent_5p upward -B34-B35 : adjacent_5p outward -B35-B36 : adjacent_5p upward -B39-B40 : adjacent_5p upward -B44-B45 : adjacent_5p upward -B47-B48 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 10 -Number of adjacent stackings = 10 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -B21-B48 : C-G Ww/Ww pairing antiparallel cis XIX -B22-B47 : A-U Ww/Ww pairing antiparallel cis XX -B23-B46 : G-C Ww/Ww pairing antiparallel cis XIX -B25-B38 : G-C Ww/Ww pairing antiparallel cis one_hbond -B26-B37 : U-A Ww/Ww pairing antiparallel cis XX -B28-B35 : C-G Ww/Ww pairing antiparallel cis XIX -B30-B34 : U-G O2'/Hh pairing -Residue conformations ------------------------------------------- -B19 : G C4p_exo anti -B20 : G C3p_endo anti -B21 : C C4p_exo anti -B22 : A C3p_endo anti -B23 : G C3p_endo anti -B24 : A C2p_exo anti -B25 : G C4p_exo anti -B26 : U C3p_endo anti -B27 : C C4p_exo anti -B28 : C C3p_endo anti -B29 : U C3p_endo anti -B30 : U C3p_exo anti -B33 : C C3p_exo anti -B34 : G C4p_exo syn -B35 : G C3p_endo anti -B36 : G C4p_exo anti -B37 : A C4p_exo anti -B38 : C C3p_endo anti -B39 : A C2p_exo anti -B40 : U C3p_endo anti -B41 : U C3p_exo anti -B42 : G C3p_endo anti -B43 : C C2p_endo anti -B44 : A C3p_endo anti -B45 : C C3p_endo anti -B46 : C C3p_endo anti -B47 : U C3p_endo anti -B48 : G C3p_endo anti -B49 : C C3p_endo anti -B50 : C C3p_endo anti -A1 : ALA -A2 : VAL -A3 : PRO -A4 : GLU -A5 : THR -A6 : ARG -A7 : PRO -A8 : ASN -A9 : HIS -A10 : THR -A11 : ILE -A12 : TYR -A13 : ILE -A14 : ASN -A15 : ASN -A16 : LEU -A17 : ASN -A18 : GLU -A19 : LYS -A20 : ILE -A21 : LYS -A22 : LYS -A23 : ASP -A24 : GLU -A25 : LEU -A26 : LYS -A27 : LYS -A28 : SER -A29 : LEU -A30 : HIS -A31 : ALA -A32 : ILE -A33 : PHE -A34 : SER -A35 : ARG -A36 : PHE -A37 : GLY -A38 : GLN -A39 : ILE -A40 : LEU -A41 : ASP -A42 : ILE -A43 : LEU -A44 : VAL -A45 : SER -A46 : ARG -A47 : SER -A48 : LEU -A49 : LYS -A50 : MET -A51 : ARG -A52 : GLY -A53 : GLN -A54 : ALA -A55 : PHE -A56 : VAL -A57 : ILE -A58 : PHE -A59 : LYS -A60 : GLU -A61 : VAL -A62 : SER -A63 : SER -A64 : ALA -A65 : THR -A66 : ASN -A67 : ALA -A68 : LEU -A69 : ARG -A70 : SER -A71 : MET -A72 : GLN -A73 : GLY -A74 : PHE -A75 : PRO -A76 : PHE -A77 : TYR -A78 : ASP -A79 : LYS -A80 : PRO -A81 : MET -A82 : ARG -A83 : ILE -A84 : GLN -A85 : TYR -A86 : ALA -A87 : LYS -A88 : THR -A89 : ASP -A90 : SER -A91 : ASP -A92 : ILE -A93 : ILE -A94 : ALA -A95 : LYS -A96 : MET -A97 : LYS -A98 : GLY -A99 : THR -A100 : PHE -A101 : VAL -Adjacent stackings ---------------------------------------------- -B20-B21 : adjacent_5p upward -B22-B23 : adjacent_5p upward -B23-B24 : adjacent_5p upward -B26-B27 : adjacent_5p upward -B35-B36 : adjacent_5p upward -B36-B37 : adjacent_5p upward -B39-B40 : adjacent_5p upward -B44-B45 : adjacent_5p upward -B47-B48 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 9 -Number of adjacent stackings = 9 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -B21-B48 : C-G Ww/Ww pairing antiparallel cis XIX -B22-B47 : A-U Ww/Ww pairing antiparallel cis XX -B23-B46 : G-C Ww/Ww pairing antiparallel cis -B25-B38 : G-C Wh/Wh pairing antiparallel cis one_hbond -B26-B37 : U-A Ww/Ww pairing antiparallel cis XX -B28-B35 : C-G Ww/Ww pairing antiparallel cis -B30-B34 : U-G O2'/Hh pairing -B40-B42 : U-G O2'/Bs pairing diff --git a/MCdata/1av6_MC b/MCdata/1av6_MC deleted file mode 100644 index a062132be5471b5bbcf279964cda49386ccefa7c..0000000000000000000000000000000000000000 --- a/MCdata/1av6_MC +++ /dev/null @@ -1,308 +0,0 @@ -Residue conformations ------------------------------------------- -B402 : G C2p_exo anti -B403 : A C3p_endo anti -B404 : A C3p_endo anti -B405 : A C3p_endo anti -B406 : A C2p_exo anti -B407 : A C3p_endo anti -A3 : VAL -A4 : VAL -A5 : SER -A6 : LEU -A7 : ASP -A8 : LYS -A9 : PRO -A10 : PHE -A11 : MET -A12 : TYR -A13 : PHE -A14 : GLU -A15 : GLU -A16 : ILE -A17 : ASP -A18 : ASN -A19 : GLU -A20 : LEU -A21 : ASP -A22 : TYR -A23 : GLU -A24 : PRO -A25 : GLU -A26 : SER -A27 : ALA -A28 : ASN -A29 : GLU -A30 : VAL -A31 : ALA -A32 : LYS -A33 : LYS -A34 : LEU -A35 : PRO -A36 : TYR -A37 : GLN -A38 : GLY -A39 : GLN -A40 : LEU -A41 : LYS -A42 : LEU -A43 : LEU -A44 : LEU -A45 : GLY -A46 : GLU -A47 : LEU -A48 : PHE -A49 : PHE -A50 : LEU -A51 : SER -A52 : LYS -A53 : LEU -A54 : GLN -A55 : ARG -A56 : HIS -A57 : GLY -A58 : ILE -A59 : LEU -A60 : ASP -A61 : GLY -A62 : ALA -A63 : THR -A64 : VAL -A65 : VAL -A66 : TYR -A67 : ILE -A68 : GLY -A69 : SER -A70 : ALA -A71 : PRO -A72 : GLY -A73 : THR -A74 : HIS -A75 : ILE -A76 : ARG -A77 : TYR -A78 : LEU -A79 : ARG -A80 : ASP -A81 : HIS -A82 : PHE -A83 : TYR -A84 : ASN -A85 : LEU -A86 : GLY -A87 : VAL -A88 : ILE -A89 : ILE -A90 : LYS -A91 : TRP -A92 : MET -A93 : LEU -A94 : ILE -A95 : ASP -A96 : GLY -A97 : ARG -A98 : HIS -A99 : HIS -A100 : ASP -A101 : PRO -A102 : ILE -A103 : LEU -A104 : ASN -A105 : GLY -A106 : LEU -A107 : ARG -A108 : ASP -A109 : VAL -A110 : THR -A111 : LEU -A112 : VAL -A113 : THR -A114 : ARG -A115 : PHE -A116 : VAL -A117 : ASP -A118 : GLU -A119 : GLU -A120 : TYR -A121 : LEU -A122 : ARG -A123 : SER -A124 : ILE -A125 : LYS -A126 : LYS -A127 : GLN -A128 : LEU -A129 : HIS -A130 : PRO -A131 : SER -A132 : LYS -A133 : ILE -A134 : ILE -A135 : LEU -A136 : ILE -A137 : SER -A138 : ASP -A139 : VAL -A140 : ARG -A141 : SER -A148 : PRO -A149 : SER -A150 : THR -A151 : ALA -A152 : ASP -A153 : LEU -A154 : LEU -A155 : SER -A156 : ASN -A157 : TYR -A158 : ALA -A159 : LEU -A160 : GLN -A161 : ASN -A162 : VAL -A163 : MET -A164 : ILE -A165 : SER -A166 : ILE -A167 : LEU -A168 : ASN -A169 : PRO -A170 : VAL -A171 : ALA -A172 : SER -A173 : SER -A174 : LEU -A175 : LYS -A176 : TRP -A177 : ARG -A178 : CYS -A179 : PRO -A180 : PHE -A181 : PRO -A182 : ASP -A183 : GLN -A184 : TRP -A185 : ILE -A186 : LYS -A187 : ASP -A188 : PHE -A189 : TYR -A190 : ILE -A191 : PRO -A192 : HIS -A193 : GLY -A194 : ASN -A195 : LYS -A196 : MET -A197 : LEU -A198 : GLN -A199 : PRO -A200 : PHE -A201 : ALA -A202 : PRO -A203 : SER -A204 : TYR -A205 : SER -A206 : ALA -A207 : GLU -A208 : MET -A209 : ARG -A210 : LEU -A211 : LEU -A212 : SER -A213 : ILE -A214 : TYR -A215 : THR -A216 : GLY -A217 : GLU -A218 : ASN -A219 : MET -A220 : ARG -A221 : LEU -A222 : THR -A223 : ARG -A224 : VAL -A225 : THR -A226 : LYS -A227 : SER -A228 : ASP -A229 : ALA -A230 : VAL -A231 : ASN -A232 : TYR -A233 : GLU -A234 : LYS -A235 : LYS -A236 : MET -A237 : TYR -A238 : TYR -A239 : LEU -A240 : ASN -A241 : LYS -A242 : ILE -A243 : VAL -A244 : ARG -A245 : ASN -A246 : LYS -A247 : VAL -A248 : VAL -A249 : VAL -A250 : ASN -A251 : PHE -A252 : ASP -A253 : TYR -A254 : PRO -A255 : ASN -A256 : GLN -A257 : GLU -A258 : TYR -A259 : ASP -A260 : TYR -A261 : PHE -A262 : HIS -A263 : MET -A264 : TYR -A265 : PHE -A266 : MET -A267 : LEU -A268 : ARG -A269 : THR -A270 : VAL -A271 : TYR -A272 : CYS -A273 : ASN -A274 : LYS -A275 : THR -A276 : PHE -A277 : PRO -A278 : THR -A279 : THR -A280 : LYS -A281 : ALA -A282 : LYS -A283 : VAL -A284 : LEU -A285 : PHE -A286 : LEU -A287 : GLN -A288 : GLN -A289 : SER -A290 : ILE -A291 : PHE -A292 : ARG -A293 : PHE -A294 : LEU -A295 : ASN -A296 : ILE -A297 : PRO -B408 : MGT -A400 : SAH -Adjacent stackings ---------------------------------------------- -B402-B403 : adjacent_5p upward -B403-B404 : adjacent_5p upward -B405-B406 : adjacent_5p upward -B406-B407 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 4 -Number of adjacent stackings = 4 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ diff --git a/MCdata/1b23_MC b/MCdata/1b23_MC deleted file mode 100644 index ed70601738d56f9fb0477fa174139f993dfdfad7..0000000000000000000000000000000000000000 --- a/MCdata/1b23_MC +++ /dev/null @@ -1,836 +0,0 @@ -Residue conformations ------------------------------------------- -R1 : G C3p_endo anti -R2 : G C3p_endo anti -R3 : C C3p_endo anti -R4 : G C3p_endo anti -R5 : C C3p_endo anti -R6 : G C3p_endo anti -R7 : U C4p_exo anti -R8 : 4SU -R9 : A C2p_endo syn -R10 : A C3p_endo anti -R11 : C C3p_endo anti -R12 : A C3p_endo anti -R13 : A C3p_endo anti -R14 : A C3p_endo anti -R15 : G C3p_endo anti -R16 : C C3p_endo anti -R18 : G C2p_endo anti -R19 : G C2p_endo anti -R20 : H2U -R21 : H2U -R22 : A C2p_exo anti -R23 : U C3p_endo anti -R24 : G C3p_endo anti -R25 : U C3p_endo anti -R26 : A C3p_endo anti -R27 : G C3p_endo anti -R28 : C C3p_endo anti -R29 : G C3p_endo anti -R30 : G C3p_endo anti -R31 : A C3p_endo anti -R32 : PSU -R33 : U C3p_endo anti -R34 : G C3p_endo anti -R35 : C C3p_endo anti -R36 : A C3p_endo anti -R37 : MIA -R38 : A C3p_endo anti -R39 : PSU -R40 : C C3p_endo anti -R41 : C C3p_endo anti -R42 : G C3p_endo anti -R43 : U C3p_endo anti -R44 : C C2p_endo anti -R45 : U C2p_endo anti -R46 : A C2p_exo anti -R48 : G C2p_endo anti -R49 : U C3p_endo anti -R50 : C C3p_endo anti -R51 : C C3p_endo anti -R52 : G C3p_endo anti -R53 : G C3p_endo anti -R54 : 5MU -R55 : PSU -R56 : C C3p_endo anti -R57 : G C3p_endo anti -R58 : A C2p_endo syn -R59 : C C3p_endo anti -R60 : U C2p_endo anti -R61 : C C3p_endo anti -R62 : C C3p_endo anti -R63 : G C2p_exo anti -R64 : G C3p_endo anti -R65 : A C3p_endo anti -R66 : A C3p_endo anti -R67 : C C3p_endo anti -R68 : G C3p_endo anti -R69 : C C3p_endo anti -R70 : G C3p_endo anti -R71 : C C3p_endo anti -R72 : C C3p_endo anti -R73 : U C3p_endo anti -R74 : C C3p_endo anti -R75 : C C3p_exo anti -R76 : A C2p_endo anti -P1 : ALA -P2 : LYS -P3 : GLY -P4 : GLU -P5 : PHE -P6 : ILE -P7 : ARG -P8 : THR -P9 : LYS -P10 : PRO -P11 : HIS -P12 : VAL -P13 : ASN -P14 : VAL -P15 : GLY -P16 : THR -P17 : ILE -P18 : GLY -P19 : HIS -P20 : VAL -P21 : ASP -P22 : HIS -P23 : GLY -P24 : LYS -P25 : THR -P26 : THR -P27 : LEU -P28 : THR -P29 : ALA -P30 : ALA -P31 : LEU -P32 : THR -P33 : TYR -P34 : VAL -P35 : ALA -P36 : ALA -P37 : ALA -P38 : GLU -P39 : ASN -P40 : PRO -P41 : ASN -P42 : VAL -P43 : GLU -P44 : VAL -P45 : LYS -P46 : ASP -P47 : TYR -P48 : GLY -P49 : ASP -P50 : ILE -P51 : ASP -P52 : LYS -P53 : ALA -P54 : PRO -P55 : GLU -P56 : GLU -P57 : ARG -P58 : ALA -P59 : ARG -P60 : GLY -P61 : ILE -P62 : THR -P63 : ILE -P64 : ASN -P65 : THR -P66 : ALA -P67 : HIS -P68 : VAL -P69 : GLU -P70 : TYR -P71 : GLU -P72 : THR -P73 : ALA -P74 : LYS -P75 : ARG -P76 : HIS -P77 : TYR -P78 : SER -P79 : HIS -P80 : VAL -P81 : ASP -P82 : CYS -P83 : PRO -P84 : GLY -P85 : HIS -P86 : ALA -P87 : ASP -P88 : TYR -P89 : ILE -P90 : LYS -P91 : ASN -P92 : MET -P93 : ILE -P94 : THR -P95 : GLY -P96 : ALA -P97 : ALA -P98 : GLN -P99 : MET -P100 : ASP -P101 : GLY -P102 : ALA -P103 : ILE -P104 : LEU -P105 : VAL -P106 : VAL -P107 : SER -P108 : ALA -P109 : ALA -P110 : ASP -P111 : GLY -P112 : PRO -P113 : MET -P114 : PRO -P115 : GLN -P116 : THR -P117 : ARG -P118 : GLU -P119 : HIS -P120 : ILE -P121 : LEU -P122 : LEU -P123 : ALA -P124 : ARG -P125 : GLN -P126 : VAL -P127 : GLY -P128 : VAL -P129 : PRO -P130 : TYR -P131 : ILE -P132 : VAL -P133 : VAL -P134 : PHE -P135 : MET -P136 : ASN -P137 : LYS -P138 : VAL -P139 : ASP -P140 : MET -P141 : VAL -P142 : ASP -P143 : ASP -P144 : PRO -P145 : GLU -P146 : LEU -P147 : LEU -P148 : ASP -P149 : LEU -P150 : VAL -P151 : GLU -P152 : MET -P153 : GLU -P154 : VAL -P155 : ARG -P156 : ASP -P157 : LEU -P158 : LEU -P159 : ASN -P160 : GLN -P161 : TYR -P162 : GLU -P163 : PHE -P164 : PRO -P165 : GLY -P166 : ASP -P167 : GLU -P168 : VAL -P169 : PRO -P170 : VAL -P171 : ILE -P172 : ARG -P173 : GLY -P174 : SER -P175 : ALA -P176 : LEU -P177 : LEU -P178 : ALA -P179 : LEU -P180 : GLU -P181 : GLU -P182 : MET -P183 : HIS -P184 : LYS -P185 : ASN -P186 : PRO -P187 : LYS -P188 : THR -P189 : LYS -P190 : ARG -P191 : GLY -P192 : GLU -P193 : ASN -P194 : GLU -P195 : TRP -P196 : VAL -P197 : ASP -P198 : LYS -P199 : ILE -P200 : TRP -P201 : GLU -P202 : LEU -P203 : LEU -P204 : ASP -P205 : ALA -P206 : ILE -P207 : ASP -P208 : GLU -P209 : TYR -P210 : ILE -P211 : PRO -P212 : THR -P213 : PRO -P214 : VAL -P215 : ARG -P216 : ASP -P217 : VAL -P218 : ASP -P219 : LYS -P220 : PRO -P221 : PHE -P222 : LEU -P223 : MET -P224 : PRO -P225 : VAL -P226 : GLU -P227 : ASP -P228 : VAL -P229 : PHE -P230 : THR -P231 : ILE -P232 : THR -P233 : GLY -P234 : ARG -P235 : GLY -P236 : THR -P237 : VAL -P238 : ALA -P239 : THR -P240 : GLY -P241 : ARG -P242 : ILE -P243 : GLU -P244 : ARG -P245 : GLY -P246 : LYS -P247 : VAL -P248 : LYS -P249 : VAL -P250 : GLY -P251 : ASP -P252 : GLU -P253 : VAL -P254 : GLU -P255 : ILE -P256 : VAL -P257 : GLY -P258 : LEU -P259 : ALA -P260 : PRO -P261 : GLU -P262 : THR -P263 : ARG -P264 : LYS -P265 : THR -P266 : VAL -P267 : VAL -P268 : THR -P269 : GLY -P270 : VAL -P271 : GLU -P272 : MET -P273 : HIS -P274 : ARG -P275 : LYS -P276 : THR -P277 : LEU -P278 : GLN -P279 : GLU -P280 : GLY -P281 : ILE -P282 : ALA -P283 : GLY -P284 : ASP -P285 : ASN -P286 : VAL -P287 : GLY -P288 : LEU -P289 : LEU -P290 : LEU -P291 : ARG -P292 : GLY -P293 : VAL -P294 : SER -P295 : ARG -P296 : GLU -P297 : GLU -P298 : VAL -P299 : GLU -P300 : ARG -P301 : GLY -P302 : GLN -P303 : VAL -P304 : LEU -P305 : ALA -P306 : LYS -P307 : PRO -P308 : GLY -P309 : SER -P310 : ILE -P311 : THR -P312 : PRO -P313 : HIS -P314 : THR -P315 : LYS -P316 : PHE -P317 : GLU -P318 : ALA -P319 : SER -P320 : VAL -P321 : TYR -P322 : ILE -P323 : LEU -P324 : LYS -P325 : LYS -P326 : GLU -P327 : GLU -P328 : GLY -P329 : GLY -P330 : ARG -P331 : HIS -P332 : THR -P333 : GLY -P334 : PHE -P335 : PHE -P336 : THR -P337 : GLY -P338 : TYR -P339 : ARG -P340 : PRO -P341 : GLN -P342 : PHE -P343 : TYR -P344 : PHE -P345 : ARG -P346 : THR -P347 : THR -P348 : ASP -P349 : VAL -P350 : THR -P351 : GLY -P352 : VAL -P353 : VAL -P354 : ARG -P355 : LEU -P356 : PRO -P357 : GLN -P358 : GLY -P359 : VAL -P360 : GLU -P361 : MET -P362 : VAL -P363 : MET -P364 : PRO -P365 : GLY -P366 : ASP -P367 : ASN -P368 : VAL -P369 : THR -P370 : PHE -P371 : THR -P372 : VAL -P373 : GLU -P374 : LEU -P375 : ILE -P376 : LYS -P377 : PRO -P378 : VAL -P379 : ALA -P380 : LEU -P381 : GLU -P382 : GLU -P383 : GLY -P384 : LEU -P385 : ARG -P386 : PHE -P387 : ALA -P388 : ILE -P389 : ARG -P390 : GLU -P391 : GLY -P392 : GLY -P393 : ARG -P394 : THR -P395 : VAL -P396 : GLY -P397 : ALA -P398 : GLY -P399 : VAL -P400 : VAL -P401 : THR -P402 : LYS -P403 : ILE -P404 : LEU -P405 : GLU -R77 : MG -R179 : MG -R976 : CYS -P407 : MG -P408 : SO4 -P409 : SO4 -P406 : GNP -R977 : HOH -R978 : HOH -R979 : HOH -R980 : HOH -R981 : HOH -R982 : HOH -R983 : HOH -R984 : HOH -R985 : HOH -R986 : HOH -R987 : HOH -R988 : HOH -R989 : HOH -R990 : HOH -R991 : HOH -R992 : HOH -R993 : HOH -R994 : HOH -R995 : HOH -R996 : HOH -R997 : HOH -R998 : HOH -R999 : HOH -R1000 : HOH -R1001 : HOH -R1002 : HOH -R1003 : HOH -R1004 : HOH -R1005 : HOH -R1006 : HOH -R1007 : HOH -R1008 : HOH -R1009 : HOH -R1010 : HOH -R1011 : HOH -R1012 : HOH -R1013 : HOH -R1014 : HOH -R1015 : HOH -R1016 : HOH -R1017 : HOH -R1018 : HOH -R1019 : HOH -R1020 : HOH -R1021 : HOH -R1022 : HOH -R1023 : HOH -R1024 : HOH -R1025 : HOH -R1026 : HOH -R1027 : HOH -R1028 : HOH -R1029 : HOH -R1030 : HOH -R1031 : HOH -R1032 : HOH -R1033 : HOH -R1034 : HOH -R1035 : HOH -R1036 : HOH -R1037 : HOH -R1038 : HOH -R1039 : HOH -R1040 : HOH -R1041 : HOH -R1042 : HOH -R1043 : HOH -R1044 : HOH -R1045 : HOH -R1046 : HOH -R1047 : HOH -R1048 : HOH -R1049 : HOH -R1050 : HOH -R1051 : HOH -R1052 : HOH -R1053 : HOH -R1054 : HOH -R1055 : HOH -R1056 : HOH -R1057 : HOH -R1058 : HOH -R1059 : HOH -R1060 : HOH -R1061 : HOH -R1062 : HOH -R1063 : HOH -P410 : HOH -P411 : HOH -P412 : HOH -P413 : HOH -P414 : HOH -P415 : HOH -P416 : HOH -P417 : HOH -P418 : HOH -P419 : HOH -P420 : HOH -P421 : HOH -P422 : HOH -P423 : HOH -P424 : HOH -P425 : HOH -P426 : HOH -P427 : HOH -P428 : HOH -P429 : HOH -P430 : HOH -P431 : HOH -P432 : HOH -P433 : HOH -P434 : HOH -P435 : HOH -P436 : HOH -P437 : HOH -P438 : HOH -P439 : HOH -P440 : HOH -P441 : HOH -P442 : HOH -P443 : HOH -P444 : HOH -P445 : HOH -P446 : HOH -P447 : HOH -P448 : HOH -P449 : HOH -P450 : HOH -P451 : HOH -P452 : HOH -P453 : HOH -P454 : HOH -P455 : HOH -P456 : HOH -P457 : HOH -P458 : HOH -P459 : HOH -P460 : HOH -P461 : HOH -P462 : HOH -P463 : HOH -P464 : HOH -P465 : HOH -P466 : HOH -P467 : HOH -P468 : HOH -P469 : HOH -P470 : HOH -P471 : HOH -P472 : HOH -P473 : HOH -P474 : HOH -P475 : HOH -P476 : HOH -P477 : HOH -P478 : HOH -P479 : HOH -P480 : HOH -P481 : HOH -P482 : HOH -P483 : HOH -P484 : HOH -P485 : HOH -P486 : HOH -P487 : HOH -P488 : HOH -P489 : HOH -P490 : HOH -P491 : HOH -P492 : HOH -P493 : HOH -P494 : HOH -P495 : HOH -P496 : HOH -P497 : HOH -P498 : HOH -P499 : HOH -P500 : HOH -P501 : HOH -P502 : HOH -P503 : HOH -P504 : HOH -P505 : HOH -P506 : HOH -P507 : HOH -P508 : HOH -P509 : HOH -P510 : HOH -P511 : HOH -P512 : HOH -P513 : HOH -P514 : HOH -P515 : HOH -P516 : HOH -P517 : HOH -P518 : HOH -P519 : HOH -P520 : HOH -P521 : HOH -P522 : HOH -P523 : HOH -P524 : HOH -P525 : HOH -P526 : HOH -P527 : HOH -P528 : HOH -P529 : HOH -P530 : HOH -P531 : HOH -P532 : HOH -P533 : HOH -P534 : HOH -P535 : HOH -P536 : HOH -P537 : HOH -P538 : HOH -P539 : HOH -P540 : HOH -P541 : HOH -P542 : HOH -P543 : HOH -P544 : HOH -P545 : HOH -P546 : HOH -P547 : HOH -P548 : HOH -P549 : HOH -P550 : HOH -P551 : HOH -P552 : HOH -P553 : HOH -P554 : HOH -P555 : HOH -P556 : HOH -P557 : HOH -P558 : HOH -P559 : HOH -P560 : HOH -P561 : HOH -P562 : HOH -P563 : HOH -P564 : HOH -P565 : HOH -P566 : HOH -P567 : HOH -P568 : HOH -P569 : HOH -P570 : HOH -P571 : HOH -P572 : HOH -P573 : HOH -P574 : HOH -P575 : HOH -P576 : HOH -P577 : HOH -P578 : HOH -P579 : HOH -P580 : HOH -P581 : HOH -P582 : HOH -P583 : HOH -Adjacent stackings ---------------------------------------------- -R1-R2 : adjacent_5p upward -R2-R3 : adjacent_5p upward -R4-R5 : adjacent_5p upward -R10-R11 : adjacent_5p upward -R12-R13 : adjacent_5p upward -R14-R15 : adjacent_5p upward -R15-R16 : adjacent_5p upward -R22-R23 : adjacent_5p upward -R24-R25 : adjacent_5p upward -R25-R26 : adjacent_5p upward -R26-R27 : adjacent_5p upward -R27-R28 : adjacent_5p upward -R28-R29 : adjacent_5p upward -R29-R30 : adjacent_5p upward -R30-R31 : adjacent_5p upward -R34-R35 : adjacent_5p upward -R41-R42 : adjacent_5p upward -R42-R43 : adjacent_5p upward -R43-R44 : adjacent_5p upward -R46-R48 : adjacent_5p upward -R49-R50 : adjacent_5p upward -R50-R51 : adjacent_5p upward -R52-R53 : adjacent_5p upward -R56-R57 : adjacent_5p upward -R59-R60 : adjacent_5p upward -R63-R64 : adjacent_5p upward -R64-R65 : adjacent_5p upward -R65-R66 : adjacent_5p upward -R66-R67 : adjacent_5p upward -R67-R68 : adjacent_5p upward -R68-R69 : adjacent_5p upward -R69-R70 : adjacent_5p upward -R70-R71 : adjacent_5p upward -R73-R74 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -R4-R70 : outward -R6-R68 : outward -R7-R49 : upward -R9-R46 : outward -R10-R26 : outward -R12-R24 : outward -R14-R22 : outward -R18-R57 : inward pairing -R18-R58 : outward -R19-R57 : outward -R29-R42 : outward -R48-R59 : upward -R51-R64 : outward -R52-R63 : outward -R53-R62 : outward -R58-R61 : upward pairing -Number of stackings = 50 -Number of adjacent stackings = 34 -Number of non adjacent stackings = 16 -Base-pairs ------------------------------------------------------ -R1-R72 : G-C Ww/Ww pairing antiparallel cis XIX -R2-R71 : G-C Ww/Ww pairing antiparallel cis one_hbond -R3-R70 : C-G Ww/Ww pairing antiparallel cis XIX -R4-R69 : G-C Ww/Ww pairing antiparallel cis XIX -R5-R68 : C-G Ww/Ww pairing antiparallel cis XIX -R6-R67 : G-C Ww/Ww pairing antiparallel cis XIX -R7-R66 : U-A Ww/Ww pairing antiparallel cis XX -R9-R11 : A-C O2'/Bh pairing -R9-R13 : A-A Hh/Ww pairing antiparallel trans V -R11-R24 : C-G Ww/Ww pairing antiparallel cis XIX -R12-R23 : A-U Ww/Ws pairing antiparallel cis XX -R13-R22 : A-A Ss/Hw pairing antiparallel trans one_hbond 41 -R14-R46 : A-A Wh/Ww pairing parallel cis one_hbond -R15-R48 : G-G Bh/Ww pairing parallel trans 113 -R16-R59 : C-C Ww/Ww pairing parallel trans XV -R18-R57 : G-G O2'/Ww O2'/Bs inward pairing -R19-R56 : G-C Ww/Ww pairing antiparallel cis XIX -R22-R46 : A-A O2P/Bh pairing -R27-R43 : G-U Ww/Ws pairing antiparallel cis XXVIII -R28-R42 : C-G Ww/Ww pairing antiparallel cis XIX -R29-R41 : G-C Ww/Ww pairing antiparallel cis XIX -R30-R40 : G-C Ws/Ww pairing antiparallel cis one_hbond -R33-R35 : U-C O2'/Bh pairing -R33-R36 : U-A Ws/C8 Ww/O2P pairing antiparallel trans one_hbond -R49-R65 : U-A Ww/Ww pairing antiparallel cis XX -R50-R64 : C-G Ww/Ww pairing antiparallel cis XIX -R51-R63 : C-G Ww/Ww pairing antiparallel cis XIX -R52-R62 : G-C Ww/Ww pairing antiparallel cis XIX -R53-R61 : G-C Ww/Ww pairing antiparallel cis XIX -R58-R61 : A-C O2'/Bh upward pairing -R60-R61 : U-C O2P/Bh O2P/Bh adjacent_5p pairing -R72-R73 : C-U Hw/Hw adjacent_5p pairing parallel cis one_hbond 101 diff --git a/MCdata/1b2m_MC b/MCdata/1b2m_MC deleted file mode 100644 index 599a8441c26a43c4d285fdb305cf51cac23d584f..0000000000000000000000000000000000000000 --- a/MCdata/1b2m_MC +++ /dev/null @@ -1,313 +0,0 @@ -Residue conformations ------------------------------------------- -C105 : G C2p_endo syn -C106 : U34 -D105 : G C2p_endo syn -D106 : U34 -E105 : G C1p_exo syn -E106 : U34 -A1 : ALA -A2 : CYS -A3 : ASP -A4 : TYR -A5 : THR -A6 : CYS -A7 : GLY -A8 : SER -A9 : ASN -A10 : CYS -A11 : TYR -A12 : SER -A13 : SER -A14 : SER -A15 : ASP -A16 : VAL -A17 : SER -A18 : THR -A19 : ALA -A20 : GLN -A21 : ALA -A22 : ALA -A23 : GLY -A24 : TYR -A25 : GLN -A26 : LEU -A27 : HIS -A28 : GLU -A29 : ASP -A30 : GLY -A31 : GLU -A32 : THR -A33 : VAL -A34 : GLY -A35 : SER -A36 : ASN -A37 : SER -A38 : TYR -A39 : PRO -A40 : HIS -A41 : LYS -A42 : TYR -A43 : ASN -A44 : ASN -A45 : TYR -A46 : GLU -A47 : GLY -A48 : PHE -A49 : ASP -A50 : PHE -A51 : SER -A52 : VAL -A53 : SER -A54 : SER -A55 : PRO -A56 : TYR -A57 : TYR -A58 : GLU -A59 : TRP -A60 : PRO -A61 : ILE -A62 : LEU -A63 : SER -A64 : SER -A65 : GLY -A66 : ASP -A67 : VAL -A68 : TYR -A69 : SER -A70 : GLY -A71 : GLY -A72 : SER -A73 : PRO -A74 : GLY -A75 : ALA -A76 : ASP -A77 : ARG -A78 : VAL -A79 : VAL -A80 : PHE -A81 : ASN -A82 : GLU -A83 : ASN -A84 : ASN -A85 : GLN -A86 : LEU -A87 : ALA -A88 : GLY -A89 : VAL -A90 : ILE -A91 : THR -A92 : HIS -A93 : THR -A94 : GLY -A95 : ALA -A96 : SER -A97 : GLY -A98 : ASN -A99 : ASN -A100 : PHE -A101 : VAL -A102 : GLU -A103 : CYS -A104 : THR -B1 : ALA -B2 : CYS -B3 : ASP -B4 : TYR -B5 : THR -B6 : CYS -B7 : GLY -B8 : SER -B9 : ASN -B10 : CYS -B11 : TYR -B12 : SER -B13 : SER -B14 : SER -B15 : ASP -B16 : VAL -B17 : SER -B18 : THR -B19 : ALA -B20 : GLN -B21 : ALA -B22 : ALA -B23 : GLY -B24 : TYR -B25 : GLN -B26 : LEU -B27 : HIS -B28 : GLU -B29 : ASP -B30 : GLY -B31 : GLU -B32 : THR -B33 : VAL -B34 : GLY -B35 : SER -B36 : ASN -B37 : SER -B38 : TYR -B39 : PRO -B40 : HIS -B41 : LYS -B42 : TYR -B43 : ASN -B44 : ASN -B45 : TYR -B46 : GLU -B47 : GLY -B48 : PHE -B49 : ASP -B50 : PHE -B51 : SER -B52 : VAL -B53 : SER -B54 : SER -B55 : PRO -B56 : TYR -B57 : TYR -B58 : GLU -B59 : TRP -B60 : PRO -B61 : ILE -B62 : LEU -B63 : SER -B64 : SER -B65 : GLY -B66 : ASP -B67 : VAL -B68 : TYR -B69 : SER -B70 : GLY -B71 : GLY -B72 : SER -B73 : PRO -B74 : GLY -B75 : ALA -B76 : ASP -B77 : ARG -B78 : VAL -B79 : VAL -B80 : PHE -B81 : ASN -B82 : GLU -B83 : ASN -B84 : ASN -B85 : GLN -B86 : LEU -B87 : ALA -B88 : GLY -B89 : VAL -B90 : ILE -B91 : THR -B92 : HIS -B93 : THR -B94 : GLY -B95 : ALA -B96 : SER -B97 : GLY -B98 : ASN -B99 : ASN -B100 : PHE -B101 : VAL -B102 : GLU -B103 : CYS -B104 : THR -C137 : HOH -D188 : HOH -D195 : HOH -A107 : HOH -A108 : HOH -A110 : HOH -A111 : HOH -A112 : HOH -A113 : HOH -A114 : HOH -A115 : HOH -A116 : HOH -A117 : HOH -A118 : HOH -A119 : HOH -A120 : HOH -A127 : HOH -A133 : HOH -A134 : HOH -A135 : HOH -A139 : HOH -A140 : HOH -A141 : HOH -A142 : HOH -A144 : HOH -A145 : HOH -A146 : HOH -A147 : HOH -A148 : HOH -A149 : HOH -A155 : HOH -A156 : HOH -A157 : HOH -A169 : HOH -A170 : HOH -A171 : HOH -A177 : HOH -A178 : HOH -A179 : HOH -A180 : HOH -A181 : HOH -A182 : HOH -A183 : HOH -A184 : HOH -A185 : HOH -A186 : HOH -A187 : HOH -A189 : HOH -A190 : HOH -A191 : HOH -A194 : HOH -B109 : HOH -B121 : HOH -B122 : HOH -B123 : HOH -B124 : HOH -B125 : HOH -B126 : HOH -B128 : HOH -B129 : HOH -B130 : HOH -B131 : HOH -B132 : HOH -B136 : HOH -B138 : HOH -B143 : HOH -B150 : HOH -B151 : HOH -B152 : HOH -B153 : HOH -B154 : HOH -B158 : HOH -B159 : HOH -B160 : HOH -B161 : HOH -B162 : HOH -B163 : HOH -B164 : HOH -B165 : HOH -B166 : HOH -B167 : HOH -B168 : HOH -B172 : HOH -B173 : HOH -B174 : HOH -B175 : HOH -B176 : HOH -B192 : HOH -B193 : HOH -B196 : HOH -B197 : HOH -B198 : HOH -Adjacent stackings ---------------------------------------------- -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 0 -Number of adjacent stackings = 0 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ diff --git a/MCdata/1b36_MC b/MCdata/1b36_MC deleted file mode 100644 index 38cb511853d45d24cbdeebf68894d8dc37e2c262..0000000000000000000000000000000000000000 --- a/MCdata/1b36_MC +++ /dev/null @@ -1,855 +0,0 @@ -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C2p_exo anti -A3 : U C3p_endo anti -A4 : G C3p_endo anti -A5 : C C3p_endo anti -A6 : A C4p_exo anti -A7 : G C3p_endo anti -A8 : A C3p_endo anti -A9 : A C2p_exo anti -A10 : A C2p_exo anti -A11 : C C3p_endo anti -A12 : A C4p_exo anti -A13 : G C3p_endo anti -A14 : C C3p_endo anti -A15 : G C4p_exo anti -A16 : C C3p_endo anti -A17 : U C3p_endo anti -A18 : U C2p_endo anti -A19 : C C1p_exo anti -A20 : G C4p_exo syn -A21 : G C3p_endo anti -A22 : C C3p_endo anti -A23 : G C3p_endo anti -A24 : C C4p_exo anti -A25 : G C3p_endo anti -A26 : U O4p_endo anti -A27 : A C3p_endo anti -A28 : U C3p_endo anti -A29 : A C2p_endo anti -A30 : U C2p_endo anti -A31 : U C3p_endo anti -A32 : A C4p_exo anti -A33 : C C3p_endo anti -A34 : G C4p_exo anti -A35 : C C3p_endo anti -A36 : A C2p_exo anti -A37 : C C2p_exo anti -A38 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A20-A21 : adjacent_5p outward -A21-A22 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A24-A25 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward pairing -A27-A28 : adjacent_5p upward -A32-A33 : adjacent_5p upward -A34-A35 : adjacent_5p upward -A36-A37 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A36 : outward -A15-A23 : outward -A17-A19 : upward -Number of stackings = 25 -Number of adjacent stackings = 22 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -A1-A38 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A37 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A36 : U-A Ww/Ww pairing antiparallel cis XX -A4-A35 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A34 : C-G Ww/Ww pairing antiparallel cis XIX -A7-A8 : G-A O2'/C8 adjacent_5p pairing -A7-A32 : G-A Ss/Hw pairing antiparallel trans one_hbond 63 -A9-A29 : A-A Hw/Hh pairing parallel trans one_hbond -A10-A27 : A-A Bh/Ss pairing antiparallel trans one_hbond 40 -A11-A26 : C-U Wh/Ws pairing antiparallel cis one_hbond 100 -A12-A25 : A-G Wh/Ss Ww/O2' pairing antiparallel trans one_hbond 63 -A13-A24 : G-C Ww/Ww pairing antiparallel cis XIX -A14-A23 : C-G Ww/Ww pairing antiparallel cis XIX -A15-A22 : G-C Ww/Ww pairing antiparallel cis XIX -A16-A21 : C-G Ww/Ww pairing antiparallel cis XIX -A17-A20 : U-G Bs/Ww pairing parallel trans one_hbond 87 -A26-A27 : U-A O2'/C8 adjacent_5p upward pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C2p_exo anti -A3 : U C3p_endo anti -A4 : G C3p_endo anti -A5 : C C4p_exo anti -A6 : A C3p_endo anti -A7 : G C2p_exo anti -A8 : A C2p_exo anti -A9 : A C4p_exo anti -A10 : A C3p_endo anti -A11 : C O4p_endo anti -A12 : A O4p_endo anti -A13 : G C3p_endo anti -A14 : C C3p_endo anti -A15 : G C4p_exo anti -A16 : C C3p_endo anti -A17 : U C3p_endo anti -A18 : U C2p_endo anti -A19 : C C1p_exo anti -A20 : G O4p_endo syn -A21 : G C3p_endo anti -A22 : C C3p_endo anti -A23 : G C3p_endo anti -A24 : C C4p_exo anti -A25 : G C3p_endo anti -A26 : U O4p_endo anti -A27 : A C3p_endo anti -A28 : U C3p_endo anti -A29 : A C1p_exo anti -A30 : U C2p_endo anti -A31 : U C3p_endo anti -A32 : A O4p_endo anti -A33 : C C3p_endo anti -A34 : G C3p_endo anti -A35 : C C3p_endo anti -A36 : A C2p_exo anti -A37 : C C2p_exo anti -A38 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A24-A25 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward pairing -A32-A33 : adjacent_5p upward -A34-A35 : adjacent_5p upward -A36-A37 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A8-A32 : outward -A17-A19 : upward -Number of stackings = 23 -Number of adjacent stackings = 21 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A1-A38 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A37 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A36 : U-A Ww/Ww pairing antiparallel cis XX -A4-A35 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A34 : C-G Ww/Ww pairing antiparallel cis XIX -A7-A8 : G-A O2'/C8 adjacent_5p pairing -A7-A32 : G-A Ss/Hh pairing antiparallel trans XI -A8-A31 : A-U Bh/Ws pairing antiparallel trans one_hbond -A10-A27 : A-A Wh/Ss pairing antiparallel trans one_hbond 40 -A11-A26 : C-U Bh/Bs pairing antiparallel cis -A12-A25 : A-G Wh/Ss pairing antiparallel cis one_hbond 63 -A13-A24 : G-C Ww/Ww pairing antiparallel cis XIX -A14-A23 : C-G Ww/Ww pairing antiparallel cis XIX -A15-A22 : G-C Ww/Ww pairing antiparallel cis XIX -A16-A21 : C-G Ww/Ww pairing antiparallel cis XIX -A17-A20 : U-G Ws/Ws pairing parallel trans one_hbond 87 -A18-A20 : U-G O2'/Hh pairing -A26-A27 : U-A O2'/C8 adjacent_5p upward pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : U C3p_endo anti -A4 : G C2p_exo anti -A5 : C C4p_exo anti -A6 : A C4p_exo anti -A7 : G C3p_endo anti -A8 : A C3p_endo anti -A9 : A C2p_exo anti -A10 : A C3p_endo anti -A11 : C C3p_endo anti -A12 : A C3p_endo anti -A13 : G C3p_endo anti -A14 : C C3p_endo anti -A15 : G C3p_endo anti -A16 : C C3p_endo anti -A17 : U C3p_endo anti -A18 : U C1p_exo anti -A19 : C C3p_exo anti -A20 : G C4p_exo syn -A21 : G C2p_exo anti -A22 : C C4p_exo anti -A23 : G C3p_endo anti -A24 : C C4p_exo anti -A25 : G C3p_endo anti -A26 : U C4p_exo anti -A27 : A C3p_endo anti -A28 : U C3p_endo anti -A29 : A C2p_endo anti -A30 : U C1p_exo anti -A31 : U C3p_endo anti -A32 : A O4p_endo anti -A33 : C C3p_endo anti -A34 : G C3p_endo anti -A35 : C C3p_endo anti -A36 : A C2p_exo anti -A37 : C C3p_endo anti -A38 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A24-A25 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A32-A33 : adjacent_5p upward -A34-A35 : adjacent_5p upward -A36-A37 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A8-A32 : outward -A15-A23 : outward -Number of stackings = 22 -Number of adjacent stackings = 20 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A1-A38 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A37 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A36 : U-A Ww/Ww pairing antiparallel cis XX -A4-A35 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A34 : C-G Ww/Ww pairing antiparallel cis XIX -A6-A33 : A-C Ww/Wh pairing antiparallel cis one_hbond 71 -A7-A8 : G-A O2'/C8 adjacent_5p pairing -A7-A32 : G-A Ss/Hw pairing antiparallel trans XI -A8-A31 : A-U Bh/Ws pairing antiparallel trans one_hbond -A9-A28 : A-U Bh/O2' pairing -A10-A27 : A-A Wh/Ss pairing antiparallel trans one_hbond 40 -A11-A26 : C-U Wh/Ws pairing antiparallel cis one_hbond 100 -A12-A25 : A-G Wh/Ss Ww/O2' pairing antiparallel trans one_hbond 63 -A13-A24 : G-C Ww/Ww pairing antiparallel cis XIX -A14-A23 : C-G Ww/Ww pairing antiparallel cis XIX -A15-A22 : G-C Ww/Ww pairing antiparallel cis XIX -A16-A21 : C-G Ww/Ww pairing antiparallel cis XIX -A18-A19 : U-C O2P/Bh adjacent_5p pairing -Residue conformations ------------------------------------------- -A1 : G C2p_exo anti -A2 : G C3p_endo anti -A3 : U C3p_endo anti -A4 : G C3p_endo anti -A5 : C C3p_endo anti -A6 : A C2p_exo anti -A7 : G C3p_endo anti -A8 : A C3p_endo anti -A9 : A C4p_exo anti -A10 : A C3p_endo anti -A11 : C C3p_endo anti -A12 : A O4p_endo anti -A13 : G C3p_endo anti -A14 : C C2p_exo anti -A15 : G C3p_endo anti -A16 : C C3p_endo anti -A17 : U C2p_exo anti -A18 : U C2p_endo anti -A19 : C C1p_exo anti -A20 : G C4p_exo syn -A21 : G C2p_exo anti -A22 : C C3p_endo anti -A23 : G C3p_endo anti -A24 : C O4p_endo anti -A25 : G C3p_endo anti -A26 : U C4p_exo anti -A27 : A C2p_exo anti -A28 : U C3p_endo anti -A29 : A C3p_exo anti -A30 : U C2p_endo anti -A31 : U C3p_endo anti -A32 : A O4p_endo anti -A33 : C C4p_exo anti -A34 : G C3p_endo anti -A35 : C C3p_endo anti -A36 : A C3p_endo anti -A37 : C C2p_exo anti -A38 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A20-A21 : adjacent_5p outward -A21-A22 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A24-A25 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward pairing -A32-A33 : adjacent_5p upward -A34-A35 : adjacent_5p upward -A36-A37 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A36 : outward -A8-A32 : outward -A15-A23 : outward -A17-A19 : upward -Number of stackings = 24 -Number of adjacent stackings = 20 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A1-A38 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A37 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A36 : U-A Ww/Ww pairing antiparallel cis XX -A4-A35 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A34 : C-G Ww/Ww pairing antiparallel cis XIX -A7-A32 : G-A Ss/Hh pairing antiparallel trans XI -A8-A31 : A-U Hw/Ws pairing antiparallel trans one_hbond -A9-A28 : A-U Ww/O2' Bh/O2' pairing -A9-A29 : A-A Hh/Hh pairing parallel trans II -A10-A27 : A-A Wh/Ss pairing antiparallel trans one_hbond 40 -A11-A26 : C-U Bh/Bs pairing antiparallel cis -A12-A25 : A-G Hh/Ss Bh/O2' pairing antiparallel trans XI -A13-A24 : G-C Ww/Ww pairing antiparallel cis XIX -A14-A23 : C-G Ww/Ww pairing antiparallel cis XIX -A15-A22 : G-C Ww/Ww pairing antiparallel cis XIX -A16-A21 : C-G Ww/Ww pairing antiparallel cis XIX -A17-A20 : U-G Bs/Ww O2'/Ww pairing parallel trans 87 -A18-A20 : U-G O2'/Hh pairing -A26-A27 : U-A O2'/C8 adjacent_5p upward pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : U C3p_endo anti -A4 : G C3p_endo anti -A5 : C C3p_endo anti -A6 : A C4p_exo anti -A7 : G C2p_exo anti -A8 : A C2p_exo anti -A9 : A O4p_endo anti -A10 : A C3p_endo anti -A11 : C C3p_endo anti -A12 : A C3p_endo anti -A13 : G C2p_exo anti -A14 : C C3p_endo anti -A15 : G C3p_endo anti -A16 : C C3p_endo anti -A17 : U C3p_endo anti -A18 : U C2p_endo anti -A19 : C C3p_exo anti -A20 : G O4p_endo syn -A21 : G C2p_exo anti -A22 : C C3p_endo anti -A23 : G C3p_endo anti -A24 : C C3p_endo anti -A25 : G C3p_endo anti -A26 : U O4p_endo anti -A27 : A C3p_endo anti -A28 : U C3p_endo anti -A29 : A C3p_exo anti -A30 : U C4p_endo anti -A31 : U C3p_endo anti -A32 : A O4p_endo anti -A33 : C C3p_endo anti -A34 : G C4p_exo anti -A35 : C C2p_exo anti -A36 : A C4p_exo anti -A37 : C C3p_endo anti -A38 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A24-A25 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A32-A33 : adjacent_5p upward -A34-A35 : adjacent_5p upward -A36-A37 : adjacent_5p upward -A37-A38 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A36 : outward -A15-A23 : outward -Number of stackings = 22 -Number of adjacent stackings = 20 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A1-A38 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A37 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A36 : U-A Ww/Ww pairing antiparallel cis XX -A4-A35 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A34 : C-G Ww/Ww pairing antiparallel cis XIX -A6-A33 : A-C Ww/Wh pairing antiparallel cis one_hbond 71 -A7-A32 : G-A Ss/Bh pairing antiparallel trans one_hbond 63 -A9-A29 : A-A Hw/Hh pairing parallel trans one_hbond -A10-A27 : A-A Bh/Ss pairing antiparallel trans one_hbond 40 -A11-A12 : C-A O2'/C8 adjacent_5p pairing -A12-A25 : A-G Bh/Ss pairing antiparallel trans one_hbond 63 -A13-A24 : G-C Ww/Ww pairing antiparallel cis XIX -A14-A23 : C-G Ww/Ww pairing antiparallel cis XIX -A15-A22 : G-C Ww/Ww pairing antiparallel cis XIX -A16-A21 : C-G Ww/Ww pairing antiparallel cis XIX -A17-A20 : U-G Ws/Ws pairing parallel trans one_hbond 87 -Residue conformations ------------------------------------------- -A1 : G C2p_exo anti -A2 : G C3p_endo anti -A3 : U C3p_endo anti -A4 : G C3p_endo anti -A5 : C C4p_exo anti -A6 : A C3p_endo anti -A7 : G C3p_endo anti -A8 : A C2p_exo anti -A9 : A O4p_endo anti -A10 : A C3p_endo anti -A11 : C C2p_exo anti -A12 : A C4p_exo anti -A13 : G C3p_endo anti -A14 : C C3p_endo anti -A15 : G C3p_endo anti -A16 : C C3p_endo anti -A17 : U C3p_endo anti -A18 : U C2p_endo anti -A19 : C C2p_endo anti -A20 : G O4p_endo syn -A21 : G C2p_exo anti -A22 : C C3p_endo anti -A23 : G C3p_endo anti -A24 : C O4p_endo anti -A25 : G C3p_endo anti -A26 : U C4p_exo anti -A27 : A C4p_exo anti -A28 : U C3p_endo anti -A29 : A C3p_exo anti -A30 : U C2p_endo anti -A31 : U C3p_endo anti -A32 : A C4p_exo anti -A33 : C C3p_endo anti -A34 : G C2p_exo anti -A35 : C C3p_endo anti -A36 : A C3p_endo anti -A37 : C C2p_exo anti -A38 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A20-A21 : adjacent_5p outward -A21-A22 : adjacent_5p upward -A22-A23 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A32-A33 : adjacent_5p upward -A34-A35 : adjacent_5p upward -A36-A37 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A8-A32 : outward -A15-A23 : outward -A17-A19 : upward -Number of stackings = 22 -Number of adjacent stackings = 19 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -A1-A38 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A37 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A36 : U-A Ww/Ww pairing antiparallel cis XX -A4-A35 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A34 : C-G Ww/Ww pairing antiparallel cis XIX -A6-A33 : A-C Ww/Wh pairing antiparallel cis one_hbond 71 -A7-A32 : G-A Ss/Hh pairing antiparallel trans XI -A8-A31 : A-U Hw/Ws pairing antiparallel trans one_hbond -A9-A10 : A-A O2'/C8 adjacent_5p pairing -A9-A28 : A-U Bh/O2' pairing -A10-A27 : A-A Bh/Ss pairing antiparallel trans one_hbond 40 -A11-A26 : C-U Wh/Ws pairing antiparallel cis one_hbond 100 -A12-A25 : A-G Hw/Ss pairing antiparallel trans one_hbond -A13-A24 : G-C Ww/Ww pairing antiparallel cis XIX -A14-A23 : C-G Ww/Ww pairing antiparallel cis XIX -A15-A22 : G-C Ww/Ww pairing antiparallel cis XIX -A16-A21 : C-G Ww/Ww pairing antiparallel cis XIX -A17-A20 : U-G Ws/Ws pairing parallel trans one_hbond 87 -A27-A28 : A-U O2'/Hh adjacent_5p pairing -Residue conformations ------------------------------------------- -A1 : G C2p_exo anti -A2 : G C4p_exo anti -A3 : U C2p_exo anti -A4 : G C2p_exo anti -A5 : C C4p_exo anti -A6 : A C2p_exo anti -A7 : G C3p_endo anti -A8 : A C3p_endo anti -A9 : A C4p_exo anti -A10 : A C3p_endo anti -A11 : C C3p_endo anti -A12 : A C4p_exo anti -A13 : G C3p_endo anti -A14 : C C3p_endo anti -A15 : G C3p_endo anti -A16 : C C3p_endo anti -A17 : U C3p_endo anti -A18 : U C2p_endo anti -A19 : C C1p_exo anti -A20 : G C4p_exo syn -A21 : G C3p_endo anti -A22 : C C3p_endo anti -A23 : G C4p_exo anti -A24 : C C4p_exo anti -A25 : G C3p_endo anti -A26 : U C4p_exo anti -A27 : A C3p_endo anti -A28 : U C3p_endo anti -A29 : A C3p_exo anti -A30 : U C1p_exo anti -A31 : U C3p_endo anti -A32 : A C4p_exo anti -A33 : C C3p_endo anti -A34 : G C3p_endo anti -A35 : C C3p_endo anti -A36 : A C2p_exo anti -A37 : C C3p_endo anti -A38 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A20-A21 : adjacent_5p outward -A21-A22 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A32-A33 : adjacent_5p upward -A34-A35 : adjacent_5p upward -A36-A37 : adjacent_5p upward -A37-A38 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A36 : outward -A8-A32 : outward -A15-A23 : outward -Number of stackings = 21 -Number of adjacent stackings = 18 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -A1-A38 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A37 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A36 : U-A Ww/Ww pairing antiparallel cis XX -A4-A35 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A34 : C-G Ww/Ww pairing antiparallel cis XIX -A7-A8 : G-A O2'/C8 adjacent_5p pairing -A7-A32 : G-A Ss/Hw pairing antiparallel trans XI -A8-A31 : A-U Hh/Ws pairing antiparallel trans XXIV -A9-A29 : A-A Hh/Hh pairing parallel trans one_hbond -A10-A27 : A-A Wh/Ss pairing antiparallel trans one_hbond 40 -A12-A25 : A-G Hh/Ss pairing antiparallel trans XI -A13-A24 : G-C Ww/Ww pairing antiparallel cis XIX -A14-A23 : C-G Ww/Ww pairing antiparallel cis XIX -A15-A22 : G-C Ww/Ww pairing antiparallel cis XIX -A16-A21 : C-G Ww/Ww pairing antiparallel cis XIX -A17-A20 : U-G Ws/Ws pairing parallel trans one_hbond 87 -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C2p_exo anti -A3 : U C3p_endo anti -A4 : G C3p_endo anti -A5 : C C3p_endo anti -A6 : A C4p_exo anti -A7 : G C3p_endo anti -A8 : A C3p_endo anti -A9 : A C3p_endo anti -A10 : A C3p_endo anti -A11 : C O4p_endo anti -A12 : A C3p_endo anti -A13 : G C3p_endo anti -A14 : C C3p_endo anti -A15 : G C4p_exo anti -A16 : C C3p_endo anti -A17 : U C3p_endo anti -A18 : U C2p_endo anti -A19 : C C1p_exo anti -A20 : G O4p_endo syn -A21 : G C2p_exo anti -A22 : C C3p_endo anti -A23 : G C3p_endo anti -A24 : C C4p_exo anti -A25 : G C3p_endo anti -A26 : U C4p_exo anti -A27 : A C4p_exo anti -A28 : U C3p_endo anti -A29 : A C1p_exo anti -A30 : U C2p_endo anti -A31 : U C4p_exo anti -A32 : A C4p_exo anti -A33 : C C2p_exo anti -A34 : G C4p_exo anti -A35 : C C3p_endo anti -A36 : A C2p_exo anti -A37 : C C4p_exo anti -A38 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A20-A21 : adjacent_5p outward -A21-A22 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A24-A25 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A32-A33 : adjacent_5p upward -A34-A35 : adjacent_5p upward -A35-A36 : adjacent_5p upward -A36-A37 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A36 : outward -A8-A32 : outward -A15-A23 : outward -A17-A19 : upward -Number of stackings = 25 -Number of adjacent stackings = 21 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A1-A38 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A37 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A36 : U-A Ww/Ww pairing antiparallel cis XX -A4-A35 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A34 : C-G Ww/Ww pairing antiparallel cis XIX -A6-A33 : A-C Ww/Bh pairing antiparallel cis one_hbond 71 -A7-A8 : G-A O2'/C8 adjacent_5p pairing -A7-A32 : G-A Ss/Hh pairing antiparallel trans XI -A8-A31 : A-U Hh/Ws pairing antiparallel trans XXIV -A9-A28 : A-U Wh/Ss Bh/O2' pairing antiparallel trans one_hbond -A9-A29 : A-A Hh/Hh pairing parallel trans II -A10-A27 : A-A Wh/Ss pairing antiparallel trans one_hbond 40 -A11-A26 : C-U Wh/Ws pairing antiparallel cis one_hbond 100 -A12-A25 : A-G Wh/Ss pairing antiparallel cis one_hbond 63 -A13-A24 : G-C Ww/Ww pairing antiparallel cis XIX -A14-A23 : C-G Ww/Ww pairing antiparallel cis XIX -A15-A22 : G-C Ww/Ww pairing antiparallel cis XIX -A16-A21 : C-G Ww/Ww pairing antiparallel cis XIX -A18-A20 : U-G O2'/Hh O2'/C8 pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : U C3p_endo anti -A4 : G C3p_endo anti -A5 : C C3p_endo anti -A6 : A C4p_exo anti -A7 : G C3p_endo anti -A8 : A C2p_exo anti -A9 : A O4p_endo anti -A10 : A C3p_endo anti -A11 : C C3p_endo anti -A12 : A C4p_exo anti -A13 : G C3p_endo anti -A14 : C C2p_exo anti -A15 : G C3p_endo anti -A16 : C C3p_endo anti -A17 : U C2p_exo anti -A18 : U C3p_exo anti -A19 : C C2p_endo anti -A20 : G O4p_endo syn -A21 : G C2p_exo anti -A22 : C C3p_endo anti -A23 : G C4p_exo anti -A24 : C O4p_endo anti -A25 : G C3p_endo anti -A26 : U O4p_endo anti -A27 : A C3p_endo anti -A28 : U C3p_endo anti -A29 : A C1p_endo anti -A30 : U C2p_endo anti -A31 : U C3p_endo anti -A32 : A C4p_exo anti -A33 : C C3p_endo anti -A34 : G C2p_exo anti -A35 : C C3p_endo anti -A36 : A C3p_endo anti -A37 : C C3p_endo anti -A38 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A24-A25 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A32-A33 : adjacent_5p upward -A34-A35 : adjacent_5p upward -A35-A36 : adjacent_5p upward -A36-A37 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A36 : outward -A8-A32 : outward -A15-A23 : outward -A17-A19 : upward -Number of stackings = 23 -Number of adjacent stackings = 19 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A1-A38 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A37 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A36 : U-A Ww/Ww pairing antiparallel cis XX -A4-A35 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A34 : C-G Ww/Ww pairing antiparallel cis XIX -A7-A8 : G-A O2'/C8 adjacent_5p pairing -A7-A32 : G-A Ss/Hh pairing antiparallel trans XI -A8-A31 : A-U Bh/Ws pairing antiparallel trans one_hbond -A9-A28 : A-U Wh/Ss pairing antiparallel trans one_hbond -A9-A29 : A-A Hw/Hh pairing parallel trans one_hbond -A10-A27 : A-A Bh/Ss pairing antiparallel trans one_hbond 40 -A13-A24 : G-C Ww/Ww pairing antiparallel cis XIX -A14-A23 : C-G Ww/Ww pairing antiparallel cis XIX -A15-A22 : G-C Ww/Ww pairing antiparallel cis XIX -A16-A21 : C-G Ww/Ww pairing antiparallel cis XIX -A17-A20 : U-G Ws/Ws pairing parallel trans one_hbond 87 -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C2p_exo anti -A3 : U C3p_endo anti -A4 : G C4p_exo anti -A5 : C C3p_endo anti -A6 : A C4p_exo anti -A7 : G C3p_endo anti -A8 : A C3p_endo anti -A9 : A O4p_endo anti -A10 : A C3p_endo anti -A11 : C C3p_endo anti -A12 : A C4p_exo anti -A13 : G C3p_endo anti -A14 : C C2p_exo anti -A15 : G C3p_endo anti -A16 : C C3p_endo anti -A17 : U C3p_endo anti -A18 : U C2p_endo anti -A19 : C C1p_exo anti -A20 : G C4p_exo syn -A21 : G C3p_endo anti -A22 : C C3p_endo anti -A23 : G C4p_exo anti -A24 : C O4p_endo anti -A25 : G C3p_endo anti -A26 : U C4p_exo anti -A27 : A C3p_endo anti -A28 : U C3p_endo anti -A29 : A C2p_endo anti -A30 : U C2p_endo anti -A31 : U C3p_endo anti -A32 : A C4p_exo anti -A33 : C C3p_endo anti -A34 : G C3p_endo anti -A35 : C C3p_endo anti -A36 : A C2p_exo anti -A37 : C C4p_exo anti -A38 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A24-A25 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward pairing -A27-A28 : adjacent_5p upward -A32-A33 : adjacent_5p upward -A34-A35 : adjacent_5p upward -A36-A37 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A36 : outward -A6-A34 : outward -A15-A23 : outward -Number of stackings = 24 -Number of adjacent stackings = 21 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -A1-A38 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A37 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A36 : U-A Ww/Ww pairing antiparallel cis XX -A4-A35 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A34 : C-G Ww/Ww pairing antiparallel cis XIX -A6-A33 : A-C Ww/Wh pairing antiparallel cis one_hbond 71 -A7-A32 : G-A Ss/Hh pairing antiparallel trans XI -A8-A31 : A-U Hh/Ws pairing antiparallel trans XXIV -A9-A28 : A-U Bh/O2' pairing -A10-A27 : A-A Bh/Ss pairing antiparallel trans one_hbond 40 -A12-A25 : A-G Wh/Ss Ww/O2' pairing antiparallel trans one_hbond 63 -A13-A24 : G-C Ww/Ww pairing antiparallel cis XIX -A14-A23 : C-G Ww/Ww pairing antiparallel cis XIX -A15-A22 : G-C Ww/Ww pairing antiparallel cis XIX -A16-A21 : C-G Ww/Ww pairing antiparallel cis XIX -A26-A27 : U-A O2'/C8 adjacent_5p upward pairing diff --git a/MCdata/1b7f_MC b/MCdata/1b7f_MC deleted file mode 100644 index 8c42b46c91b6cee4044039abfc4a7b6e828b6e41..0000000000000000000000000000000000000000 --- a/MCdata/1b7f_MC +++ /dev/null @@ -1,453 +0,0 @@ -Residue conformations ------------------------------------------- -P1 : G C1p_exo syn -P2 : U C2p_endo anti -P3 : U C1p_exo anti -P4 : G C2p_endo anti -P5 : U C2p_endo anti -P6 : U C1p_exo anti -P7 : U C2p_exo anti -P8 : U C4p_exo anti -P9 : U C2p_endo anti -P10 : U C2p_endo anti -P11 : U C2p_exo anti -P12 : U C4p_endo syn -Q1 : G O4p_endo syn -Q2 : U O4p_exo syn -Q3 : U C2p_endo anti -Q4 : G C3p_exo anti -Q5 : U C2p_endo anti -Q6 : U C1p_exo anti -Q7 : U C2p_exo anti -Q8 : U C3p_endo anti -Q9 : U C2p_endo anti -Q10 : U C2p_endo anti -Q11 : U O4p_endo anti -Q12 : U O4p_endo syn -A123 : SER -A124 : ASN -A125 : THR -A126 : ASN -A127 : LEU -A128 : ILE -A129 : VAL -A130 : ASN -A131 : TYR -A132 : LEU -A133 : PRO -A134 : GLN -A135 : ASP -A136 : MET -A137 : THR -A138 : ASP -A139 : ARG -A140 : GLU -A141 : LEU -A142 : TYR -A143 : ALA -A144 : LEU -A145 : PHE -A146 : ARG -A147 : ALA -A148 : ILE -A149 : GLY -A150 : PRO -A151 : ILE -A152 : ASN -A153 : THR -A154 : CYS -A155 : ARG -A156 : ILE -A157 : MET -A158 : ARG -A159 : ASP -A160 : TYR -A161 : LYS -A162 : THR -A163 : GLY -A164 : TYR -A165 : SER -A166 : TYR -A167 : GLY -A168 : TYR -A169 : ALA -A170 : PHE -A171 : VAL -A172 : ASP -A173 : PHE -A174 : THR -A175 : SER -A176 : GLU -A177 : MET -A178 : ASP -A179 : SER -A180 : GLN -A181 : ARG -A182 : ALA -A183 : ILE -A184 : LYS -A185 : VAL -A186 : LEU -A187 : ASN -A188 : GLY -A189 : ILE -A190 : THR -A191 : VAL -A192 : ARG -A193 : ASN -A194 : LYS -A195 : ARG -A196 : LEU -A197 : LYS -A198 : VAL -A199 : SER -A200 : TYR -A201 : ALA -A202 : ARG -A203 : PRO -A204 : GLY -A205 : GLY -A206 : GLU -A207 : SER -A208 : ILE -A209 : LYS -A210 : ASP -A211 : THR -A212 : ASN -A213 : LEU -A214 : TYR -A215 : VAL -A216 : THR -A217 : ASN -A218 : LEU -A219 : PRO -A220 : ARG -A221 : THR -A222 : ILE -A223 : THR -A224 : ASP -A225 : ASP -A226 : GLN -A227 : LEU -A228 : ASP -A229 : THR -A230 : ILE -A231 : PHE -A232 : GLY -A233 : LYS -A234 : TYR -A235 : GLY -A236 : SER -A237 : ILE -A238 : VAL -A239 : GLN -A240 : LYS -A241 : ASN -A242 : ILE -A243 : LEU -A244 : ARG -A245 : ASP -A246 : LYS -A247 : LEU -A248 : THR -A249 : GLY -A250 : ARG -A251 : PRO -A252 : ARG -A253 : GLY -A254 : VAL -A255 : ALA -A256 : PHE -A257 : VAL -A258 : ARG -A259 : TYR -A260 : ASN -A261 : LYS -A262 : ARG -A263 : GLU -A264 : GLU -A265 : ALA -A266 : GLN -A267 : GLU -A268 : ALA -A269 : ILE -A270 : SER -A271 : ALA -A272 : LEU -A273 : ASN -A274 : ASN -A275 : VAL -A276 : ILE -A277 : PRO -A278 : GLU -A279 : GLY -A280 : GLY -A281 : SER -A282 : GLN -A283 : PRO -A284 : LEU -A285 : SER -A286 : VAL -A287 : ARG -A288 : LEU -A289 : ALA -B123 : SER -B124 : ASN -B125 : THR -B126 : ASN -B127 : LEU -B128 : ILE -B129 : VAL -B130 : ASN -B131 : TYR -B132 : LEU -B133 : PRO -B134 : GLN -B135 : ASP -B136 : MET -B137 : THR -B138 : ASP -B139 : ARG -B140 : GLU -B141 : LEU -B142 : TYR -B143 : ALA -B144 : LEU -B145 : PHE -B146 : ARG -B147 : ALA -B148 : ILE -B149 : GLY -B150 : PRO -B151 : ILE -B152 : ASN -B153 : THR -B154 : CYS -B155 : ARG -B156 : ILE -B157 : MET -B158 : ARG -B159 : ASP -B160 : TYR -B161 : LYS -B162 : THR -B163 : GLY -B164 : TYR -B165 : SER -B166 : TYR -B167 : GLY -B168 : TYR -B169 : ALA -B170 : PHE -B171 : VAL -B172 : ASP -B173 : PHE -B174 : THR -B175 : SER -B176 : GLU -B177 : MET -B178 : ASP -B179 : SER -B180 : GLN -B181 : ARG -B182 : ALA -B183 : ILE -B184 : LYS -B185 : VAL -B186 : LEU -B187 : ASN -B188 : GLY -B189 : ILE -B190 : THR -B191 : VAL -B192 : ARG -B193 : ASN -B194 : LYS -B195 : ARG -B196 : LEU -B197 : LYS -B198 : VAL -B199 : SER -B200 : TYR -B201 : ALA -B202 : ARG -B203 : PRO -B204 : GLY -B205 : GLY -B206 : GLU -B207 : SER -B208 : ILE -B209 : LYS -B210 : ASP -B211 : THR -B212 : ASN -B213 : LEU -B214 : TYR -B215 : VAL -B216 : THR -B217 : ASN -B218 : LEU -B219 : PRO -B220 : ARG -B221 : THR -B222 : ILE -B223 : THR -B224 : ASP -B225 : ASP -B226 : GLN -B227 : LEU -B228 : ASP -B229 : THR -B230 : ILE -B231 : PHE -B232 : GLY -B233 : LYS -B234 : TYR -B235 : GLY -B236 : SER -B237 : ILE -B238 : VAL -B239 : GLN -B240 : LYS -B241 : ASN -B242 : ILE -B243 : LEU -B244 : ARG -B245 : ASP -B246 : LYS -B247 : LEU -B248 : THR -B249 : GLY -B250 : ARG -B251 : PRO -B252 : ARG -B253 : GLY -B254 : VAL -B255 : ALA -B256 : PHE -B257 : VAL -B258 : ARG -B259 : TYR -B260 : ASN -B261 : LYS -B262 : ARG -B263 : GLU -B264 : GLU -B265 : ALA -B266 : GLN -B267 : GLU -B268 : ALA -B269 : ILE -B270 : SER -B271 : ALA -B272 : LEU -B273 : ASN -B274 : ASN -B275 : VAL -B276 : ILE -B277 : PRO -B278 : GLU -B279 : GLY -B280 : GLY -B281 : SER -B282 : GLN -B283 : PRO -B284 : LEU -B285 : SER -B286 : VAL -B287 : ARG -B288 : LEU -B289 : ALA -P42 : HOH -P59 : HOH -P62 : HOH -P104 : HOH -P116 : HOH -P128 : HOH -P149 : HOH -Q20 : HOH -Q32 : HOH -Q48 : HOH -Q78 : HOH -Q123 : HOH -Q132 : HOH -Q143 : HOH -Q145 : HOH -A290 : HOH -A291 : HOH -A292 : HOH -A293 : HOH -A294 : HOH -A295 : HOH -A296 : HOH -A297 : HOH -A298 : HOH -A299 : HOH -A300 : HOH -A301 : HOH -A302 : HOH -A303 : HOH -A304 : HOH -A305 : HOH -A306 : HOH -A307 : HOH -A308 : HOH -A309 : HOH -A310 : HOH -A311 : HOH -A312 : HOH -A313 : HOH -A314 : HOH -A315 : HOH -A316 : HOH -A317 : HOH -A318 : HOH -A319 : HOH -A320 : HOH -A321 : HOH -A322 : HOH -A323 : HOH -A324 : HOH -A325 : HOH -B290 : HOH -B291 : HOH -B292 : HOH -B293 : HOH -B294 : HOH -B295 : HOH -B296 : HOH -B297 : HOH -B298 : HOH -B299 : HOH -B300 : HOH -B301 : HOH -B302 : HOH -B303 : HOH -B304 : HOH -B305 : HOH -B306 : HOH -B307 : HOH -B308 : HOH -B309 : HOH -B310 : HOH -B311 : HOH -B312 : HOH -B313 : HOH -B314 : HOH -B315 : HOH -B316 : HOH -B317 : HOH -B318 : HOH -B319 : HOH -B320 : HOH -B321 : HOH -B322 : HOH -Adjacent stackings ---------------------------------------------- -P7-P8 : adjacent_5p upward -Q7-Q8 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 2 -Number of adjacent stackings = 2 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -Q3-Q4 : U-G O2P/Hh O2P/Hh adjacent_5p pairing -Q9-Q10 : U-U Ss/Hh adjacent_5p pairing parallel cis one_hbond diff --git a/MCdata/1bau_MC b/MCdata/1bau_MC deleted file mode 100644 index 9fa7853ff16976ddd205eb8d105804af74b15b89..0000000000000000000000000000000000000000 --- a/MCdata/1bau_MC +++ /dev/null @@ -1,108 +0,0 @@ -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : A C3p_endo anti -A5 : A C3p_endo anti -A6 : U C3p_endo anti -A7 : G C2p_endo anti -A8 : A C3p_endo anti -A9 : A C3p_endo anti -A10 : G C3p_endo anti -A11 : C C3p_endo anti -A12 : G C3p_endo anti -A13 : C C3p_endo anti -A14 : G C3p_endo anti -A15 : C C3p_endo anti -A16 : A C3p_endo anti -A17 : C C3p_endo anti -A18 : G C3p_endo anti -A19 : U C3p_endo anti -A20 : U C3p_endo anti -A21 : G C3p_endo anti -A22 : C C3p_endo anti -A23 : C C3p_endo anti -B1 : G C3p_endo anti -B2 : G C3p_endo anti -B3 : C C3p_endo anti -B4 : A C3p_endo anti -B5 : A C3p_endo anti -B6 : U C3p_endo anti -B7 : G C2p_endo anti -B8 : A C3p_endo anti -B9 : A C3p_endo anti -B10 : G C3p_endo anti -B11 : C C3p_endo anti -B12 : G C3p_endo anti -B13 : C C3p_endo anti -B14 : G C3p_endo anti -B15 : C C3p_endo anti -B16 : A C3p_endo anti -B17 : C C3p_endo anti -B18 : G C3p_endo anti -B19 : U C3p_endo anti -B20 : U C3p_endo anti -B21 : G C3p_endo anti -B22 : C C3p_endo anti -B23 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A22-A23 : adjacent_5p upward -B1-B2 : adjacent_5p upward -B2-B3 : adjacent_5p upward -B4-B5 : adjacent_5p upward -B5-B6 : adjacent_5p upward -B6-B7 : adjacent_5p upward -B10-B11 : adjacent_5p upward -B12-B13 : adjacent_5p upward -B14-B15 : adjacent_5p upward -B15-B16 : adjacent_5p upward -B18-B19 : adjacent_5p upward -B19-B20 : adjacent_5p upward -B21-B22 : adjacent_5p upward -B22-B23 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A21 : outward -A9-B17 : outward -B4-B21 : outward -Number of stackings = 29 -Number of adjacent stackings = 26 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -A1-A23 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A22 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A21 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A20 : A-U Ww/Ww pairing antiparallel cis XX -A5-A19 : A-U Ww/Ww pairing antiparallel cis XX -A6-A18 : U-G Ws/Ww pairing antiparallel cis XXVIII -A8-A10 : A-G C8/O2P pairing -A8-A11 : A-C Bh/O2P pairing -A8-B9 : A-A O2'/C8 pairing -A9-B8 : A-A C8/O2' pairing -A9-B16 : A-A Wh/Ss pairing antiparallel cis one_hbond 40 -A10-B15 : G-C Ww/Ww pairing antiparallel cis 127 -A11-B14 : C-G Ww/Ww pairing antiparallel cis 128 -A12-B13 : G-C Ww/Ww pairing antiparallel cis 128 -A13-B12 : C-G Ww/Ww pairing antiparallel cis 128 -A14-B11 : G-C Ww/Ww pairing antiparallel cis XIX -A15-B10 : C-G Ww/Ww pairing antiparallel cis XIX -A16-B9 : A-A Ss/Wh pairing antiparallel cis one_hbond 40 -B1-B23 : G-C Ww/Ww pairing antiparallel cis XIX -B2-B22 : G-C Ww/Ww pairing antiparallel cis XIX -B3-B21 : C-G Ww/Ww pairing antiparallel cis XIX -B4-B20 : A-U Ww/Ww pairing antiparallel cis XX -B5-B19 : A-U Ww/Ww pairing antiparallel cis XX -B6-B18 : U-G Ws/Ww pairing antiparallel cis XXVIII -B8-B10 : A-G C8/O2P pairing -B8-B11 : A-C Bh/O2P pairing diff --git a/MCdata/1bgz_MC b/MCdata/1bgz_MC deleted file mode 100644 index 066ddcc8975b3c745a4bc601d753afe14ed710e3..0000000000000000000000000000000000000000 --- a/MCdata/1bgz_MC +++ /dev/null @@ -1,325 +0,0 @@ -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : G C3p_endo anti -A4 : A C3p_endo anti -A5 : U C3p_exo anti -A6 : A C3p_endo anti -A7 : C C3p_endo anti -A8 : U C3p_endo anti -A9 : G C3p_endo anti -A10 : C C3p_endo anti -A11 : U C3p_endo anti -A12 : U C3p_exo anti -A13 : C C3p_exo anti -A14 : G C3p_endo syn -A15 : G C3p_endo anti -A16 : U C3p_endo anti -A17 : A C3p_exo anti -A18 : A C3p_endo anti -A19 : G C3p_endo anti -A20 : U C3p_endo anti -A21 : C C3p_endo anti -A22 : C C3p_endo anti -A23 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A14-A15 : adjacent_5p outward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A22-A23 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 14 -Number of adjacent stackings = 14 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-A23 : G-C Wh/Ww pairing antiparallel cis one_hbond -A2-A22 : G-C Ww/Ww pairing antiparallel cis one_hbond -A3-A21 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A20 : A-U Ww/Ww pairing antiparallel cis XX -A5-A7 : U-C O2'/Bh pairing -A5-A17 : U-A O2'/Bh pairing -A7-A19 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A18 : U-A Ww/Ww pairing antiparallel cis XX -A9-A16 : G-U Ww/Ws pairing antiparallel cis XXVIII -A10-A15 : C-G Ws/Ww pairing antiparallel cis one_hbond 130 -A12-A13 : U-C O2P/Ww adjacent_5p pairing -A17-A18 : A-A Ss/Hw adjacent_5p pairing parallel cis one_hbond -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : G C3p_endo anti -A4 : A C3p_endo anti -A5 : U C3p_exo anti -A6 : A C3p_endo anti -A7 : C C3p_endo anti -A8 : U C3p_endo anti -A9 : G C3p_endo anti -A10 : C C3p_endo anti -A11 : U C3p_endo anti -A12 : U C3p_exo anti -A13 : C C3p_exo anti -A14 : G C3p_endo syn -A15 : G C3p_endo anti -A16 : U C3p_endo anti -A17 : A C3p_exo anti -A18 : A C3p_endo anti -A19 : G C3p_endo anti -A20 : U C3p_endo anti -A21 : C C3p_endo anti -A22 : C C3p_endo anti -A23 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A14-A15 : adjacent_5p outward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A20-A21 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 13 -Number of adjacent stackings = 13 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A2-A22 : G-C Ww/Ww pairing antiparallel cis -A3-A21 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A20 : A-U Ww/Ww pairing antiparallel cis XX -A5-A7 : U-C O2'/Bh pairing -A5-A17 : U-A O2'/Bh pairing -A7-A19 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A17 : U-A Wh/Bs pairing antiparallel trans one_hbond -A8-A18 : U-A Ww/Ww pairing antiparallel cis XX -A9-A16 : G-U Ww/Ws pairing antiparallel cis XXVIII -A10-A15 : C-G Ws/Ww pairing antiparallel cis one_hbond 130 -A12-A13 : U-C O2P/Bh adjacent_5p pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : G C3p_endo anti -A4 : A C3p_endo anti -A5 : U C3p_exo anti -A6 : A C3p_endo anti -A7 : C C3p_endo anti -A8 : U C3p_endo anti -A9 : G C3p_endo anti -A10 : C C3p_endo anti -A11 : U C3p_endo anti -A12 : U C3p_exo anti -A13 : C C3p_exo anti -A14 : G C3p_endo syn -A15 : G C3p_endo anti -A16 : U C3p_endo anti -A17 : A C3p_exo anti -A18 : A C3p_endo anti -A19 : G C3p_endo anti -A20 : U C3p_endo anti -A21 : C C3p_endo anti -A22 : C C3p_endo anti -A23 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A14-A15 : adjacent_5p outward -A16-A17 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A20-A21 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 12 -Number of adjacent stackings = 12 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-A23 : G-C Ww/Ww pairing antiparallel cis one_hbond -A2-A22 : G-C Ww/Ww pairing antiparallel cis -A3-A21 : G-C Ww/Ww pairing antiparallel cis -A4-A20 : A-U Ww/Ww pairing antiparallel cis XX -A5-A7 : U-C O2'/Bh pairing -A5-A17 : U-A O2'/Bh pairing -A7-A19 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A18 : U-A Ww/Ww pairing antiparallel cis XX -A9-A16 : G-U Ww/Ws pairing antiparallel cis XXVIII -A10-A15 : C-G Ww/Ww pairing antiparallel cis one_hbond 130 -A12-A13 : U-C O2P/Bh adjacent_5p pairing -A17-A18 : A-A Ss/Hw adjacent_5p pairing parallel cis one_hbond -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : G C3p_endo anti -A4 : A C3p_endo anti -A5 : U C3p_exo anti -A6 : A C3p_endo anti -A7 : C C3p_endo anti -A8 : U C3p_endo anti -A9 : G C3p_endo anti -A10 : C C3p_endo anti -A11 : U C3p_endo anti -A12 : U C3p_exo anti -A13 : C C3p_exo anti -A14 : G C3p_endo syn -A15 : G C3p_endo anti -A16 : U C3p_endo anti -A17 : A C3p_exo anti -A18 : A C3p_endo anti -A19 : G C3p_endo anti -A20 : U C3p_endo anti -A21 : C C3p_endo anti -A22 : C C3p_endo anti -A23 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A14-A15 : adjacent_5p outward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A22-A23 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 15 -Number of adjacent stackings = 15 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-A23 : G-C Ww/Ww pairing antiparallel cis one_hbond -A2-A22 : G-C Ww/Ww pairing antiparallel cis one_hbond -A3-A21 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A20 : A-U Ww/Ww pairing antiparallel cis XX -A5-A7 : U-C Ws/Hw pairing parallel cis one_hbond 99 -A8-A18 : U-A Ww/Ww pairing antiparallel cis XX -A9-A16 : G-U Ww/Ws pairing antiparallel cis XXVIII -A10-A15 : C-G Ww/Ww pairing antiparallel cis one_hbond 130 -A12-A13 : U-C O2P/Bh adjacent_5p pairing -A17-A18 : A-A Ss/Hw adjacent_5p pairing parallel cis one_hbond -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : G C3p_endo anti -A4 : A C3p_endo anti -A5 : U C3p_exo anti -A6 : A C3p_endo anti -A7 : C C3p_endo anti -A8 : U C3p_endo anti -A9 : G C3p_endo anti -A10 : C C3p_endo anti -A11 : U C3p_endo anti -A12 : U C3p_exo anti -A13 : C C3p_exo anti -A14 : G C3p_endo syn -A15 : G C3p_endo anti -A16 : U C3p_endo anti -A17 : A C3p_exo anti -A18 : A C3p_endo anti -A19 : G C3p_endo anti -A20 : U C3p_endo anti -A21 : C C3p_endo anti -A22 : C C3p_endo anti -A23 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A14-A15 : adjacent_5p outward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A22-A23 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 15 -Number of adjacent stackings = 15 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-A23 : G-C Ww/Ww pairing antiparallel cis one_hbond -A2-A22 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A21 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A20 : A-U Ww/Ww pairing antiparallel cis XX -A5-A7 : U-C Ws/Hw pairing parallel cis one_hbond 99 -A7-A19 : C-G Ww/Ww pairing antiparallel cis one_hbond -A8-A18 : U-A Ww/Ww pairing antiparallel cis XX -A9-A16 : G-U Ww/Ws pairing antiparallel cis XXVIII -A10-A15 : C-G Ws/Ww pairing antiparallel cis one_hbond 130 -A12-A13 : U-C O2P/Ww adjacent_5p pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : G C3p_endo anti -A4 : A C3p_endo anti -A5 : U C3p_exo anti -A6 : A C3p_endo anti -A7 : C C3p_endo anti -A8 : U C3p_endo anti -A9 : G C3p_endo anti -A10 : C C3p_endo anti -A11 : U C3p_endo anti -A12 : U C3p_exo anti -A13 : C C3p_exo anti -A14 : G C3p_endo syn -A15 : G C3p_endo anti -A16 : U C3p_endo anti -A17 : A C3p_exo anti -A18 : A C3p_endo anti -A19 : G C3p_endo anti -A20 : U C3p_endo anti -A21 : C C3p_endo anti -A22 : C C3p_endo anti -A23 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A14-A15 : adjacent_5p outward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A20-A21 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 13 -Number of adjacent stackings = 13 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-A23 : G-C Ww/Ww pairing antiparallel cis one_hbond -A2-A22 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A21 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A20 : A-U Ww/Ww pairing antiparallel cis XX -A5-A7 : U-C Ws/Hw pairing parallel cis one_hbond 99 -A8-A18 : U-A Ww/Ww pairing antiparallel cis XX -A9-A16 : G-U Ww/Ws pairing antiparallel cis XXVIII -A12-A13 : U-C O2P/Bh adjacent_5p pairing diff --git a/MCdata/1biv_MC b/MCdata/1biv_MC deleted file mode 100644 index f306446e8dae02751f3987f8187c565c893c7fc7..0000000000000000000000000000000000000000 --- a/MCdata/1biv_MC +++ /dev/null @@ -1,426 +0,0 @@ -Residue conformations ------------------------------------------- -A4 : G C2p_exo anti -A5 : G C3p_endo anti -A6 : C C3p_endo anti -A7 : U C3p_endo anti -A8 : C C3p_endo anti -A9 : G C3p_endo anti -A10 : U C2p_endo anti -A11 : G C2p_endo anti -A12 : U C2p_endo anti -A13 : A C3p_endo anti -A14 : G C3p_endo anti -A15 : C C3p_endo anti -A16 : U C3p_endo anti -A17 : C C2p_endo syn -A18 : A C2p_endo anti -A19 : U C4p_exo anti -A20 : U C2p_endo anti -A21 : A C2p_endo anti -A22 : G C3p_endo anti -A23 : C C3p_endo anti -A24 : U C3p_endo anti -A25 : C C3p_endo anti -A26 : C C3p_endo anti -A27 : G C3p_endo anti -A28 : A C2p_exo anti -A29 : G C3p_endo anti -A30 : C C3p_endo anti -A31 : C C2p_exo anti -B65 : SER -B66 : GLY -B67 : PRO -B68 : ARG -B69 : PRO -B70 : ARG -B71 : GLY -B72 : THR -B73 : ARG -B74 : GLY -B75 : LYS -B76 : GLY -B77 : ARG -B78 : ARG -B79 : ILE -B80 : ARG -B81 : ARG -Adjacent stackings ---------------------------------------------- -A5-A6 : adjacent_5p upward -A10-A11 : adjacent_5p downward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A22-A23 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A28-A29 : adjacent_5p upward -A29-A30 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A5-A31 : outward -A9-A27 : outward -A11-A13 : upward -Number of stackings = 17 -Number of adjacent stackings = 14 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -A4-A31 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A30 : G-C Ww/Ww pairing antiparallel cis XIX -A6-A29 : C-G Ww/Ww pairing antiparallel cis XIX -A7-A28 : U-A Ww/Ww pairing antiparallel cis XX -A8-A27 : C-G Ww/Ww pairing antiparallel cis XIX -A9-A26 : G-C Ww/Ww pairing antiparallel cis XIX -A9-B77 : G-ARG pairing one_hbond -A10-A13 : U-A Ww/Hh pairing parallel cis XXIII -A11-A25 : G-C Ww/Ww pairing antiparallel cis XIX -A11-B73 : G-ARG pairing one_hbond -A13-A24 : A-U Ww/Ww pairing antiparallel cis XX -A14-A23 : G-C Ww/Ww pairing antiparallel cis XIX -A14-B70 : G-ARG pairing -A15-A22 : C-G Ww/Ww pairing antiparallel cis XIX -A16-A21 : U-A Ww/Ww pairing antiparallel cis XX -Residue conformations ------------------------------------------- -A4 : G C2p_exo anti -A5 : G C3p_endo anti -A6 : C C3p_endo anti -A7 : U C3p_endo anti -A8 : C C3p_endo anti -A9 : G C3p_endo anti -A10 : U C2p_endo anti -A11 : G C2p_endo anti -A12 : U C2p_endo anti -A13 : A C3p_endo anti -A14 : G C3p_endo anti -A15 : C C3p_endo anti -A16 : U C3p_endo anti -A17 : C C3p_exo anti -A18 : A C1p_exo anti -A19 : U C4p_exo anti -A20 : U C2p_endo anti -A21 : A C2p_endo anti -A22 : G C3p_endo anti -A23 : C C3p_endo anti -A24 : U C3p_endo anti -A25 : C C3p_endo anti -A26 : C C3p_endo anti -A27 : G C3p_endo anti -A28 : A C3p_endo anti -A29 : G C4p_exo anti -A30 : C C3p_endo anti -A31 : C C3p_endo anti -B65 : SER -B66 : GLY -B67 : PRO -B68 : ARG -B69 : PRO -B70 : ARG -B71 : GLY -B72 : THR -B73 : ARG -B74 : GLY -B75 : LYS -B76 : GLY -B77 : ARG -B78 : ARG -B79 : ILE -B80 : ARG -B81 : ARG -Adjacent stackings ---------------------------------------------- -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A10-A11 : adjacent_5p downward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A22-A23 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A28-A29 : adjacent_5p upward -A29-A30 : adjacent_5p upward -A30-A31 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A8-A28 : outward -A9-A27 : outward -A14-A24 : outward -Number of stackings = 19 -Number of adjacent stackings = 16 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -A4-A31 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A30 : G-C Ww/Ww pairing antiparallel cis XIX -A6-A29 : C-G Ww/Ww pairing antiparallel cis XIX -A7-A28 : U-A Ww/Ww pairing antiparallel cis XX -A8-A27 : C-G Ww/Ww pairing antiparallel cis -A9-A26 : G-C Ww/Ww pairing antiparallel cis XIX -A11-A25 : G-C Ww/Ww pairing antiparallel cis XIX -A12-A26 : U-C Ww/O2' pairing -A13-A24 : A-U Ww/Ww pairing antiparallel cis XX -A14-A23 : G-C Ww/Ww pairing antiparallel cis XIX -A14-B70 : G-ARG pairing one_hbond -A15-A22 : C-G Ww/Ww pairing antiparallel cis XIX -A16-A21 : U-A Ww/Ww pairing antiparallel cis XX -A17-A18 : C-A O2'/Hh adjacent_5p pairing -Residue conformations ------------------------------------------- -A4 : G C3p_endo anti -A5 : G C3p_endo anti -A6 : C C3p_endo anti -A7 : U C3p_endo anti -A8 : C C3p_endo anti -A9 : G C4p_exo anti -A10 : U C2p_endo anti -A11 : G C2p_endo anti -A12 : U C2p_endo anti -A13 : A C3p_endo anti -A14 : G C3p_endo anti -A15 : C C3p_endo anti -A16 : U C3p_endo anti -A17 : C C2p_endo anti -A18 : A C2p_endo anti -A19 : U C4p_exo anti -A20 : U C2p_endo anti -A21 : A C2p_endo anti -A22 : G C3p_endo anti -A23 : C C3p_endo anti -A24 : U C3p_endo anti -A25 : C C3p_endo anti -A26 : C C3p_endo anti -A27 : G C3p_endo anti -A28 : A C4p_exo anti -A29 : G C3p_endo anti -A30 : C C3p_endo anti -A31 : C C2p_exo anti -B65 : SER -B66 : GLY -B67 : PRO -B68 : ARG -B69 : PRO -B70 : ARG -B71 : GLY -B72 : THR -B73 : ARG -B74 : GLY -B75 : LYS -B76 : GLY -B77 : ARG -B78 : ARG -B79 : ILE -B80 : ARG -B81 : ARG -Adjacent stackings ---------------------------------------------- -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A10-A11 : adjacent_5p downward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A22-A23 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A28-A29 : adjacent_5p upward -A29-A30 : adjacent_5p upward -A30-A31 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A9-A27 : outward -A11-A13 : upward -Number of stackings = 18 -Number of adjacent stackings = 16 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A4-A31 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A30 : G-C Ww/Ww pairing antiparallel cis XIX -A6-A29 : C-G Ww/Ww pairing antiparallel cis XIX -A7-A28 : U-A Ww/Ww pairing antiparallel cis XX -A8-A27 : C-G Ww/Ww pairing antiparallel cis XIX -A9-A26 : G-C Ww/Ww pairing antiparallel cis XIX -A9-B77 : G-ARG pairing one_hbond -A10-A13 : U-A Ww/Hh pairing parallel cis XXIII -A11-A25 : G-C Ww/Ww pairing antiparallel cis XIX -A11-B73 : G-ARG pairing one_hbond -A13-A24 : A-U Ww/Ww pairing antiparallel cis XX -A14-A23 : G-C Ww/Ww pairing antiparallel cis XIX -A14-B70 : G-ARG pairing one_hbond -A15-A22 : C-G Ww/Ww pairing antiparallel cis XIX -A16-A21 : U-A Ww/Ww pairing antiparallel cis XX -A17-A18 : C-A O2'/Hh adjacent_5p pairing -Residue conformations ------------------------------------------- -A4 : G C3p_endo anti -A5 : G C3p_endo anti -A6 : C C3p_endo anti -A7 : U C3p_endo anti -A8 : C C3p_endo anti -A9 : G C3p_endo anti -A10 : U C2p_endo anti -A11 : G C2p_endo anti -A12 : U C2p_endo anti -A13 : A C3p_endo anti -A14 : G C3p_endo anti -A15 : C C3p_endo anti -A16 : U C3p_endo anti -A17 : C C2p_endo anti -A18 : A C1p_exo anti -A19 : U C4p_exo anti -A20 : U C2p_endo anti -A21 : A C2p_endo anti -A22 : G C3p_endo anti -A23 : C C4p_exo anti -A24 : U C3p_endo anti -A25 : C C3p_endo anti -A26 : C C3p_endo anti -A27 : G C3p_endo anti -A28 : A C2p_exo anti -A29 : G C3p_endo anti -A30 : C C3p_endo anti -A31 : C C3p_endo anti -B65 : SER -B66 : GLY -B67 : PRO -B68 : ARG -B69 : PRO -B70 : ARG -B71 : GLY -B72 : THR -B73 : ARG -B74 : GLY -B75 : LYS -B76 : GLY -B77 : ARG -B78 : ARG -B79 : ILE -B80 : ARG -B81 : ARG -Adjacent stackings ---------------------------------------------- -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A10-A11 : adjacent_5p downward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A22-A23 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A28-A29 : adjacent_5p upward -A29-A30 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A5-A31 : outward -A8-A28 : outward -A9-A27 : outward -A11-A13 : upward -A13-A25 : outward -Number of stackings = 21 -Number of adjacent stackings = 16 -Number of non adjacent stackings = 5 -Base-pairs ------------------------------------------------------ -A4-A31 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A30 : G-C Ww/Ww pairing antiparallel cis XIX -A6-A29 : C-G Ww/Ww pairing antiparallel cis XIX -A7-A28 : U-A Ww/Ww pairing antiparallel cis XX -A8-A27 : C-G Ww/Ww pairing antiparallel cis XIX -A9-A26 : G-C Ww/Ww pairing antiparallel cis XIX -A10-A13 : U-A Ww/Hh pairing parallel cis XXIII -A11-A25 : G-C Ww/Ww pairing antiparallel cis XIX -A11-B73 : G-ARG pairing one_hbond -A13-A24 : A-U Ww/Ww pairing antiparallel cis XX -A14-A23 : G-C Ww/Ww pairing antiparallel cis XIX -A14-B70 : G-ARG pairing one_hbond -A15-A22 : C-G Ww/Ww pairing antiparallel cis XIX -A16-A21 : U-A Ww/Ww pairing antiparallel cis XX -Residue conformations ------------------------------------------- -A4 : G C1p_exo anti -A5 : G C3p_endo anti -A6 : C C3p_endo anti -A7 : U C3p_endo anti -A8 : C C3p_endo anti -A9 : G C3p_endo anti -A10 : U C1p_exo anti -A11 : G C2p_endo anti -A12 : U C2p_endo anti -A13 : A C4p_exo anti -A14 : G C3p_endo anti -A15 : C C3p_endo anti -A16 : U C3p_endo anti -A17 : C C2p_endo anti -A18 : A C2p_endo anti -A19 : U C4p_exo anti -A20 : U C2p_endo anti -A21 : A C2p_endo anti -A22 : G C3p_endo anti -A23 : C C4p_exo anti -A24 : U C3p_endo anti -A25 : C C3p_endo anti -A26 : C C3p_endo anti -A27 : G C3p_endo anti -A28 : A C3p_endo anti -A29 : G C3p_endo anti -A30 : C C3p_endo anti -A31 : C C3p_endo anti -B65 : SER -B66 : GLY -B67 : PRO -B68 : ARG -B69 : PRO -B70 : ARG -B71 : GLY -B72 : THR -B73 : ARG -B74 : GLY -B75 : LYS -B76 : GLY -B77 : ARG -B78 : ARG -B79 : ILE -B80 : ARG -B81 : ARG -Adjacent stackings ---------------------------------------------- -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A10-A11 : adjacent_5p downward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A22-A23 : adjacent_5p upward -A24-A25 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A28-A29 : adjacent_5p upward -A29-A30 : adjacent_5p upward -A30-A31 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A9-A27 : outward -A13-A25 : outward -Number of stackings = 16 -Number of adjacent stackings = 14 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A4-A5 : G-G O2'/Hh adjacent_5p pairing -A4-A31 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A30 : G-C Ww/Ww pairing antiparallel cis XIX -A6-A29 : C-G Ww/Ww pairing antiparallel cis XIX -A7-A28 : U-A Ww/Ww pairing antiparallel cis XX -A8-A27 : C-G Ww/Ww pairing antiparallel cis XIX -A9-A26 : G-C Ww/Ww pairing antiparallel cis XIX -A9-B77 : G-ARG pairing one_hbond -A10-A13 : U-A Ww/Hh pairing parallel cis XXIII -A11-A25 : G-C Ww/Ww pairing antiparallel cis XIX -A13-A24 : A-U Ww/Ww pairing antiparallel cis XX -A14-A23 : G-C Ww/Ww pairing antiparallel cis XIX -A14-B70 : G-ARG pairing -A15-A22 : C-G Ww/Ww pairing antiparallel cis XIX -A16-A21 : U-A Ww/Ww pairing antiparallel cis XX -A17-A18 : C-A O2'/Hh adjacent_5p pairing diff --git a/MCdata/1bj2_MC b/MCdata/1bj2_MC deleted file mode 100644 index 775b2f882fed4596bfb0900f3f7aca44ce33a647..0000000000000000000000000000000000000000 --- a/MCdata/1bj2_MC +++ /dev/null @@ -1,787 +0,0 @@ -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C4p_exo anti -A4 : A C3p_endo anti -A5 : A C3p_endo anti -A6 : C C3p_endo anti -A7 : G C3p_endo anti -A8 : G C4p_exo anti -A9 : A C4p_exo anti -A10 : U C3p_endo anti -A11 : G C3p_endo anti -A12 : G C3p_endo anti -A13 : U C4p_exo anti -A14 : U C4p_exo anti -A15 : C C3p_endo anti -A16 : G C3p_endo anti -A17 : U C3p_endo anti -A18 : U C3p_endo anti -A19 : G C3p_endo anti -A20 : C C3p_endo anti -A21 : C C3p_endo anti -B1 : G C3p_endo anti -B2 : C C3p_endo anti -B3 : A C3p_endo anti -B4 : C C3p_endo anti -B5 : C C3p_endo anti -B6 : G C4p_exo anti -B7 : A C3p_endo anti -B8 : A C3p_endo anti -B9 : C C4p_exo anti -B10 : C C4p_exo anti -B11 : A C3p_endo anti -B12 : U C3p_endo anti -B13 : C C3p_endo anti -B14 : C C2p_exo anti -B15 : G C3p_endo anti -B16 : G C3p_endo anti -B17 : U C3p_endo anti -B18 : G C3p_endo anti -B19 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A20-A21 : adjacent_5p upward -B2-B3 : adjacent_5p upward -B3-B4 : adjacent_5p upward -B7-B8 : adjacent_5p upward -B8-B9 : adjacent_5p upward -B9-B10 : adjacent_5p upward -B10-B11 : adjacent_5p upward -B11-B12 : adjacent_5p upward -B15-B16 : adjacent_5p upward -B16-B17 : adjacent_5p upward -B17-B18 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A19 : outward -A5-A18 : outward -A7-A16 : outward -A7-B7 : upward -A9-B13 : outward -B3-B18 : outward -B5-B16 : outward -B6-B15 : outward -Number of stackings = 31 -Number of adjacent stackings = 23 -Number of non adjacent stackings = 8 -Base-pairs ------------------------------------------------------ -A1-A21 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A20 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A19 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A18 : A-U Ww/Ww pairing antiparallel cis XX -A5-A17 : A-U Ww/Ww pairing antiparallel cis XX -A6-A16 : C-G Ww/Ww pairing antiparallel cis XIX -A7-A15 : G-C Ww/Ww pairing antiparallel cis XIX -A8-B13 : G-C Ww/Ww pairing antiparallel cis XIX -A9-B12 : A-U Ww/Ww pairing antiparallel cis XX -A10-B11 : U-A Ww/Ww pairing antiparallel cis XX -A11-B10 : G-C Ww/Ww pairing antiparallel cis XIX -A12-B9 : G-C Ww/Ww pairing antiparallel cis XIX -A13-B8 : U-A Ww/Ww pairing antiparallel cis XX -A14-B7 : U-A Ww/Ww pairing antiparallel cis XX -B1-B19 : G-C Ww/Ww pairing antiparallel cis XIX -B2-B18 : C-G Ww/Ww pairing antiparallel cis XIX -B3-B17 : A-U Ww/Ww pairing antiparallel cis XX -B4-B16 : C-G Ww/Ww pairing antiparallel cis XIX -B5-B15 : C-G Ww/Ww pairing antiparallel cis XIX -B6-B14 : G-C Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : A C3p_endo anti -A5 : A C3p_endo anti -A6 : C C3p_endo anti -A7 : G C3p_endo anti -A8 : G C3p_endo anti -A9 : A C2p_exo anti -A10 : U C3p_endo anti -A11 : G C3p_endo anti -A12 : G C3p_endo anti -A13 : U C3p_endo anti -A14 : U C3p_endo anti -A15 : C C3p_endo anti -A16 : G C3p_endo anti -A17 : U C3p_endo anti -A18 : U C3p_endo anti -A19 : G C3p_endo anti -A20 : C C3p_endo anti -A21 : C C3p_endo anti -B1 : G C3p_endo anti -B2 : C C3p_endo anti -B3 : A C3p_endo anti -B4 : C C3p_endo anti -B5 : C C3p_endo anti -B6 : G C3p_endo anti -B7 : A C4p_exo anti -B8 : A C4p_exo anti -B9 : C C4p_exo anti -B10 : C C4p_exo anti -B11 : A C3p_endo anti -B12 : U C3p_endo anti -B13 : C C3p_endo anti -B14 : C C4p_exo anti -B15 : G C3p_endo anti -B16 : G C3p_endo anti -B17 : U C3p_endo anti -B18 : G C3p_endo anti -B19 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A19-A20 : adjacent_5p upward -B2-B3 : adjacent_5p upward -B3-B4 : adjacent_5p upward -B7-B8 : adjacent_5p upward -B8-B9 : adjacent_5p upward -B9-B10 : adjacent_5p upward -B10-B11 : adjacent_5p upward -B11-B12 : adjacent_5p upward -B15-B16 : adjacent_5p upward -B16-B17 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A19 : outward -A5-A18 : outward -A7-A16 : outward -A7-B7 : upward -A8-B6 : downward -A8-B14 : outward -A9-B13 : outward -A14-B8 : outward -A15-B7 : outward -B5-B16 : outward -B6-B15 : outward -Number of stackings = 31 -Number of adjacent stackings = 20 -Number of non adjacent stackings = 11 -Base-pairs ------------------------------------------------------ -A1-A21 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A20 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A19 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A18 : A-U Ww/Ww pairing antiparallel cis XX -A5-A17 : A-U Ww/Ww pairing antiparallel cis XX -A6-A16 : C-G Ww/Ww pairing antiparallel cis XIX -A7-A15 : G-C Ww/Ww pairing antiparallel cis XIX -A8-B13 : G-C Ww/Ww pairing antiparallel cis XIX -A9-B12 : A-U Ww/Ww pairing antiparallel cis XX -A10-B11 : U-A Ww/Ww pairing antiparallel cis XX -A11-B10 : G-C Ww/Ww pairing antiparallel cis XIX -A12-B9 : G-C Ww/Ww pairing antiparallel cis XIX -A13-B8 : U-A Ww/Ww pairing antiparallel cis XX -A14-B7 : U-A Ww/Ww pairing antiparallel cis XX -B1-B19 : G-C Ww/Ww pairing antiparallel cis XIX -B2-B18 : C-G Ww/Ww pairing antiparallel cis XIX -B3-B17 : A-U Ww/Ww pairing antiparallel cis XX -B4-B16 : C-G Ww/Ww pairing antiparallel cis XIX -B5-B15 : C-G Ww/Ww pairing antiparallel cis XIX -B6-B14 : G-C Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -A1 : G C4p_exo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : A C3p_endo anti -A5 : A C3p_endo anti -A6 : C C4p_exo anti -A7 : G C3p_endo anti -A8 : G C3p_endo anti -A9 : A C3p_endo anti -A10 : U C3p_endo anti -A11 : G C3p_endo anti -A12 : G C3p_endo anti -A13 : U C3p_endo anti -A14 : U C3p_endo anti -A15 : C C4p_exo anti -A16 : G C3p_endo anti -A17 : U C3p_endo anti -A18 : U C3p_endo anti -A19 : G C3p_endo anti -A20 : C C3p_endo anti -A21 : C C3p_endo anti -B1 : G C3p_endo anti -B2 : C C3p_endo anti -B3 : A C3p_endo anti -B4 : C C3p_endo anti -B5 : C C4p_exo anti -B6 : G C3p_endo anti -B7 : A C4p_exo anti -B8 : A C4p_exo anti -B9 : C C3p_endo anti -B10 : C C3p_endo anti -B11 : A C3p_endo anti -B12 : U C3p_endo anti -B13 : C C3p_endo anti -B14 : C C4p_exo anti -B15 : G C3p_endo anti -B16 : G C3p_endo anti -B17 : U C3p_endo anti -B18 : G C3p_endo anti -B19 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A20-A21 : adjacent_5p upward -B2-B3 : adjacent_5p upward -B3-B4 : adjacent_5p upward -B7-B8 : adjacent_5p upward -B8-B9 : adjacent_5p upward -B10-B11 : adjacent_5p upward -B11-B12 : adjacent_5p upward -B14-B15 : adjacent_5p upward -B15-B16 : adjacent_5p upward -B16-B17 : adjacent_5p upward -B17-B18 : adjacent_5p upward -B18-B19 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A5-A18 : outward -A7-A16 : outward -A7-B7 : upward -A8-B6 : downward -A8-B14 : outward -A11-B11 : outward -A12-B10 : outward -A14-B8 : outward -B5-B16 : outward -B6-B15 : outward -Number of stackings = 35 -Number of adjacent stackings = 25 -Number of non adjacent stackings = 10 -Base-pairs ------------------------------------------------------ -A1-A21 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A20 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A19 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A18 : A-U Ww/Ww pairing antiparallel cis XX -A5-A17 : A-U Ww/Ww pairing antiparallel cis XX -A6-A16 : C-G Ww/Ww pairing antiparallel cis XIX -A7-A15 : G-C Ww/Ww pairing antiparallel cis XIX -A8-B13 : G-C Ww/Ww pairing antiparallel cis XIX -A9-B12 : A-U Ww/Ww pairing antiparallel cis XX -A10-B11 : U-A Ww/Ww pairing antiparallel cis XX -A11-B10 : G-C Ww/Ww pairing antiparallel cis XIX -A12-B9 : G-C Ww/Ww pairing antiparallel cis XIX -A13-B8 : U-A Ww/Ww pairing antiparallel cis XX -A14-B7 : U-A Ww/Ww pairing antiparallel cis XX -B1-B19 : G-C Ww/Ww pairing antiparallel cis XIX -B2-B18 : C-G Ww/Ww pairing antiparallel cis XIX -B3-B17 : A-U Ww/Ww pairing antiparallel cis XX -B4-B16 : C-G Ww/Ww pairing antiparallel cis XIX -B5-B15 : C-G Ww/Ww pairing antiparallel cis XIX -B6-B14 : G-C Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -A1 : G C4p_exo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : A C3p_endo anti -A5 : A C3p_endo anti -A6 : C C3p_endo anti -A7 : G C3p_endo anti -A8 : G C4p_exo anti -A9 : A C3p_endo anti -A10 : U C3p_endo anti -A11 : G C3p_endo anti -A12 : G C3p_endo anti -A13 : U C3p_endo anti -A14 : U C3p_endo anti -A15 : C C3p_endo anti -A16 : G C3p_endo anti -A17 : U C3p_endo anti -A18 : U C3p_endo anti -A19 : G C3p_endo anti -A20 : C C3p_endo anti -A21 : C C3p_endo anti -B1 : G C3p_endo anti -B2 : C C3p_endo anti -B3 : A C3p_endo anti -B4 : C C3p_endo anti -B5 : C C3p_endo anti -B6 : G C3p_endo anti -B7 : A C4p_exo anti -B8 : A C4p_exo anti -B9 : C C3p_endo anti -B10 : C C3p_endo anti -B11 : A C3p_endo anti -B12 : U C3p_endo anti -B13 : C C3p_endo anti -B14 : C C3p_endo anti -B15 : G C3p_endo anti -B16 : G C3p_endo anti -B17 : U C3p_endo anti -B18 : G C3p_endo anti -B19 : C C4p_exo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A19-A20 : adjacent_5p upward -B2-B3 : adjacent_5p upward -B3-B4 : adjacent_5p upward -B7-B8 : adjacent_5p upward -B8-B9 : adjacent_5p upward -B10-B11 : adjacent_5p upward -B11-B12 : adjacent_5p upward -B15-B16 : adjacent_5p upward -B16-B17 : adjacent_5p upward -B17-B18 : adjacent_5p upward -B18-B19 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A2-A21 : outward -A4-A19 : outward -A7-A16 : outward -A7-B7 : upward -A8-B6 : downward -A8-B14 : outward -A11-B11 : outward -A12-B10 : outward -B6-B15 : outward -Number of stackings = 32 -Number of adjacent stackings = 23 -Number of non adjacent stackings = 9 -Base-pairs ------------------------------------------------------ -A1-A21 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A20 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A19 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A18 : A-U Ww/Ww pairing antiparallel cis XX -A5-A17 : A-U Ww/Ww pairing antiparallel cis XX -A6-A16 : C-G Ww/Ww pairing antiparallel cis XIX -A7-A15 : G-C Ww/Ww pairing antiparallel cis XIX -A8-B13 : G-C Ww/Ww pairing antiparallel cis XIX -A9-B12 : A-U Ww/Ww pairing antiparallel cis XX -A10-B11 : U-A Ww/Ww pairing antiparallel cis XX -A11-B10 : G-C Ww/Ww pairing antiparallel cis XIX -A12-B9 : G-C Ww/Ww pairing antiparallel cis XIX -A13-B8 : U-A Ww/Ww pairing antiparallel cis XX -A14-B7 : U-A Ww/Ww pairing antiparallel cis XX -B1-B19 : G-C Ww/Ww pairing antiparallel cis XIX -B2-B18 : C-G Ww/Ww pairing antiparallel cis XIX -B3-B17 : A-U Ww/Ww pairing antiparallel cis XX -B4-B16 : C-G Ww/Ww pairing antiparallel cis XIX -B5-B15 : C-G Ww/Ww pairing antiparallel cis XIX -B6-B14 : G-C Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : A C3p_endo anti -A5 : A C3p_endo anti -A6 : C C3p_endo anti -A7 : G C3p_endo anti -A8 : G C3p_endo anti -A9 : A C4p_exo anti -A10 : U C3p_endo anti -A11 : G C3p_endo anti -A12 : G C3p_endo anti -A13 : U C3p_endo anti -A14 : U C3p_endo anti -A15 : C C3p_endo anti -A16 : G C3p_endo anti -A17 : U C3p_endo anti -A18 : U C3p_endo anti -A19 : G C3p_endo anti -A20 : C C3p_endo anti -A21 : C C3p_endo anti -B1 : G C3p_endo anti -B2 : C C4p_exo anti -B3 : A C3p_endo anti -B4 : C C3p_endo anti -B5 : C C3p_endo anti -B6 : G C3p_endo anti -B7 : A C4p_exo anti -B8 : A C4p_exo anti -B9 : C C4p_exo anti -B10 : C C4p_exo anti -B11 : A C3p_endo anti -B12 : U C3p_endo anti -B13 : C C3p_endo anti -B14 : C C3p_endo anti -B15 : G C3p_endo anti -B16 : G C3p_endo anti -B17 : U C3p_endo anti -B18 : G C3p_endo anti -B19 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A19-A20 : adjacent_5p upward -B2-B3 : adjacent_5p upward -B3-B4 : adjacent_5p upward -B7-B8 : adjacent_5p upward -B8-B9 : adjacent_5p upward -B9-B10 : adjacent_5p upward -B10-B11 : adjacent_5p upward -B11-B12 : adjacent_5p upward -B15-B16 : adjacent_5p upward -B16-B17 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A2-A21 : outward -A4-A19 : outward -A5-A18 : outward -A7-A16 : outward -A7-B7 : upward -A8-B6 : downward -A11-B11 : outward -A12-B10 : outward -B3-B18 : outward -B5-B16 : outward -B6-B15 : outward -Number of stackings = 32 -Number of adjacent stackings = 21 -Number of non adjacent stackings = 11 -Base-pairs ------------------------------------------------------ -A1-A21 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A20 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A19 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A18 : A-U Ww/Ww pairing antiparallel cis XX -A5-A17 : A-U Ww/Ww pairing antiparallel cis XX -A6-A16 : C-G Ww/Ww pairing antiparallel cis XIX -A7-A15 : G-C Ww/Ww pairing antiparallel cis XIX -A8-B13 : G-C Ww/Ww pairing antiparallel cis XIX -A9-B12 : A-U Ww/Ww pairing antiparallel cis XX -A10-B11 : U-A Ww/Ww pairing antiparallel cis XX -A11-B10 : G-C Ww/Ww pairing antiparallel cis XIX -A12-B9 : G-C Ww/Ww pairing antiparallel cis XIX -A13-B8 : U-A Ww/Ww pairing antiparallel cis XX -A14-B7 : U-A Ww/Ww pairing antiparallel cis XX -B1-B19 : G-C Ww/Ww pairing antiparallel cis XIX -B2-B18 : C-G Ww/Ww pairing antiparallel cis XIX -B3-B17 : A-U Ww/Ww pairing antiparallel cis XX -B4-B16 : C-G Ww/Ww pairing antiparallel cis XIX -B5-B15 : C-G Ww/Ww pairing antiparallel cis XIX -B6-B14 : G-C Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -A1 : G C4p_exo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : A C3p_endo anti -A5 : A C3p_endo anti -A6 : C C3p_endo anti -A7 : G C3p_endo anti -A8 : G C4p_exo anti -A9 : A C2p_exo anti -A10 : U C3p_endo anti -A11 : G C3p_endo anti -A12 : G C3p_endo anti -A13 : U C3p_endo anti -A14 : U C3p_endo anti -A15 : C C4p_exo anti -A16 : G C3p_endo anti -A17 : U C3p_endo anti -A18 : U C3p_endo anti -A19 : G C4p_exo anti -A20 : C C3p_endo anti -A21 : C C3p_endo anti -B1 : G C3p_endo anti -B2 : C C3p_endo anti -B3 : A C3p_endo anti -B4 : C C3p_endo anti -B5 : C C4p_exo anti -B6 : G C3p_endo anti -B7 : A C4p_exo anti -B8 : A C4p_exo anti -B9 : C C3p_endo anti -B10 : C C3p_endo anti -B11 : A C3p_endo anti -B12 : U C3p_endo anti -B13 : C C3p_endo anti -B14 : C C4p_exo anti -B15 : G C3p_endo anti -B16 : G C3p_endo anti -B17 : U C3p_endo anti -B18 : G C3p_endo anti -B19 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A19-A20 : adjacent_5p upward -B2-B3 : adjacent_5p upward -B3-B4 : adjacent_5p upward -B7-B8 : adjacent_5p upward -B8-B9 : adjacent_5p upward -B9-B10 : adjacent_5p upward -B10-B11 : adjacent_5p upward -B11-B12 : adjacent_5p upward -B14-B15 : adjacent_5p upward -B15-B16 : adjacent_5p upward -B16-B17 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A5-A18 : outward -A7-A16 : outward -A7-B7 : upward -A8-B6 : downward -A8-B14 : outward -A11-B11 : outward -B6-B15 : outward -Number of stackings = 30 -Number of adjacent stackings = 23 -Number of non adjacent stackings = 7 -Base-pairs ------------------------------------------------------ -A1-A21 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A20 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A19 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A18 : A-U Ww/Ww pairing antiparallel cis XX -A5-A17 : A-U Ww/Ww pairing antiparallel cis XX -A6-A16 : C-G Ww/Ww pairing antiparallel cis XIX -A7-A15 : G-C Ww/Ww pairing antiparallel cis XIX -A8-B13 : G-C Ww/Ww pairing antiparallel cis XIX -A9-B12 : A-U Ww/Ww pairing antiparallel cis XX -A10-B11 : U-A Ww/Ww pairing antiparallel cis XX -A11-B10 : G-C Ww/Ww pairing antiparallel cis XIX -A12-B9 : G-C Ww/Ww pairing antiparallel cis XIX -A13-B8 : U-A Ww/Ww pairing antiparallel cis XX -A14-B7 : U-A Ww/Ww pairing antiparallel cis XX -B1-B19 : G-C Ww/Ww pairing antiparallel cis XIX -B2-B18 : C-G Ww/Ww pairing antiparallel cis XIX -B3-B17 : A-U Ww/Ww pairing antiparallel cis XX -B4-B16 : C-G Ww/Ww pairing antiparallel cis XIX -B5-B15 : C-G Ww/Ww pairing antiparallel cis XIX -B6-B14 : G-C Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : A C3p_endo anti -A5 : A C3p_endo anti -A6 : C C3p_endo anti -A7 : G C3p_endo anti -A8 : G C3p_endo anti -A9 : A C3p_endo anti -A10 : U C3p_endo anti -A11 : G C3p_endo anti -A12 : G C3p_endo anti -A13 : U C4p_exo anti -A14 : U C4p_exo anti -A15 : C C4p_exo anti -A16 : G C3p_endo anti -A17 : U C3p_endo anti -A18 : U C3p_endo anti -A19 : G C3p_endo anti -A20 : C C3p_endo anti -A21 : C C3p_endo anti -B1 : G C3p_endo anti -B2 : C C3p_endo anti -B3 : A C3p_endo anti -B4 : C C3p_endo anti -B5 : C C4p_exo anti -B6 : G C4p_exo anti -B7 : A C4p_exo anti -B8 : A C3p_endo anti -B9 : C C3p_endo anti -B10 : C C3p_endo anti -B11 : A C3p_endo anti -B12 : U C3p_endo anti -B13 : C C2p_exo anti -B14 : C C3p_endo anti -B15 : G C3p_endo anti -B16 : G C3p_endo anti -B17 : U C3p_endo anti -B18 : G C3p_endo anti -B19 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A19-A20 : adjacent_5p upward -B1-B2 : adjacent_5p upward -B2-B3 : adjacent_5p upward -B3-B4 : adjacent_5p upward -B5-B6 : adjacent_5p upward -B7-B8 : adjacent_5p upward -B8-B9 : adjacent_5p upward -B10-B11 : adjacent_5p upward -B11-B12 : adjacent_5p upward -B15-B16 : adjacent_5p upward -B16-B17 : adjacent_5p upward -B18-B19 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A2-A21 : outward -A4-A19 : outward -A7-A16 : outward -A8-B6 : downward -A9-B13 : outward -A11-B11 : outward -B3-B18 : outward -Number of stackings = 28 -Number of adjacent stackings = 21 -Number of non adjacent stackings = 7 -Base-pairs ------------------------------------------------------ -A1-A21 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A20 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A19 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A18 : A-U Ww/Ww pairing antiparallel cis XX -A5-A17 : A-U Ww/Ww pairing antiparallel cis XX -A6-A16 : C-G Ww/Ww pairing antiparallel cis XIX -A7-A15 : G-C Ww/Ww pairing antiparallel cis XIX -A7-B7 : G-A Bs/O2' pairing -A8-B13 : G-C Ww/Ww pairing antiparallel cis XIX -A9-B7 : A-A O2P/Hh pairing -A9-B12 : A-U Ww/Ww pairing antiparallel cis XX -A10-B11 : U-A Ww/Ww pairing antiparallel cis XX -A11-B10 : G-C Ww/Ww pairing antiparallel cis XIX -A12-B9 : G-C Ww/Ww pairing antiparallel cis XIX -A13-B8 : U-A Ww/Ww pairing antiparallel cis XX -A14-B7 : U-A Ww/Ww pairing antiparallel cis XX -B1-B19 : G-C Ww/Ww pairing antiparallel cis XIX -B2-B18 : C-G Ww/Ww pairing antiparallel cis XIX -B3-B17 : A-U Ww/Ww pairing antiparallel cis XX -B4-B16 : C-G Ww/Ww pairing antiparallel cis XIX -B5-B15 : C-G Ww/Ww pairing antiparallel cis XIX -B6-B14 : G-C Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C4p_exo anti -A4 : A C3p_endo anti -A5 : A C3p_endo anti -A6 : C C4p_exo anti -A7 : G C4p_exo anti -A8 : G C3p_endo anti -A9 : A C3p_endo anti -A10 : U C3p_endo anti -A11 : G C3p_endo anti -A12 : G C3p_endo anti -A13 : U C3p_endo anti -A14 : U C4p_exo anti -A15 : C C4p_exo anti -A16 : G C3p_endo anti -A17 : U C3p_endo anti -A18 : U C3p_endo anti -A19 : G C3p_endo anti -A20 : C C3p_endo anti -A21 : C C3p_endo anti -B1 : G C3p_endo anti -B2 : C C3p_endo anti -B3 : A C3p_endo anti -B4 : C C3p_endo anti -B5 : C C3p_endo anti -B6 : G C3p_endo anti -B7 : A C4p_exo anti -B8 : A C4p_exo anti -B9 : C C3p_endo anti -B10 : C C4p_exo anti -B11 : A C3p_endo anti -B12 : U C3p_endo anti -B13 : C C3p_endo anti -B14 : C C3p_endo anti -B15 : G C3p_endo anti -B16 : G C3p_endo anti -B17 : U C3p_endo anti -B18 : G C3p_endo anti -B19 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A19-A20 : adjacent_5p upward -B2-B3 : adjacent_5p upward -B3-B4 : adjacent_5p upward -B5-B6 : adjacent_5p upward -B7-B8 : adjacent_5p upward -B8-B9 : adjacent_5p upward -B10-B11 : adjacent_5p upward -B11-B12 : adjacent_5p upward -B14-B15 : adjacent_5p upward -B15-B16 : adjacent_5p upward -B16-B17 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A5-A18 : outward -A7-A16 : outward -A7-B7 : upward -A8-B6 : downward -A9-B13 : outward -A12-B10 : outward -B5-B16 : outward -Number of stackings = 30 -Number of adjacent stackings = 23 -Number of non adjacent stackings = 7 -Base-pairs ------------------------------------------------------ -A1-A21 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A20 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A19 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A18 : A-U Ww/Ww pairing antiparallel cis XX -A5-A17 : A-U Ww/Ww pairing antiparallel cis XX -A6-A16 : C-G Ww/Ww pairing antiparallel cis XIX -A7-A15 : G-C Ww/Ww pairing antiparallel cis XIX -A8-B13 : G-C Ww/Ww pairing antiparallel cis XIX -A9-B12 : A-U Ww/Ww pairing antiparallel cis XX -A10-B11 : U-A Ww/Ww pairing antiparallel cis XX -A11-B10 : G-C Ww/Ww pairing antiparallel cis XIX -A12-B9 : G-C Ww/Ww pairing antiparallel cis XIX -A13-B8 : U-A Ww/Ww pairing antiparallel cis XX -A14-B7 : U-A Ww/Ww pairing antiparallel cis XX -B1-B19 : G-C Ww/Ww pairing antiparallel cis XIX -B2-B18 : C-G Ww/Ww pairing antiparallel cis XIX -B3-B17 : A-U Ww/Ww pairing antiparallel cis XX -B4-B16 : C-G Ww/Ww pairing antiparallel cis XIX -B5-B15 : C-G Ww/Ww pairing antiparallel cis XIX -B6-B14 : G-C Ww/Ww pairing antiparallel cis XIX diff --git a/MCdata/1bmv_MC b/MCdata/1bmv_MC deleted file mode 100644 index bff6d30edb7ce7ebb4fd6dceab06651308554936..0000000000000000000000000000000000000000 --- a/MCdata/1bmv_MC +++ /dev/null @@ -1,583 +0,0 @@ -Residue conformations ------------------------------------------- -M1 : G C3p_endo anti -M2 : G C3p_endo anti -M3 : U C3p_endo anti -M4 : C C3p_endo anti -M5 : A C3p_endo anti -M6 : A C3p_endo anti -M7 : A C3p_endo anti -M8 : A C3p_endo anti -M9 : U C3p_endo anti -M10 : G C3p_endo anti -M11 : C C3p_endo anti -'1'1001 : SER -'1'1002 : ILE -'1'1003 : SER -'1'1004 : GLN -'1'1005 : GLN -'1'1006 : THR -'1'1007 : VAL -'1'1008 : TRP -'1'1009 : ASN -'1'1010 : GLN -'1'1011 : MET -'1'1012 : ALA -'1'1013 : THR -'1'1014 : VAL -'1'1015 : ARG -'1'1016 : THR -'1'1017 : PRO -'1'1018 : LEU -'1'1019 : ASN -'1'1020 : PHE -'1'1021 : ASP -'1'1022 : SER -'1'1023 : SER -'1'1024 : LYS -'1'1025 : GLN -'1'1026 : SER -'1'1027 : PHE -'1'1028 : CYS -'1'1029 : GLN -'1'1030 : PHE -'1'1031 : SER -'1'1032 : VAL -'1'1033 : ASP -'1'1034 : LEU -'1'1035 : LEU -'1'1036 : GLY -'1'1037 : GLY -'1'1038 : GLY -'1'1039 : ILE -'1'1040 : SER -'1'1041 : VAL -'1'1042 : ASP -'1'1043 : LYS -'1'1044 : THR -'1'1045 : GLY -'1'1046 : ASP -'1'1047 : TRP -'1'1048 : ILE -'1'1049 : THR -'1'1050 : LEU -'1'1051 : VAL -'1'1052 : GLN -'1'1053 : ASN -'1'1054 : SER -'1'1055 : PRO -'1'1056 : ILE -'1'1057 : SER -'1'1058 : ASN -'1'1059 : LEU -'1'1060 : LEU -'1'1061 : ARG -'1'1062 : VAL -'1'1063 : ALA -'1'1064 : ALA -'1'1065 : TRP -'1'1066 : LYS -'1'1067 : LYS -'1'1068 : GLY -'1'1069 : CYS -'1'1070 : LEU -'1'1071 : MET -'1'1072 : VAL -'1'1073 : LYS -'1'1074 : VAL -'1'1075 : VAL -'1'1076 : MET -'1'1077 : SER -'1'1078 : GLY -'1'1079 : ASN -'1'1080 : ALA -'1'1081 : ALA -'1'1082 : VAL -'1'1083 : LYS -'1'1084 : ARG -'1'1085 : SER -'1'1086 : ASP -'1'1087 : TRP -'1'1088 : ALA -'1'1089 : SER -'1'1090 : LEU -'1'1091 : VAL -'1'1092 : GLN -'1'1093 : VAL -'1'1094 : PHE -'1'1095 : LEU -'1'1096 : THR -'1'1097 : ASN -'1'1098 : SER -'1'1099 : ASN -'1'1100 : SER -'1'1101 : THR -'1'1102 : GLU -'1'1103 : HIS -'1'1104 : PHE -'1'1105 : ASP -'1'1106 : ALA -'1'1107 : CYS -'1'1108 : ARG -'1'1109 : TRP -'1'1110 : THR -'1'1111 : LYS -'1'1112 : SER -'1'1113 : GLU -'1'1114 : PRO -'1'1115 : HIS -'1'1116 : SER -'1'1117 : TRP -'1'1118 : GLU -'1'1119 : LEU -'1'1120 : ILE -'1'1121 : PHE -'1'1122 : PRO -'1'1123 : ILE -'1'1124 : GLU -'1'1125 : VAL -'1'1126 : CYS -'1'1127 : GLY -'1'1128 : PRO -'1'1129 : ASN -'1'1130 : ASN -'1'1131 : GLY -'1'1132 : PHE -'1'1133 : GLU -'1'1134 : MET -'1'1135 : TRP -'1'1136 : SER -'1'1137 : SER -'1'1138 : GLU -'1'1139 : TRP -'1'1140 : ALA -'1'1141 : ASN -'1'1142 : GLN -'1'1143 : THR -'1'1144 : SER -'1'1145 : TRP -'1'1146 : HIS -'1'1147 : LEU -'1'1148 : SER -'1'1149 : PHE -'1'1150 : LEU -'1'1151 : VAL -'1'1152 : ASP -'1'1153 : ASN -'1'1154 : PRO -'1'1155 : LYS -'1'1156 : GLN -'1'1157 : SER -'1'1158 : THR -'1'1159 : THR -'1'1160 : PHE -'1'1161 : ASP -'1'1162 : VAL -'1'1163 : LEU -'1'1164 : LEU -'1'1165 : GLY -'1'1166 : ILE -'1'1167 : SER -'1'1168 : GLN -'1'1169 : ASN -'1'1170 : PHE -'1'1171 : GLU -'1'1172 : ILE -'1'1173 : ALA -'1'1174 : GLY -'1'1175 : ASN -'1'1176 : THR -'1'1177 : LEU -'1'1178 : MET -'1'1179 : PRO -'1'1180 : ALA -'1'1181 : PHE -'1'1182 : SER -'1'1183 : VAL -'1'1184 : PRO -'1'1185 : GLN -'2'3001 : MET -'2'3002 : GLU -'2'3003 : THR -'2'3004 : ASN -'2'3005 : LEU -'2'3006 : PHE -'2'3007 : LYS -'2'3008 : LEU -'2'3009 : SER -'2'3010 : LEU -'2'3011 : ASP -'2'3012 : ASP -'2'3013 : VAL -'2'3014 : GLU -'2'3015 : THR -'2'3016 : PRO -'2'3017 : LYS -'2'3018 : GLY -'2'3019 : SER -'2'3020 : MET -'2'3021 : LEU -'2'3022 : ASP -'2'3023 : LEU -'2'3024 : LYS -'2'3025 : ILE -'2'3026 : SER -'2'3027 : GLN -'2'3028 : SER -'2'3029 : LYS -'2'3030 : ILE -'2'3031 : ALA -'2'3032 : LEU -'2'3033 : PRO -'2'3034 : LYS -'2'3035 : ASN -'2'3036 : THR -'2'3037 : VAL -'2'3038 : GLY -'2'3039 : GLY -'2'3040 : THR -'2'3041 : ILE -'2'3042 : LEU -'2'3043 : ARG -'2'3044 : SER -'2'3045 : ASP -'2'3046 : LEU -'2'3047 : LEU -'2'3048 : ALA -'2'3049 : ASN -'2'3050 : PHE -'2'3051 : LEU -'2'3052 : THR -'2'3053 : GLU -'2'3054 : GLY -'2'3055 : ASN -'2'3056 : PHE -'2'3057 : ARG -'2'3058 : ALA -'2'3059 : SER -'2'3060 : VAL -'2'3061 : ASP -'2'3062 : LEU -'2'3063 : GLN -'2'3064 : ARG -'2'3065 : THR -'2'3066 : HIS -'2'3067 : ARG -'2'3068 : ILE -'2'3069 : LYS -'2'3070 : GLY -'2'3071 : MET -'2'3072 : ILE -'2'3073 : LYS -'2'3074 : MET -'2'3075 : VAL -'2'3076 : ALA -'2'3077 : THR -'2'3078 : VAL -'2'3079 : GLY -'2'3080 : ILE -'2'3081 : PRO -'2'3082 : GLU -'2'3083 : ASN -'2'3084 : THR -'2'3085 : GLY -'2'3086 : ILE -'2'3087 : ALA -'2'3088 : LEU -'2'3089 : ALA -'2'3090 : CYS -'2'3091 : ALA -'2'3092 : MET -'2'3093 : ASN -'2'3094 : SER -'2'3095 : SER -'2'3096 : ILE -'2'3097 : ARG -'2'3098 : GLY -'2'3099 : ARG -'2'3100 : ALA -'2'3101 : SER -'2'3102 : SER -'2'3103 : ASP -'2'3104 : ILE -'2'3105 : TYR -'2'3106 : THR -'2'3107 : ILE -'2'3108 : CYS -'2'3109 : SER -'2'3110 : GLN -'2'3111 : ASP -'2'3112 : CYS -'2'3113 : GLU -'2'3114 : LEU -'2'3115 : TRP -'2'3116 : ASN -'2'3117 : PRO -'2'3118 : ALA -'2'3119 : CYS -'2'3120 : THR -'2'3121 : LYS -'2'3122 : ALA -'2'3123 : MET -'2'3124 : THR -'2'3125 : MET -'2'3126 : SER -'2'3127 : PHE -'2'3128 : ASN -'2'3129 : PRO -'2'3130 : ASN -'2'3131 : PRO -'2'3132 : CYS -'2'3133 : SER -'2'3134 : ASP -'2'3135 : ALA -'2'3136 : TRP -'2'3137 : SER -'2'3138 : LEU -'2'3139 : GLU -'2'3140 : PHE -'2'3141 : LEU -'2'3142 : LYS -'2'3143 : ARG -'2'3144 : THR -'2'3145 : GLY -'2'3146 : PHE -'2'3147 : HIS -'2'3148 : CYS -'2'3149 : ASP -'2'3150 : ILE -'2'3151 : ILE -'2'3152 : CYS -'2'3153 : VAL -'2'3154 : THR -'2'3155 : GLY -'2'3156 : TRP -'2'3157 : THR -'2'3158 : ALA -'2'3159 : THR -'2'3160 : PRO -'2'3161 : MET -'2'3162 : GLN -'2'3163 : ASP -'2'3164 : VAL -'2'3165 : GLN -'2'3166 : VAL -'2'3167 : THR -'2'3168 : ILE -'2'3169 : ASP -'2'3170 : TRP -'2'3171 : PHE -'2'3172 : ILE -'2'3173 : SER -'2'3174 : SER -'2'3175 : GLN -'2'3176 : GLU -'2'3177 : CYS -'2'3178 : VAL -'2'3179 : PRO -'2'3180 : ARG -'2'3181 : THR -'2'3182 : TYR -'2'2001 : CYS -'2'2002 : VAL -'2'2003 : LEU -'2'2004 : ASN -'2'2005 : PRO -'2'2006 : GLN -'2'2007 : ASN -'2'2008 : PRO -'2'2009 : PHE -'2'2010 : VAL -'2'2011 : LEU -'2'2012 : ASN -'2'2013 : ARG -'2'2014 : TRP -'2'2015 : MET -'2'2016 : GLY -'2'2017 : LYS -'2'2018 : LEU -'2'2019 : THR -'2'2020 : PHE -'2'2021 : PRO -'2'2022 : GLN -'2'2023 : GLY -'2'2024 : THR -'2'2025 : SER -'2'2026 : ARG -'2'2027 : SER -'2'2028 : VAL -'2'2029 : LYS -'2'2030 : ARG -'2'2031 : MET -'2'2032 : PRO -'2'2033 : LEU -'2'2034 : SER -'2'2035 : ILE -'2'2036 : GLY -'2'2037 : GLY -'2'2038 : GLY -'2'2039 : ALA -'2'2040 : GLY -'2'2041 : ALA -'2'2042 : LYS -'2'2043 : SER -'2'2044 : ALA -'2'2045 : ILE -'2'2046 : LEU -'2'2047 : MET -'2'2048 : ASN -'2'2049 : MET -'2'2050 : PRO -'2'2051 : ASN -'2'2052 : ALA -'2'2053 : VAL -'2'2054 : LEU -'2'2055 : SER -'2'2056 : MET -'2'2057 : TRP -'2'2058 : ARG -'2'2059 : TYR -'2'2060 : PHE -'2'2061 : VAL -'2'2062 : GLY -'2'2063 : ASP -'2'2064 : LEU -'2'2065 : VAL -'2'2066 : PHE -'2'2067 : GLU -'2'2068 : VAL -'2'2069 : SER -'2'2070 : LYS -'2'2071 : MET -'2'2072 : THR -'2'2073 : SER -'2'2074 : PRO -'2'2075 : TYR -'2'2076 : ILE -'2'2077 : LYS -'2'2078 : CYS -'2'2079 : THR -'2'2080 : VAL -'2'2081 : SER -'2'2082 : PHE -'2'2083 : PHE -'2'2084 : ILE -'2'2085 : ALA -'2'2086 : PHE -'2'2087 : GLY -'2'2088 : ASN -'2'2089 : LEU -'2'2090 : ALA -'2'2091 : ASP -'2'2092 : ASP -'2'2093 : THR -'2'2094 : ILE -'2'2095 : ASN -'2'2096 : PHE -'2'2097 : GLU -'2'2098 : ALA -'2'2099 : PHE -'2'2100 : PRO -'2'2101 : HIS -'2'2102 : LYS -'2'2103 : LEU -'2'2104 : VAL -'2'2105 : GLN -'2'2106 : PHE -'2'2107 : GLY -'2'2108 : GLU -'2'2109 : ILE -'2'2110 : GLN -'2'2111 : GLU -'2'2112 : LYS -'2'2113 : VAL -'2'2114 : VAL -'2'2115 : LEU -'2'2116 : LYS -'2'2117 : PHE -'2'2118 : SER -'2'2119 : GLN -'2'2120 : GLU -'2'2121 : GLU -'2'2122 : PHE -'2'2123 : LEU -'2'2124 : THR -'2'2125 : ALA -'2'2126 : TRP -'2'2127 : SER -'2'2128 : THR -'2'2129 : GLN -'2'2130 : VAL -'2'2131 : ARG -'2'2132 : PRO -'2'2133 : ALA -'2'2134 : THR -'2'2135 : THR -'2'2136 : LEU -'2'2137 : LEU -'2'2138 : ALA -'2'2139 : ASP -'2'2140 : GLY -'2'2141 : CYS -'2'2142 : PRO -'2'2143 : TYR -'2'2144 : LEU -'2'2145 : TYR -'2'2146 : ALA -'2'2147 : MET -'2'2148 : VAL -'2'2149 : HIS -'2'2150 : ASP -'2'2151 : SER -'2'2152 : SER -'2'2153 : VAL -'2'2154 : SER -'2'2155 : THR -'2'2156 : ILE -'2'2157 : PRO -'2'2158 : GLY -'2'2159 : ASP -'2'2160 : PHE -'2'2161 : VAL -'2'2162 : ILE -'2'2163 : GLY -'2'2164 : VAL -'2'2165 : LYS -'2'2166 : LEU -'2'2167 : THR -'2'2168 : ILE -'2'2169 : ILE -'2'2170 : GLU -'2'2171 : ASN -'2'2172 : MET -'2'2173 : CYS -'2'2174 : ALA -'2'2175 : TYR -'2'2176 : GLY -'2'2177 : LEU -'2'2178 : ASN -'2'2179 : PRO -'2'2180 : GLY -'2'2181 : ILE -'2'2182 : SER -'2'2183 : GLY -'2'2184 : SER -'2'2185 : ARG -'2'2186 : LEU -'2'2187 : LEU -'2'2188 : GLY -'2'2189 : THR -'2'2190 : ILE -'2'2191 : PRO -'2'2192 : GLN -Adjacent stackings ---------------------------------------------- -M1-M2 : adjacent_5p upward -M2-M3 : adjacent_5p upward -M3-M4 : adjacent_5p upward -M4-M5 : adjacent_5p upward -M5-M6 : adjacent_5p upward -M6-M7 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 6 -Number of adjacent stackings = 6 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ diff --git a/MCdata/1bn0_MC b/MCdata/1bn0_MC deleted file mode 100644 index 4d73b5ead7f912cce34d5deee2eeba10632c2f8e..0000000000000000000000000000000000000000 --- a/MCdata/1bn0_MC +++ /dev/null @@ -1,529 +0,0 @@ -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C2p_exo anti -A3 : A C2p_exo anti -A4 : C C3p_endo anti -A5 : U C3p_endo anti -A6 : A C3p_endo anti -A7 : G C2p_exo anti -A8 : C C3p_endo anti -A9 : G C4p_exo anti -A10 : G C2p_endo syn -A11 : A O4p_endo syn -A12 : G C2p_exo anti -A13 : G C1p_endo anti -A14 : C C3p_endo anti -A15 : U C2p_exo anti -A16 : A C4p_exo anti -A17 : G C3p_endo anti -A18 : U C2p_exo anti -A19 : C C3p_endo anti -A20 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A6-A16 : outward -Number of stackings = 11 -Number of adjacent stackings = 10 -Number of non adjacent stackings = 1 -Base-pairs ------------------------------------------------------ -A1-A20 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A19 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A18 : A-U Ww/Ww pairing antiparallel cis XX -A4-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A5-A16 : U-A Ww/Ww pairing antiparallel cis one_hbond -A6-A15 : A-U Ww/Ww pairing antiparallel cis XX -A7-A14 : G-C Ww/Ww pairing antiparallel cis XIX -A8-A13 : C-G Ww/Ww pairing antiparallel cis XIX -A9-A11 : G-A Wh/Hw pairing parallel cis one_hbond -A11-A13 : A-G Ss/O2P pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C2p_exo anti -A3 : A C2p_exo anti -A4 : C C3p_endo anti -A5 : U C3p_endo anti -A6 : A C3p_endo anti -A7 : G C2p_exo anti -A8 : C C3p_endo anti -A9 : G C3p_endo anti -A10 : G C3p_endo anti -A11 : A C4p_endo syn -A12 : G C2p_exo anti -A13 : G C2p_exo anti -A14 : C C3p_endo anti -A15 : U C2p_exo anti -A16 : A C4p_exo anti -A17 : G C2p_exo anti -A18 : U C1p_endo anti -A19 : C C4p_exo anti -A20 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 11 -Number of adjacent stackings = 11 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-A20 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A19 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A18 : A-U Ww/Ww pairing antiparallel cis XX -A4-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A5-A16 : U-A Ww/Ww pairing antiparallel cis XX -A6-A15 : A-U Ww/Ww pairing antiparallel cis XX -A7-A14 : G-C Ww/Ww pairing antiparallel cis XIX -A8-A13 : C-G Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C2p_exo anti -A3 : A C2p_exo anti -A4 : C C3p_endo anti -A5 : U C3p_endo anti -A6 : A C3p_endo anti -A7 : G C2p_exo anti -A8 : C C3p_endo anti -A9 : G C2p_exo anti -A10 : G C3p_exo syn -A11 : A O4p_endo syn -A12 : G C4p_endo anti -A13 : G C2p_exo anti -A14 : C C3p_endo anti -A15 : U C2p_exo anti -A16 : A C4p_exo anti -A17 : G C2p_exo anti -A18 : U C2p_exo anti -A19 : C C3p_endo anti -A20 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 13 -Number of adjacent stackings = 13 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-A20 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A19 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A18 : A-U Ww/Ww pairing antiparallel cis XX -A4-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A5-A16 : U-A Ww/Ww pairing antiparallel cis XX -A6-A15 : A-U Ww/Ww pairing antiparallel cis XX -A7-A14 : G-C Ww/Ww pairing antiparallel cis XIX -A8-A13 : C-G Ww/Ww pairing antiparallel cis XIX -A10-A11 : G-A O2'/Hh adjacent_5p pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C2p_exo anti -A3 : A C2p_exo anti -A4 : C C3p_endo anti -A5 : U C3p_endo anti -A6 : A C3p_endo anti -A7 : G C2p_exo anti -A8 : C C3p_endo anti -A9 : G C2p_exo anti -A10 : G C4p_exo anti -A11 : A C2p_endo syn -A12 : G O4p_exo anti -A13 : G C2p_exo anti -A14 : C C3p_endo anti -A15 : U C2p_exo anti -A16 : A C4p_exo anti -A17 : G C2p_exo anti -A18 : U C2p_exo anti -A19 : C C3p_endo anti -A20 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A6-A16 : outward -Number of stackings = 14 -Number of adjacent stackings = 13 -Number of non adjacent stackings = 1 -Base-pairs ------------------------------------------------------ -A1-A20 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A19 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A18 : A-U Ww/Ww pairing antiparallel cis XX -A4-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A5-A16 : U-A Ww/Ww pairing antiparallel cis XX -A6-A15 : A-U Ww/Ww pairing antiparallel cis XX -A7-A14 : G-C Ww/Ww pairing antiparallel cis XIX -A8-A13 : C-G Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -A1 : G C2p_exo anti -A2 : G C3p_endo anti -A3 : A C2p_exo anti -A4 : C C3p_endo anti -A5 : U C3p_endo anti -A6 : A C3p_endo anti -A7 : G C2p_exo anti -A8 : C C3p_endo anti -A9 : G C1p_endo anti -A10 : G C2p_endo syn -A11 : A O4p_exo syn -A12 : G C2p_exo anti -A13 : G C2p_exo anti -A14 : C C3p_endo anti -A15 : U C2p_endo anti -A16 : A C4p_exo anti -A17 : G C3p_endo anti -A18 : U C2p_exo anti -A19 : C C1p_exo anti -A20 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 11 -Number of adjacent stackings = 11 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-A20 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A19 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A18 : A-U Ww/Ww pairing antiparallel cis XX -A4-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A5-A16 : U-A Ww/Ww pairing antiparallel cis XX -A6-A15 : A-U Ww/Ww pairing antiparallel cis XX -A7-A14 : G-C Ww/Ww pairing antiparallel cis XIX -A8-A13 : C-G Ww/Ww pairing antiparallel cis XIX -A9-A10 : G-G O2'/Ss adjacent_5p pairing -A10-A11 : G-A O2'/Hh adjacent_5p pairing -Residue conformations ------------------------------------------- -A1 : G C2p_exo anti -A2 : G C2p_exo anti -A3 : A C2p_exo anti -A4 : C C3p_endo anti -A5 : U C3p_endo anti -A6 : A C2p_endo anti -A7 : G C2p_endo syn -A8 : C C2p_exo anti -A9 : G C2p_exo anti -A10 : G C2p_endo syn -A11 : A C2p_endo syn -A12 : G C2p_exo anti -A13 : G C2p_exo anti -A14 : C C3p_endo anti -A15 : U C2p_endo anti -A16 : A C4p_exo anti -A17 : G C3p_endo anti -A18 : U C2p_exo anti -A19 : C C1p_exo anti -A20 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A6-A7 : adjacent_5p upward pairing -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A6-A16 : outward -Number of stackings = 11 -Number of adjacent stackings = 10 -Number of non adjacent stackings = 1 -Base-pairs ------------------------------------------------------ -A1-A20 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A19 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A18 : A-U Ww/Ww pairing antiparallel cis XX -A4-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A5-A16 : U-A Ww/Ww pairing antiparallel cis XX -A6-A7 : A-G O2'/C8 adjacent_5p upward pairing -A6-A15 : A-U Ww/Ww pairing antiparallel cis XX -A7-A14 : G-C Ww/Ww pairing antiparallel cis XIX -A8-A13 : C-G Ww/Ww pairing antiparallel cis XIX -A10-A11 : G-A O2'/Hh adjacent_5p pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C2p_exo anti -A3 : A C2p_exo anti -A4 : C C3p_endo anti -A5 : U C3p_endo anti -A6 : A C3p_endo anti -A7 : G C2p_exo anti -A8 : C C3p_endo anti -A9 : G C2p_exo anti -A10 : G C4p_exo anti -A11 : A C2p_endo syn -A12 : G O4p_exo anti -A13 : G C2p_exo anti -A14 : C C3p_endo anti -A15 : U C2p_endo anti -A16 : A C4p_exo anti -A17 : G C3p_endo anti -A18 : U C2p_exo anti -A19 : C C1p_exo anti -A20 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A9-A11 : inward -Number of stackings = 14 -Number of adjacent stackings = 13 -Number of non adjacent stackings = 1 -Base-pairs ------------------------------------------------------ -A1-A20 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A19 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A18 : A-U Ww/Ww pairing antiparallel cis XX -A4-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A5-A16 : U-A Ww/Ww pairing antiparallel cis XX -A6-A15 : A-U Ww/Ww pairing antiparallel cis XX -A7-A14 : G-C Ww/Ww pairing antiparallel cis XIX -A8-A13 : C-G Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : A C2p_exo anti -A4 : C C3p_endo anti -A5 : U C3p_endo anti -A6 : A C3p_endo anti -A7 : G C2p_exo anti -A8 : C C3p_endo anti -A9 : G C3p_endo anti -A10 : G C2p_endo syn -A11 : A O4p_endo anti -A12 : G C4p_endo anti -A13 : G C2p_exo anti -A14 : C C2p_exo anti -A15 : U C2p_endo anti -A16 : A C4p_exo anti -A17 : G C2p_exo anti -A18 : U O4p_exo anti -A19 : C C4p_exo anti -A20 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A6-A16 : outward -Number of stackings = 12 -Number of adjacent stackings = 11 -Number of non adjacent stackings = 1 -Base-pairs ------------------------------------------------------ -A1-A20 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A19 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A18 : A-U Ww/Ww pairing antiparallel cis XX -A4-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A5-A16 : U-A Ww/Ww pairing antiparallel cis XX -A6-A15 : A-U Ww/Ww pairing antiparallel cis XX -A7-A14 : G-C Ww/Ww pairing antiparallel cis XIX -A8-A13 : C-G Ww/Ww pairing antiparallel cis XIX -A9-A10 : G-G O2'/Ss adjacent_5p pairing -A10-A11 : G-A O2'/Hh adjacent_5p pairing -Residue conformations ------------------------------------------- -A1 : G C1p_endo anti -A2 : G C3p_endo anti -A3 : A C2p_exo anti -A4 : C C3p_endo anti -A5 : U C3p_endo anti -A6 : A C3p_endo anti -A7 : G C2p_exo anti -A8 : C C3p_endo anti -A9 : G C3p_endo anti -A10 : G C3p_exo syn -A11 : A C2p_endo anti -A12 : G C4p_endo anti -A13 : G C2p_exo anti -A14 : C C2p_exo anti -A15 : U C2p_endo anti -A16 : A C4p_exo anti -A17 : G C2p_exo anti -A18 : U C2p_exo anti -A19 : C C2p_endo anti -A20 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 12 -Number of adjacent stackings = 12 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-A20 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A19 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A18 : A-U Ww/Ww pairing antiparallel cis XX -A4-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A5-A16 : U-A Ww/Ww pairing antiparallel cis XX -A6-A15 : A-U Ww/Ww pairing antiparallel cis XX -A7-A14 : G-C Ww/Ww pairing antiparallel cis XIX -A8-A13 : C-G Ww/Ww pairing antiparallel cis XIX -A10-A11 : G-A O2'/C8 adjacent_5p pairing -A11-A12 : A-G Ss/O2P adjacent_5p pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : A C2p_exo anti -A4 : C C3p_endo anti -A5 : U C3p_endo anti -A6 : A C3p_endo anti -A7 : G C2p_exo anti -A8 : C C3p_endo anti -A9 : G C1p_endo anti -A10 : G C3p_exo syn -A11 : A O4p_endo anti -A12 : G C4p_endo anti -A13 : G C2p_exo anti -A14 : C C2p_exo anti -A15 : U C2p_endo anti -A16 : A C4p_exo anti -A17 : G C2p_exo anti -A18 : U C2p_exo anti -A19 : C C4p_exo anti -A20 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 11 -Number of adjacent stackings = 11 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-A20 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A19 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A18 : A-U Ww/Ww pairing antiparallel cis XX -A4-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A5-A16 : U-A Ww/Ww pairing antiparallel cis XX -A6-A15 : A-U Ww/Ww pairing antiparallel cis XX -A7-A14 : G-C Ww/Ww pairing antiparallel cis XIX -A8-A13 : C-G Ww/Ww pairing antiparallel cis XIX -A9-A10 : G-G O2'/Hh adjacent_5p pairing -Residue conformations ------------------------------------------- -A1 : G C2p_exo anti -A2 : G C3p_endo anti -A3 : A C2p_exo anti -A4 : C C3p_endo anti -A5 : U C3p_endo anti -A6 : A C3p_endo anti -A7 : G C2p_exo anti -A8 : C C3p_endo anti -A9 : G C1p_endo anti -A10 : G C2p_endo syn -A11 : A C1p_exo syn -A12 : G C4p_endo anti -A13 : G C2p_exo anti -A14 : C C3p_endo anti -A15 : U C2p_endo anti -A16 : A C4p_exo anti -A17 : G C3p_endo anti -A18 : U C2p_exo anti -A19 : C C1p_exo anti -A20 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A6-A16 : outward -Number of stackings = 11 -Number of adjacent stackings = 10 -Number of non adjacent stackings = 1 -Base-pairs ------------------------------------------------------ -A1-A20 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A19 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A18 : A-U Ww/Ww pairing antiparallel cis XX -A4-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A5-A16 : U-A Ww/Ww pairing antiparallel cis XX -A6-A15 : A-U Ww/Ww pairing antiparallel cis XX -A7-A14 : G-C Ww/Ww pairing antiparallel cis XIX -A8-A13 : C-G Ww/Ww pairing antiparallel cis XIX -A10-A11 : G-A O2'/C8 adjacent_5p pairing diff --git a/MCdata/1br3_MC b/MCdata/1br3_MC deleted file mode 100644 index 04ceee959f8a6de5ed8b284bf45c76b0927c6e10..0000000000000000000000000000000000000000 --- a/MCdata/1br3_MC +++ /dev/null @@ -1,85 +0,0 @@ -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : A C3p_endo anti -A4 : C C3p_endo anti -A5 : A C2p_exo anti -A6 : G C3p_endo anti -A7 : A C3p_endo anti -A8 : U C3p_endo anti -A9 : G C3p_endo anti -A10 : G C3p_endo anti -A11 : G C3p_endo anti -A12 : A C3p_endo anti -A13 : G C3p_endo anti -B14 : G C3p_endo anti -B15 : C C3p_endo anti -B16 : T C3p_endo anti -B17 : C C3p_endo anti -B18 : C C3p_endo anti -B19 : C C4p_exo anti -B20 : A O4p_endo anti -B21 : G C2p_endo anti -B22 : G C3p_endo anti -B23 : C C4p_exo anti -B24 : T C2p_endo anti -B25 : A C3p_exo anti -B26 : G C2p_endo anti -B27 : C C4p_exo anti -B28 : T C2p_endo anti -B29 : A C3p_exo syn -B30 : C C1p_exo anti -B31 : A C1p_exo anti -B32 : A C1p_exo syn -B33 : C C2p_endo anti -B34 : G C2p_endo anti -B35 : A C2p_endo anti -B36 : C C2p_exo anti -B37 : T C3p_endo anti -B38 : G C3p_endo anti -B39 : T C3p_endo anti -B40 : C C3p_endo anti -B41 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A12-A13 : adjacent_5p upward -B14-B15 : adjacent_5p upward -B16-B17 : adjacent_5p upward -B18-B19 : adjacent_5p upward -B19-B20 : adjacent_5p upward -B20-B21 : adjacent_5p upward -B22-B23 : adjacent_5p upward -B24-B25 : adjacent_5p upward -B25-B26 : adjacent_5p upward -B26-B27 : adjacent_5p upward -B27-B28 : adjacent_5p upward -B31-B32 : adjacent_5p inward -B33-B34 : adjacent_5p upward -B34-B35 : adjacent_5p upward -B38-B39 : adjacent_5p upward -B39-B40 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A5-B38 : outward -B29-B31 : upward -Number of stackings = 28 -Number of adjacent stackings = 26 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A1-B41 : G-C Ww/Ww pairing antiparallel cis XIX -A2-B40 : G-C Ww/Ww pairing antiparallel cis XIX -A3-B39 : A-T Ww/Ww pairing antiparallel cis -A4-B38 : C-G Ww/Ww pairing antiparallel cis XIX -A5-B37 : A-T Ww/Ws pairing antiparallel cis -A6-B36 : G-C Ww/Ww pairing antiparallel cis XIX -B28-B29 : T-A O2P/Bh adjacent_5p pairing -B28-B35 : T-A Ww/Ww pairing antiparallel cis -B29-B33 : A-C Ss/Hw pairing antiparallel trans one_hbond 72 diff --git a/MCdata/1bvj_MC b/MCdata/1bvj_MC deleted file mode 100644 index e2085e96f350a674ac02f428bf3e5085687d5ccf..0000000000000000000000000000000000000000 --- a/MCdata/1bvj_MC +++ /dev/null @@ -1,1303 +0,0 @@ -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C3p_endo anti -A5 : A C3p_exo anti -A6 : C C2p_endo anti -A7 : G C4p_exo anti -A8 : G C4p_exo anti -A9 : U C3p_endo anti -A10 : G C2p_exo anti -A11 : U C3p_endo anti -A12 : A C2p_exo anti -A13 : A C3p_endo anti -A14 : A C2p_exo anti -A15 : A C3p_endo anti -A16 : A C3p_endo anti -A17 : U C3p_endo anti -A18 : C C3p_endo anti -A19 : U C3p_endo anti -A20 : C C3p_endo anti -A21 : G C3p_endo anti -A22 : C C3p_endo anti -A23 : C C2p_exo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward pairing -A16-A17 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A22-A23 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A21 : outward -A5-A7 : upward -Number of stackings = 19 -Number of adjacent stackings = 17 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A1-A23 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A22 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A21 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A20 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A19 : A-U Ww/Ww pairing antiparallel cis XX -A6-A14 : C-A Ww/O2P pairing -A7-A18 : G-C Ww/Ww pairing antiparallel cis XIX -A8-A17 : G-U Ww/Ws pairing antiparallel cis XXVIII -A9-A16 : U-A Ww/Ww pairing antiparallel cis XX -A10-A14 : G-A Ww/O2P pairing -A10-A15 : G-A Ss/Hh pairing antiparallel trans XI -A11-A13 : U-A O2'/Hh Ww/O2P pairing -A11-A14 : U-A O2'/Bh Ww/O2P pairing -A15-A16 : A-A O2P/Hh adjacent_5p upward pairing -Residue conformations ------------------------------------------- -A1 : G C4p_exo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C3p_endo anti -A5 : A C2p_endo anti -A6 : C C4p_exo anti -A7 : G C4p_exo anti -A8 : G C4p_exo anti -A9 : U C3p_endo anti -A10 : G C2p_exo anti -A11 : U C4p_exo anti -A12 : A C3p_endo anti -A13 : A C3p_endo anti -A14 : A C2p_exo anti -A15 : A C3p_endo anti -A16 : A C3p_endo anti -A17 : U C3p_endo anti -A18 : C C2p_exo anti -A19 : U C3p_endo anti -A20 : C C3p_endo anti -A21 : G C3p_endo anti -A22 : C C3p_endo anti -A23 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward pairing -A16-A17 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A22-A23 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A21 : outward -A5-A7 : upward -A8-A18 : outward -Number of stackings = 19 -Number of adjacent stackings = 16 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -A1-A23 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A22 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A21 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A20 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A6 : A-C O2'/Hh adjacent_5p pairing -A5-A19 : A-U Ww/Ww pairing antiparallel cis XX -A6-A20 : C-C Hw/Ss Bh/O2' pairing parallel trans one_hbond -A7-A18 : G-C Ww/Ww pairing antiparallel cis XIX -A8-A17 : G-U Ww/Ws pairing antiparallel cis XXVIII -A9-A16 : U-A Ww/Ww pairing antiparallel cis XX -A10-A14 : G-A Ww/O2P pairing -A10-A15 : G-A Ss/Hh O2'/Bh pairing antiparallel trans XI -A11-A13 : U-A O2'/Hh Ww/O2P pairing -A11-A14 : U-A Ww/O2P pairing -A15-A16 : A-A O2P/Hh adjacent_5p upward pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C3p_endo anti -A5 : A C4p_exo anti -A6 : C C2p_endo anti -A7 : G C4p_exo anti -A8 : G C4p_exo anti -A9 : U C3p_endo anti -A10 : G C2p_exo anti -A11 : U C3p_endo anti -A12 : A C2p_exo anti -A13 : A C3p_endo anti -A14 : A C1p_endo anti -A15 : A O4p_endo anti -A16 : A C4p_exo anti -A17 : U C4p_exo anti -A18 : C C3p_endo anti -A19 : U C3p_endo anti -A20 : C C3p_endo anti -A21 : G C3p_endo anti -A22 : C C3p_endo anti -A23 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A22-A23 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A21 : outward -A5-A7 : upward -A8-A18 : outward -Number of stackings = 19 -Number of adjacent stackings = 16 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -A1-A23 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A22 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A21 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A20 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A19 : A-U Ww/Ww pairing antiparallel cis XX -A7-A18 : G-C Ww/Ww pairing antiparallel cis XIX -A8-A17 : G-U Ww/Ws pairing antiparallel cis XXVIII -A9-A16 : U-A Ww/Ww pairing antiparallel cis XX -A10-A15 : G-A O2'/Bh pairing -A11-A13 : U-A O2'/Hh pairing -A11-A14 : U-A Ww/O2P pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C3p_endo anti -A5 : A C3p_exo anti -A6 : C C2p_endo anti -A7 : G C4p_exo anti -A8 : G C3p_endo anti -A9 : U C3p_endo anti -A10 : G C2p_exo anti -A11 : U C3p_endo anti -A12 : A C4p_endo anti -A13 : A C3p_endo anti -A14 : A C2p_exo anti -A15 : A C3p_endo anti -A16 : A O4p_endo anti -A17 : U C4p_exo anti -A18 : C C2p_exo anti -A19 : U C3p_endo anti -A20 : C C3p_endo anti -A21 : G C3p_endo anti -A22 : C C3p_endo anti -A23 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A12-A13 : adjacent_5p upward pairing -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A22-A23 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A21 : outward -A5-A7 : upward -A10-A16 : outward -Number of stackings = 19 -Number of adjacent stackings = 16 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -A1-A23 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A22 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A21 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A20 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A19 : A-U Ww/Ww pairing antiparallel cis XX -A6-A14 : C-A Bh/O2P pairing -A7-A18 : G-C Ww/Ww pairing antiparallel cis XIX -A8-A17 : G-U Ww/Ws pairing antiparallel cis XXVIII -A9-A16 : U-A Ww/Ww pairing antiparallel cis XX -A10-A15 : G-A Ws/Hh pairing antiparallel trans one_hbond 54 -A11-A13 : U-A O2'/Hh pairing -A11-A14 : U-A O2'/Bh Ww/O2P pairing -A12-A13 : A-A O2P/Hh adjacent_5p upward pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C4p_exo anti -A5 : A C4p_exo anti -A6 : C C4p_exo anti -A7 : G C4p_exo anti -A8 : G C4p_exo anti -A9 : U C3p_endo anti -A10 : G C2p_exo anti -A11 : U C3p_endo anti -A12 : A O4p_exo anti -A13 : A C3p_endo anti -A14 : A C2p_exo anti -A15 : A C1p_endo anti -A16 : A O4p_endo anti -A17 : U C4p_exo anti -A18 : C C3p_endo anti -A19 : U C3p_endo anti -A20 : C C3p_endo anti -A21 : G C2p_exo anti -A22 : C C3p_endo anti -A23 : C C2p_exo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A22-A23 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A21 : outward -A5-A7 : upward -A8-A18 : outward -Number of stackings = 20 -Number of adjacent stackings = 17 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -A1-A23 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A22 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A21 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A20 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A6 : A-C O2'/Hh adjacent_5p pairing -A5-A19 : A-U Ww/Ww pairing antiparallel cis XX -A7-A18 : G-C Ww/Ww pairing antiparallel cis XIX -A8-A17 : G-U Ww/Ws pairing antiparallel cis XXVIII -A9-A16 : U-A Ww/Ww pairing antiparallel cis XX -A10-A14 : G-A Ww/O2P pairing -A10-A15 : G-A Ss/Hh pairing antiparallel trans one_hbond -A11-A13 : U-A O2'/Hh pairing -A11-A14 : U-A Ww/O2P pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C3p_endo anti -A5 : A C4p_exo anti -A6 : C C3p_endo anti -A7 : G C4p_exo anti -A8 : G C4p_exo anti -A9 : U C2p_exo anti -A10 : G C2p_exo anti -A11 : U C3p_endo anti -A12 : A C1p_endo anti -A13 : A C3p_endo anti -A14 : A C3p_exo anti -A15 : A C4p_exo anti -A16 : A O4p_endo anti -A17 : U C4p_exo anti -A18 : C C3p_endo anti -A19 : U C3p_endo anti -A20 : C C3p_endo anti -A21 : G C3p_endo anti -A22 : C C3p_endo anti -A23 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A22-A23 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A21 : outward -A5-A7 : upward -A10-A16 : outward -Number of stackings = 20 -Number of adjacent stackings = 17 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -A1-A23 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A22 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A21 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A20 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A19 : A-U Ww/Ww pairing antiparallel cis XX -A7-A18 : G-C Ww/Ww pairing antiparallel cis XIX -A8-A17 : G-U Ww/Ws pairing antiparallel cis XXVIII -A9-A16 : U-A Ww/Ww pairing antiparallel cis XX -A10-A14 : G-A Ww/O2P pairing -A10-A15 : G-A Sw/Hh pairing antiparallel trans one_hbond -A11-A13 : U-A O2'/Bh O2'/Hh pairing -A11-A14 : U-A O2'/Bh Ww/O2P pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C2p_exo anti -A3 : C C3p_endo anti -A4 : G C3p_endo anti -A5 : A C4p_exo anti -A6 : C C2p_endo anti -A7 : G C3p_endo anti -A8 : G C3p_endo anti -A9 : U C3p_endo anti -A10 : G C2p_exo anti -A11 : U C3p_endo anti -A12 : A C3p_endo anti -A13 : A C3p_endo anti -A14 : A C3p_exo anti -A15 : A C3p_endo anti -A16 : A O4p_endo anti -A17 : U C4p_exo anti -A18 : C C3p_endo anti -A19 : U C3p_endo anti -A20 : C C3p_endo anti -A21 : G C3p_endo anti -A22 : C C3p_endo anti -A23 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A22-A23 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A21 : outward -A5-A7 : upward -A10-A16 : outward -Number of stackings = 18 -Number of adjacent stackings = 15 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -A1-A23 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A22 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A21 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A20 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A19 : A-U Ww/Ww pairing antiparallel cis XX -A7-A18 : G-C Ww/Ww pairing antiparallel cis XIX -A8-A17 : G-U Ww/Ws pairing antiparallel cis XXVIII -A9-A16 : U-A Ww/Ww pairing antiparallel cis XX -A10-A15 : G-A Ss/Hh pairing antiparallel trans XI -A11-A13 : U-A O2'/Hh Ww/O2P pairing -A11-A14 : U-A Ww/O2P pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C3p_endo anti -A5 : A C1p_exo anti -A6 : C C2p_endo anti -A7 : G C4p_exo anti -A8 : G C4p_exo anti -A9 : U C3p_endo anti -A10 : G C2p_exo anti -A11 : U C3p_endo anti -A12 : A C4p_endo anti -A13 : A C3p_endo anti -A14 : A C3p_exo anti -A15 : A C4p_exo anti -A16 : A C3p_endo anti -A17 : U C3p_endo anti -A18 : C C2p_exo anti -A19 : U C3p_endo anti -A20 : C C3p_endo anti -A21 : G C3p_endo anti -A22 : C C3p_endo anti -A23 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A22-A23 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A21 : outward -A5-A7 : upward -A8-A18 : outward -Number of stackings = 18 -Number of adjacent stackings = 15 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -A1-A23 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A22 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A21 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A20 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A19 : A-U Ww/Ww pairing antiparallel cis XX -A6-A14 : C-A Bh/O2P pairing -A7-A18 : G-C Ww/Ww pairing antiparallel cis XIX -A8-A17 : G-U Ww/Ws pairing antiparallel cis XXVIII -A9-A16 : U-A Ww/Ww pairing antiparallel cis XX -A10-A14 : G-A O2'/Bh pairing -A10-A15 : G-A Sw/Hh pairing antiparallel trans one_hbond -A11-A12 : U-A O2'/Hh adjacent_5p pairing -A11-A13 : U-A O2'/Hh pairing -A11-A14 : U-A Ww/O2P pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C3p_endo anti -A5 : A C2p_endo anti -A6 : C C2p_endo anti -A7 : G C4p_exo anti -A8 : G C4p_exo anti -A9 : U C3p_endo anti -A10 : G C1p_endo anti -A11 : U C3p_endo anti -A12 : A C3p_endo anti -A13 : A C3p_endo anti -A14 : A C2p_exo anti -A15 : A C3p_endo anti -A16 : A C3p_endo anti -A17 : U C3p_endo anti -A18 : C C3p_endo anti -A19 : U C3p_endo anti -A20 : C C4p_exo anti -A21 : G C3p_endo anti -A22 : C C3p_endo anti -A23 : C C2p_exo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward pairing -A16-A17 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A22-A23 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A21 : outward -A5-A7 : upward -A8-A18 : outward -Number of stackings = 19 -Number of adjacent stackings = 16 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -A1-A23 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A22 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A21 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A20 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A19 : A-U Ww/Ww pairing antiparallel cis XX -A6-A14 : C-A Ww/O2P Bh/O2P pairing -A7-A18 : G-C Ww/Ww pairing antiparallel cis XIX -A8-A17 : G-U Ww/Ws pairing antiparallel cis XXVIII -A9-A16 : U-A Ww/Ww pairing antiparallel cis XX -A10-A14 : G-A Ww/O2P pairing -A10-A15 : G-A Ss/Hh pairing antiparallel trans XI -A11-A13 : U-A O2'/Hh Ww/O2P pairing -A11-A14 : U-A Ww/O2P pairing -A15-A16 : A-A O2P/Hh adjacent_5p upward pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C3p_endo anti -A5 : A C4p_exo anti -A6 : C C4p_exo anti -A7 : G C4p_exo anti -A8 : G C4p_exo anti -A9 : U C3p_endo anti -A10 : G C2p_exo anti -A11 : U C3p_endo anti -A12 : A C1p_exo anti -A13 : A C2p_endo anti -A14 : A C3p_endo anti -A15 : A C2p_exo anti -A16 : A C3p_endo anti -A17 : U C3p_endo anti -A18 : C C3p_endo anti -A19 : U C3p_endo anti -A20 : C C3p_endo anti -A21 : G C3p_endo anti -A22 : C C3p_endo anti -A23 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A22-A23 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A21 : outward -A5-A7 : upward -A8-A18 : outward -Number of stackings = 21 -Number of adjacent stackings = 18 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -A1-A23 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A22 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A21 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A20 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A6 : A-C O2'/Hh adjacent_5p pairing -A5-A19 : A-U Ww/Ww pairing antiparallel cis XX -A6-A7 : C-G O2P/Hh adjacent_5p pairing -A7-A18 : G-C Ww/Ww pairing antiparallel cis XIX -A8-A17 : G-U Ww/Ws pairing antiparallel cis XXVIII -A9-A16 : U-A Ww/Ww pairing antiparallel cis XX -A11-A13 : U-A O2'/Hh pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C3p_endo anti -A5 : A O4p_endo anti -A6 : C C2p_endo anti -A7 : G C4p_exo anti -A8 : G C4p_exo anti -A9 : U C4p_exo anti -A10 : G C2p_exo anti -A11 : U C4p_exo anti -A12 : A C3p_endo anti -A13 : A C3p_endo anti -A14 : A C2p_exo anti -A15 : A C3p_endo anti -A16 : A C3p_endo anti -A17 : U C4p_exo anti -A18 : C C3p_endo anti -A19 : U C3p_endo anti -A20 : C C4p_exo anti -A21 : G C3p_endo anti -A22 : C C3p_endo anti -A23 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A21-A22 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A21 : outward -A5-A7 : upward -A8-A18 : outward -Number of stackings = 19 -Number of adjacent stackings = 16 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -A1-A23 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A22 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A21 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A20 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A19 : A-U Ww/Ww pairing antiparallel cis XX -A6-A14 : C-A Bh/O2P pairing -A7-A18 : G-C Ww/Ww pairing antiparallel cis XIX -A8-A17 : G-U Ww/Ws pairing antiparallel cis XXVIII -A9-A15 : U-A Ws/Wh pairing antiparallel trans one_hbond 46 -A9-A16 : U-A Ww/Ww pairing antiparallel cis XX -A11-A13 : U-A O2'/Hh pairing -A11-A14 : U-A Ww/O2P pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C3p_endo anti -A5 : A C3p_endo anti -A6 : C C4p_exo syn -A7 : G C4p_exo anti -A8 : G C3p_endo anti -A9 : U C3p_endo anti -A10 : G C2p_exo anti -A11 : U C3p_endo anti -A12 : A C4p_endo anti -A13 : A C3p_endo anti -A14 : A C3p_exo anti -A15 : A C3p_endo anti -A16 : A C3p_endo anti -A17 : U C3p_endo anti -A18 : C C3p_endo anti -A19 : U C3p_endo anti -A20 : C C3p_endo anti -A21 : G C2p_exo anti -A22 : C C3p_endo anti -A23 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A22-A23 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A21 : outward -A5-A7 : upward -A8-A18 : outward -Number of stackings = 21 -Number of adjacent stackings = 18 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -A1-A23 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A22 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A21 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A20 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A6 : A-C O2'/Hh adjacent_5p pairing -A5-A19 : A-U Ww/Ww pairing antiparallel cis XX -A6-A7 : C-G O2P/Hh adjacent_5p pairing -A7-A18 : G-C Ww/Ww pairing antiparallel cis XIX -A8-A17 : G-U Ww/Ws pairing antiparallel cis XXVIII -A9-A16 : U-A Ww/Ww pairing antiparallel cis XX -A11-A13 : U-A O2'/Hh pairing -A11-A14 : U-A Ww/O2P pairing -Residue conformations ------------------------------------------- -A1 : G C4p_exo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C4p_exo anti -A5 : A O4p_endo anti -A6 : C C4p_exo anti -A7 : G C4p_exo anti -A8 : G C4p_exo anti -A9 : U C3p_endo anti -A10 : G C2p_exo anti -A11 : U C3p_endo anti -A12 : A C2p_exo anti -A13 : A C3p_endo anti -A14 : A C2p_exo anti -A15 : A O4p_endo anti -A16 : A C3p_endo anti -A17 : U C3p_endo anti -A18 : C C3p_endo anti -A19 : U C3p_endo anti -A20 : C C3p_endo anti -A21 : G C2p_exo anti -A22 : C C3p_endo anti -A23 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A22-A23 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A21 : outward -A5-A7 : upward pairing -A8-A18 : outward -Number of stackings = 17 -Number of adjacent stackings = 14 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -A1-A23 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A22 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A21 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A20 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A6 : A-C O2'/Hh adjacent_5p pairing -A5-A7 : A-G O2'/Hh upward pairing -A5-A19 : A-U Ww/Ww pairing antiparallel cis XX -A7-A18 : G-C Ww/Ww pairing antiparallel cis XIX -A8-A17 : G-U Ww/Ws pairing antiparallel cis XXVIII -A9-A15 : U-A Ws/Wh pairing antiparallel trans one_hbond 46 -A9-A16 : U-A Ww/Ww pairing antiparallel cis XX -A10-A14 : G-A O2'/Bh pairing -A10-A15 : G-A Sw/Hh pairing antiparallel trans one_hbond -A11-A13 : U-A O2'/Hh pairing -A11-A14 : U-A Ww/O2P pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C2p_exo anti -A5 : A O4p_endo anti -A6 : C C1p_exo anti -A7 : G C4p_exo anti -A8 : G C3p_endo anti -A9 : U C3p_endo anti -A10 : G C2p_exo anti -A11 : U C3p_endo anti -A12 : A C1p_endo anti -A13 : A C3p_endo anti -A14 : A C2p_exo anti -A15 : A C3p_endo anti -A16 : A C4p_exo anti -A17 : U C4p_exo anti -A18 : C C3p_endo anti -A19 : U C3p_endo anti -A20 : C C3p_endo anti -A21 : G C3p_endo anti -A22 : C C3p_endo anti -A23 : C C2p_exo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward pairing -A16-A17 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A22-A23 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A21 : outward -A5-A7 : upward -A8-A18 : outward -Number of stackings = 21 -Number of adjacent stackings = 18 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -A1-A23 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A22 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A21 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A20 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A19 : A-U Ww/Ww pairing antiparallel cis XX -A7-A18 : G-C Ww/Ww pairing antiparallel cis XIX -A8-A17 : G-U Ww/Ws pairing antiparallel cis XXVIII -A9-A16 : U-A Ww/Ww pairing antiparallel cis XX -A10-A14 : G-A Ww/O2P pairing -A10-A15 : G-A Ss/Hh pairing antiparallel trans XI -A11-A13 : U-A O2'/Hh pairing -A11-A14 : U-A O2'/Bh Ww/O2P pairing -A15-A16 : A-A O2P/Hh adjacent_5p upward pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C3p_endo anti -A5 : A C3p_exo anti -A6 : C C2p_endo anti -A7 : G C4p_exo anti -A8 : G C3p_endo anti -A9 : U C3p_endo anti -A10 : G C2p_exo anti -A11 : U C3p_endo anti -A12 : A C3p_endo anti -A13 : A C3p_endo anti -A14 : A C2p_exo anti -A15 : A C3p_endo anti -A16 : A C3p_endo anti -A17 : U C3p_endo anti -A18 : C C3p_endo anti -A19 : U C3p_endo anti -A20 : C C3p_endo anti -A21 : G C2p_exo anti -A22 : C C3p_endo anti -A23 : C C2p_exo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A22-A23 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A21 : outward -A5-A7 : upward -A8-A18 : outward -Number of stackings = 20 -Number of adjacent stackings = 17 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -A1-A23 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A22 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A21 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A20 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A19 : A-U Ww/Ww pairing antiparallel cis XX -A6-A14 : C-A Bh/O2P pairing -A7-A18 : G-C Ww/Ww pairing antiparallel cis XIX -A8-A17 : G-U Ww/Ws pairing antiparallel cis XXVIII -A9-A16 : U-A Ww/Ww pairing antiparallel cis XX -A10-A14 : G-A O2'/Bh pairing -A10-A15 : G-A Ss/Hh pairing antiparallel trans XI -A11-A13 : U-A O2'/Hh pairing -A11-A14 : U-A Ww/O2P pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C3p_endo anti -A5 : A C4p_exo anti -A6 : C C2p_endo anti -A7 : G C4p_exo anti -A8 : G C4p_exo anti -A9 : U C3p_endo anti -A10 : G C2p_exo anti -A11 : U C3p_endo anti -A12 : A C1p_endo anti -A13 : A C3p_endo anti -A14 : A C2p_exo anti -A15 : A C3p_endo anti -A16 : A C2p_exo anti -A17 : U C4p_exo anti -A18 : C C3p_endo anti -A19 : U C3p_endo anti -A20 : C C3p_endo anti -A21 : G C2p_exo anti -A22 : C C3p_endo anti -A23 : C C2p_exo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A22-A23 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A21 : outward -A5-A7 : upward -Number of stackings = 19 -Number of adjacent stackings = 17 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A1-A23 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A22 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A21 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A20 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A19 : A-U Ww/Ww pairing antiparallel cis XX -A7-A18 : G-C Ww/Ww pairing antiparallel cis XIX -A8-A17 : G-U Ww/Ws pairing antiparallel cis XXVIII -A9-A16 : U-A Ww/Ww pairing antiparallel cis XX -A10-A14 : G-A Ww/O2P pairing -A10-A15 : G-A Ss/Hh pairing antiparallel trans XI -A11-A13 : U-A O2'/Bh O2'/Hh pairing -A11-A14 : U-A Ww/O2P pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C3p_endo anti -A5 : A C3p_exo anti -A6 : C C2p_endo anti -A7 : G C4p_exo anti -A8 : G C4p_exo anti -A9 : U C3p_endo anti -A10 : G C2p_exo anti -A11 : U C3p_endo anti -A12 : A C1p_endo anti -A13 : A C3p_endo anti -A14 : A C2p_exo anti -A15 : A C3p_endo anti -A16 : A O4p_endo anti -A17 : U C4p_exo anti -A18 : C C3p_endo anti -A19 : U C3p_endo anti -A20 : C C3p_endo anti -A21 : G C3p_endo anti -A22 : C C3p_endo anti -A23 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward pairing -A16-A17 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A22-A23 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A21 : outward -A5-A7 : upward -Number of stackings = 19 -Number of adjacent stackings = 17 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A1-A23 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A22 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A21 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A20 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A6 : A-C O2P/Bh adjacent_5p pairing -A5-A19 : A-U Ww/Ww pairing antiparallel cis XX -A7-A18 : G-C Ww/Ww pairing antiparallel cis XIX -A8-A17 : G-U Ww/Ws pairing antiparallel cis XXVIII -A9-A16 : U-A Ww/Ww pairing antiparallel cis XX -A10-A14 : G-A Ww/O2P pairing -A10-A15 : G-A Ss/Hh pairing antiparallel trans XI -A11-A13 : U-A O2'/Hh pairing -A11-A14 : U-A O2'/Bh Ww/O2P pairing -A15-A16 : A-A O2P/Hh adjacent_5p upward pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C2p_exo anti -A5 : A C1p_exo anti -A6 : C C1p_exo anti -A7 : G C4p_exo anti -A8 : G C4p_exo anti -A9 : U C3p_endo anti -A10 : G C2p_exo anti -A11 : U C3p_endo anti -A12 : A C4p_endo anti -A13 : A C3p_endo anti -A14 : A C2p_exo anti -A15 : A C3p_endo anti -A16 : A C3p_endo anti -A17 : U C3p_endo anti -A18 : C C3p_endo anti -A19 : U C3p_endo anti -A20 : C C2p_exo anti -A21 : G C3p_endo anti -A22 : C C3p_endo anti -A23 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward pairing -A16-A17 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A22-A23 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A21 : outward -A5-A7 : upward -Number of stackings = 18 -Number of adjacent stackings = 16 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A1-A23 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A22 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A21 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A20 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A19 : A-U Ww/Ww pairing antiparallel cis XX -A7-A18 : G-C Ww/Ww pairing antiparallel cis XIX -A8-A17 : G-U Ww/Ws pairing antiparallel cis XXVIII -A9-A16 : U-A Ww/Ww pairing antiparallel cis XX -A10-A14 : G-A Ww/O2P pairing -A10-A15 : G-A Sw/Hh pairing antiparallel trans one_hbond -A11-A13 : U-A O2'/Hh pairing -A11-A14 : U-A O2'/Bh Ww/O2P pairing -A15-A16 : A-A O2P/Hh adjacent_5p upward pairing -Residue conformations ------------------------------------------- -A1 : G C4p_exo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C2p_exo anti -A5 : A C3p_exo anti -A6 : C C1p_exo anti -A7 : G C4p_exo anti -A8 : G C4p_exo anti -A9 : U C3p_endo anti -A10 : G C2p_exo anti -A11 : U C3p_endo anti -A12 : A O4p_endo anti -A13 : A C3p_endo anti -A14 : A C2p_exo anti -A15 : A C2p_exo anti -A16 : A C2p_exo anti -A17 : U C4p_exo anti -A18 : C C3p_endo anti -A19 : U C3p_endo anti -A20 : C C3p_endo anti -A21 : G C2p_exo anti -A22 : C C3p_endo anti -A23 : C C2p_exo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A22-A23 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A21 : outward -A5-A7 : upward -Number of stackings = 18 -Number of adjacent stackings = 16 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A1-A23 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A22 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A21 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A20 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A6 : A-C O2P/Bh adjacent_5p pairing -A5-A19 : A-U Ww/Ww pairing antiparallel cis XX -A7-A18 : G-C Ww/Ww pairing antiparallel cis XIX -A8-A17 : G-U Ww/Ws pairing antiparallel cis XXVIII -A9-A16 : U-A Ww/Ww pairing antiparallel cis XX -A10-A14 : G-A Ww/O2P pairing -A11-A14 : U-A O2'/Bh Ww/O2P pairing -A15-A16 : A-A O2P/Hh adjacent_5p pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C3p_endo anti -A5 : A C4p_exo anti -A6 : C C1p_exo anti -A7 : G C4p_exo anti -A8 : G C3p_endo anti -A9 : U C3p_endo anti -A10 : G C2p_exo anti -A11 : U C3p_endo anti -A12 : A C3p_exo anti -A13 : A C3p_endo anti -A14 : A C2p_exo anti -A15 : A C3p_endo anti -A16 : A C3p_endo anti -A17 : U C4p_exo anti -A18 : C C3p_endo anti -A19 : U C3p_endo anti -A20 : C C3p_endo anti -A21 : G C3p_endo anti -A22 : C C3p_endo anti -A23 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A22-A23 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A21 : outward -A5-A7 : upward -A8-A18 : outward -Number of stackings = 21 -Number of adjacent stackings = 18 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -A1-A23 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A22 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A21 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A20 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A19 : A-U Ww/Ww pairing antiparallel cis XX -A6-A15 : C-A Bh/O2P pairing -A7-A18 : G-C Ww/Ww pairing antiparallel cis XIX -A8-A17 : G-U Ww/Ws pairing antiparallel cis XXVIII -A9-A16 : U-A Ww/Ww pairing antiparallel cis XX -A10-A14 : G-A Ww/O2P pairing -A10-A15 : G-A Ss/Hh pairing antiparallel trans XI -A11-A13 : U-A O2'/Hh pairing -A11-A14 : U-A O2'/Bh Ww/O2P pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C3p_endo anti -A5 : A C3p_endo anti -A6 : C O4p_endo anti -A7 : G C4p_exo anti -A8 : G C3p_endo anti -A9 : U C3p_endo anti -A10 : G C2p_exo anti -A11 : U C3p_endo anti -A12 : A C4p_endo anti -A13 : A C3p_endo anti -A14 : A C3p_exo anti -A15 : A C2p_exo anti -A16 : A C3p_endo anti -A17 : U C2p_exo anti -A18 : C C3p_endo anti -A19 : U C3p_endo anti -A20 : C C3p_endo anti -A21 : G C2p_exo anti -A22 : C C3p_endo anti -A23 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A22-A23 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A21 : outward -A5-A7 : upward -Number of stackings = 20 -Number of adjacent stackings = 18 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A1-A23 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A22 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A21 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A20 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A19 : A-U Ww/Ww pairing antiparallel cis XX -A7-A18 : G-C Ww/Ww pairing antiparallel cis XIX -A8-A17 : G-U Ww/Ws pairing antiparallel cis XXVIII -A9-A16 : U-A Ww/Ww pairing antiparallel cis XX -A10-A14 : G-A Ww/O2P pairing -A11-A13 : U-A O2'/Hh pairing -A11-A14 : U-A Ww/O2P pairing diff --git a/MCdata/1byj_MC b/MCdata/1byj_MC deleted file mode 100644 index b22090948568864dd4a7ee9036deaf267f9de721..0000000000000000000000000000000000000000 --- a/MCdata/1byj_MC +++ /dev/null @@ -1,2623 +0,0 @@ -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : C C3p_endo anti -A7 : A C3p_endo anti -A8 : C C3p_endo anti -A9 : A C3p_endo anti -A10 : C C3p_endo anti -A11 : C C3p_endo anti -A12 : U C3p_endo anti -A13 : U C1p_exo anti -A14 : C C2p_endo anti -A15 : G C4p_exo syn -A16 : G C2p_exo anti -A17 : G C3p_endo anti -A18 : U C3p_endo anti -A19 : G C3p_endo anti -A20 : A C3p_endo anti -A21 : A C3p_endo anti -A22 : G C3p_endo anti -A23 : U C3p_endo anti -A24 : C C3p_endo anti -A25 : G C3p_endo anti -A26 : C C3p_endo anti -A27 : C O4p_endo anti -A28 : GE1 -A29 : GE2 -A30 : GE3 -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A15-A16 : adjacent_5p outward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A22-A23 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A25 : outward -A9-A19 : outward -A12-A14 : upward -Number of stackings = 21 -Number of adjacent stackings = 18 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -A1-A27 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A26 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A25 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A24 : G-C Ww/Ww pairing antiparallel cis XIX -A6-A22 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A19 : C-G Ww/Ww pairing antiparallel cis XIX -A9-A18 : A-U Ww/Ww pairing antiparallel cis XX -A10-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A11-A16 : C-G Ww/Ww pairing antiparallel cis XIX -A12-A15 : U-G Bs/Ww pairing parallel trans 87 -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : C C3p_endo anti -A7 : A C3p_endo anti -A8 : C C3p_endo anti -A9 : A C3p_endo anti -A10 : C C3p_endo anti -A11 : C C3p_endo anti -A12 : U C3p_endo anti -A13 : U C1p_exo anti -A14 : C C2p_endo anti -A15 : G C4p_exo syn -A16 : G C2p_exo anti -A17 : G C3p_endo anti -A18 : U C3p_endo anti -A19 : G C3p_endo anti -A20 : A C3p_endo anti -A21 : A C3p_endo anti -A22 : G C3p_endo anti -A23 : U C3p_endo anti -A24 : C C3p_endo anti -A25 : G C3p_endo anti -A26 : C C3p_endo anti -A27 : C O4p_endo anti -A28 : GE1 -A29 : GE2 -A30 : GE3 -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A15-A16 : adjacent_5p outward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A22-A23 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A25 : outward -A7-A22 : outward -A9-A19 : outward -A12-A14 : upward -Number of stackings = 22 -Number of adjacent stackings = 18 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A1-A27 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A26 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A25 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A24 : G-C Ww/Ww pairing antiparallel cis XIX -A6-A22 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A19 : C-G Ww/Ww pairing antiparallel cis XIX -A9-A18 : A-U Ww/Ww pairing antiparallel cis XX -A10-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A11-A16 : C-G Ww/Ww pairing antiparallel cis XIX -A12-A15 : U-G Bs/Ww pairing parallel trans 87 -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : C C3p_endo anti -A7 : A C3p_endo anti -A8 : C C3p_endo anti -A9 : A C3p_endo anti -A10 : C C3p_endo anti -A11 : C C3p_endo anti -A12 : U C3p_endo anti -A13 : U C1p_exo anti -A14 : C C2p_endo anti -A15 : G C4p_exo syn -A16 : G C2p_exo anti -A17 : G C3p_endo anti -A18 : U C3p_endo anti -A19 : G C3p_endo anti -A20 : A C3p_endo anti -A21 : A C3p_endo anti -A22 : G C3p_endo anti -A23 : U C3p_endo anti -A24 : C C3p_endo anti -A25 : G C3p_endo anti -A26 : C C3p_endo anti -A27 : C O4p_endo anti -A28 : GE1 -A29 : GE2 -A30 : GE3 -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A15-A16 : adjacent_5p outward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A22-A23 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A25 : outward -A7-A22 : outward -A9-A19 : outward -A12-A14 : upward -Number of stackings = 22 -Number of adjacent stackings = 18 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A1-A27 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A26 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A25 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A24 : G-C Ww/Ww pairing antiparallel cis XIX -A6-A22 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A19 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A21 : C-A Ws/Wh pairing antiparallel cis one_hbond 78 -A9-A18 : A-U Ww/Ww pairing antiparallel cis XX -A10-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A11-A16 : C-G Ww/Ww pairing antiparallel cis XIX -A12-A15 : U-G Bs/Ww pairing parallel trans 87 -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : C C3p_endo anti -A7 : A C3p_endo anti -A8 : C C3p_endo anti -A9 : A C3p_endo anti -A10 : C C3p_endo anti -A11 : C C3p_endo anti -A12 : U C3p_endo anti -A13 : U C1p_exo anti -A14 : C C2p_endo anti -A15 : G C4p_exo syn -A16 : G C2p_exo anti -A17 : G C3p_endo anti -A18 : U C3p_endo anti -A19 : G C3p_endo anti -A20 : A C2p_endo anti -A21 : A C3p_endo anti -A22 : G C3p_endo anti -A23 : U C3p_endo anti -A24 : C C3p_endo anti -A25 : G C3p_endo anti -A26 : C C3p_endo anti -A27 : C O4p_endo anti -A28 : GE1 -A29 : GE2 -A30 : GE3 -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A15-A16 : adjacent_5p outward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A22-A23 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A25 : outward -A7-A22 : outward -A9-A19 : outward -A12-A14 : upward -Number of stackings = 22 -Number of adjacent stackings = 18 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A1-A27 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A26 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A25 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A24 : G-C Ww/Ww pairing antiparallel cis XIX -A6-A22 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A19 : C-G Ww/Ww pairing antiparallel cis XIX -A9-A18 : A-U Ww/Ww pairing antiparallel cis XX -A10-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A11-A16 : C-G Ww/Ww pairing antiparallel cis XIX -A12-A15 : U-G Bs/Ww pairing parallel trans 87 -A19-A20 : G-A O2'/Hh adjacent_5p pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : C C3p_endo anti -A7 : A C3p_endo anti -A8 : C C3p_endo anti -A9 : A C3p_endo anti -A10 : C C3p_endo anti -A11 : C C3p_endo anti -A12 : U C3p_endo anti -A13 : U C1p_exo anti -A14 : C C2p_endo anti -A15 : G C4p_exo syn -A16 : G C2p_exo anti -A17 : G C3p_endo anti -A18 : U C3p_endo anti -A19 : G C3p_endo anti -A20 : A C3p_endo anti -A21 : A C3p_endo anti -A22 : G C3p_endo anti -A23 : U C3p_endo anti -A24 : C C3p_endo anti -A25 : G C3p_endo anti -A26 : C C3p_endo anti -A27 : C O4p_endo anti -A28 : GE1 -A29 : GE2 -A30 : GE3 -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A15-A16 : adjacent_5p outward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A22-A23 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A25 : outward -A7-A22 : outward -A9-A19 : outward -A12-A14 : upward -Number of stackings = 22 -Number of adjacent stackings = 18 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A1-A27 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A26 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A25 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A24 : G-C Ww/Ww pairing antiparallel cis XIX -A6-A22 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A19 : C-G Ww/Ww pairing antiparallel cis XIX -A9-A18 : A-U Ww/Ww pairing antiparallel cis XX -A10-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A11-A16 : C-G Ww/Ww pairing antiparallel cis XIX -A12-A15 : U-G Bs/Ww pairing parallel trans 87 -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : C C3p_endo anti -A7 : A C3p_endo anti -A8 : C C3p_endo anti -A9 : A C3p_endo anti -A10 : C C3p_endo anti -A11 : C C3p_endo anti -A12 : U C3p_endo anti -A13 : U C1p_exo anti -A14 : C C2p_endo anti -A15 : G C4p_exo syn -A16 : G C2p_exo anti -A17 : G C3p_endo anti -A18 : U C3p_endo anti -A19 : G C3p_endo anti -A20 : A C3p_endo anti -A21 : A C3p_endo anti -A22 : G C3p_endo anti -A23 : U C3p_endo anti -A24 : C C3p_endo anti -A25 : G C3p_endo anti -A26 : C C3p_endo anti -A27 : C O4p_endo anti -A28 : GE1 -A29 : GE2 -A30 : GE3 -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A15-A16 : adjacent_5p outward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A22-A23 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A25 : outward -A7-A22 : outward -A9-A19 : outward -A12-A14 : upward -Number of stackings = 22 -Number of adjacent stackings = 18 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A1-A27 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A26 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A25 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A24 : G-C Ww/Ww pairing antiparallel cis XIX -A6-A22 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A19 : C-G Ww/Ww pairing antiparallel cis XIX -A9-A18 : A-U Ww/Ww pairing antiparallel cis XX -A10-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A11-A16 : C-G Ww/Ww pairing antiparallel cis XIX -A12-A15 : U-G Bs/Ww pairing parallel trans 87 -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : C C3p_endo anti -A7 : A C3p_endo anti -A8 : C C3p_endo anti -A9 : A C3p_endo anti -A10 : C C3p_endo anti -A11 : C C3p_endo anti -A12 : U C3p_endo anti -A13 : U C1p_exo anti -A14 : C C2p_endo anti -A15 : G C4p_exo syn -A16 : G C2p_exo anti -A17 : G C3p_endo anti -A18 : U C3p_endo anti -A19 : G C3p_endo anti -A20 : A C3p_endo anti -A21 : A C4p_exo anti -A22 : G C3p_endo anti -A23 : U C3p_endo anti -A24 : C C3p_endo anti -A25 : G C3p_endo anti -A26 : C C3p_endo anti -A27 : C O4p_endo anti -A28 : GE1 -A29 : GE2 -A30 : GE3 -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A15-A16 : adjacent_5p outward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A22-A23 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A25 : outward -A7-A22 : outward -A9-A19 : outward -A12-A14 : upward -Number of stackings = 22 -Number of adjacent stackings = 18 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A1-A27 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A26 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A25 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A24 : G-C Ww/Ww pairing antiparallel cis XIX -A6-A22 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A19 : C-G Ww/Ww pairing antiparallel cis XIX -A9-A18 : A-U Ww/Ww pairing antiparallel cis XX -A10-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A11-A16 : C-G Ww/Ww pairing antiparallel cis XIX -A12-A15 : U-G Bs/Ww pairing parallel trans 87 -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : C C3p_endo anti -A7 : A C3p_endo anti -A8 : C C3p_endo anti -A9 : A C3p_endo anti -A10 : C C3p_endo anti -A11 : C C3p_endo anti -A12 : U C3p_endo anti -A13 : U C1p_exo anti -A14 : C C2p_endo anti -A15 : G C4p_exo syn -A16 : G C2p_exo anti -A17 : G C3p_endo anti -A18 : U C3p_endo anti -A19 : G C3p_endo anti -A20 : A C3p_endo anti -A21 : A C3p_endo anti -A22 : G C3p_endo anti -A23 : U C3p_endo anti -A24 : C C3p_endo anti -A25 : G C3p_endo anti -A26 : C C3p_endo anti -A27 : C O4p_endo anti -A28 : GE1 -A29 : GE2 -A30 : GE3 -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A15-A16 : adjacent_5p outward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A22-A23 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A25 : outward -A7-A22 : outward -A9-A19 : outward -A12-A14 : upward -Number of stackings = 22 -Number of adjacent stackings = 18 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A1-A27 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A26 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A25 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A24 : G-C Ww/Ww pairing antiparallel cis XIX -A6-A22 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A19 : C-G Ww/Ww pairing antiparallel cis XIX -A9-A18 : A-U Ww/Ww pairing antiparallel cis XX -A10-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A11-A16 : C-G Ww/Ww pairing antiparallel cis XIX -A12-A15 : U-G Bs/Ww pairing parallel trans 87 -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : C C3p_endo anti -A7 : A C3p_endo anti -A8 : C C3p_endo anti -A9 : A C3p_endo anti -A10 : C C3p_endo anti -A11 : C C3p_endo anti -A12 : U C3p_endo anti -A13 : U C1p_exo anti -A14 : C C2p_endo anti -A15 : G C4p_exo syn -A16 : G C2p_exo anti -A17 : G C3p_endo anti -A18 : U C3p_endo anti -A19 : G C3p_endo anti -A20 : A C3p_endo anti -A21 : A C4p_exo anti -A22 : G C3p_endo anti -A23 : U C3p_endo anti -A24 : C C3p_endo anti -A25 : G C3p_endo anti -A26 : C C3p_endo anti -A27 : C O4p_endo anti -A28 : GE1 -A29 : GE2 -A30 : GE3 -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A15-A16 : adjacent_5p outward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A22-A23 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A25 : outward -A7-A22 : outward -A9-A19 : outward -A12-A14 : upward -Number of stackings = 22 -Number of adjacent stackings = 18 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A1-A27 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A26 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A25 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A24 : G-C Ww/Ww pairing antiparallel cis XIX -A6-A22 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A19 : C-G Ww/Ww pairing antiparallel cis XIX -A9-A18 : A-U Ww/Ww pairing antiparallel cis XX -A10-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A11-A16 : C-G Ww/Ww pairing antiparallel cis XIX -A12-A15 : U-G Bs/Ww pairing parallel trans 87 -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : C C3p_endo anti -A7 : A C3p_endo anti -A8 : C C3p_endo anti -A9 : A C3p_endo anti -A10 : C C3p_endo anti -A11 : C C3p_endo anti -A12 : U C3p_endo anti -A13 : U C1p_exo anti -A14 : C C2p_endo anti -A15 : G C4p_exo syn -A16 : G C2p_exo anti -A17 : G C3p_endo anti -A18 : U C3p_endo anti -A19 : G C3p_endo anti -A20 : A C3p_endo anti -A21 : A C4p_exo anti -A22 : G C3p_endo anti -A23 : U C3p_endo anti -A24 : C C3p_endo anti -A25 : G C3p_endo anti -A26 : C C3p_endo anti -A27 : C O4p_endo anti -A28 : GE1 -A29 : GE2 -A30 : GE3 -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A15-A16 : adjacent_5p outward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A22-A23 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A25 : outward -A7-A22 : outward -A9-A19 : outward -A12-A14 : upward -Number of stackings = 21 -Number of adjacent stackings = 17 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A1-A27 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A26 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A25 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A24 : G-C Ww/Ww pairing antiparallel cis XIX -A6-A22 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A19 : C-G Ww/Ww pairing antiparallel cis XIX -A9-A18 : A-U Ww/Ww pairing antiparallel cis XX -A10-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A11-A16 : C-G Ww/Ww pairing antiparallel cis XIX -A12-A15 : U-G Bs/Ww pairing parallel trans 87 -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : C C3p_endo anti -A7 : A C3p_endo anti -A8 : C C3p_endo anti -A9 : A C3p_endo anti -A10 : C C3p_endo anti -A11 : C C3p_endo anti -A12 : U C3p_endo anti -A13 : U C1p_exo anti -A14 : C C2p_endo anti -A15 : G C4p_exo syn -A16 : G C2p_exo anti -A17 : G C3p_endo anti -A18 : U C3p_endo anti -A19 : G C3p_endo anti -A20 : A C3p_endo anti -A21 : A C3p_endo anti -A22 : G C3p_endo anti -A23 : U C3p_endo anti -A24 : C C3p_endo anti -A25 : G C3p_endo anti -A26 : C C3p_endo anti -A27 : C O4p_endo anti -A28 : GE1 -A29 : GE2 -A30 : GE3 -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A15-A16 : adjacent_5p outward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A22-A23 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A25 : outward -A7-A22 : outward -A9-A19 : outward -A12-A14 : upward -Number of stackings = 22 -Number of adjacent stackings = 18 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A1-A27 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A26 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A25 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A24 : G-C Ww/Ww pairing antiparallel cis XIX -A6-A22 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A19 : C-G Ww/Ww pairing antiparallel cis XIX -A9-A18 : A-U Ww/Ww pairing antiparallel cis XX -A10-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A11-A16 : C-G Ww/Ww pairing antiparallel cis XIX -A12-A15 : U-G Bs/Ww pairing parallel trans 87 -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : C C3p_endo anti -A7 : A C3p_endo anti -A8 : C C3p_endo anti -A9 : A C3p_endo anti -A10 : C C3p_endo anti -A11 : C C3p_endo anti -A12 : U C3p_endo anti -A13 : U C1p_exo anti -A14 : C C2p_endo anti -A15 : G C4p_exo syn -A16 : G C2p_exo anti -A17 : G C3p_endo anti -A18 : U C3p_endo anti -A19 : G C3p_endo anti -A20 : A C3p_endo anti -A21 : A C3p_endo anti -A22 : G C3p_endo anti -A23 : U C3p_endo anti -A24 : C C3p_endo anti -A25 : G C3p_endo anti -A26 : C C3p_endo anti -A27 : C O4p_endo anti -A28 : GE1 -A29 : GE2 -A30 : GE3 -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A15-A16 : adjacent_5p outward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A22-A23 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A25 : outward -A7-A22 : outward -A9-A19 : outward -A12-A14 : upward -Number of stackings = 22 -Number of adjacent stackings = 18 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A1-A27 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A26 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A25 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A24 : G-C Ww/Ww pairing antiparallel cis XIX -A6-A22 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A19 : C-G Ww/Ww pairing antiparallel cis XIX -A9-A18 : A-U Ww/Ww pairing antiparallel cis XX -A10-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A11-A16 : C-G Ww/Ww pairing antiparallel cis XIX -A12-A15 : U-G Bs/Ww pairing parallel trans 87 -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : C C3p_endo anti -A7 : A C3p_endo anti -A8 : C C3p_endo anti -A9 : A C3p_endo anti -A10 : C C3p_endo anti -A11 : C C3p_endo anti -A12 : U C3p_endo anti -A13 : U C1p_exo anti -A14 : C C2p_endo anti -A15 : G C4p_exo syn -A16 : G C2p_exo anti -A17 : G C3p_endo anti -A18 : U C3p_endo anti -A19 : G C3p_endo anti -A20 : A C3p_endo anti -A21 : A C4p_exo anti -A22 : G C3p_endo anti -A23 : U C3p_endo anti -A24 : C C3p_endo anti -A25 : G C3p_endo anti -A26 : C C3p_endo anti -A27 : C O4p_endo anti -A28 : GE1 -A29 : GE2 -A30 : GE3 -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A15-A16 : adjacent_5p outward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A22-A23 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A25 : outward -A7-A22 : outward -A9-A19 : outward -A12-A14 : upward -Number of stackings = 22 -Number of adjacent stackings = 18 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A1-A27 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A26 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A25 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A24 : G-C Ww/Ww pairing antiparallel cis XIX -A6-A22 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A19 : C-G Ww/Ww pairing antiparallel cis XIX -A9-A18 : A-U Ww/Ww pairing antiparallel cis XX -A10-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A11-A16 : C-G Ww/Ww pairing antiparallel cis XIX -A12-A15 : U-G Bs/Ww pairing parallel trans 87 -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : C C3p_endo anti -A7 : A C3p_endo anti -A8 : C C3p_endo anti -A9 : A C3p_endo anti -A10 : C C3p_endo anti -A11 : C C3p_endo anti -A12 : U C3p_endo anti -A13 : U C1p_exo anti -A14 : C C2p_endo anti -A15 : G C4p_exo syn -A16 : G C2p_exo anti -A17 : G C3p_endo anti -A18 : U C3p_endo anti -A19 : G C3p_endo anti -A20 : A C3p_endo anti -A21 : A C4p_exo anti -A22 : G C3p_endo anti -A23 : U C3p_endo anti -A24 : C C3p_endo anti -A25 : G C3p_endo anti -A26 : C C3p_endo anti -A27 : C O4p_endo anti -A28 : GE1 -A29 : GE2 -A30 : GE3 -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A15-A16 : adjacent_5p outward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A22-A23 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A25 : outward -A7-A22 : outward -A9-A19 : outward -A12-A14 : upward -Number of stackings = 22 -Number of adjacent stackings = 18 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A1-A27 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A26 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A25 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A24 : G-C Ww/Ww pairing antiparallel cis XIX -A6-A22 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A19 : C-G Ww/Ww pairing antiparallel cis XIX -A9-A18 : A-U Ww/Ww pairing antiparallel cis XX -A10-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A11-A16 : C-G Ww/Ww pairing antiparallel cis XIX -A12-A15 : U-G Bs/Ww pairing parallel trans 87 -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : C C3p_endo anti -A7 : A C3p_endo anti -A8 : C C3p_endo anti -A9 : A C3p_endo anti -A10 : C C3p_endo anti -A11 : C C3p_endo anti -A12 : U C3p_endo anti -A13 : U C1p_exo anti -A14 : C C2p_endo anti -A15 : G C4p_exo syn -A16 : G C2p_exo anti -A17 : G C3p_endo anti -A18 : U C3p_endo anti -A19 : G C3p_endo anti -A20 : A C3p_endo anti -A21 : A C4p_exo anti -A22 : G C3p_endo anti -A23 : U C3p_endo anti -A24 : C C3p_endo anti -A25 : G C3p_endo anti -A26 : C C3p_endo anti -A27 : C O4p_endo anti -A28 : GE1 -A29 : GE2 -A30 : GE3 -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A15-A16 : adjacent_5p outward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A22-A23 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A25 : outward -A7-A22 : outward -A9-A19 : outward -A12-A14 : upward -Number of stackings = 22 -Number of adjacent stackings = 18 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A1-A27 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A26 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A25 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A24 : G-C Ww/Ww pairing antiparallel cis XIX -A6-A22 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A19 : C-G Ww/Ww pairing antiparallel cis XIX -A9-A18 : A-U Ww/Ww pairing antiparallel cis XX -A10-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A11-A16 : C-G Ww/Ww pairing antiparallel cis XIX -A12-A15 : U-G Bs/Ww pairing parallel trans 87 -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : C C3p_endo anti -A7 : A C3p_endo anti -A8 : C C3p_endo anti -A9 : A C3p_endo anti -A10 : C C3p_endo anti -A11 : C C3p_endo anti -A12 : U C3p_endo anti -A13 : U C1p_exo anti -A14 : C C2p_endo anti -A15 : G C4p_exo syn -A16 : G C2p_exo anti -A17 : G C3p_endo anti -A18 : U C3p_endo anti -A19 : G C3p_endo anti -A20 : A C3p_endo anti -A21 : A C3p_endo anti -A22 : G C3p_endo anti -A23 : U C3p_endo anti -A24 : C C3p_endo anti -A25 : G C3p_endo anti -A26 : C C3p_endo anti -A27 : C O4p_endo anti -A28 : GE1 -A29 : GE2 -A30 : GE3 -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A15-A16 : adjacent_5p outward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A22-A23 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A25 : outward -A7-A22 : outward -A9-A19 : outward -A12-A14 : upward -Number of stackings = 22 -Number of adjacent stackings = 18 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A1-A27 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A26 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A25 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A24 : G-C Ww/Ww pairing antiparallel cis XIX -A6-A22 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A19 : C-G Ww/Ww pairing antiparallel cis -A9-A18 : A-U Ww/Ww pairing antiparallel cis XX -A10-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A11-A16 : C-G Ww/Ww pairing antiparallel cis XIX -A12-A15 : U-G Bs/Ww pairing parallel trans 87 -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : C C3p_endo anti -A7 : A C3p_endo anti -A8 : C C3p_endo anti -A9 : A C3p_endo anti -A10 : C C3p_endo anti -A11 : C C3p_endo anti -A12 : U C3p_endo anti -A13 : U C1p_exo anti -A14 : C C2p_endo anti -A15 : G C4p_exo syn -A16 : G C2p_exo anti -A17 : G C3p_endo anti -A18 : U C3p_endo anti -A19 : G C3p_endo anti -A20 : A C3p_endo anti -A21 : A C3p_endo anti -A22 : G C3p_endo anti -A23 : U C3p_endo anti -A24 : C C3p_endo anti -A25 : G C3p_endo anti -A26 : C C3p_endo anti -A27 : C O4p_endo anti -A28 : GE1 -A29 : GE2 -A30 : GE3 -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A15-A16 : adjacent_5p outward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A22-A23 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A25 : outward -A7-A22 : outward -A9-A19 : outward -A12-A14 : upward -Number of stackings = 22 -Number of adjacent stackings = 18 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A1-A27 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A26 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A25 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A24 : G-C Ww/Ww pairing antiparallel cis XIX -A6-A22 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A19 : C-G Ww/Ww pairing antiparallel cis XIX -A9-A18 : A-U Ww/Ww pairing antiparallel cis XX -A10-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A11-A16 : C-G Ww/Ww pairing antiparallel cis XIX -A12-A15 : U-G Bs/Ww pairing parallel trans 87 -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : C C3p_endo anti -A7 : A C3p_endo anti -A8 : C C3p_endo anti -A9 : A C3p_endo anti -A10 : C C3p_endo anti -A11 : C C3p_endo anti -A12 : U C3p_endo anti -A13 : U C1p_exo anti -A14 : C C2p_endo anti -A15 : G C4p_exo syn -A16 : G C2p_exo anti -A17 : G C3p_endo anti -A18 : U C3p_endo anti -A19 : G C3p_endo anti -A20 : A C3p_endo anti -A21 : A C3p_endo anti -A22 : G C3p_endo anti -A23 : U C3p_endo anti -A24 : C C3p_endo anti -A25 : G C3p_endo anti -A26 : C C3p_endo anti -A27 : C O4p_endo anti -A28 : GE1 -A29 : GE2 -A30 : GE3 -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A15-A16 : adjacent_5p outward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A22-A23 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A25 : outward -A7-A22 : outward -A9-A19 : outward -A12-A14 : upward -Number of stackings = 22 -Number of adjacent stackings = 18 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A1-A27 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A26 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A25 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A24 : G-C Ww/Ww pairing antiparallel cis XIX -A6-A22 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A19 : C-G Ww/Ww pairing antiparallel cis XIX -A9-A18 : A-U Ww/Ww pairing antiparallel cis XX -A10-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A11-A16 : C-G Ww/Ww pairing antiparallel cis XIX -A12-A15 : U-G Bs/Ww pairing parallel trans 87 -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : C C3p_endo anti -A7 : A C3p_endo anti -A8 : C C3p_endo anti -A9 : A C3p_endo anti -A10 : C C3p_endo anti -A11 : C C3p_endo anti -A12 : U C3p_endo anti -A13 : U C1p_exo anti -A14 : C C2p_endo anti -A15 : G C4p_exo syn -A16 : G C2p_exo anti -A17 : G C3p_endo anti -A18 : U C3p_endo anti -A19 : G C3p_endo anti -A20 : A C3p_endo anti -A21 : A C3p_endo anti -A22 : G C3p_endo anti -A23 : U C3p_endo anti -A24 : C C3p_endo anti -A25 : G C3p_endo anti -A26 : C C3p_endo anti -A27 : C O4p_endo anti -A28 : GE1 -A29 : GE2 -A30 : GE3 -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A15-A16 : adjacent_5p outward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A22-A23 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A25 : outward -A7-A22 : outward -A9-A19 : outward -A12-A14 : upward -Number of stackings = 22 -Number of adjacent stackings = 18 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A1-A27 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A26 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A25 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A24 : G-C Ww/Ww pairing antiparallel cis XIX -A6-A22 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A19 : C-G Ww/Ww pairing antiparallel cis XIX -A9-A18 : A-U Ww/Ww pairing antiparallel cis XX -A10-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A11-A16 : C-G Ww/Ww pairing antiparallel cis XIX -A12-A15 : U-G Bs/Ww pairing parallel trans 87 -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : C C3p_endo anti -A7 : A C3p_endo anti -A8 : C C3p_endo anti -A9 : A C3p_endo anti -A10 : C C3p_endo anti -A11 : C C3p_endo anti -A12 : U C3p_endo anti -A13 : U C1p_exo anti -A14 : C C2p_endo anti -A15 : G C4p_exo syn -A16 : G C2p_exo anti -A17 : G C3p_endo anti -A18 : U C3p_endo anti -A19 : G C3p_endo anti -A20 : A C3p_endo anti -A21 : A C3p_endo anti -A22 : G C3p_endo anti -A23 : U C3p_endo anti -A24 : C C3p_endo anti -A25 : G C3p_endo anti -A26 : C C3p_endo anti -A27 : C O4p_endo anti -A28 : GE1 -A29 : GE2 -A30 : GE3 -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A15-A16 : adjacent_5p outward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A22-A23 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A25 : outward -A7-A22 : outward -A9-A19 : outward -A12-A14 : upward -Number of stackings = 22 -Number of adjacent stackings = 18 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A1-A27 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A26 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A25 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A24 : G-C Ww/Ww pairing antiparallel cis XIX -A6-A22 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A19 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A21 : C-A Ws/Wh pairing antiparallel cis one_hbond 78 -A9-A18 : A-U Ww/Ww pairing antiparallel cis XX -A10-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A11-A16 : C-G Ww/Ww pairing antiparallel cis XIX -A12-A15 : U-G Bs/Ww pairing parallel trans 87 -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : C C3p_endo anti -A7 : A C3p_endo anti -A8 : C C3p_endo anti -A9 : A C3p_endo anti -A10 : C C3p_endo anti -A11 : C C3p_endo anti -A12 : U C3p_endo anti -A13 : U C1p_exo anti -A14 : C C2p_endo anti -A15 : G C4p_exo syn -A16 : G C2p_exo anti -A17 : G C3p_endo anti -A18 : U C3p_endo anti -A19 : G C3p_endo anti -A20 : A C3p_endo anti -A21 : A C4p_exo anti -A22 : G C3p_endo anti -A23 : U C3p_endo anti -A24 : C C3p_endo anti -A25 : G C3p_endo anti -A26 : C C3p_endo anti -A27 : C O4p_endo anti -A28 : GE1 -A29 : GE2 -A30 : GE3 -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A15-A16 : adjacent_5p outward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A22-A23 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A25 : outward -A7-A22 : outward -A9-A19 : outward -A12-A14 : upward -Number of stackings = 22 -Number of adjacent stackings = 18 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A1-A27 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A26 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A25 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A24 : G-C Ww/Ww pairing antiparallel cis XIX -A6-A22 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A19 : C-G Ww/Ww pairing antiparallel cis XIX -A9-A18 : A-U Ww/Ww pairing antiparallel cis XX -A10-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A11-A16 : C-G Ww/Ww pairing antiparallel cis XIX -A12-A15 : U-G Bs/Ww pairing parallel trans 87 -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : C C3p_endo anti -A7 : A C3p_endo anti -A8 : C C3p_endo anti -A9 : A C3p_endo anti -A10 : C C3p_endo anti -A11 : C C3p_endo anti -A12 : U C3p_endo anti -A13 : U C1p_exo anti -A14 : C C2p_endo anti -A15 : G C4p_exo syn -A16 : G C2p_exo anti -A17 : G C3p_endo anti -A18 : U C3p_endo anti -A19 : G C3p_endo anti -A20 : A C3p_endo anti -A21 : A C4p_exo anti -A22 : G C3p_endo anti -A23 : U C3p_endo anti -A24 : C C3p_endo anti -A25 : G C3p_endo anti -A26 : C C3p_endo anti -A27 : C O4p_endo anti -A28 : GE1 -A29 : GE2 -A30 : GE3 -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A15-A16 : adjacent_5p outward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A22-A23 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A25 : outward -A7-A22 : outward -A9-A19 : outward -A12-A14 : upward -Number of stackings = 22 -Number of adjacent stackings = 18 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A1-A27 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A26 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A25 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A24 : G-C Ww/Ww pairing antiparallel cis XIX -A6-A22 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A19 : C-G Ww/Ww pairing antiparallel cis XIX -A9-A18 : A-U Ww/Ww pairing antiparallel cis XX -A10-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A11-A16 : C-G Ww/Ww pairing antiparallel cis XIX -A12-A15 : U-G Bs/Ww pairing parallel trans 87 -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : C C3p_endo anti -A7 : A C3p_endo anti -A8 : C C3p_endo anti -A9 : A C3p_endo anti -A10 : C C3p_endo anti -A11 : C C3p_endo anti -A12 : U C3p_endo anti -A13 : U C1p_exo anti -A14 : C C2p_endo anti -A15 : G C4p_exo syn -A16 : G C2p_exo anti -A17 : G C3p_endo anti -A18 : U C3p_endo anti -A19 : G C3p_endo anti -A20 : A C3p_endo anti -A21 : A C3p_endo anti -A22 : G C3p_endo anti -A23 : U C3p_endo anti -A24 : C C3p_endo anti -A25 : G C3p_endo anti -A26 : C C3p_endo anti -A27 : C O4p_endo anti -A28 : GE1 -A29 : GE2 -A30 : GE3 -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A15-A16 : adjacent_5p outward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A22-A23 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A25 : outward -A7-A22 : outward -A9-A19 : outward -A12-A14 : upward -Number of stackings = 22 -Number of adjacent stackings = 18 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A1-A27 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A26 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A25 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A24 : G-C Ww/Ww pairing antiparallel cis XIX -A6-A22 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A19 : C-G Ww/Ww pairing antiparallel cis XIX -A9-A18 : A-U Ww/Ww pairing antiparallel cis XX -A10-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A11-A16 : C-G Ww/Ww pairing antiparallel cis XIX -A12-A15 : U-G Bs/Ww pairing parallel trans 87 -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : C C3p_endo anti -A7 : A C3p_endo anti -A8 : C C3p_endo anti -A9 : A C3p_endo anti -A10 : C C3p_endo anti -A11 : C C3p_endo anti -A12 : U C3p_endo anti -A13 : U C1p_exo anti -A14 : C C2p_endo anti -A15 : G C4p_exo syn -A16 : G C2p_exo anti -A17 : G C3p_endo anti -A18 : U C3p_endo anti -A19 : G C3p_endo anti -A20 : A C3p_endo anti -A21 : A C3p_endo anti -A22 : G C3p_endo anti -A23 : U C3p_endo anti -A24 : C C3p_endo anti -A25 : G C3p_endo anti -A26 : C C3p_endo anti -A27 : C O4p_endo anti -A28 : GE1 -A29 : GE2 -A30 : GE3 -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A15-A16 : adjacent_5p outward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A22-A23 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A25 : outward -A7-A22 : outward -A9-A19 : outward -A12-A14 : upward -Number of stackings = 22 -Number of adjacent stackings = 18 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A1-A27 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A26 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A25 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A24 : G-C Ww/Ww pairing antiparallel cis XIX -A6-A22 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A19 : C-G Ww/Ww pairing antiparallel cis XIX -A9-A18 : A-U Ww/Ww pairing antiparallel cis XX -A10-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A11-A16 : C-G Ww/Ww pairing antiparallel cis XIX -A12-A15 : U-G Bs/Ww pairing parallel trans 87 -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : C C3p_endo anti -A7 : A C3p_endo anti -A8 : C C3p_endo anti -A9 : A C3p_endo anti -A10 : C C3p_endo anti -A11 : C C3p_endo anti -A12 : U C3p_endo anti -A13 : U C1p_exo anti -A14 : C C2p_endo anti -A15 : G C4p_exo syn -A16 : G C2p_exo anti -A17 : G C3p_endo anti -A18 : U C3p_endo anti -A19 : G C3p_endo anti -A20 : A C3p_endo anti -A21 : A C4p_exo anti -A22 : G C3p_endo anti -A23 : U C3p_endo anti -A24 : C C3p_endo anti -A25 : G C3p_endo anti -A26 : C C3p_endo anti -A27 : C O4p_endo anti -A28 : GE1 -A29 : GE2 -A30 : GE3 -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A15-A16 : adjacent_5p outward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A22-A23 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A25 : outward -A7-A22 : outward -A9-A19 : outward -A12-A14 : upward -Number of stackings = 22 -Number of adjacent stackings = 18 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A1-A27 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A26 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A25 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A24 : G-C Ww/Ww pairing antiparallel cis XIX -A6-A22 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A19 : C-G Ww/Ww pairing antiparallel cis XIX -A9-A18 : A-U Ww/Ww pairing antiparallel cis XX -A10-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A11-A16 : C-G Ww/Ww pairing antiparallel cis XIX -A12-A15 : U-G Bs/Ww pairing parallel trans 87 -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : C C3p_endo anti -A7 : A C3p_endo anti -A8 : C C3p_endo anti -A9 : A C3p_endo anti -A10 : C C3p_endo anti -A11 : C C3p_endo anti -A12 : U C3p_endo anti -A13 : U C1p_exo anti -A14 : C C2p_endo anti -A15 : G C4p_exo syn -A16 : G C2p_exo anti -A17 : G C3p_endo anti -A18 : U C3p_endo anti -A19 : G C3p_endo anti -A20 : A C3p_endo anti -A21 : A C4p_exo anti -A22 : G C3p_endo anti -A23 : U C3p_endo anti -A24 : C C3p_endo anti -A25 : G C3p_endo anti -A26 : C C3p_endo anti -A27 : C O4p_endo anti -A28 : GE1 -A29 : GE2 -A30 : GE3 -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A15-A16 : adjacent_5p outward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A22-A23 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A25 : outward -A7-A22 : outward -A9-A19 : outward -A12-A14 : upward -Number of stackings = 22 -Number of adjacent stackings = 18 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A1-A27 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A26 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A25 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A24 : G-C Ww/Ww pairing antiparallel cis XIX -A6-A22 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A19 : C-G Ww/Ww pairing antiparallel cis XIX -A9-A18 : A-U Ww/Ww pairing antiparallel cis XX -A10-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A11-A16 : C-G Ww/Ww pairing antiparallel cis XIX -A12-A15 : U-G Bs/Ww pairing parallel trans 87 -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : C C3p_endo anti -A7 : A C3p_endo anti -A8 : C C3p_endo anti -A9 : A C3p_endo anti -A10 : C C3p_endo anti -A11 : C C3p_endo anti -A12 : U C3p_endo anti -A13 : U C1p_exo anti -A14 : C C2p_endo anti -A15 : G C4p_exo syn -A16 : G C2p_exo anti -A17 : G C3p_endo anti -A18 : U C3p_endo anti -A19 : G C3p_endo anti -A20 : A C3p_endo anti -A21 : A C3p_endo anti -A22 : G C3p_endo anti -A23 : U C3p_endo anti -A24 : C C3p_endo anti -A25 : G C3p_endo anti -A26 : C C3p_endo anti -A27 : C O4p_endo anti -A28 : GE1 -A29 : GE2 -A30 : GE3 -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A15-A16 : adjacent_5p outward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A22-A23 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A25 : outward -A9-A19 : outward -A12-A14 : upward -Number of stackings = 21 -Number of adjacent stackings = 18 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -A1-A27 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A26 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A25 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A24 : G-C Ww/Ww pairing antiparallel cis XIX -A6-A22 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A19 : C-G Ww/Ww pairing antiparallel cis XIX -A9-A18 : A-U Ww/Ww pairing antiparallel cis XX -A10-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A11-A16 : C-G Ww/Ww pairing antiparallel cis XIX -A12-A15 : U-G Bs/Ww pairing parallel trans 87 -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : C C3p_endo anti -A7 : A C3p_endo anti -A8 : C C3p_endo anti -A9 : A C3p_endo anti -A10 : C C3p_endo anti -A11 : C C3p_endo anti -A12 : U C3p_endo anti -A13 : U C1p_exo anti -A14 : C C2p_endo anti -A15 : G C4p_exo syn -A16 : G C2p_exo anti -A17 : G C3p_endo anti -A18 : U C3p_endo anti -A19 : G C3p_endo anti -A20 : A C3p_endo anti -A21 : A C3p_endo anti -A22 : G C3p_endo anti -A23 : U C3p_endo anti -A24 : C C3p_endo anti -A25 : G C3p_endo anti -A26 : C C3p_endo anti -A27 : C O4p_endo anti -A28 : GE1 -A29 : GE2 -A30 : GE3 -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A15-A16 : adjacent_5p outward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A22-A23 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A25 : outward -A7-A22 : outward -A9-A19 : outward -A12-A14 : upward -Number of stackings = 22 -Number of adjacent stackings = 18 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A1-A27 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A26 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A25 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A24 : G-C Ww/Ww pairing antiparallel cis XIX -A6-A22 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A19 : C-G Ww/Ww pairing antiparallel cis XIX -A9-A18 : A-U Ww/Ww pairing antiparallel cis XX -A10-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A11-A16 : C-G Ww/Ww pairing antiparallel cis XIX -A12-A15 : U-G Bs/Ww pairing parallel trans 87 -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : C C3p_endo anti -A7 : A C3p_endo anti -A8 : C C3p_endo anti -A9 : A C3p_endo anti -A10 : C C3p_endo anti -A11 : C C3p_endo anti -A12 : U C3p_endo anti -A13 : U C1p_exo anti -A14 : C C2p_endo anti -A15 : G C4p_exo syn -A16 : G C2p_exo anti -A17 : G C3p_endo anti -A18 : U C3p_endo anti -A19 : G C3p_endo anti -A20 : A C3p_endo anti -A21 : A C4p_exo anti -A22 : G C3p_endo anti -A23 : U C3p_endo anti -A24 : C C3p_endo anti -A25 : G C3p_endo anti -A26 : C C3p_endo anti -A27 : C O4p_endo anti -A28 : GE1 -A29 : GE2 -A30 : GE3 -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A15-A16 : adjacent_5p outward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A22-A23 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A25 : outward -A7-A22 : outward -A9-A19 : outward -A12-A14 : upward -Number of stackings = 22 -Number of adjacent stackings = 18 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A1-A27 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A26 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A25 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A24 : G-C Ww/Ww pairing antiparallel cis XIX -A6-A22 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A19 : C-G Ww/Ww pairing antiparallel cis XIX -A9-A18 : A-U Ww/Ww pairing antiparallel cis XX -A10-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A11-A16 : C-G Ww/Ww pairing antiparallel cis XIX -A12-A15 : U-G Bs/Ww pairing parallel trans 87 -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : C C3p_endo anti -A7 : A C3p_endo anti -A8 : C C3p_endo anti -A9 : A C3p_endo anti -A10 : C C3p_endo anti -A11 : C C3p_endo anti -A12 : U C3p_endo anti -A13 : U C1p_exo anti -A14 : C C2p_endo anti -A15 : G C4p_exo syn -A16 : G C2p_exo anti -A17 : G C3p_endo anti -A18 : U C3p_endo anti -A19 : G C3p_endo anti -A20 : A C3p_endo anti -A21 : A C3p_endo anti -A22 : G C3p_endo anti -A23 : U C3p_endo anti -A24 : C C3p_endo anti -A25 : G C3p_endo anti -A26 : C C3p_endo anti -A27 : C O4p_endo anti -A28 : GE1 -A29 : GE2 -A30 : GE3 -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A15-A16 : adjacent_5p outward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A22-A23 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A25 : outward -A7-A22 : outward -A9-A19 : outward -A12-A14 : upward -Number of stackings = 22 -Number of adjacent stackings = 18 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A1-A27 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A26 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A25 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A24 : G-C Ww/Ww pairing antiparallel cis XIX -A6-A22 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A19 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A21 : C-A Ws/Wh pairing antiparallel cis one_hbond 78 -A9-A18 : A-U Ww/Ww pairing antiparallel cis XX -A10-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A11-A16 : C-G Ww/Ww pairing antiparallel cis XIX -A12-A15 : U-G Bs/Ww pairing parallel trans 87 -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : C C3p_endo anti -A7 : A C3p_endo anti -A8 : C C3p_endo anti -A9 : A C3p_endo anti -A10 : C C3p_endo anti -A11 : C C3p_endo anti -A12 : U C3p_endo anti -A13 : U C1p_exo anti -A14 : C C2p_endo anti -A15 : G C4p_exo syn -A16 : G C2p_exo anti -A17 : G C3p_endo anti -A18 : U C3p_endo anti -A19 : G C3p_endo anti -A20 : A C2p_endo anti -A21 : A C4p_exo anti -A22 : G C3p_endo anti -A23 : U C3p_endo anti -A24 : C C3p_endo anti -A25 : G C3p_endo anti -A26 : C C3p_endo anti -A27 : C O4p_endo anti -A28 : GE1 -A29 : GE2 -A30 : GE3 -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A15-A16 : adjacent_5p outward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A22-A23 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A25 : outward -A9-A19 : outward -A12-A14 : upward -Number of stackings = 22 -Number of adjacent stackings = 19 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -A1-A27 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A26 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A25 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A24 : G-C Ww/Ww pairing antiparallel cis XIX -A6-A22 : C-G Ww/Ww pairing antiparallel cis XIX -A7-A21 : A-A Ss/Hw O2'/Bh pairing antiparallel trans one_hbond 41 -A8-A19 : C-G Ww/Ww pairing antiparallel cis XIX -A9-A18 : A-U Ww/Ww pairing antiparallel cis XX -A10-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A11-A16 : C-G Ww/Ww pairing antiparallel cis XIX -A12-A15 : U-G Bs/Ww pairing parallel trans 87 -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : C C3p_endo anti -A7 : A C3p_endo anti -A8 : C C3p_endo anti -A9 : A C3p_endo anti -A10 : C C3p_endo anti -A11 : C C3p_endo anti -A12 : U C3p_endo anti -A13 : U C1p_exo anti -A14 : C C2p_endo anti -A15 : G C4p_exo syn -A16 : G C2p_exo anti -A17 : G C3p_endo anti -A18 : U C3p_endo anti -A19 : G C3p_endo anti -A20 : A C3p_endo anti -A21 : A C3p_endo anti -A22 : G C3p_endo anti -A23 : U C3p_endo anti -A24 : C C3p_endo anti -A25 : G C3p_endo anti -A26 : C C3p_endo anti -A27 : C O4p_endo anti -A28 : GE1 -A29 : GE2 -A30 : GE3 -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A15-A16 : adjacent_5p outward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A22-A23 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A25 : outward -A7-A22 : outward -A9-A19 : outward -A12-A14 : upward -Number of stackings = 22 -Number of adjacent stackings = 18 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A1-A27 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A26 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A25 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A24 : G-C Ww/Ww pairing antiparallel cis XIX -A6-A22 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A19 : C-G Ww/Ww pairing antiparallel cis XIX -A9-A18 : A-U Ww/Ww pairing antiparallel cis XX -A10-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A11-A16 : C-G Ww/Ww pairing antiparallel cis XIX -A12-A15 : U-G Bs/Ww pairing parallel trans 87 -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : C C3p_endo anti -A7 : A C3p_endo anti -A8 : C C3p_endo anti -A9 : A C3p_endo anti -A10 : C C3p_endo anti -A11 : C C3p_endo anti -A12 : U C3p_endo anti -A13 : U C1p_exo anti -A14 : C C2p_endo anti -A15 : G C4p_exo syn -A16 : G C2p_exo anti -A17 : G C3p_endo anti -A18 : U C3p_endo anti -A19 : G C4p_exo anti -A20 : A C3p_endo anti -A21 : A C3p_endo anti -A22 : G C3p_endo anti -A23 : U C3p_endo anti -A24 : C C3p_endo anti -A25 : G C3p_endo anti -A26 : C C3p_endo anti -A27 : C O4p_endo anti -A28 : GE1 -A29 : GE2 -A30 : GE3 -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A15-A16 : adjacent_5p outward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A22-A23 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A25 : outward -A7-A22 : outward -A9-A19 : outward -A12-A14 : upward -Number of stackings = 21 -Number of adjacent stackings = 17 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A1-A27 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A26 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A25 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A24 : G-C Ww/Ww pairing antiparallel cis XIX -A6-A22 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A19 : C-G Ww/Ww pairing antiparallel cis XIX -A9-A18 : A-U Ww/Ww pairing antiparallel cis XX -A10-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A11-A16 : C-G Ww/Ww pairing antiparallel cis XIX -A12-A15 : U-G Bs/Ww pairing parallel trans 87 -A13-A15 : U-G O2'/Hh pairing -A19-A20 : G-A O2'/Hh adjacent_5p pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : C C3p_endo anti -A7 : A C3p_endo anti -A8 : C C3p_endo anti -A9 : A C3p_endo anti -A10 : C C3p_endo anti -A11 : C C3p_endo anti -A12 : U C3p_endo anti -A13 : U C1p_exo anti -A14 : C C2p_endo anti -A15 : G C4p_exo syn -A16 : G C2p_exo anti -A17 : G C3p_endo anti -A18 : U C3p_endo anti -A19 : G C3p_endo anti -A20 : A C3p_endo anti -A21 : A C3p_endo anti -A22 : G C3p_endo anti -A23 : U C3p_endo anti -A24 : C C3p_endo anti -A25 : G C3p_endo anti -A26 : C C3p_endo anti -A27 : C O4p_endo anti -A28 : GE1 -A29 : GE2 -A30 : GE3 -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A15-A16 : adjacent_5p outward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A22-A23 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A25 : outward -A7-A22 : outward -A9-A19 : outward -A12-A14 : upward -Number of stackings = 22 -Number of adjacent stackings = 18 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A1-A27 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A26 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A25 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A24 : G-C Ww/Ww pairing antiparallel cis XIX -A6-A22 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A19 : C-G Ww/Ww pairing antiparallel cis XIX -A9-A18 : A-U Ww/Ww pairing antiparallel cis XX -A10-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A11-A16 : C-G Ww/Ww pairing antiparallel cis XIX -A12-A15 : U-G Bs/Ww pairing parallel trans 87 -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : C C3p_endo anti -A7 : A C3p_endo anti -A8 : C C3p_endo anti -A9 : A C3p_endo anti -A10 : C C3p_endo anti -A11 : C C3p_endo anti -A12 : U C3p_endo anti -A13 : U C1p_exo anti -A14 : C C2p_endo anti -A15 : G C4p_exo syn -A16 : G C2p_exo anti -A17 : G C3p_endo anti -A18 : U C3p_endo anti -A19 : G C3p_endo anti -A20 : A C2p_endo anti -A21 : A C3p_endo anti -A22 : G C3p_endo anti -A23 : U C3p_endo anti -A24 : C C3p_endo anti -A25 : G C3p_endo anti -A26 : C C3p_endo anti -A27 : C O4p_endo anti -A28 : GE1 -A29 : GE2 -A30 : GE3 -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A15-A16 : adjacent_5p outward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A22-A23 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A25 : outward -A7-A22 : outward -A9-A19 : outward -A12-A14 : upward -Number of stackings = 21 -Number of adjacent stackings = 17 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A1-A27 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A26 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A25 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A24 : G-C Ww/Ww pairing antiparallel cis XIX -A6-A22 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A19 : C-G Ww/Ww pairing antiparallel cis XIX -A9-A18 : A-U Ww/Ww pairing antiparallel cis XX -A10-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A11-A16 : C-G Ww/Ww pairing antiparallel cis XIX -A12-A15 : U-G Bs/Ww pairing parallel trans 87 -A19-A20 : G-A O2'/Hh adjacent_5p pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : C C3p_endo anti -A7 : A C3p_endo anti -A8 : C C3p_endo anti -A9 : A C3p_endo anti -A10 : C C3p_endo anti -A11 : C C3p_endo anti -A12 : U C3p_endo anti -A13 : U C1p_exo anti -A14 : C C2p_endo anti -A15 : G C4p_exo syn -A16 : G C2p_exo anti -A17 : G C3p_endo anti -A18 : U C3p_endo anti -A19 : G C3p_endo anti -A20 : A C3p_endo anti -A21 : A C3p_endo anti -A22 : G C3p_endo anti -A23 : U C3p_endo anti -A24 : C C3p_endo anti -A25 : G C3p_endo anti -A26 : C C3p_endo anti -A27 : C O4p_endo anti -A28 : GE1 -A29 : GE2 -A30 : GE3 -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A15-A16 : adjacent_5p outward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A22-A23 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A25 : outward -A9-A19 : outward -A12-A14 : upward -Number of stackings = 21 -Number of adjacent stackings = 18 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -A1-A27 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A26 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A25 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A24 : G-C Ww/Ww pairing antiparallel cis XIX -A6-A22 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A19 : C-G Ww/Ww pairing antiparallel cis XIX -A9-A18 : A-U Ww/Ww pairing antiparallel cis XX -A10-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A11-A16 : C-G Ww/Ww pairing antiparallel cis XIX -A12-A15 : U-G Bs/Ww pairing parallel trans 87 -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : C C3p_endo anti -A7 : A C3p_endo anti -A8 : C C3p_endo anti -A9 : A C3p_endo anti -A10 : C C3p_endo anti -A11 : C C3p_endo anti -A12 : U C3p_endo anti -A13 : U C1p_exo anti -A14 : C C2p_endo anti -A15 : G C4p_exo syn -A16 : G C2p_exo anti -A17 : G C3p_endo anti -A18 : U C3p_endo anti -A19 : G C3p_endo anti -A20 : A C3p_endo anti -A21 : A C3p_endo anti -A22 : G C3p_endo anti -A23 : U C3p_endo anti -A24 : C C3p_endo anti -A25 : G C3p_endo anti -A26 : C C3p_endo anti -A27 : C O4p_endo anti -A28 : GE1 -A29 : GE2 -A30 : GE3 -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A15-A16 : adjacent_5p outward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A22-A23 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A25 : outward -A7-A22 : outward -A9-A19 : outward -A12-A14 : upward -Number of stackings = 22 -Number of adjacent stackings = 18 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A1-A27 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A26 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A25 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A24 : G-C Ww/Ww pairing antiparallel cis XIX -A6-A22 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A19 : C-G Ww/Ww pairing antiparallel cis XIX -A9-A18 : A-U Ww/Ww pairing antiparallel cis XX -A10-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A11-A16 : C-G Ww/Ww pairing antiparallel cis XIX -A12-A15 : U-G Bs/Ww pairing parallel trans 87 -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : C C3p_endo anti -A7 : A C3p_endo anti -A8 : C C3p_endo anti -A9 : A C3p_endo anti -A10 : C C3p_endo anti -A11 : C C3p_endo anti -A12 : U C3p_endo anti -A13 : U C1p_exo anti -A14 : C C2p_endo anti -A15 : G C4p_exo syn -A16 : G C2p_exo anti -A17 : G C3p_endo anti -A18 : U C3p_endo anti -A19 : G C3p_endo anti -A20 : A C3p_endo anti -A21 : A C3p_endo anti -A22 : G C3p_endo anti -A23 : U C3p_endo anti -A24 : C C3p_endo anti -A25 : G C3p_endo anti -A26 : C C3p_endo anti -A27 : C O4p_endo anti -A28 : GE1 -A29 : GE2 -A30 : GE3 -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A15-A16 : adjacent_5p outward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A22-A23 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A25 : outward -A7-A22 : outward -A9-A19 : outward -A12-A14 : upward -Number of stackings = 21 -Number of adjacent stackings = 17 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A1-A27 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A26 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A25 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A24 : G-C Ww/Ww pairing antiparallel cis XIX -A6-A22 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A19 : C-G Ww/Ww pairing antiparallel cis XIX -A9-A18 : A-U Ww/Ww pairing antiparallel cis XX -A10-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A11-A16 : C-G Ww/Ww pairing antiparallel cis XIX -A12-A15 : U-G Bs/Ww pairing parallel trans 87 diff --git a/MCdata/1byx_MC b/MCdata/1byx_MC deleted file mode 100644 index b9b7f1c3846685edec3f1fa0f9ec0740ef16c05a..0000000000000000000000000000000000000000 --- a/MCdata/1byx_MC +++ /dev/null @@ -1,832 +0,0 @@ -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : C C3p_endo anti -A3 : A C2p_exo anti -A4 : G C2p_exo anti -A5 : U C3p_endo anti -A6 : G C3p_endo anti -A7 : G C3p_endo anti -A8 : C C2p_exo anti -B101 : G C2p_exo anti -B102 : C C3p_endo anti -B103 : C C3p_endo anti -B104 : A C2p_exo anti -B105 : C C3p_endo anti -B106 : T C3p_endo anti -B107 : G C2p_endo anti -B108 : C C3p_exo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p inward -B103-B104 : adjacent_5p upward -B104-B105 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A3-B107 : outward -A6-B104 : outward -Number of stackings = 11 -Number of adjacent stackings = 9 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A2-B107 : C-G Ww/Ww pairing antiparallel cis XIX -A3-B106 : A-T Ww/Ww pairing antiparallel cis -A4-B105 : G-C Ww/Ww pairing antiparallel cis XIX -A5-B104 : U-A Ww/Ww pairing antiparallel cis XX -A6-B103 : G-C Ww/Ww pairing antiparallel cis XIX -A7-B102 : G-C Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -A1 : G C2p_exo anti -A2 : C C3p_endo anti -A3 : A C3p_endo anti -A4 : G C2p_exo anti -A5 : U C3p_endo anti -A6 : G C3p_endo anti -A7 : G C2p_exo anti -A8 : C C2p_exo anti -B101 : G C3p_endo anti -B102 : C C3p_endo anti -B103 : C C3p_endo anti -B104 : A C3p_endo anti -B105 : C C3p_endo anti -B106 : T C3p_endo anti -B107 : G C2p_endo anti -B108 : C C3p_exo anti -Adjacent stackings ---------------------------------------------- -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p inward -B101-B102 : adjacent_5p upward -B102-B103 : adjacent_5p upward -B103-B104 : adjacent_5p upward -B104-B105 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A3-B107 : outward -A6-B104 : outward -Number of stackings = 12 -Number of adjacent stackings = 10 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A2-B107 : C-G Ww/Ww pairing antiparallel cis XIX -A3-B106 : A-T Ww/Ww pairing antiparallel cis -A4-B105 : G-C Ww/Ww pairing antiparallel cis XIX -A5-B104 : U-A Ww/Ww pairing antiparallel cis XX -A6-B103 : G-C Ww/Ww pairing antiparallel cis XIX -A7-B102 : G-C Ww/Ww pairing antiparallel cis XIX -A8-B101 : C-G Ww/Ws pairing parallel trans one_hbond -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : C C3p_endo anti -A3 : A C3p_endo anti -A4 : G C2p_exo anti -A5 : U C3p_endo anti -A6 : G C3p_endo anti -A7 : G C2p_exo anti -A8 : C C3p_endo anti -B101 : G C1p_endo syn -B102 : C C2p_exo anti -B103 : C C3p_endo anti -B104 : A C3p_endo anti -B105 : C C3p_endo anti -B106 : T C3p_endo anti -B107 : G C2p_endo anti -B108 : C C2p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -B102-B103 : adjacent_5p upward -B104-B105 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A3-B107 : outward -A6-B104 : outward -Number of stackings = 10 -Number of adjacent stackings = 8 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A2-B107 : C-G Ww/Ww pairing antiparallel cis XIX -A3-B106 : A-T Ww/Ww pairing antiparallel cis -A4-B105 : G-C Ww/Ww pairing antiparallel cis XIX -A5-B104 : U-A Ww/Ww pairing antiparallel cis XX -A6-B103 : G-C Ww/Ww pairing antiparallel cis XIX -A7-B102 : G-C Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -A1 : G C2p_exo anti -A2 : C C3p_endo anti -A3 : A C3p_endo anti -A4 : G C2p_exo anti -A5 : U C3p_endo anti -A6 : G C3p_endo anti -A7 : G C3p_endo anti -A8 : C C3p_endo anti -B101 : G C2p_exo syn -B102 : C C3p_endo anti -B103 : C C3p_endo anti -B104 : A C3p_endo anti -B105 : C C3p_endo anti -B106 : T C3p_endo anti -B107 : G C2p_endo anti -B108 : C C2p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -B102-B103 : adjacent_5p upward -B103-B104 : adjacent_5p upward -B104-B105 : adjacent_5p upward -B105-B106 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A3-B107 : outward -A6-B104 : outward -Number of stackings = 13 -Number of adjacent stackings = 11 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A2-B107 : C-G Ww/Ww pairing antiparallel cis XIX -A3-B106 : A-T Ww/Ww pairing antiparallel cis -A4-B105 : G-C Ww/Ww pairing antiparallel cis XIX -A5-B104 : U-A Ww/Ww pairing antiparallel cis XX -A6-B103 : G-C Ww/Ww pairing antiparallel cis XIX -A7-B102 : G-C Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : C C3p_endo anti -A3 : A C2p_exo anti -A4 : G C2p_exo anti -A5 : U C3p_endo anti -A6 : G C3p_endo anti -A7 : G C3p_endo anti -A8 : C C3p_endo anti -B101 : G C3p_endo anti -B102 : C C2p_exo anti -B103 : C C3p_endo anti -B104 : A C3p_endo anti -B105 : C C3p_endo anti -B106 : T C3p_endo anti -B107 : G C2p_endo anti -B108 : C C3p_exo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -B101-B102 : adjacent_5p upward -B102-B103 : adjacent_5p upward -B103-B104 : adjacent_5p upward -B104-B105 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A3-B107 : outward -A6-B104 : outward -Number of stackings = 12 -Number of adjacent stackings = 10 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A2-B107 : C-G Ww/Ww pairing antiparallel cis XIX -A3-B106 : A-T Ww/Ww pairing antiparallel cis -A4-B105 : G-C Ww/Ww pairing antiparallel cis XIX -A5-B104 : U-A Ww/Ww pairing antiparallel cis XX -A6-B103 : G-C Ww/Ww pairing antiparallel cis XIX -A7-A8 : G-C O2P/Bh adjacent_5p pairing -A7-B102 : G-C Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : C C3p_endo anti -A3 : A C2p_exo anti -A4 : G C2p_exo anti -A5 : U C3p_endo anti -A6 : G C3p_endo anti -A7 : G C3p_endo anti -A8 : C C3p_endo anti -B101 : G C3p_endo anti -B102 : C C2p_exo anti -B103 : C C3p_endo anti -B104 : A C3p_endo anti -B105 : C C3p_endo anti -B106 : T C3p_endo anti -B107 : G C2p_endo anti -B108 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -B101-B102 : adjacent_5p upward -B102-B103 : adjacent_5p upward -B104-B105 : adjacent_5p upward -B105-B106 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A3-B107 : outward -A6-B104 : outward -Number of stackings = 12 -Number of adjacent stackings = 10 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A2-B107 : C-G Ww/Ww pairing antiparallel cis XIX -A4-B105 : G-C Ww/Ww pairing antiparallel cis XIX -A5-B104 : U-A Ww/Ww pairing antiparallel cis XX -A6-B103 : G-C Ww/Ww pairing antiparallel cis -A7-A8 : G-C O2P/Bh adjacent_5p pairing -A7-B102 : G-C Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -A1 : G C2p_exo syn -A2 : C C2p_exo anti -A3 : A C3p_endo anti -A4 : G C2p_exo anti -A5 : U C3p_endo anti -A6 : G C3p_endo anti -A7 : G C2p_exo anti -A8 : C C3p_endo anti -B101 : G C2p_exo anti -B102 : C C3p_endo anti -B103 : C C3p_endo anti -B104 : A C3p_endo anti -B105 : C C3p_endo anti -B106 : T C3p_endo anti -B107 : G C2p_endo anti -B108 : C C3p_exo anti -Adjacent stackings ---------------------------------------------- -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -B101-B102 : adjacent_5p upward -B102-B103 : adjacent_5p upward -B103-B104 : adjacent_5p upward -B104-B105 : adjacent_5p upward -B105-B106 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A3-B107 : outward -A6-B104 : outward -Number of stackings = 11 -Number of adjacent stackings = 9 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A2-B107 : C-G Ww/Ww pairing antiparallel cis -A3-B106 : A-T Ww/Ww pairing antiparallel cis -A4-B105 : G-C Ww/Ww pairing antiparallel cis XIX -A5-B104 : U-A Ww/Ww pairing antiparallel cis XX -A6-B103 : G-C Ww/Ww pairing antiparallel cis XIX -A7-A8 : G-C O2P/Bh adjacent_5p pairing -A7-B102 : G-C Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -A1 : G C2p_exo anti -A2 : C C3p_endo anti -A3 : A C3p_endo anti -A4 : G C2p_exo anti -A5 : U C3p_endo anti -A6 : G C3p_endo anti -A7 : G C2p_exo anti -A8 : C C3p_endo anti -B101 : G C2p_exo anti -B102 : C C3p_endo anti -B103 : C C3p_endo anti -B104 : A C3p_endo anti -B105 : C C3p_endo anti -B106 : T C3p_endo anti -B107 : G C2p_endo anti -B108 : C C2p_exo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p inward -B102-B103 : adjacent_5p upward -B103-B104 : adjacent_5p upward -B104-B105 : adjacent_5p upward -B105-B106 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A3-B107 : outward -A6-B104 : outward -Number of stackings = 13 -Number of adjacent stackings = 11 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A2-B107 : C-G Ww/Ww pairing antiparallel cis XIX -A3-B106 : A-T Ww/Ww pairing antiparallel cis -A4-B105 : G-C Ww/Ww pairing antiparallel cis XIX -A5-B104 : U-A Ww/Ww pairing antiparallel cis XX -A6-B103 : G-C Ww/Ww pairing antiparallel cis XIX -A7-B102 : G-C Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -A1 : G C2p_exo anti -A2 : C C3p_endo anti -A3 : A C3p_endo anti -A4 : G C2p_exo anti -A5 : U C3p_endo anti -A6 : G C3p_endo anti -A7 : G C2p_exo anti -A8 : C C2p_exo anti -B101 : G C1p_endo syn -B102 : C C3p_endo anti -B103 : C C3p_endo anti -B104 : A C3p_endo anti -B105 : C C3p_endo anti -B106 : T C3p_endo anti -B107 : G C2p_endo anti -B108 : C C2p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p inward -B102-B103 : adjacent_5p upward -B104-B105 : adjacent_5p upward -B106-B107 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A3-B107 : outward -A6-B104 : outward -Number of stackings = 12 -Number of adjacent stackings = 10 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A2-B107 : C-G Ww/Ww pairing antiparallel cis XIX -A3-B106 : A-T Ww/Ww pairing antiparallel cis -A4-B105 : G-C Ww/Ww pairing antiparallel cis XIX -A5-B104 : U-A Ww/Ww pairing antiparallel cis XX -A6-B103 : G-C Ww/Ww pairing antiparallel cis XIX -A7-B102 : G-C Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -A1 : G C1p_endo anti -A2 : C C3p_endo anti -A3 : A C2p_exo anti -A4 : G C2p_exo anti -A5 : U C3p_endo anti -A6 : G C3p_endo anti -A7 : G C3p_endo anti -A8 : C C3p_endo anti -B101 : G C3p_endo anti -B102 : C C3p_endo anti -B103 : C C3p_endo anti -B104 : A C3p_endo anti -B105 : C C3p_endo anti -B106 : T C3p_endo anti -B107 : G C2p_endo anti -B108 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -B101-B102 : adjacent_5p upward -B102-B103 : adjacent_5p upward -B103-B104 : adjacent_5p upward -B104-B105 : adjacent_5p upward -B105-B106 : adjacent_5p upward -B107-B108 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A3-B107 : outward -A6-B104 : outward -Number of stackings = 14 -Number of adjacent stackings = 12 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A1-B108 : G-C Ww/Ww pairing antiparallel cis XIX -A2-B107 : C-G Ww/Ww pairing antiparallel cis XIX -A3-B106 : A-T Ww/Ww pairing antiparallel cis -A4-B105 : G-C Ww/Ww pairing antiparallel cis XIX -A5-B104 : U-A Ww/Ww pairing antiparallel cis -A6-B103 : G-C Ww/Ww pairing antiparallel cis XIX -A7-B102 : G-C Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -A1 : G C1p_endo syn -A2 : C C3p_endo anti -A3 : A C2p_exo anti -A4 : G C2p_exo anti -A5 : U C3p_endo anti -A6 : G C3p_endo anti -A7 : G C3p_endo anti -A8 : C C3p_endo anti -B101 : G C3p_endo anti -B102 : C C2p_exo anti -B103 : C C3p_endo anti -B104 : A C3p_endo anti -B105 : C C3p_endo anti -B106 : T C3p_endo anti -B107 : G C2p_endo anti -B108 : C C2p_endo anti -Adjacent stackings ---------------------------------------------- -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -B101-B102 : adjacent_5p upward -B102-B103 : adjacent_5p upward -B103-B104 : adjacent_5p upward -B104-B105 : adjacent_5p upward -B105-B106 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A3-B107 : outward -A6-B104 : outward -Number of stackings = 12 -Number of adjacent stackings = 10 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A2-B107 : C-G Ww/Ww pairing antiparallel cis XIX -A3-B106 : A-T Ww/Ww pairing antiparallel cis -A4-B105 : G-C Ww/Ww pairing antiparallel cis XIX -A5-B104 : U-A Ww/Ww pairing antiparallel cis XX -A6-B103 : G-C Ww/Ww pairing antiparallel cis XIX -A7-B102 : G-C Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : C C3p_endo anti -A3 : A C2p_exo anti -A4 : G C2p_exo anti -A5 : U C3p_endo anti -A6 : G C3p_endo anti -A7 : G C2p_exo anti -A8 : C C3p_endo anti -B101 : G C2p_exo anti -B102 : C C3p_endo anti -B103 : C C3p_endo anti -B104 : A C2p_exo anti -B105 : C C3p_endo anti -B106 : T C3p_endo anti -B107 : G C2p_endo anti -B108 : C C2p_endo anti -Adjacent stackings ---------------------------------------------- -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward pairing -B101-B102 : adjacent_5p upward -B102-B103 : adjacent_5p upward -B104-B105 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A3-B107 : outward -A6-B104 : outward -Number of stackings = 11 -Number of adjacent stackings = 9 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A2-B107 : C-G Ww/Ww pairing antiparallel cis XIX -A3-B106 : A-T Ww/Ww pairing antiparallel cis -A4-B105 : G-C Ww/Ww pairing antiparallel cis XIX -A5-B104 : U-A Ww/Ww pairing antiparallel cis XX -A6-B103 : G-C Ww/Ww pairing antiparallel cis XIX -A7-A8 : G-C O2P/Bh adjacent_5p upward pairing -A7-B102 : G-C Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -A1 : G C2p_exo anti -A2 : C C3p_endo anti -A3 : A C2p_exo anti -A4 : G C2p_exo anti -A5 : U C3p_endo anti -A6 : G C3p_endo anti -A7 : G C3p_endo anti -A8 : C C3p_endo anti -B101 : G C2p_exo anti -B102 : C C3p_endo anti -B103 : C C3p_endo anti -B104 : A C2p_exo anti -B105 : C C3p_endo anti -B106 : T C3p_endo anti -B107 : G C2p_endo anti -B108 : C C2p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward pairing -B101-B102 : adjacent_5p upward -B102-B103 : adjacent_5p upward -B104-B105 : adjacent_5p upward -B105-B106 : adjacent_5p upward -B107-B108 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A3-B107 : outward -A6-B104 : outward -Number of stackings = 14 -Number of adjacent stackings = 12 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A1-B108 : G-C Ww/Ww pairing antiparallel cis XIX -A2-B107 : C-G Ww/Ww pairing antiparallel cis XIX -A3-B106 : A-T Ww/Ws pairing antiparallel cis -A4-B105 : G-C Ww/Ww pairing antiparallel cis XIX -A5-B104 : U-A Ww/Ww pairing antiparallel cis XX -A6-B103 : G-C Ww/Ww pairing antiparallel cis XIX -A7-A8 : G-C O2P/Bh adjacent_5p upward pairing -A7-B102 : G-C Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : C C3p_endo anti -A3 : A C3p_endo anti -A4 : G C2p_exo anti -A5 : U C3p_endo anti -A6 : G C3p_endo anti -A7 : G C2p_exo anti -A8 : C C3p_endo anti -B101 : G C1p_endo syn -B102 : C C3p_endo anti -B103 : C C3p_endo anti -B104 : A C3p_endo anti -B105 : C C3p_endo anti -B106 : T C3p_endo anti -B107 : G C2p_endo anti -B108 : C C2p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -B102-B103 : adjacent_5p upward -B104-B105 : adjacent_5p upward -B105-B106 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A3-B107 : outward -A6-B104 : outward -Number of stackings = 11 -Number of adjacent stackings = 9 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A2-B107 : C-G Ww/Ww pairing antiparallel cis XIX -A3-B106 : A-T Ww/Ww pairing antiparallel cis -A4-B105 : G-C Ww/Ww pairing antiparallel cis XIX -A5-B104 : U-A Ww/Ww pairing antiparallel cis XX -A6-B103 : G-C Ww/Ww pairing antiparallel cis XIX -A7-B102 : G-C Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -A1 : G C2p_exo anti -A2 : C C3p_endo anti -A3 : A C2p_exo anti -A4 : G C2p_exo anti -A5 : U C3p_endo anti -A6 : G C3p_endo anti -A7 : G C2p_exo anti -A8 : C C3p_endo anti -B101 : G C2p_exo anti -B102 : C C3p_endo anti -B103 : C C3p_endo anti -B104 : A C3p_endo anti -B105 : C C3p_endo anti -B106 : T C3p_endo anti -B107 : G C3p_endo anti -B108 : C C3p_exo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p inward -B102-B103 : adjacent_5p upward -B103-B104 : adjacent_5p upward -B104-B105 : adjacent_5p upward -B105-B106 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A3-B107 : outward -A6-B104 : outward -Number of stackings = 12 -Number of adjacent stackings = 10 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A1-B108 : G-C Ws/Ww pairing antiparallel cis one_hbond -A2-B107 : C-G Ww/Ww pairing antiparallel cis XIX -A3-B106 : A-T Ww/Ww pairing antiparallel cis -A4-B105 : G-C Ww/Ww pairing antiparallel cis XIX -A5-B104 : U-A Ww/Ww pairing antiparallel cis XX -A6-B103 : G-C Ww/Ww pairing antiparallel cis XIX -A7-B102 : G-C Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -A1 : G C2p_exo anti -A2 : C C3p_endo anti -A3 : A C3p_endo anti -A4 : G C2p_exo anti -A5 : U C3p_endo anti -A6 : G C3p_endo anti -A7 : G C2p_exo anti -A8 : C C3p_endo anti -B101 : G C3p_endo anti -B102 : C C3p_endo anti -B103 : C C3p_endo anti -B104 : A C3p_endo anti -B105 : C C3p_endo anti -B106 : T C3p_endo anti -B107 : G C2p_endo anti -B108 : C O4p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p inward -B102-B103 : adjacent_5p upward -B103-B104 : adjacent_5p upward -B104-B105 : adjacent_5p upward -B105-B106 : adjacent_5p upward -B107-B108 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A3-B107 : outward -A6-B104 : outward -Number of stackings = 14 -Number of adjacent stackings = 12 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A2-B107 : C-G Ww/Ww pairing antiparallel cis XIX -A3-B106 : A-T Ww/Ww pairing antiparallel cis -A4-B105 : G-C Ww/Ww pairing antiparallel cis XIX -A5-B104 : U-A Ww/Ww pairing antiparallel cis XX -A6-B103 : G-C Ww/Ww pairing antiparallel cis XIX -A7-B102 : G-C Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -A1 : G C2p_exo anti -A2 : C C3p_endo anti -A3 : A C2p_exo anti -A4 : G C2p_exo anti -A5 : U C3p_endo anti -A6 : G C3p_endo anti -A7 : G C2p_exo anti -A8 : C C3p_endo anti -B101 : G C1p_endo syn -B102 : C C3p_endo anti -B103 : C C3p_endo anti -B104 : A C3p_endo anti -B105 : C C3p_endo anti -B106 : T C3p_endo anti -B107 : G C3p_endo anti -B108 : C C2p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p inward -B102-B103 : adjacent_5p upward -B103-B104 : adjacent_5p upward -B104-B105 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A3-B107 : outward -A6-B104 : outward -Number of stackings = 12 -Number of adjacent stackings = 10 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A2-B107 : C-G Ww/Ww pairing antiparallel cis XIX -A3-B106 : A-T Ww/Ww pairing antiparallel cis -A4-B105 : G-C Ww/Ww pairing antiparallel cis XIX -A5-B104 : U-A Ww/Ww pairing antiparallel cis XX -A6-B103 : G-C Ww/Ww pairing antiparallel cis XIX -A7-B102 : G-C Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -A1 : G C2p_exo syn -A2 : C C3p_endo anti -A3 : A C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : G C3p_endo anti -A7 : G C2p_exo anti -A8 : C C2p_exo anti -B101 : G C1p_endo syn -B102 : C C3p_endo anti -B103 : C C3p_endo anti -B104 : A C3p_endo anti -B105 : C C3p_endo anti -B106 : T C3p_endo anti -B107 : G C2p_endo anti -B108 : C C1p_endo anti -Adjacent stackings ---------------------------------------------- -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p inward -B102-B103 : adjacent_5p upward -B103-B104 : adjacent_5p upward -B104-B105 : adjacent_5p upward -B105-B106 : adjacent_5p upward -B106-B107 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A3-B107 : outward -A6-B104 : outward -Number of stackings = 13 -Number of adjacent stackings = 11 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A2-B107 : C-G Ww/Ww pairing antiparallel cis XIX -A3-B106 : A-T Ww/Ww pairing antiparallel cis -A4-B105 : G-C Ww/Ww pairing antiparallel cis XIX -A5-B104 : U-A Ww/Ww pairing antiparallel cis XX -A6-B103 : G-C Ww/Ww pairing antiparallel cis XIX -A7-B102 : G-C Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : C C3p_endo anti -A3 : A C3p_endo anti -A4 : G C2p_exo anti -A5 : U C3p_endo anti -A6 : G C3p_endo anti -A7 : G C3p_endo anti -A8 : C C3p_endo anti -B101 : G C1p_endo syn -B102 : C C3p_endo anti -B103 : C C3p_endo anti -B104 : A C3p_endo anti -B105 : C C3p_endo anti -B106 : T C3p_endo anti -B107 : G C2p_endo anti -B108 : C C2p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -B102-B103 : adjacent_5p upward -B103-B104 : adjacent_5p upward -B104-B105 : adjacent_5p upward -B105-B106 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A3-B107 : outward -A6-B104 : outward -Number of stackings = 12 -Number of adjacent stackings = 10 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A2-B107 : C-G Ww/Ww pairing antiparallel cis XIX -A3-B106 : A-T Ww/Ww pairing antiparallel cis -A4-B105 : G-C Ww/Ww pairing antiparallel cis XIX -A5-B104 : U-A Ww/Ww pairing antiparallel cis XX -A6-B103 : G-C Ww/Ww pairing antiparallel cis XIX -A7-B102 : G-C Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -A1 : G C2p_exo anti -A2 : C C3p_endo anti -A3 : A C3p_endo anti -A4 : G C2p_exo anti -A5 : U C3p_endo anti -A6 : G C3p_endo anti -A7 : G C3p_endo anti -A8 : C C3p_endo anti -B101 : G C2p_exo anti -B102 : C C3p_endo anti -B103 : C C3p_endo anti -B104 : A C3p_endo anti -B105 : C C3p_endo anti -B106 : T C3p_endo anti -B107 : G C2p_endo anti -B108 : C C2p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -B101-B102 : adjacent_5p upward -B102-B103 : adjacent_5p upward -B103-B104 : adjacent_5p upward -B104-B105 : adjacent_5p upward -B105-B106 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A3-B107 : outward -A6-B104 : outward -Number of stackings = 13 -Number of adjacent stackings = 11 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A2-B107 : C-G Ww/Ww pairing antiparallel cis XIX -A3-B106 : A-T Ww/Ww pairing antiparallel cis -A4-B105 : G-C Ww/Ww pairing antiparallel cis XIX -A5-B104 : U-A Ww/Ww pairing antiparallel cis XX -A6-B103 : G-C Ww/Ww pairing antiparallel cis XIX -A7-B102 : G-C Ww/Ww pairing antiparallel cis XIX diff --git a/MCdata/1bz2_MC b/MCdata/1bz2_MC deleted file mode 100644 index 8f702ee2fa0bfb5d5ae9cf9d8a9344ca21bba8d4..0000000000000000000000000000000000000000 --- a/MCdata/1bz2_MC +++ /dev/null @@ -1,43 +0,0 @@ -Residue conformations ------------------------------------------- -A27 : U C3p_endo anti -A28 : C C3p_endo anti -A29 : A C3p_endo anti -A30 : G C3p_endo anti -A31 : A C3p_endo anti -A32 : C C3p_endo anti -A33 : U C4p_exo anti -A34 : U O4p_endo anti -A35 : U C1p_exo anti -A36 : U O4p_endo anti -A37 : A O4p_endo anti -A38 : A C3p_endo anti -A39 : U C3p_endo anti -A40 : C C3p_endo anti -A41 : U C3p_endo anti -A42 : G C3p_endo anti -A43 : A C3p_endo anti -Adjacent stackings ---------------------------------------------- -A27-A28 : adjacent_5p upward -A28-A29 : adjacent_5p upward -A29-A30 : adjacent_5p upward -A30-A31 : adjacent_5p upward -A31-A32 : adjacent_5p upward -A32-A33 : adjacent_5p upward -A38-A39 : adjacent_5p upward -A39-A40 : adjacent_5p upward -A40-A41 : adjacent_5p upward -A41-A42 : adjacent_5p upward -A42-A43 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A29-A42 : outward -Number of stackings = 12 -Number of adjacent stackings = 11 -Number of non adjacent stackings = 1 -Base-pairs ------------------------------------------------------ -A27-A43 : U-A Ww/Ww pairing antiparallel cis XX -A28-A42 : C-G Ww/Ww pairing antiparallel cis XIX -A29-A41 : A-U Ww/Ww pairing antiparallel cis XX -A30-A40 : G-C Ww/Ww pairing antiparallel cis XIX -A31-A39 : A-U Ww/Ww pairing antiparallel cis XX -A32-A38 : C-A Ww/Wh pairing antiparallel cis one_hbond 75 -A36-A37 : U-A O2P/Hh O2P/Hh adjacent_5p pairing diff --git a/MCdata/1bz3_MC b/MCdata/1bz3_MC deleted file mode 100644 index 99581fe906ddf8f377989cab958e931d1e4eb5ea..0000000000000000000000000000000000000000 --- a/MCdata/1bz3_MC +++ /dev/null @@ -1,43 +0,0 @@ -Residue conformations ------------------------------------------- -A27 : U C3p_endo anti -A28 : C C3p_endo anti -A29 : A C3p_endo anti -A30 : G C3p_endo anti -A31 : A C3p_endo anti -A32 : C C3p_endo anti -A33 : U O4p_endo anti -A34 : U C1p_exo anti -A35 : U C1p_exo anti -A36 : U C2p_endo anti -A37 : A C4p_exo anti -A38 : A C3p_endo anti -A39 : U C3p_endo anti -A40 : C C3p_endo anti -A41 : U C3p_endo anti -A42 : G C3p_endo anti -A43 : A C4p_exo anti -Adjacent stackings ---------------------------------------------- -A27-A28 : adjacent_5p upward -A28-A29 : adjacent_5p upward -A29-A30 : adjacent_5p upward -A30-A31 : adjacent_5p upward -A31-A32 : adjacent_5p upward -A32-A33 : adjacent_5p upward -A37-A38 : adjacent_5p upward -A38-A39 : adjacent_5p upward -A39-A40 : adjacent_5p upward -A40-A41 : adjacent_5p upward -A42-A43 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A29-A42 : outward -Number of stackings = 12 -Number of adjacent stackings = 11 -Number of non adjacent stackings = 1 -Base-pairs ------------------------------------------------------ -A27-A43 : U-A Ww/Ww pairing antiparallel cis XX -A28-A42 : C-G Ww/Ww pairing antiparallel cis XIX -A29-A41 : A-U Ww/Ww pairing antiparallel cis one_hbond -A30-A40 : G-C Ww/Ww pairing antiparallel cis XIX -A31-A39 : A-U Ww/Ww pairing antiparallel cis XX -A32-A38 : C-A Ww/Ww pairing antiparallel cis 75 -A33-A37 : U-A Ww/Ww pairing antiparallel cis one_hbond diff --git a/MCdata/1bzt_MC b/MCdata/1bzt_MC deleted file mode 100644 index 97248018f67dcd4487700eefbd8704f75d6965ed..0000000000000000000000000000000000000000 --- a/MCdata/1bzt_MC +++ /dev/null @@ -1,36 +0,0 @@ -Residue conformations ------------------------------------------- -A27 : U C3p_endo anti -A28 : C C3p_endo anti -A29 : A C3p_endo anti -A30 : G C3p_endo anti -A31 : A C3p_endo anti -A32 : C C3p_endo anti -A33 : U O4p_endo anti -A34 : U O4p_endo anti -A35 : U C1p_exo anti -A36 : U C1p_exo anti -A37 : A O4p_endo anti -A38 : A C3p_endo anti -A39 : PSU -A40 : C C3p_endo anti -A41 : U C3p_endo anti -A42 : G C3p_endo anti -A43 : A C3p_endo anti -Adjacent stackings ---------------------------------------------- -A29-A30 : adjacent_5p upward -A30-A31 : adjacent_5p upward -A31-A32 : adjacent_5p upward -A32-A33 : adjacent_5p upward -A42-A43 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A29-A42 : outward -A30-A41 : outward -Number of stackings = 7 -Number of adjacent stackings = 5 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A27-A43 : U-A Ww/Ww pairing antiparallel cis XX -A28-A42 : C-G Ww/Ww pairing antiparallel cis XIX -A29-A41 : A-U Ww/Ww pairing antiparallel cis XX -A30-A40 : G-C Ww/Ww pairing antiparallel cis XIX -A32-A38 : C-A Ww/Ww pairing antiparallel cis 75 diff --git a/MCdata/1bzu_MC b/MCdata/1bzu_MC deleted file mode 100644 index 4dbbb0ff624f27edb6813f173be266e664dd4986..0000000000000000000000000000000000000000 --- a/MCdata/1bzu_MC +++ /dev/null @@ -1,36 +0,0 @@ -Residue conformations ------------------------------------------- -A27 : U C3p_endo anti -A28 : C C3p_endo anti -A29 : A C3p_endo anti -A30 : G C3p_endo anti -A31 : A C3p_endo anti -A32 : C C3p_endo anti -A33 : U C4p_exo anti -A34 : U O4p_endo anti -A35 : U C1p_exo anti -A36 : U O4p_endo anti -A37 : A C4p_exo anti -A38 : A C3p_endo anti -A39 : PSU -A40 : C C3p_endo anti -A41 : U C3p_endo anti -A42 : G C3p_endo anti -A43 : A C3p_endo anti -Adjacent stackings ---------------------------------------------- -A29-A30 : adjacent_5p upward -A30-A31 : adjacent_5p upward -A31-A32 : adjacent_5p upward -A37-A38 : adjacent_5p upward -A40-A41 : adjacent_5p upward -A42-A43 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A29-A42 : outward -Number of stackings = 7 -Number of adjacent stackings = 6 -Number of non adjacent stackings = 1 -Base-pairs ------------------------------------------------------ -A27-A43 : U-A Ww/Ww pairing antiparallel cis one_hbond -A28-A42 : C-G Ww/Ww pairing antiparallel cis XIX -A29-A41 : A-U Ww/Ww pairing antiparallel cis XX -A30-A40 : G-C Ww/Ww pairing antiparallel cis XIX -A32-A38 : C-A Ws/Hw pairing antiparallel trans one_hbond diff --git a/MCdata/1c04_MC b/MCdata/1c04_MC deleted file mode 100644 index 1364d7cda235c7a5ff41461c6bd27c2dde8c38f9..0000000000000000000000000000000000000000 --- a/MCdata/1c04_MC +++ /dev/null @@ -1,710 +0,0 @@ -Residue conformations ------------------------------------------- -E1 : G C3p_endo anti -E2 : C C3p_endo anti -E3 : C C3p_endo anti -E4 : A C3p_endo anti -E5 : G C2p_exo anti -E6 : G C3p_endo anti -E7 : A C4p_exo anti -E8 : U C3p_endo anti -E9 : G C3p_endo anti -E10 : U C3p_exo anti -E11 : A C2p_endo anti -E12 : G C3p_endo anti -E13 : G C3p_endo anti -E14 : C C3p_endo anti -E15 : U C3p_endo anti -E16 : U C3p_endo anti -E17 : A C4p_exo anti -E18 : G C3p_endo anti -E19 : A C2p_endo syn -E20 : A C1p_exo anti -E21 : G C3p_endo anti -E22 : C C3p_endo anti -E23 : A C3p_endo anti -E24 : G C3p_endo anti -E25 : C C3p_endo anti -E26 : C C3p_endo anti -E27 : A C3p_endo anti -E28 : U C3p_endo anti -E29 : C C3p_endo anti -E30 : A C3p_endo anti -E31 : U C3p_endo anti -E32 : U C4p_exo anti -E33 : U C2p_exo anti -E34 : A C3p_endo anti -E35 : A C3p_endo anti -E36 : A C3p_endo syn -E37 : G C3p_endo anti -E38 : A C3p_exo syn -E39 : A C2p_endo anti -E40 : A C3p_endo anti -E41 : G C2p_exo anti -E42 : C C3p_endo anti -E43 : G C3p_endo anti -E44 : U C3p_endo anti -E45 : A C3p_endo anti -E46 : A C3p_endo anti -E47 : U C3p_endo anti -E48 : A C3p_endo anti -E49 : G C3p_endo anti -E50 : C C3p_endo anti -E51 : U C3p_endo anti -E52 : C C3p_endo anti -E53 : A C3p_endo anti -E54 : C C2p_exo anti -E55 : U C3p_endo anti -E56 : G C3p_endo anti -E57 : G C3p_endo anti -E58 : U C3p_endo anti -F1 : G C3p_endo anti -F2 : G C3p_endo anti -F3 : G C3p_endo anti -F4 : U C3p_endo anti -F5 : G C3p_endo anti -F6 : C C4p_exo anti -F7 : U C3p_endo anti -F8 : C C3p_endo anti -F9 : A C2p_endo anti -F10 : G C2p_endo anti -F11 : U C2p_exo anti -F12 : A C3p_endo anti -F13 : C C3p_endo anti -F14 : G C3p_endo anti -F15 : A C3p_endo anti -F16 : G C3p_endo anti -F17 : A C2p_exo anti -F18 : G C3p_endo anti -F19 : G C3p_endo anti -F20 : A C3p_endo anti -F21 : A C3p_endo anti -F22 : C C3p_endo anti -F23 : C C3p_endo anti -F24 : G C3p_endo anti -F25 : C C3p_endo anti -F26 : A C3p_endo anti -F27 : C C3p_endo anti -F28 : C C3p_endo anti -F29 : C C3p_endo anti -A60 : GLN -A61 : TYR -A62 : ARG -A63 : ILE -A64 : ILE -A65 : ASP -A66 : PHE -A67 : LYS -A68 : ARG -A69 : ASP -A70 : LYS -A71 : ASP -A72 : GLY -A73 : ILE -A74 : PRO -A75 : GLY -A76 : ARG -A77 : VAL -A78 : ALA -A79 : THR -A80 : ILE -A81 : GLU -A82 : TYR -A83 : ASP -A84 : PRO -A85 : ASN -A86 : ARG -A87 : SER -A88 : ALA -A89 : ASN -A90 : ILE -A91 : ALA -A92 : LEU -A93 : ILE -A94 : ASN -A95 : TYR -A96 : ALA -A97 : ASP -A98 : GLY -A99 : GLU -A100 : LYS -A101 : ARG -A102 : TYR -A103 : ILE -A104 : ILE -A105 : ALA -A106 : PRO -A107 : LYS -A108 : ASN -A109 : LEU -A110 : LYS -A111 : VAL -A112 : GLY -A113 : MSE -A114 : GLU -A115 : ILE -A116 : MSE -A117 : SER -A118 : GLY -A119 : PRO -A120 : ASP -A121 : ALA -A122 : ASP -A123 : ILE -A124 : LYS -A125 : ILE -A126 : GLY -A127 : ASN -A128 : ALA -A129 : LEU -A130 : PRO -A131 : LEU -A132 : GLU -A133 : ASN -A134 : ILE -A135 : PRO -A136 : VAL -A137 : GLY -A138 : THR -A139 : LEU -A140 : VAL -A141 : HIS -A142 : ASN -A143 : ILE -A144 : GLU -A145 : LEU -A146 : LYS -A147 : PRO -A148 : GLY -A149 : ARG -A150 : GLY -A151 : GLY -A152 : GLN -A153 : LEU -A154 : VAL -A155 : ARG -A156 : ALA -A157 : ALA -A158 : GLY -A159 : THR -A160 : SER -A161 : ALA -A162 : GLN -A163 : VAL -A164 : LEU -A165 : GLY -A166 : LYS -A167 : GLU -A168 : GLY -A169 : LYS -A170 : TYR -A171 : VAL -A172 : ILE -A173 : VAL -A174 : ARG -A175 : LEU -A176 : ALA -A177 : SER -A178 : GLY -A179 : GLU -A180 : VAL -A181 : ARG -A182 : MSE -A183 : ILE -A184 : LEU -A185 : GLY -A186 : LYS -A187 : CYS -A188 : ARG -A189 : ALA -A190 : THR -A191 : VAL -A192 : GLY -A193 : GLU -A194 : VAL -B7 : PRO -B8 : ILE -B9 : GLU -B10 : ILE -B11 : PRO -B12 : ALA -B13 : GLY -B14 : VAL -B15 : THR -B16 : VAL -B17 : THR -B18 : VAL -B19 : ASN -B20 : GLY -B21 : ASN -B22 : THR -B23 : VAL -B24 : THR -B25 : VAL -B26 : LYS -B27 : GLY -B28 : PRO -B29 : LYS -B30 : GLY -B31 : GLU -B32 : LEU -B33 : THR -B34 : ARG -B35 : THR -B36 : PHE -B37 : HIS -B38 : PRO -B39 : ASP -B40 : MET -B41 : THR -B42 : ILE -B43 : THR -B44 : VAL -B45 : GLU -B46 : GLY -B47 : ASN -B48 : VAL -B49 : ILE -B50 : THR -B51 : VAL -B52 : THR -B53 : ARG -B54 : PRO -B55 : SER -B56 : ASP -B57 : GLU -B58 : LYS -B59 : HIS -B60 : HIS -B61 : ARG -B62 : ALA -B63 : LEU -B64 : HIS -B65 : GLY -B66 : THR -B67 : THR -B68 : ARG -B69 : SER -B70 : LEU -B71 : LEU -B72 : ALA -B73 : ASN -B74 : MET -B75 : VAL -B76 : GLU -B77 : GLY -B78 : VAL -B79 : SER -B80 : LYS -B81 : GLY -B82 : TYR -B83 : GLU -B84 : LYS -B85 : ALA -B86 : LEU -B87 : GLU -B88 : LEU -B89 : VAL -B90 : GLY -B91 : VAL -B92 : GLY -B93 : TYR -B94 : ARG -B95 : ALA -B96 : SER -B97 : LYS -B98 : GLN -B99 : GLY -B100 : LYS -B101 : LYS -B102 : LEU -B103 : VAL -B104 : LEU -B105 : SER -B106 : VAL -B107 : GLY -B108 : TYR -B109 : SER -B110 : HIS -B111 : PRO -B112 : VAL -B113 : GLU -B114 : ILE -B115 : GLU -B116 : PRO -B117 : GLU -B118 : GLU -B119 : GLY -B120 : LEU -B121 : GLU -B122 : ILE -B123 : GLU -B124 : VAL -B125 : PRO -B126 : SER -B127 : GLN -B128 : THR -B129 : LYS -B130 : ILE -B131 : ILE -B132 : VAL -B133 : LYS -B134 : GLY -B135 : ALA -B136 : ASP -B137 : LYS -B138 : GLN -B139 : ARG -B140 : VAL -B141 : GLY -B142 : GLU -B143 : LEU -B144 : ALA -B145 : ALA -B146 : ASN -B147 : ILE -B148 : ARG -B149 : ALA -B150 : VAL -B151 : ARG -B152 : PRO -B153 : PRO -B154 : GLU -B155 : PRO -B156 : TYR -B157 : LYS -B158 : GLY -B159 : LYS -B160 : GLY -B161 : ILE -B162 : ARG -B163 : TYR -B164 : GLU -B165 : GLY -B166 : GLU -B167 : LEU -B168 : VAL -B169 : ARG -B170 : LEU -C6 : LYS -C7 : THR -C8 : PRO -C9 : PRO -C10 : ALA -C11 : ALA -C12 : VAL -C13 : LEU -C14 : LEU -C15 : LYS -C16 : LYS -C17 : ALA -C18 : ALA -C19 : GLY -C20 : ILE -C21 : GLU -C22 : SER -C23 : GLY -C24 : SER -C25 : GLY -C26 : GLU -C27 : PRO -C28 : ASN -C29 : ARG -C30 : ASN -C31 : LYS -C32 : VAL -C33 : ALA -C34 : THR -C35 : ILE -C36 : LYS -C37 : ARG -C38 : ASP -C39 : LYS -C40 : VAL -C41 : ARG -C42 : GLU -C43 : ILE -C44 : ALA -C45 : GLU -C46 : LEU -C47 : LYS -C48 : MET -C49 : PRO -C50 : ASP -C51 : LEU -C52 : ASN -C53 : ALA -C54 : ALA -C55 : SER -C56 : ILE -C57 : GLU -C58 : ALA -C59 : ALA -C60 : MET -C61 : ARG -C62 : MET -C63 : ILE -C64 : GLU -C65 : GLY -C66 : THR -C67 : ALA -C68 : ARG -C69 : SER -C70 : MET -C71 : GLY -C72 : ILE -D1 : MET -D2 : ILE -D3 : GLN -D4 : GLN -D5 : GLU -D6 : SER -D7 : ARG -D8 : LEU -D9 : LYS -D10 : VAL -D11 : ALA -D12 : ASP -D13 : ASN -D14 : SER -D15 : GLY -D16 : ALA -D17 : ARG -D18 : GLU -D19 : VAL -D20 : LEU -D21 : VAL -D22 : ILE -D23 : LYS -D24 : VAL -D25 : LEU -D26 : GLY -D27 : GLY -D28 : SER -D29 : GLY -D30 : ARG -D31 : ARG -D32 : TYR -D33 : ALA -D34 : ASN -D35 : ILE -D36 : GLY -D37 : ASP -D38 : VAL -D39 : VAL -D40 : VAL -D41 : ALA -D42 : THR -D43 : VAL -D44 : LYS -D45 : ASP -D46 : ALA -D47 : THR -D48 : PRO -D49 : GLY -D50 : GLY -D51 : VAL -D52 : VAL -D53 : LYS -D54 : LYS -D55 : GLY -D56 : GLN -D57 : VAL -D58 : VAL -D59 : LYS -D60 : ALA -D61 : VAL -D62 : VAL -D63 : VAL -D64 : ARG -D65 : THR -D66 : LYS -D67 : ARG -D68 : GLY -D69 : VAL -D70 : ARG -D71 : ARG -D72 : PRO -D73 : ASP -D74 : GLY -D75 : SER -D76 : TYR -D77 : ILE -D78 : ARG -D79 : PHE -D80 : ASP -D81 : GLU -D82 : ASN -D83 : ALA -D84 : CYS -D85 : VAL -D86 : ILE -D87 : ILE -D88 : ARG -D89 : ASP -D90 : ASP -D91 : LYS -D92 : SER -D93 : PRO -D94 : ARG -D95 : GLY -D96 : THR -D97 : ARG -D98 : ILE -D99 : PHE -D100 : GLY -D101 : PRO -D102 : VAL -D103 : ALA -D104 : ARG -D105 : GLU -D106 : LEU -D107 : ARG -D108 : ASP -D109 : LYS -D110 : ASP -D111 : PHE -D112 : MET -D113 : LYS -D114 : ILE -D115 : ILE -D116 : SER -D117 : LEU -D118 : ALA -D119 : PRO -D120 : GLU -D121 : VAL -D122 : ILE -Adjacent stackings ---------------------------------------------- -E1-E2 : adjacent_5p upward -E4-E5 : adjacent_5p upward -E5-E6 : adjacent_5p upward -E7-E8 : adjacent_5p upward -E9-E10 : adjacent_5p inward -E12-E13 : adjacent_5p upward -E13-E14 : adjacent_5p upward -E14-E15 : adjacent_5p upward -E15-E16 : adjacent_5p upward -E17-E18 : adjacent_5p upward -E18-E19 : adjacent_5p upward -E21-E22 : adjacent_5p upward -E23-E24 : adjacent_5p upward -E24-E25 : adjacent_5p upward -E26-E27 : adjacent_5p upward -E27-E28 : adjacent_5p upward -E29-E30 : adjacent_5p upward -E30-E31 : adjacent_5p upward -E31-E32 : adjacent_5p upward -E32-E33 : adjacent_5p upward -E34-E35 : adjacent_5p upward -E35-E36 : adjacent_5p inward -E40-E41 : adjacent_5p upward -E41-E42 : adjacent_5p upward -E42-E43 : adjacent_5p upward -E43-E44 : adjacent_5p upward -E45-E46 : adjacent_5p upward -E46-E47 : adjacent_5p upward -E47-E48 : adjacent_5p upward -E48-E49 : adjacent_5p upward -E49-E50 : adjacent_5p upward -E50-E51 : adjacent_5p upward -E51-E52 : adjacent_5p upward -E52-E53 : adjacent_5p upward -E53-E54 : adjacent_5p upward pairing -E56-E57 : adjacent_5p upward -E57-E58 : adjacent_5p upward -F1-F2 : adjacent_5p upward -F2-F3 : adjacent_5p upward -F3-F4 : adjacent_5p upward -F4-F5 : adjacent_5p upward -F5-F6 : adjacent_5p upward -F6-F7 : adjacent_5p upward -F8-F9 : adjacent_5p inward -F11-F12 : adjacent_5p upward -F12-F13 : adjacent_5p upward -F13-F14 : adjacent_5p upward -F15-F16 : adjacent_5p upward -F16-F17 : adjacent_5p upward -F18-F19 : adjacent_5p upward -F20-F21 : adjacent_5p upward -F21-F22 : adjacent_5p upward -F26-F27 : adjacent_5p upward -F27-F28 : adjacent_5p upward -F28-F29 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -E4-E56 : outward -E7-E36 : outward -E9-E30 : outward -E11-E20 : outward -E12-E27 : outward -E13-E26 : outward -E19-E23 : upward -E21-E39 : downward pairing -E29-E38 : downward -E37-E39 : upward -E37-E53 : outward -E40-E52 : outward -F5-F26 : outward -F9-F11 : outward -F10-F19 : inward pairing -F12-F20 : outward -F14-F18 : outward -Number of stackings = 72 -Number of adjacent stackings = 55 -Number of non adjacent stackings = 17 -Base-pairs ------------------------------------------------------ -E1-E58 : G-U Ww/Ws pairing antiparallel cis XXVIII -E2-E57 : C-G Ww/Ww pairing antiparallel cis XIX -E3-E56 : C-G Ww/Ww pairing antiparallel cis XIX -E4-E55 : A-U Ww/Ww pairing antiparallel cis XX -E5-E35 : G-A Ss/Ss O2'/Ww pairing parallel trans 57 -E5-E54 : G-C Ww/Ww pairing antiparallel cis XIX -E6-E52 : G-C Ww/O2P pairing -E6-E53 : G-A Ss/Hh O2'/Bh pairing antiparallel trans XI -E7-E31 : A-U Ww/Ww pairing antiparallel cis XX -E7-E37 : A-G Bh/O2P pairing -E8-E30 : U-A Ww/Ww pairing antiparallel cis XX -E9-E29 : G-C Ww/Ww pairing antiparallel cis XIX -E10-E38 : U-A Ww/Hh pairing parallel cis XXIII -E12-E26 : G-C Ww/Ww pairing antiparallel cis XIX -E13-E25 : G-C Ww/Ww pairing antiparallel cis XIX -E14-E24 : C-G Ww/Ww pairing antiparallel cis XIX -E15-E19 : U-A Ww/O2' pairing -E15-E23 : U-A Ws/Wh pairing antiparallel trans one_hbond 46 -E16-E18 : U-G O2'/Hh pairing -E16-E19 : U-A Ss/C8 pairing antiparallel trans one_hbond -E18-E45 : G-A Bs/O2' pairing -E20-E47 : A-U Ww/O2' pairing -E21-E39 : G-A Bs/O2' Ss/O2' downward pairing -E21-E41 : G-G Ww/Hh pairing parallel cis VI -E21-E50 : G-C Wh/Wh pairing antiparallel trans one_hbond -E22-E42 : C-C Ww/Hh pairing parallel cis -E27-E38 : A-A Ww/O2' pairing -E32-E36 : U-A Ww/Ww pairing parallel trans XXI -E33-E35 : U-A O2'/Hh pairing -E34-E55 : A-U Bs/Ss Ss/O2' pairing antiparallel cis one_hbond -E36-E53 : A-A O2'/Ww pairing -E37-E52 : G-C Ww/Ww pairing antiparallel cis 122 -E40-E51 : A-U Ww/Ww pairing antiparallel cis XX -E41-E50 : G-C Ww/Ww pairing antiparallel cis XIX -E42-E49 : C-G Ww/Ww pairing antiparallel cis XIX -E43-E48 : G-A Ss/Hh O2'/Bh pairing antiparallel trans XI -E44-E46 : U-A O2'/Bh O2'/Hh pairing -E44-E47 : U-U Ww/O2P pairing -E53-E54 : A-C O2P/Bh adjacent_5p upward pairing -F1-F29 : G-C Ww/Ww pairing antiparallel cis XIX -F2-F28 : G-C Ww/Ww pairing antiparallel cis XIX -F3-F27 : G-C Ww/Ww pairing antiparallel cis XIX -F4-F26 : U-A Ww/Ww pairing antiparallel cis XX -F5-F25 : G-C Ww/Ww pairing antiparallel cis XIX -F6-F24 : C-G Ww/Ww pairing antiparallel cis XIX -F7-F23 : U-C Ws/Hw pairing antiparallel trans one_hbond -F9-F21 : A-A Bh/O2P pairing -F10-F11 : G-U Sw/Hw adjacent_5p pairing parallel cis one_hbond 89 -F10-F19 : G-G O2'/Ww inward pairing -F10-F20 : G-A Ww/O2P Bs/O2P pairing -F11-F19 : U-G O2P/Ww O2P/Bs pairing -F11-F20 : U-A Ww/Hh pairing antiparallel trans XXIV -F12-F19 : A-G Hh/Ss pairing antiparallel trans XI -F13-F18 : C-G Ww/Ww pairing antiparallel cis XIX -F14-F16 : G-G O2'/Hh pairing -F14-F17 : G-A Ss/Hh Bs/O2P pairing antiparallel trans XI diff --git a/MCdata/1c0a_MC b/MCdata/1c0a_MC deleted file mode 100644 index c9ea70c2316f59a818394acd41b8ad69f42a7992..0000000000000000000000000000000000000000 --- a/MCdata/1c0a_MC +++ /dev/null @@ -1,1270 +0,0 @@ -Residue conformations ------------------------------------------- -B601 : G C3p_endo anti -B602 : G C3p_endo anti -B603 : A C3p_endo anti -B604 : G C3p_endo anti -B605 : C C3p_endo anti -B606 : G C3p_endo anti -B607 : G C2p_endo anti -B608 : 4SU -B609 : A C2p_endo anti -B610 : G C3p_endo anti -B611 : U C3p_endo anti -B612 : U C3p_endo anti -B613 : C C3p_endo anti -B614 : A C3p_endo anti -B615 : G C3p_endo anti -B616 : H2U -B617 : C C2p_endo anti -B618 : G C2p_endo anti -B619 : G C2p_endo syn -B620 : H2U -B620.A : H2U -B621 : A C2p_endo anti -B622 : G C3p_endo anti -B623 : A C3p_endo anti -B624 : A C3p_endo anti -B625 : U C3p_endo anti -B626 : A C3p_endo anti -B627 : C C3p_endo anti -B628 : C C3p_endo anti -B629 : U C3p_endo anti -B630 : G C3p_endo anti -B631 : C C3p_endo anti -B632 : C C3p_endo anti -B633 : U C2p_endo anti -B634 : QUO -B635 : U C3p_endo anti -B636 : C C3p_endo anti -B637 : A C2p_endo syn -B638 : C C3p_endo anti -B639 : G C3p_endo anti -B640 : C C3p_endo anti -B641 : A C3p_endo anti -B642 : G C3p_endo anti -B643 : G C3p_endo anti -B644 : G C3p_endo anti -B645 : G C3p_endo anti -B646 : G7M -B647 : U C2p_endo anti -B648 : C C2p_endo anti -B649 : G C3p_endo anti -B650 : C C3p_endo anti -B651 : G C3p_endo anti -B652 : G C3p_endo anti -B653 : G C3p_endo anti -B654 : 5MU -B655 : PSU -B656 : C C3p_endo anti -B657 : G C3p_endo anti -B658 : A C2p_endo syn -B659 : G C3p_endo anti -B660 : U C2p_endo anti -B661 : C C3p_endo anti -B662 : C C3p_endo anti -B663 : C C3p_endo anti -B664 : G C3p_endo anti -B665 : PSU -B666 : C C3p_endo anti -B667 : C C3p_endo anti -B668 : G C3p_endo anti -B669 : U C3p_endo anti -B670 : U C3p_endo anti -B671 : C C3p_endo anti -B672 : C C3p_endo anti -B673 : G C3p_endo anti -B674 : C C3p_endo anti -B675 : C C3p_endo anti -B676 : A C2p_endo anti -A1 : MET -A2 : ARG -A3 : THR -A4 : GLU -A5 : TYR -A6 : CYS -A7 : GLY -A8 : GLN -A9 : LEU -A10 : ARG -A11 : LEU -A12 : SER -A13 : HIS -A14 : VAL -A15 : GLY -A16 : GLN -A17 : GLN -A18 : VAL -A19 : THR -A20 : LEU -A21 : CYS -A22 : GLY -A23 : TRP -A24 : VAL -A25 : ASN -A26 : ARG -A27 : ARG -A28 : ARG -A29 : ASP -A30 : LEU -A31 : GLY -A32 : SER -A33 : LEU -A34 : ILE -A35 : PHE -A36 : ILE -A37 : ASP -A38 : MET -A39 : ARG -A40 : ASP -A41 : ARG -A42 : GLU -A43 : GLY -A44 : ILE -A45 : VAL -A46 : GLN -A47 : VAL -A48 : PHE -A49 : PHE -A50 : ASP -A51 : PRO -A52 : ASP -A53 : ARG -A54 : ALA -A55 : ASP -A56 : ALA -A57 : LEU -A58 : LYS -A59 : LEU -A60 : ALA -A61 : SER -A62 : GLU -A63 : LEU -A64 : ARG -A65 : ASN -A66 : GLU -A67 : PHE -A68 : CYS -A69 : ILE -A70 : GLN -A71 : VAL -A72 : THR -A73 : GLY -A74 : THR -A75 : VAL -A76 : ARG -A77 : ALA -A78 : ARG -A79 : ASP -A80 : GLU -A81 : LYS -A82 : ASN -A83 : ILE -A84 : ASN -A85 : ARG -A86 : ASP -A87 : MET -A88 : ALA -A89 : THR -A90 : GLY -A91 : GLU -A92 : ILE -A93 : GLU -A94 : VAL -A95 : LEU -A96 : ALA -A97 : SER -A98 : SER -A99 : LEU -A100 : THR -A101 : ILE -A102 : ILE -A103 : ASN -A104 : ARG -A105 : ALA -A106 : ASP -A107 : VAL -A108 : LEU -A109 : PRO -A110 : LEU -A111 : ASP -A112 : SER -A113 : ASN -A114 : HIS -A115 : VAL -A116 : ASN -A117 : THR -A118 : GLU -A119 : GLU -A120 : ALA -A121 : ARG -A122 : LEU -A123 : LYS -A124 : TYR -A125 : ARG -A126 : TYR -A127 : LEU -A128 : ASP -A129 : LEU -A130 : ARG -A131 : ARG -A132 : PRO -A133 : GLU -A134 : MET -A135 : ALA -A136 : GLN -A137 : ARG -A138 : LEU -A139 : LYS -A140 : THR -A141 : ARG -A142 : ALA -A143 : LYS -A144 : ILE -A145 : THR -A146 : SER -A147 : LEU -A148 : VAL -A149 : ARG -A150 : ARG -A151 : PHE -A152 : MET -A153 : ASP -A154 : ASP -A155 : HIS -A156 : GLY -A157 : PHE -A158 : LEU -A159 : ASP -A160 : ILE -A161 : GLU -A162 : THR -A163 : PRO -A164 : MET -A165 : LEU -A166 : THR -A167 : LYS -A168 : ALA -A169 : THR -A170 : PRO -A171 : GLU -A172 : GLY -A173 : ALA -A174 : ARG -A175 : ASP -A176 : TYR -A177 : LEU -A178 : VAL -A179 : PRO -A180 : SER -A181 : ARG -A182 : VAL -A183 : HIS -A184 : LYS -A185 : GLY -A186 : LYS -A187 : PHE -A188 : TYR -A189 : ALA -A190 : LEU -A191 : PRO -A192 : GLN -A193 : SER -A194 : PRO -A195 : GLN -A196 : LEU -A197 : PHE -A198 : LYS -A199 : GLN -A200 : LEU -A201 : LEU -A202 : MET -A203 : MET -A204 : SER -A205 : GLY -A206 : PHE -A207 : ASP -A208 : ARG -A209 : TYR -A210 : TYR -A211 : GLN -A212 : ILE -A213 : VAL -A214 : LYS -A215 : CYS -A216 : PHE -A217 : ARG -A218 : ASP -A219 : GLU -A220 : ASP -A221 : LEU -A222 : ARG -A223 : ALA -A224 : ASP -A225 : ARG -A226 : GLN -A227 : PRO -A228 : GLU -A229 : PHE -A230 : THR -A231 : GLN -A232 : ILE -A233 : ASP -A234 : VAL -A235 : GLU -A236 : THR -A237 : SER -A238 : PHE -A239 : MET -A240 : THR -A241 : ALA -A242 : PRO -A243 : GLN -A244 : VAL -A245 : ARG -A246 : GLU -A247 : VAL -A248 : MET -A249 : GLU -A250 : ALA -A251 : LEU -A252 : VAL -A253 : ARG -A254 : HIS -A255 : LEU -A256 : TRP -A257 : LEU -A258 : GLU -A259 : VAL -A260 : LYS -A261 : GLY -A262 : VAL -A263 : ASP -A264 : LEU -A265 : GLY -A266 : ASP -A267 : PHE -A268 : PRO -A269 : VAL -A270 : MET -A271 : THR -A272 : PHE -A273 : ALA -A274 : GLU -A275 : ALA -A276 : GLU -A277 : ARG -A278 : ARG -A279 : TYR -A280 : GLY -A281 : SER -A282 : ASP -A283 : LYS -A284 : PRO -A285 : ASP -A286 : LEU -A287 : ARG -A288 : ASN -A289 : PRO -A290 : MET -A291 : GLU -A292 : LEU -A293 : THR -A294 : ASP -A295 : VAL -A296 : ALA -A297 : ASP -A298 : LEU -A299 : LEU -A300 : LYS -A301 : SER -A302 : VAL -A303 : GLU -A304 : PHE -A305 : ALA -A306 : VAL -A307 : PHE -A308 : ALA -A309 : GLY -A310 : PRO -A311 : ALA -A312 : ASN -A313 : ASP -A314 : PRO -A315 : LYS -A316 : GLY -A317 : ARG -A318 : VAL -A319 : ALA -A320 : ALA -A321 : LEU -A322 : ARG -A323 : VAL -A324 : PRO -A325 : GLY -A326 : GLY -A327 : ALA -A328 : SER -A329 : LEU -A330 : THR -A331 : ARG -A332 : LYS -A333 : GLN -A334 : ILE -A335 : ASP -A336 : GLU -A337 : TYR -A338 : GLY -A339 : ASN -A340 : PHE -A341 : VAL -A342 : LYS -A343 : ILE -A344 : TYR -A345 : GLY -A346 : ALA -A347 : LYS -A348 : GLY -A349 : LEU -A350 : ALA -A351 : TYR -A352 : ILE -A353 : LYS -A354 : VAL -A355 : ASN -A356 : GLU -A357 : ARG -A358 : ALA -A359 : LYS -A360 : GLY -A361 : LEU -A362 : GLU -A363 : GLY -A364 : ILE -A365 : ASN -A366 : SER -A367 : PRO -A368 : VAL -A369 : ALA -A370 : LYS -A371 : PHE -A372 : LEU -A373 : ASN -A374 : ALA -A375 : GLU -A376 : ILE -A377 : ILE -A378 : GLU -A379 : ASP -A380 : ILE -A381 : LEU -A382 : ASP -A383 : ARG -A384 : THR -A385 : ALA -A386 : ALA -A387 : GLN -A388 : ASP -A389 : GLY -A390 : ASP -A391 : MET -A392 : ILE -A393 : PHE -A394 : PHE -A395 : GLY -A396 : ALA -A397 : ASP -A398 : ASN -A399 : LYS -A400 : LYS -A401 : ILE -A402 : VAL -A403 : ALA -A404 : ASP -A405 : ALA -A406 : MET -A407 : GLY -A408 : ALA -A409 : LEU -A410 : ARG -A411 : LEU -A412 : LYS -A413 : VAL -A414 : GLY -A415 : LYS -A416 : ASP -A417 : LEU -A418 : GLY -A419 : LEU -A420 : THR -A421 : ASP -A422 : GLU -A423 : SER -A424 : LYS -A425 : TRP -A426 : ALA -A427 : PRO -A428 : LEU -A429 : TRP -A430 : VAL -A431 : ILE -A432 : ASP -A433 : PHE -A434 : PRO -A435 : MET -A436 : PHE -A437 : GLU -A438 : ASP -A439 : ASP -A440 : GLY -A441 : GLU -A442 : GLY -A443 : GLY -A444 : LEU -A445 : THR -A446 : ALA -A447 : MET -A448 : HIS -A449 : HIS -A450 : PRO -A451 : PHE -A452 : THR -A453 : SER -A454 : PRO -A455 : LYS -A456 : ASP -A457 : MET -A458 : THR -A459 : ALA -A460 : ALA -A461 : GLU -A462 : LEU -A463 : LYS -A464 : ALA -A465 : ALA -A466 : PRO -A467 : GLU -A468 : ASN -A469 : ALA -A470 : VAL -A471 : ALA -A472 : ASN -A473 : ALA -A474 : TYR -A475 : ASP -A476 : MET -A477 : VAL -A478 : ILE -A479 : ASN -A480 : GLY -A481 : TYR -A482 : GLU -A483 : VAL -A484 : GLY -A485 : GLY -A486 : GLY -A487 : SER -A488 : VAL -A489 : ARG -A490 : ILE -A491 : HIS -A492 : ASN -A493 : GLY -A494 : ASP -A495 : MET -A496 : GLN -A497 : GLN -A498 : THR -A499 : VAL -A500 : PHE -A501 : GLY -A502 : ILE -A503 : LEU -A504 : GLY -A505 : ILE -A506 : ASN -A507 : GLU -A508 : GLU -A509 : GLU -A510 : GLN -A511 : ARG -A512 : GLU -A513 : LYS -A514 : PHE -A515 : GLY -A516 : PHE -A517 : LEU -A518 : LEU -A519 : ASP -A520 : ALA -A521 : LEU -A522 : LYS -A523 : TYR -A524 : GLY -A525 : THR -A526 : PRO -A527 : PRO -A528 : HIS -A529 : ALA -A530 : GLY -A531 : LEU -A532 : ALA -A533 : PHE -A534 : GLY -A535 : LEU -A536 : ASP -A537 : ARG -A538 : LEU -A539 : THR -A540 : MET -A541 : LEU -A542 : LEU -A543 : THR -A544 : GLY -A545 : THR -A546 : ASP -A547 : ASN -A548 : ILE -A549 : ARG -A550 : ASP -A551 : VAL -A552 : ILE -A553 : ALA -A554 : PHE -A555 : PRO -A556 : LYS -A557 : THR -A558 : THR -A559 : ALA -A560 : ALA -A561 : ALA -A562 : CYS -A563 : LEU -A564 : MET -A565 : THR -A566 : GLU -A567 : ALA -A568 : PRO -A569 : SER -A570 : PHE -A571 : ALA -A572 : ASN -A573 : PRO -A574 : THR -A575 : ALA -A576 : LEU -A577 : ALA -A578 : GLU -A579 : LEU -A580 : SER -A581 : ILE -A582 : GLN -A583 : VAL -A584 : VAL -A585 : LYS -B701 : SO4 -A800 : AMP -A831 : AMO -B1011 : HOH -B1015 : HOH -B1024 : HOH -B1056 : HOH -B1080 : HOH -B1088 : HOH -B1096 : HOH -B1097 : HOH -B1111 : HOH -B1112 : HOH -B1113 : HOH -B1135 : HOH -B1137 : HOH -B1139 : HOH -B1149 : HOH -B1150 : HOH -B1157 : HOH -B1160 : HOH -B1174 : HOH -B1187 : HOH -B1189 : HOH -B1190 : HOH -B1201 : HOH -B1204 : HOH -B1205 : HOH -B1206 : HOH -B1207 : HOH -B1209 : HOH -B1210 : HOH -B1211 : HOH -B1213 : HOH -B1215 : HOH -B1216 : HOH -B1221 : HOH -B1222 : HOH -B1223 : HOH -B1228 : HOH -B1230 : HOH -B1232 : HOH -B1234 : HOH -B1244 : HOH -B1245 : HOH -B1249 : HOH -B1250 : HOH -B1261 : HOH -B1270 : HOH -B1272 : HOH -B1276 : HOH -B1277 : HOH -B1291 : HOH -B1299 : HOH -B1306 : HOH -B1312 : HOH -B1313 : HOH -B1316 : HOH -B1318 : HOH -B1325 : HOH -B1331 : HOH -B1334 : HOH -B1338 : HOH -B1342 : HOH -B1344 : HOH -B1350 : HOH -B1356 : HOH -B1357 : HOH -B1358 : HOH -B1359 : HOH -B1361 : HOH -B1365 : HOH -B1382 : HOH -B1384 : HOH -B1385 : HOH -B1388 : HOH -B1390 : HOH -B1392 : HOH -B1398 : HOH -B1402 : HOH -B1408 : HOH -B1411 : HOH -B1412 : HOH -B1416 : HOH -B1418 : HOH -B1423 : HOH -B1425 : HOH -B1427 : HOH -B1429 : HOH -B1431 : HOH -B1434 : HOH -B1438 : HOH -B1449 : HOH -B1453 : HOH -B1455 : HOH -B1465 : HOH -B1471 : HOH -B1479 : HOH -B1483 : HOH -B1485 : HOH -B1493 : HOH -B1496 : HOH -B1502 : HOH -B1503 : HOH -B1505 : HOH -B1508 : HOH -B1509 : HOH -B1510 : HOH -B1513 : HOH -B1514 : HOH -A1001 : HOH -A1002 : HOH -A1003 : HOH -A1004 : HOH -A1005 : HOH -A1006 : HOH -A1007 : HOH -A1008 : HOH -A1009 : HOH -A1010 : HOH -A1012 : HOH -A1013 : HOH -A1014 : HOH -A1016 : HOH -A1017 : HOH -A1018 : HOH -A1019 : HOH -A1020 : HOH -A1021 : HOH -A1022 : HOH -A1023 : HOH -A1025 : HOH -A1026 : HOH -A1027 : HOH -A1028 : HOH -A1029 : HOH -A1030 : HOH -A1031 : HOH -A1032 : HOH -A1033 : HOH -A1034 : HOH -A1035 : HOH -A1036 : HOH -A1037 : HOH -A1038 : HOH -A1039 : HOH -A1040 : HOH -A1041 : HOH -A1042 : HOH -A1043 : HOH -A1044 : HOH -A1045 : HOH -A1046 : HOH -A1047 : HOH -A1048 : HOH -A1049 : HOH -A1050 : HOH -A1051 : HOH -A1052 : HOH -A1053 : HOH -A1054 : HOH -A1055 : HOH -A1057 : HOH -A1058 : HOH -A1059 : HOH -A1060 : HOH -A1061 : HOH -A1062 : HOH -A1063 : HOH -A1064 : HOH -A1065 : HOH -A1066 : HOH -A1067 : HOH -A1068 : HOH -A1069 : HOH -A1070 : HOH -A1071 : HOH -A1072 : HOH -A1073 : HOH -A1074 : HOH -A1075 : HOH -A1076 : HOH -A1077 : HOH -A1078 : HOH -A1079 : HOH -A1081 : HOH -A1082 : HOH -A1083 : HOH -A1084 : HOH -A1085 : HOH -A1086 : HOH -A1087 : HOH -A1089 : HOH -A1090 : HOH -A1091 : HOH -A1092 : HOH -A1093 : HOH -A1094 : HOH -A1095 : HOH -A1098 : HOH -A1099 : HOH -A1100 : HOH -A1101 : HOH -A1102 : HOH -A1103 : HOH -A1104 : HOH -A1105 : HOH -A1106 : HOH -A1107 : HOH -A1108 : HOH -A1109 : HOH -A1110 : HOH -A1114 : HOH -A1115 : HOH -A1116 : HOH -A1117 : HOH -A1118 : HOH -A1119 : HOH -A1120 : HOH -A1121 : HOH -A1122 : HOH -A1123 : HOH -A1124 : HOH -A1125 : HOH -A1126 : HOH -A1127 : HOH -A1128 : HOH -A1129 : HOH -A1130 : HOH -A1131 : HOH -A1132 : HOH -A1133 : HOH -A1134 : HOH -A1136 : HOH -A1138 : HOH -A1140 : HOH -A1141 : HOH -A1142 : HOH -A1143 : HOH -A1144 : HOH -A1145 : HOH -A1146 : HOH -A1147 : HOH -A1148 : HOH -A1151 : HOH -A1152 : HOH -A1153 : HOH -A1154 : HOH -A1155 : HOH -A1156 : HOH -A1158 : HOH -A1159 : HOH -A1161 : HOH -A1162 : HOH -A1163 : HOH -A1164 : HOH -A1165 : HOH -A1166 : HOH -A1167 : HOH -A1168 : HOH -A1169 : HOH -A1170 : HOH -A1171 : HOH -A1172 : HOH -A1173 : HOH -A1175 : HOH -A1176 : HOH -A1177 : HOH -A1178 : HOH -A1179 : HOH -A1180 : HOH -A1181 : HOH -A1182 : HOH -A1183 : HOH -A1184 : HOH -A1185 : HOH -A1186 : HOH -A1188 : HOH -A1191 : HOH -A1192 : HOH -A1193 : HOH -A1194 : HOH -A1195 : HOH -A1196 : HOH -A1197 : HOH -A1198 : HOH -A1199 : HOH -A1200 : HOH -A1202 : HOH -A1203 : HOH -A1208 : HOH -A1212 : HOH -A1214 : HOH -A1217 : HOH -A1218 : HOH -A1219 : HOH -A1220 : HOH -A1224 : HOH -A1225 : HOH -A1226 : HOH -A1227 : HOH -A1229 : HOH -A1231 : HOH -A1233 : HOH -A1235 : HOH -A1236 : HOH -A1237 : HOH -A1238 : HOH -A1239 : HOH -A1240 : HOH -A1241 : HOH -A1242 : HOH -A1243 : HOH -A1246 : HOH -A1247 : HOH -A1248 : HOH -A1251 : HOH -A1252 : HOH -A1253 : HOH -A1254 : HOH -A1255 : HOH -A1256 : HOH -A1257 : HOH -A1258 : HOH -A1259 : HOH -A1260 : HOH -A1262 : HOH -A1263 : HOH -A1264 : HOH -A1265 : HOH -A1266 : HOH -A1267 : HOH -A1268 : HOH -A1269 : HOH -A1271 : HOH -A1273 : HOH -A1274 : HOH -A1275 : HOH -A1278 : HOH -A1279 : HOH -A1280 : HOH -A1281 : HOH -A1282 : HOH -A1283 : HOH -A1284 : HOH -A1285 : HOH -A1286 : HOH -A1287 : HOH -A1288 : HOH -A1289 : HOH -A1290 : HOH -A1292 : HOH -A1293 : HOH -A1294 : HOH -A1295 : HOH -A1296 : HOH -A1297 : HOH -A1298 : HOH -A1300 : HOH -A1301 : HOH -A1302 : HOH -A1303 : HOH -A1304 : HOH -A1305 : HOH -A1307 : HOH -A1308 : HOH -A1309 : HOH -A1310 : HOH -A1311 : HOH -A1314 : HOH -A1315 : HOH -A1317 : HOH -A1319 : HOH -A1320 : HOH -A1321 : HOH -A1322 : HOH -A1323 : HOH -A1324 : HOH -A1326 : HOH -A1327 : HOH -A1328 : HOH -A1329 : HOH -A1330 : HOH -A1332 : HOH -A1333 : HOH -A1335 : HOH -A1336 : HOH -A1337 : HOH -A1339 : HOH -A1340 : HOH -A1341 : HOH -A1343 : HOH -A1345 : HOH -A1346 : HOH -A1347 : HOH -A1348 : HOH -A1349 : HOH -A1351 : HOH -A1352 : HOH -A1353 : HOH -A1354 : HOH -A1355 : HOH -A1360 : HOH -A1362 : HOH -A1363 : HOH -A1364 : HOH -A1366 : HOH -A1367 : HOH -A1368 : HOH -A1369 : HOH -A1370 : HOH -A1371 : HOH -A1372 : HOH -A1373 : HOH -A1374 : HOH -A1375 : HOH -A1376 : HOH -A1377 : HOH -A1378 : HOH -A1379 : HOH -A1380 : HOH -A1381 : HOH -A1383 : HOH -A1386 : HOH -A1387 : HOH -A1389 : HOH -A1391 : HOH -A1393 : HOH -A1394 : HOH -A1395 : HOH -A1396 : HOH -A1397 : HOH -A1399 : HOH -A1400 : HOH -A1401 : HOH -A1403 : HOH -A1404 : HOH -A1405 : HOH -A1406 : HOH -A1407 : HOH -A1409 : HOH -A1410 : HOH -A1413 : HOH -A1414 : HOH -A1415 : HOH -A1417 : HOH -A1419 : HOH -A1420 : HOH -A1421 : HOH -A1422 : HOH -A1424 : HOH -A1426 : HOH -A1428 : HOH -A1430 : HOH -A1432 : HOH -A1433 : HOH -A1435 : HOH -A1436 : HOH -A1437 : HOH -A1439 : HOH -A1440 : HOH -A1441 : HOH -A1442 : HOH -A1443 : HOH -A1444 : HOH -A1445 : HOH -A1446 : HOH -A1447 : HOH -A1448 : HOH -A1450 : HOH -A1451 : HOH -A1452 : HOH -A1454 : HOH -A1456 : HOH -A1457 : HOH -A1458 : HOH -A1459 : HOH -A1460 : HOH -A1461 : HOH -A1462 : HOH -A1463 : HOH -A1464 : HOH -A1466 : HOH -A1467 : HOH -A1468 : HOH -A1469 : HOH -A1470 : HOH -A1472 : HOH -A1473 : HOH -A1474 : HOH -A1475 : HOH -A1476 : HOH -A1477 : HOH -A1478 : HOH -A1480 : HOH -A1481 : HOH -A1482 : HOH -A1484 : HOH -A1486 : HOH -A1487 : HOH -A1488 : HOH -A1489 : HOH -A1490 : HOH -A1491 : HOH -A1492 : HOH -A1494 : HOH -A1495 : HOH -A1497 : HOH -A1498 : HOH -A1499 : HOH -A1500 : HOH -A1501 : HOH -A1504 : HOH -A1506 : HOH -A1507 : HOH -A1511 : HOH -A1512 : HOH -Adjacent stackings ---------------------------------------------- -B601-B602 : adjacent_5p upward -B602-B603 : adjacent_5p upward -B603-B604 : adjacent_5p upward -B604-B605 : adjacent_5p upward -B606-B607 : adjacent_5p upward -B610-B611 : adjacent_5p upward -B611-B612 : adjacent_5p upward -B612-B613 : adjacent_5p upward -B614-B615 : adjacent_5p upward -B622-B623 : adjacent_5p upward -B623-B624 : adjacent_5p upward -B624-B625 : adjacent_5p upward -B625-B626 : adjacent_5p upward -B626-B627 : adjacent_5p upward -B627-B628 : adjacent_5p upward -B628-B629 : adjacent_5p upward -B630-B631 : adjacent_5p upward -B631-B632 : adjacent_5p upward -B635-B636 : adjacent_5p upward -B638-B639 : adjacent_5p upward -B639-B640 : adjacent_5p upward -B640-B641 : adjacent_5p upward -B641-B642 : adjacent_5p upward -B642-B643 : adjacent_5p upward -B643-B644 : adjacent_5p upward -B644-B645 : adjacent_5p upward -B649-B650 : adjacent_5p upward -B650-B651 : adjacent_5p upward -B651-B652 : adjacent_5p upward -B652-B653 : adjacent_5p upward -B656-B657 : adjacent_5p upward -B659-B660 : adjacent_5p upward -B662-B663 : adjacent_5p upward -B663-B664 : adjacent_5p upward -B666-B667 : adjacent_5p upward -B667-B668 : adjacent_5p upward -B668-B669 : adjacent_5p upward -B670-B671 : adjacent_5p upward -B672-B673 : adjacent_5p upward -B673-B674 : adjacent_5p upward pairing -B674-B675 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -B606-B668 : outward -B607-B649 : upward -B609-B645 : inward -B614-B622 : outward -B615-B659 : upward -B618-B657 : inward pairing -B618-B658 : outward -B619-B657 : outward -B621-B648 : outward -B630-B641 : outward -B651-B664 : outward -B658-B661 : upward -Number of stackings = 53 -Number of adjacent stackings = 41 -Number of non adjacent stackings = 12 -Base-pairs ------------------------------------------------------ -B601-B672 : G-C Ww/Ww pairing antiparallel cis XIX -B602-B671 : G-C Ww/Ww pairing antiparallel cis XIX -B603-B670 : A-U Ww/Ww pairing antiparallel cis XX -B604-B669 : G-U Ww/Ws pairing antiparallel cis XXVIII -B605-B668 : C-G Ww/Ww pairing antiparallel cis XIX -B606-B667 : G-C Ww/Ww pairing antiparallel cis XIX -B607-B666 : G-C Ww/Ww pairing antiparallel cis XIX -B609-B610 : A-G O2'/Hh adjacent_5p pairing -B609-B623 : A-A Hh/Hh pairing parallel trans II -B610-B625 : G-U Ww/Ws pairing antiparallel cis XXVIII -B611-B624 : U-A Ww/Ww pairing antiparallel cis XX -B612-B623 : U-A Ww/Ww pairing antiparallel cis XX -B613-B622 : C-G Ww/Ww pairing antiparallel cis XIX -B615-B648 : G-C Ww/Ww pairing parallel trans XXII -B618-B657 : G-G O2'/Bs inward pairing -B619-B656 : G-C Ww/Ww pairing antiparallel cis XIX -B621-B647 : A-U O2P/Ww pairing -B625-B645 : U-G Wh/Ws pairing antiparallel cis one_hbond 94 -B626-B644 : A-G Ww/Ww pairing antiparallel cis VIII -B627-B643 : C-G Ww/Ww pairing antiparallel cis XIX -B628-B642 : C-G Ww/Ww pairing antiparallel cis XIX -B629-B641 : U-A Ww/Ww pairing antiparallel cis XX -B630-B640 : G-C Ww/Ww pairing antiparallel cis XIX -B631-B639 : C-G Ww/Ww pairing antiparallel cis -B632-B638 : C-C Ws/Wh pairing antiparallel cis one_hbond 137 -B650-B664 : C-G Ww/Ww pairing antiparallel cis XIX -B651-B663 : G-C Ww/Ww pairing antiparallel cis XIX -B652-B662 : G-C Ww/Ww pairing antiparallel cis XIX -B653-B661 : G-C Ww/Ww pairing antiparallel cis XIX -B660-B661 : U-C O2P/Bh adjacent_5p pairing -B673-B674 : G-C O2P/Bh adjacent_5p upward pairing diff --git a/MCdata/1c0o_MC b/MCdata/1c0o_MC deleted file mode 100644 index 5670021c0d4f6465070384feea7c447ce616c1f9..0000000000000000000000000000000000000000 --- a/MCdata/1c0o_MC +++ /dev/null @@ -1,744 +0,0 @@ -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : G C3p_endo anti -A4 : U C3p_endo anti -A5 : C C3p_endo anti -A6 : U C3p_endo anti -A7 : U C2p_endo anti -A8 : C C2p_endo anti -A9 : G C3p_endo syn -A10 : G C3p_endo anti -A11 : G C3p_endo anti -A12 : U C3p_endo anti -A13 : C C3p_endo anti -A14 : C C3p_endo anti -A15 : NCO -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A9-A10 : adjacent_5p outward pairing -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 9 -Number of adjacent stackings = 9 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-A14 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A13 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A12 : G-U Ww/Ws pairing antiparallel cis XXVIII -A4-A11 : U-G Ws/Ww pairing antiparallel cis XXVIII -A5-A10 : C-G Ww/Ww pairing antiparallel cis XIX -A7-A8 : U-C O2P/Bh adjacent_5p pairing -A7-A9 : U-G O2'/Hh pairing -A9-A10 : G-G Bs/O2P adjacent_5p outward pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : G C3p_endo anti -A4 : U C3p_endo anti -A5 : C C3p_endo anti -A6 : U C3p_endo anti -A7 : U C2p_endo anti -A8 : C C2p_endo anti -A9 : G C3p_endo syn -A10 : G C3p_endo anti -A11 : G C3p_endo anti -A12 : U C3p_endo anti -A13 : C C3p_endo anti -A14 : C C3p_endo anti -A15 : NCO -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A9-A10 : adjacent_5p outward pairing -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A13-A14 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 8 -Number of adjacent stackings = 8 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-A14 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A13 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A12 : G-U Ww/Ws pairing antiparallel cis XXVIII -A4-A11 : U-G Ws/Ww pairing antiparallel cis XXVIII -A5-A10 : C-G Ww/Ww pairing antiparallel cis XIX -A7-A8 : U-C O2P/Bh adjacent_5p pairing -A7-A9 : U-G O2'/Hh pairing -A9-A10 : G-G Bs/O2P adjacent_5p outward pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : G C3p_endo anti -A4 : U C3p_endo anti -A5 : C C3p_endo anti -A6 : U C3p_endo anti -A7 : U C2p_endo anti -A8 : C C2p_endo anti -A9 : G C3p_endo syn -A10 : G C3p_endo anti -A11 : G C3p_endo anti -A12 : U C3p_endo anti -A13 : C C3p_endo anti -A14 : C C3p_endo anti -A15 : NCO -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A9-A10 : adjacent_5p outward pairing -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 10 -Number of adjacent stackings = 10 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-A14 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A13 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A12 : G-U Ww/Ws pairing antiparallel cis XXVIII -A4-A11 : U-G Ws/Ww pairing antiparallel cis XXVIII -A5-A10 : C-G Ww/Ww pairing antiparallel cis XIX -A6-A9 : U-G Bs/Ww pairing parallel trans one_hbond -A7-A8 : U-C O2P/Bh adjacent_5p pairing -A7-A9 : U-G O2'/Hh pairing -A9-A10 : G-G Bs/O2P adjacent_5p outward pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : G C3p_endo anti -A4 : U C3p_endo anti -A5 : C C3p_endo anti -A6 : U C3p_endo anti -A7 : U C2p_endo anti -A8 : C C2p_endo anti -A9 : G C3p_endo syn -A10 : G C3p_endo anti -A11 : G C3p_endo anti -A12 : U C3p_endo anti -A13 : C C3p_endo anti -A14 : C C3p_endo anti -A15 : NCO -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A9-A10 : adjacent_5p outward pairing -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 9 -Number of adjacent stackings = 9 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-A14 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A13 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A12 : G-U Ww/Ws pairing antiparallel cis XXVIII -A4-A11 : U-G Ws/Ww pairing antiparallel cis XXVIII -A5-A10 : C-G Ww/Ww pairing antiparallel cis XIX -A7-A8 : U-C O2P/Bh adjacent_5p pairing -A7-A9 : U-G O2'/Hh pairing -A9-A10 : G-G Bs/O2P adjacent_5p outward pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : G C3p_endo anti -A4 : U C3p_endo anti -A5 : C C3p_endo anti -A6 : U C3p_endo anti -A7 : U C2p_endo anti -A8 : C C2p_endo anti -A9 : G C3p_endo syn -A10 : G C3p_endo anti -A11 : G C3p_endo anti -A12 : U C3p_endo anti -A13 : C C3p_endo anti -A14 : C C3p_endo anti -A15 : NCO -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A9-A10 : adjacent_5p outward pairing -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A13-A14 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 8 -Number of adjacent stackings = 8 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-A14 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A13 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A12 : G-U Ww/Ws pairing antiparallel cis XXVIII -A4-A11 : U-G Ws/Ww pairing antiparallel cis XXVIII -A5-A10 : C-G Ww/Ww pairing antiparallel cis XIX -A7-A8 : U-C O2P/Bh adjacent_5p pairing -A7-A9 : U-G O2'/Hh pairing -A9-A10 : G-G Bs/O2P adjacent_5p outward pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : G C3p_endo anti -A4 : U C3p_endo anti -A5 : C C3p_endo anti -A6 : U C3p_endo anti -A7 : U C2p_endo anti -A8 : C C2p_endo anti -A9 : G C3p_endo syn -A10 : G C3p_endo anti -A11 : G C3p_endo anti -A12 : U C3p_endo anti -A13 : C C3p_endo anti -A14 : C C3p_endo anti -A15 : NCO -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A9-A10 : adjacent_5p outward pairing -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 9 -Number of adjacent stackings = 9 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-A14 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A13 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A12 : G-U Ww/Ws pairing antiparallel cis XXVIII -A4-A11 : U-G Ws/Ww pairing antiparallel cis XXVIII -A5-A10 : C-G Ww/Ww pairing antiparallel cis XIX -A7-A8 : U-C O2P/Bh adjacent_5p pairing -A7-A9 : U-G O2'/Hh pairing -A9-A10 : G-G Bs/O2P adjacent_5p outward pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : G C3p_endo anti -A4 : U C3p_endo anti -A5 : C C3p_endo anti -A6 : U C3p_endo anti -A7 : U C2p_endo anti -A8 : C C2p_endo anti -A9 : G C3p_endo syn -A10 : G C3p_endo anti -A11 : G C3p_endo anti -A12 : U C3p_endo anti -A13 : C C3p_endo anti -A14 : C C3p_endo anti -A15 : NCO -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A9-A10 : adjacent_5p outward pairing -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A13-A14 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 8 -Number of adjacent stackings = 8 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-A14 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A13 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A12 : G-U Ww/Ws pairing antiparallel cis XXVIII -A4-A11 : U-G Ws/Ww pairing antiparallel cis XXVIII -A5-A10 : C-G Ww/Ww pairing antiparallel cis XIX -A6-A9 : U-G Bs/Ww pairing parallel trans one_hbond -A7-A8 : U-C O2P/Bh adjacent_5p pairing -A7-A9 : U-G O2'/Hh pairing -A9-A10 : G-G Bs/O2P adjacent_5p outward pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : G C3p_endo anti -A4 : U C3p_endo anti -A5 : C C3p_endo anti -A6 : U C3p_endo anti -A7 : U C2p_endo anti -A8 : C C2p_endo anti -A9 : G C3p_endo syn -A10 : G C3p_endo anti -A11 : G C3p_endo anti -A12 : U C3p_endo anti -A13 : C C3p_endo anti -A14 : C C3p_endo anti -A15 : NCO -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A9-A10 : adjacent_5p outward pairing -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A13-A14 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 9 -Number of adjacent stackings = 9 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-A14 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A13 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A12 : G-U Ww/Ws pairing antiparallel cis XXVIII -A4-A11 : U-G Ws/Ww pairing antiparallel cis XXVIII -A5-A10 : C-G Ww/Ww pairing antiparallel cis XIX -A7-A8 : U-C O2P/Bh adjacent_5p pairing -A7-A9 : U-G O2'/Hh pairing -A9-A10 : G-G Bs/O2P adjacent_5p outward pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : G C3p_endo anti -A4 : U C3p_endo anti -A5 : C C3p_endo anti -A6 : U C3p_endo anti -A7 : U C2p_endo anti -A8 : C C2p_endo anti -A9 : G C3p_endo syn -A10 : G C3p_endo anti -A11 : G C3p_endo anti -A12 : U C3p_endo anti -A13 : C C3p_endo anti -A14 : C C3p_endo anti -A15 : NCO -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A9-A10 : adjacent_5p outward pairing -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A13-A14 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 8 -Number of adjacent stackings = 8 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-A14 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A13 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A12 : G-U Ww/Ws pairing antiparallel cis XXVIII -A4-A11 : U-G Ws/Ww pairing antiparallel cis XXVIII -A5-A10 : C-G Ww/Ww pairing antiparallel cis XIX -A6-A9 : U-G Bs/Ww pairing parallel trans one_hbond -A7-A8 : U-C O2P/Bh adjacent_5p pairing -A7-A9 : U-G O2'/Hh pairing -A9-A10 : G-G Bs/O2P adjacent_5p outward pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : G C3p_endo anti -A4 : U C3p_endo anti -A5 : C C3p_endo anti -A6 : U C3p_endo anti -A7 : U C2p_endo anti -A8 : C C2p_endo anti -A9 : G C3p_endo syn -A10 : G C3p_endo anti -A11 : G C3p_endo anti -A12 : U C3p_endo anti -A13 : C C3p_endo anti -A14 : C C3p_endo anti -A15 : NCO -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A9-A10 : adjacent_5p outward pairing -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 9 -Number of adjacent stackings = 9 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-A14 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A13 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A12 : G-U Ww/Ws pairing antiparallel cis XXVIII -A4-A11 : U-G Ws/Ww pairing antiparallel cis XXVIII -A5-A10 : C-G Ww/Ww pairing antiparallel cis XIX -A7-A8 : U-C O2P/Bh adjacent_5p pairing -A7-A9 : U-G O2'/Hh pairing -A9-A10 : G-G Bs/O2P adjacent_5p outward pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : G C3p_endo anti -A4 : U C3p_endo anti -A5 : C C3p_endo anti -A6 : U C3p_endo anti -A7 : U C2p_endo anti -A8 : C C2p_endo anti -A9 : G C3p_endo syn -A10 : G C3p_endo anti -A11 : G C3p_endo anti -A12 : U C3p_endo anti -A13 : C C3p_endo anti -A14 : C C3p_endo anti -A15 : NCO -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A9-A10 : adjacent_5p outward pairing -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A13-A14 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 8 -Number of adjacent stackings = 8 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-A14 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A13 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A12 : G-U Ww/Ws pairing antiparallel cis XXVIII -A4-A11 : U-G Ws/Ww pairing antiparallel cis XXVIII -A5-A10 : C-G Ww/Ww pairing antiparallel cis XIX -A6-A9 : U-G Bs/Ww pairing parallel trans 87 -A7-A8 : U-C O2P/Bh adjacent_5p pairing -A7-A9 : U-G O2'/Hh pairing -A9-A10 : G-G Bs/O2P adjacent_5p outward pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : G C3p_endo anti -A4 : U C3p_endo anti -A5 : C C3p_endo anti -A6 : U C3p_endo anti -A7 : U C2p_endo anti -A8 : C C2p_endo anti -A9 : G C3p_endo syn -A10 : G C3p_endo anti -A11 : G C3p_endo anti -A12 : U C3p_endo anti -A13 : C C3p_endo anti -A14 : C C3p_endo anti -A15 : NCO -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A13-A14 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 7 -Number of adjacent stackings = 7 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-A14 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A13 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A12 : G-U Ww/Ws pairing antiparallel cis XXVIII -A4-A11 : U-G Ws/Ww pairing antiparallel cis XXVIII -A5-A10 : C-G Ww/Ww pairing antiparallel cis XIX -A6-A9 : U-G Bs/Ww pairing parallel trans 87 -A7-A8 : U-C O2P/Bh adjacent_5p pairing -A7-A9 : U-G O2'/Hh pairing -A9-A10 : G-G Bs/O2P adjacent_5p pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : G C3p_endo anti -A4 : U C3p_endo anti -A5 : C C3p_endo anti -A6 : U C3p_endo anti -A7 : U C2p_endo anti -A8 : C C2p_endo anti -A9 : G C3p_endo syn -A10 : G C3p_endo anti -A11 : G C3p_endo anti -A12 : U C3p_endo anti -A13 : C C3p_endo anti -A14 : C C3p_endo anti -A15 : NCO -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A9-A10 : adjacent_5p outward pairing -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 10 -Number of adjacent stackings = 10 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-A14 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A13 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A12 : G-U Ww/Ws pairing antiparallel cis XXVIII -A4-A11 : U-G Ws/Ww pairing antiparallel cis XXVIII -A5-A10 : C-G Ww/Ww pairing antiparallel cis XIX -A7-A8 : U-C O2P/Bh adjacent_5p pairing -A7-A9 : U-G O2'/Hh pairing -A9-A10 : G-G Bs/O2P adjacent_5p outward pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : G C3p_endo anti -A4 : U C3p_endo anti -A5 : C C3p_endo anti -A6 : U C3p_endo anti -A7 : U C2p_endo anti -A8 : C C2p_endo anti -A9 : G C3p_endo syn -A10 : G C3p_endo anti -A11 : G C3p_endo anti -A12 : U C3p_endo anti -A13 : C C3p_endo anti -A14 : C C3p_endo anti -A15 : NCO -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A9-A10 : adjacent_5p outward pairing -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A13-A14 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 8 -Number of adjacent stackings = 8 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-A14 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A13 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A12 : G-U Ww/Ws pairing antiparallel cis XXVIII -A4-A11 : U-G Ws/Ww pairing antiparallel cis XXVIII -A5-A10 : C-G Ww/Ww pairing antiparallel cis XIX -A6-A9 : U-G Bs/Ww pairing parallel trans one_hbond -A7-A8 : U-C O2P/Bh adjacent_5p pairing -A7-A9 : U-G O2'/Hh pairing -A9-A10 : G-G Bs/O2P adjacent_5p outward pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : G C3p_endo anti -A4 : U C3p_endo anti -A5 : C C3p_endo anti -A6 : U C3p_endo anti -A7 : U C2p_endo anti -A8 : C C2p_endo anti -A9 : G C3p_endo syn -A10 : G C3p_endo anti -A11 : G C3p_endo anti -A12 : U C3p_endo anti -A13 : C C3p_endo anti -A14 : C C3p_endo anti -A15 : NCO -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A9-A10 : adjacent_5p outward pairing -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 10 -Number of adjacent stackings = 10 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-A14 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A13 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A12 : G-U Ww/Ws pairing antiparallel cis XXVIII -A4-A11 : U-G Ws/Ww pairing antiparallel cis XXVIII -A5-A10 : C-G Ww/Ww pairing antiparallel cis XIX -A7-A8 : U-C O2P/Bh adjacent_5p pairing -A7-A9 : U-G O2'/Hh pairing -A9-A10 : G-G Bs/O2P adjacent_5p outward pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : G C3p_endo anti -A4 : U C3p_endo anti -A5 : C C3p_endo anti -A6 : U C3p_endo anti -A7 : U C2p_endo anti -A8 : C C2p_endo anti -A9 : G C3p_endo syn -A10 : G C3p_endo anti -A11 : G C3p_endo anti -A12 : U C3p_endo anti -A13 : C C3p_endo anti -A14 : C C3p_endo anti -A15 : NCO -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A9-A10 : adjacent_5p outward pairing -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A13-A14 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 9 -Number of adjacent stackings = 9 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-A14 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A13 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A12 : G-U Ww/Ws pairing antiparallel cis XXVIII -A4-A11 : U-G Ws/Ww pairing antiparallel cis XXVIII -A5-A10 : C-G Ww/Ww pairing antiparallel cis XIX -A7-A8 : U-C O2P/Bh adjacent_5p pairing -A7-A9 : U-G O2'/Hh pairing -A9-A10 : G-G Bs/O2P adjacent_5p outward pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : G C3p_endo anti -A4 : U C3p_endo anti -A5 : C C3p_endo anti -A6 : U C3p_endo anti -A7 : U C2p_endo anti -A8 : C C2p_endo anti -A9 : G C3p_endo syn -A10 : G C3p_endo anti -A11 : G C3p_endo anti -A12 : U C3p_endo anti -A13 : C C3p_endo anti -A14 : C C3p_endo anti -A15 : NCO -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A9-A10 : adjacent_5p outward pairing -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 10 -Number of adjacent stackings = 10 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-A14 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A13 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A12 : G-U Ww/Ws pairing antiparallel cis XXVIII -A4-A11 : U-G Ws/Ww pairing antiparallel cis XXVIII -A5-A10 : C-G Ww/Ww pairing antiparallel cis XIX -A6-A9 : U-G Bs/Ww pairing parallel trans one_hbond -A7-A8 : U-C O2P/Bh adjacent_5p pairing -A7-A9 : U-G O2'/Hh pairing -A9-A10 : G-G Bs/O2P adjacent_5p outward pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : G C3p_endo anti -A4 : U C3p_endo anti -A5 : C C3p_endo anti -A6 : U C3p_endo anti -A7 : U C2p_endo anti -A8 : C C2p_endo anti -A9 : G C3p_endo syn -A10 : G C3p_endo anti -A11 : G C3p_endo anti -A12 : U C3p_endo anti -A13 : C C3p_endo anti -A14 : C C3p_endo anti -A15 : NCO -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A9-A10 : adjacent_5p outward pairing -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A13-A14 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 8 -Number of adjacent stackings = 8 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-A14 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A13 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A12 : G-U Ww/Ws pairing antiparallel cis XXVIII -A4-A11 : U-G Ws/Ww pairing antiparallel cis XXVIII -A5-A10 : C-G Ww/Ww pairing antiparallel cis XIX -A7-A8 : U-C O2P/Bh adjacent_5p pairing -A7-A9 : U-G O2'/Hh pairing -A9-A10 : G-G Bs/O2P adjacent_5p outward pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : G C3p_endo anti -A4 : U C3p_endo anti -A5 : C C3p_endo anti -A6 : U C3p_endo anti -A7 : U C2p_endo anti -A8 : C C2p_endo anti -A9 : G C3p_endo syn -A10 : G C3p_endo anti -A11 : G C3p_endo anti -A12 : U C3p_endo anti -A13 : C C3p_endo anti -A14 : C C3p_endo anti -A15 : NCO -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A9-A10 : adjacent_5p outward pairing -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 10 -Number of adjacent stackings = 10 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-A14 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A13 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A12 : G-U Ww/Ws pairing antiparallel cis XXVIII -A4-A11 : U-G Ws/Ww pairing antiparallel cis XXVIII -A5-A10 : C-G Ww/Ww pairing antiparallel cis XIX -A7-A8 : U-C O2P/Bh adjacent_5p pairing -A7-A9 : U-G O2'/Hh pairing -A9-A10 : G-G Bs/O2P adjacent_5p outward pairing diff --git a/MCdata/1c2q_MC b/MCdata/1c2q_MC deleted file mode 100644 index aa67b6d6eb2266582cdb4e385d7d9447e759f75e..0000000000000000000000000000000000000000 --- a/MCdata/1c2q_MC +++ /dev/null @@ -1,50 +0,0 @@ -Residue conformations ------------------------------------------- -A1 : A O4p_endo anti -A2 : T C1p_exo anti -A3 : G C2p_endo anti -A4 : G C2p_endo anti -A5 : T3P -A6 : G C4p_exo anti -A7 : C C3p_endo anti -A8 : T O4p_endo anti -A9 : C C4p_exo anti -B10 : G C4p_exo anti -B11 : A C3p_endo anti -B12 : G C3p_endo anti -B13 : C C3p_endo anti -B14 : A C3p_endo anti -B15 : C C3p_endo anti -B16 : C C3p_endo anti -B17 : A C3p_endo anti -B18 : U C4p_exo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -B10-B11 : adjacent_5p upward -B11-B12 : adjacent_5p upward -B12-B13 : adjacent_5p upward -B13-B14 : adjacent_5p upward -B14-B15 : adjacent_5p upward -B15-B16 : adjacent_5p upward -B16-B17 : adjacent_5p upward -B17-B18 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A3-B17 : outward -A6-B14 : outward -Number of stackings = 16 -Number of adjacent stackings = 14 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A1-B18 : A-U Ww/Ww pairing antiparallel cis XX -A2-B17 : T-A Ww/Ww pairing antiparallel cis -A3-B16 : G-C Ww/Ww pairing antiparallel cis XIX -A4-B15 : G-C Ww/Ww pairing antiparallel cis XIX -A5-B14 : T3P-A pairing antiparallel one_hbond -A6-B13 : G-C Ww/Ww pairing antiparallel cis XIX -A7-B12 : C-G Ww/Ww pairing antiparallel cis XIX -A8-B11 : T-A Ww/Ww pairing antiparallel cis -A9-B10 : C-G Ww/Ww pairing antiparallel cis XIX diff --git a/MCdata/1c2w_MC b/MCdata/1c2w_MC deleted file mode 100644 index e0386f6d2c17f3dcf1633c0aafea9897e8e1a119..0000000000000000000000000000000000000000 --- a/MCdata/1c2w_MC +++ /dev/null @@ -1,6098 +0,0 @@ -Residue conformations ------------------------------------------- -B1 : G C3p_endo anti -B2 : G C3p_endo anti -B3 : U C3p_endo anti -B4 : U C3p_endo anti -B5 : A C3p_endo anti -B6 : A C3p_endo anti -B7 : G C3p_endo anti -B8 : C C3p_endo anti -B9 : G C3p_endo anti -B10 : A C3p_endo syn -B11 : C C3p_endo syn -B12 : U C3p_endo anti -B13 : A C3p_endo anti -B14 : A C3p_endo anti -B15 : G C3p_endo anti -B16 : C C3p_endo anti -B17 : G C3p_endo anti -B18 : U C3p_endo anti -B19 : A C3p_endo anti -B20 : C C3p_endo anti -B21 : A C3p_endo anti -B22 : C C3p_endo anti -B23 : G C3p_endo anti -B24 : G C3p_endo anti -B25 : U C3p_endo anti -B26 : G C3p_endo anti -B27 : G C3p_endo anti -B28 : A C3p_endo anti -B29 : U C3p_endo anti -B30 : G C3p_endo anti -B31 : C C3p_endo anti -B32 : C C3p_endo anti -B33 : C C3p_endo anti -B34 : U C3p_endo syn -B35 : G C3p_endo anti -B36 : G C3p_endo anti -B37 : C C3p_endo anti -B38 : A C3p_endo anti -B39 : G C3p_endo anti -B40 : U C3p_endo anti -B41 : C C3p_endo anti -B42 : A C3p_endo anti -B43 : G C3p_endo anti -B44 : A C3p_endo anti -B45 : G C3p_endo anti -B46 : G C3p_endo anti -B47 : C C3p_endo anti -B48 : G C3p_endo anti -B49 : A C3p_endo anti -B50 : U C3p_endo anti -B51 : G C3p_endo anti -B52 : A C3p_endo anti -B53 : A C3p_endo syn -B54 : G C3p_endo anti -B55 : G C3p_endo anti -B56 : A C3p_endo anti -B57 : C C3p_endo anti -B58 : G C3p_endo anti -B59 : U C3p_endo anti -B60 : G C3p_endo syn -B61 : C C3p_endo anti -B62 : U C3p_endo anti -B63 : A C3p_endo anti -B64 : A C3p_endo syn -B65 : U C3p_endo anti -B66 : C C3p_endo anti -B67 : U C3p_endo anti -B68 : G C3p_endo anti -B69 : C C3p_endo anti -B70 : G C3p_endo anti -B71 : A C3p_endo anti -B72 : U C3p_endo anti -B73 : A C3p_endo anti -B74 : A C3p_endo anti -B75 : G C3p_endo syn -B76 : C C3p_endo anti -B77 : G C3p_endo anti -B78 : U C3p_endo anti -B79 : C C3p_endo anti -B80 : G C3p_endo anti -B81 : G C3p_endo anti -B82 : U C3p_endo anti -B83 : A C3p_endo syn -B84 : A C3p_endo syn -B85 : G C3p_endo anti -B86 : G C3p_endo anti -B87 : U C3p_endo anti -B88 : G C3p_endo anti -B89 : A C3p_endo anti -B90 : U C3p_endo anti -B91 : A C3p_endo anti -B92 : U C3p_endo anti -B93 : G C3p_endo anti -B94 : A C3p_endo syn -B95 : A C3p_endo anti -B96 : C C3p_endo anti -B97 : C C3p_endo anti -B98 : G C3p_endo syn -B99 : U C3p_endo anti -B100 : U C3p_endo anti -B101 : A C3p_endo syn -B102 : U C3p_endo anti -B103 : A C3p_endo syn -B104 : A C3p_endo anti -B105 : C C3p_endo anti -B106 : C C3p_endo anti -B107 : G C3p_endo anti -B108 : G C3p_endo anti -B109 : C C3p_endo anti -B110 : G C3p_endo anti -B111 : A C3p_endo anti -B112 : U C3p_endo anti -B113 : U C3p_endo anti -B114 : U C3p_endo anti -B115 : C C3p_endo anti -B116 : C C3p_endo anti -B117 : G C3p_endo anti -B118 : A C3p_endo anti -B119 : A C3p_endo anti -B120 : U C3p_endo anti -B121 : G C3p_endo anti -B122 : G C3p_endo anti -B123 : G C3p_endo anti -B124 : G C3p_endo anti -B125 : A C3p_endo anti -B126 : A C3p_endo anti -B127 : A C3p_endo anti -B128 : C C3p_endo anti -B129 : C C3p_endo anti -B130 : C C3p_endo anti -B131 : A C3p_endo anti -B132 : G C3p_endo anti -B133 : U C3p_endo anti -B134 : G C3p_endo anti -B135 : U C3p_endo anti -B136 : G C3p_endo anti -B137 : U C3p_endo anti -B138 : U C3p_endo anti -B139 : U C3p_endo syn -B140 : C C3p_endo anti -B141 : G C3p_endo syn -B142 : A C3p_endo anti -B143 : C C3p_endo anti -B144 : A C3p_endo anti -B145 : C C3p_endo anti -B146 : A C3p_endo anti -B147 : C C3p_endo anti -B148 : U C3p_endo anti -B149 : A C3p_endo anti -B150 : U C3p_endo anti -B151 : C C3p_endo anti -B152 : A C3p_endo anti -B153 : U C3p_endo anti -B154 : U C3p_endo anti -B155 : A C3p_endo anti -B156 : A C3p_endo anti -B157 : C C3p_endo anti -B158 : U C3p_endo anti -B159 : G C3p_endo anti -B160 : A C3p_endo anti -B161 : A C3p_endo anti -B162 : U C3p_endo anti -B163 : C C3p_endo anti -B164 : C C3p_endo anti -B165 : A C3p_endo anti -B166 : U C3p_endo anti -B167 : A C3p_endo anti -B168 : G C3p_endo anti -B169 : G C3p_endo anti -B170 : U C3p_endo anti -B171 : U C3p_endo anti -B172 : A C3p_endo anti -B173 : A C3p_endo anti -B174 : U C3p_endo anti -B175 : G C3p_endo anti -B176 : A C3p_endo anti -B177 : G C3p_endo syn -B178 : G C3p_endo syn -B179 : C C3p_endo anti -B180 : G C3p_endo anti -B181 : A C3p_endo anti -B182 : A C3p_endo anti -B183 : C C3p_endo anti -B184 : C C3p_endo anti -B185 : G C3p_endo anti -B186 : G C3p_endo anti -B187 : G C3p_endo anti -B188 : G C3p_endo anti -B189 : G C3p_endo anti -B190 : A C3p_endo anti -B191 : A C3p_endo anti -B192 : C C3p_endo anti -B193 : U C3p_endo anti -B194 : G C3p_endo anti -B195 : A C3p_endo anti -B196 : A C3p_endo anti -B197 : A C3p_endo anti -B198 : C C3p_endo anti -B199 : A C3p_endo anti -B200 : U C3p_endo anti -B201 : C C3p_endo anti -B202 : U C3p_endo anti -B203 : A C3p_endo anti -B204 : A C3p_endo anti -B205 : G C3p_endo anti -B206 : U C3p_endo anti -B207 : A C3p_endo anti -B208 : C C3p_endo anti -B209 : C C3p_endo anti -B210 : C C3p_endo anti -B211 : C C3p_endo anti -B212 : G C3p_endo anti -B213 : A C3p_endo syn -B214 : G C3p_endo syn -B215 : G C3p_endo anti -B216 : A C3p_endo anti -B217 : A C3p_endo anti -B218 : A C3p_endo anti -B219 : A C3p_endo anti -B220 : G C3p_endo syn -B221 : A C3p_endo syn -B222 : A C3p_endo anti -B223 : A C3p_endo syn -B224 : U C3p_endo anti -B225 : C C3p_endo anti -B226 : A C3p_endo anti -B227 : A C3p_endo syn -B228 : C C3p_endo anti -B229 : C C3p_endo anti -B230 : G C3p_endo anti -B231 : A C3p_endo anti -B232 : G C3p_endo syn -B233 : A C3p_endo anti -B234 : U C3p_endo anti -B235 : U C3p_endo anti -B236 : C C3p_endo anti -B237 : C C3p_endo anti -B238 : C C3p_endo anti -B239 : C C3p_endo anti -B240 : C C3p_endo anti -B241 : A C3p_endo syn -B242 : G C3p_endo syn -B243 : U C3p_endo anti -B244 : A C3p_endo anti -B245 : G C3p_endo anti -B246 : C C3p_endo anti -B247 : G C3p_endo anti -B248 : G C3p_endo anti -B249 : C C3p_endo anti -B250 : G C3p_endo anti -B251 : A C3p_endo anti -B252 : G C3p_endo anti -B253 : C C3p_endo anti -B254 : G C3p_endo syn -B255 : A C3p_endo syn -B256 : A C3p_endo anti -B257 : C C3p_endo anti -B258 : G C3p_endo anti -B259 : G C3p_endo anti -B260 : G C3p_endo anti -B261 : G C3p_endo anti -B262 : A C3p_endo anti -B263 : G C3p_endo syn -B264 : C C3p_endo anti -B265 : A C3p_endo anti -B266 : G C3p_endo anti -B267 : C C3p_endo anti -B268 : C C3p_endo anti -B269 : C C3p_endo syn -B270 : A C3p_endo anti -B271 : G C3p_endo anti -B272 : A C3p_endo anti -B273 : G C3p_endo anti -B274 : C C3p_endo anti -B275 : C C3p_endo anti -B276 : U C3p_endo anti -B277 : G C3p_endo syn -B278 : A C3p_endo anti -B279 : A C3p_endo syn -B280 : U C3p_endo anti -B281 : C C3p_endo anti -B282 : A C3p_endo anti -B283 : G C3p_endo anti -B284 : U C3p_endo anti -B285 : G C3p_endo anti -B286 : U C3p_endo anti -B287 : G C3p_endo anti -B288 : U C3p_endo anti -B289 : G C3p_endo anti -B290 : U C3p_endo anti -B291 : G C3p_endo anti -B292 : U C3p_endo anti -B293 : U C3p_endo anti -B294 : A C3p_endo anti -B295 : G C3p_endo anti -B296 : U C3p_endo anti -B297 : G C3p_endo anti -B298 : G C3p_endo syn -B299 : A C3p_endo anti -B300 : A C3p_endo syn -B301 : G C3p_endo anti -B302 : C C3p_endo anti -B303 : G C3p_endo anti -B304 : U C3p_endo anti -B305 : C C3p_endo anti -B306 : U C3p_endo anti -B307 : G C3p_endo anti -B308 : G C3p_endo anti -B309 : A C3p_endo anti -B310 : A C3p_endo anti -B311 : A C3p_endo anti -B312 : G C3p_endo anti -B313 : G C3p_endo anti -B314 : C C3p_endo anti -B315 : G C3p_endo anti -B316 : C C3p_endo anti -B317 : G C3p_endo anti -B318 : C C3p_endo anti -B319 : G C3p_endo anti -B320 : A C3p_endo anti -B321 : U C3p_endo anti -B322 : A C3p_endo syn -B323 : C C3p_endo anti -B324 : A C3p_endo anti -B325 : G C3p_endo anti -B326 : G C3p_endo anti -B327 : G C3p_endo anti -B328 : U C3p_endo anti -B329 : G C3p_endo anti -B330 : A C3p_endo anti -B331 : C C3p_endo anti -B332 : A C3p_endo syn -B333 : G C3p_endo anti -B334 : C C3p_endo anti -B335 : C C3p_endo anti -B336 : C C3p_endo anti -B337 : C C3p_endo anti -B338 : G C3p_endo syn -B339 : U C3p_endo syn -B340 : A C3p_endo anti -B341 : C C3p_endo anti -B342 : A C3p_endo anti -B343 : C C3p_endo anti -B344 : A C3p_endo anti -B345 : A C3p_endo anti -B346 : A C3p_endo anti -B347 : A C3p_endo anti -B348 : A C3p_endo anti -B349 : U C3p_endo anti -B350 : G C3p_endo anti -B351 : C C3p_endo anti -B352 : A C3p_endo anti -B353 : C C3p_endo anti -B354 : A C3p_endo anti -B355 : U C3p_endo anti -B356 : G C3p_endo anti -B357 : C C3p_endo anti -B358 : U C3p_endo anti -B359 : G C3p_endo anti -B360 : U C3p_endo anti -B361 : G C3p_endo syn -B362 : A C3p_endo anti -B363 : G C3p_endo anti -B364 : C C3p_endo anti -B365 : U C3p_endo anti -B366 : C C3p_endo anti -B367 : G C3p_endo anti -B368 : A C3p_endo syn -B369 : U C3p_endo anti -B370 : G C3p_endo anti -B371 : A C3p_endo anti -B372 : G C3p_endo syn -B373 : U C3p_endo anti -B374 : A C3p_endo syn -B375 : G C3p_endo anti -B376 : G C3p_endo anti -B377 : G C3p_endo anti -B378 : C C3p_endo anti -B379 : G C3p_endo anti -B380 : G C3p_endo anti -B381 : G C3p_endo anti -B382 : A C3p_endo anti -B383 : C C3p_endo anti -B384 : A C3p_endo syn -B385 : C C3p_endo anti -B386 : G C3p_endo anti -B387 : U C3p_endo anti -B388 : G C3p_endo anti -B389 : G C3p_endo anti -B390 : U C3p_endo anti -B391 : A C3p_endo anti -B392 : U C3p_endo anti -B393 : C C3p_endo anti -B394 : C C3p_endo anti -B395 : U C3p_endo anti -B396 : G C3p_endo anti -B397 : U C3p_endo anti -B398 : C C3p_endo anti -B399 : U C3p_endo anti -B400 : G C3p_endo anti -B401 : A C3p_endo syn -B402 : A C3p_endo anti -B403 : U C3p_endo anti -B404 : A C3p_endo syn -B405 : U C3p_endo anti -B406 : G C3p_endo anti -B407 : G C3p_endo anti -B408 : G C3p_endo anti -B409 : G C3p_endo anti -B410 : G C3p_endo anti -B411 : G C3p_endo anti -B412 : A C3p_endo anti -B413 : C C3p_endo anti -B414 : C C3p_endo anti -B415 : A C3p_endo anti -B416 : U C3p_endo anti -B417 : C C3p_endo anti -B418 : C C3p_endo anti -B419 : U C3p_endo anti -B420 : C C3p_endo anti -B421 : C C3p_endo anti -B422 : A C3p_endo anti -B423 : A C3p_endo anti -B424 : G C3p_endo anti -B425 : G C3p_endo anti -B426 : C C3p_endo anti -B427 : U C3p_endo anti -B428 : A C3p_endo anti -B429 : A C3p_endo anti -B430 : A C3p_endo anti -B431 : U C3p_endo anti -B432 : A C3p_endo syn -B433 : C C3p_endo anti -B434 : U C3p_endo anti -B435 : C C3p_endo anti -B436 : C C3p_endo anti -B437 : U C3p_endo anti -B438 : G C3p_endo anti -B439 : A C3p_endo anti -B440 : C C3p_endo anti -B441 : U C3p_endo anti -B442 : G C3p_endo anti -B443 : A C3p_endo anti -B444 : C C3p_endo anti -B445 : C C3p_endo anti -B446 : G C3p_endo anti -B447 : A C3p_endo anti -B448 : U C3p_endo anti -B449 : A C3p_endo syn -B450 : G C3p_endo syn -B451 : U C3p_endo anti -B452 : G C3p_endo anti -B453 : A C3p_endo anti -B454 : A C3p_endo anti -B455 : C C3p_endo anti -B456 : C C3p_endo anti -B457 : A C3p_endo syn -B458 : G C3p_endo anti -B459 : U C3p_endo anti -B460 : A C3p_endo anti -B461 : C C3p_endo anti -B462 : C C3p_endo anti -B463 : G C3p_endo anti -B464 : U C3p_endo anti -B465 : G C3p_endo syn -B466 : A C3p_endo anti -B467 : G C3p_endo anti -B468 : G C3p_endo anti -B469 : G C3p_endo anti -B470 : A C3p_endo anti -B471 : A C3p_endo anti -B472 : A C3p_endo anti -B473 : G C3p_endo anti -B474 : G C3p_endo anti -B475 : C C3p_endo anti -B476 : G C3p_endo anti -B477 : A C3p_endo syn -B478 : A C3p_endo anti -B479 : A C3p_endo anti -B480 : A C3p_endo anti -B481 : G C3p_endo syn -B482 : A C3p_endo syn -B483 : A C3p_endo anti -B484 : C C3p_endo anti -B485 : C C3p_endo anti -B486 : C C3p_endo anti -B487 : C C3p_endo anti -B488 : G C3p_endo anti -B489 : G C3p_endo syn -B490 : C C3p_endo anti -B491 : G C3p_endo anti -B492 : A C3p_endo syn -B493 : G C3p_endo anti -B494 : G C3p_endo anti -B495 : G C3p_endo anti -B496 : G C3p_endo anti -B497 : A C3p_endo syn -B498 : G C3p_endo anti -B499 : U C3p_endo anti -B500 : G C3p_endo syn -B501 : A C3p_endo anti -B502 : A C3p_endo anti -B503 : A C3p_endo anti -B504 : A C3p_endo anti -B505 : A C3p_endo syn -B506 : G C3p_endo anti -B507 : A C3p_endo anti -B508 : A C3p_endo syn -B509 : C C3p_endo anti -B510 : C C3p_endo anti -B511 : U C3p_endo anti -B512 : G C3p_endo anti -B513 : A C3p_endo syn -B514 : A C3p_endo anti -B515 : A C3p_endo anti -B516 : C C3p_endo anti -B517 : C C3p_endo anti -B518 : G C3p_endo anti -B519 : U C3p_endo anti -B520 : G C3p_endo anti -B521 : U C3p_endo anti -B522 : A C3p_endo anti -B523 : C C3p_endo anti -B524 : G C3p_endo anti -B525 : U C3p_endo anti -B526 : A C3p_endo anti -B527 : C C3p_endo anti -B528 : A C3p_endo syn -B529 : A C3p_endo anti -B530 : G C3p_endo anti -B531 : C C3p_endo anti -B532 : A C3p_endo anti -B533 : G C3p_endo anti -B534 : U C3p_endo anti -B535 : G C3p_endo anti -B536 : G C3p_endo anti -B537 : G C3p_endo syn -B538 : A C3p_endo anti -B539 : G C3p_endo anti -B540 : C C3p_endo anti -B541 : A C3p_endo anti -B542 : C C3p_endo anti -B543 : G C3p_endo anti -B544 : C C3p_endo anti -B545 : U C3p_endo anti -B546 : U C3p_endo anti -B547 : A C3p_endo anti -B548 : G C3p_endo anti -B549 : G C3p_endo anti -B550 : C C3p_endo anti -B551 : G C3p_endo anti -B552 : U C3p_endo anti -B553 : G C3p_endo anti -B554 : U C3p_endo anti -B555 : G C3p_endo anti -B556 : A C3p_endo anti -B557 : C C3p_endo anti -B558 : U C3p_endo anti -B559 : G C3p_endo anti -B560 : C C3p_endo anti -B561 : G C3p_endo anti -B562 : U C3p_endo anti -B563 : A C3p_endo anti -B564 : C C3p_endo anti -B565 : C C3p_endo anti -B566 : U C3p_endo anti -B567 : U C3p_endo anti -B568 : U C3p_endo anti -B569 : U C3p_endo anti -B570 : G C3p_endo anti -B571 : U C3p_endo anti -B572 : A C3p_endo anti -B573 : U C3p_endo anti -B574 : A C3p_endo anti -B575 : A C3p_endo anti -B576 : U C3p_endo anti -B577 : G C3p_endo syn -B578 : G C3p_endo anti -B579 : G C3p_endo anti -B580 : U C3p_endo anti -B581 : C C3p_endo anti -B582 : A C3p_endo anti -B583 : G C3p_endo anti -B584 : C C3p_endo anti -B585 : G C3p_endo anti -B586 : A C3p_endo syn -B587 : C C3p_endo syn -B588 : U C3p_endo anti -B589 : U C3p_endo anti -B590 : A C3p_endo anti -B591 : U C3p_endo anti -B592 : A C3p_endo anti -B593 : U C3p_endo anti -B594 : U C3p_endo anti -B595 : C C3p_endo anti -B596 : U C3p_endo anti -B597 : G C3p_endo anti -B598 : U C3p_endo anti -B599 : A C3p_endo anti -B600 : G C3p_endo anti -B601 : C C3p_endo anti -B602 : A C3p_endo anti -B603 : A C3p_endo anti -B604 : G C3p_endo anti -B605 : G C3p_endo anti -B606 : U C3p_endo anti -B607 : U C3p_endo anti -B608 : A C3p_endo syn -B609 : A C3p_endo syn -B610 : C C3p_endo anti -B611 : C C3p_endo anti -B612 : G C3p_endo anti -B613 : A C3p_endo anti -B614 : A C3p_endo anti -B615 : U C3p_endo anti -B616 : A C3p_endo anti -B617 : G C3p_endo anti -B618 : G C3p_endo anti -B619 : G C3p_endo anti -B620 : G C3p_endo syn -B621 : A C3p_endo anti -B622 : G C3p_endo anti -B623 : C C3p_endo anti -B624 : C C3p_endo anti -B625 : G C3p_endo anti -B626 : A C3p_endo anti -B627 : A C3p_endo syn -B628 : G C3p_endo anti -B629 : G C3p_endo anti -B630 : G C3p_endo anti -B631 : A C3p_endo anti -B632 : A C3p_endo anti -B633 : A C3p_endo syn -B634 : C C3p_endo anti -B635 : C C3p_endo anti -B636 : G C3p_endo anti -B637 : A C3p_endo anti -B638 : G C3p_endo anti -B639 : U C3p_endo anti -B640 : C C3p_endo anti -B641 : U C3p_endo anti -B642 : U C3p_endo anti -B643 : A C3p_endo anti -B644 : A C3p_endo anti -B645 : C C3p_endo anti -B646 : U C3p_endo anti -B647 : G C3p_endo anti -B648 : G C3p_endo anti -B649 : G C3p_endo anti -B650 : C C3p_endo anti -B651 : G C3p_endo anti -B652 : U C3p_endo anti -B653 : U C3p_endo anti -B654 : A C3p_endo anti -B655 : A C3p_endo anti -B656 : G C3p_endo anti -B657 : U C3p_endo anti -B658 : U C3p_endo anti -B659 : G C3p_endo anti -B660 : C C3p_endo anti -B661 : A C3p_endo anti -B662 : G C3p_endo anti -B663 : G C3p_endo anti -B664 : G C3p_endo anti -B665 : U C3p_endo anti -B666 : A C3p_endo anti -B667 : U C3p_endo anti -B668 : A C3p_endo anti -B669 : G C3p_endo anti -B670 : A C3p_endo syn -B671 : C C3p_endo anti -B672 : C C3p_endo anti -B673 : C C3p_endo anti -B674 : G C3p_endo syn -B675 : A C3p_endo anti -B676 : A C3p_endo syn -B677 : A C3p_endo anti -B678 : C C3p_endo anti -B679 : C C3p_endo anti -B680 : C C3p_endo anti -B681 : G C3p_endo anti -B682 : G C3p_endo anti -B683 : U C3p_endo anti -B684 : G C3p_endo syn -B685 : A C3p_endo anti -B686 : U C3p_endo anti -B687 : C C3p_endo anti -B688 : U C3p_endo anti -B689 : A C3p_endo anti -B690 : G C3p_endo anti -B691 : C C3p_endo anti -B692 : C C3p_endo anti -B693 : A C3p_endo anti -B694 : U C3p_endo anti -B695 : G C3p_endo anti -B696 : G C3p_endo anti -B697 : G C3p_endo anti -B698 : C C3p_endo anti -B699 : A C3p_endo anti -B700 : G C3p_endo anti -B701 : G C3p_endo anti -B702 : U C3p_endo anti -B703 : U C3p_endo anti -B704 : G C3p_endo syn -B705 : A C3p_endo syn -B706 : A C3p_endo anti -B707 : G C3p_endo anti -B708 : G C3p_endo anti -B709 : U C3p_endo anti -B710 : U C3p_endo anti -B711 : G C3p_endo anti -B712 : G C3p_endo anti -B713 : G C3p_endo anti -B714 : U C3p_endo anti -B715 : A C3p_endo anti -B716 : A C3p_endo anti -B717 : C C3p_endo anti -B718 : A C3p_endo anti -B719 : C C3p_endo anti -B720 : U C3p_endo anti -B721 : A C3p_endo anti -B722 : A C3p_endo anti -B723 : C C3p_endo anti -B724 : U C3p_endo anti -B725 : G C3p_endo syn -B726 : G C3p_endo anti -B727 : A C3p_endo syn -B728 : G C3p_endo syn -B729 : G C3p_endo anti -B730 : A C3p_endo anti -B731 : C C3p_endo anti -B732 : C C3p_endo anti -B733 : G C3p_endo anti -B734 : A C3p_endo anti -B735 : A C3p_endo anti -B736 : C C3p_endo anti -B737 : C C3p_endo anti -B738 : G C3p_endo anti -B739 : A C3p_endo anti -B740 : C C3p_endo anti -B741 : U C3p_endo anti -B742 : A C3p_endo anti -B743 : A C3p_endo anti -B744 : U C3p_endo anti -B745 : 7MG -B746 : PSU -B747 : 5MU -B748 : G C3p_endo syn -B749 : A C3p_endo anti -B750 : A C3p_endo anti -B751 : A C3p_endo anti -B752 : A C3p_endo anti -B753 : A C3p_endo anti -B754 : U C3p_endo anti -B755 : U C3p_endo anti -B756 : A C3p_endo anti -B757 : G C3p_endo anti -B758 : C C3p_endo anti -B759 : G C3p_endo anti -B760 : G C3p_endo anti -B761 : A C3p_endo anti -B762 : U C3p_endo syn -B763 : G C3p_endo anti -B764 : A C3p_endo anti -B765 : C C3p_endo anti -B766 : U C3p_endo anti -B767 : U C3p_endo anti -B768 : G C3p_endo anti -B769 : U C3p_endo anti -B770 : G C3p_endo anti -B771 : G C3p_endo anti -B772 : C C3p_endo anti -B773 : U C3p_endo anti -B774 : G C3p_endo anti -B775 : G C3p_endo anti -B776 : G C3p_endo anti -B777 : G C3p_endo anti -B778 : G C3p_endo anti -B779 : U C3p_endo anti -B780 : G C3p_endo anti -B781 : A C3p_endo anti -B782 : A C3p_endo anti -B783 : A C3p_endo anti -B784 : G C3p_endo anti -B785 : G C3p_endo syn -B786 : C C3p_endo anti -B787 : C C3p_endo anti -B788 : A C3p_endo anti -B789 : A C3p_endo syn -B790 : U C3p_endo anti -B791 : C C3p_endo anti -B792 : A C3p_endo anti -B793 : A C3p_endo anti -B794 : A C3p_endo anti -B795 : C C3p_endo anti -B796 : C C3p_endo anti -B797 : G C3p_endo anti -B798 : G C3p_endo anti -B799 : G C3p_endo anti -B800 : A C3p_endo syn -B801 : G C3p_endo anti -B802 : A C3p_endo syn -B803 : U C3p_endo syn -B804 : A C3p_endo syn -B805 : G C3p_endo anti -B806 : C C3p_endo anti -B807 : U C3p_endo syn -B808 : G C3p_endo anti -B809 : G C3p_endo anti -B810 : U C3p_endo anti -B811 : U C3p_endo syn -B812 : C C3p_endo anti -B813 : U C3p_endo anti -B814 : C C3p_endo anti -B815 : C C3p_endo anti -B816 : C C3p_endo anti -B817 : C C3p_endo anti -B818 : G C3p_endo anti -B819 : A C3p_endo syn -B820 : A C3p_endo syn -B821 : A C3p_endo syn -B822 : G C3p_endo anti -B823 : C C3p_endo anti -B824 : U C3p_endo anti -B825 : A C3p_endo anti -B826 : U C3p_endo anti -B827 : U C3p_endo anti -B828 : U C3p_endo anti -B829 : A C3p_endo anti -B830 : G C3p_endo anti -B831 : G C3p_endo anti -B832 : U C3p_endo anti -B833 : A C3p_endo anti -B834 : G C3p_endo anti -B835 : C C3p_endo anti -B836 : G C3p_endo anti -B837 : C C3p_endo anti -B838 : C C3p_endo anti -B839 : U C3p_endo anti -B840 : C C3p_endo anti -B841 : G C3p_endo anti -B842 : U C3p_endo anti -B843 : G C3p_endo anti -B844 : A C3p_endo anti -B845 : A C3p_endo anti -B846 : U C3p_endo anti -B847 : U C3p_endo anti -B848 : C C3p_endo anti -B849 : A C3p_endo anti -B850 : U C3p_endo anti -B851 : C C3p_endo anti -B852 : U C3p_endo anti -B853 : C C3p_endo anti -B854 : C C3p_endo anti -B855 : G C3p_endo anti -B856 : G C3p_endo anti -B857 : G C3p_endo anti -B858 : G C3p_endo anti -B859 : G C3p_endo syn -B860 : U C3p_endo anti -B861 : A C3p_endo syn -B862 : G C3p_endo anti -B863 : A C3p_endo syn -B864 : G C3p_endo anti -B865 : C C3p_endo anti -B866 : A C3p_endo anti -B867 : C C3p_endo anti -B868 : U C3p_endo anti -B869 : G C3p_endo anti -B870 : U C3p_endo anti -B871 : U C3p_endo anti -B872 : U C3p_endo anti -B873 : C C3p_endo anti -B874 : G C3p_endo anti -B875 : G C3p_endo anti -B876 : C C3p_endo anti -B877 : A C3p_endo anti -B878 : A C3p_endo syn -B879 : G C3p_endo anti -B880 : G C3p_endo anti -B881 : G C3p_endo anti -B882 : G C3p_endo anti -B883 : G C3p_endo anti -B884 : U C3p_endo anti -B885 : C C3p_endo anti -B886 : A C3p_endo anti -B887 : U C3p_endo anti -B888 : C C3p_endo anti -B889 : C C3p_endo anti -B890 : C C3p_endo anti -B891 : G C3p_endo anti -B892 : A C3p_endo anti -B893 : C C3p_endo anti -B894 : U C3p_endo anti -B895 : U C3p_endo anti -B896 : A C3p_endo anti -B897 : C C3p_endo anti -B898 : C C3p_endo anti -B899 : A C3p_endo anti -B900 : A C3p_endo syn -B901 : C C3p_endo anti -B902 : C C3p_endo anti -B903 : C C3p_endo anti -B904 : G C3p_endo anti -B905 : A C3p_endo anti -B906 : U C3p_endo anti -B907 : G C3p_endo anti -B908 : C C3p_endo anti -B909 : A C3p_endo anti -B910 : A C3p_endo anti -B911 : A C3p_endo anti -B912 : C C3p_endo anti -B913 : U C3p_endo anti -B914 : G C3p_endo anti -B915 : C C3p_endo anti -B916 : G C3p_endo anti -B917 : A C3p_endo anti -B918 : A C3p_endo anti -B919 : U C3p_endo anti -B920 : A C3p_endo anti -B921 : C C3p_endo anti -B922 : C C3p_endo anti -B923 : G C3p_endo anti -B924 : G C3p_endo anti -B925 : A C3p_endo anti -B926 : G C3p_endo anti -B927 : A C3p_endo syn -B928 : A C3p_endo anti -B929 : U C3p_endo anti -B930 : G C3p_endo anti -B931 : U C3p_endo anti -B932 : U C3p_endo anti -B933 : A C3p_endo syn -B934 : U C3p_endo anti -B935 : C C3p_endo anti -B936 : A C3p_endo anti -B937 : C C3p_endo anti -B938 : G C3p_endo anti -B939 : G C3p_endo anti -B940 : G C3p_endo anti -B941 : A C3p_endo anti -B942 : G C3p_endo anti -B943 : A C3p_endo syn -B944 : C C3p_endo anti -B945 : A C3p_endo anti -B946 : C C3p_endo anti -B947 : A C3p_endo anti -B948 : C C3p_endo anti -B949 : G C3p_endo anti -B950 : G C3p_endo anti -B951 : C C3p_endo anti -B952 : G C3p_endo anti -B953 : G C3p_endo anti -B954 : G C3p_endo anti -B955 : U C3p_endo anti -B956 : G C3p_endo anti -B957 : C C3p_endo anti -B958 : U C3p_endo anti -B959 : A C3p_endo anti -B960 : A C3p_endo anti -B961 : C C3p_endo anti -B962 : G C3p_endo anti -B963 : U C3p_endo anti -B964 : C C3p_endo anti -B965 : C C3p_endo anti -B966 : G C3p_endo anti -B967 : U C3p_endo anti -B968 : C C3p_endo anti -B969 : G C3p_endo anti -B970 : U C3p_endo anti -B971 : G C3p_endo anti -B972 : A C3p_endo syn -B973 : A C3p_endo syn -B974 : G C3p_endo anti -B975 : A C3p_endo syn -B976 : G C3p_endo anti -B977 : G C3p_endo anti -B978 : G C3p_endo anti -B979 : A C3p_endo anti -B980 : A C3p_endo anti -B981 : A C3p_endo anti -B982 : C C3p_endo anti -B983 : A C3p_endo anti -B984 : A C3p_endo anti -B985 : C C3p_endo anti -B986 : C C3p_endo anti -B987 : C C3p_endo anti -B988 : A C3p_endo syn -B989 : G C3p_endo anti -B990 : A C3p_endo anti -B991 : C C3p_endo anti -B992 : C C3p_endo anti -B993 : G C3p_endo anti -B994 : C C3p_endo anti -B995 : C C3p_endo anti -B996 : A C3p_endo anti -B997 : G C3p_endo anti -B998 : C C3p_endo anti -B999 : U C3p_endo anti -B1000 : A C3p_endo anti -B1001 : A C3p_endo anti -B1002 : G C3p_endo anti -B1003 : G C3p_endo anti -B1004 : U C3p_endo anti -B1005 : C C3p_endo anti -B1006 : C C3p_endo anti -B1007 : C C3p_endo anti -B1008 : A C3p_endo anti -B1009 : A C3p_endo anti -B1010 : A C3p_endo syn -B1011 : G C3p_endo anti -B1012 : U C3p_endo anti -B1013 : C C3p_endo anti -B1014 : A C3p_endo anti -B1015 : U C3p_endo anti -B1016 : G C3p_endo anti -B1017 : G C3p_endo anti -B1018 : U C3p_endo anti -B1019 : U C3p_endo anti -B1020 : A C3p_endo anti -B1021 : A C3p_endo anti -B1022 : G C3p_endo anti -B1023 : U C3p_endo anti -B1024 : G C3p_endo syn -B1025 : G C3p_endo anti -B1026 : G C3p_endo anti -B1027 : A C3p_endo anti -B1028 : A C3p_endo anti -B1029 : A C3p_endo syn -B1030 : C C3p_endo anti -B1031 : G C3p_endo anti -B1032 : A C3p_endo anti -B1033 : U C3p_endo anti -B1034 : G C3p_endo anti -B1035 : U C3p_endo anti -B1036 : G C3p_endo anti -B1037 : G C3p_endo anti -B1038 : G C3p_endo anti -B1039 : A C3p_endo anti -B1040 : A C3p_endo anti -B1041 : G C3p_endo anti -B1042 : G C3p_endo anti -B1043 : C C3p_endo anti -B1044 : C C3p_endo anti -B1045 : C C3p_endo anti -B1046 : A C3p_endo anti -B1047 : G C3p_endo anti -B1048 : A C3p_endo anti -B1049 : C C3p_endo anti -B1050 : A C3p_endo anti -B1051 : G C3p_endo anti -B1052 : C C3p_endo anti -B1053 : C C3p_endo anti -B1054 : A C3p_endo anti -B1055 : G C2p_exo anti -B1056 : G C3p_endo anti -B1057 : A C4p_exo anti -B1058 : U C3p_endo anti -B1059 : G C3p_endo anti -B1060 : U C3p_exo anti -B1061 : U C2p_endo anti -B1062 : G C3p_endo anti -B1063 : G C3p_endo anti -B1064 : C C3p_endo anti -B1065 : U C3p_endo anti -B1066 : U C3p_endo anti -B1067 : A C4p_exo anti -B1068 : G C3p_endo anti -B1069 : A C2p_endo syn -B1070 : A C1p_exo anti -B1071 : G C3p_endo anti -B1072 : C C3p_endo anti -B1073 : A C3p_endo anti -B1074 : G C3p_endo anti -B1075 : C C3p_endo anti -B1076 : C C3p_endo anti -B1077 : A C3p_endo anti -B1078 : U C3p_endo anti -B1079 : C C3p_endo anti -B1080 : A C3p_endo anti -B1081 : U C3p_endo anti -B1082 : U C4p_exo anti -B1083 : U C2p_exo anti -B1084 : A C3p_endo anti -B1085 : A C3p_endo anti -B1086 : A C3p_endo syn -B1087 : G C3p_endo anti -B1088 : A C3p_exo syn -B1089 : A C2p_endo anti -B1090 : A C3p_endo anti -B1091 : G C2p_exo anti -B1092 : C C3p_endo anti -B1093 : G C3p_endo anti -B1094 : U C3p_endo anti -B1095 : A C3p_endo anti -B1096 : A C3p_endo anti -B1097 : U C3p_endo anti -B1098 : A C3p_endo anti -B1099 : G C3p_endo anti -B1100 : C C3p_endo anti -B1101 : U C3p_endo anti -B1102 : C C3p_endo anti -B1103 : A C3p_endo anti -B1104 : C C2p_exo anti -B1105 : U C3p_endo anti -B1106 : G C3p_endo anti -B1107 : G C3p_endo anti -B1108 : U C3p_endo anti -B1109 : C C3p_endo anti -B1110 : G C3p_endo syn -B1111 : A C3p_endo anti -B1112 : G C3p_endo anti -B1113 : U C3p_endo anti -B1114 : C C3p_endo anti -B1115 : G C3p_endo anti -B1116 : G C3p_endo anti -B1117 : C C3p_endo anti -B1118 : C C3p_endo anti -B1119 : U C3p_endo anti -B1120 : G C3p_endo anti -B1121 : C C3p_endo anti -B1122 : G C3p_endo anti -B1123 : C C3p_endo anti -B1124 : G C3p_endo anti -B1125 : G C3p_endo anti -B1126 : A C3p_endo anti -B1127 : A C3p_endo anti -B1128 : G C3p_endo syn -B1129 : A C3p_endo anti -B1130 : U C3p_endo anti -B1131 : G C3p_endo anti -B1132 : U C3p_endo anti -B1133 : A C3p_endo anti -B1134 : A C3p_endo anti -B1135 : C C3p_endo anti -B1136 : G C3p_endo anti -B1137 : G C3p_endo anti -B1138 : G C3p_endo anti -B1139 : G C3p_endo anti -B1140 : C C3p_endo anti -B1141 : U C3p_endo anti -B1142 : A C3p_endo syn -B1143 : A C3p_endo anti -B1144 : A C3p_endo anti -B1145 : C C3p_endo anti -B1146 : C C3p_endo anti -B1147 : A C3p_endo anti -B1148 : U C3p_endo anti -B1149 : G C3p_endo anti -B1150 : C C3p_endo anti -B1151 : A C3p_endo anti -B1152 : C C3p_endo anti -B1153 : C C3p_endo anti -B1154 : G C3p_endo anti -B1155 : A C3p_endo anti -B1156 : A C3p_endo anti -B1157 : G C3p_endo anti -B1158 : C C3p_endo anti -B1159 : U C3p_endo anti -B1160 : G C3p_endo anti -B1161 : C C3p_endo anti -B1162 : G C3p_endo anti -B1163 : G C3p_endo anti -B1164 : C C3p_endo anti -B1165 : A C3p_endo anti -B1166 : G C3p_endo anti -B1167 : C C3p_endo anti -B1168 : G C3p_endo anti -B1169 : A C3p_endo anti -B1170 : C C3p_endo anti -B1171 : G C3p_endo anti -B1172 : C C3p_endo anti -B1173 : U C3p_endo anti -B1174 : U C3p_endo anti -B1175 : A C3p_endo anti -B1176 : U C3p_endo anti -B1177 : G C3p_endo anti -B1178 : C C3p_endo anti -B1179 : G C3p_endo anti -B1180 : U C3p_endo anti -B1181 : U C3p_endo anti -B1182 : G C3p_endo anti -B1183 : U C3p_endo anti -B1184 : U C3p_endo anti -B1185 : G C3p_endo anti -B1186 : G C3p_endo anti -B1187 : G C3p_endo anti -B1188 : U C3p_endo anti -B1189 : A C3p_endo anti -B1190 : G C3p_endo anti -B1191 : G C3p_endo anti -B1192 : G C3p_endo anti -B1193 : G C3p_endo anti -B1194 : A C3p_endo anti -B1195 : G C3p_endo anti -B1196 : C C3p_endo anti -B1197 : G C3p_endo anti -B1198 : U C3p_endo anti -B1199 : U C3p_endo anti -B1200 : C C3p_endo anti -B1201 : U C3p_endo anti -B1202 : G C3p_endo anti -B1203 : U C3p_endo anti -B1204 : A C3p_endo anti -B1205 : A C3p_endo anti -B1206 : G C3p_endo anti -B1207 : C C3p_endo anti -B1208 : C C3p_endo anti -B1209 : U C3p_endo anti -B1210 : G C3p_endo anti -B1211 : C C3p_endo anti -B1212 : G C3p_endo anti -B1213 : A C3p_endo syn -B1214 : A C3p_endo syn -B1215 : G C3p_endo anti -B1216 : G C3p_endo anti -B1217 : U C3p_endo anti -B1218 : G C3p_endo anti -B1219 : U C3p_endo anti -B1220 : G C3p_endo anti -B1221 : C C3p_endo anti -B1222 : U C3p_endo anti -B1223 : G C3p_endo syn -B1224 : U C3p_endo anti -B1225 : G C3p_endo anti -B1226 : A C3p_endo anti -B1227 : G C3p_endo anti -B1228 : G C3p_endo anti -B1229 : C C3p_endo anti -B1230 : A C3p_endo anti -B1231 : U C3p_endo anti -B1232 : G C3p_endo anti -B1233 : C C3p_endo anti -B1234 : U C3p_endo anti -B1235 : G C3p_endo anti -B1236 : G C3p_endo syn -B1237 : A C3p_endo anti -B1238 : G C3p_endo anti -B1239 : G C3p_endo anti -B1240 : U C3p_endo anti -B1241 : A C3p_endo anti -B1242 : U C3p_endo anti -B1243 : C C3p_endo anti -B1244 : A C3p_endo anti -B1245 : G C3p_endo anti -B1246 : A C3p_endo anti -B1247 : A C3p_endo anti -B1248 : G C3p_endo anti -B1249 : U C3p_endo anti -B1250 : G C3p_endo anti -B1251 : C C3p_endo syn -B1252 : G C3p_endo anti -B1253 : A C3p_endo anti -B1254 : A C3p_endo anti -B1255 : U C3p_endo syn -B1256 : G C3p_endo anti -B1257 : C C3p_endo anti -B1258 : U C3p_endo anti -B1259 : G C3p_endo anti -B1260 : A C3p_endo anti -B1261 : C C3p_endo anti -B1262 : A C3p_endo anti -B1263 : U C3p_endo anti -B1264 : A C3p_endo anti -B1265 : A C3p_endo anti -B1266 : G C3p_endo anti -B1267 : U C3p_endo anti -B1268 : A C3p_endo anti -B1269 : A C3p_endo anti -B1270 : C C3p_endo anti -B1271 : G C3p_endo anti -B1272 : A C3p_endo anti -B1273 : U C3p_endo anti -B1274 : A C3p_endo anti -B1275 : A C3p_endo anti -B1276 : A C3p_endo anti -B1277 : G C3p_endo anti -B1278 : C C3p_endo anti -B1279 : G C3p_endo anti -B1280 : G C3p_endo anti -B1281 : G C3p_endo anti -B1282 : U C3p_endo anti -B1283 : G C3p_endo anti -B1284 : A C3p_endo anti -B1285 : A C3p_endo anti -B1286 : A C3p_endo anti -B1287 : A C3p_endo anti -B1288 : G C3p_endo anti -B1289 : C C3p_endo anti -B1290 : C C3p_endo anti -B1291 : C C3p_endo anti -B1292 : G C3p_endo anti -B1293 : C C3p_endo anti -B1294 : U C3p_endo anti -B1295 : C C3p_endo anti -B1296 : G C3p_endo anti -B1297 : C C3p_endo anti -B1298 : C C3p_endo anti -B1299 : G C3p_endo anti -B1300 : G C3p_endo anti -B1301 : A C3p_endo anti -B1302 : A C3p_endo anti -B1303 : G C3p_endo anti -B1304 : A C3p_endo anti -B1305 : C C3p_endo anti -B1306 : C C3p_endo anti -B1307 : A C3p_endo anti -B1308 : A C3p_endo syn -B1309 : G C3p_endo anti -B1310 : G C3p_endo syn -B1311 : G C3p_endo anti -B1312 : U C3p_endo anti -B1313 : U C3p_endo anti -B1314 : C C3p_endo anti -B1315 : C C3p_endo anti -B1316 : U C3p_endo anti -B1317 : G C3p_endo anti -B1318 : U C3p_endo anti -B1319 : C C3p_endo anti -B1320 : C C3p_endo anti -B1321 : A C3p_endo syn -B1322 : A C3p_endo syn -B1323 : C C3p_endo anti -B1324 : G C3p_endo anti -B1325 : U C3p_endo anti -B1326 : U C3p_endo anti -B1327 : A C3p_endo syn -B1328 : A C3p_endo syn -B1329 : U C3p_endo anti -B1330 : C C3p_endo anti -B1331 : G C3p_endo anti -B1332 : G C3p_endo anti -B1333 : G C3p_endo anti -B1334 : G C3p_endo anti -B1335 : C C3p_endo anti -B1336 : A C3p_endo anti -B1337 : G C3p_endo anti -B1338 : G C3p_endo anti -B1339 : G C3p_endo anti -B1340 : U C3p_endo syn -B1341 : G C3p_endo anti -B1342 : A C3p_endo anti -B1343 : G C3p_endo anti -B1344 : U C3p_endo anti -B1345 : C C3p_endo anti -B1346 : G C3p_endo anti -B1347 : A C3p_endo anti -B1348 : C C3p_endo anti -B1349 : C C3p_endo anti -B1350 : C C3p_endo anti -B1351 : C C3p_endo anti -B1352 : U C3p_endo anti -B1353 : A C3p_endo syn -B1354 : A C3p_endo anti -B1355 : G C3p_endo anti -B1356 : G C3p_endo anti -B1357 : C C3p_endo anti -B1358 : G C3p_endo syn -B1359 : A C3p_endo syn -B1360 : G C3p_endo syn -B1361 : G C3p_endo anti -B1362 : C C3p_endo anti -B1363 : C C3p_endo anti -B1364 : G C3p_endo anti -B1365 : A C3p_endo anti -B1366 : A C3p_endo anti -B1367 : A C3p_endo anti -B1368 : G C3p_endo anti -B1369 : G C3p_endo anti -B1370 : C C3p_endo anti -B1371 : G C3p_endo anti -B1372 : U C3p_endo anti -B1373 : A C3p_endo syn -B1374 : G C3p_endo anti -B1375 : U C3p_endo anti -B1376 : C C3p_endo anti -B1377 : G C3p_endo anti -B1378 : A C3p_endo anti -B1379 : U C3p_endo anti -B1380 : G C3p_endo anti -B1381 : G C3p_endo anti -B1382 : G C3p_endo anti -B1383 : A C3p_endo anti -B1384 : A C3p_endo anti -B1385 : A C3p_endo anti -B1386 : C C3p_endo anti -B1387 : A C3p_endo anti -B1388 : G C3p_endo anti -B1389 : G C3p_endo anti -B1390 : U C3p_endo anti -B1391 : U C3p_endo anti -B1392 : A C3p_endo anti -B1393 : A C3p_endo anti -B1394 : U C3p_endo anti -B1395 : A C3p_endo anti -B1396 : U C3p_endo anti -B1397 : U C3p_endo anti -B1398 : C C3p_endo anti -B1399 : C C3p_endo anti -B1400 : U C3p_endo anti -B1401 : G C3p_endo anti -B1402 : U C3p_endo anti -B1403 : A C3p_endo anti -B1404 : C C3p_endo anti -B1405 : U C3p_endo anti -B1406 : U C3p_endo anti -B1407 : G C3p_endo anti -B1408 : G C3p_endo anti -B1409 : U C3p_endo anti -B1410 : G C3p_endo anti -B1411 : U C3p_endo anti -B1412 : U C3p_endo anti -B1413 : A C3p_endo anti -B1414 : C C3p_endo anti -B1415 : U C3p_endo anti -B1416 : G C3p_endo anti -B1417 : C C3p_endo anti -B1418 : G C3p_endo anti -B1419 : A C3p_endo anti -B1420 : A C3p_endo anti -B1421 : G C3p_endo anti -B1422 : G C3p_endo anti -B1423 : G C3p_endo anti -B1424 : G C3p_endo anti -B1425 : G C3p_endo syn -B1426 : G C3p_endo anti -B1427 : A C3p_endo anti -B1428 : C C3p_endo anti -B1429 : G C3p_endo anti -B1430 : C C3p_endo anti -B1431 : A C3p_endo anti -B1432 : G C3p_endo anti -B1433 : A C3p_endo anti -B1434 : A C3p_endo anti -B1435 : G C3p_endo anti -B1436 : G C3p_endo anti -B1437 : C C3p_endo anti -B1438 : U C3p_endo anti -B1439 : A C3p_endo syn -B1440 : U C3p_endo anti -B1441 : G C3p_endo anti -B1442 : U C3p_endo anti -B1443 : U C3p_endo anti -B1444 : G C3p_endo anti -B1445 : G C3p_endo syn -B1446 : C C3p_endo anti -B1447 : C C3p_endo anti -B1448 : G C3p_endo anti -B1449 : G C3p_endo anti -B1450 : G C3p_endo anti -B1451 : C C3p_endo anti -B1452 : G C3p_endo anti -B1453 : A C3p_endo anti -B1454 : C C3p_endo anti -B1455 : G C3p_endo anti -B1456 : G C3p_endo anti -B1457 : U C3p_endo anti -B1458 : U C3p_endo anti -B1459 : G C3p_endo anti -B1460 : U C3p_endo anti -B1461 : C C3p_endo anti -B1462 : C C3p_endo anti -B1463 : C C3p_endo anti -B1464 : G C3p_endo anti -B1465 : G C3p_endo anti -B1466 : U C3p_endo anti -B1467 : U C3p_endo anti -B1468 : U C3p_endo anti -B1469 : A C3p_endo syn -B1470 : A C3p_endo syn -B1471 : G C3p_endo anti -B1472 : C C3p_endo anti -B1473 : G C3p_endo anti -B1474 : U C3p_endo anti -B1475 : G C3p_endo anti -B1476 : U C3p_endo anti -B1477 : A C3p_endo syn -B1478 : G C3p_endo anti -B1479 : G C3p_endo anti -B1480 : C C3p_endo anti -B1481 : U C3p_endo anti -B1482 : G C3p_endo anti -B1483 : G C3p_endo anti -B1484 : U C3p_endo anti -B1485 : U C3p_endo anti -B1486 : U C3p_endo anti -B1487 : U C3p_endo anti -B1488 : C C3p_endo anti -B1489 : C C3p_endo anti -B1490 : A C3p_endo anti -B1491 : G C3p_endo anti -B1492 : G C3p_endo anti -B1493 : C C3p_endo anti -B1494 : A C3p_endo anti -B1495 : A C3p_endo anti -B1496 : A C3p_endo anti -B1497 : U C3p_endo anti -B1498 : C C3p_endo anti -B1499 : C C3p_endo anti -B1500 : G C3p_endo anti -B1501 : G C3p_endo anti -B1502 : A C3p_endo anti -B1503 : A C3p_endo anti -B1504 : A C3p_endo anti -B1505 : A C3p_endo anti -B1506 : U C3p_endo anti -B1507 : C C3p_endo anti -B1508 : A C3p_endo anti -B1509 : A C3p_endo anti -B1510 : G C3p_endo anti -B1511 : G C3p_endo anti -B1512 : C C3p_endo anti -B1513 : U C3p_endo anti -B1514 : G C3p_endo anti -B1515 : A C3p_endo anti -B1516 : G C3p_endo anti -B1517 : G C3p_endo anti -B1518 : C C3p_endo anti -B1519 : G C3p_endo anti -B1520 : U C3p_endo anti -B1521 : G C3p_endo anti -B1522 : A C3p_endo syn -B1523 : U C3p_endo anti -B1524 : G C3p_endo anti -B1525 : A C3p_endo anti -B1526 : C C3p_endo anti -B1527 : G C3p_endo anti -B1528 : A C3p_endo anti -B1529 : G C3p_endo anti -B1530 : G C3p_endo anti -B1531 : C C3p_endo anti -B1532 : A C3p_endo anti -B1533 : C C3p_endo anti -B1534 : U C3p_endo anti -B1535 : A C3p_endo anti -B1536 : C C3p_endo anti -B1537 : G C3p_endo anti -B1538 : G C3p_endo anti -B1539 : U C3p_endo anti -B1540 : G C3p_endo anti -B1541 : C C3p_endo anti -B1542 : U C3p_endo anti -B1543 : G C3p_endo anti -B1544 : A C3p_endo anti -B1545 : A C3p_endo syn -B1546 : G C3p_endo syn -B1547 : C C3p_endo anti -B1548 : A C3p_endo anti -B1549 : A C3p_endo anti -B1550 : C C3p_endo anti -B1551 : A C3p_endo anti -B1552 : A C3p_endo anti -B1553 : A C3p_endo anti -B1554 : U C3p_endo anti -B1555 : G C3p_endo anti -B1556 : C C3p_endo anti -B1557 : C C3p_endo anti -B1558 : C C3p_endo anti -B1559 : U C3p_endo anti -B1560 : G C3p_endo syn -B1561 : C C3p_endo anti -B1562 : U C3p_endo anti -B1563 : U C3p_endo anti -B1564 : C C3p_endo anti -B1565 : C C3p_endo syn -B1566 : A C3p_endo anti -B1567 : G C3p_endo anti -B1568 : G C3p_endo anti -B1569 : A C3p_endo syn -B1570 : A C3p_endo anti -B1571 : A C3p_endo anti -B1572 : A C3p_endo anti -B1573 : G C3p_endo anti -B1574 : C C3p_endo anti -B1575 : C C3p_endo anti -B1576 : U C3p_endo anti -B1577 : C C3p_endo anti -B1578 : U C3p_endo anti -B1579 : A C3p_endo anti -B1580 : A C3p_endo anti -B1581 : G C3p_endo syn -B1582 : C C3p_endo anti -B1583 : A C3p_endo anti -B1584 : U C3p_endo anti -B1585 : C C3p_endo anti -B1586 : A C3p_endo syn -B1587 : G C3p_endo anti -B1588 : G C3p_endo anti -B1589 : U C3p_endo anti -B1590 : A C3p_endo anti -B1591 : A C3p_endo anti -B1592 : C C3p_endo anti -B1593 : A C3p_endo anti -B1594 : U C3p_endo anti -B1595 : C C3p_endo anti -B1596 : A C3p_endo anti -B1597 : A C3p_endo anti -B1598 : A C3p_endo anti -B1599 : U C3p_endo anti -B1600 : C C3p_endo anti -B1601 : G C3p_endo anti -B1602 : U C3p_endo anti -B1603 : A C3p_endo anti -B1604 : C C3p_endo anti -B1605 : C C3p_endo syn -B1606 : C C3p_endo anti -B1607 : C C3p_endo anti -B1608 : A C3p_endo anti -B1609 : A C3p_endo anti -B1610 : A C3p_endo syn -B1611 : C C3p_endo anti -B1612 : C C3p_endo anti -B1613 : G C3p_endo anti -B1614 : A C3p_endo anti -B1615 : C C3p_endo anti -B1616 : A C3p_endo anti -B1617 : C C3p_endo anti -B1618 : 1MA -B1619 : G C3p_endo anti -B1620 : G C3p_endo anti -B1621 : U C3p_endo anti -B1622 : G C3p_endo anti -B1623 : G C3p_endo anti -B1624 : U C3p_endo anti -B1625 : C C3p_endo anti -B1626 : A C3p_endo anti -B1627 : G C3p_endo anti -B1628 : G C3p_endo anti -B1629 : U C3p_endo anti -B1630 : A C3p_endo anti -B1631 : G C3p_endo anti -B1632 : A C3p_endo anti -B1633 : G C3p_endo anti -B1634 : A C3p_endo anti -B1635 : A C3p_endo anti -B1636 : U C3p_endo anti -B1637 : A C3p_endo anti -B1638 : C C3p_endo anti -B1639 : C C3p_endo anti -B1640 : A C3p_endo anti -B1641 : A C3p_endo syn -B1642 : G C3p_endo anti -B1643 : G C3p_endo anti -B1644 : C C3p_endo anti -B1645 : G C3p_endo anti -B1646 : C C3p_endo anti -B1647 : U C3p_endo anti -B1648 : U C3p_endo anti -B1649 : G C3p_endo anti -B1650 : A C3p_endo anti -B1651 : G C3p_endo anti -B1652 : A C3p_endo anti -B1653 : G C3p_endo anti -B1654 : A C3p_endo syn -B1655 : A C3p_endo syn -B1656 : C C3p_endo anti -B1657 : U C3p_endo anti -B1658 : C C3p_endo anti -B1659 : G C3p_endo anti -B1660 : G C3p_endo anti -B1661 : G C3p_endo anti -B1662 : U C3p_endo anti -B1663 : G C3p_endo anti -B1664 : A C3p_endo anti -B1665 : A C3p_endo anti -B1666 : G C3p_endo anti -B1667 : G C3p_endo anti -B1668 : A C3p_endo anti -B1669 : A C3p_endo anti -B1670 : C C3p_endo anti -B1671 : U C3p_endo anti -B1672 : A C3p_endo anti -B1673 : G C3p_endo anti -B1674 : G C3p_endo syn -B1675 : C C3p_endo anti -B1676 : A C3p_endo anti -B1677 : A C3p_endo anti -B1678 : A C3p_endo anti -B1679 : A C3p_endo syn -B1680 : U C3p_endo anti -B1681 : G C3p_endo anti -B1682 : G C3p_endo anti -B1683 : U C3p_endo anti -B1684 : G C3p_endo anti -B1685 : C C3p_endo anti -B1686 : C C3p_endo anti -B1687 : G C3p_endo anti -B1688 : U C3p_endo anti -B1689 : A C3p_endo anti -B1690 : A C3p_endo syn -B1691 : C C3p_endo anti -B1692 : U C3p_endo anti -B1693 : U C3p_endo anti -B1694 : C C3p_endo anti -B1695 : G C3p_endo syn -B1696 : G C3p_endo anti -B1697 : G C3p_endo anti -B1698 : A C3p_endo anti -B1699 : G C3p_endo anti -B1700 : A C3p_endo anti -B1701 : A C3p_endo anti -B1702 : G C3p_endo anti -B1703 : G C3p_endo anti -B1704 : C C3p_endo anti -B1705 : A C3p_endo anti -B1706 : C C3p_endo anti -B1707 : G C3p_endo anti -B1708 : C C3p_endo anti -B1709 : U C3p_endo anti -B1710 : G C3p_endo anti -B1711 : A C3p_endo anti -B1712 : U C3p_endo anti -B1713 : A C3p_endo anti -B1714 : U C3p_endo anti -B1715 : G C3p_endo anti -B1716 : U C3p_endo anti -B1717 : A C3p_endo anti -B1718 : G C3p_endo anti -B1719 : G C3p_endo syn -B1720 : U C3p_endo syn -B1721 : G C3p_endo anti -B1722 : A C3p_endo anti -B1723 : G C3p_endo syn -B1724 : G C3p_endo anti -B1725 : U C3p_endo anti -B1726 : C C3p_endo anti -B1727 : C C3p_endo anti -B1728 : C C3p_endo anti -B1729 : U C3p_endo anti -B1730 : C C3p_endo anti -B1731 : G C3p_endo anti -B1732 : C C3p_endo anti -B1733 : G C3p_endo anti -B1734 : G C3p_endo anti -B1735 : A C3p_endo anti -B1736 : U C3p_endo anti -B1737 : G C3p_endo anti -B1738 : G C3p_endo anti -B1739 : A C3p_endo anti -B1740 : G C3p_endo syn -B1741 : C C3p_endo anti -B1742 : U C3p_endo anti -B1743 : G C3p_endo anti -B1744 : A C3p_endo anti -B1745 : A C3p_endo anti -B1746 : A C3p_endo anti -B1747 : U C3p_endo anti -B1748 : C C3p_endo anti -B1749 : A C3p_endo anti -B1750 : G C3p_endo anti -B1751 : U C3p_endo anti -B1752 : C C3p_endo anti -B1753 : G C3p_endo anti -B1754 : A C3p_endo anti -B1755 : A C3p_endo anti -B1756 : G C3p_endo anti -B1757 : A C3p_endo anti -B1758 : U C3p_endo anti -B1759 : A C3p_endo anti -B1760 : C C3p_endo anti -B1761 : C C3p_endo anti -B1762 : A C3p_endo anti -B1763 : G C3p_endo syn -B1764 : C C3p_endo anti -B1765 : U C3p_endo anti -B1766 : G C3p_endo anti -B1767 : G C3p_endo anti -B1768 : C C3p_endo anti -B1769 : U C3p_endo anti -B1770 : G C3p_endo anti -B1771 : C C3p_endo anti -B1772 : A C3p_endo anti -B1773 : A C3p_endo anti -B1774 : C C3p_endo anti -B1775 : U C3p_endo anti -B1776 : G C3p_endo anti -B1777 : U C3p_endo anti -B1778 : U C3p_endo anti -B1779 : U C3p_endo anti -B1780 : A C3p_endo anti -B1781 : U C3p_endo anti -B1782 : U C3p_endo anti -B1783 : A C3p_endo anti -B1784 : A C3p_endo anti -B1785 : A C3p_endo anti -B1786 : A C3p_endo anti -B1787 : A C3p_endo anti -B1788 : C C3p_endo anti -B1789 : A C3p_endo anti -B1790 : C C3p_endo anti -B1791 : A C3p_endo anti -B1792 : G C3p_endo anti -B1793 : C C3p_endo anti -B1794 : A C3p_endo anti -B1795 : C C3p_endo anti -B1796 : U C3p_endo anti -B1797 : G C3p_endo anti -B1798 : U C3p_endo anti -B1799 : G C3p_endo anti -B1800 : C C3p_endo anti -B1801 : A C3p_endo anti -B1802 : A C3p_endo syn -B1803 : A C3p_endo syn -B1804 : C C3p_endo anti -B1805 : A C3p_endo anti -B1806 : C C3p_endo anti -B1807 : G C3p_endo syn -B1808 : A C3p_endo anti -B1809 : A C3p_endo anti -B1810 : A C3p_endo anti -B1811 : G C3p_endo anti -B1812 : U C3p_endo anti -B1813 : G C3p_endo anti -B1814 : G C3p_endo anti -B1815 : A C3p_endo syn -B1816 : C C3p_endo anti -B1817 : G C3p_endo syn -B1818 : U C3p_endo anti -B1819 : A C3p_endo syn -B1820 : U C3p_endo anti -B1821 : A C3p_endo anti -B1822 : C C3p_endo anti -B1823 : G C3p_endo anti -B1824 : G C3p_endo anti -B1825 : U C3p_endo anti -B1826 : G C3p_endo anti -B1827 : U C3p_endo anti -B1828 : G C3p_endo anti -B1829 : A C3p_endo anti -B1830 : C C3p_endo anti -B1831 : G C3p_endo anti -B1832 : C C3p_endo anti -B1833 : C C3p_endo anti -B1834 : U C3p_endo anti -B1835 : G C3p_endo anti -B1836 : C C3p_endo anti -B1837 : C C3p_endo anti -B1838 : C C3p_endo syn -B1839 : G C3p_endo syn -B1840 : G C3p_endo anti -B1841 : U C3p_endo anti -B1842 : G C3p_endo anti -B1843 : C C3p_endo anti -B1844 : C C3p_endo anti -B1845 : G C3p_endo anti -B1846 : G C3p_endo anti -B1847 : A C3p_endo anti -B1848 : A C3p_endo anti -B1849 : G C3p_endo anti -B1850 : G C3p_endo anti -B1851 : U C3p_endo anti -B1852 : U C3p_endo anti -B1853 : A C3p_endo anti -B1854 : A C3p_endo anti -B1855 : U C3p_endo anti -B1856 : U C3p_endo anti -B1857 : G C3p_endo anti -B1858 : A C3p_endo anti -B1859 : U C3p_endo anti -B1860 : G C3p_endo anti -B1861 : G C3p_endo anti -B1862 : G C3p_endo anti -B1863 : G C3p_endo anti -B1864 : U C3p_endo anti -B1865 : U C3p_endo anti -B1866 : A C3p_endo syn -B1867 : G C3p_endo anti -B1868 : C C3p_endo anti -B1869 : G C3p_endo anti -B1870 : C C3p_endo anti -B1871 : A C3p_endo anti -B1872 : A C3p_endo anti -B1873 : G C3p_endo anti -B1874 : C C3p_endo anti -B1875 : G C3p_endo anti -B1876 : A C3p_endo syn -B1877 : A C3p_endo anti -B1878 : G C3p_endo anti -B1879 : C C3p_endo anti -B1880 : U C3p_endo anti -B1881 : C C3p_endo anti -B1882 : U C3p_endo anti -B1883 : U C3p_endo anti -B1884 : G C3p_endo anti -B1885 : A C3p_endo anti -B1886 : U C3p_endo anti -B1887 : C C3p_endo anti -B1888 : G C3p_endo anti -B1889 : A C3p_endo anti -B1890 : A C3p_endo anti -B1891 : G C3p_endo syn -B1892 : C C3p_endo anti -B1893 : C C3p_endo anti -B1894 : C C3p_endo anti -B1895 : C C3p_endo anti -B1896 : G C3p_endo anti -B1897 : G C3p_endo anti -B1898 : U C3p_endo anti -B1899 : A C3p_endo anti -B1900 : A C3p_endo syn -B1901 : A C3p_endo anti -B1902 : C C3p_endo anti -B1903 : G C3p_endo anti -B1904 : G C3p_endo anti -B1905 : C C3p_endo anti -B1906 : G C3p_endo anti -B1907 : G C3p_endo anti -B1908 : C C3p_endo anti -B1909 : C C3p_endo anti -B1910 : G C3p_endo anti -B1911 : PSU -B1912 : A C3p_endo anti -B1913 : A C3p_endo anti -B1914 : C C3p_endo anti -B1915 : 5MU -B1916 : A C3p_endo anti -B1917 : PSU -B1918 : A C3p_endo anti -B1919 : A C3p_endo anti -B1920 : C C3p_endo anti -B1921 : G C3p_endo anti -B1922 : G C3p_endo anti -B1923 : U C3p_endo anti -B1924 : C C3p_endo anti -B1925 : C C3p_endo syn -B1926 : U C3p_endo anti -B1927 : A C3p_endo syn -B1928 : A C3p_endo syn -B1929 : G C3p_endo anti -B1930 : G C3p_endo syn -B1931 : U C3p_endo anti -B1932 : A C3p_endo anti -B1933 : G C3p_endo anti -B1934 : C C3p_endo anti -B1935 : G C3p_endo anti -B1936 : A C3p_endo anti -B1937 : A C3p_endo anti -B1938 : A C3p_endo anti -B1939 : 5MU -B1940 : U C3p_endo anti -B1941 : C C3p_endo anti -B1942 : C C3p_endo anti -B1943 : U C3p_endo syn -B1944 : U C3p_endo anti -B1945 : G C3p_endo anti -B1946 : U C3p_endo anti -B1947 : C C3p_endo anti -B1948 : G C3p_endo anti -B1949 : G C3p_endo anti -B1950 : G C3p_endo anti -B1951 : U C3p_endo syn -B1952 : A C3p_endo syn -B1953 : A C3p_endo anti -B1954 : G C3p_endo anti -B1955 : U C3p_endo anti -B1956 : U C3p_endo anti -B1957 : C C3p_endo anti -B1958 : C C3p_endo anti -B1959 : G C3p_endo anti -B1960 : A C3p_endo anti -B1961 : C C3p_endo anti -B1962 : C C3p_endo anti -B1963 : U C3p_endo anti -B1964 : G C3p_endo anti -B1965 : C C3p_endo anti -B1966 : A C3p_endo anti -B1967 : C C3p_endo anti -B1968 : G C3p_endo anti -B1969 : A C3p_endo anti -B1970 : A C3p_endo anti -B1971 : U C3p_endo anti -B1972 : G C3p_endo anti -B1973 : G C3p_endo anti -B1974 : C C3p_endo anti -B1975 : G C3p_endo anti -B1976 : U C3p_endo anti -B1977 : A C3p_endo syn -B1978 : A C3p_endo anti -B1979 : U C3p_endo anti -B1980 : G C3p_endo anti -B1981 : A C3p_endo anti -B1982 : U C3p_endo anti -B1983 : G C3p_endo anti -B1984 : G C3p_endo anti -B1985 : C C3p_endo anti -B1986 : C C3p_endo anti -B1987 : A C3p_endo anti -B1988 : G C3p_endo anti -B1989 : G C3p_endo anti -B1990 : C C3p_endo anti -B1991 : U C3p_endo anti -B1992 : G C3p_endo anti -B1993 : U C3p_endo anti -B1994 : C C3p_endo anti -B1995 : U C3p_endo anti -B1996 : C C3p_endo anti -B1997 : C C3p_endo anti -B1998 : A C3p_endo anti -B1999 : C C3p_endo anti -B2000 : C C3p_endo anti -B2001 : C C3p_endo anti -B2002 : G C3p_endo anti -B2003 : A C3p_endo anti -B2004 : G C3p_endo anti -B2005 : A C3p_endo anti -B2006 : C C3p_endo anti -B2007 : U C3p_endo anti -B2008 : C C3p_endo anti -B2009 : A C3p_endo anti -B2010 : G C3p_endo anti -B2011 : U C3p_endo anti -B2012 : G C3p_endo anti -B2013 : A C3p_endo anti -B2014 : A C3p_endo anti -B2015 : A C3p_endo anti -B2016 : U C3p_endo anti -B2017 : U C3p_endo anti -B2018 : G C3p_endo anti -B2019 : A C3p_endo anti -B2020 : A C3p_endo syn -B2021 : C C3p_endo syn -B2022 : U C3p_endo anti -B2023 : C C3p_endo anti -B2024 : G C3p_endo anti -B2025 : C C3p_endo anti -B2026 : U C3p_endo anti -B2027 : G C3p_endo anti -B2028 : U C3p_endo anti -B2029 : G C3p_endo syn -B2030 : 1MA -B2031 : A C3p_endo anti -B2032 : G C3p_endo anti -B2033 : A C3p_endo anti -B2034 : U C3p_endo anti -B2035 : G C3p_endo anti -B2036 : C C3p_endo anti -B2037 : A C3p_endo anti -B2038 : G C3p_endo anti -B2039 : U C3p_endo anti -B2040 : G C3p_endo anti -B2041 : U C3p_endo anti -B2042 : A C3p_endo anti -B2043 : C C3p_endo anti -B2044 : C C3p_endo anti -B2045 : C C3p_endo anti -B2046 : G C3p_endo anti -B2047 : C C3p_endo anti -B2048 : G C3p_endo anti -B2049 : G C3p_endo anti -B2050 : C C3p_endo anti -B2051 : A C3p_endo anti -B2052 : A C3p_endo anti -B2053 : G C3p_endo anti -B2054 : A C3p_endo anti -B2055 : C C3p_endo anti -B2056 : G C3p_endo anti -B2057 : G C3p_endo anti -B2058 : A C3p_endo syn -B2059 : A C3p_endo syn -B2060 : A C3p_endo anti -B2061 : G C3p_endo anti -B2062 : A C3p_endo anti -B2063 : C C3p_endo anti -B2064 : C C3p_endo anti -B2065 : C C3p_endo anti -B2066 : C C3p_endo anti -B2067 : G C3p_endo anti -B2068 : U C3p_endo anti -B2069 : 7MG -B2070 : A C3p_endo anti -B2071 : A C3p_endo anti -B2072 : C C3p_endo anti -B2073 : C C3p_endo anti -B2074 : U C3p_endo anti -B2075 : U C3p_endo anti -B2076 : U C3p_endo syn -B2077 : A C3p_endo anti -B2078 : C C3p_endo anti -B2079 : U C3p_endo anti -B2080 : A C3p_endo anti -B2081 : U C3p_endo anti -B2082 : A C3p_endo syn -B2083 : G C3p_endo anti -B2084 : C C3p_endo anti -B2085 : U C3p_endo anti -B2086 : U C3p_endo anti -B2087 : G C3p_endo anti -B2088 : A C3p_endo anti -B2089 : C C3p_endo anti -B2090 : A C3p_endo anti -B2091 : C C3p_endo anti -B2092 : U C3p_endo anti -B2093 : G C3p_endo anti -B2094 : A C3p_endo anti -B2095 : A C3p_endo anti -B2096 : C C3p_endo anti -B2097 : A C3p_endo anti -B2098 : U C3p_endo anti -B2099 : U C3p_endo anti -B2100 : G C3p_endo anti -B2101 : A C3p_endo anti -B2102 : G C3p_endo anti -B2103 : C C3p_endo anti -B2104 : C C3p_endo anti -B2105 : U C3p_endo anti -B2106 : U C3p_endo anti -B2107 : G C3p_endo anti -B2108 : A C3p_endo anti -B2109 : U C3p_endo anti -B2110 : G C3p_endo syn -B2111 : U C3p_endo anti -B2112 : G C3p_endo anti -B2113 : U C3p_endo syn -B2114 : A C3p_endo anti -B2115 : G C3p_endo anti -B2116 : G C3p_endo anti -B2117 : A C3p_endo anti -B2118 : U C3p_endo anti -B2119 : A C3p_endo anti -B2120 : G C3p_endo anti -B2121 : G C3p_endo anti -B2122 : U C3p_endo anti -B2123 : G C3p_endo anti -B2124 : G C3p_endo anti -B2125 : G C3p_endo anti -B2126 : A C3p_endo anti -B2127 : G C3p_endo anti -B2128 : G C3p_endo anti -B2129 : C C3p_endo anti -B2130 : U C3p_endo anti -B2131 : U C3p_endo anti -B2132 : U C3p_endo anti -B2133 : G C3p_endo anti -B2134 : A C3p_endo syn -B2135 : A C3p_endo anti -B2136 : G C3p_endo anti -B2137 : U C3p_endo anti -B2138 : G C3p_endo anti -B2139 : U C3p_endo syn -B2140 : G C3p_endo anti -B2141 : G C3p_endo anti -B2142 : A C3p_endo anti -B2143 : C C3p_endo anti -B2144 : G C3p_endo anti -B2145 : C C3p_endo anti -B2146 : C C3p_endo anti -B2147 : A C3p_endo anti -B2148 : G C3p_endo anti -B2149 : U C3p_endo anti -B2150 : C C3p_endo anti -B2151 : U C3p_endo anti -B2152 : G C3p_endo anti -B2153 : C C3p_endo anti -B2154 : A C3p_endo anti -B2155 : U C3p_endo anti -B2156 : G C3p_endo anti -B2157 : G C3p_endo anti -B2158 : A C3p_endo anti -B2159 : G C3p_endo anti -B2160 : C C3p_endo anti -B2161 : C C3p_endo anti -B2162 : G C3p_endo anti -B2163 : A C3p_endo anti -B2164 : C C3p_endo anti -B2165 : C C3p_endo anti -B2166 : U C3p_endo anti -B2167 : U C3p_endo anti -B2168 : G C3p_endo anti -B2169 : A C3p_endo anti -B2170 : A C3p_endo anti -B2171 : A C3p_endo anti -B2172 : U C3p_endo anti -B2173 : A C3p_endo anti -B2174 : C C3p_endo anti -B2175 : C C3p_endo anti -B2176 : A C3p_endo anti -B2177 : C C3p_endo anti -B2178 : C C3p_endo anti -B2179 : C C3p_endo anti -B2180 : U C3p_endo anti -B2181 : U C3p_endo anti -B2182 : U C3p_endo anti -B2183 : A C3p_endo anti -B2184 : A C3p_endo anti -B2185 : U C3p_endo anti -B2186 : G C3p_endo anti -B2187 : U C3p_endo anti -B2188 : U C3p_endo anti -B2189 : U C3p_endo anti -B2190 : G C3p_endo anti -B2191 : A C3p_endo anti -B2192 : U C3p_endo anti -B2193 : G C3p_endo anti -B2194 : U C3p_endo anti -B2195 : U C3p_endo anti -B2196 : C C3p_endo anti -B2197 : U C3p_endo anti -B2198 : A C3p_endo anti -B2199 : A C3p_endo syn -B2200 : C C3p_endo anti -B2201 : G C3p_endo anti -B2202 : U C3p_endo anti -B2203 : U C3p_endo anti -B2204 : G C3p_endo anti -B2205 : A C3p_endo anti -B2206 : C C3p_endo anti -B2207 : C C3p_endo anti -B2208 : C C3p_endo anti -B2209 : G C3p_endo anti -B2210 : U C3p_endo anti -B2211 : A C3p_endo anti -B2212 : A C3p_endo anti -B2213 : U C3p_endo anti -B2214 : C C3p_endo anti -B2215 : C C3p_endo anti -B2216 : G C3p_endo anti -B2217 : G C3p_endo anti -B2218 : G C3p_endo anti -B2219 : U C3p_endo anti -B2220 : U C3p_endo anti -B2221 : G C3p_endo anti -B2222 : C C3p_endo anti -B2223 : G C3p_endo anti -B2224 : G C3p_endo anti -B2225 : A C3p_endo anti -B2226 : C C3p_endo syn -B2227 : A C3p_endo anti -B2228 : G C3p_endo anti -B2229 : U C3p_endo anti -B2230 : G C3p_endo anti -B2231 : U C3p_endo anti -B2232 : C C3p_endo anti -B2233 : U C3p_endo anti -B2234 : G C3p_endo anti -B2235 : G C3p_endo anti -B2236 : U C3p_endo anti -B2237 : G C3p_endo anti -B2238 : G C3p_endo anti -B2239 : G C3p_endo anti -B2240 : U C3p_endo anti -B2241 : A C3p_endo anti -B2242 : G C3p_endo anti -B2243 : U C3p_endo anti -B2244 : U C3p_endo anti -B2245 : U C3p_endo anti -B2246 : G C3p_endo anti -B2247 : A C3p_endo anti -B2248 : C C3p_endo anti -B2249 : U C3p_endo anti -B2250 : G C3p_endo anti -B2251 : 7MG -B2252 : G C3p_endo syn -B2253 : G C3p_endo anti -B2254 : C C3p_endo anti -B2255 : G C3p_endo anti -B2256 : G C3p_endo anti -B2257 : U C3p_endo anti -B2258 : C C3p_endo anti -B2259 : U C3p_endo anti -B2260 : C C3p_endo anti -B2261 : C C3p_endo anti -B2262 : U C3p_endo anti -B2263 : C C3p_endo anti -B2264 : C C3p_endo anti -B2265 : U C3p_endo anti -B2266 : A C3p_endo anti -B2267 : A C3p_endo anti -B2268 : A C3p_endo anti -B2269 : G C3p_endo anti -B2270 : A C3p_endo anti -B2271 : G C3p_endo anti -B2272 : U C3p_endo anti -B2273 : A C3p_endo anti -B2274 : A C3p_endo anti -B2275 : C C3p_endo anti -B2276 : G C3p_endo anti -B2277 : G C3p_endo anti -B2278 : A C3p_endo anti -B2279 : G C3p_endo anti -B2280 : G C3p_endo anti -B2281 : A C3p_endo anti -B2282 : G C3p_endo anti -B2283 : C C3p_endo anti -B2284 : A C3p_endo anti -B2285 : C C3p_endo anti -B2286 : G C3p_endo anti -B2287 : A C3p_endo anti -B2288 : A C3p_endo anti -B2289 : G C3p_endo anti -B2290 : G C3p_endo anti -B2291 : U C3p_endo anti -B2292 : U C3p_endo anti -B2293 : G C3p_endo anti -B2294 : G C3p_endo anti -B2295 : C C3p_endo anti -B2296 : U C3p_endo anti -B2297 : A C3p_endo anti -B2298 : A C3p_endo anti -B2299 : U C3p_endo anti -B2300 : C C3p_endo anti -B2301 : C C3p_endo anti -B2302 : U C3p_endo anti -B2303 : G C3p_endo anti -B2304 : G C3p_endo anti -B2305 : U C3p_endo anti -B2306 : C C3p_endo anti -B2307 : G C3p_endo anti -B2308 : G C3p_endo anti -B2309 : A C3p_endo anti -B2310 : C C3p_endo anti -B2311 : A C3p_endo anti -B2312 : U C3p_endo anti -B2313 : C C3p_endo anti -B2314 : A C3p_endo anti -B2315 : G C3p_endo anti -B2316 : G C3p_endo anti -B2317 : A C3p_endo anti -B2318 : G C3p_endo anti -B2319 : G C3p_endo syn -B2320 : U C3p_endo anti -B2321 : U C3p_endo anti -B2322 : A C3p_endo anti -B2323 : G C3p_endo anti -B2324 : U C3p_endo anti -B2325 : G C3p_endo anti -B2326 : C C3p_endo anti -B2327 : A C3p_endo anti -B2328 : A C3p_endo anti -B2329 : U C3p_endo anti -B2330 : G C3p_endo anti -B2331 : G C3p_endo anti -B2332 : C C3p_endo anti -B2333 : A C3p_endo anti -B2334 : U C3p_endo anti -B2335 : A C3p_endo anti -B2336 : A C3p_endo anti -B2337 : G C3p_endo anti -B2338 : C C3p_endo anti -B2339 : C C3p_endo anti -B2340 : A C3p_endo anti -B2341 : G C3p_endo anti -B2342 : C C3p_endo anti -B2343 : U C3p_endo anti -B2344 : U C3p_endo anti -B2345 : G C3p_endo anti -B2346 : A C3p_endo anti -B2347 : C C3p_endo anti -B2348 : U C3p_endo anti -B2349 : G C3p_endo anti -B2350 : C C3p_endo anti -B2351 : G C3p_endo syn -B2352 : A C3p_endo anti -B2353 : G C3p_endo anti -B2354 : C C3p_endo anti -B2355 : G C3p_endo anti -B2356 : U C3p_endo anti -B2357 : G C3p_endo anti -B2358 : A C3p_endo anti -B2359 : C C3p_endo anti -B2360 : G C3p_endo anti -B2361 : G C3p_endo anti -B2362 : C C3p_endo anti -B2363 : G C3p_endo anti -B2364 : C C3p_endo anti -B2365 : G C3p_endo anti -B2366 : A C3p_endo anti -B2367 : G C3p_endo anti -B2368 : C C3p_endo anti -B2369 : A C3p_endo anti -B2370 : G C3p_endo anti -B2371 : G C3p_endo syn -B2372 : U C3p_endo anti -B2373 : G C3p_endo anti -B2374 : C C3p_endo anti -B2375 : G C3p_endo anti -B2376 : A C3p_endo anti -B2377 : A C3p_endo anti -B2378 : A C3p_endo anti -B2379 : G C3p_endo anti -B2380 : C C3p_endo anti -B2381 : A C3p_endo anti -B2382 : G C3p_endo anti -B2383 : G C3p_endo anti -B2384 : U C3p_endo anti -B2385 : C C3p_endo anti -B2386 : A C3p_endo anti -B2387 : U C3p_endo anti -B2388 : A C3p_endo anti -B2389 : G C3p_endo anti -B2390 : U C3p_endo anti -B2391 : G C3p_endo syn -B2392 : A C3p_endo anti -B2393 : U C3p_endo anti -B2394 : C C3p_endo anti -B2395 : C C3p_endo anti -B2396 : G C3p_endo anti -B2397 : G C3p_endo anti -B2398 : U C3p_endo anti -B2399 : G C3p_endo anti -B2400 : G C3p_endo anti -B2401 : U C3p_endo anti -B2402 : U C3p_endo anti -B2403 : C C3p_endo anti -B2404 : U C3p_endo anti -B2405 : G C3p_endo syn -B2406 : A C3p_endo anti -B2407 : A C3p_endo anti -B2408 : U C3p_endo anti -B2409 : G C3p_endo anti -B2410 : G C3p_endo anti -B2411 : A C3p_endo anti -B2412 : A C3p_endo anti -B2413 : G C3p_endo anti -B2414 : G C3p_endo anti -B2415 : G C3p_endo anti -B2416 : C C3p_endo anti -B2417 : C C3p_endo anti -B2418 : A C3p_endo anti -B2419 : U C3p_endo anti -B2420 : C C3p_endo anti -B2421 : G C3p_endo anti -B2422 : C C3p_endo anti -B2423 : U C3p_endo anti -B2424 : C C3p_endo anti -B2425 : A C3p_endo syn -B2426 : A C3p_endo syn -B2427 : C C3p_endo anti -B2428 : G C3p_endo anti -B2429 : G C3p_endo syn -B2430 : A C3p_endo anti -B2431 : U C3p_endo anti -B2432 : A C3p_endo anti -B2433 : A C3p_endo anti -B2434 : A C3p_endo anti -B2435 : A C3p_endo anti -B2436 : G C3p_endo anti -B2437 : G C3p_endo anti -B2438 : U C3p_endo anti -B2439 : A C3p_endo anti -B2440 : C C3p_endo anti -B2441 : U C3p_endo anti -B2442 : C C3p_endo anti -B2443 : C C3p_endo anti -B2444 : G C3p_endo anti -B2445 : G C3p_endo anti -B2446 : G C3p_endo anti -B2447 : G C3p_endo anti -B2448 : A C3p_endo anti -B2449 : 5MU -B2450 : A C3p_endo anti -B2451 : A C3p_endo anti -B2452 : C C3p_endo anti -B2453 : A C3p_endo anti -B2454 : G C3p_endo anti -B2455 : G C3p_endo anti -B2456 : C C3p_endo anti -B2457 : U C3p_endo anti -B2458 : G C3p_endo anti -B2459 : A C3p_endo anti -B2460 : U C3p_endo anti -B2461 : A C3p_endo anti -B2462 : C C3p_endo anti -B2463 : C C3p_endo anti -B2464 : G C3p_endo anti -B2465 : C C3p_endo anti -B2466 : C C3p_endo anti -B2467 : C C3p_endo anti -B2468 : A C3p_endo anti -B2469 : A C3p_endo syn -B2470 : G C3p_endo anti -B2471 : A C3p_endo anti -B2472 : G C3p_endo anti -B2473 : U C3p_endo anti -B2474 : U C3p_endo anti -B2475 : C C3p_endo anti -B2476 : A C3p_endo anti -B2477 : U C3p_endo anti -B2478 : A C3p_endo anti -B2479 : U C3p_endo anti -B2480 : C C3p_endo anti -B2481 : G C3p_endo anti -B2482 : A C3p_endo anti -B2483 : C C3p_endo anti -B2484 : G C3p_endo anti -B2485 : G C3p_endo anti -B2486 : C C3p_endo anti -B2487 : G C3p_endo anti -B2488 : G C3p_endo anti -B2489 : U C3p_endo anti -B2490 : G C3p_endo anti -B2491 : U C3p_endo anti -B2492 : U C3p_endo anti -B2493 : U C3p_endo anti -B2494 : G C3p_endo anti -B2495 : G C3p_endo anti -B2496 : C C3p_endo anti -B2497 : A C3p_endo anti -B2498 : 5MC -B2499 : C C3p_endo anti -B2500 : U C3p_endo anti -B2501 : C C3p_endo anti -B2502 : G C3p_endo anti -B2503 : A C3p_endo anti -B2504 : U C3p_endo anti -B2505 : G C3p_endo syn -B2506 : U C3p_endo anti -B2507 : C C3p_endo anti -B2508 : G C3p_endo anti -B2509 : G C3p_endo anti -B2510 : C C3p_endo anti -B2511 : U C3p_endo anti -B2512 : C C3p_endo anti -B2513 : A C3p_endo anti -B2514 : U C3p_endo anti -B2515 : C C3p_endo anti -B2516 : A C3p_endo anti -B2517 : C C3p_endo anti -B2518 : A C3p_endo anti -B2519 : U C3p_endo anti -B2520 : C C3p_endo anti -B2521 : C C3p_endo anti -B2522 : U C3p_endo anti -B2523 : G C3p_endo anti -B2524 : G C3p_endo anti -B2525 : G C3p_endo anti -B2526 : G C3p_endo anti -B2527 : C C3p_endo anti -B2528 : U C3p_endo anti -B2529 : G C3p_endo anti -B2530 : A C3p_endo anti -B2531 : A C3p_endo anti -B2532 : G C3p_endo anti -B2533 : U C3p_endo anti -B2534 : A C3p_endo anti -B2535 : G C3p_endo anti -B2536 : G C3p_endo anti -B2537 : U C3p_endo anti -B2538 : C C3p_endo anti -B2539 : C C3p_endo anti -B2540 : C C3p_endo anti -B2541 : A C3p_endo anti -B2542 : A C3p_endo anti -B2543 : G C3p_endo anti -B2544 : G C3p_endo anti -B2545 : G C3p_endo anti -B2546 : U C3p_endo anti -B2547 : A C3p_endo anti -B2548 : U C3p_endo anti -B2549 : G C3p_endo anti -B2550 : G C3p_endo anti -B2551 : C C3p_endo anti -B2552 : U C3p_endo anti -B2553 : G C3p_endo anti -B2554 : U C3p_endo anti -B2555 : U C3p_endo anti -B2556 : C C3p_endo syn -B2557 : G C3p_endo anti -B2558 : C C3p_endo anti -B2559 : C C3p_endo anti -B2560 : A C3p_endo anti -B2561 : U C3p_endo anti -B2562 : U C3p_endo anti -B2563 : U C3p_endo anti -B2564 : A C3p_endo syn -B2565 : A C3p_endo syn -B2566 : A C3p_endo anti -B2567 : G C3p_endo anti -B2568 : U C3p_endo anti -B2569 : G C3p_endo anti -B2570 : G C3p_endo anti -B2571 : U C3p_endo anti -B2572 : A C3p_endo anti -B2573 : C C3p_endo anti -B2574 : G C3p_endo syn -B2575 : C C3p_endo syn -B2576 : G C3p_endo anti -B2577 : A C3p_endo anti -B2578 : G C3p_endo anti -B2579 : C C3p_endo anti -B2580 : U C3p_endo anti -B2581 : G C3p_endo anti -B2582 : G C3p_endo anti -B2583 : G C3p_endo anti -B2584 : U C3p_endo anti -B2585 : U C3p_endo anti -B2586 : U C3p_endo anti -B2587 : A C3p_endo anti -B2588 : G C3p_endo anti -B2589 : A C3p_endo anti -B2590 : A C3p_endo anti -B2591 : C C3p_endo anti -B2592 : G C3p_endo anti -B2593 : U C3p_endo anti -B2594 : C C3p_endo anti -B2595 : G C3p_endo anti -B2596 : U C3p_endo anti -B2597 : G C3p_endo anti -B2598 : A C3p_endo syn -B2599 : G C3p_endo anti -B2600 : A C3p_endo anti -B2601 : C C3p_endo anti -B2602 : A C3p_endo anti -B2603 : G C3p_endo anti -B2604 : U C3p_endo anti -B2605 : U C3p_endo anti -B2606 : C C3p_endo anti -B2607 : G C3p_endo anti -B2608 : G C3p_endo anti -B2609 : U C3p_endo syn -B2610 : C C3p_endo anti -B2611 : C C3p_endo anti -B2612 : C C3p_endo anti -B2613 : U C3p_endo anti -B2614 : A C3p_endo anti -B2615 : U C3p_endo anti -B2616 : C C3p_endo anti -B2617 : U C3p_endo anti -B2618 : G C3p_endo anti -B2619 : C C3p_endo anti -B2620 : C C3p_endo anti -B2621 : G C3p_endo anti -B2622 : U C3p_endo anti -B2623 : G C3p_endo anti -B2624 : G C3p_endo anti -B2625 : G C3p_endo anti -B2626 : C C3p_endo anti -B2627 : G C3p_endo anti -B2628 : C C3p_endo anti -B2629 : U C3p_endo anti -B2630 : G C3p_endo anti -B2631 : G C3p_endo anti -B2632 : A C3p_endo anti -B2633 : G C3p_endo anti -B2634 : A C3p_endo anti -B2635 : A C3p_endo anti -B2636 : C C3p_endo anti -B2637 : U C3p_endo anti -B2638 : G C3p_endo anti -B2639 : A C3p_endo anti -B2640 : G C3p_endo anti -B2641 : G C3p_endo anti -B2642 : G C3p_endo anti -B2643 : G C3p_endo anti -B2644 : G C3p_endo anti -B2645 : G C3p_endo syn -B2646 : C C3p_endo anti -B2647 : U C3p_endo anti -B2648 : G C3p_endo anti -B2649 : C C3p_endo anti -B2650 : U C3p_endo anti -B2651 : C C3p_endo anti -B2652 : C C3p_endo anti -B2653 : U C3p_endo anti -B2654 : A C2p_endo anti -B2655 : G C2p_endo anti -B2656 : U C2p_exo anti -B2657 : A C3p_endo anti -B2658 : C C3p_endo anti -B2659 : G C3p_endo anti -B2660 : A O4p_endo anti -B2661 : G O4p_endo anti -B2662 : A C4p_exo anti -B2663 : G C3p_endo anti -B2664 : G C3p_endo anti -B2665 : A C3p_endo anti -B2666 : C C3p_endo anti -B2667 : C C3p_endo anti -B2668 : G C3p_endo anti -B2669 : G C3p_endo anti -B2670 : A C3p_endo anti -B2671 : G C3p_endo anti -B2672 : U C3p_endo anti -B2673 : G C3p_endo anti -B2674 : G C3p_endo anti -B2675 : A C3p_endo anti -B2676 : C C3p_endo anti -B2677 : G C3p_endo anti -B2678 : C C3p_endo anti -B2679 : A C3p_endo anti -B2680 : U C3p_endo anti -B2681 : C C3p_endo anti -B2682 : A C3p_endo anti -B2683 : C C3p_endo anti -B2684 : U C3p_endo anti -B2685 : G C3p_endo syn -B2686 : G C3p_endo anti -B2687 : U C3p_endo anti -B2688 : G C3p_endo anti -B2689 : U C3p_endo anti -B2690 : U C3p_endo anti -B2691 : C C3p_endo anti -B2692 : G C3p_endo anti -B2693 : G C3p_endo anti -B2694 : G C3p_endo anti -B2695 : U C3p_endo anti -B2696 : U C3p_endo anti -B2697 : G C3p_endo anti -B2698 : U C3p_endo anti -B2699 : C C3p_endo anti -B2700 : A C3p_endo anti -B2701 : U C3p_endo anti -B2702 : G C3p_endo anti -B2703 : C C3p_endo anti -B2704 : C C3p_endo anti -B2705 : A C3p_endo anti -B2706 : A C3p_endo anti -B2707 : U C3p_endo anti -B2708 : G C3p_endo anti -B2709 : G C3p_endo anti -B2710 : C C3p_endo anti -B2711 : A C3p_endo anti -B2712 : C C3p_endo anti -B2713 : U C3p_endo anti -B2714 : G C3p_endo anti -B2715 : C C3p_endo anti -B2716 : C C3p_endo anti -B2717 : C C3p_endo anti -B2718 : G C3p_endo anti -B2719 : G C3p_endo anti -B2720 : U C3p_endo anti -B2721 : A C3p_endo anti -B2722 : G C3p_endo anti -B2723 : C C3p_endo anti -B2724 : U C3p_endo anti -B2725 : A C3p_endo syn -B2726 : A C3p_endo syn -B2727 : A C3p_endo anti -B2728 : U C3p_endo anti -B2729 : G C3p_endo anti -B2730 : C C3p_endo anti -B2731 : G C3p_endo anti -B2732 : G C3p_endo syn -B2733 : A C3p_endo syn -B2734 : A C3p_endo anti -B2735 : G C3p_endo anti -B2736 : A C3p_endo anti -B2737 : G C3p_endo anti -B2738 : A C3p_endo syn -B2739 : U C3p_endo anti -B2740 : A C3p_endo syn -B2741 : A C3p_endo syn -B2742 : G C3p_endo anti -B2743 : U C3p_endo anti -B2744 : G C3p_endo anti -B2745 : C C3p_endo anti -B2746 : U C3p_endo anti -B2747 : G C3p_endo anti -B2748 : A C3p_endo syn -B2749 : A C3p_endo syn -B2750 : A C3p_endo anti -B2751 : G C3p_endo anti -B2752 : C C3p_endo anti -B2753 : A C3p_endo anti -B2754 : U C3p_endo anti -B2755 : C C3p_endo anti -B2756 : U C3p_endo anti -B2757 : A C3p_endo anti -B2758 : A C3p_endo anti -B2759 : G C3p_endo anti -B2760 : C C3p_endo anti -B2761 : A C3p_endo anti -B2762 : C C3p_endo anti -B2763 : G C3p_endo anti -B2764 : A C3p_endo syn -B2765 : A C3p_endo anti -B2766 : A C3p_endo syn -B2767 : C C3p_endo anti -B2768 : U C3p_endo anti -B2769 : U C3p_endo anti -B2770 : G C3p_endo anti -B2771 : C C3p_endo anti -B2772 : C C3p_endo anti -B2773 : C C3p_endo anti -B2774 : C C3p_endo anti -B2775 : G C3p_endo anti -B2776 : A C3p_endo anti -B2777 : G C3p_endo syn -B2778 : A C3p_endo syn -B2779 : U C3p_endo anti -B2780 : G C3p_endo syn -B2781 : A C3p_endo anti -B2782 : G C3p_endo anti -B2783 : U C3p_endo anti -B2784 : U C3p_endo anti -B2785 : C C3p_endo anti -B2786 : U C3p_endo anti -B2787 : C C3p_endo anti -B2788 : C C3p_endo anti -B2789 : C C3p_endo anti -B2790 : U C3p_endo anti -B2791 : G C3p_endo anti -B2792 : A C3p_endo anti -B2793 : C C3p_endo anti -B2794 : C C3p_endo anti -B2795 : C C3p_endo anti -B2796 : U C3p_endo anti -B2797 : U C3p_endo anti -B2798 : U C3p_endo syn -B2799 : A C3p_endo anti -B2800 : A C3p_endo anti -B2801 : G C3p_endo anti -B2802 : G C3p_endo anti -B2803 : G C3p_endo anti -B2804 : U C3p_endo anti -B2805 : C C3p_endo anti -B2806 : C C3p_endo anti -B2807 : U C3p_endo anti -B2808 : G C3p_endo syn -B2809 : A C3p_endo anti -B2810 : A C3p_endo syn -B2811 : G C3p_endo anti -B2812 : G C3p_endo anti -B2813 : A C3p_endo anti -B2814 : A C3p_endo anti -B2815 : C C3p_endo anti -B2816 : G C3p_endo anti -B2817 : U C3p_endo anti -B2818 : U C3p_endo anti -B2819 : G C3p_endo anti -B2820 : A C3p_endo anti -B2821 : A C3p_endo anti -B2822 : G C3p_endo syn -B2823 : A C3p_endo anti -B2824 : C C3p_endo anti -B2825 : G C3p_endo anti -B2826 : A C3p_endo anti -B2827 : C C3p_endo anti -B2828 : G C3p_endo anti -B2829 : A C3p_endo anti -B2830 : C C3p_endo anti -B2831 : G C3p_endo anti -B2832 : U C3p_endo anti -B2833 : U C3p_endo anti -B2834 : G C3p_endo anti -B2835 : A C3p_endo syn -B2836 : U C3p_endo anti -B2837 : A C3p_endo anti -B2838 : G C3p_endo anti -B2839 : G C3p_endo anti -B2840 : C C3p_endo anti -B2841 : C C3p_endo anti -B2842 : G C3p_endo anti -B2843 : G C3p_endo anti -B2844 : G C3p_endo syn -B2845 : U C3p_endo anti -B2846 : G C3p_endo anti -B2847 : U C3p_endo anti -B2848 : G C3p_endo syn -B2849 : U C3p_endo anti -B2850 : A C3p_endo syn -B2851 : A C3p_endo anti -B2852 : G C3p_endo anti -B2853 : C C3p_endo anti -B2854 : G C3p_endo anti -B2855 : C C3p_endo anti -B2856 : A C3p_endo anti -B2857 : G C3p_endo anti -B2858 : C C3p_endo anti -B2859 : G C3p_endo anti -B2860 : A C3p_endo anti -B2861 : U C3p_endo anti -B2862 : G C3p_endo anti -B2863 : C C3p_endo anti -B2864 : G C3p_endo anti -B2865 : U C3p_endo anti -B2866 : U C3p_endo anti -B2867 : G C3p_endo syn -B2868 : A C3p_endo syn -B2869 : G C3p_endo anti -B2870 : C C3p_endo anti -B2871 : U C3p_endo anti -B2872 : A C3p_endo syn -B2873 : A C3p_endo anti -B2874 : C C3p_endo anti -B2875 : C C3p_endo anti -B2876 : G C3p_endo anti -B2877 : G C3p_endo anti -B2878 : U C3p_endo anti -B2879 : A C3p_endo anti -B2880 : C C3p_endo anti -B2881 : U C3p_endo anti -B2882 : A C3p_endo anti -B2883 : A C3p_endo syn -B2884 : U C3p_endo anti -B2885 : G C3p_endo anti -B2886 : A C3p_endo anti -B2887 : A C3p_endo anti -B2888 : C C3p_endo anti -B2889 : C C3p_endo anti -B2890 : G C3p_endo anti -B2891 : U C3p_endo anti -B2892 : G C3p_endo anti -B2893 : A C3p_endo anti -B2894 : G C3p_endo anti -B2895 : G C3p_endo anti -B2896 : C C3p_endo anti -B2897 : U C3p_endo anti -B2898 : U C3p_endo anti -B2899 : A C3p_endo anti -B2900 : A C3p_endo anti -B2901 : C C3p_endo anti -B2902 : C C3p_endo anti -B2903 : U C3p_endo anti -B2904 : U C3p_endo syn -Adjacent stackings ---------------------------------------------- -B1-B2 : adjacent_5p upward -B2-B3 : adjacent_5p upward -B3-B4 : adjacent_5p upward -B5-B6 : adjacent_5p upward -B6-B7 : adjacent_5p upward -B7-B8 : adjacent_5p upward -B13-B14 : adjacent_5p upward -B17-B18 : adjacent_5p upward -B19-B20 : adjacent_5p upward -B21-B22 : adjacent_5p upward -B23-B24 : adjacent_5p upward -B24-B25 : adjacent_5p upward -B30-B31 : adjacent_5p upward -B35-B36 : adjacent_5p upward -B38-B39 : adjacent_5p upward -B39-B40 : adjacent_5p upward -B42-B43 : adjacent_5p upward -B44-B45 : adjacent_5p upward -B54-B55 : adjacent_5p upward -B55-B56 : adjacent_5p upward -B58-B59 : adjacent_5p upward -B68-B69 : adjacent_5p upward -B77-B78 : adjacent_5p upward -B80-B81 : adjacent_5p upward -B81-B82 : adjacent_5p upward -B85-B86 : adjacent_5p upward -B86-B87 : adjacent_5p upward -B88-B89 : adjacent_5p upward -B95-B96 : adjacent_5p upward -B104-B105 : adjacent_5p upward -B107-B108 : adjacent_5p upward -B108-B109 : adjacent_5p upward -B121-B122 : adjacent_5p upward -B122-B123 : adjacent_5p upward -B131-B132 : adjacent_5p upward -B132-B133 : adjacent_5p upward -B134-B135 : adjacent_5p upward -B136-B137 : adjacent_5p upward -B140-B141 : adjacent_5p inward -B141-B142 : adjacent_5p outward pairing -B142-B143 : adjacent_5p upward -B144-B145 : adjacent_5p upward -B146-B147 : adjacent_5p upward -B152-B153 : adjacent_5p upward -B155-B156 : adjacent_5p upward -B156-B157 : adjacent_5p upward -B162-B163 : adjacent_5p upward -B164-B165 : adjacent_5p upward -B165-B166 : adjacent_5p upward -B169-B170 : adjacent_5p upward -B172-B173 : adjacent_5p upward -B173-B174 : adjacent_5p upward -B175-B176 : adjacent_5p upward -B185-B186 : adjacent_5p upward -B186-B187 : adjacent_5p upward -B187-B188 : adjacent_5p upward -B191-B192 : adjacent_5p upward -B194-B195 : adjacent_5p upward -B197-B198 : adjacent_5p upward pairing -B204-B205 : adjacent_5p upward -B205-B206 : adjacent_5p upward -B227-B228 : adjacent_5p outward -B230-B231 : adjacent_5p upward -B245-B246 : adjacent_5p upward -B248-B249 : adjacent_5p upward -B250-B251 : adjacent_5p upward -B251-B252 : adjacent_5p upward -B252-B253 : adjacent_5p upward -B253-B254 : adjacent_5p inward pairing -B258-B259 : adjacent_5p upward -B259-B260 : adjacent_5p upward -B260-B261 : adjacent_5p upward -B261-B262 : adjacent_5p upward -B265-B266 : adjacent_5p upward -B266-B267 : adjacent_5p upward -B271-B272 : adjacent_5p upward -B272-B273 : adjacent_5p upward -B273-B274 : adjacent_5p upward -B282-B283 : adjacent_5p upward -B283-B284 : adjacent_5p upward -B285-B286 : adjacent_5p upward -B287-B288 : adjacent_5p upward -B289-B290 : adjacent_5p upward -B291-B292 : adjacent_5p upward -B295-B296 : adjacent_5p upward -B301-B302 : adjacent_5p upward -B303-B304 : adjacent_5p upward -B308-B309 : adjacent_5p upward -B309-B310 : adjacent_5p upward -B310-B311 : adjacent_5p upward -B311-B312 : adjacent_5p upward -B312-B313 : adjacent_5p upward -B313-B314 : adjacent_5p upward -B315-B316 : adjacent_5p upward -B317-B318 : adjacent_5p upward -B325-B326 : adjacent_5p upward -B326-B327 : adjacent_5p upward -B333-B334 : adjacent_5p upward -B342-B343 : adjacent_5p upward -B347-B348 : adjacent_5p upward -B348-B349 : adjacent_5p upward -B350-B351 : adjacent_5p upward -B352-B353 : adjacent_5p upward -B354-B355 : adjacent_5p upward -B356-B357 : adjacent_5p upward -B363-B364 : adjacent_5p upward -B375-B376 : adjacent_5p upward -B376-B377 : adjacent_5p upward -B377-B378 : adjacent_5p upward -B379-B380 : adjacent_5p upward -B380-B381 : adjacent_5p upward -B381-B382 : adjacent_5p upward -B386-B387 : adjacent_5p upward -B388-B389 : adjacent_5p upward -B389-B390 : adjacent_5p upward -B390-B391 : adjacent_5p upward -B396-B397 : adjacent_5p upward -B406-B407 : adjacent_5p upward -B407-B408 : adjacent_5p upward -B408-B409 : adjacent_5p upward -B409-B410 : adjacent_5p upward -B415-B416 : adjacent_5p upward -B424-B425 : adjacent_5p upward -B425-B426 : adjacent_5p upward -B438-B439 : adjacent_5p upward -B439-B440 : adjacent_5p upward -B446-B447 : adjacent_5p upward pairing -B457-B458 : adjacent_5p inward -B467-B468 : adjacent_5p upward -B472-B473 : adjacent_5p upward pairing -B473-B474 : adjacent_5p upward -B474-B475 : adjacent_5p upward -B492-B493 : adjacent_5p outward -B493-B494 : adjacent_5p upward -B494-B495 : adjacent_5p upward -B495-B496 : adjacent_5p upward -B515-B516 : adjacent_5p upward -B518-B519 : adjacent_5p upward -B520-B521 : adjacent_5p upward -B522-B523 : adjacent_5p upward -B533-B534 : adjacent_5p upward -B535-B536 : adjacent_5p upward -B539-B540 : adjacent_5p upward -B541-B542 : adjacent_5p upward -B543-B544 : adjacent_5p upward -B547-B548 : adjacent_5p upward -B548-B549 : adjacent_5p upward -B549-B550 : adjacent_5p upward -B551-B552 : adjacent_5p upward -B553-B554 : adjacent_5p upward -B559-B560 : adjacent_5p upward -B579-B580 : adjacent_5p upward -B582-B583 : adjacent_5p upward -B583-B584 : adjacent_5p upward -B590-B591 : adjacent_5p upward -B592-B593 : adjacent_5p upward -B593-B594 : adjacent_5p upward -B594-B595 : adjacent_5p upward -B597-B598 : adjacent_5p upward -B599-B600 : adjacent_5p upward -B600-B601 : adjacent_5p upward -B604-B605 : adjacent_5p upward -B605-B606 : adjacent_5p upward -B613-B614 : adjacent_5p upward -B614-B615 : adjacent_5p upward -B617-B618 : adjacent_5p upward -B621-B622 : adjacent_5p upward -B622-B623 : adjacent_5p upward -B628-B629 : adjacent_5p upward -B638-B639 : adjacent_5p upward -B639-B640 : adjacent_5p upward -B641-B642 : adjacent_5p upward -B647-B648 : adjacent_5p upward -B648-B649 : adjacent_5p upward -B649-B650 : adjacent_5p upward -B656-B657 : adjacent_5p upward -B659-B660 : adjacent_5p upward -B661-B662 : adjacent_5p upward -B662-B663 : adjacent_5p upward -B663-B664 : adjacent_5p upward -B664-B665 : adjacent_5p upward -B666-B667 : adjacent_5p upward -B681-B682 : adjacent_5p upward -B682-B683 : adjacent_5p upward -B689-B690 : adjacent_5p upward -B690-B691 : adjacent_5p upward -B693-B694 : adjacent_5p upward -B695-B696 : adjacent_5p upward -B696-B697 : adjacent_5p upward -B700-B701 : adjacent_5p upward -B701-B702 : adjacent_5p upward -B707-B708 : adjacent_5p upward -B708-B709 : adjacent_5p upward -B711-B712 : adjacent_5p upward -B715-B716 : adjacent_5p upward -B716-B717 : adjacent_5p upward -B717-B718 : adjacent_5p upward -B721-B722 : adjacent_5p upward -B722-B723 : adjacent_5p upward -B729-B730 : adjacent_5p upward -B730-B731 : adjacent_5p upward -B742-B743 : adjacent_5p upward -B743-B744 : adjacent_5p upward -B750-B751 : adjacent_5p upward -B751-B752 : adjacent_5p upward -B752-B753 : adjacent_5p upward -B753-B754 : adjacent_5p upward -B756-B757 : adjacent_5p upward -B757-B758 : adjacent_5p upward -B759-B760 : adjacent_5p upward -B768-B769 : adjacent_5p upward -B770-B771 : adjacent_5p upward -B771-B772 : adjacent_5p upward -B774-B775 : adjacent_5p upward -B777-B778 : adjacent_5p upward -B794-B795 : adjacent_5p upward -B797-B798 : adjacent_5p upward -B798-B799 : adjacent_5p upward -B805-B806 : adjacent_5p upward -B808-B809 : adjacent_5p upward -B822-B823 : adjacent_5p upward -B825-B826 : adjacent_5p upward -B829-B830 : adjacent_5p upward -B830-B831 : adjacent_5p upward -B831-B832 : adjacent_5p upward -B833-B834 : adjacent_5p upward -B834-B835 : adjacent_5p upward -B841-B842 : adjacent_5p upward -B843-B844 : adjacent_5p upward -B845-B846 : adjacent_5p downward -B849-B850 : adjacent_5p upward -B855-B856 : adjacent_5p upward -B862-B863 : adjacent_5p inward -B869-B870 : adjacent_5p upward -B874-B875 : adjacent_5p upward -B879-B880 : adjacent_5p upward -B881-B882 : adjacent_5p upward -B882-B883 : adjacent_5p upward -B883-B884 : adjacent_5p upward -B887-B888 : adjacent_5p upward -B888-B889 : adjacent_5p upward -B889-B890 : adjacent_5p upward -B891-B892 : adjacent_5p upward -B892-B893 : adjacent_5p upward -B904-B905 : adjacent_5p upward -B907-B908 : adjacent_5p upward -B923-B924 : adjacent_5p upward -B924-B925 : adjacent_5p upward -B925-B926 : adjacent_5p upward -B928-B929 : adjacent_5p upward -B936-B937 : adjacent_5p upward -B938-B939 : adjacent_5p upward -B939-B940 : adjacent_5p upward -B947-B948 : adjacent_5p upward -B949-B950 : adjacent_5p upward -B950-B951 : adjacent_5p upward -B952-B953 : adjacent_5p upward -B953-B954 : adjacent_5p upward -B954-B955 : adjacent_5p upward -B955-B956 : adjacent_5p upward pairing -B962-B963 : adjacent_5p upward -B966-B967 : adjacent_5p upward -B969-B970 : adjacent_5p upward -B976-B977 : adjacent_5p upward -B977-B978 : adjacent_5p upward -B981-B982 : adjacent_5p upward -B983-B984 : adjacent_5p upward pairing -B984-B985 : adjacent_5p upward -B993-B994 : adjacent_5p upward -B996-B997 : adjacent_5p upward -B997-B998 : adjacent_5p upward -B1002-B1003 : adjacent_5p upward -B1003-B1004 : adjacent_5p upward -B1014-B1015 : adjacent_5p upward -B1016-B1017 : adjacent_5p upward -B1017-B1018 : adjacent_5p upward -B1021-B1022 : adjacent_5p downward pairing -B1034-B1035 : adjacent_5p upward -B1036-B1037 : adjacent_5p upward -B1037-B1038 : adjacent_5p upward -B1041-B1042 : adjacent_5p upward -B1042-B1043 : adjacent_5p upward -B1051-B1052 : adjacent_5p upward -B1054-B1055 : adjacent_5p upward -B1055-B1056 : adjacent_5p upward -B1057-B1058 : adjacent_5p upward -B1059-B1060 : adjacent_5p inward -B1062-B1063 : adjacent_5p upward -B1063-B1064 : adjacent_5p upward -B1064-B1065 : adjacent_5p upward -B1065-B1066 : adjacent_5p upward -B1067-B1068 : adjacent_5p upward -B1068-B1069 : adjacent_5p upward -B1071-B1072 : adjacent_5p upward -B1073-B1074 : adjacent_5p upward -B1074-B1075 : adjacent_5p upward -B1076-B1077 : adjacent_5p upward -B1077-B1078 : adjacent_5p upward -B1079-B1080 : adjacent_5p upward -B1080-B1081 : adjacent_5p upward -B1081-B1082 : adjacent_5p upward -B1082-B1083 : adjacent_5p upward -B1084-B1085 : adjacent_5p upward -B1085-B1086 : adjacent_5p inward -B1090-B1091 : adjacent_5p upward -B1091-B1092 : adjacent_5p upward -B1092-B1093 : adjacent_5p upward -B1093-B1094 : adjacent_5p upward -B1095-B1096 : adjacent_5p upward -B1096-B1097 : adjacent_5p upward -B1097-B1098 : adjacent_5p upward -B1098-B1099 : adjacent_5p upward -B1099-B1100 : adjacent_5p upward -B1100-B1101 : adjacent_5p upward -B1101-B1102 : adjacent_5p upward -B1102-B1103 : adjacent_5p upward -B1103-B1104 : adjacent_5p upward pairing -B1106-B1107 : adjacent_5p upward -B1107-B1108 : adjacent_5p upward -B1112-B1113 : adjacent_5p upward -B1116-B1117 : adjacent_5p upward -B1120-B1121 : adjacent_5p upward -B1137-B1138 : adjacent_5p upward -B1143-B1144 : adjacent_5p upward -B1144-B1145 : adjacent_5p upward -B1147-B1148 : adjacent_5p upward -B1149-B1150 : adjacent_5p upward -B1151-B1152 : adjacent_5p upward -B1156-B1157 : adjacent_5p upward -B1157-B1158 : adjacent_5p upward -B1160-B1161 : adjacent_5p upward -B1162-B1163 : adjacent_5p upward -B1165-B1166 : adjacent_5p upward -B1166-B1167 : adjacent_5p upward -B1168-B1169 : adjacent_5p upward -B1169-B1170 : adjacent_5p upward -B1171-B1172 : adjacent_5p upward -B1175-B1176 : adjacent_5p upward -B1177-B1178 : adjacent_5p upward -B1179-B1180 : adjacent_5p upward -B1182-B1183 : adjacent_5p upward -B1190-B1191 : adjacent_5p upward -B1191-B1192 : adjacent_5p upward -B1192-B1193 : adjacent_5p upward -B1193-B1194 : adjacent_5p upward -B1194-B1195 : adjacent_5p upward -B1206-B1207 : adjacent_5p upward -B1215-B1216 : adjacent_5p upward -B1216-B1217 : adjacent_5p upward -B1218-B1219 : adjacent_5p upward -B1220-B1221 : adjacent_5p upward -B1226-B1227 : adjacent_5p upward pairing -B1227-B1228 : adjacent_5p upward -B1228-B1229 : adjacent_5p upward -B1230-B1231 : adjacent_5p upward -B1232-B1233 : adjacent_5p upward -B1237-B1238 : adjacent_5p upward -B1238-B1239 : adjacent_5p upward -B1239-B1240 : adjacent_5p upward -B1244-B1245 : adjacent_5p upward -B1245-B1246 : adjacent_5p upward -B1246-B1247 : adjacent_5p upward -B1256-B1257 : adjacent_5p upward -B1259-B1260 : adjacent_5p upward -B1260-B1261 : adjacent_5p upward -B1269-B1270 : adjacent_5p upward -B1276-B1277 : adjacent_5p upward -B1277-B1278 : adjacent_5p upward -B1279-B1280 : adjacent_5p upward -B1280-B1281 : adjacent_5p upward -B1287-B1288 : adjacent_5p upward -B1292-B1293 : adjacent_5p upward -B1296-B1297 : adjacent_5p upward -B1303-B1304 : adjacent_5p upward -B1304-B1305 : adjacent_5p upward -B1317-B1318 : adjacent_5p upward -B1325-B1326 : adjacent_5p upward -B1332-B1333 : adjacent_5p upward -B1333-B1334 : adjacent_5p upward -B1334-B1335 : adjacent_5p upward -B1336-B1337 : adjacent_5p upward -B1337-B1338 : adjacent_5p upward -B1338-B1339 : adjacent_5p upward -B1343-B1344 : adjacent_5p upward -B1346-B1347 : adjacent_5p upward -B1355-B1356 : adjacent_5p upward -B1356-B1357 : adjacent_5p upward -B1361-B1362 : adjacent_5p upward -B1367-B1368 : adjacent_5p upward -B1368-B1369 : adjacent_5p upward -B1369-B1370 : adjacent_5p upward -B1374-B1375 : adjacent_5p upward -B1380-B1381 : adjacent_5p upward -B1381-B1382 : adjacent_5p upward -B1384-B1385 : adjacent_5p upward -B1385-B1386 : adjacent_5p upward -B1387-B1388 : adjacent_5p upward -B1388-B1389 : adjacent_5p upward -B1401-B1402 : adjacent_5p upward -B1403-B1404 : adjacent_5p upward -B1407-B1408 : adjacent_5p upward -B1408-B1409 : adjacent_5p upward -B1410-B1411 : adjacent_5p upward -B1413-B1414 : adjacent_5p upward -B1420-B1421 : adjacent_5p upward -B1421-B1422 : adjacent_5p upward -B1422-B1423 : adjacent_5p upward -B1423-B1424 : adjacent_5p upward -B1431-B1432 : adjacent_5p upward -B1435-B1436 : adjacent_5p upward -B1436-B1437 : adjacent_5p upward -B1441-B1442 : adjacent_5p upward -B1448-B1449 : adjacent_5p upward -B1449-B1450 : adjacent_5p upward -B1456-B1457 : adjacent_5p upward -B1457-B1458 : adjacent_5p upward -B1464-B1465 : adjacent_5p upward -B1471-B1472 : adjacent_5p upward -B1473-B1474 : adjacent_5p upward -B1478-B1479 : adjacent_5p upward -B1479-B1480 : adjacent_5p upward -B1482-B1483 : adjacent_5p upward -B1483-B1484 : adjacent_5p upward -B1491-B1492 : adjacent_5p upward -B1500-B1501 : adjacent_5p upward -B1501-B1502 : adjacent_5p upward -B1502-B1503 : adjacent_5p upward -B1503-B1504 : adjacent_5p upward -B1504-B1505 : adjacent_5p upward -B1505-B1506 : adjacent_5p upward -B1511-B1512 : adjacent_5p upward -B1517-B1518 : adjacent_5p upward -B1519-B1520 : adjacent_5p upward -B1529-B1530 : adjacent_5p upward -B1530-B1531 : adjacent_5p upward -B1532-B1533 : adjacent_5p upward -B1535-B1536 : adjacent_5p upward -B1536-B1537 : adjacent_5p upward -B1537-B1538 : adjacent_5p upward -B1538-B1539 : adjacent_5p upward -B1540-B1541 : adjacent_5p upward -B1546-B1547 : adjacent_5p outward -B1548-B1549 : adjacent_5p upward -B1549-B1550 : adjacent_5p upward -B1555-B1556 : adjacent_5p upward -B1562-B1563 : adjacent_5p upward -B1563-B1564 : adjacent_5p upward -B1576-B1577 : adjacent_5p upward -B1587-B1588 : adjacent_5p upward -B1588-B1589 : adjacent_5p upward -B1590-B1591 : adjacent_5p upward -B1591-B1592 : adjacent_5p upward -B1593-B1594 : adjacent_5p upward -B1596-B1597 : adjacent_5p upward -B1616-B1617 : adjacent_5p upward -B1619-B1620 : adjacent_5p upward -B1622-B1623 : adjacent_5p upward -B1623-B1624 : adjacent_5p upward -B1627-B1628 : adjacent_5p upward -B1628-B1629 : adjacent_5p upward -B1635-B1636 : adjacent_5p upward -B1637-B1638 : adjacent_5p upward -B1642-B1643 : adjacent_5p upward -B1643-B1644 : adjacent_5p upward -B1649-B1650 : adjacent_5p upward -B1650-B1651 : adjacent_5p upward -B1659-B1660 : adjacent_5p upward -B1660-B1661 : adjacent_5p upward -B1661-B1662 : adjacent_5p upward -B1665-B1666 : adjacent_5p upward -B1666-B1667 : adjacent_5p upward -B1680-B1681 : adjacent_5p downward -B1682-B1683 : adjacent_5p upward -B1684-B1685 : adjacent_5p upward -B1700-B1701 : adjacent_5p upward -B1701-B1702 : adjacent_5p upward -B1702-B1703 : adjacent_5p upward -B1703-B1704 : adjacent_5p upward -B1705-B1706 : adjacent_5p upward -B1707-B1708 : adjacent_5p upward -B1710-B1711 : adjacent_5p upward -B1711-B1712 : adjacent_5p upward -B1717-B1718 : adjacent_5p upward -B1724-B1725 : adjacent_5p upward -B1729-B1730 : adjacent_5p upward -B1730-B1731 : adjacent_5p upward -B1731-B1732 : adjacent_5p upward -B1732-B1733 : adjacent_5p upward -B1733-B1734 : adjacent_5p upward -B1734-B1735 : adjacent_5p upward -B1735-B1736 : adjacent_5p upward -B1740-B1741 : adjacent_5p outward -B1746-B1747 : adjacent_5p upward -B1749-B1750 : adjacent_5p upward -B1750-B1751 : adjacent_5p upward -B1766-B1767 : adjacent_5p upward -B1767-B1768 : adjacent_5p upward -B1776-B1777 : adjacent_5p upward -B1781-B1782 : adjacent_5p upward -B1782-B1783 : adjacent_5p upward -B1783-B1784 : adjacent_5p upward -B1784-B1785 : adjacent_5p upward -B1785-B1786 : adjacent_5p upward -B1786-B1787 : adjacent_5p upward -B1787-B1788 : adjacent_5p upward -B1792-B1793 : adjacent_5p upward -B1794-B1795 : adjacent_5p upward -B1796-B1797 : adjacent_5p upward -B1797-B1798 : adjacent_5p upward -B1805-B1806 : adjacent_5p upward -B1809-B1810 : adjacent_5p upward pairing -B1811-B1812 : adjacent_5p upward -B1821-B1822 : adjacent_5p upward -B1823-B1824 : adjacent_5p upward -B1824-B1825 : adjacent_5p upward -B1826-B1827 : adjacent_5p upward -B1829-B1830 : adjacent_5p upward -B1831-B1832 : adjacent_5p upward -B1835-B1836 : adjacent_5p upward -B1840-B1841 : adjacent_5p upward -B1842-B1843 : adjacent_5p upward -B1845-B1846 : adjacent_5p upward -B1849-B1850 : adjacent_5p upward -B1860-B1861 : adjacent_5p upward -B1861-B1862 : adjacent_5p upward -B1862-B1863 : adjacent_5p upward -B1863-B1864 : adjacent_5p upward -B1867-B1868 : adjacent_5p upward -B1871-B1872 : adjacent_5p upward pairing -B1873-B1874 : adjacent_5p upward -B1877-B1878 : adjacent_5p upward -B1878-B1879 : adjacent_5p upward -B1896-B1897 : adjacent_5p upward -B1897-B1898 : adjacent_5p upward -B1901-B1902 : adjacent_5p upward -B1903-B1904 : adjacent_5p upward -B1904-B1905 : adjacent_5p upward -B1906-B1907 : adjacent_5p upward -B1907-B1908 : adjacent_5p upward -B1913-B1914 : adjacent_5p upward -B1919-B1920 : adjacent_5p upward -B1921-B1922 : adjacent_5p upward -B1922-B1923 : adjacent_5p upward -B1945-B1946 : adjacent_5p upward -B1948-B1949 : adjacent_5p upward -B1949-B1950 : adjacent_5p upward -B1959-B1960 : adjacent_5p upward -B1960-B1961 : adjacent_5p upward -B1972-B1973 : adjacent_5p upward -B1973-B1974 : adjacent_5p upward -B1975-B1976 : adjacent_5p upward -B1983-B1984 : adjacent_5p upward -B1984-B1985 : adjacent_5p upward -B1987-B1988 : adjacent_5p upward -B1998-B1999 : adjacent_5p upward -B2002-B2003 : adjacent_5p upward -B2003-B2004 : adjacent_5p upward -B2009-B2010 : adjacent_5p upward -B2010-B2011 : adjacent_5p upward -B2016-B2017 : adjacent_5p upward -B2024-B2025 : adjacent_5p upward -B2032-B2033 : adjacent_5p upward -B2033-B2034 : adjacent_5p upward -B2034-B2035 : adjacent_5p upward -B2037-B2038 : adjacent_5p upward -B2038-B2039 : adjacent_5p upward -B2046-B2047 : adjacent_5p upward -B2048-B2049 : adjacent_5p upward -B2049-B2050 : adjacent_5p upward -B2052-B2053 : adjacent_5p upward -B2053-B2054 : adjacent_5p upward -B2056-B2057 : adjacent_5p upward -B2071-B2072 : adjacent_5p upward -B2077-B2078 : adjacent_5p upward -B2080-B2081 : adjacent_5p upward -B2083-B2084 : adjacent_5p upward -B2085-B2086 : adjacent_5p upward -B2087-B2088 : adjacent_5p upward -B2088-B2089 : adjacent_5p upward -B2090-B2091 : adjacent_5p upward -B2093-B2094 : adjacent_5p upward -B2094-B2095 : adjacent_5p upward -B2095-B2096 : adjacent_5p upward -B2097-B2098 : adjacent_5p upward -B2100-B2101 : adjacent_5p upward -B2101-B2102 : adjacent_5p upward -B2102-B2103 : adjacent_5p upward -B2107-B2108 : adjacent_5p upward -B2111-B2112 : adjacent_5p downward pairing -B2120-B2121 : adjacent_5p upward -B2121-B2122 : adjacent_5p upward -B2123-B2124 : adjacent_5p upward -B2127-B2128 : adjacent_5p upward -B2128-B2129 : adjacent_5p upward -B2136-B2137 : adjacent_5p upward -B2138-B2139 : adjacent_5p inward -B2139-B2140 : adjacent_5p outward -B2140-B2141 : adjacent_5p upward -B2141-B2142 : adjacent_5p upward -B2142-B2143 : adjacent_5p upward -B2148-B2149 : adjacent_5p upward -B2152-B2153 : adjacent_5p upward -B2154-B2155 : adjacent_5p upward -B2159-B2160 : adjacent_5p upward -B2176-B2177 : adjacent_5p upward -B2183-B2184 : adjacent_5p upward -B2186-B2187 : adjacent_5p upward -B2190-B2191 : adjacent_5p upward -B2191-B2192 : adjacent_5p upward -B2193-B2194 : adjacent_5p upward -B2201-B2202 : adjacent_5p upward -B2204-B2205 : adjacent_5p upward -B2205-B2206 : adjacent_5p upward -B2216-B2217 : adjacent_5p upward -B2217-B2218 : adjacent_5p upward -B2218-B2219 : adjacent_5p upward -B2221-B2222 : adjacent_5p upward -B2226-B2227 : adjacent_5p outward -B2227-B2228 : adjacent_5p upward -B2228-B2229 : adjacent_5p upward -B2230-B2231 : adjacent_5p upward -B2234-B2235 : adjacent_5p upward -B2235-B2236 : adjacent_5p upward -B2239-B2240 : adjacent_5p upward -B2241-B2242 : adjacent_5p upward -B2242-B2243 : adjacent_5p upward -B2246-B2247 : adjacent_5p upward -B2247-B2248 : adjacent_5p upward -B2255-B2256 : adjacent_5p upward -B2256-B2257 : adjacent_5p upward -B2269-B2270 : adjacent_5p upward -B2271-B2272 : adjacent_5p upward -B2272-B2273 : adjacent_5p upward -B2273-B2274 : adjacent_5p upward -B2274-B2275 : adjacent_5p upward -B2276-B2277 : adjacent_5p upward -B2277-B2278 : adjacent_5p upward -B2278-B2279 : adjacent_5p upward -B2279-B2280 : adjacent_5p upward -B2280-B2281 : adjacent_5p upward -B2284-B2285 : adjacent_5p upward -B2288-B2289 : adjacent_5p upward -B2289-B2290 : adjacent_5p upward -B2290-B2291 : adjacent_5p upward -B2293-B2294 : adjacent_5p upward -B2294-B2295 : adjacent_5p upward -B2303-B2304 : adjacent_5p upward -B2307-B2308 : adjacent_5p upward -B2309-B2310 : adjacent_5p upward -B2310-B2311 : adjacent_5p upward -B2311-B2312 : adjacent_5p upward -B2314-B2315 : adjacent_5p upward -B2315-B2316 : adjacent_5p upward -B2316-B2317 : adjacent_5p upward -B2323-B2324 : adjacent_5p upward -B2328-B2329 : adjacent_5p upward -B2331-B2332 : adjacent_5p upward -B2336-B2337 : adjacent_5p upward -B2337-B2338 : adjacent_5p upward -B2340-B2341 : adjacent_5p upward -B2341-B2342 : adjacent_5p upward -B2349-B2350 : adjacent_5p upward -B2353-B2354 : adjacent_5p upward -B2363-B2364 : adjacent_5p upward -B2367-B2368 : adjacent_5p upward -B2369-B2370 : adjacent_5p upward -B2373-B2374 : adjacent_5p upward -B2379-B2380 : adjacent_5p upward -B2382-B2383 : adjacent_5p upward -B2383-B2384 : adjacent_5p upward -B2386-B2387 : adjacent_5p upward -B2396-B2397 : adjacent_5p upward -B2397-B2398 : adjacent_5p upward -B2399-B2400 : adjacent_5p upward -B2400-B2401 : adjacent_5p upward -B2407-B2408 : adjacent_5p upward -B2409-B2410 : adjacent_5p upward -B2412-B2413 : adjacent_5p upward -B2413-B2414 : adjacent_5p upward -B2414-B2415 : adjacent_5p upward -B2415-B2416 : adjacent_5p upward -B2418-B2419 : adjacent_5p upward -B2434-B2435 : adjacent_5p upward -B2435-B2436 : adjacent_5p upward -B2436-B2437 : adjacent_5p upward -B2437-B2438 : adjacent_5p upward -B2444-B2445 : adjacent_5p upward -B2445-B2446 : adjacent_5p upward -B2446-B2447 : adjacent_5p upward -B2455-B2456 : adjacent_5p upward -B2458-B2459 : adjacent_5p upward -B2459-B2460 : adjacent_5p upward -B2461-B2462 : adjacent_5p upward -B2464-B2465 : adjacent_5p upward -B2470-B2471 : adjacent_5p upward -B2478-B2479 : adjacent_5p upward -B2484-B2485 : adjacent_5p upward -B2485-B2486 : adjacent_5p upward -B2487-B2488 : adjacent_5p upward -B2488-B2489 : adjacent_5p upward -B2490-B2491 : adjacent_5p upward -B2494-B2495 : adjacent_5p upward -B2495-B2496 : adjacent_5p upward -B2508-B2509 : adjacent_5p upward -B2509-B2510 : adjacent_5p upward -B2513-B2514 : adjacent_5p upward -B2516-B2517 : adjacent_5p upward -B2518-B2519 : adjacent_5p upward -B2523-B2524 : adjacent_5p upward -B2524-B2525 : adjacent_5p upward -B2525-B2526 : adjacent_5p upward -B2526-B2527 : adjacent_5p upward -B2532-B2533 : adjacent_5p upward -B2533-B2534 : adjacent_5p upward -B2535-B2536 : adjacent_5p upward -B2536-B2537 : adjacent_5p upward -B2543-B2544 : adjacent_5p upward -B2544-B2545 : adjacent_5p upward -B2545-B2546 : adjacent_5p upward -B2547-B2548 : adjacent_5p upward -B2549-B2550 : adjacent_5p upward -B2550-B2551 : adjacent_5p upward -B2557-B2558 : adjacent_5p upward -B2560-B2561 : adjacent_5p upward -B2567-B2568 : adjacent_5p upward -B2569-B2570 : adjacent_5p upward -B2570-B2571 : adjacent_5p upward -B2576-B2577 : adjacent_5p upward -B2577-B2578 : adjacent_5p upward -B2578-B2579 : adjacent_5p upward -B2581-B2582 : adjacent_5p upward -B2588-B2589 : adjacent_5p upward -B2589-B2590 : adjacent_5p upward -B2590-B2591 : adjacent_5p upward -B2592-B2593 : adjacent_5p upward -B2598-B2599 : adjacent_5p outward -B2599-B2600 : adjacent_5p upward -B2600-B2601 : adjacent_5p upward -B2603-B2604 : adjacent_5p upward -B2618-B2619 : adjacent_5p upward -B2621-B2622 : adjacent_5p upward -B2623-B2624 : adjacent_5p upward -B2624-B2625 : adjacent_5p upward -B2630-B2631 : adjacent_5p upward -B2631-B2632 : adjacent_5p upward -B2632-B2633 : adjacent_5p upward -B2633-B2634 : adjacent_5p upward -B2634-B2635 : adjacent_5p upward -B2635-B2636 : adjacent_5p upward -B2640-B2641 : adjacent_5p upward -B2641-B2642 : adjacent_5p upward -B2642-B2643 : adjacent_5p upward -B2648-B2649 : adjacent_5p upward -B2657-B2658 : adjacent_5p upward pairing -B2658-B2659 : adjacent_5p upward -B2660-B2661 : adjacent_5p upward -B2661-B2662 : adjacent_5p upward -B2663-B2664 : adjacent_5p upward -B2665-B2666 : adjacent_5p upward -B2668-B2669 : adjacent_5p upward -B2669-B2670 : adjacent_5p upward -B2670-B2671 : adjacent_5p upward -B2671-B2672 : adjacent_5p upward -B2673-B2674 : adjacent_5p upward -B2677-B2678 : adjacent_5p upward -B2679-B2680 : adjacent_5p upward -B2692-B2693 : adjacent_5p upward -B2693-B2694 : adjacent_5p upward -B2694-B2695 : adjacent_5p upward -B2697-B2698 : adjacent_5p upward -B2700-B2701 : adjacent_5p upward -B2703-B2704 : adjacent_5p upward -B2705-B2706 : adjacent_5p upward -B2706-B2707 : adjacent_5p upward -B2708-B2709 : adjacent_5p upward -B2709-B2710 : adjacent_5p upward -B2714-B2715 : adjacent_5p upward -B2727-B2728 : adjacent_5p upward -B2729-B2730 : adjacent_5p upward -B2735-B2736 : adjacent_5p upward -B2736-B2737 : adjacent_5p upward -B2742-B2743 : adjacent_5p upward -B2744-B2745 : adjacent_5p upward -B2756-B2757 : adjacent_5p upward -B2757-B2758 : adjacent_5p upward -B2758-B2759 : adjacent_5p upward -B2759-B2760 : adjacent_5p upward -B2761-B2762 : adjacent_5p upward -B2774-B2775 : adjacent_5p upward -B2781-B2782 : adjacent_5p upward -B2782-B2783 : adjacent_5p upward -B2791-B2792 : adjacent_5p upward -B2792-B2793 : adjacent_5p upward -B2800-B2801 : adjacent_5p upward -B2801-B2802 : adjacent_5p upward -B2802-B2803 : adjacent_5p upward -B2803-B2804 : adjacent_5p upward -B2808-B2809 : adjacent_5p inward -B2811-B2812 : adjacent_5p upward -B2812-B2813 : adjacent_5p upward -B2813-B2814 : adjacent_5p upward -B2814-B2815 : adjacent_5p upward -B2816-B2817 : adjacent_5p upward -B2822-B2823 : adjacent_5p outward -B2826-B2827 : adjacent_5p upward -B2828-B2829 : adjacent_5p upward -B2829-B2830 : adjacent_5p upward -B2831-B2832 : adjacent_5p upward -B2837-B2838 : adjacent_5p upward -B2838-B2839 : adjacent_5p upward -B2839-B2840 : adjacent_5p upward -B2842-B2843 : adjacent_5p upward -B2851-B2852 : adjacent_5p upward -B2852-B2853 : adjacent_5p upward -B2854-B2855 : adjacent_5p upward -B2860-B2861 : adjacent_5p upward -B2862-B2863 : adjacent_5p upward -B2864-B2865 : adjacent_5p upward -B2876-B2877 : adjacent_5p upward -B2877-B2878 : adjacent_5p upward -B2895-B2896 : adjacent_5p upward -B2899-B2900 : adjacent_5p upward -B2900-B2901 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -B5-B2899 : outward -B16-B1197 : downward -B17-B524 : outward -B19-B522 : outward -B21-B520 : outward -B23-B518 : outward -B29-B805 : outward -B30-B476 : outward -B38-B442 : outward -B42-B438 : outward -B43-B44 : upward -B58-B70 : outward -B77-B110 : outward -B80-B107 : outward -B91-B498 : upward pairing -B98-B101 : outward -B134-B146 : outward -B136-B144 : outward -B152-B175 : outward -B155-B172 : outward -B157-B158 : upward -B159-B167 : outward -B185-B212 : outward -B188-B191 : upward -B191-B208 : outward -B262-B430 : upward -B265-B369 : outward -B269-B271 : outward -B270-B2157 : outward -B282-B359 : outward -B285-B356 : outward -B287-B354 : outward -B289-B352 : outward -B291-B350 : outward -B297-B342 : outward -B303-B315 : outward -B363-B428 : downward -B379-B396 : outward -B415-B2409 : outward -B445-B470 : upward -B454-B458 : upward -B464-B466 : upward -B489-B491 : outward -B489-B510 : inward -B499-B505 : downward -B501-B504 : downward -B524-B810 : inward -B527-B1189 : inward pairing -B528-B530 : outward pairing -B535-B559 : outward -B541-B553 : outward -B543-B551 : outward -B570-B2043 : downward pairing -B582-B1259 : outward -B590-B668 : outward -B592-B666 : outward -B597-B661 : outward -B599-B659 : outward -B630-B632 : upward -B675-B1249 : downward -B681-B797 : outward -B684-B790 : upward -B689-B774 : outward -B693-B770 : outward -B695-B768 : outward -B706-B727 : downward pairing -B711-B721 : outward -B738-B759 : outward -B742-B756 : outward -B779-B792 : outward -B818-B820 : downward -B825-B833 : outward -B841-B938 : outward -B843-B936 : outward -B849-B930 : outward -B850-B851 : upward -B855-B923 : outward -B869-B909 : outward -B874-B904 : outward -B926-B928 : upward -B947-B971 : outward -B949-B969 : outward -B952-B966 : outward -B991-B1185 : downward -B993-B1162 : outward -B1014-B1149 : outward -B1016-B1147 : outward -B1031-B1124 : outward -B1032-B1126 : outward -B1034-B1123 : outward -B1036-B1120 : outward -B1054-B1106 : outward -B1057-B1086 : outward -B1059-B1080 : outward -B1061-B1070 : outward -B1062-B1077 : outward -B1063-B1076 : outward -B1069-B1073 : upward -B1071-B1089 : downward pairing -B1079-B1088 : downward -B1087-B1089 : upward -B1087-B1103 : outward -B1090-B1102 : outward -B1159-B1160 : upward -B1165-B1185 : outward -B1168-B1182 : outward -B1171-B1179 : outward -B1202-B1244 : outward -B1218-B1232 : outward -B1220-B1230 : outward -B1279-B1292 : outward -B1285-B2012 : downward pairing -B1294-B1295 : upward -B1296-B1645 : outward -B1302-B1606 : inward -B1307-B1622 : outward -B1311-B1640 : outward pairing -B1317-B1336 : outward -B1320-B1323 : upward -B1324-B1331 : outward -B1346-B1601 : outward -B1359-B1370 : downward -B1359-B1371 : inward pairing -B1387-B1401 : outward -B1407-B1596 : outward -B1410-B1593 : outward -B1413-B1590 : outward -B1419-B1631 : outward -B1425-B1567 : outward -B1429-B1430 : upward -B1441-B1551 : outward -B1444-B1548 : outward -B1448-B1464 : outward -B1450-B1526 : inward -B1473-B1519 : outward -B1482-B1508 : outward -B1532-B1540 : outward -B1570-B1572 : downward pairing -B1630-B1637 : outward -B1649-B2009 : outward -B1659-B2002 : outward -B1663-B1665 : upward -B1663-B1998 : outward -B1684-B1705 : outward -B1710-B1749 : outward -B1714-B1737 : upward -B1717-B1743 : outward -B1722-B1724 : upward -B1722-B1740 : downward pairing -B1766-B1987 : outward -B1770-B1983 : outward -B1772-B1980 : outward -B1776-B1789 : outward -B1794-B1826 : outward -B1797-B1823 : outward -B1799-B1821 : outward -B1805-B1813 : outward -B1831-B1975 : outward -B1845-B1896 : outward -B1848-B1857 : upward -B1854-B1858 : inward -B1867-B1877 : outward -B1910-B1921 : outward -B1936-B1938 : inward -B1945-B2433 : downward -B1948-B1959 : outward -B1971-B2554 : inward -B2023-B2024 : upward -B2024-B2040 : outward -B2027-B2037 : outward -B2046-B2623 : outward -B2048-B2621 : outward -B2059-B2555 : inward -B2060-B2448 : upward pairing -B2067-B2444 : outward -B2080-B2241 : outward -B2090-B2230 : outward -B2097-B2193 : outward -B2100-B2190 : outward -B2107-B2183 : outward -B2123-B2176 : outward -B2136-B2156 : outward -B2138-B2154 : outward -B2140-B2152 : outward -B2201-B2223 : outward -B2202-B2204 : upward -B2204-B2221 : outward -B2209-B2216 : outward -B2250-B2255 : outward -B2293-B2340 : outward -B2303-B2314 : outward -B2330-B2386 : outward -B2349-B2369 : outward -B2355-B2363 : outward -B2373-B2381 : outward -B2377-B2394 : inward -B2396-B2421 : outward -B2399-B2418 : outward -B2442-B2443 : upward pairing -B2451-B2563 : outward pairing -B2458-B2494 : outward -B2461-B2490 : outward -B2464-B2487 : outward -B2508-B2581 : outward -B2516-B2569 : outward -B2521-B2522 : upward -B2523-B2541 : outward -B2549-B2560 : outward -B2639-B2641 : inward pairing -B2648-B2673 : outward -B2654-B2656 : outward -B2656-B2664 : inward -B2657-B2665 : outward -B2659-B2663 : outward -B2677-B2731 : outward -B2679-B2729 : outward -B2681-B2683 : upward -B2682-B2688 : outward pairing -B2682-B2720 : inward -B2687-B2722 : downward -B2688-B2725 : inward pairing -B2692-B2718 : outward -B2697-B2711 : outward -B2700-B2708 : outward -B2744-B2761 : outward -B2816-B2831 : outward -B2819-B2828 : outward -B2837-B2882 : outward -B2842-B2876 : outward -B2845-B2867 : inward -B2851-B2868 : outward -B2854-B2864 : outward -B2856-B2862 : outward -B2884-B2887 : upward pairing -Number of stackings = 1057 -Number of adjacent stackings = 823 -Number of non adjacent stackings = 234 -Base-pairs ------------------------------------------------------ -B1-B2902 : G-C Ww/Ww pairing antiparallel cis XIX -B1-B2904 : G-U O2P/Ww pairing -B2-B2901 : G-C Ww/Ww pairing antiparallel cis XIX -B3-B2900 : U-A Ww/Ww pairing antiparallel cis XX -B4-B2899 : U-A Ww/Ww pairing antiparallel cis XX -B5-B2898 : A-U Ww/Ww pairing antiparallel cis XX -B6-B2897 : A-U Ww/Ww pairing antiparallel cis XX -B7-B2896 : G-C Ww/Ww pairing antiparallel cis XIX -B8-B9 : C-G O2P/Hh O2P/C8 adjacent_5p pairing -B8-B2895 : C-G Ww/Ww pairing antiparallel cis XIX -B9-B526 : G-A Sw/Ss Bs/O2' Ss/O2' pairing antiparallel cis one_hbond -B9-B527 : G-C Ss/O2P pairing -B9-B1192 : G-G Hh/O2P pairing -B9-B1193 : G-G O2P/Hh pairing -B10-B525 : A-U Ww/O2P pairing -B10-B587 : A-C Ss/O2P pairing -B10-B810 : A-U Wh/Bs pairing parallel trans one_hbond -B12-B813 : U-U O2'/Hh pairing -B12-B1195 : U-G O2P/Ss O2P/C8 pairing -B13-B584 : A-C Ss/Bh O2'/Bh pairing parallel trans one_hbond -B13-B585 : A-G O2P/Ss pairing -B14-B1256 : A-G O2'/Hh pairing -B15-B1197 : G-G O2P/Ww O2P/Bs pairing -B15-B1252 : G-G Ww/Bh pairing antiparallel trans one_hbond 115 -B15-B1255 : G-U C8/O2' pairing -B16-B524 : C-G Ww/Ww pairing antiparallel cis XIX -B16-B1198 : C-U O2P/Hh pairing -B17-B523 : G-C Ww/Ww pairing antiparallel cis XIX -B17-B809 : G-G O2'/Bs pairing -B18-B522 : U-A Ww/Ww pairing antiparallel cis XX -B19-B521 : A-U Ww/Ww pairing antiparallel cis XX -B19-B669 : A-G O2P/Hh pairing -B20-B520 : C-G Ww/Ww pairing antiparallel cis XIX -B20-B669 : C-G O2P/Hh pairing -B21-B519 : A-U Ww/Ww pairing antiparallel cis XX -B22-B518 : C-G Ww/Ww pairing antiparallel cis XIX -B23-B507 : G-A Bs/O2' pairing -B23-B508 : G-A Ss/O2P Ss/O2P pairing -B23-B517 : G-C Ww/Ww pairing antiparallel cis XIX -B24-B26 : G-G Sw/Hh pairing antiparallel trans one_hbond 108 -B24-B516 : G-C Ww/Ww pairing antiparallel cis XIX -B25-B515 : U-A Ww/Ww pairing antiparallel cis XX -B27-B515 : G-A Hh/O2' C8/O2' pairing -B27-B516 : G-C Ww/O2P pairing -B27-B1249 : G-U Bs/O2P Ss/O2P pairing -B28-B673 : A-C Hh/O2' pairing -B28-B674 : A-G Bh/O2P pairing -B28-B675 : A-A Ss/O2P pairing -B28-B801 : A-G Bh/O2P pairing -B28-B1249 : A-U C8/O2P pairing -B28-B1250 : A-G Ss/O2P C8/O2P pairing -B28-B1252 : A-G Hh/C8 pairing parallel cis one_hbond -B29-B476 : U-G Ws/Ws pairing antiparallel cis one_hbond -B29-B1250 : U-G O2P/Ww O2P/Bs O2P/Ss pairing -B30-B475 : G-C Ww/Ww pairing antiparallel cis XIX -B30-B1250 : G-G O2P/Ww O2P/Bs O2P/Ss pairing -B31-B474 : C-G Ww/Ww pairing antiparallel cis XIX -B32-B473 : C-G Ww/Ww pairing antiparallel cis XIX -B33-B677 : C-A O2'/Ss pairing -B34-B678 : U-C Hh/O2P pairing -B35-B445 : G-C Ww/Ww pairing antiparallel cis XIX -B36-B444 : G-C Ww/Ww pairing antiparallel cis XIX -B37-B442 : C-G Ww/Ww pairing antiparallel cis XIX -B38-B441 : A-U Ww/Ww pairing antiparallel cis XX -B39-B227 : G-A O2P/Bh pairing -B39-B440 : G-C Ww/Ww pairing antiparallel cis XIX -B40-B228 : U-C O2P/Ww pairing -B40-B439 : U-A Ww/Ww pairing antiparallel cis XX -B41-B438 : C-G Ww/Ww pairing antiparallel cis XIX -B42-B437 : A-U Ww/Ww pairing antiparallel cis XX -B43-B436 : G-C Ww/Ww pairing antiparallel cis XIX -B44-B434 : A-U Ww/Ww pairing antiparallel cis XX -B45-B46 : G-G O2P/Hh adjacent_5p pairing -B45-B433 : G-C Ww/Ww pairing antiparallel cis XIX -B51-B175 : G-G O2'/Bs pairing -B51-B176 : G-A O2'/Ss pairing -B52-B53 : A-A Ss/O2P pairing -B52-B117 : A-G O2'/Bs pairing -B52-B118 : A-A Bh/O2P Hh/O2P pairing -B52-B176 : A-A O2P/Ww O2P/Ss pairing -B53-B174 : A-U Hh/O2P C8/O2P pairing -B53-B175 : A-G Ss/O2P pairing -B54-B116 : G-C Ww/Ww pairing antiparallel cis XIX -B55-B73 : G-A Hh/Bh pairing parallel trans 30 -B55-B115 : G-C Ww/Ww pairing antiparallel cis XIX -B56-B114 : A-U Ww/Ww pairing antiparallel cis XX -B57-B70 : C-G Ww/Ww pairing antiparallel cis XIX -B58-B69 : G-C Ww/Ww pairing antiparallel cis XIX -B59-B64 : U-A Ss/Bs pairing parallel cis one_hbond -B59-B68 : U-G Ws/Ws pairing antiparallel cis one_hbond -B61-B89 : C-A Ww/O2P pairing -B61-B91 : C-A Bh/O2' pairing -B61-B93 : C-G Ww/Ww pairing antiparallel cis XIX -B61-B496 : C-G Ww/O2P pairing -B63-B64 : A-A Ss/Wh adjacent_5p pairing antiparallel trans one_hbond 40 -B63-B70 : A-G Bh/O2' pairing -B64-B69 : A-C Bh/O2' pairing -B64-B86 : A-G Bh/O2P Hh/O2P pairing -B65-B89 : U-A Ww/Ww pairing antiparallel cis XX -B66-B68 : C-G O2P/C8 pairing -B66-B88 : C-G Ww/Ww pairing antiparallel cis XIX -B67-B74 : U-A Ww/Ww pairing antiparallel cis XX -B71-B72 : A-U O2P/Ww adjacent_5p pairing -B71-B102 : A-U Hw/Hw pairing antiparallel cis one_hbond -B71-B106 : A-C Ss/O2P C8/O2P pairing -B71-B107 : A-G Wh/Hw pairing parallel cis one_hbond -B73-B100 : A-U O2P/Ww pairing -B73-B118 : A-A O2P/Ss pairing -B74-B106 : A-C Hh/O2P pairing -B75-B112 : G-U Hh/O2P pairing -B75-B113 : G-U Ss/O2P pairing -B76-B110 : C-G Ww/Ww pairing antiparallel cis XIX -B76-B112 : C-U Bh/O2' pairing -B76-B119 : C-A Bh/O2' pairing -B77-B99 : G-U O2P/Hh O2P/Ww Hh/O2' pairing -B77-B109 : G-C Ww/Ww pairing antiparallel cis XIX -B77-B147 : G-C C8/O2P pairing -B78-B99 : U-U O2P/Hh pairing -B78-B108 : U-G Ws/Ws pairing antiparallel cis one_hbond -B78-B126 : U-A O2'/Bh pairing -B79-B107 : C-G Ww/Ww pairing antiparallel cis XIX -B79-B126 : C-A O2P/Bh O2P/Hh pairing -B80-B106 : G-C Ww/Ww pairing antiparallel cis XIX -B81-B98 : G-G Hw/Ww pairing parallel trans one_hbond -B81-B105 : G-C Ww/Ww pairing antiparallel cis XIX -B82-B84 : U-A O2'/Ss O2'/C8 pairing -B82-B104 : U-A Ww/Ww pairing antiparallel cis XX -B83-B84 : A-A O2P/Ss adjacent_5p pairing -B83-B89 : A-A Hh/O2' C8/O2' pairing -B84-B86 : A-G Hw/Wh pairing antiparallel cis one_hbond 67 -B85-B97 : G-C Ww/Ww pairing antiparallel cis XIX -B86-B88 : G-G O2P/Ww pairing -B86-B96 : G-C Ww/Ww pairing antiparallel cis XIX -B86-B497 : G-A O2'/Ww pairing -B87-B88 : U-G O2P/Hh pairing -B87-B95 : U-A Ww/Ww pairing antiparallel cis XX -B88-B93 : G-G O2P/Bs pairing -B90-B91 : U-A O2P/Hh O2P/C8 adjacent_5p pairing -B91-B94 : A-A Ss/Wh pairing antiparallel trans one_hbond 40 -B91-B498 : A-G O2'/Hh upward pairing -B92-B498 : U-G O2'/C8 pairing -B93-B496 : G-G Bs/O2P pairing -B93-B498 : G-G Bs/O2P Ss/O2P pairing -B93-B499 : G-U Hh/O2P pairing -B93-B504 : G-A C8/O2P pairing -B94-B95 : A-A O2P/Ss O2P/C8 adjacent_5p pairing -B98-B99 : G-U Bs/O2P Ss/O2P adjacent_5p pairing -B98-B103 : G-A O2P/Ss pairing -B98-B106 : G-C Hw/Bh pairing antiparallel trans 122 -B99-B102 : U-U O2P/Hh pairing -B100-B101 : U-A O2P/C8 O2'/Ww O2'/Bh adjacent_5p pairing -B100-B119 : U-A O2P/Ss pairing -B101-B104 : A-A Ss/O2P pairing -B101-B105 : A-C Ww/O2P pairing -B102-B119 : U-A Ww/Ww pairing antiparallel cis XX -B103-B104 : A-A Hh/Hh adjacent_5p pairing antiparallel cis 36 -B110-B111 : G-A Hh/O2' pairing -B111-B112 : A-U Ss/O2P adjacent_5p pairing -B112-B119 : U-A O2'/Ss O2'/C8 pairing -B113-B115 : U-C Ww/O2P pairing -B113-B119 : U-A O2P/C8 pairing -B117-B177 : G-G Bs/O2P pairing -B120-B121 : U-G Hh/O2P adjacent_5p pairing -B120-B148 : U-U Hh/O2P Hh/O2P pairing -B121-B130 : G-C Ww/Ww pairing antiparallel cis XIX -B122-B125 : G-A O2P/C8 O2P/Ss O2P/C8 pairing -B122-B129 : G-C Ww/Ww pairing antiparallel cis XIX -B123-B128 : G-C Ww/Ww pairing antiparallel cis XIX -B124-B128 : G-C Hw/Wh pairing parallel cis one_hbond -B127-B128 : A-C O2P/Bh adjacent_5p pairing -B128-B1327 : C-A O2P/Ss pairing -B129-B1327 : C-A O2P/Ww O2P/Bh O2P/Ww pairing -B131-B148 : A-U Ww/Ww pairing antiparallel cis XX -B132-B147 : G-C Ww/Ww pairing antiparallel cis XIX -B133-B146 : U-A Ww/Ww pairing antiparallel cis XX -B134-B145 : G-C Ww/Ww pairing antiparallel cis XIX -B135-B144 : U-A Ww/Ww pairing antiparallel cis XX -B136-B143 : G-C Ww/Ww pairing antiparallel cis XIX -B136-B1325 : G-U Bs/O2' pairing -B136-B1326 : G-U Bs/O2' Ss/O2' pairing -B137-B142 : U-A Ww/Ww pairing antiparallel cis XX -B141-B142 : G-A O2P/Bh adjacent_5p outward pairing -B141-B1324 : G-G Ww/O2' pairing -B141-B1331 : G-G C8/Ss pairing parallel cis one_hbond -B143-B1326 : C-U O2'/Ww pairing -B143-B1328 : C-A O2P/C8 O2P/Ww O2P/Ss pairing -B144-B1326 : A-U Ss/O2' pairing -B144-B1327 : A-A O2P/Ww O2P/Bh O2P/Hh pairing -B144-B1328 : A-A O2P/Ss pairing -B150-B176 : U-A Ww/Ww pairing antiparallel cis XX -B151-B175 : C-G Ww/Ww pairing antiparallel cis XIX -B152-B174 : A-U Ww/Ww pairing antiparallel cis XX -B153-B173 : U-A Ww/Ww pairing antiparallel cis XX -B154-B172 : U-A Ww/Ww pairing antiparallel cis XX -B155-B171 : A-U Ww/Ww pairing antiparallel cis XX -B156-B170 : A-U Ww/Ww pairing antiparallel cis XX -B157-B169 : C-G Ww/Ww pairing antiparallel cis XIX -B158-B160 : U-A O2P/Bh pairing -B158-B167 : U-A Ww/Ww pairing antiparallel cis XX -B159-B160 : G-A O2P/Hh adjacent_5p pairing -B159-B166 : G-U Ws/Ws pairing antiparallel cis one_hbond -B160-B161 : A-A O2'/Hh adjacent_5p pairing -B160-B163 : A-C O2'/Bh pairing -B166-B168 : U-G O2'/Hh pairing -B168-B1552 : G-A Bs/O2P pairing -B175-B178 : G-G O2'/Bs O2'/Ss pairing -B178-B179 : G-C Hh/Hw adjacent_5p pairing antiparallel cis one_hbond 116 -B179-B195 : C-A Ww/O2P Bh/O2P pairing -B180-B189 : G-G O2'/Ww pairing -B180-B198 : G-C C8/O2P pairing -B181-B189 : A-G O2P/Ww O2P/Bs pairing -B181-B195 : A-A O2P/Bh pairing -B182-B188 : A-G Bs/Hh pairing antiparallel trans one_hbond -B182-B204 : A-A O2P/Bh pairing -B184-B212 : C-G Ww/Ww pairing antiparallel cis XIX -B185-B211 : G-C Ww/Ww pairing antiparallel cis XIX -B186-B210 : G-C Ww/Ww pairing antiparallel cis XIX -B186-B218 : G-A O2'/Ss pairing -B187-B209 : G-C Ww/Ww pairing antiparallel cis XIX -B188-B190 : G-A O2P/Ss O2P/Hh O2P/C8 pairing -B188-B208 : G-C Ww/Ww pairing antiparallel cis XIX -B189-B192 : G-C Hh/O2P pairing -B190-B216 : A-A Hw/Ss pairing parallel trans one_hbond -B191-B206 : A-U Ww/Ww pairing antiparallel cis XX -B192-B205 : C-G Ww/Ww pairing antiparallel cis XIX -B193-B204 : U-A Ww/Ww pairing antiparallel cis XX -B194-B201 : G-C Ww/Ww pairing antiparallel cis XIX -B195-B196 : A-A O2'/Hh adjacent_5p pairing -B195-B200 : A-U Ww/Ww pairing antiparallel cis XX -B196-B197 : A-A O2'/Hh adjacent_5p pairing -B197-B198 : A-C O2P/Bh adjacent_5p upward pairing -B198-B199 : C-A Ws/Hw O2'/Hh O2'/C8 adjacent_5p pairing parallel cis one_hbond 80 -B201-B203 : C-A O2P/Hh Hh/O2P pairing -B202-B204 : U-A O2'/Ss O2'/C8 pairing -B203-B204 : A-A O2P/Hh O2P/C8 adjacent_5p pairing -B210-B217 : C-A Ss/Bs O2'/Ww O2'/Bh pairing antiparallel trans one_hbond -B211-B213 : C-A Ss/Bs O2'/Ss O2'/C8 pairing parallel cis one_hbond -B213-B219 : A-A Hh/O2P pairing -B213-B244 : A-A O2P/C8 pairing -B214-B243 : G-U Bs/O2P pairing -B214-B254 : G-G Ww/O2' pairing -B214-B256 : G-A O2'/Ss C8/O2' pairing -B215-B216 : G-A Ss/O2P C8/O2P adjacent_5p pairing -B216-B218 : A-A O2P/Ss pairing -B216-B256 : A-A O2P/Hh O2P/Bh pairing -B216-B257 : A-C Hh/Wh pairing parallel cis one_hbond 69 -B219-B256 : A-A O2P/Ww O2P/Ss pairing -B219-B276 : A-U Ss/Ww pairing parallel trans one_hbond 42 -B220-B258 : G-G C8/Hw O2'/Hh pairing antiparallel cis one_hbond -B221-B222 : A-A O2'/C8 Hh/O2' adjacent_5p pairing -B221-B278 : A-A Ww/Ss Ss/O2' pairing antiparallel cis -B221-B279 : A-A Ss/O2P C8/O2P pairing -B222-B223 : A-A O2P/Ww O2P/Bh adjacent_5p pairing -B222-B224 : A-U O2'/Ww pairing -B222-B261 : A-G O2P/Hh pairing -B222-B278 : A-A Ww/O2' pairing -B223-B260 : A-G Wh/Hh Bh/O2P Hh/O2P pairing parallel cis one_hbond 61 -B223-B261 : A-G O2P/Hh Ss/O2P pairing -B223-B262 : A-A O2P/Bh O2P/Hh pairing -B223-B279 : A-A Hh/O2P pairing -B224-B231 : U-A Ww/Ww pairing antiparallel cis XX -B225-B226 : C-A O2'/Hh adjacent_5p pairing -B225-B227 : C-A Hh/O2P pairing -B225-B228 : C-C Bh/O2P pairing -B225-B230 : C-G Ww/Ww pairing antiparallel cis XIX -B225-B281 : C-C O2P/Bh pairing -B226-B356 : A-G Ss/O2P Ss/O2P C8/O2P pairing -B226-B357 : A-C O2P/Bh Hh/O2P pairing -B226-B432 : A-A Bs/Ss Ww/O2P Bh/O2P pairing antiparallel cis one_hbond -B227-B355 : A-U Ss/O2P C8/O2P pairing -B227-B432 : A-A Ww/C8 Ss/O2' pairing parallel cis one_hbond -B228-B229 : C-C O2P/Bh adjacent_5p pairing -B228-B433 : C-C Ww/O2P Bh/O2P pairing -B229-B433 : C-C Hh/O2P pairing -B230-B432 : G-A Bs/O2P pairing -B233-B235 : A-U Ss/O2P pairing -B234-B430 : U-A Ww/Ww pairing antiparallel cis XX -B235-B262 : U-A Ww/Ww pairing antiparallel cis XX -B235-B277 : U-G O2P/Hh pairing -B236-B261 : C-G Ww/Ww pairing antiparallel cis XIX -B236-B277 : C-G O2P/Hh pairing -B237-B260 : C-G Ww/Ww pairing antiparallel cis XIX -B237-B428 : C-A O2'/Bh O2'/Hh pairing -B238-B259 : C-G Ww/Ww pairing antiparallel cis XIX -B238-B277 : C-G Bh/O2P pairing -B239-B258 : C-G Ww/Ww pairing antiparallel cis XIX -B239-B277 : C-G Bh/O2P pairing -B240-B274 : C-C Hh/O2P pairing -B241-B275 : A-C Bh/O2P pairing -B242-B255 : G-A O2P/Hh Bs/O2' pairing -B244-B249 : A-C Ss/O2P C8/O2P pairing -B245-B253 : G-C Ww/Ww pairing antiparallel cis XIX -B246-B252 : C-G Ww/Ww pairing antiparallel cis XIX -B247-B248 : G-G O2'/Hh adjacent_5p pairing -B249-B250 : C-G Wh/Hw adjacent_5p pairing parallel cis one_hbond -B253-B254 : C-G O2P/Ww O2P/Bs adjacent_5p inward pairing -B254-B255 : G-A C8/O2P adjacent_5p pairing -B255-B275 : A-C Hh/O2' C8/O2' pairing -B255-B276 : A-U Ww/O2P Bh/O2P pairing -B257-B258 : C-G Bh/O2' adjacent_5p pairing -B261-B428 : G-A Sw/Ss pairing parallel cis one_hbond 57 -B261-B429 : G-A Bs/O2P Ss/O2P pairing -B262-B263 : A-G O2'/Bs O2'/Ss adjacent_5p pairing -B263-B359 : G-G O2P/Ss pairing -B263-B360 : G-U Ss/O2P pairing -B263-B362 : G-A Hh/O2P pairing -B264-B369 : C-U O2P/Ww pairing -B265-B427 : A-U Ww/Ww pairing antiparallel cis XX -B266-B426 : G-C Ww/Ww pairing antiparallel cis XIX -B267-B269 : C-C O2'/Hh pairing -B267-B425 : C-G Ww/Ww pairing antiparallel cis XIX -B268-B424 : C-G Ww/Ww pairing antiparallel cis XIX -B269-B426 : C-C Wh/Bs pairing antiparallel trans one_hbond -B270-B2134 : A-A Bh/O2P pairing -B271-B366 : G-C Ww/Ww pairing antiparallel cis XIX -B271-B2156 : G-G O2'/Hh pairing -B272-B365 : A-U Ww/Ww pairing antiparallel cis XX -B272-B2136 : A-G O2P/Hh pairing -B273-B364 : G-C Ww/Ww pairing antiparallel cis XIX -B274-B363 : C-G Ww/Ww pairing antiparallel cis XIX -B281-B359 : C-G Ww/Ww pairing antiparallel cis XIX -B281-B430 : C-A Bh/O2P pairing -B282-B358 : A-U Ww/Ww pairing antiparallel cis XX -B282-B370 : A-G O2'/Bs pairing -B283-B357 : G-C Ww/Ww pairing antiparallel cis XIX -B284-B356 : U-G Ws/Ws pairing antiparallel cis one_hbond -B284-B373 : U-U O2P/Hh O2P/Ww pairing -B285-B355 : G-U Ws/Ws pairing antiparallel cis one_hbond -B286-B354 : U-A Ww/Ww pairing antiparallel cis XX -B287-B353 : G-C Ww/Ww pairing antiparallel cis XIX -B288-B352 : U-A Ww/Ww pairing antiparallel cis XX -B289-B351 : G-C Ww/Ww pairing antiparallel cis XIX -B290-B350 : U-G Ws/Ws pairing antiparallel cis one_hbond -B291-B349 : G-U Ws/Ws pairing antiparallel cis one_hbond -B292-B348 : U-A Ww/Ww pairing antiparallel cis XX -B293-B295 : U-G O2'/Hh pairing -B293-B347 : U-A Ww/Ww pairing antiparallel cis XX -B294-B295 : A-G O2P/C8 adjacent_5p pairing -B294-B326 : A-G Ss/Sw pairing parallel cis one_hbond 57 -B294-B327 : A-G O2'/Ss O2'/C8 pairing -B294-B337 : A-C Bh/O2' pairing -B295-B343 : G-C Ww/Ww pairing antiparallel cis XIX -B296-B342 : U-A Ww/Ww pairing antiparallel cis XX -B297-B341 : G-C Ww/Ww pairing antiparallel cis XIX -B299-B340 : A-A Ww/O2P pairing -B301-B316 : G-C Ww/Ww pairing antiparallel cis XIX -B302-B315 : C-G Ww/Ww pairing antiparallel cis XIX -B303-B314 : G-C Ww/Ww pairing antiparallel cis XIX -B304-B313 : U-G Ws/Ws pairing antiparallel cis one_hbond -B305-B312 : C-G Ww/Ww pairing antiparallel cis XIX -B306-B311 : U-A Ww/Ww pairing antiparallel cis XX -B309-B311 : A-A O2P/Bh pairing -B311-B483 : A-A O2P/Hh pairing -B317-B319 : G-G O2'/Hh pairing -B317-B334 : G-C Ww/Ww pairing antiparallel cis XIX -B318-B333 : C-G Ww/Ww pairing antiparallel cis XIX -B319-B320 : G-A Ss/O2' adjacent_5p pairing -B319-B323 : G-C Ww/Ww pairing antiparallel cis XIX -B319-B324 : G-A Ww/O2' Bs/O2' Ss/O2' pairing -B320-B325 : A-G C8/O2P pairing -B321-B324 : U-A O2P/Ss O2P/C8 pairing -B323-B325 : C-G O2'/Ww pairing -B325-B329 : G-G Hw/Ww pairing antiparallel trans one_hbond -B325-B337 : G-C Ww/Ww pairing antiparallel cis XIX -B326-B336 : G-C Ww/Ww pairing antiparallel cis XIX -B327-B328 : G-U O2P/Ww Hh/O2' adjacent_5p pairing -B327-B335 : G-C Ww/Ww pairing antiparallel cis XIX -B329-B335 : G-C O2'/Bh pairing -B330-B333 : A-G O2'/Bs pairing -B330-B334 : A-C Ss/O2' C8/O2' pairing -B335-B341 : C-C O2'/Bh pairing -B340-B346 : A-A Ss/O2' pairing -B344-B347 : A-A Bh/O2P Hh/O2P pairing -B344-B400 : A-G Bh/O2P pairing -B346-B466 : A-A O2P/Ww pairing -B356-B432 : G-A O2P/Ss pairing -B359-B430 : G-A Ww/O2P pairing -B362-B363 : A-G O2'/Hh adjacent_5p pairing -B362-B427 : A-U Hh/O2' pairing -B365-B368 : U-A O2P/Hh O2P/C8 pairing -B366-B368 : C-A O2P/Ss pairing -B367-B368 : G-A O2'/Ss Ss/O2P adjacent_5p pairing -B370-B429 : G-A O2P/Bh O2P/Hh pairing -B375-B399 : G-U Ws/Ws pairing antiparallel cis one_hbond -B375-B401 : G-A Bs/O2' Bs/O2P pairing -B376-B398 : G-C Ww/Ww pairing antiparallel cis XIX -B377-B403 : G-U O2P/Hh pairing -B378-B396 : C-G Ww/Ww pairing antiparallel cis XIX -B379-B395 : G-U Ws/Ws pairing antiparallel cis one_hbond -B380-B394 : G-C Ww/Ww pairing antiparallel cis XIX -B381-B393 : G-C Ww/Ww pairing antiparallel cis XIX -B382-B383 : A-C Ww/O2' adjacent_5p pairing -B382-B392 : A-U Ww/Ww pairing antiparallel cis XX -B383-B386 : C-G Bh/O2P pairing -B383-B387 : C-U Wh/Hw pairing parallel cis one_hbond 103 -B383-B391 : C-A O2'/Bh pairing -B384-B391 : A-A O2P/Ww pairing -B388-B406 : G-G Bs/O2P Ss/O2P pairing -B406-B421 : G-C Ww/Ww pairing antiparallel cis XIX -B407-B420 : G-C Ww/Ww pairing antiparallel cis XIX -B408-B419 : G-U Ws/Ws pairing antiparallel cis one_hbond -B409-B418 : G-C Ww/Ww pairing antiparallel cis XIX -B410-B417 : G-C Ww/Ww pairing antiparallel cis XIX -B411-B2406 : G-A O2'/Hh O2'/C8 pairing -B411-B2407 : G-A Hh/Wh pairing antiparallel cis one_hbond 60 -B412-B2405 : A-G O2'/Bs pairing -B412-B2406 : A-A O2P/Bh pairing -B413-B2405 : C-G O2P/Bs pairing -B413-B2410 : C-G Ww/Ww pairing antiparallel cis XIX -B414-B2409 : C-G Ww/Ww pairing antiparallel cis XIX -B415-B2408 : A-U Ww/Ww pairing antiparallel cis XX -B416-B2407 : U-A Ww/Ww pairing antiparallel cis XX -B423-B424 : A-G Ww/O2' pairing -B425-B2157 : G-G O2'/Hh pairing -B428-B429 : A-A Ss/O2P adjacent_5p pairing -B435-B436 : C-C O2'/Hh pairing -B435-B438 : C-G Ww/O2P pairing -B441-B443 : U-A O2P/Bh pairing -B446-B447 : G-A O2P/Bh O2P/Hh adjacent_5p upward pairing -B446-B479 : G-A Ww/O2' Bs/O2' pairing -B447-B472 : A-A Bh/O2' pairing -B447-B473 : A-G C8/O2P pairing -B447-B479 : A-A O2'/Ss pairing -B448-B474 : U-G Hh/O2P pairing -B448-B478 : U-A O2'/Ss pairing -B449-B452 : A-G O2P/Hh pairing -B449-B594 : A-U Ww/O2' Ss/O2' pairing -B450-B451 : G-U Ss/O2P adjacent_5p pairing -B450-B452 : G-G O2P/Ss O2P/C8 pairing -B450-B592 : G-A Hh/Bs pairing antiparallel cis one_hbond -B451-B462 : U-C Hw/Hw pairing antiparallel cis one_hbond -B453-B454 : A-A Ss/O2P adjacent_5p pairing -B453-B475 : A-C Bh/O2P Hh/O2P pairing -B453-B476 : A-G Bh/O2P pairing -B453-B477 : A-A Hw/Ww pairing antiparallel cis one_hbond -B453-B478 : A-A O2P/Ss pairing -B455-B655 : C-A O2'/Ss pairing -B457-B459 : A-U Ss/O2P C8/O2P pairing -B457-B657 : A-U C8/O2P pairing -B457-B658 : A-U Bh/O2P Bh/O2P Hh/O2P Hh/O2P pairing -B458-B657 : G-U Bs/O2P pairing -B458-B658 : G-U Ww/O2P pairing -B459-B465 : U-G Ww/O2P pairing -B459-B478 : U-A Ws/Ww pairing parallel cis -B460-B593 : A-U Bh/O2P Bh/O2P Hh/O2P pairing -B461-B465 : C-G Bh/O2P pairing -B461-B468 : C-G Ww/Ww pairing antiparallel cis XIX -B462-B465 : C-G Bh/O2P pairing -B462-B467 : C-G Ww/Ww pairing antiparallel cis XIX -B465-B468 : G-G Hh/O2P C8/O2P pairing -B465-B479 : G-A O2P/Bh O2P/Bh pairing -B470-B471 : A-A Ww/O2' adjacent_5p pairing -B471-B472 : A-A Hh/O2P C8/O2P adjacent_5p pairing -B471-B676 : A-A Ww/O2P pairing -B471-B677 : A-A Ww/C8 Ww/O2P pairing antiparallel trans one_hbond -B471-B1250 : A-G Hh/O2' pairing -B472-B473 : A-G O2P/Hh adjacent_5p upward pairing -B475-B477 : C-A O2P/Bh pairing -B477-B478 : A-A Ss/O2P C8/O2P adjacent_5p pairing -B480-B514 : A-A O2'/Bh pairing -B480-B670 : A-A O2P/C8 pairing -B484-B496 : C-G Ww/Ww pairing antiparallel cis XIX -B485-B495 : C-G Ww/Ww pairing antiparallel cis XIX -B486-B494 : C-G Ww/Ww pairing antiparallel cis XIX -B487-B491 : C-G Hw/Wh pairing antiparallel cis one_hbond 123 -B487-B493 : C-G Ww/Ww pairing antiparallel cis XIX -B487-B505 : C-A O2'/Hh O2'/C8 pairing -B487-B509 : C-C O2P/Bh pairing -B488-B510 : G-C Ss/Wh O2'/Bh pairing parallel trans one_hbond 119 -B489-B509 : G-C O2P/Bh pairing -B490-B491 : C-G O2P/Hh adjacent_5p pairing -B490-B510 : C-C Bh/O2' pairing -B491-B492 : G-A Bs/O2P Ss/O2P adjacent_5p pairing -B491-B493 : G-G Ww/Bh pairing parallel cis 113 -B494-B499 : G-U Sw/Bh pairing parallel cis one_hbond 92 -B494-B505 : G-A Bs/O2P pairing -B495-B505 : G-A Bs/O2P Ss/O2P pairing -B500-B501 : G-A C8/O2' adjacent_5p pairing -B500-B504 : G-A Ss/O2P C8/O2P pairing -B500-B505 : G-A O2'/C8 Hh/O2P pairing -B501-B502 : A-A O2P/Hh O2P/C8 adjacent_5p pairing -B501-B505 : A-A Ss/O2P pairing -B502-B503 : A-A C8/O2P adjacent_5p pairing -B506-B1244 : G-A Bs/O2' pairing -B507-B517 : A-C Ss/O2' pairing -B507-B518 : A-G Hh/O2' pairing -B507-B1245 : A-G Hh/O2P C8/O2P pairing -B507-B1246 : A-A Ss/O2P C8/O2P pairing -B508-B518 : A-G O2P/Bs O2P/Ss pairing -B512-B514 : G-A Bs/O2P Ss/O2P pairing -B512-B515 : G-A Ww/O2P Bs/O2P pairing -B512-B516 : G-C Hw/Hh pairing parallel trans 121 -B514-B669 : A-G O2P/Bs O2P/Ss pairing -B514-B670 : A-A Ss/O2' pairing -B518-B1247 : G-A O2P/Bh O2P/Hh pairing -B524-B586 : G-A O2P/Ss pairing -B524-B809 : G-G Bs/O2' pairing -B526-B811 : A-U O2P/Hh O2P/Ww pairing -B527-B1189 : C-A O2'/Bh inward pairing -B528-B530 : A-G Hh/O2P outward pairing -B528-B565 : A-C Bh/O2P pairing -B528-B1189 : A-A O2P/Hh pairing -B529-B942 : A-G Ww/O2P Bh/O2P pairing -B529-B947 : A-A Hh/O2' C8/O2' pairing -B529-B973 : A-A Ss/O2P Hh/O2' pairing -B530-B564 : G-C O2P/Bh pairing -B533-B560 : G-C Ww/Ww pairing antiparallel cis XIX -B533-B561 : G-G Bs/O2' pairing -B533-B562 : G-U Bs/O2P pairing -B534-B559 : U-G Ws/Ws pairing antiparallel cis one_hbond -B535-B558 : G-U Ws/Ws pairing antiparallel cis one_hbond -B536-B557 : G-C Ww/Ww pairing antiparallel cis XIX -B536-B949 : G-G O2P/Bs pairing -B536-B950 : G-G O2P/Ss pairing -B538-B539 : A-G O2'/C8 adjacent_5p pairing -B539-B554 : G-U Ws/Ws pairing antiparallel cis one_hbond -B540-B553 : C-G Ww/Ww pairing antiparallel cis XIX -B541-B552 : A-U Ww/Ww pairing antiparallel cis XX -B542-B551 : C-G Ww/Ww pairing antiparallel cis XIX -B543-B550 : G-C Ww/Ww pairing antiparallel cis XIX -B544-B549 : C-G Ww/Ww pairing antiparallel cis XIX -B563-B988 : A-A Wh/Ww pairing antiparallel cis one_hbond 37 -B564-B565 : C-C Ww/O2P adjacent_5p pairing -B566-B836 : U-G Ww/O2P pairing -B566-B837 : U-C Hh/O2P pairing -B566-B1189 : U-A O2P/Ss pairing -B568-B569 : U-U Hh/O2P Ww/O2P adjacent_5p pairing -B568-B832 : U-U Ww/O2' pairing -B569-B2042 : U-A O2P/Ww O2P/Bh pairing -B570-B572 : G-A C8/Ss C8/O2' pairing antiparallel cis one_hbond -B570-B573 : G-U Ww/O2' pairing -B570-B2043 : G-C Bs/O2P Ss/O2P downward pairing -B570-B2044 : G-C Ww/O2P Bs/O2P pairing -B570-B2045 : G-C Hw/Hw pairing parallel trans one_hbond 121 -B571-B573 : U-U Hh/O2P pairing -B571-B2047 : U-C Hw/Hw pairing parallel cis one_hbond 101 -B572-B2623 : A-G Bh/Hh pairing parallel trans one_hbond 61 -B573-B2045 : U-C Hh/O2P pairing -B573-B2046 : U-G Ww/O2P pairing -B574-B2039 : A-U Ss/O2P Hh/O2P C8/O2P pairing -B574-B2040 : A-G Ss/O2P C8/O2P pairing -B574-B2042 : A-A Hh/O2P pairing -B575-B2625 : A-G Bh/O2' pairing -B577-B579 : G-G Hh/O2' pairing -B577-B2018 : G-G Bs/O2' pairing -B579-B1261 : G-C Ww/Ww pairing antiparallel cis XIX -B580-B1260 : U-A Ww/Ww pairing antiparallel cis XX -B581-B1259 : C-G Ww/Ww pairing antiparallel cis XIX -B582-B1258 : A-U Ww/Ww pairing antiparallel cis XX -B583-B1257 : G-C Ww/Ww pairing antiparallel cis XIX -B584-B585 : C-G O2P/Ss adjacent_5p pairing -B584-B1256 : C-G Ww/Ww pairing antiparallel cis XIX -B585-B1195 : G-G C8/O2' pairing -B586-B1196 : A-C O2P/Hh pairing -B589-B668 : U-A Ww/Ww pairing antiparallel cis XX -B590-B667 : A-U Ww/Ww pairing antiparallel cis XX -B591-B666 : U-A Ww/Ww pairing antiparallel cis XX -B592-B665 : A-U Ww/Ww pairing antiparallel cis XX -B593-B664 : U-G Ws/Ws pairing antiparallel cis one_hbond -B594-B663 : U-G Ws/Ws pairing antiparallel cis one_hbond -B595-B662 : C-G Ww/Ww pairing antiparallel cis XIX -B596-B661 : U-A Ww/Ww pairing antiparallel cis XX -B597-B660 : G-C Ww/Ww pairing antiparallel cis XIX -B598-B659 : U-G Ws/Ws pairing antiparallel cis one_hbond -B599-B658 : A-U Ww/Ww pairing antiparallel cis XX -B600-B657 : G-U Ws/Ws pairing antiparallel cis one_hbond -B601-B656 : C-G Ww/Ww pairing antiparallel cis XIX -B603-B658 : A-U Bh/O2' Hh/O2' pairing -B604-B624 : G-C Ww/Ww pairing antiparallel cis XIX -B605-B623 : G-C Ww/Ww pairing antiparallel cis XIX -B606-B622 : U-G Ws/Ws pairing antiparallel cis one_hbond -B607-B621 : U-A Ww/Ww pairing antiparallel cis XX -B608-B610 : A-C O2'/Bh pairing -B608-B616 : A-A Bh/O2P pairing -B608-B618 : A-G C8/Hw pairing parallel trans one_hbond -B610-B618 : C-G Ww/Ww pairing antiparallel cis XIX -B611-B617 : C-G Ww/Ww pairing antiparallel cis XIX -B612-B613 : G-A O2'/Hh adjacent_5p pairing -B619-B621 : G-A O2'/Hh pairing -B628-B635 : G-C Ww/Ww pairing antiparallel cis XIX -B629-B634 : G-C Ww/Ww pairing antiparallel cis XIX -B630-B631 : G-A O2'/Hh adjacent_5p pairing -B633-B634 : A-C O2P/Hh adjacent_5p pairing -B635-B637 : C-A O2P/Hh pairing -B637-B651 : A-G O2P/Hh pairing -B638-B650 : G-C Ww/Ww pairing antiparallel cis XIX -B639-B649 : U-G Ws/Ws pairing antiparallel cis one_hbond -B640-B648 : C-G Ww/Ww pairing antiparallel cis XIX -B641-B647 : U-G Ws/Ws pairing antiparallel cis one_hbond -B645-B647 : C-G Ww/O2' pairing -B646-B654 : U-A O2P/Hh pairing -B648-B653 : G-U Hh/O2P pairing -B650-B652 : C-U Bh/O2P pairing -B651-B652 : G-U Ws/Hw adjacent_5p pairing antiparallel cis one_hbond -B654-B655 : A-A Bs/Hh adjacent_5p pairing parallel cis one_hbond -B669-B670 : G-A Ss/O2P C8/O2P adjacent_5p pairing -B670-B671 : A-C Ww/O2P Ss/O2P pairing -B670-B672 : A-C Ww/O2P Ss/O2P pairing -B671-B809 : C-G Ww/Ww pairing antiparallel cis XIX -B672-B808 : C-G Ww/Ww pairing antiparallel cis XIX -B672-B1251 : C-C O2P/Ww pairing -B673-B1249 : C-U Ww/O2P pairing -B674-B1247 : G-A Bs/O2' pairing -B674-B1248 : G-G Bs/O2P pairing -B675-B801 : A-G O2P/Ss pairing -B676-B1250 : A-G O2P/C8 pairing -B678-B799 : C-G Ww/Ww pairing antiparallel cis XIX -B679-B798 : C-G Ww/Ww pairing antiparallel cis XIX -B680-B797 : C-G Ww/Ww pairing antiparallel cis XIX -B681-B796 : G-C Ww/Ww pairing antiparallel cis XIX -B682-B795 : G-C Ww/Ww pairing antiparallel cis XIX -B683-B684 : U-G O2P/Ww adjacent_5p pairing -B683-B777 : U-G Ww/O2P pairing -B683-B794 : U-A Ww/Ww pairing antiparallel cis XX -B684-B788 : G-A O2'/Ss pairing -B685-B686 : A-U Ss/O2P C8/O2P adjacent_5p pairing -B685-B788 : A-A O2P/Ss pairing -B686-B687 : U-C O2P/Bh adjacent_5p pairing -B687-B775 : C-G Ww/Ww pairing antiparallel cis XIX -B687-B788 : C-A Bh/O2P pairing -B688-B774 : U-G Ws/Ws pairing antiparallel cis one_hbond -B689-B773 : A-U Ww/Ww pairing antiparallel cis XX -B690-B772 : G-C Ww/Ww pairing antiparallel cis XIX -B691-B771 : C-G Ww/Ww pairing antiparallel cis XIX -B692-B770 : C-G Ww/Ww pairing antiparallel cis XIX -B693-B769 : A-U Ww/Ww pairing antiparallel cis XX -B694-B768 : U-G Ws/Ws pairing antiparallel cis one_hbond -B695-B767 : G-U Ws/Ws pairing antiparallel cis one_hbond -B696-B766 : G-U Ws/Ws pairing antiparallel cis one_hbond -B697-B765 : G-C Ww/Ww pairing antiparallel cis XIX -B698-B763 : C-G Ww/Ww pairing antiparallel cis XIX -B698-B1948 : C-G Bh/O2' pairing -B698-B1964 : C-G O2P/Hh pairing -B699-B734 : A-A Wh/Ww pairing parallel cis one_hbond -B699-B1964 : A-G O2P/Hh pairing -B700-B732 : G-C Ww/Ww pairing antiparallel cis XIX -B701-B731 : G-C Ww/Ww pairing antiparallel cis XIX -B702-B730 : U-A Ww/Ww pairing antiparallel cis XX -B703-B704 : U-G Ws/Ws adjacent_5p pairing parallel cis one_hbond 87 -B703-B726 : U-G Ss/Ws pairing parallel trans one_hbond -B703-B729 : U-G Ws/Ws pairing antiparallel cis one_hbond -B704-B705 : G-A O2'/Hh adjacent_5p pairing -B705-B725 : A-G Bh/O2P Bh/O2' Hh/O2P pairing -B706-B707 : A-G O2'/Hh adjacent_5p pairing -B706-B727 : A-A Bh/O2' downward pairing -B707-B724 : G-U Ws/Ws pairing antiparallel cis one_hbond -B708-B723 : G-C Ww/Ww pairing antiparallel cis XIX -B709-B722 : U-A Ww/Ww pairing antiparallel cis XX -B710-B721 : U-A Ww/Ww pairing antiparallel cis XX -B711-B720 : G-U Ws/Ws pairing antiparallel cis one_hbond -B712-B713 : G-G O2P/Hh adjacent_5p pairing -B712-B719 : G-C Ww/Ww pairing antiparallel cis XIX -B725-B727 : G-A O2'/Ww pairing -B726-B727 : G-A O2P/Ss O2P/C8 adjacent_5p pairing -B733-B760 : G-G Bs/O2' pairing -B734-B760 : A-G O2'/Bs pairing -B736-B760 : C-G Ww/Ww pairing antiparallel cis XIX -B737-B759 : C-G Ww/Ww pairing antiparallel cis XIX -B738-B758 : G-C Ww/Ww pairing antiparallel cis XIX -B740-B757 : C-G Ww/Ww pairing antiparallel cis XIX -B741-B756 : U-A Ww/Ww pairing antiparallel cis XX -B741-B1951 : U-U Hh/O2P pairing -B742-B755 : A-U Ww/Ww pairing antiparallel cis XX -B743-B754 : A-U Ww/Ww pairing antiparallel cis XX -B744-B753 : U-A Ww/Ww pairing antiparallel cis XX -B749-B752 : A-A O2P/Bh pairing -B749-B2614 : A-A Ss/Wh O2'/Ww pairing antiparallel cis one_hbond 40 -B757-B1951 : G-U Bs/O2P pairing -B761-B762 : A-U Ww/Ww adjacent_5p pairing antiparallel cis XX -B764-B1948 : A-G Hw/Ss Bh/O2' pairing parallel trans one_hbond -B764-B1959 : A-G Ww/Sw pairing parallel cis one_hbond -B772-B784 : C-G O2'/Bs O2'/Ss pairing -B774-B787 : G-C O2P/Bh pairing -B775-B777 : G-G O2P/C8 pairing -B777-B787 : G-C Ww/Ww pairing antiparallel cis XIX -B777-B788 : G-A Bs/O2' Ss/O2' pairing -B777-B789 : G-A Bs/O2P pairing -B777-B794 : G-A O2P/Ww pairing -B778-B779 : G-U Hh/O2' adjacent_5p pairing -B778-B786 : G-C Ww/Ww pairing antiparallel cis XIX -B778-B789 : G-A O2'/Hh O2'/C8 C8/O2P pairing -B780-B786 : G-C O2'/Bh pairing -B780-B787 : G-C O2'/Bh pairing -B782-B783 : A-A O2P/Bh adjacent_5p pairing -B783-B784 : A-G Hh/O2P C8/O2P adjacent_5p pairing -B788-B790 : A-U Ww/Hh pairing parallel cis one_hbond -B792-B794 : A-A Hh/Hw Ww/O2P pairing parallel trans one_hbond -B796-B1253 : C-A O2P/Ww pairing -B797-B1253 : G-A O2P/C8 O2P/Hh pairing -B798-B801 : G-G O2P/C8 pairing -B799-B800 : G-A O2P/C8 adjacent_5p pairing -B800-B1200 : A-C Hw/Ss Bh/O2' pairing parallel cis one_hbond -B802-B1199 : A-U Bh/O2' pairing -B803-B1254 : U-A O2P/Hh O2P/C8 pairing -B804-B807 : A-U O2P/Ww pairing -B804-B1254 : A-A O2'/Bh O2'/Hh O2P/Bh pairing -B805-B1252 : G-G Ss/O2P pairing -B805-B1254 : G-A O2P/Hh O2P/C8 pairing -B806-B808 : C-G O2P/Ss pairing -B810-B1197 : U-G Hh/Hh pairing parallel trans -B812-B1195 : C-G Ww/Ww pairing antiparallel cis XIX -B813-B1194 : U-A Ww/Ww pairing antiparallel cis XX -B814-B1193 : C-G Ww/Ww pairing antiparallel cis XIX -B815-B1192 : C-G Ww/Ww pairing antiparallel cis XIX -B816-B1191 : C-G Ww/Ww pairing antiparallel cis XIX -B817-B1190 : C-G Ww/Ww pairing antiparallel cis XIX -B818-B819 : G-A O2'/Hh adjacent_5p pairing -B821-B822 : A-G O2'/Hh adjacent_5p pairing -B821-B2628 : A-C Ss/Hw Hh/O2P pairing antiparallel trans one_hbond 72 -B822-B835 : G-C Ww/Ww pairing antiparallel cis XIX -B823-B834 : C-G Ww/Ww pairing antiparallel cis XIX -B823-B1154 : C-G O2'/Bs pairing -B824-B833 : U-A Ww/Ww pairing antiparallel cis XX -B825-B832 : A-U Ww/Ww pairing antiparallel cis XX -B826-B831 : U-G Ws/Ws pairing antiparallel cis one_hbond -B833-B977 : A-G Ss/O2' pairing -B836-B838 : G-C Bs/O2' pairing -B837-B961 : C-C Bh/Ww pairing parallel trans 134 -B837-B976 : C-G O2'/Hh pairing -B838-B940 : C-G Ww/Ww pairing antiparallel cis XIX -B839-B939 : U-G Ws/Ws pairing antiparallel cis one_hbond -B839-B961 : U-C O2P/Bh pairing -B840-B938 : C-G Ww/Ww pairing antiparallel cis XIX -B841-B932 : G-U O2P/Ww pairing -B841-B937 : G-C Ww/Ww pairing antiparallel cis XIX -B842-B936 : U-A Ww/Ww pairing antiparallel cis XX -B843-B935 : G-C Ww/Ww pairing antiparallel cis XIX -B844-B934 : A-U Ww/Ww pairing antiparallel cis XX -B845-B848 : A-C O2P/Bh pairing -B845-B849 : A-A Hh/Hh pairing parallel trans II -B846-B848 : U-C Ww/O2P pairing -B848-B930 : C-G Ww/Ww pairing antiparallel cis XIX -B849-B929 : A-U Ww/Ww pairing antiparallel cis XX -B850-B928 : U-A Ww/Ww pairing antiparallel cis XX -B851-B926 : C-G Ww/Ww pairing antiparallel cis XIX -B852-B925 : U-A Ww/Ww pairing antiparallel cis XX -B853-B924 : C-G Ww/Ww pairing antiparallel cis XIX -B854-B923 : C-G Ww/Ww pairing antiparallel cis XIX -B855-B922 : G-C Ww/Ww pairing antiparallel cis XIX -B856-B858 : G-G O2P/Hh pairing -B856-B921 : G-C Ww/Ww pairing antiparallel cis XIX -B857-B858 : G-G O2P/C8 O2'/Hh adjacent_5p pairing -B857-B912 : G-C O2'/Ww pairing -B858-B859 : G-G O2P/Ss O2P/Hh O2P/C8 adjacent_5p pairing -B858-B912 : G-C O2P/Bh pairing -B858-B919 : G-U Ws/Ws pairing antiparallel cis one_hbond -B859-B861 : G-A Ss/Hw pairing parallel cis one_hbond -B859-B912 : G-C Ss/Hw pairing parallel trans one_hbond -B860-B917 : U-A Ww/Ww pairing antiparallel cis XX -B861-B911 : A-A C8/Ss pairing antiparallel cis one_hbond -B862-B915 : G-C Ww/Ww pairing antiparallel cis XIX -B863-B864 : A-G Ss/O2P Hh/O2' adjacent_5p pairing -B864-B908 : G-C Hh/O2P pairing -B864-B909 : G-A Ww/O2P pairing -B866-B915 : A-C O2'/Hh Ss/O2' pairing -B868-B909 : U-A Ww/Ww pairing antiparallel cis XX -B869-B908 : G-C Ww/Ww pairing antiparallel cis XIX -B870-B907 : U-G Ws/Ws pairing antiparallel cis one_hbond -B872-B905 : U-A Ww/Ww pairing antiparallel cis XX -B873-B904 : C-G Ww/Ww pairing antiparallel cis XIX -B874-B903 : G-C Ww/Ww pairing antiparallel cis XIX -B875-B899 : G-A Bs/O2' pairing -B875-B902 : G-C Ww/Ww pairing antiparallel cis XIX -B879-B898 : G-C Ww/Ww pairing antiparallel cis XIX -B880-B897 : G-C Ww/Ww pairing antiparallel cis XIX -B881-B895 : G-U Ws/Ws pairing antiparallel cis one_hbond -B882-B894 : G-U Ws/Ws pairing antiparallel cis one_hbond -B883-B893 : G-C Ww/Ww pairing antiparallel cis XIX -B884-B892 : U-A Ww/Ww pairing antiparallel cis XX -B885-B891 : C-G Ww/Ww pairing antiparallel cis XIX -B886-B890 : A-C Wh/Ws pairing antiparallel trans one_hbond 78 -B895-B896 : U-A O2'/Hh O2'/C8 adjacent_5p pairing -B896-B897 : A-C O2'/Hh adjacent_5p pairing -B898-B900 : C-A Hh/O2P Ww/O2P pairing -B900-B902 : A-C O2'/Bh pairing -B905-B906 : A-U O2P/Ww adjacent_5p pairing -B906-B907 : U-G O2'/Hh adjacent_5p pairing -B909-B910 : A-A O2P/Hh adjacent_5p pairing -B914-B916 : G-G Sw/Ss Ss/O2' pairing parallel cis one_hbond -B914-B917 : G-A O2P/Bh O2'/Hh C8/O2P pairing -B916-B2595 : G-G Hh/O2P pairing -B918-B919 : A-U O2P/Hh adjacent_5p pairing -B918-B2597 : A-G Ss/O2P pairing -B920-B921 : A-C O2P/Hh Hh/O2' adjacent_5p pairing -B920-B2597 : A-G Bs/Hw O2'/C8 pairing parallel cis one_hbond -B927-B928 : A-A O2'/Hh adjacent_5p pairing -B929-B931 : U-U Hh/Hw pairing parallel cis one_hbond -B933-B935 : A-C Hh/O2P pairing -B933-B936 : A-A Bh/O2P pairing -B941-B973 : A-A O2'/Hh O2'/C8 pairing -B942-B943 : G-A O2'/Ww adjacent_5p pairing -B942-B971 : G-G O2P/Bs pairing -B946-B971 : C-G Ww/Ww pairing antiparallel cis XIX -B947-B970 : A-U Ww/Ww pairing antiparallel cis XX -B947-B972 : A-A Ss/Hw pairing parallel cis one_hbond -B948-B969 : C-G Ww/Ww pairing antiparallel cis XIX -B949-B968 : G-C Ww/Ww pairing antiparallel cis XIX -B950-B967 : G-U Ws/Ws pairing antiparallel cis one_hbond -B951-B966 : C-G Ww/Ww pairing antiparallel cis XIX -B952-B965 : G-C Ww/Ww pairing antiparallel cis XIX -B953-B964 : G-C Ww/Ww pairing antiparallel cis XIX -B954-B963 : G-U Ws/Ws pairing antiparallel cis one_hbond -B955-B956 : U-G O2P/Hh adjacent_5p upward pairing -B955-B962 : U-G Ws/Ws pairing antiparallel cis one_hbond -B957-B959 : C-A Ww/Bh pairing parallel trans one_hbond -B971-B972 : G-A O2'/Ss pairing -B974-B975 : G-A Ss/O2P adjacent_5p pairing -B976-B987 : G-C Ww/Ww pairing antiparallel cis XIX -B977-B979 : G-A O2P/Bh pairing -B977-B986 : G-C Ww/Ww pairing antiparallel cis XIX -B978-B979 : G-A O2P/Hh adjacent_5p pairing -B978-B985 : G-C Ww/Ww pairing antiparallel cis XIX -B979-B980 : A-A O2'/Ww adjacent_5p pairing -B979-B982 : A-C O2'/Bh Ww/O2P Ss/O2P pairing -B980-B982 : A-C Ww/Hw pairing antiparallel cis one_hbond -B983-B984 : A-A O2P/Hh adjacent_5p upward pairing -B990-B992 : A-C Hh/O2P C8/O2P pairing -B990-B993 : A-G Bh/O2P pairing -B990-B1157 : A-G C8/O2P pairing -B991-B1163 : C-G Ww/Ww pairing antiparallel cis XIX -B992-B1162 : C-G Ww/Ww pairing antiparallel cis XIX -B993-B1161 : G-C Ww/Ww pairing antiparallel cis XIX -B994-B1160 : C-G Ww/Ww pairing antiparallel cis XIX -B996-B1159 : A-U Ww/Ww pairing antiparallel cis XX -B997-B1158 : G-C Ww/Ww pairing antiparallel cis XIX -B998-B1157 : C-G Ww/Ww pairing antiparallel cis XIX -B999-B1156 : U-A Ww/Ww pairing antiparallel cis XX -B1000-B1150 : A-C Hh/Hh Hh/O2P pairing parallel cis one_hbond -B1002-B1153 : G-C Ww/Ww pairing antiparallel cis XIX -B1003-B1008 : G-A Bs/O2' pairing -B1003-B1009 : G-A Bs/O2P pairing -B1003-B1152 : G-C Ww/Ww pairing antiparallel cis XIX -B1004-B1010 : U-A O2P/Ww O2P/Bh pairing -B1004-B1151 : U-A Ww/Ww pairing antiparallel cis XX -B1005-B1010 : C-A O2P/Hh pairing -B1005-B1138 : C-G Ww/Ww pairing antiparallel cis XIX -B1006-B1137 : C-G Ww/Ww pairing antiparallel cis XIX -B1007-B1009 : C-A O2'/Bh O2'/Hh pairing -B1009-B1011 : A-G O2'/Hh O2'/C8 pairing -B1009-B1151 : A-A Bs/Ss pairing parallel trans one_hbond -B1011-B1150 : G-C Ww/Ww pairing antiparallel cis XIX -B1013-B1149 : C-G Ww/Ww pairing antiparallel cis XIX -B1014-B1148 : A-U Ww/Ww pairing antiparallel cis XX -B1015-B1147 : U-A Ww/Ww pairing antiparallel cis XX -B1016-B1146 : G-C Ww/Ww pairing antiparallel cis XIX -B1016-B2753 : G-A O2P/C8 O2P/Hh pairing -B1016-B2754 : G-U O2'/Ww pairing -B1017-B1145 : G-C Ww/Ww pairing antiparallel cis XIX -B1017-B2753 : G-A O2P/Hh O2P/C8 pairing -B1018-B1144 : U-A Ww/Ww pairing antiparallel cis XX -B1019-B1027 : U-A O2'/Hh pairing -B1019-B1028 : U-A Ww/O2P pairing -B1019-B1143 : U-A Ww/Ww pairing antiparallel cis XX -B1020-B1027 : A-A O2P/Hh pairing -B1020-B1133 : A-A Bh/O2P Hh/O2P pairing -B1020-B2752 : A-C Hh/Bh pairing antiparallel trans one_hbond -B1021-B1022 : A-G Ss/O2P adjacent_5p downward pairing -B1021-B1133 : A-A O2P/C8 O2'/Bh pairing -B1022-B2462 : G-C Hh/O2P pairing -B1023-B2465 : U-C Ss/Hw O2P/Bh O2'/Bh pairing parallel trans one_hbond -B1023-B2482 : U-A Ww/O2' pairing -B1023-B2484 : U-G Hh/Hh pairing antiparallel trans -B1024-B2467 : G-C Hh/O2P pairing -B1024-B2469 : G-A O2'/Ww O2'/Ss pairing -B1024-B2470 : G-G O2'/Hh pairing -B1025-B2470 : G-G O2P/Hh pairing -B1025-B2478 : G-A Ss/O2P pairing -B1026-B1134 : G-A O2'/Bh pairing -B1027-B1134 : A-A O2P/Ss O2'/Bh O2'/Hh pairing -B1028-B1143 : A-A O2P/Ww pairing -B1028-B1144 : A-A O2'/Ss Ss/O2' pairing -B1030-B1124 : C-G Ww/Ww pairing antiparallel cis XIX -B1030-B1126 : C-A Bh/O2P pairing -B1031-B1123 : G-C Ww/Ww pairing antiparallel cis XIX -B1032-B1034 : A-G O2'/Hh pairing -B1032-B2751 : A-G O2P/Ww pairing -B1033-B1034 : U-G O2'/Hh O2'/C8 adjacent_5p pairing -B1033-B1035 : U-U Hh/O2P pairing -B1033-B1127 : U-A O2P/Ww pairing -B1033-B2750 : U-A O2P/Hh O2P/Bh pairing -B1033-B2751 : U-G O2P/Hh pairing -B1034-B1121 : G-C Ww/Ww pairing antiparallel cis XIX -B1035-B1120 : U-G Ws/Ws pairing antiparallel cis one_hbond -B1036-B1119 : G-U Ws/Ws pairing antiparallel cis one_hbond -B1037-B1118 : G-C Ww/Ww pairing antiparallel cis XIX -B1038-B1039 : G-A C8/O2' adjacent_5p pairing -B1038-B1117 : G-C Ww/Ww pairing antiparallel cis XIX -B1039-B1045 : A-C Bh/O2' pairing -B1040-B1041 : A-G O2'/Hh adjacent_5p pairing -B1040-B1045 : A-C Bh/O2' pairing -B1040-B1048 : A-A O2P/Ss pairing -B1040-B1050 : A-A C8/O2' pairing -B1041-B1114 : G-C Ww/Ww pairing antiparallel cis XIX -B1041-B1115 : G-G Sw/Hh pairing antiparallel trans one_hbond 108 -B1042-B1113 : G-U Ws/Ws pairing antiparallel cis one_hbond -B1043-B1112 : C-G Ww/Ww pairing antiparallel cis XIX -B1046-B1111 : A-A O2P/Ss pairing -B1047-B1052 : G-C O2P/Bh Hh/O2P pairing -B1047-B1053 : G-C O2P/Bh Hh/O2P pairing -B1050-B1051 : A-G O2P/Hh adjacent_5p pairing -B1050-B1052 : A-C O2P/Bh pairing -B1051-B1108 : G-U Ww/Ws pairing antiparallel cis XXVIII -B1052-B1107 : C-G Ww/Ww pairing antiparallel cis XIX -B1053-B1106 : C-G Ww/Ww pairing antiparallel cis XIX -B1054-B1105 : A-U Ww/Ww pairing antiparallel cis XX -B1055-B1085 : G-A Ss/Ss O2'/Ww pairing parallel trans 57 -B1055-B1104 : G-C Ww/Ww pairing antiparallel cis XIX -B1056-B1102 : G-C Ww/O2P pairing -B1056-B1103 : G-A Ss/Hh O2'/Bh pairing antiparallel trans XI -B1057-B1081 : A-U Ww/Ww pairing antiparallel cis XX -B1057-B1087 : A-G Bh/O2P pairing -B1058-B1080 : U-A Ww/Ww pairing antiparallel cis XX -B1059-B1079 : G-C Ww/Ww pairing antiparallel cis XIX -B1060-B1088 : U-A Ww/Hh pairing parallel cis XXIII -B1062-B1076 : G-C Ww/Ww pairing antiparallel cis XIX -B1063-B1075 : G-C Ww/Ww pairing antiparallel cis XIX -B1064-B1074 : C-G Ww/Ww pairing antiparallel cis XIX -B1065-B1069 : U-A Ww/O2' pairing -B1065-B1073 : U-A Ws/Wh pairing antiparallel trans one_hbond 46 -B1066-B1068 : U-G O2'/Hh pairing -B1066-B1069 : U-A Ss/C8 pairing antiparallel trans one_hbond -B1068-B1095 : G-A Bs/O2' pairing -B1070-B1097 : A-U Ww/O2' pairing -B1071-B1089 : G-A Bs/O2' Ss/O2' downward pairing -B1071-B1091 : G-G Ww/Hh pairing parallel cis VI -B1071-B1100 : G-C Wh/Wh pairing antiparallel trans one_hbond -B1072-B1092 : C-C Ww/Hh pairing parallel cis -B1077-B1088 : A-A Ww/O2' pairing -B1082-B1086 : U-A Ww/Ww pairing parallel trans XXI -B1083-B1085 : U-A O2'/Hh pairing -B1084-B1105 : A-U Bs/Ss Ss/O2' pairing antiparallel cis one_hbond -B1086-B1103 : A-A O2'/Ww pairing -B1087-B1102 : G-C Ww/Ww pairing antiparallel cis 122 -B1090-B1101 : A-U Ww/Ww pairing antiparallel cis XX -B1091-B1100 : G-C Ww/Ww pairing antiparallel cis XIX -B1092-B1099 : C-G Ww/Ww pairing antiparallel cis XIX -B1093-B1098 : G-A Ss/Hh O2'/Bh pairing antiparallel trans XI -B1094-B1096 : U-A O2'/Bh O2'/Hh pairing -B1094-B1097 : U-U Ww/O2P pairing -B1103-B1104 : A-C O2P/Bh adjacent_5p upward pairing -B1115-B2748 : G-A Ww/O2' pairing -B1115-B2749 : G-A Bs/O2P pairing -B1117-B1128 : C-G O2P/Bs pairing -B1117-B2750 : C-A O2P/Ss pairing -B1117-B2751 : C-G O2P/Hh O2P/C8 pairing -B1118-B2750 : C-A O2P/Ww pairing -B1119-B1127 : U-A O2P/Bh pairing -B1123-B1126 : C-A Bh/Hh pairing parallel trans one_hbond 69 -B1124-B1126 : G-A Wh/C8 pairing parallel trans one_hbond -B1127-B2750 : A-A Ww/Wh pairing parallel cis one_hbond -B1128-B2751 : G-G O2P/Bs O2P/Ss Bs/O2P pairing -B1129-B1130 : A-U Ss/O2P C8/O2P adjacent_5p pairing -B1130-B2749 : U-A Ww/O2' pairing -B1132-B2753 : U-A O2P/Ss pairing -B1133-B1142 : A-A O2'/Ss pairing -B1133-B1143 : A-A O2'/Hh pairing -B1133-B2463 : A-C Bh/O2P pairing -B1133-B2752 : A-C O2P/Bh pairing -B1134-B1140 : A-C Ss/O2' pairing -B1134-B1143 : A-A O2P/Ss O2P/C8 pairing -B1136-B2583 : G-G Bs/O2' pairing -B1137-B2583 : G-G O2'/Ss O2'/C8 pairing -B1138-B1139 : G-G O2P/Hh adjacent_5p pairing -B1142-B1143 : A-A O2P/C8 adjacent_5p pairing -B1153-B1156 : C-A O2P/Hh O2P/C8 pairing -B1155-B1156 : A-A O2'/Hh O2'/C8 adjacent_5p pairing -B1164-B1185 : C-G Ww/Ww pairing antiparallel cis XIX -B1165-B1184 : A-U Ww/Ww pairing antiparallel cis XX -B1166-B1183 : G-U Ws/Ws pairing antiparallel cis one_hbond -B1167-B1182 : C-G Ww/Ww pairing antiparallel cis XIX -B1168-B1181 : G-U Ws/Ws pairing antiparallel cis one_hbond -B1169-B1180 : A-U Ww/Ww pairing antiparallel cis XX -B1170-B1179 : C-G Ww/Ww pairing antiparallel cis XIX -B1171-B1178 : G-C Ww/Ww pairing antiparallel cis XIX -B1172-B1177 : C-G Ww/Ww pairing antiparallel cis XIX -B1193-B2895 : G-G O2P/Bs pairing -B1198-B1247 : U-A Ww/Ww pairing antiparallel cis XX -B1199-B1246 : U-A Ww/Ww pairing antiparallel cis XX -B1200-B1245 : C-G Ww/Ww pairing antiparallel cis XIX -B1201-B1244 : U-A Ww/Ww pairing antiparallel cis XX -B1202-B1203 : G-U Ss/Hh adjacent_5p pairing antiparallel trans one_hbond -B1202-B1243 : G-C Ww/Ww pairing antiparallel cis XIX -B1205-B1206 : A-G O2'/Hh adjacent_5p pairing -B1205-B1211 : A-C C8/Ws pairing parallel cis one_hbond -B1206-B1240 : G-U Ws/Ws pairing antiparallel cis one_hbond -B1207-B1239 : C-G Ww/Ww pairing antiparallel cis XIX -B1208-B1238 : C-G Ww/Ww pairing antiparallel cis XIX -B1209-B1212 : U-G O2P/Hh pairing -B1209-B1237 : U-A Ww/Ww pairing antiparallel cis XX -B1211-B1236 : C-G Hh/Ss pairing antiparallel trans one_hbond -B1213-B1234 : A-U Bh/O2' pairing -B1214-B1235 : A-G O2P/Ww pairing -B1215-B1234 : G-U Ws/Ws pairing antiparallel cis one_hbond -B1215-B1235 : G-G Bh/Ws pairing parallel trans one_hbond -B1216-B1233 : G-C Ww/Ww pairing antiparallel cis XIX -B1217-B1232 : U-G Ws/Ws pairing antiparallel cis one_hbond -B1218-B1231 : G-U Ws/Ws pairing antiparallel cis one_hbond -B1219-B1230 : U-A Ww/Ww pairing antiparallel cis XX -B1220-B1229 : G-C Ww/Ww pairing antiparallel cis XIX -B1221-B1228 : C-G Ww/Ww pairing antiparallel cis XIX -B1222-B1224 : U-U Ww/O2P pairing -B1222-B1227 : U-G Ws/Ws pairing antiparallel cis one_hbond -B1224-B1225 : U-G O2'/Hh adjacent_5p pairing -B1226-B1227 : A-G O2P/Hh adjacent_5p upward pairing -B1240-B1241 : U-A Hw/C8 adjacent_5p pairing antiparallel cis one_hbond -B1241-B1243 : A-C O2'/Hh O2'/Ww pairing -B1252-B1254 : G-A Bs/O2' pairing -B1254-B1255 : A-U Ss/O2P adjacent_5p pairing -B1262-B2014 : A-A O2P/Ww pairing -B1262-B2017 : A-U Ww/Ww pairing antiparallel cis XX -B1263-B1269 : U-A Ww/O2P pairing -B1265-B1616 : A-A Ss/O2' pairing -B1266-B1270 : G-C Bs/O2' pairing -B1266-B1282 : G-U Ww/O2' pairing -B1266-B1647 : G-U O2'/Ww pairing -B1268-B2003 : A-A Ww/O2P pairing -B1269-B2011 : A-U Ww/Ww pairing antiparallel cis XX -B1270-B2010 : C-G Ww/Ww pairing antiparallel cis XIX -B1271-B1272 : G-A Bs/O2P adjacent_5p pairing -B1271-B1649 : G-G O2'/Hh pairing -B1272-B1650 : A-A Ss/O2P C8/O2P pairing -B1274-B1288 : A-G Ss/O2P pairing -B1275-B1277 : A-G Hw/Hw pairing antiparallel cis one_hbond -B1276-B1294 : A-U Ww/Ww pairing antiparallel cis XX -B1277-B1293 : G-C Ww/Ww pairing antiparallel cis XIX -B1278-B1292 : C-G Ww/Ww pairing antiparallel cis XIX -B1279-B1291 : G-C Ww/Ww pairing antiparallel cis XIX -B1280-B1290 : G-C Ww/Ww pairing antiparallel cis XIX -B1281-B1282 : G-U Hh/Hh adjacent_5p pairing antiparallel cis one_hbond -B1281-B1289 : G-C Ww/Ww pairing antiparallel cis XIX -B1281-B1647 : G-U Bs/O2' pairing -B1281-B2013 : G-A O2P/Ww O2P/Ss pairing -B1282-B1285 : U-A Ss/Hw O2'/Bh pairing antiparallel trans one_hbond 45 -B1282-B1286 : U-A Ws/Bh pairing antiparallel trans one_hbond -B1283-B2012 : G-G O2P/Ww pairing -B1283-B2014 : G-A O2'/Ww pairing -B1284-B2012 : A-G O2P/Ss Hh/O2P pairing -B1284-B2013 : A-A O2P/Hh pairing -B1285-B1286 : A-A Hh/Hw adjacent_5p pairing parallel cis one_hbond -B1285-B2011 : A-U Ss/O2' C8/O2' pairing -B1285-B2012 : A-G O2P/Hh Ss/O2P C8/O2P downward pairing -B1292-B1310 : G-G O2P/Ss O2P/C8 pairing -B1294-B1311 : U-G O2P/Hh O2P/Hh pairing -B1294-B1640 : U-A O2P/Bh pairing -B1295-B1311 : C-G Hw/Hw pairing antiparallel trans one_hbond -B1295-B1645 : C-G Ww/Ww pairing antiparallel cis XIX -B1296-B1644 : G-C Ww/Ww pairing antiparallel cis XIX -B1297-B1643 : C-G Ww/Ww pairing antiparallel cis XIX -B1298-B1338 : C-G O2P/Bs pairing -B1298-B1339 : C-G O2P/Ss O2P/Bs pairing -B1298-B1642 : C-G Ww/Ww pairing antiparallel cis XIX -B1299-B1300 : G-G Ss/O2P C8/O2P adjacent_5p pairing -B1299-B1643 : G-G Ww/O2' Bs/O2' pairing -B1301-B1303 : A-G Ww/O2' Bh/O2' pairing -B1302-B1303 : A-G O2'/Hh pairing -B1302-B1607 : A-C Ss/O2P pairing -B1302-B1608 : A-A Bh/O2P pairing -B1303-B1625 : G-C Ww/Ww pairing antiparallel cis XIX -B1304-B1607 : A-C O2P/Bh pairing -B1304-B1624 : A-U Ww/Ww pairing antiparallel cis XX -B1304-B1646 : A-C O2'/Bh pairing -B1305-B1310 : C-G O2'/Ww O2'/Bs pairing -B1305-B1623 : C-G Ww/Ww pairing antiparallel cis XIX -B1305-B1646 : C-C O2P/Ww pairing -B1306-B1622 : C-G Ww/Ww pairing antiparallel cis XIX -B1307-B1621 : A-U Ww/Ww pairing antiparallel cis XX -B1308-B1309 : A-G C8/Hh adjacent_5p pairing antiparallel cis one_hbond -B1310-B1644 : G-C Hh/O2P Hh/O2P pairing -B1311-B1312 : G-U Bs/O2P Bs/O2P Ss/O2P adjacent_5p pairing -B1311-B1640 : G-A O2'/Ss outward pairing -B1312-B1641 : U-A O2P/Ww pairing -B1312-B1642 : U-G O2P/Hh pairing -B1313-B1339 : U-G Ws/Ws pairing antiparallel cis one_hbond -B1314-B1338 : C-G Ww/Ww pairing antiparallel cis XIX -B1315-B1337 : C-G Ww/Ww pairing antiparallel cis XIX -B1316-B1336 : U-A Ww/Ww pairing antiparallel cis XX -B1317-B1335 : G-C Ww/Ww pairing antiparallel cis XIX -B1318-B1334 : U-G Ws/Ws pairing antiparallel cis one_hbond -B1319-B1322 : C-A O2P/Bh O2P/Hh pairing -B1319-B1333 : C-G Ww/Ww pairing antiparallel cis XIX -B1320-B1322 : C-A O2P/C8 pairing -B1320-B1332 : C-G Ww/Ww pairing antiparallel cis XIX -B1323-B1331 : C-G Ww/Ww pairing antiparallel cis XIX -B1324-B1330 : G-C Ww/Ww pairing antiparallel cis XIX -B1341-B1592 : G-C Bs/O2P pairing -B1343-B1404 : G-C Ww/Ww pairing antiparallel cis XIX -B1344-B1403 : U-A Ww/Ww pairing antiparallel cis XX -B1345-B1601 : C-G Ww/Ww pairing antiparallel cis XIX -B1346-B1348 : G-C O2'/Hh pairing -B1346-B1600 : G-C Ww/Ww pairing antiparallel cis XIX -B1347-B1599 : A-U Ww/Ww pairing antiparallel cis XX -B1348-B1349 : C-C O2'/Hh adjacent_5p pairing -B1349-B1382 : C-G Ww/Ww pairing antiparallel cis XIX -B1350-B1381 : C-G Ww/Ww pairing antiparallel cis XIX -B1351-B1377 : C-G Ww/O2' pairing -B1351-B1378 : C-A Bh/O2P pairing -B1351-B1380 : C-G Ww/Ww pairing antiparallel cis XIX -B1352-B1354 : U-A O2P/Hh pairing -B1352-B1374 : U-G Ww/O2P pairing -B1353-B1373 : A-A Ww/O2' C8/O2P pairing -B1355-B1376 : G-C Ww/Ww pairing antiparallel cis XIX -B1356-B1375 : G-U Ws/Ws pairing antiparallel cis one_hbond -B1357-B1374 : C-G Ww/Ww pairing antiparallel cis XIX -B1358-B1359 : G-A Bs/O2P Ss/O2P adjacent_5p pairing -B1358-B1361 : G-G Ws/Wh pairing parallel cis one_hbond -B1359-B1371 : A-G O2P/Hh Hh/O2P inward pairing -B1360-B1361 : G-G O2P/Hh adjacent_5p pairing -B1361-B1370 : G-C Ww/Ww pairing antiparallel cis XIX -B1362-B1365 : C-A O2P/Ss pairing -B1362-B1369 : C-G Ww/Ww pairing antiparallel cis XIX -B1363-B1364 : C-G O2'/Hh adjacent_5p pairing -B1363-B1365 : C-A O2P/Bh O2P/Hh pairing -B1363-B1368 : C-G Ww/Ww pairing antiparallel cis XIX -B1364-B1366 : G-A O2'/Hh pairing -B1364-B1367 : G-A O2'/Bh pairing -B1365-B1366 : A-A O2P/Hh adjacent_5p pairing -B1365-B1367 : A-A O2P/Bh pairing -B1370-B1373 : C-A O2P/Ww O2P/Bh pairing -B1371-B1373 : G-A O2'/Ss Ss/O2P C8/O2P pairing -B1375-B1378 : U-A O2P/Bh pairing -B1376-B1378 : C-A O2P/Ss pairing -B1377-B1378 : G-A Hh/Ww adjacent_5p pairing parallel cis 61 -B1377-B1380 : G-G O2P/C8 pairing -B1385-B1402 : A-U Ww/Ww pairing antiparallel cis XX -B1386-B1401 : C-G Ww/Ww pairing antiparallel cis XIX -B1387-B1400 : A-U Ww/Ww pairing antiparallel cis XX -B1388-B1399 : G-C Ww/Ww pairing antiparallel cis XIX -B1389-B1398 : G-C Ww/Ww pairing antiparallel cis XIX -B1392-B1394 : A-U Hw/Ss Bh/O2' Hh/O2' pairing parallel cis one_hbond -B1392-B1395 : A-A Bh/O2P pairing -B1394-B1395 : U-A Ww/Hh adjacent_5p pairing antiparallel cis 52 -B1405-B1597 : U-A Ww/Ww pairing antiparallel cis XX -B1406-B1596 : U-A Ww/Ww pairing antiparallel cis XX -B1407-B1595 : G-C Ww/Ww pairing antiparallel cis XIX -B1408-B1594 : G-U Ws/Ws pairing antiparallel cis one_hbond -B1409-B1593 : U-A Ww/Ww pairing antiparallel cis XX -B1410-B1592 : G-C Ww/Ww pairing antiparallel cis XIX -B1411-B1591 : U-A Ww/Ww pairing antiparallel cis XX -B1412-B1590 : U-A Ww/Ww pairing antiparallel cis XX -B1413-B1589 : A-U Ww/Ww pairing antiparallel cis XX -B1414-B1586 : C-A Bh/O2P pairing -B1414-B1588 : C-G Ww/Ww pairing antiparallel cis XIX -B1415-B1583 : U-A O2P/Bh O2P/Hh pairing -B1415-B1587 : U-G Ws/Ws pairing antiparallel cis one_hbond -B1416-B1465 : G-G Ws/Ss Bs/O2' pairing antiparallel cis one_hbond -B1416-B1583 : G-A O2P/Bh pairing -B1417-B1635 : C-A Ss/Bs Ww/O2' Bh/O2' pairing parallel trans one_hbond -B1418-B1581 : G-G Ww/Hh pairing parallel trans one_hbond 111 -B1418-B1583 : G-A Bs/O2P pairing -B1418-B1634 : G-A O2'/Ww O2'/Bh pairing -B1418-B1635 : G-A O2P/Bh Bs/O2P Bs/O2P pairing -B1419-B1573 : A-G O2'/Hh pairing -B1420-B1569 : A-A O2P/Ww O2P/Ss pairing -B1420-B1578 : A-U Ww/Ww pairing antiparallel cis XX -B1421-B1569 : G-A O2P/Ss O2P/C8 pairing -B1421-B1577 : G-C Ww/Ww pairing antiparallel cis XIX -B1422-B1568 : G-G Hw/C8 pairing parallel trans one_hbond -B1422-B1576 : G-U Ws/Ws pairing antiparallel cis one_hbond -B1423-B1575 : G-C Ww/Ww pairing antiparallel cis XIX -B1424-B1565 : G-C Sw/Bs O2'/Hh pairing antiparallel trans one_hbond 128 -B1424-B1567 : G-G Hh/O2P pairing -B1424-B1574 : G-C Ww/Ww pairing antiparallel cis XIX -B1425-B1566 : G-A Bs/O2P pairing -B1426-B1431 : G-A Ww/O2' pairing -B1426-B1566 : G-A O2P/Ss O2P/Ss pairing -B1426-B1567 : G-G O2P/Hh O2P/C8 pairing -B1427-B1572 : A-A O2P/Ss pairing -B1428-B1630 : C-A Hh/O2' pairing -B1429-B1564 : G-C Ww/Ww pairing antiparallel cis XIX -B1430-B1566 : C-A Ss/Hw O2'/Ww O2'/Bh pairing antiparallel trans one_hbond 77 -B1431-B1562 : A-U Ww/Ww pairing antiparallel cis XX -B1432-B1433 : G-A O2P/Hh adjacent_5p pairing -B1432-B1561 : G-C Ww/Ww pairing antiparallel cis XIX -B1434-B1435 : A-G O2'/Hh adjacent_5p pairing -B1435-B1557 : G-C Ww/Ww pairing antiparallel cis XIX -B1436-B1439 : G-A O2P/Ww pairing -B1436-B1556 : G-C Ww/Ww pairing antiparallel cis XIX -B1437-B1438 : C-U O2P/Hh adjacent_5p pairing -B1437-B1555 : C-G Ww/Ww pairing antiparallel cis XIX -B1440-B1551 : U-A Ww/Ww pairing antiparallel cis XX -B1441-B1550 : G-C Ww/Ww pairing antiparallel cis XIX -B1442-B1549 : U-A Ww/Ww pairing antiparallel cis XX -B1443-B1548 : U-A Ww/Ww pairing antiparallel cis XX -B1444-B1445 : G-G O2P/Ww adjacent_5p pairing -B1444-B1547 : G-C Ww/Ww pairing antiparallel cis XIX -B1445-B1446 : G-C O2P/Hh adjacent_5p pairing -B1445-B1543 : G-G O2'/Hh pairing -B1446-B1465 : C-G Ww/Ww pairing antiparallel cis XIX -B1447-B1464 : C-G Ww/Ww pairing antiparallel cis XIX -B1448-B1463 : G-C Ww/Ww pairing antiparallel cis XIX -B1449-B1462 : G-C Ww/Ww pairing antiparallel cis XIX -B1449-B1544 : G-A Hw/Bs pairing antiparallel trans one_hbond -B1450-B1452 : G-G Bs/O2P pairing -B1450-B1461 : G-C Ww/Ww pairing antiparallel cis XIX -B1450-B1468 : G-U O2'/Ww pairing -B1451-B1526 : C-C Hh/O2P pairing -B1452-B1453 : G-A C8/O2P adjacent_5p pairing -B1452-B1460 : G-U Hw/Hh pairing antiparallel cis one_hbond -B1452-B1526 : G-C O2P/Hh pairing -B1454-B1470 : C-A Ww/O2' Bh/O2' pairing -B1455-B1526 : G-C Hh/O2P pairing -B1459-B1461 : G-C Ss/O2P pairing -B1459-B1462 : G-C Bs/O2P pairing -B1459-B1543 : G-G Ww/O2' Bs/O2' pairing -B1459-B1544 : G-A Bs/O2P pairing -B1463-B1544 : C-A Bh/O2' pairing -B1464-B1466 : G-U Sw/Ss Ss/O2' pairing antiparallel cis one_hbond -B1464-B1544 : G-A Hh/O2' pairing -B1467-B1468 : U-U Hh/O2P adjacent_5p pairing -B1468-B1527 : U-G O2'/Ss O2'/C8 pairing -B1469-B1473 : A-G Hh/O2P C8/O2P pairing -B1469-B1474 : A-U Bh/O2P pairing -B1470-B1472 : A-C Ss/O2P pairing -B1470-B1528 : A-A O2P/Hh pairing -B1471-B1520 : G-U Ws/Ws pairing antiparallel cis one_hbond -B1471-B1523 : G-U Ss/Hh pairing antiparallel cis one_hbond -B1471-B1536 : G-C Ww/O2' pairing -B1472-B1515 : C-A O2P/Hh pairing -B1472-B1519 : C-G Ww/Ww pairing antiparallel cis XIX -B1472-B1528 : C-A O2'/Ww O2'/Ss pairing -B1473-B1518 : G-C Ww/Ww pairing antiparallel cis XIX -B1474-B1517 : U-G Ws/Ws pairing antiparallel cis one_hbond -B1476-B1517 : U-G Ww/O2P pairing -B1477-B1478 : A-G C8/O2P adjacent_5p pairing -B1478-B1513 : G-U Ws/Ws pairing antiparallel cis one_hbond -B1478-B1515 : G-A O2'/Bh pairing -B1478-B1516 : G-G C8/O2P pairing -B1479-B1512 : G-C Ww/Ww pairing antiparallel cis XIX -B1480-B1511 : C-G Ww/Ww pairing antiparallel cis XIX -B1481-B1508 : U-A Ww/Ww pairing antiparallel cis XX -B1482-B1507 : G-C Ww/Ww pairing antiparallel cis XIX -B1483-B1506 : G-U Ws/Ws pairing antiparallel cis one_hbond -B1484-B1505 : U-A Ww/Ww pairing antiparallel cis XX -B1485-B1504 : U-A Ww/Ww pairing antiparallel cis XX -B1486-B1503 : U-A Ww/Ww pairing antiparallel cis XX -B1487-B1502 : U-A Ww/Ww pairing antiparallel cis XX -B1488-B1501 : C-G Ww/Ww pairing antiparallel cis XIX -B1489-B1500 : C-G Ww/Ww pairing antiparallel cis XIX -B1491-B1496 : G-A Bh/Bs pairing antiparallel trans one_hbond -B1491-B1499 : G-C Ww/Ww pairing antiparallel cis XIX -B1492-B1498 : G-C Ww/Ww pairing antiparallel cis XIX -B1495-B1496 : A-A O2P/Hh adjacent_5p pairing -B1509-B1510 : A-G O2'/Hh adjacent_5p pairing -B1515-B1516 : A-G Ss/O2P adjacent_5p pairing -B1516-B1520 : G-U Ww/Hw pairing parallel cis one_hbond -B1519-B1521 : G-G Ws/Bh pairing antiparallel cis one_hbond 115 -B1520-B1522 : U-A O2'/Ww O2'/Ss pairing -B1520-B1536 : U-C Ww/O2' pairing -B1521-B1522 : G-A Ww/O2' adjacent_5p pairing -B1522-B1528 : A-A O2'/Ss Hh/O2' C8/O2' pairing -B1522-B1537 : A-G Bh/O2P pairing -B1523-B1527 : U-G O2P/Bs O2P/Ss pairing -B1523-B1528 : U-A O2P/Ww O2P/Ss pairing -B1524-B1539 : G-U Ww/O2P pairing -B1527-B1529 : G-G Bs/O2P Ss/O2P Ss/O2P C8/O2P pairing -B1528-B1529 : A-G O2P/Hh adjacent_5p pairing -B1529-B1542 : G-U Ws/Ws pairing antiparallel cis one_hbond -B1530-B1541 : G-C Ww/Ww pairing antiparallel cis XIX -B1531-B1540 : C-G Ww/Ww pairing antiparallel cis XIX -B1532-B1539 : A-U Ww/Ww pairing antiparallel cis XX -B1533-B1535 : C-A Bh/O2P pairing -B1533-B1538 : C-G Ww/Ww pairing antiparallel cis XIX -B1534-B1535 : U-A O2'/Hh adjacent_5p pairing -B1543-B1544 : G-A Ss/C8 adjacent_5p pairing parallel cis one_hbond -B1545-B1546 : A-G O2'/Ss adjacent_5p pairing -B1551-B1552 : A-A O2P/Ss O2P/C8 Hh/O2' adjacent_5p pairing -B1552-B1555 : A-G Ww/O2P pairing -B1553-B1555 : A-G O2'/Hh O2P/Hh pairing -B1557-B1560 : C-G O2P/Bs pairing -B1559-B1561 : U-C O2'/Bh pairing -B1568-B1570 : G-A O2P/C8 O2'/Bh pairing -B1568-B1572 : G-A O2P/C8 O2'/Hh pairing -B1568-B1574 : G-C O2'/Bh pairing -B1568-B1575 : G-C O2'/Bh pairing -B1568-B1580 : G-A Ws/Ww pairing antiparallel trans one_hbond -B1569-B1570 : A-A O2P/Ww O2P/Bh O2'/Hh O2'/C8 adjacent_5p pairing -B1569-B1571 : A-A Hh/O2P pairing -B1569-B1572 : A-A C8/O2P pairing -B1569-B1573 : A-G O2P/C8 pairing -B1570-B1572 : A-A Ss/O2P downward pairing -B1571-B1572 : A-A Ss/O2P adjacent_5p pairing -B1572-B1573 : A-G Ss/O2P adjacent_5p pairing -B1572-B1574 : A-C Hh/Hw pairing parallel trans one_hbond -B1573-B1631 : G-G Ss/O2' pairing -B1576-B1580 : U-A O2P/Ww O2P/Bh pairing -B1577-B1579 : C-A O2P/Bh O2P/Hh O2P/Hh pairing -B1577-B1580 : C-A O2P/Hh pairing -B1578-B1579 : U-A O2P/Hh O2P/C8 adjacent_5p pairing -B1579-B1580 : A-A Ss/O2P adjacent_5p pairing -B1580-B1632 : A-A Ss/O2P pairing -B1581-B1629 : G-U Bs/O2P pairing -B1581-B1630 : G-A Bs/O2P pairing -B1581-B1632 : G-A Ww/O2P pairing -B1582-B1628 : C-G O2P/Hh pairing -B1582-B1634 : C-A Ws/C8 pairing parallel cis one_hbond -B1583-B1637 : A-A Ww/O2P Ww/O2P Ss/O2P pairing -B1583-B1638 : A-C Bh/O2P pairing -B1586-B1587 : A-G O2'/Hh O2'/C8 adjacent_5p pairing -B1586-B1588 : A-G C8/O2P pairing -B1586-B1589 : A-U Hh/O2P pairing -B1596-B1598 : A-A O2P/Hh pairing -B1598-B1599 : A-U C8/O2P pairing -B1608-B1622 : A-G Ss/O2P pairing -B1609-B1610 : A-A Ss/O2P adjacent_5p pairing -B1609-B1621 : A-U C8/O2' pairing -B1610-B1611 : A-C Ss/O2P adjacent_5p pairing -B1610-B1612 : A-C Ww/O2P pairing -B1611-B1620 : C-G Ww/Ww pairing antiparallel cis XIX -B1612-B1619 : C-G Ww/Ww pairing antiparallel cis XIX -B1613-B1615 : G-C Ss/Ww pairing parallel trans 119 -B1626-B1642 : A-G Hh/Sw pairing antiparallel cis one_hbond -B1627-B1639 : G-C Ww/Ww pairing antiparallel cis XIX -B1627-B1641 : G-A O2'/C8 pairing -B1628-B1638 : G-C Ww/Ww pairing antiparallel cis XIX -B1629-B1637 : U-A Ww/Ww pairing antiparallel cis XX -B1630-B1636 : A-U Ww/Ww pairing antiparallel cis XX -B1631-B1632 : G-A O2'/Hh adjacent_5p pairing -B1634-B1635 : A-A Hh/O2P C8/O2P adjacent_5p pairing -B1641-B1642 : A-G Ss/O2P adjacent_5p pairing -B1648-B2009 : U-A Ww/Ww pairing antiparallel cis XX -B1649-B2008 : G-C Ww/Ww pairing antiparallel cis XIX -B1650-B2007 : A-U Ww/Ww pairing antiparallel cis XX -B1651-B1652 : G-A Bs/O2' adjacent_5p pairing -B1651-B2006 : G-C Ww/Ww pairing antiparallel cis XIX -B1653-B1654 : G-A O2'/Ss adjacent_5p pairing -B1656-B2004 : C-G Ww/Ww pairing antiparallel cis XIX -B1657-B2003 : U-A Ww/Ww pairing antiparallel cis XX -B1658-B1996 : C-C O2P/Bh pairing -B1658-B2002 : C-G Ww/Ww pairing antiparallel cis XIX -B1659-B1996 : G-C O2P/Ww O2P/Bh pairing -B1659-B2001 : G-C Ww/Ww pairing antiparallel cis XIX -B1660-B2000 : G-C Ww/Ww pairing antiparallel cis XIX -B1661-B1999 : G-C Ww/Ww pairing antiparallel cis XIX -B1662-B1998 : U-A Ww/Ww pairing antiparallel cis XX -B1663-B1997 : G-C Ww/Ww pairing antiparallel cis XIX -B1664-B1665 : A-A O2'/Hh adjacent_5p pairing -B1664-B1759 : A-A Ww/O2P Bh/O2P pairing -B1665-B1995 : A-U Ww/Ww pairing antiparallel cis XX -B1666-B1994 : G-C Ww/Ww pairing antiparallel cis XIX -B1667-B1758 : G-U Hh/Ww pairing antiparallel trans one_hbond 95 -B1667-B1993 : G-U Ws/Ws pairing antiparallel cis one_hbond -B1668-B1753 : A-G O2'/Bs pairing -B1669-B1991 : A-U Ww/Ww pairing antiparallel cis XX -B1670-B1749 : C-A Ww/O2' Bh/O2' pairing -B1670-B1753 : C-G Ws/C8 O2'/C8 pairing antiparallel cis one_hbond -B1671-B1672 : U-A Bs/C8 adjacent_5p pairing antiparallel trans one_hbond -B1671-B1751 : U-U Hh/O2P pairing -B1672-B1673 : A-G C8/O2' adjacent_5p pairing -B1672-B1674 : A-G Ss/O2P C8/O2P pairing -B1672-B1678 : A-A Ss/Wh pairing antiparallel cis one_hbond 40 -B1672-B1702 : A-G Ww/O2P pairing -B1673-B1682 : G-G O2P/Hh pairing -B1673-B1988 : G-G Bs/O2P pairing -B1674-B1678 : G-A O2P/Ww pairing -B1674-B1681 : G-G Hh/O2P pairing -B1674-B1701 : G-A Bs/O2P Ss/O2P pairing -B1674-B1702 : G-G O2'/Hh pairing -B1675-B1677 : C-A O2'/Ss O2'/C8 pairing -B1675-B1678 : C-A O2P/Hh O2P/C8 pairing -B1678-B1684 : A-G O2'/Hh pairing -B1678-B1685 : A-C O2'/Bh pairing -B1679-B1685 : A-C O2P/Bh pairing -B1679-B1686 : A-C O2P/Bh pairing -B1679-B1690 : A-A Ww/C8 pairing parallel cis one_hbond -B1679-B1700 : A-A Hh/O2P pairing -B1680-B1682 : U-G Ww/O2P pairing -B1680-B1700 : U-A O2P/C8 pairing -B1682-B1706 : G-C Ww/Ww pairing antiparallel cis XIX -B1683-B1705 : U-A Ww/Ww pairing antiparallel cis XX -B1684-B1704 : G-C Ww/Ww pairing antiparallel cis XIX -B1685-B1703 : C-G Ww/Ww pairing antiparallel cis XIX -B1686-B1702 : C-G Ww/Ww pairing antiparallel cis XIX -B1689-B1692 : A-U Hh/O2P C8/O2P pairing -B1689-B1693 : A-U Bh/O2P pairing -B1689-B1695 : A-G Ww/O2P Ss/O2P pairing -B1689-B1696 : A-G Ww/O2P pairing -B1690-B1691 : A-C Bh/O2' Hh/O2' adjacent_5p pairing -B1691-B1697 : C-G Ww/Sw pairing antiparallel cis one_hbond 125 -B1691-B1699 : C-G O2P/Hh pairing -B1692-B1697 : U-G Hh/O2' pairing -B1693-B1698 : U-A O2P/Hh pairing -B1694-B1695 : C-G O2'/Ww O2'/Bs adjacent_5p pairing -B1694-B1697 : C-G Bh/O2P pairing -B1694-B1698 : C-A Bh/O2P pairing -B1696-B2703 : G-C O2P/Bh pairing -B1697-B2704 : G-C O2P/Bh pairing -B1697-B2705 : G-A O2P/Bh pairing -B1698-B2702 : A-G O2P/Ss pairing -B1701-B1989 : A-G O2'/Hh pairing -B1702-B1989 : G-G O2P/Hh pairing -B1707-B1751 : G-U Ws/Ws pairing antiparallel cis one_hbond -B1708-B1750 : C-G Ww/Ww pairing antiparallel cis XIX -B1709-B1749 : U-A Ww/Ww pairing antiparallel cis XX -B1710-B1748 : G-C Ww/Ww pairing antiparallel cis XIX -B1711-B1747 : A-U Ww/Ww pairing antiparallel cis XX -B1712-B1746 : U-A Ww/Ww pairing antiparallel cis XX -B1713-B1741 : A-C Bh/O2P pairing -B1713-B1742 : A-U Ww/O2P pairing -B1714-B1717 : U-A O2P/Bh pairing -B1714-B1741 : U-C Bs/Hw pairing antiparallel trans one_hbond 97 -B1715-B1737 : G-G Hh/Sw pairing antiparallel trans one_hbond 108 -B1715-B1738 : G-G O2P/Hh pairing -B1716-B1743 : U-G Ws/Ws pairing antiparallel cis one_hbond -B1717-B1742 : A-U Ww/Ww pairing antiparallel cis XX -B1718-B1741 : G-C Ww/Ww pairing antiparallel cis XIX -B1719-B1732 : G-C Hh/O2P pairing -B1721-B1737 : G-G O2'/Ww pairing -B1721-B1738 : G-G Bs/O2' pairing -B1721-B1739 : G-A O2P/Ww O2P/Bh pairing -B1722-B1739 : A-A O2P/Ss O2P/C8 pairing -B1722-B1740 : A-G O2P/Ww downward pairing -B1724-B1736 : G-U Ws/Ws pairing antiparallel cis one_hbond -B1725-B1735 : U-A Ww/Ww pairing antiparallel cis XX -B1726-B1734 : C-G Ww/Ww pairing antiparallel cis XIX -B1727-B1733 : C-G Ww/Ww pairing antiparallel cis XIX -B1728-B1732 : C-C Wh/Ww pairing parallel trans one_hbond -B1734-B1739 : G-A O2P/Ww O2P/Bh pairing -B1735-B1739 : A-A O2P/C8 Hh/O2' pairing -B1736-B1740 : U-G Hh/O2P Ww/O2P pairing -B1737-B1740 : G-G Hh/Bs Hh/O2P pairing parallel cis 33 -B1743-B1744 : G-A O2'/Hh adjacent_5p pairing -B1744-B1746 : A-A Ss/O2P pairing -B1754-B1988 : A-G O2P/Ss pairing -B1754-B1989 : A-G C8/O2' pairing -B1754-B1990 : A-C Ww/O2P Bh/O2P Bh/O2P pairing -B1755-B1988 : A-G O2P/Bs pairing -B1757-B1760 : A-C O2'/Hh pairing -B1762-B1992 : A-G Bs/Wh pairing antiparallel trans one_hbond -B1764-B1988 : C-G Ww/Ww pairing antiparallel cis XIX -B1765-B1987 : U-A Ww/Ww pairing antiparallel cis XX -B1766-B1986 : G-C Ww/Ww pairing antiparallel cis XIX -B1767-B1985 : G-C Ww/Ww pairing antiparallel cis XIX -B1768-B1984 : C-G Ww/Ww pairing antiparallel cis XIX -B1769-B1983 : U-G Ws/Ws pairing antiparallel cis one_hbond -B1770-B1982 : G-U Ws/Ws pairing antiparallel cis one_hbond -B1771-B1980 : C-G Ww/Ww pairing antiparallel cis XIX -B1772-B1773 : A-A Ss/O2' adjacent_5p pairing -B1772-B1979 : A-U Ww/Ww pairing antiparallel cis XX -B1774-B1784 : C-A Ww/O2P pairing -B1775-B1789 : U-A Ww/Ww pairing antiparallel cis XX -B1776-B1788 : G-C Ww/Ww pairing antiparallel cis XIX -B1777-B1787 : U-A Ww/Ww pairing antiparallel cis XX -B1778-B1786 : U-A Ww/Ww pairing antiparallel cis XX -B1779-B1785 : U-A Ww/Ww pairing antiparallel cis XX -B1780-B1784 : A-A Hh/Wh pairing antiparallel trans one_hbond -B1780-B2544 : A-G Hh/O2' pairing -B1784-B2544 : A-G Ww/O2' pairing -B1787-B2556 : A-C Ww/O2P Ss/O2P pairing -B1787-B2557 : A-G Ss/O2P C8/O2P pairing -B1790-B1828 : C-G O2'/Hh pairing -B1790-B1830 : C-C Ww/O2P Bh/O2P pairing -B1790-B1942 : C-C Ws/Wh pairing antiparallel cis one_hbond 137 -B1791-B1930 : A-G Ss/O2P pairing -B1791-B1932 : A-A Bh/O2' pairing -B1791-B1934 : A-C Ss/Hh O2'/Hh pairing parallel cis one_hbond -B1791-B1942 : A-C Hh/O2P Hh/O2P pairing -B1791-B2441 : A-U Hh/O2' pairing -B1792-B1819 : G-A O2P/Ww pairing -B1792-B1827 : G-U Ws/Ws pairing antiparallel cis one_hbond -B1792-B1934 : G-C O2P/Bh pairing -B1792-B1943 : G-U O2'/Ww pairing -B1793-B1826 : C-G Ww/Ww pairing antiparallel cis XIX -B1794-B1825 : A-U Ww/Ww pairing antiparallel cis XX -B1795-B1824 : C-G Ww/Ww pairing antiparallel cis XIX -B1795-B1965 : C-C O2'/Bh pairing -B1796-B1817 : U-G O2P/Ww O2P/Ww pairing -B1796-B1823 : U-G Ws/Ws pairing antiparallel cis one_hbond -B1797-B1815 : G-A O2P/C8 pairing -B1797-B1817 : G-G O2P/Bs pairing -B1797-B1822 : G-C Ww/Ww pairing antiparallel cis XIX -B1798-B1821 : U-A Ww/Ww pairing antiparallel cis XX -B1799-B1820 : G-U Ws/Ws pairing antiparallel cis one_hbond -B1801-B1802 : A-A Hh/O2P adjacent_5p pairing -B1801-B1816 : A-C Ss/O2' C8/O2' pairing -B1802-B1813 : A-G Hh/Ss Bh/O2' pairing antiparallel trans XI -B1803-B1897 : A-G Bh/O2P pairing -B1804-B1813 : C-G Ww/Ww pairing antiparallel cis XIX -B1805-B1812 : A-U Ww/Ww pairing antiparallel cis XX -B1806-B1809 : C-A Bh/O2P pairing -B1806-B1811 : C-G Ww/Ww pairing antiparallel cis XIX -B1808-B1810 : A-A O2P/Bh pairing -B1809-B1810 : A-A O2P/Bh adjacent_5p upward pairing -B1810-B1811 : A-G O2P/Hh adjacent_5p pairing -B1813-B1814 : G-G Bh/C8 adjacent_5p pairing antiparallel cis one_hbond -B1814-B1815 : G-A O2'/Ss O2P/Ww O2P/Bh adjacent_5p pairing -B1814-B1816 : G-C O2P/Ww pairing -B1819-B1934 : A-C Wh/Ww pairing parallel trans one_hbond -B1825-B1966 : U-A O2'/Ss pairing -B1826-B1968 : G-G O2'/Hh pairing -B1827-B1829 : U-A Ww/O2P pairing -B1828-B2443 : G-C Ww/O2' Bs/O2' pairing -B1829-B1969 : A-A C8/O2' pairing -B1829-B1970 : A-A Bh/O2' Hh/O2P C8/O2P pairing -B1829-B1976 : A-U Ww/Ww pairing antiparallel cis XX -B1830-B1970 : C-A Bh/O2' pairing -B1830-B1975 : C-G Ww/Ww pairing antiparallel cis XIX -B1831-B1974 : G-C Ww/Ww pairing antiparallel cis XIX -B1832-B1973 : C-G Ww/Ww pairing antiparallel cis XIX -B1833-B1834 : C-U O2P/Hh adjacent_5p pairing -B1833-B1972 : C-G Ww/Ww pairing antiparallel cis XIX -B1835-B1905 : G-C Ww/Ww pairing antiparallel cis XIX -B1836-B1904 : C-G Ww/Ww pairing antiparallel cis XIX -B1837-B1838 : C-C Ws/Hh adjacent_5p pairing parallel trans one_hbond -B1837-B1903 : C-G Ww/Ww pairing antiparallel cis XIX -B1838-B1840 : C-G O2'/C8 pairing -B1840-B1902 : G-C Ww/Ww pairing antiparallel cis XIX -B1841-B1901 : U-A Ww/Ww pairing antiparallel cis XX -B1842-B1898 : G-U Ws/Ws pairing antiparallel cis one_hbond -B1843-B1897 : C-G Ww/Ww pairing antiparallel cis XIX -B1844-B1896 : C-G Ww/Ww pairing antiparallel cis XIX -B1845-B1895 : G-C Ww/Ww pairing antiparallel cis XIX -B1846-B1847 : G-A O2P/Hh O2P/Hh adjacent_5p pairing -B1846-B1894 : G-C Ww/Ww pairing antiparallel cis XIX -B1847-B2231 : A-U Ss/O2' C8/O2' pairing -B1848-B1852 : A-U Hh/O2' C8/O2' pairing -B1848-B2089 : A-C O2P/Hh pairing -B1848-B2090 : A-A Bh/Ss Hh/O2' pairing antiparallel trans one_hbond 40 -B1849-B1889 : G-A O2P/Ss pairing -B1849-B1893 : G-C Ww/Ww pairing antiparallel cis XIX -B1850-B1890 : G-A O2P/Bh pairing -B1850-B1892 : G-C Ww/Ww pairing antiparallel cis XIX -B1852-B1856 : U-U O2P/Ww pairing -B1852-B1857 : U-G O2'/Hh pairing -B1853-B1855 : A-U Ss/O2P pairing -B1853-B1857 : A-G O2P/C8 pairing -B1853-B1886 : A-U O2P/Ww pairing -B1853-B1887 : A-C Hh/O2P pairing -B1853-B1888 : A-G O2'/C8 pairing -B1854-B1855 : A-U Ss/O2P adjacent_5p pairing -B1854-B1859 : A-U Bh/O2' pairing -B1854-B1888 : A-G O2P/Hh O2P/C8 pairing -B1855-B1858 : U-A O2P/Hh pairing -B1855-B1884 : U-G O2'/Ss Hh/O2' Ww/O2' pairing -B1855-B1885 : U-A Ww/O2' pairing -B1855-B1886 : U-U Hh/O2P pairing -B1856-B1890 : U-A O2'/Ww pairing -B1857-B1858 : G-A Bs/O2P Ss/O2P adjacent_5p pairing -B1857-B1886 : G-U O2P/Ww pairing -B1857-B2230 : G-G Bs/O2' Ss/O2' pairing -B1858-B1885 : A-A O2'/Ww pairing -B1859-B1885 : U-A O2P/Ww O2P/Bh pairing -B1860-B1882 : G-U Ws/Ws pairing antiparallel cis one_hbond -B1860-B1883 : G-U Sw/Ws pairing parallel trans one_hbond -B1861-B1881 : G-C Ww/Ww pairing antiparallel cis XIX -B1862-B1880 : G-U Ws/Ws pairing antiparallel cis one_hbond -B1863-B1879 : G-C Ww/Ww pairing antiparallel cis XIX -B1864-B1878 : U-G Ws/Ws pairing antiparallel cis one_hbond -B1865-B1877 : U-A Ww/Ww pairing antiparallel cis XX -B1867-B1874 : G-C Ww/Ww pairing antiparallel cis XIX -B1868-B1873 : C-G Ww/Ww pairing antiparallel cis XIX -B1870-B1872 : C-A Hh/Ww pairing parallel trans one_hbond -B1870-B2159 : C-G O2'/Hh pairing -B1871-B1872 : A-A O2P/Hh Ww/O2' adjacent_5p upward pairing -B1871-B2132 : A-U Ww/O2P Bh/O2P pairing -B1871-B2133 : A-G Wh/Hh pairing parallel cis one_hbond 61 -B1872-B1875 : A-G O2P/Ww O2P/Bs pairing -B1873-B2134 : G-A O2P/Bh pairing -B1874-B1875 : C-G Bh/O2' adjacent_5p pairing -B1876-B1877 : A-A O2P/Hh adjacent_5p pairing -B1882-B1883 : U-U O2'/Hh adjacent_5p pairing -B1883-B1884 : U-G O2'/C8 adjacent_5p pairing -B1886-B1887 : U-C O2'/Hh adjacent_5p pairing -B1887-B1888 : C-G O2P/Hh adjacent_5p pairing -B1900-B1901 : A-A O2'/Hh adjacent_5p pairing -B1900-B1902 : A-C Hh/Wh pairing antiparallel trans one_hbond -B1905-B1928 : C-A O2'/Hh O2'/C8 pairing -B1906-B1924 : G-C Ww/Ww pairing antiparallel cis XIX -B1906-B1938 : G-A O2P/Hh pairing -B1907-B1923 : G-U Ws/Ws pairing antiparallel cis one_hbond -B1907-B1938 : G-A O2P/Bh pairing -B1908-B1922 : C-G Ww/Ww pairing antiparallel cis XIX -B1909-B1921 : C-G Ww/Ww pairing antiparallel cis XIX -B1910-B1920 : G-C Ww/Ww pairing antiparallel cis XIX -B1912-B1916 : A-A Ww/O2P pairing -B1924-B1926 : C-U Bh/O2P pairing -B1926-B1927 : U-A O2P/Bh O2P/Hh adjacent_5p pairing -B1928-B1936 : A-A Ss/O2' pairing -B1928-B1941 : A-C O2'/Bh pairing -B1929-B1930 : G-G Ss/Ws adjacent_5p pairing parallel cis one_hbond -B1932-B1937 : A-A Hh/O2P pairing -B1932-B1941 : A-C O2P/Ww O2P/Bh pairing -B1933-B1935 : G-G O2'/Bs O2'/Ss pairing -B1933-B1936 : G-A Hh/C8 pairing parallel trans one_hbond -B1933-B2063 : G-C C8/O2P pairing -B1934-B1935 : C-G O2P/C8 adjacent_5p pairing -B1934-B1972 : C-G O2P/Bs O2P/Ss pairing -B1935-B1940 : G-U Bs/O2P pairing -B1935-B1973 : G-G Hh/O2' pairing -B1935-B2062 : G-A Bh/Bs pairing antiparallel cis one_hbond -B1937-B1938 : A-A O2P/Hh O2P/C8 adjacent_5p pairing -B1938-B2064 : A-C Ss/O2P pairing -B1940-B2063 : U-C Bs/Hh pairing parallel cis one_hbond -B1940-B2553 : U-G Ww/O2' pairing -B1941-B1972 : C-G O2'/C8 pairing -B1941-B2062 : C-A O2P/Ss pairing -B1943-B1944 : U-U Hh/O2P adjacent_5p pairing -B1945-B1961 : G-C Ww/Ww pairing antiparallel cis XIX -B1946-B1960 : U-A Ww/Ww pairing antiparallel cis XX -B1946-B1963 : U-U O2'/Hh pairing -B1947-B1959 : C-G Ww/Ww pairing antiparallel cis XIX -B1948-B1958 : G-C Ww/Ww pairing antiparallel cis XIX -B1949-B1957 : G-C Ww/Ww pairing antiparallel cis XIX -B1950-B1952 : G-A Ww/O2P pairing -B1950-B1956 : G-U Ws/Ws pairing antiparallel cis one_hbond -B1952-B1954 : A-G Ww/O2P pairing -B1952-B1968 : A-G O2'/Bs pairing -B1954-B2058 : G-A O2'/Ss pairing -B1955-B2058 : U-A O2P/Ss pairing -B1963-B1965 : U-C Ww/O2P pairing -B1964-B1965 : G-C O2'/Hh adjacent_5p pairing -B1965-B1966 : C-A O2'/Hh O2'/C8 adjacent_5p pairing -B1971-B1974 : U-C O2P/Bh pairing -B1991-B1992 : U-G O2P/Hh adjacent_5p pairing -B2004-B2005 : G-A O2P/Hh adjacent_5p pairing -B2007-B2846 : U-G O2P/Hh pairing -B2013-B2014 : A-A O2P/Bh adjacent_5p pairing -B2015-B2018 : A-G O2'/Ww pairing -B2017-B2018 : U-G O2P/Hh adjacent_5p pairing -B2023-B2040 : C-G Ww/Ww pairing antiparallel cis XIX -B2024-B2039 : G-U Ws/Ws pairing antiparallel cis one_hbond -B2025-B2038 : C-G Ww/Ww pairing antiparallel cis XIX -B2026-B2037 : U-A Ww/Ww pairing antiparallel cis XX -B2027-B2036 : G-C Ww/Ww pairing antiparallel cis XIX -B2042-B2043 : A-C O2'/Hh adjacent_5p pairing -B2043-B2625 : C-G Ww/Ww pairing antiparallel cis XIX -B2044-B2624 : C-G Ww/Ww pairing antiparallel cis XIX -B2045-B2623 : C-G Ww/Ww pairing antiparallel cis XIX -B2046-B2622 : G-U Ws/Ws pairing antiparallel cis one_hbond -B2047-B2621 : C-G Ww/Ww pairing antiparallel cis XIX -B2048-B2620 : G-C Ww/Ww pairing antiparallel cis XIX -B2049-B2619 : G-C Ww/Ww pairing antiparallel cis XIX -B2050-B2618 : C-G Ww/Ww pairing antiparallel cis XIX -B2051-B2609 : A-U Hh/O2P pairing -B2051-B2610 : A-C Ss/O2P pairing -B2052-B2617 : A-U Ww/Ww pairing antiparallel cis XX -B2053-B2616 : G-C Ww/Ww pairing antiparallel cis XIX -B2054-B2055 : A-C O2P/Hh adjacent_5p pairing -B2054-B2615 : A-U Ww/Ww pairing antiparallel cis XX -B2056-B2612 : G-C Ww/Ww pairing antiparallel cis XIX -B2057-B2611 : G-C Ww/Ww pairing antiparallel cis XIX -B2058-B2068 : A-U Hw/Ws Ss/O2' pairing antiparallel cis one_hbond -B2059-B2556 : A-C Bh/O2P pairing -B2060-B2447 : A-G Ss/O2P pairing -B2060-B2448 : A-A Bh/O2' upward pairing -B2060-B2557 : A-G O2'/Bs O2'/Ss pairing -B2060-B2558 : A-C O2'/Hh pairing -B2061-B2553 : G-G Bs/O2P pairing -B2061-B2554 : G-U Ss/O2P pairing -B2061-B2557 : G-G O2P/Bs pairing -B2062-B2063 : A-C O2P/Bh adjacent_5p pairing -B2062-B2064 : A-C O2P/Bh pairing -B2063-B2447 : C-G Ww/Ww pairing antiparallel cis XIX -B2063-B2553 : C-G Bh/O2' pairing -B2064-B2446 : C-G Ww/Ww pairing antiparallel cis XIX -B2065-B2440 : C-C O2P/Ww pairing -B2065-B2445 : C-G Ww/Ww pairing antiparallel cis XIX -B2066-B2440 : C-C O2P/Hh pairing -B2066-B2444 : C-G Ww/Ww pairing antiparallel cis XIX -B2067-B2068 : G-U O2'/Hh O2'/Ww adjacent_5p pairing -B2067-B2443 : G-C Ww/Ww pairing antiparallel cis XIX -B2070-B2441 : A-U Ww/Ww pairing antiparallel cis XX -B2071-B2438 : A-U Ww/Ww pairing antiparallel cis XX -B2072-B2437 : C-G Ww/Ww pairing antiparallel cis XIX -B2072-B2439 : C-A O2'/Bh O2'/Hh pairing -B2073-B2436 : C-G Ww/Ww pairing antiparallel cis XIX -B2074-B2435 : U-A Ww/Ww pairing antiparallel cis XX -B2075-B2434 : U-A Ww/Ww pairing antiparallel cis XX -B2077-B2243 : A-U Ww/Ww pairing antiparallel cis XX -B2077-B2430 : A-A Bh/O2' pairing -B2078-B2242 : C-G Ww/Ww pairing antiparallel cis XIX -B2079-B2241 : U-A Ww/Ww pairing antiparallel cis XX -B2080-B2082 : A-A O2P/Ww pairing -B2080-B2240 : A-U Ww/Ww pairing antiparallel cis XX -B2081-B2082 : U-A Ww/O2' adjacent_5p pairing -B2081-B2239 : U-G Ws/Ws pairing antiparallel cis one_hbond -B2083-B2236 : G-U Ws/Ws pairing antiparallel cis one_hbond -B2083-B2238 : G-G Sw/Hw pairing parallel cis one_hbond -B2084-B2235 : C-G Ww/Ww pairing antiparallel cis XIX -B2085-B2234 : U-G Ws/Ws pairing antiparallel cis one_hbond -B2086-B2087 : U-G O2'/Hh O2'/C8 adjacent_5p pairing -B2087-B2232 : G-C Ww/Ww pairing antiparallel cis XIX -B2088-B2231 : A-U Ww/Ww pairing antiparallel cis XX -B2089-B2230 : C-G Ww/Ww pairing antiparallel cis XIX -B2090-B2229 : A-U Ww/Ww pairing antiparallel cis XX -B2091-B2228 : C-G Ww/Ww pairing antiparallel cis XIX -B2092-B2227 : U-A Ww/Ww pairing antiparallel cis XX -B2093-B2196 : G-C Ww/Ww pairing antiparallel cis XIX -B2094-B2195 : A-U Ww/Ww pairing antiparallel cis XX -B2095-B2194 : A-U Ww/Ww pairing antiparallel cis XX -B2096-B2193 : C-G Ww/Ww pairing antiparallel cis XIX -B2097-B2192 : A-U Ww/Ww pairing antiparallel cis XX -B2098-B2191 : U-A Ww/Ww pairing antiparallel cis XX -B2099-B2190 : U-G Ws/Ws pairing antiparallel cis one_hbond -B2100-B2189 : G-U Ws/Ws pairing antiparallel cis one_hbond -B2101-B2188 : A-U Ww/Ww pairing antiparallel cis XX -B2102-B2187 : G-U Ws/Ws pairing antiparallel cis one_hbond -B2103-B2186 : C-G Ww/Ww pairing antiparallel cis XIX -B2104-B2112 : C-G O2'/Hh pairing -B2105-B2184 : U-A Ww/Ww pairing antiparallel cis XX -B2106-B2112 : U-G O2P/Ww pairing -B2106-B2183 : U-A Ww/Ww pairing antiparallel cis XX -B2107-B2112 : G-G Hh/O2P pairing -B2107-B2182 : G-U Ws/Ws pairing antiparallel cis one_hbond -B2108-B2112 : A-G Hh/O2P pairing -B2108-B2181 : A-U Ww/Ww pairing antiparallel cis XX -B2109-B2120 : U-G Hw/Sw pairing parallel trans one_hbond 89 -B2111-B2112 : U-G Hh/O2P Ww/O2P adjacent_5p downward pairing -B2111-B2113 : U-U O2P/Ww pairing -B2111-B2178 : U-C O2'/Bh pairing -B2112-B2113 : G-U Bs/O2P Bs/O2P pairing -B2112-B2177 : G-C Ww/O2P Bs/O2P pairing -B2112-B2178 : G-C O2'/Hh Ss/O2P C8/O2P pairing -B2113-B2177 : U-C O2P/Bh pairing -B2113-B2178 : U-C O2P/Bh pairing -B2114-B2115 : A-G O2P/Hh Ss/O2P adjacent_5p pairing -B2114-B2121 : A-G Ss/O2P pairing -B2115-B2122 : G-U C8/Hw pairing parallel cis one_hbond -B2117-B2171 : A-A Ww/O2' Bh/O2' pairing -B2117-B2172 : A-U O2'/Ww Ww/O2P pairing -B2118-B2172 : U-U O2P/Ww pairing -B2120-B2178 : G-C Ww/Ww pairing antiparallel cis XIX -B2121-B2177 : G-C Ww/Ww pairing antiparallel cis XIX -B2122-B2176 : U-A Ww/Ww pairing antiparallel cis XX -B2123-B2175 : G-C Ww/Ww pairing antiparallel cis XIX -B2124-B2174 : G-C Ww/Ww pairing antiparallel cis XIX -B2127-B2161 : G-C Ww/Ww pairing antiparallel cis XIX -B2128-B2160 : G-C Ww/Ww pairing antiparallel cis XIX -B2129-B2159 : C-G Ww/Ww pairing antiparallel cis XIX -B2133-B2157 : G-G Ww/O2' Bs/O2P pairing -B2136-B2155 : G-U Ws/Ws pairing antiparallel cis one_hbond -B2137-B2154 : U-A Ww/Ww pairing antiparallel cis XX -B2138-B2153 : G-C Ww/Ww pairing antiparallel cis XIX -B2140-B2151 : G-U Ws/Ws pairing antiparallel cis one_hbond -B2141-B2150 : G-C Ww/Ww pairing antiparallel cis XIX -B2142-B2149 : A-U Ww/Ww pairing antiparallel cis XX -B2143-B2145 : C-C O2'/Ww O2'/Bh pairing -B2143-B2148 : C-G Ww/Ww pairing antiparallel cis XIX -B2146-B2147 : C-A O2'/Hh adjacent_5p pairing -B2147-B2148 : A-G O2P/Hh adjacent_5p pairing -B2156-B2157 : G-G Ss/O2P Ss/O2P adjacent_5p pairing -B2161-B2168 : C-G O2'/Ww pairing -B2162-B2164 : G-C O2P/Ww pairing -B2163-B2164 : A-C Ss/O2P adjacent_5p pairing -B2163-B2168 : A-G O2P/Hh pairing -B2164-B2165 : C-C O2P/Hh adjacent_5p pairing -B2165-B2168 : C-G O2'/Ss O2P/Ww O2P/Bs pairing -B2167-B2169 : U-A O2P/Hh pairing -B2170-B2172 : A-U Ss/O2P pairing -B2179-B2181 : C-U Bh/O2P pairing -B2200-B2223 : C-G Ww/Ww pairing antiparallel cis XIX -B2201-B2222 : G-C Ww/Ww pairing antiparallel cis XIX -B2202-B2221 : U-G Ws/Ws pairing antiparallel cis one_hbond -B2204-B2220 : G-U Ws/Ws pairing antiparallel cis one_hbond -B2205-B2219 : A-U Ww/Ww pairing antiparallel cis XX -B2206-B2218 : C-G Ww/Ww pairing antiparallel cis XIX -B2207-B2217 : C-G Ww/Ww pairing antiparallel cis XIX -B2208-B2216 : C-G Ww/Ww pairing antiparallel cis XIX -B2209-B2215 : G-C Ww/Ww pairing antiparallel cis XIX -B2211-B2212 : A-A O2'/Hh adjacent_5p pairing -B2224-B2225 : G-A Sw/Hh adjacent_5p pairing parallel cis one_hbond 53 -B2237-B2238 : G-G O2'/Hh adjacent_5p pairing -B2246-B2258 : G-C Ww/Ww pairing antiparallel cis XIX -B2247-B2257 : A-U Ww/Ww pairing antiparallel cis XX -B2248-B2256 : C-G Ww/Ww pairing antiparallel cis XIX -B2249-B2255 : U-G Ws/Ws pairing antiparallel cis one_hbond -B2250-B2252 : G-G Bs/O2P pairing -B2250-B2254 : G-C Ww/Ww pairing antiparallel cis XIX -B2252-B2254 : G-C Hh/O2' pairing -B2254-B2429 : C-G O2P/Hh pairing -B2259-B2281 : U-A Ww/Ww pairing antiparallel cis XX -B2259-B2426 : U-A O2P/Ww pairing -B2260-B2280 : C-G Ww/Ww pairing antiparallel cis XIX -B2260-B2426 : C-A O2P/Ww pairing -B2261-B2279 : C-G Ww/Ww pairing antiparallel cis XIX -B2262-B2278 : U-A Ww/Ww pairing antiparallel cis XX -B2263-B2277 : C-G Ww/Ww pairing antiparallel cis XIX -B2263-B2424 : C-C O2P/Hh pairing -B2264-B2276 : C-G Ww/Ww pairing antiparallel cis XIX -B2268-B2269 : A-G Ss/O2P adjacent_5p pairing -B2273-B2425 : A-A O2P/Hh pairing -B2275-B2427 : C-C O2'/Ww pairing -B2283-B2387 : C-U Bh/O2' pairing -B2283-B2388 : C-A Hh/O2P pairing -B2284-B2384 : A-U Ww/Ww pairing antiparallel cis XX -B2284-B2388 : A-A Bh/O2' pairing -B2284-B2389 : A-G Hh/O2P pairing -B2285-B2383 : C-G Ww/Ww pairing antiparallel cis XIX -B2286-B2344 : G-U Bs/Bs pairing parallel trans -B2287-B2288 : A-A O2'/Hh adjacent_5p pairing -B2288-B2344 : A-U Ww/Ww pairing antiparallel cis XX -B2289-B2343 : G-U Ws/Ws pairing antiparallel cis one_hbond -B2290-B2342 : G-C Ww/Ww pairing antiparallel cis XIX -B2290-B2346 : G-A O2'/Bh pairing -B2291-B2341 : U-G Ws/Ws pairing antiparallel cis one_hbond -B2292-B2340 : U-A Ww/Ww pairing antiparallel cis XX -B2293-B2339 : G-C Ww/Ww pairing antiparallel cis XIX -B2294-B2338 : G-C Ww/Ww pairing antiparallel cis XIX -B2295-B2337 : C-G Ww/Ww pairing antiparallel cis XIX -B2296-B2336 : U-A Ww/Ww pairing antiparallel cis XX -B2297-B2321 : A-U Ww/Ww pairing antiparallel cis XX -B2299-B2317 : U-A Ww/Ww pairing antiparallel cis XX -B2300-B2316 : C-G Ww/Ww pairing antiparallel cis XIX -B2301-B2315 : C-G Ww/Ww pairing antiparallel cis XIX -B2302-B2314 : U-A Ww/Ww pairing antiparallel cis XX -B2303-B2313 : G-C Ww/Ww pairing antiparallel cis XIX -B2304-B2312 : G-U Ws/Ws pairing antiparallel cis one_hbond -B2305-B2308 : U-G O2'/Hh pairing -B2318-B2319 : G-G Ss/Ws O2'/Bs adjacent_5p pairing parallel trans one_hbond -B2319-B2322 : G-A O2'/Ss O2'/C8 pairing -B2323-B2332 : G-C Ww/Ww pairing antiparallel cis XIX -B2323-B2333 : G-A Bs/O2' pairing -B2324-B2331 : U-G Ws/Ws pairing antiparallel cis one_hbond -B2328-B2387 : A-U Ww/Ww pairing antiparallel cis XX -B2329-B2386 : U-A Ww/Ww pairing antiparallel cis XX -B2330-B2385 : G-C Ww/Ww pairing antiparallel cis XIX -B2344-B2381 : U-A O2'/Bh pairing -B2345-B2380 : G-C O2P/Ww O2P/Bh O2P/Bh pairing -B2345-B2381 : G-A O2P/Hh pairing -B2345-B2382 : G-G O2'/Ss Ss/O2' pairing -B2346-B2382 : A-G O2P/Bs pairing -B2347-B2370 : C-G Ww/Ww pairing antiparallel cis XIX -B2347-B2372 : C-U Bh/O2P pairing -B2348-B2369 : U-A Ww/Ww pairing antiparallel cis XX -B2349-B2368 : G-C Ww/Ww pairing antiparallel cis XIX -B2350-B2352 : C-A O2P/Hh pairing -B2350-B2367 : C-G Ww/Ww pairing antiparallel cis XIX -B2353-B2364 : G-C Ww/Ww pairing antiparallel cis XIX -B2354-B2363 : C-G Ww/Ww pairing antiparallel cis XIX -B2355-B2362 : G-C Ww/Ww pairing antiparallel cis XIX -B2359-B2360 : C-G O2P/Hh adjacent_5p pairing -B2361-B2363 : G-G Hh/O2P pairing -B2364-B2366 : C-A O2'/Hh O2'/C8 pairing -B2365-B2366 : G-A O2P/Ss adjacent_5p pairing -B2372-B2381 : U-A Ww/Ww pairing antiparallel cis XX -B2373-B2380 : G-C Ww/Ww pairing antiparallel cis XIX -B2374-B2379 : C-G Ww/Ww pairing antiparallel cis XIX -B2376-B2394 : A-C Ss/O2P pairing -B2376-B2396 : A-G Ss/O2P pairing -B2376-B2397 : A-G Hh/O2P pairing -B2378-B2394 : A-C O2P/Hh pairing -B2379-B2393 : G-U O2'/Hh Ss/O2' C8/O2' pairing -B2380-B2392 : C-A O2P/Ww pairing -B2387-B2388 : U-A O2P/Hh O2P/C8 adjacent_5p pairing -B2395-B2421 : C-G Ww/Ww pairing antiparallel cis XIX -B2396-B2420 : G-C Ww/Ww pairing antiparallel cis XIX -B2397-B2419 : G-U Ws/Ws pairing antiparallel cis one_hbond -B2398-B2418 : U-A Ww/Ww pairing antiparallel cis XX -B2399-B2417 : G-C Ww/Ww pairing antiparallel cis XIX -B2400-B2416 : G-C Ww/Ww pairing antiparallel cis XIX -B2401-B2415 : U-G Ws/Ws pairing antiparallel cis one_hbond -B2402-B2414 : U-G Ws/Ws pairing antiparallel cis one_hbond -B2403-B2413 : C-G Ww/Ww pairing antiparallel cis XIX -B2404-B2412 : U-A Ww/Ww pairing antiparallel cis XX -B2410-B2411 : G-A O2P/Hh adjacent_5p pairing -B2411-B2412 : A-A Ss/O2P adjacent_5p pairing -B2433-B2434 : A-A O2P/Hh adjacent_5p pairing -B2439-B2440 : A-C Ss/O2P adjacent_5p pairing -B2442-B2443 : C-C O2P/Bh upward pairing -B2445-B2554 : G-U O2P/Hh pairing -B2446-B2557 : G-G O2P/Bs O2P/Ss pairing -B2450-B2566 : A-A O2'/Hh pairing -B2451-B2563 : A-U O2P/Ww outward pairing -B2452-B2517 : C-C Hh/O2' pairing -B2453-B2454 : A-G Ss/O2P adjacent_5p pairing -B2454-B2647 : G-U Bs/O2P pairing -B2455-B2496 : G-C Ww/Ww pairing antiparallel cis XIX -B2455-B2500 : G-U C8/Wh O2P/Ww pairing parallel cis one_hbond -B2455-B2665 : G-A Ww/O2' Ss/O2' pairing -B2456-B2495 : C-G Ww/Ww pairing antiparallel cis XIX -B2457-B2494 : U-G Ws/Ws pairing antiparallel cis one_hbond -B2458-B2492 : G-U Ws/Ws pairing antiparallel cis one_hbond -B2459-B2491 : A-U Ww/Ww pairing antiparallel cis XX -B2460-B2490 : U-G Ws/Ws pairing antiparallel cis one_hbond -B2461-B2482 : A-A O2P/Bh O2P/Ww pairing -B2461-B2489 : A-U Ww/Ww pairing antiparallel cis XX -B2462-B2482 : C-A O2P/Ww O2P/Bh pairing -B2462-B2488 : C-G Ww/Ww pairing antiparallel cis XIX -B2463-B2487 : C-G Ww/Ww pairing antiparallel cis XIX -B2464-B2486 : G-C Ww/Ww pairing antiparallel cis XIX -B2465-B2468 : C-A O2P/Ss O2P/C8 pairing -B2465-B2485 : C-G Ww/Ww pairing antiparallel cis XIX -B2466-B2469 : C-A O2P/Hh O2P/Bh pairing -B2466-B2484 : C-G Ww/Ww pairing antiparallel cis XIX -B2470-B2480 : G-C Ww/Ww pairing antiparallel cis XIX -B2471-B2472 : A-G O2'/Hh adjacent_5p pairing -B2471-B2479 : A-U Ww/Ww pairing antiparallel cis XX -B2481-B2482 : G-A Ss/O2P adjacent_5p pairing -B2481-B2484 : G-G O2'/Hh pairing -B2487-B2505 : G-G Sw/Hh pairing parallel cis one_hbond 109 -B2488-B2505 : G-G O2'/C8 pairing -B2488-B2575 : G-C O2P/Bh pairing -B2489-B2501 : U-C O2P/Hh pairing -B2489-B2575 : U-C O2P/Bh pairing -B2491-B2766 : U-A O2P/Hh pairing -B2496-B2497 : C-A Ss/C8 adjacent_5p pairing antiparallel trans one_hbond -B2497-B2657 : A-A O2'/Ww O2'/Bh pairing -B2497-B2662 : A-A O2P/Bh pairing -B2497-B2663 : A-G O2P/Bs pairing -B2497-B2665 : A-A O2'/C8 pairing -B2501-B2575 : C-C Ww/Wh pairing antiparallel cis one_hbond 131 -B2502-B2769 : G-U Ww/O2P Bs/O2P Ss/O2P pairing -B2504-B2580 : U-U Ww/Hh pairing antiparallel trans 81 -B2505-B2506 : G-U Hh/O2P C8/O2P pairing -B2506-B2582 : U-G Ws/Ws pairing antiparallel cis one_hbond -B2507-B2581 : C-G Ww/Ww pairing antiparallel cis XIX -B2508-B2580 : G-U Ws/Ws pairing antiparallel cis one_hbond -B2509-B2579 : G-C Ww/Ww pairing antiparallel cis XIX -B2510-B2578 : C-G Ww/Ww pairing antiparallel cis XIX -B2511-B2577 : U-A Ww/Ww pairing antiparallel cis XX -B2512-B2576 : C-G Ww/Ww pairing antiparallel cis XIX -B2513-B2571 : A-U Ww/Ww pairing antiparallel cis XX -B2514-B2570 : U-G Ws/Ws pairing antiparallel cis one_hbond -B2515-B2569 : C-G Ww/Ww pairing antiparallel cis XIX -B2516-B2568 : A-U Ww/Ww pairing antiparallel cis XX -B2517-B2567 : C-G Ww/Ww pairing antiparallel cis XIX -B2518-B2546 : A-U Ww/Ww pairing antiparallel cis XX -B2518-B2563 : A-U Hh/O2P pairing -B2519-B2545 : U-G Ws/Ws pairing antiparallel cis one_hbond -B2520-B2544 : C-G Ww/Ww pairing antiparallel cis XIX -B2521-B2543 : C-G Ww/Ww pairing antiparallel cis XIX -B2522-B2541 : U-A Ww/Ww pairing antiparallel cis XX -B2523-B2540 : G-C Ww/Ww pairing antiparallel cis XIX -B2524-B2539 : G-C Ww/Ww pairing antiparallel cis XIX -B2525-B2538 : G-C Ww/Ww pairing antiparallel cis XIX -B2526-B2537 : G-U Ws/Ws pairing antiparallel cis one_hbond -B2527-B2536 : C-G Ww/Ww pairing antiparallel cis XIX -B2528-B2529 : U-G O2P/Hh adjacent_5p pairing -B2528-B2535 : U-G Ws/Ws pairing antiparallel cis one_hbond -B2529-B2530 : G-A O2'/Hh adjacent_5p pairing -B2529-B2532 : G-G Ww/O2P Bs/O2P pairing -B2543-B2610 : G-C O2P/Ww pairing -B2545-B2564 : G-A O2P/Hh pairing -B2547-B2561 : A-U Ww/Ww pairing antiparallel cis XX -B2548-B2560 : U-A Ww/Ww pairing antiparallel cis XX -B2549-B2559 : G-C Ww/Ww pairing antiparallel cis XIX -B2550-B2558 : G-C Ww/Ww pairing antiparallel cis XIX -B2551-B2557 : C-G Ww/Ww pairing antiparallel cis XIX -B2552-B2553 : U-G O2P/Hh adjacent_5p pairing -B2555-B2557 : U-G O2P/Hh pairing -B2556-B2558 : C-C Hh/O2P pairing -B2563-B2566 : U-A Ww/O2P pairing -B2572-B2674 : A-G O2P/Bs pairing -B2574-B2768 : G-U Ww/O2P pairing -B2582-B2583 : G-G O2P/Hh adjacent_5p pairing -B2587-B2588 : A-G Ss/O2P adjacent_5p pairing -B2588-B2606 : G-C Ww/Ww pairing antiparallel cis XIX -B2589-B2605 : A-U Ww/Ww pairing antiparallel cis XX -B2590-B2604 : A-U Ww/Ww pairing antiparallel cis XX -B2591-B2603 : C-G Ww/Ww pairing antiparallel cis XIX -B2592-B2601 : G-C Ww/Ww pairing antiparallel cis XIX -B2593-B2600 : U-A Ww/Ww pairing antiparallel cis XX -B2594-B2599 : C-G Ww/Ww pairing antiparallel cis XIX -B2607-B2608 : G-G Hh/O2P adjacent_5p pairing -B2630-B2788 : G-C Ww/Ww pairing antiparallel cis XIX -B2631-B2787 : G-C Ww/Ww pairing antiparallel cis XIX -B2632-B2786 : A-U Ww/Ww pairing antiparallel cis XX -B2633-B2785 : G-C Ww/Ww pairing antiparallel cis XIX -B2634-B2784 : A-U Ww/Ww pairing antiparallel cis XX -B2635-B2783 : A-U Ww/Ww pairing antiparallel cis XX -B2636-B2782 : C-G Ww/Ww pairing antiparallel cis XIX -B2637-B2777 : U-G O2'/Ss pairing -B2637-B2781 : U-A Ww/Ww pairing antiparallel cis XX -B2638-B2732 : G-G Ww/O2' Bs/O2' pairing -B2638-B2771 : G-C Ww/O2P Bs/O2P pairing -B2638-B2777 : G-G O2'/Bs pairing -B2639-B2641 : A-G Hh/O2P inward pairing -B2639-B2642 : A-G Bs/Hw Bh/O2P pairing antiparallel trans one_hbond -B2639-B2731 : A-G Bh/O2P Hh/O2P pairing -B2639-B2732 : A-G Ww/O2P Ss/O2P pairing -B2639-B2777 : A-G O2'/Hh pairing -B2640-B2774 : G-C Ww/Ww pairing antiparallel cis XIX -B2641-B2773 : G-C Ww/Ww pairing antiparallel cis XIX -B2642-B2772 : G-C Ww/Ww pairing antiparallel cis XIX -B2643-B2771 : G-C Ww/Ww pairing antiparallel cis XIX -B2644-B2673 : G-G Hh/O2P pairing -B2644-B2674 : G-G O2'/Hh pairing -B2646-B2674 : C-G Ww/Ww pairing antiparallel cis XIX -B2647-B2673 : U-G Ws/Ws pairing antiparallel cis one_hbond -B2648-B2672 : G-U Ws/Ws pairing antiparallel cis one_hbond -B2649-B2671 : C-G Ww/Ww pairing antiparallel cis XIX -B2650-B2670 : U-A Ww/Ww pairing antiparallel cis XX -B2651-B2669 : C-G Ww/Ww pairing antiparallel cis XIX -B2652-B2668 : C-G Ww/Ww pairing antiparallel cis XIX -B2654-B2666 : A-C Hh/Wh pairing parallel trans one_hbond 69 -B2655-B2665 : G-A Ww/O2P Bs/O2P pairing -B2656-B2665 : U-A Ws/Hh pairing antiparallel trans XXIV -B2657-B2658 : A-C O2P/Bh adjacent_5p upward pairing -B2657-B2664 : A-G Hh/Ss Bh/O2' pairing antiparallel trans XI -B2658-B2663 : C-G Ww/Ww pairing antiparallel cis XIX -B2659-B2661 : G-G O2'/Hh pairing -B2659-B2662 : G-A Ss/Hh O2'/Bh pairing antiparallel trans XI -B2667-B2668 : C-G O2'/C8 adjacent_5p pairing -B2675-B2677 : A-G Ss/O2P pairing -B2676-B2731 : C-G Ww/Ww pairing antiparallel cis XIX -B2677-B2730 : G-C Ww/Ww pairing antiparallel cis XIX -B2678-B2729 : C-G Ww/Ww pairing antiparallel cis XIX -B2679-B2728 : A-U Ww/Ww pairing antiparallel cis XX -B2680-B2727 : U-A Ww/Ww pairing antiparallel cis XX -B2681-B2684 : C-U Wh/Hw pairing parallel cis one_hbond 103 -B2682-B2688 : A-G Hh/O2' C8/O2' outward pairing -B2682-B2721 : A-A Ss/O2P pairing -B2683-B2684 : C-U Ws/Hh adjacent_5p pairing parallel cis one_hbond -B2683-B2721 : C-A O2P/Ss pairing -B2685-B2687 : G-U Hh/O2P pairing -B2685-B2722 : G-G O2'/Ss pairing -B2685-B2723 : G-C Ss/O2P pairing -B2686-B2687 : G-U Ww/O2' adjacent_5p pairing -B2686-B2729 : G-G Bs/O2' pairing -B2688-B2724 : G-U Hh/O2' pairing -B2688-B2725 : G-A C8/O2P inward pairing -B2690-B2727 : U-A O2'/Hh pairing -B2691-B2718 : C-G Ww/Ww pairing antiparallel cis XIX -B2692-B2717 : G-C Ww/Ww pairing antiparallel cis XIX -B2693-B2716 : G-C Ww/Ww pairing antiparallel cis XIX -B2694-B2715 : G-C Ww/Ww pairing antiparallel cis XIX -B2695-B2714 : U-G Ws/Ws pairing antiparallel cis one_hbond -B2696-B2711 : U-A Ww/Ww pairing antiparallel cis XX -B2697-B2710 : G-C Ww/Ww pairing antiparallel cis XIX -B2698-B2709 : U-G Ws/Ws pairing antiparallel cis one_hbond -B2699-B2708 : C-G Ww/Ww pairing antiparallel cis XIX -B2700-B2707 : A-U Ww/Ww pairing antiparallel cis XX -B2701-B2706 : U-A Ww/Ww pairing antiparallel cis XX -B2704-B2706 : C-A O2P/Bh pairing -B2712-B2713 : C-U O2P/Hh adjacent_5p pairing -B2714-B2726 : G-A O2P/Bh pairing -B2719-B2721 : G-A O2P/Bh O2P/Hh pairing -B2724-B2725 : U-A O2'/Ww adjacent_5p pairing -B2733-B2772 : A-C O2P/Bh pairing -B2733-B2778 : A-A Hh/C8 pairing antiparallel cis one_hbond -B2734-B2776 : A-A C8/O2' pairing -B2735-B2769 : G-U Ws/Ws pairing antiparallel cis one_hbond -B2735-B2775 : G-G C8/Bh pairing parallel trans one_hbond -B2736-B2768 : A-U Ww/Ww pairing antiparallel cis XX -B2737-B2767 : G-C Ww/Ww pairing antiparallel cis XIX -B2738-B2741 : A-A O2P/Hh O2P/C8 pairing -B2740-B2741 : A-A Ss/O2P adjacent_5p pairing -B2740-B2742 : A-G C8/O2P pairing -B2741-B2742 : A-G O2P/Hh adjacent_5p pairing -B2742-B2762 : G-C Ww/Ww pairing antiparallel cis XIX -B2743-B2761 : U-A Ww/Ww pairing antiparallel cis XX -B2744-B2760 : G-C Ww/Ww pairing antiparallel cis XIX -B2745-B2759 : C-G Ww/Ww pairing antiparallel cis XIX -B2746-B2747 : U-G O2P/Hh adjacent_5p pairing -B2746-B2758 : U-A Ww/Ww pairing antiparallel cis XX -B2747-B2748 : G-A O2'/Ss adjacent_5p pairing -B2762-B2765 : C-A O2'/Ww pairing -B2763-B2765 : G-A O2'/Hh Bs/O2P pairing -B2764-B2765 : A-A O2P/Bh O2P/Hh adjacent_5p pairing -B2770-B2772 : G-C Hh/O2P pairing -B2776-B2778 : A-A Bh/O2P pairing -B2777-B2778 : G-A Bs/O2' adjacent_5p pairing -B2789-B2890 : C-G Bh/O2' pairing -B2791-B2805 : G-C Ww/Ww pairing antiparallel cis XIX -B2791-B2891 : G-U Hh/O2' pairing -B2792-B2804 : A-U Ww/Ww pairing antiparallel cis XX -B2793-B2803 : C-G Ww/Ww pairing antiparallel cis XIX -B2794-B2802 : C-G Ww/Ww pairing antiparallel cis XIX -B2795-B2801 : C-G Ww/Ww pairing antiparallel cis XIX -B2796-B2800 : U-A Ww/Ww pairing antiparallel cis XX -B2798-B2799 : U-A O2'/Hh adjacent_5p pairing -B2798-B2800 : U-A O2P/Ss pairing -B2798-B2894 : U-G O2'/Bs pairing -B2799-B2800 : A-A O2P/Bh O2P/Hh adjacent_5p pairing -B2799-B2894 : A-G Ss/O2P pairing -B2805-B2806 : C-C O2P/Bh adjacent_5p pairing -B2806-B2807 : C-U Hh/O2' adjacent_5p pairing -B2808-B2890 : G-G O2P/Ww O2P/Bs pairing -B2809-B2810 : A-A O2'/Ss adjacent_5p pairing -B2811-B2889 : G-C Ww/Ww pairing antiparallel cis XIX -B2812-B2888 : G-C Ww/Ww pairing antiparallel cis XIX -B2813-B2833 : A-U Ww/Ww pairing antiparallel cis XX -B2814-B2832 : A-U Ww/Ww pairing antiparallel cis XX -B2815-B2831 : C-G Ww/Ww pairing antiparallel cis XIX -B2816-B2830 : G-C Ww/Ww pairing antiparallel cis XIX -B2817-B2829 : U-A Ww/Ww pairing antiparallel cis XX -B2818-B2820 : U-A O2P/Bh pairing -B2818-B2821 : U-A O2P/Bh pairing -B2818-B2828 : U-G Ws/Ws pairing antiparallel cis one_hbond -B2819-B2820 : G-A O2P/Hh adjacent_5p pairing -B2819-B2821 : G-A O2P/Bh pairing -B2819-B2827 : G-C Ww/Ww pairing antiparallel cis XIX -B2821-B2822 : A-G O2'/Ss O2'/C8 Ss/O2P adjacent_5p pairing -B2821-B2823 : A-A C8/O2P pairing -B2834-B2879 : G-A O2'/Bh pairing -B2835-B2879 : A-A O2P/Bh pairing -B2836-B2882 : U-A Ww/Ww pairing antiparallel cis XX -B2836-B2885 : U-G Ws/Sw pairing parallel trans one_hbond -B2837-B2881 : A-U Ww/Ww pairing antiparallel cis XX -B2838-B2880 : G-C Ww/Ww pairing antiparallel cis XIX -B2839-B2878 : G-U Ws/Ws pairing antiparallel cis one_hbond -B2840-B2877 : C-G Ww/Ww pairing antiparallel cis XIX -B2841-B2876 : C-G Ww/Ww pairing antiparallel cis XIX -B2842-B2875 : G-C Ww/Ww pairing antiparallel cis XIX -B2843-B2847 : G-U Hw/Ww pairing parallel trans one_hbond -B2843-B2874 : G-C Ww/Ww pairing antiparallel cis XIX -B2844-B2866 : G-U Hh/O2P pairing -B2845-B2848 : U-G O2'/Hh O2P/Ww pairing -B2846-B2848 : G-G O2P/Ss O2'/Hh pairing -B2847-B2848 : U-G O2P/Ww adjacent_5p pairing -B2847-B2875 : U-C Wh/Wh pairing antiparallel cis one_hbond -B2848-B2872 : G-A C8/O2P pairing -B2848-B2874 : G-C O2P/Bh pairing -B2849-B2872 : U-A Hh/O2' pairing -B2851-B2866 : A-U Ww/Ww pairing antiparallel cis XX -B2851-B2872 : A-A O2P/Hh pairing -B2852-B2865 : G-U Ws/Ws pairing antiparallel cis one_hbond -B2853-B2864 : C-G Ww/Ww pairing antiparallel cis XIX -B2854-B2863 : G-C Ww/Ww pairing antiparallel cis XIX -B2855-B2862 : C-G Ww/Ww pairing antiparallel cis XIX -B2856-B2858 : A-C C8/O2P pairing -B2856-B2861 : A-U Ww/Ww pairing antiparallel cis XX -B2866-B2867 : U-G O2'/Bs O2'/Ss adjacent_5p pairing -B2867-B2868 : G-A O2'/Ss adjacent_5p pairing -B2869-B2870 : G-C Bs/O2P Ss/O2P adjacent_5p pairing -B2869-B2873 : G-A Hh/O2' pairing -B2879-B2882 : A-A Hh/Hw pairing antiparallel cis one_hbond 36 -B2879-B2886 : A-A Ww/O2' pairing -B2882-B2886 : A-A Hh/O2P pairing -B2883-B2886 : A-A Ww/O2P pairing -B2883-B2890 : A-G O2'/C8 pairing -B2884-B2887 : U-A O2P/Bh O2P/Hh upward pairing -B2884-B2888 : U-C Wh/Hw pairing parallel cis one_hbond -B2884-B2889 : U-C Hw/Hw pairing parallel cis one_hbond 101 -B2885-B2889 : G-C Hh/O2P pairing -B2887-B2889 : A-C Ww/O2P Ss/O2P pairing -B2887-B2890 : A-G Bh/O2' pairing -B2894-B2895 : G-G Hh/O2' adjacent_5p pairing -B2901-B2903 : C-U O2P/Hh pairing -B2902-B2903 : C-U Bh/O2' adjacent_5p pairing -B2902-B2904 : C-U Bh/O2P pairing diff --git a/MCdata/1c2x_MC b/MCdata/1c2x_MC deleted file mode 100644 index 486cc066c08975c15c87caeb9b63875fc14b3e07..0000000000000000000000000000000000000000 --- a/MCdata/1c2x_MC +++ /dev/null @@ -1,241 +0,0 @@ -Residue conformations ------------------------------------------- -C1 : U C3p_endo anti -C2 : G C3p_endo anti -C3 : C C3p_endo anti -C4 : C C3p_endo anti -C5 : U C3p_endo anti -C6 : G C3p_endo anti -C7 : G C3p_endo anti -C8 : C C3p_endo anti -C9 : G C3p_endo anti -C10 : G C3p_endo anti -C11 : C C3p_endo anti -C12 : C C3p_endo anti -C13 : G C3p_endo anti -C14 : U C3p_endo anti -C15 : A C3p_endo anti -C16 : G C3p_endo anti -C17 : C C3p_endo anti -C18 : G C3p_endo anti -C19 : C C3p_endo anti -C20 : G C3p_endo anti -C21 : G C3p_endo anti -C22 : U C3p_endo anti -C23 : G C3p_endo anti -C24 : G C3p_endo anti -C25 : U C3p_endo anti -C26 : C C3p_endo anti -C27 : C C3p_endo anti -C28 : C C3p_endo anti -C29 : A C3p_endo anti -C30 : C C3p_endo anti -C31 : C C3p_endo anti -C32 : U C3p_endo anti -C33 : G C3p_endo anti -C34 : A C3p_endo anti -C35 : C C3p_endo anti -C36 : C C3p_endo anti -C37 : C C3p_endo anti -C38 : C C3p_endo anti -C39 : A C3p_endo anti -C40 : U C3p_endo anti -C41 : G C3p_endo anti -C42 : C C3p_endo anti -C43 : C C3p_endo anti -C44 : G C3p_endo anti -C45 : A C3p_endo anti -C46 : A C3p_endo anti -C47 : C C3p_endo anti -C48 : U C3p_endo anti -C49 : C C3p_endo anti -C50 : A C3p_endo anti -C51 : G C3p_endo anti -C52 : A C3p_endo anti -C53 : A C3p_endo anti -C54 : G C3p_endo anti -C55 : U C3p_endo anti -C56 : G C3p_endo anti -C57 : A C3p_endo syn -C58 : A C3p_endo anti -C59 : A C3p_endo anti -C60 : C C3p_endo anti -C61 : G C3p_endo anti -C62 : C C3p_endo anti -C63 : C C3p_endo anti -C64 : G C3p_endo anti -C65 : U C3p_endo anti -C66 : A C3p_endo anti -C67 : G C3p_endo anti -C68 : C C3p_endo anti -C69 : G C3p_endo anti -C70 : C C3p_endo anti -C71 : C C3p_endo anti -C72 : G C3p_endo anti -C73 : A C2p_exo anti -C74 : U C3p_endo anti -C75 : G C3p_endo anti -C76 : G C3p_endo anti -C77 : U C3p_endo anti -C78 : A C3p_endo anti -C79 : G C3p_endo anti -C80 : U C3p_endo anti -C81 : G C3p_endo anti -C82 : U C3p_endo anti -C83 : G C3p_endo anti -C84 : G C3p_endo anti -C85 : G C3p_endo anti -C86 : G C3p_endo anti -C87 : U C4p_exo anti -C88 : C C2p_endo anti -C89 : U C3p_endo anti -C90 : C C2p_exo anti -C91 : C C3p_endo anti -C92 : C C3p_endo anti -C93 : C C3p_endo anti -C94 : A C3p_endo anti -C95 : U C3p_endo anti -C96 : G C3p_endo anti -C97 : C C3p_endo anti -C98 : G C3p_endo anti -C99 : A C2p_exo anti -C100 : G C3p_endo anti -C101 : A C2p_exo anti -C102 : G C3p_endo anti -C103 : U C3p_endo anti -C104 : A C3p_endo anti -C105 : G C3p_endo anti -C106 : G C3p_endo anti -C107 : G C3p_endo anti -C108 : A C3p_endo anti -C109 : A C3p_endo anti -C110 : C C3p_endo anti -C111 : U C3p_endo anti -C112 : G C3p_endo anti -C113 : C C3p_endo anti -C114 : C C3p_endo anti -C115 : A C3p_endo anti -C116 : G C3p_endo anti -C117 : G C3p_endo anti -C118 : C C3p_endo anti -C119 : A C3p_endo anti -C120 : U C3p_endo anti -Adjacent stackings ---------------------------------------------- -C2-C3 : adjacent_5p upward -C6-C7 : adjacent_5p upward -C7-C8 : adjacent_5p upward -C9-C10 : adjacent_5p upward -C16-C17 : adjacent_5p upward -C17-C18 : adjacent_5p upward -C18-C19 : adjacent_5p upward -C20-C21 : adjacent_5p upward -C21-C22 : adjacent_5p upward -C33-C34 : adjacent_5p upward -C50-C51 : adjacent_5p upward -C61-C62 : adjacent_5p upward -C64-C65 : adjacent_5p upward -C67-C68 : adjacent_5p upward -C71-C72 : adjacent_5p upward -C73-C74 : adjacent_5p upward -C76-C77 : adjacent_5p upward -C77-C78 : adjacent_5p upward -C78-C79 : adjacent_5p upward -C79-C80 : adjacent_5p upward -C81-C82 : adjacent_5p upward -C82-C83 : adjacent_5p upward -C83-C84 : adjacent_5p upward -C84-C85 : adjacent_5p upward -C85-C86 : adjacent_5p upward -C93-C94 : adjacent_5p upward -C94-C95 : adjacent_5p upward -C96-C97 : adjacent_5p upward -C97-C98 : adjacent_5p upward -C99-C100 : adjacent_5p upward -C100-C101 : adjacent_5p upward -C101-C102 : adjacent_5p upward -C102-C103 : adjacent_5p upward -C103-C104 : adjacent_5p upward -C104-C105 : adjacent_5p upward -C105-C106 : adjacent_5p upward -C112-C113 : adjacent_5p upward -C115-C116 : adjacent_5p upward -C116-C117 : adjacent_5p upward -C117-C118 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -C2-C119 : outward -C6-C115 : outward -C9-C112 : outward -C18-C67 : outward -C20-C64 : outward -C23-C61 : outward -C33-C50 : outward -C73-C104 : outward -C78-C99 : outward -C81-C96 : outward -C83-C94 : outward -Number of stackings = 51 -Number of adjacent stackings = 40 -Number of non adjacent stackings = 11 -Base-pairs ------------------------------------------------------ -C1-C119 : U-A Ww/Ww pairing antiparallel cis XX -C2-C118 : G-C Ww/Ww pairing antiparallel cis XIX -C3-C117 : C-G Ww/Ww pairing antiparallel cis XIX -C4-C116 : C-G Ww/Ww pairing antiparallel cis XIX -C5-C115 : U-A Ww/Ww pairing antiparallel cis XX -C6-C23 : G-G O2P/Bs O2P/Ss pairing -C6-C114 : G-C Ww/Ww pairing antiparallel cis XIX -C7-C113 : G-C Ww/Ww pairing antiparallel cis XIX -C8-C112 : C-G Ww/Ww pairing antiparallel cis XIX -C9-C111 : G-U Ws/Ws pairing antiparallel cis one_hbond -C10-C110 : G-C Ww/Ww pairing antiparallel cis XIX -C11-C12 : C-C O2P/Hh adjacent_5p pairing -C12-C15 : C-A Bh/O2' pairing -C15-C60 : A-C Ww/O2P Bh/O2P Bh/O2P pairing -C16-C66 : G-A Hw/Wh pairing antiparallel trans one_hbond 64 -C16-C68 : G-C Ww/Ww pairing antiparallel cis XIX -C17-C59 : C-A O2P/Ww O2P/Bh pairing -C17-C67 : C-G Ww/Ww pairing antiparallel cis XIX -C18-C59 : G-A O2P/Ww pairing -C18-C65 : G-U Ws/Ws pairing antiparallel cis one_hbond -C19-C64 : C-G Ww/Ww pairing antiparallel cis XIX -C20-C63 : G-C Ww/Ww pairing antiparallel cis XIX -C21-C62 : G-C Ww/Ww pairing antiparallel cis XIX -C22-C61 : U-G Ws/Ws pairing antiparallel cis one_hbond -C23-C60 : G-C Ww/Ww pairing antiparallel cis XIX -C24-C25 : G-U Sw/Ss adjacent_5p pairing antiparallel cis one_hbond -C24-C56 : G-G C8/O2P pairing -C25-C31 : U-C Ww/O2' pairing -C25-C60 : U-C O2P/Bh pairing -C29-C32 : A-U Hh/O2P pairing -C31-C51 : C-G Ww/Ww pairing antiparallel cis XIX -C31-C58 : C-A O2P/Hh O2P/C8 pairing -C32-C50 : U-A Ww/Ww pairing antiparallel cis XX -C32-C55 : U-U O2'/Ww pairing -C33-C49 : G-C Ww/Ww pairing antiparallel cis XIX -C34-C48 : A-U Ww/Ww pairing antiparallel cis XX -C39-C40 : A-U O2P/Hh adjacent_5p pairing -C42-C44 : C-G Bs/C8 pairing antiparallel cis one_hbond -C47-C51 : C-G Wh/Hw pairing parallel cis one_hbond -C51-C53 : G-A O2P/Bh O2P/Hh pairing -C51-C57 : G-A Hw/C8 Ww/O2' pairing parallel cis one_hbond -C66-C67 : A-G O2'/Hh adjacent_5p pairing -C68-C69 : C-G O2P/C8 adjacent_5p pairing -C70-C106 : C-G Ww/Ww pairing antiparallel cis XIX -C71-C105 : C-G Ww/Ww pairing antiparallel cis XIX -C72-C102 : G-G Hh/O2P pairing -C72-C103 : G-U Ww/O2P Bs/O2P pairing -C72-C104 : G-A Ss/Hh pairing antiparallel trans XI -C73-C103 : A-U Hh/Ws pairing antiparallel trans XXIV -C74-C102 : U-G Hh/Ww pairing antiparallel trans one_hbond 91 -C75-C76 : G-G Ww/O2' Bs/O2' pairing -C76-C100 : G-G Ww/Bh pairing antiparallel trans 115 -C77-C99 : U-A Ws/Hh pairing antiparallel trans XXIV -C78-C98 : A-G Hh/Ss Bh/O2' pairing antiparallel trans XI -C79-C97 : G-C Ww/Ww pairing antiparallel cis XIX -C80-C96 : U-G Ws/Ww pairing antiparallel cis XXVIII -C81-C95 : G-U Ww/Ws pairing antiparallel cis XXVIII -C82-C94 : U-A Ww/Ww pairing antiparallel cis XX -C83-C93 : G-C Ww/Ww pairing antiparallel cis XIX -C84-C92 : G-C Ww/Ww pairing antiparallel cis XIX -C85-C91 : G-C Ww/Ww pairing antiparallel cis XIX -C86-C90 : G-C Bs/Ww pairing antiparallel cis 128 -C89-C90 : U-C O2P/Ww O2P/Bh adjacent_5p pairing diff --git a/MCdata/1c4l_MC b/MCdata/1c4l_MC deleted file mode 100644 index aa375cacb82f23d9c56835609a334c8dc5c2e9e8..0000000000000000000000000000000000000000 --- a/MCdata/1c4l_MC +++ /dev/null @@ -1,49 +0,0 @@ -Residue conformations ------------------------------------------- -A1 : C C4p_exo anti -A2 : G C3p_endo anti -A3 : A C3p_endo anti -A4 : C C3p_endo anti -A5 : U C3p_endo anti -A6 : C C3p_endo anti -A7 : A C3p_endo anti -A8 : G C3p_endo anti -A9 : G C3p_endo anti -B10 : C C4p_exo anti -B11 : C C3p_endo anti -B12 : U C4p_exo anti -B13 : G C3p_endo anti -B14 : C C2p_exo anti -B15 : G C4p_exo anti -B16 : U C3p_endo anti -B17 : C O4p_endo anti -B18 : G C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -B10-B11 : adjacent_5p upward -B11-B12 : adjacent_5p upward -B12-B13 : adjacent_5p upward -B13-B14 : adjacent_5p upward -B14-B15 : adjacent_5p upward -B15-B16 : adjacent_5p upward -B17-B18 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A2-B18 : outward -A7-B13 : outward -Number of stackings = 16 -Number of adjacent stackings = 14 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A1-B18 : C-G Ww/Ww pairing antiparallel cis XIX -A2-B17 : G-C Ww/Ww pairing antiparallel cis XIX -A3-B16 : A-U Ww/Ww pairing antiparallel cis XX -A4-B15 : C-G Ww/Ww pairing antiparallel cis XIX -A6-B13 : C-G Ww/Ww pairing antiparallel cis XIX -A7-B12 : A-U Ww/Ww pairing antiparallel cis XX -A8-B11 : G-C Ww/Ww pairing antiparallel cis XIX -A9-B10 : G-C Ww/Ww pairing antiparallel cis XIX diff --git a/MCdata/1c9s_MC b/MCdata/1c9s_MC deleted file mode 100644 index 119026353fc8e6a7360d63eedee63f481165a4aa..0000000000000000000000000000000000000000 --- a/MCdata/1c9s_MC +++ /dev/null @@ -1,2899 +0,0 @@ -Residue conformations ------------------------------------------- -W101 : G C3p_endo anti -W102 : A C2p_exo anti -W103 : U C2p_endo anti -W104 : G C2p_endo anti -W105 : A C3p_endo anti -W106 : G C3p_endo anti -W107 : A C3p_endo anti -W108 : U C2p_endo anti -W109 : G C2p_endo anti -W110 : A C3p_endo anti -W111 : G C3p_endo anti -W112 : A C3p_endo anti -W113 : U C2p_endo anti -W114 : G C2p_endo anti -W115 : A C3p_endo anti -W116 : G C4p_exo anti -W117 : A C3p_endo anti -W118 : U C2p_endo anti -W119 : G C1p_exo anti -W120 : A C3p_endo anti -W121 : G C3p_endo anti -W122 : A C3p_endo anti -W123 : U C2p_endo anti -W124 : G C2p_endo anti -W125 : A C3p_endo anti -W126 : G C3p_endo anti -W127 : A C2p_exo anti -W128 : U C2p_endo syn -W129 : G C3p_exo anti -W130 : A C3p_endo anti -W131 : G C3p_endo anti -W132 : A C3p_endo anti -W133 : U C2p_endo anti -W134 : G C2p_endo anti -W135 : A C3p_endo anti -W136 : G C3p_endo anti -W137 : A C3p_endo anti -W138 : U C2p_endo anti -W139 : G C2p_endo anti -W140 : A C3p_endo anti -W141 : G C3p_endo anti -W142 : A C3p_endo anti -W143 : U C2p_endo anti -W144 : G C2p_endo anti -W145 : A C3p_endo anti -W146 : G C3p_endo anti -W147 : A C3p_endo anti -W148 : U C2p_endo anti -W149 : G C2p_endo anti -W150 : A C3p_endo anti -W151 : G C3p_endo anti -W152 : A C3p_endo anti -W153 : U C2p_endo anti -W154 : G C2p_endo anti -W155 : A C3p_endo anti -A7 : SER -A8 : ASP -A9 : PHE -A10 : VAL -A11 : VAL -A12 : ILE -A13 : LYS -A14 : ALA -A15 : LEU -A16 : GLU -A17 : ASP -A18 : GLY -A19 : VAL -A20 : ASN -A21 : VAL -A22 : ILE -A23 : GLY -A24 : LEU -A25 : THR -A26 : ARG -A27 : GLY -A28 : ALA -A29 : ASP -A30 : THR -A31 : ARG -A32 : PHE -A33 : HIS -A34 : HIS -A35 : SER -A36 : GLU -A37 : LYS -A38 : LEU -A39 : ASP -A40 : LYS -A41 : GLY -A42 : GLU -A43 : VAL -A44 : LEU -A45 : ILE -A46 : ALA -A47 : GLN -A48 : PHE -A49 : THR -A50 : GLU -A51 : HIS -A52 : THR -A53 : SER -A54 : ALA -A55 : ILE -A56 : LYS -A57 : VAL -A58 : ARG -A59 : GLY -A60 : LYS -A61 : ALA -A62 : TYR -A63 : ILE -A64 : GLN -A65 : THR -A66 : ARG -A67 : HIS -A68 : GLY -A69 : VAL -A70 : ILE -A71 : GLU -A72 : SER -A73 : GLU -A74 : GLY -A75 : LYS -B7 : SER -B8 : ASP -B9 : PHE -B10 : VAL -B11 : VAL -B12 : ILE -B13 : LYS -B14 : ALA -B15 : LEU -B16 : GLU -B17 : ASP -B18 : GLY -B19 : VAL -B20 : ASN -B21 : VAL -B22 : ILE -B23 : GLY -B24 : LEU -B25 : THR -B26 : ARG -B27 : GLY -B28 : ALA -B29 : ASP -B30 : THR -B31 : ARG -B32 : PHE -B33 : HIS -B34 : HIS -B35 : SER -B36 : GLU -B37 : LYS -B38 : LEU -B39 : ASP -B40 : LYS -B41 : GLY -B42 : GLU -B43 : VAL -B44 : LEU -B45 : ILE -B46 : ALA -B47 : GLN -B48 : PHE -B49 : THR -B50 : GLU -B51 : HIS -B52 : THR -B53 : SER -B54 : ALA -B55 : ILE -B56 : LYS -B57 : VAL -B58 : ARG -B59 : GLY -B60 : LYS -B61 : ALA -B62 : TYR -B63 : ILE -B64 : GLN -B65 : THR -B66 : ARG -B67 : HIS -B68 : GLY -B69 : VAL -B70 : ILE -B71 : GLU -B72 : SER -B73 : GLU -B74 : GLY -C6 : ASN -C7 : SER -C8 : ASP -C9 : PHE -C10 : VAL -C11 : VAL -C12 : ILE -C13 : LYS -C14 : ALA -C15 : LEU -C16 : GLU -C17 : ASP -C18 : GLY -C19 : VAL -C20 : ASN -C21 : VAL -C22 : ILE -C23 : GLY -C24 : LEU -C25 : THR -C26 : ARG -C27 : GLY -C28 : ALA -C29 : ASP -C30 : THR -C31 : ARG -C32 : PHE -C33 : HIS -C34 : HIS -C35 : SER -C36 : GLU -C37 : LYS -C38 : LEU -C39 : ASP -C40 : LYS -C41 : GLY -C42 : GLU -C43 : VAL -C44 : LEU -C45 : ILE -C46 : ALA -C47 : GLN -C48 : PHE -C49 : THR -C50 : GLU -C51 : HIS -C52 : THR -C53 : SER -C54 : ALA -C55 : ILE -C56 : LYS -C57 : VAL -C58 : ARG -C59 : GLY -C60 : LYS -C61 : ALA -C62 : TYR -C63 : ILE -C64 : GLN -C65 : THR -C66 : ARG -C67 : HIS -C68 : GLY -C69 : VAL -C70 : ILE -C71 : GLU -C72 : SER -C73 : GLU -C74 : GLY -D7 : SER -D8 : ASP -D9 : PHE -D10 : VAL -D11 : VAL -D12 : ILE -D13 : LYS -D14 : ALA -D15 : LEU -D16 : GLU -D17 : ASP -D18 : GLY -D19 : VAL -D20 : ASN -D21 : VAL -D22 : ILE -D23 : GLY -D24 : LEU -D25 : THR -D26 : ARG -D27 : GLY -D28 : ALA -D29 : ASP -D30 : THR -D31 : ARG -D32 : PHE -D33 : HIS -D34 : HIS -D35 : SER -D36 : GLU -D37 : LYS -D38 : LEU -D39 : ASP -D40 : LYS -D41 : GLY -D42 : GLU -D43 : VAL -D44 : LEU -D45 : ILE -D46 : ALA -D47 : GLN -D48 : PHE -D49 : THR -D50 : GLU -D51 : HIS -D52 : THR -D53 : SER -D54 : ALA -D55 : ILE -D56 : LYS -D57 : VAL -D58 : ARG -D59 : GLY -D60 : LYS -D61 : ALA -D62 : TYR -D63 : ILE -D64 : GLN -D65 : THR -D66 : ARG -D67 : HIS -D68 : GLY -D69 : VAL -D70 : ILE -D71 : GLU -D72 : SER -D73 : GLU -D74 : GLY -D75 : LYS -E7 : SER -E8 : ASP -E9 : PHE -E10 : VAL -E11 : VAL -E12 : ILE -E13 : LYS -E14 : ALA -E15 : LEU -E16 : GLU -E17 : ASP -E18 : GLY -E19 : VAL -E20 : ASN -E21 : VAL -E22 : ILE -E23 : GLY -E24 : LEU -E25 : THR -E26 : ARG -E27 : GLY -E28 : ALA -E29 : ASP -E30 : THR -E31 : ARG -E32 : PHE -E33 : HIS -E34 : HIS -E35 : SER -E36 : GLU -E37 : LYS -E38 : LEU -E39 : ASP -E40 : LYS -E41 : GLY -E42 : GLU -E43 : VAL -E44 : LEU -E45 : ILE -E46 : ALA -E47 : GLN -E48 : PHE -E49 : THR -E50 : GLU -E51 : HIS -E52 : THR -E53 : SER -E54 : ALA -E55 : ILE -E56 : LYS -E57 : VAL -E58 : ARG -E59 : GLY -E60 : LYS -E61 : ALA -E62 : TYR -E63 : ILE -E64 : GLN -E65 : THR -E66 : ARG -E67 : HIS -E68 : GLY -E69 : VAL -E70 : ILE -E71 : GLU -E72 : SER -E73 : GLU -E74 : GLY -F7 : SER -F8 : ASP -F9 : PHE -F10 : VAL -F11 : VAL -F12 : ILE -F13 : LYS -F14 : ALA -F15 : LEU -F16 : GLU -F17 : ASP -F18 : GLY -F19 : VAL -F20 : ASN -F21 : VAL -F22 : ILE -F23 : GLY -F24 : LEU -F25 : THR -F26 : ARG -F27 : GLY -F28 : ALA -F29 : ASP -F30 : THR -F31 : ARG -F32 : PHE -F33 : HIS -F34 : HIS -F35 : SER -F36 : GLU -F37 : LYS -F38 : LEU -F39 : ASP -F40 : LYS -F41 : GLY -F42 : GLU -F43 : VAL -F44 : LEU -F45 : ILE -F46 : ALA -F47 : GLN -F48 : PHE -F49 : THR -F50 : GLU -F51 : HIS -F52 : THR -F53 : SER -F54 : ALA -F55 : ILE -F56 : LYS -F57 : VAL -F58 : ARG -F59 : GLY -F60 : LYS -F61 : ALA -F62 : TYR -F63 : ILE -F64 : GLN -F65 : THR -F66 : ARG -F67 : HIS -F68 : GLY -F69 : VAL -F70 : ILE -F71 : GLU -F72 : SER -F73 : GLU -F74 : GLY -F75 : LYS -G6 : ASN -G7 : SER -G8 : ASP -G9 : PHE -G10 : VAL -G11 : VAL -G12 : ILE -G13 : LYS -G14 : ALA -G15 : LEU -G16 : GLU -G17 : ASP -G18 : GLY -G19 : VAL -G20 : ASN -G21 : VAL -G22 : ILE -G23 : GLY -G24 : LEU -G25 : THR -G26 : ARG -G27 : GLY -G28 : ALA -G29 : ASP -G30 : THR -G31 : ARG -G32 : PHE -G33 : HIS -G34 : HIS -G35 : SER -G36 : GLU -G37 : LYS -G38 : LEU -G39 : ASP -G40 : LYS -G41 : GLY -G42 : GLU -G43 : VAL -G44 : LEU -G45 : ILE -G46 : ALA -G47 : GLN -G48 : PHE -G49 : THR -G50 : GLU -G51 : HIS -G52 : THR -G53 : SER -G54 : ALA -G55 : ILE -G56 : LYS -G57 : VAL -G58 : ARG -G59 : GLY -G60 : LYS -G61 : ALA -G62 : TYR -G63 : ILE -G64 : GLN -G65 : THR -G66 : ARG -G67 : HIS -G68 : GLY -G69 : VAL -G70 : ILE -G71 : GLU -G72 : SER -G73 : GLU -G74 : GLY -G75 : LYS -H7 : SER -H8 : ASP -H9 : PHE -H10 : VAL -H11 : VAL -H12 : ILE -H13 : LYS -H14 : ALA -H15 : LEU -H16 : GLU -H17 : ASP -H18 : GLY -H19 : VAL -H20 : ASN -H21 : VAL -H22 : ILE -H23 : GLY -H24 : LEU -H25 : THR -H26 : ARG -H27 : GLY -H28 : ALA -H29 : ASP -H30 : THR -H31 : ARG -H32 : PHE -H33 : HIS -H34 : HIS -H35 : SER -H36 : GLU -H37 : LYS -H38 : LEU -H39 : ASP -H40 : LYS -H41 : GLY -H42 : GLU -H43 : VAL -H44 : LEU -H45 : ILE -H46 : ALA -H47 : GLN -H48 : PHE -H49 : THR -H50 : GLU -H51 : HIS -H52 : THR -H53 : SER -H54 : ALA -H55 : ILE -H56 : LYS -H57 : VAL -H58 : ARG -H59 : GLY -H60 : LYS -H61 : ALA -H62 : TYR -H63 : ILE -H64 : GLN -H65 : THR -H66 : ARG -H67 : HIS -H68 : GLY -H69 : VAL -H70 : ILE -H71 : GLU -H72 : SER -H73 : GLU -H74 : GLY -H75 : LYS -I7 : SER -I8 : ASP -I9 : PHE -I10 : VAL -I11 : VAL -I12 : ILE -I13 : LYS -I14 : ALA -I15 : LEU -I16 : GLU -I17 : ASP -I18 : GLY -I19 : VAL -I20 : ASN -I21 : VAL -I22 : ILE -I23 : GLY -I24 : LEU -I25 : THR -I26 : ARG -I27 : GLY -I28 : ALA -I29 : ASP -I30 : THR -I31 : ARG -I32 : PHE -I33 : HIS -I34 : HIS -I35 : SER -I36 : GLU -I37 : LYS -I38 : LEU -I39 : ASP -I40 : LYS -I41 : GLY -I42 : GLU -I43 : VAL -I44 : LEU -I45 : ILE -I46 : ALA -I47 : GLN -I48 : PHE -I49 : THR -I50 : GLU -I51 : HIS -I52 : THR -I53 : SER -I54 : ALA -I55 : ILE -I56 : LYS -I57 : VAL -I58 : ARG -I59 : GLY -I60 : LYS -I61 : ALA -I62 : TYR -I63 : ILE -I64 : GLN -I65 : THR -I66 : ARG -I67 : HIS -I68 : GLY -I69 : VAL -I70 : ILE -I71 : GLU -I72 : SER -I73 : GLU -I74 : GLY -I75 : LYS -J7 : SER -J8 : ASP -J9 : PHE -J10 : VAL -J11 : VAL -J12 : ILE -J13 : LYS -J14 : ALA -J15 : LEU -J16 : GLU -J17 : ASP -J18 : GLY -J19 : VAL -J20 : ASN -J21 : VAL -J22 : ILE -J23 : GLY -J24 : LEU -J25 : THR -J26 : ARG -J27 : GLY -J28 : ALA -J29 : ASP -J30 : THR -J31 : ARG -J32 : PHE -J33 : HIS -J34 : HIS -J35 : SER -J36 : GLU -J37 : LYS -J38 : LEU -J39 : ASP -J40 : LYS -J41 : GLY -J42 : GLU -J43 : VAL -J44 : LEU -J45 : ILE -J46 : ALA -J47 : GLN -J48 : PHE -J49 : THR -J50 : GLU -J51 : HIS -J52 : THR -J53 : SER -J54 : ALA -J55 : ILE -J56 : LYS -J57 : VAL -J58 : ARG -J59 : GLY -J60 : LYS -J61 : ALA -J62 : TYR -J63 : ILE -J64 : GLN -J65 : THR -J66 : ARG -J67 : HIS -J68 : GLY -J69 : VAL -J70 : ILE -J71 : GLU -J72 : SER -J73 : GLU -K7 : SER -K8 : ASP -K9 : PHE -K10 : VAL -K11 : VAL -K12 : ILE -K13 : LYS -K14 : ALA -K15 : LEU -K16 : GLU -K17 : ASP -K18 : GLY -K19 : VAL -K20 : ASN -K21 : VAL -K22 : ILE -K23 : GLY -K24 : LEU -K25 : THR -K26 : ARG -K27 : GLY -K28 : ALA -K29 : ASP -K30 : THR -K31 : ARG -K32 : PHE -K33 : HIS -K34 : HIS -K35 : SER -K36 : GLU -K37 : LYS -K38 : LEU -K39 : ASP -K40 : LYS -K41 : GLY -K42 : GLU -K43 : VAL -K44 : LEU -K45 : ILE -K46 : ALA -K47 : GLN -K48 : PHE -K49 : THR -K50 : GLU -K51 : HIS -K52 : THR -K53 : SER -K54 : ALA -K55 : ILE -K56 : LYS -K57 : VAL -K58 : ARG -K59 : GLY -K60 : LYS -K61 : ALA -K62 : TYR -K63 : ILE -K64 : GLN -K65 : THR -K66 : ARG -K67 : HIS -K68 : GLY -K69 : VAL -K70 : ILE -K71 : GLU -K72 : SER -K73 : GLU -K74 : GLY -K75 : LYS -L5 : THR -L6 : ASN -L7 : SER -L8 : ASP -L9 : PHE -L10 : VAL -L11 : VAL -L12 : ILE -L13 : LYS -L14 : ALA -L15 : LEU -L16 : GLU -L17 : ASP -L18 : GLY -L19 : VAL -L20 : ASN -L21 : VAL -L22 : ILE -L23 : GLY -L24 : LEU -L25 : THR -L26 : ARG -L27 : GLY -L28 : ALA -L29 : ASP -L30 : THR -L31 : ARG -L32 : PHE -L33 : HIS -L34 : HIS -L35 : SER -L36 : GLU -L37 : LYS -L38 : LEU -L39 : ASP -L40 : LYS -L41 : GLY -L42 : GLU -L43 : VAL -L44 : LEU -L45 : ILE -L46 : ALA -L47 : GLN -L48 : PHE -L49 : THR -L50 : GLU -L51 : HIS -L52 : THR -L53 : SER -L54 : ALA -L55 : ILE -L56 : LYS -L57 : VAL -L58 : ARG -L59 : GLY -L60 : LYS -L61 : ALA -L62 : TYR -L63 : ILE -L64 : GLN -L65 : THR -L66 : ARG -L67 : HIS -L68 : GLY -L69 : VAL -L70 : ILE -L71 : GLU -L72 : SER -L73 : GLU -L74 : GLY -M5 : THR -M6 : ASN -M7 : SER -M8 : ASP -M9 : PHE -M10 : VAL -M11 : VAL -M12 : ILE -M13 : LYS -M14 : ALA -M15 : LEU -M16 : GLU -M17 : ASP -M18 : GLY -M19 : VAL -M20 : ASN -M21 : VAL -M22 : ILE -M23 : GLY -M24 : LEU -M25 : THR -M26 : ARG -M27 : GLY -M28 : ALA -M29 : ASP -M30 : THR -M31 : ARG -M32 : PHE -M33 : HIS -M34 : HIS -M35 : SER -M36 : GLU -M37 : LYS -M38 : LEU -M39 : ASP -M40 : LYS -M41 : GLY -M42 : GLU -M43 : VAL -M44 : LEU -M45 : ILE -M46 : ALA -M47 : GLN -M48 : PHE -M49 : THR -M50 : GLU -M51 : HIS -M52 : THR -M53 : SER -M54 : ALA -M55 : ILE -M56 : LYS -M57 : VAL -M58 : ARG -M59 : GLY -M60 : LYS -M61 : ALA -M62 : TYR -M63 : ILE -M64 : GLN -M65 : THR -M66 : ARG -M67 : HIS -M68 : GLY -M69 : VAL -M70 : ILE -M71 : GLU -M72 : SER -M73 : GLU -M74 : GLY -M75 : LYS -N5 : THR -N6 : ASN -N7 : SER -N8 : ASP -N9 : PHE -N10 : VAL -N11 : VAL -N12 : ILE -N13 : LYS -N14 : ALA -N15 : LEU -N16 : GLU -N17 : ASP -N18 : GLY -N19 : VAL -N20 : ASN -N21 : VAL -N22 : ILE -N23 : GLY -N24 : LEU -N25 : THR -N26 : ARG -N27 : GLY -N28 : ALA -N29 : ASP -N30 : THR -N31 : ARG -N32 : PHE -N33 : HIS -N34 : HIS -N35 : SER -N36 : GLU -N37 : LYS -N38 : LEU -N39 : ASP -N40 : LYS -N41 : GLY -N42 : GLU -N43 : VAL -N44 : LEU -N45 : ILE -N46 : ALA -N47 : GLN -N48 : PHE -N49 : THR -N50 : GLU -N51 : HIS -N52 : THR -N53 : SER -N54 : ALA -N55 : ILE -N56 : LYS -N57 : VAL -N58 : ARG -N59 : GLY -N60 : LYS -N61 : ALA -N62 : TYR -N63 : ILE -N64 : GLN -N65 : THR -N66 : ARG -N67 : HIS -N68 : GLY -N69 : VAL -N70 : ILE -N71 : GLU -N72 : SER -N73 : GLU -N74 : GLY -O5 : THR -O6 : ASN -O7 : SER -O8 : ASP -O9 : PHE -O10 : VAL -O11 : VAL -O12 : ILE -O13 : LYS -O14 : ALA -O15 : LEU -O16 : GLU -O17 : ASP -O18 : GLY -O19 : VAL -O20 : ASN -O21 : VAL -O22 : ILE -O23 : GLY -O24 : LEU -O25 : THR -O26 : ARG -O27 : GLY -O28 : ALA -O29 : ASP -O30 : THR -O31 : ARG -O32 : PHE -O33 : HIS -O34 : HIS -O35 : SER -O36 : GLU -O37 : LYS -O38 : LEU -O39 : ASP -O40 : LYS -O41 : GLY -O42 : GLU -O43 : VAL -O44 : LEU -O45 : ILE -O46 : ALA -O47 : GLN -O48 : PHE -O49 : THR -O50 : GLU -O51 : HIS -O52 : THR -O53 : SER -O54 : ALA -O55 : ILE -O56 : LYS -O57 : VAL -O58 : ARG -O59 : GLY -O60 : LYS -O61 : ALA -O62 : TYR -O63 : ILE -O64 : GLN -O65 : THR -O66 : ARG -O67 : HIS -O68 : GLY -O69 : VAL -O70 : ILE -O71 : GLU -O72 : SER -O73 : GLU -O74 : GLY -O75 : LYS -P5 : THR -P6 : ASN -P7 : SER -P8 : ASP -P9 : PHE -P10 : VAL -P11 : VAL -P12 : ILE -P13 : LYS -P14 : ALA -P15 : LEU -P16 : GLU -P17 : ASP -P18 : GLY -P19 : VAL -P20 : ASN -P21 : VAL -P22 : ILE -P23 : GLY -P24 : LEU -P25 : THR -P26 : ARG -P27 : GLY -P28 : ALA -P29 : ASP -P30 : THR -P31 : ARG -P32 : PHE -P33 : HIS -P34 : HIS -P35 : SER -P36 : GLU -P37 : LYS -P38 : LEU -P39 : ASP -P40 : LYS -P41 : GLY -P42 : GLU -P43 : VAL -P44 : LEU -P45 : ILE -P46 : ALA -P47 : GLN -P48 : PHE -P49 : THR -P50 : GLU -P51 : HIS -P52 : THR -P53 : SER -P54 : ALA -P55 : ILE -P56 : LYS -P57 : VAL -P58 : ARG -P59 : GLY -P60 : LYS -P61 : ALA -P62 : TYR -P63 : ILE -P64 : GLN -P65 : THR -P66 : ARG -P67 : HIS -P68 : GLY -P69 : VAL -P70 : ILE -P71 : GLU -P72 : SER -P73 : GLU -P74 : GLY -Q5 : THR -Q6 : ASN -Q7 : SER -Q8 : ASP -Q9 : PHE -Q10 : VAL -Q11 : VAL -Q12 : ILE -Q13 : LYS -Q14 : ALA -Q15 : LEU -Q16 : GLU -Q17 : ASP -Q18 : GLY -Q19 : VAL -Q20 : ASN -Q21 : VAL -Q22 : ILE -Q23 : GLY -Q24 : LEU -Q25 : THR -Q26 : ARG -Q27 : GLY -Q28 : ALA -Q29 : ASP -Q30 : THR -Q31 : ARG -Q32 : PHE -Q33 : HIS -Q34 : HIS -Q35 : SER -Q36 : GLU -Q37 : LYS -Q38 : LEU -Q39 : ASP -Q40 : LYS -Q41 : GLY -Q42 : GLU -Q43 : VAL -Q44 : LEU -Q45 : ILE -Q46 : ALA -Q47 : GLN -Q48 : PHE -Q49 : THR -Q50 : GLU -Q51 : HIS -Q52 : THR -Q53 : SER -Q54 : ALA -Q55 : ILE -Q56 : LYS -Q57 : VAL -Q58 : ARG -Q59 : GLY -Q60 : LYS -Q61 : ALA -Q62 : TYR -Q63 : ILE -Q64 : GLN -Q65 : THR -Q66 : ARG -Q67 : HIS -Q68 : GLY -Q69 : VAL -Q70 : ILE -Q71 : GLU -Q72 : SER -Q73 : GLU -Q74 : GLY -R5 : THR -R6 : ASN -R7 : SER -R8 : ASP -R9 : PHE -R10 : VAL -R11 : VAL -R12 : ILE -R13 : LYS -R14 : ALA -R15 : LEU -R16 : GLU -R17 : ASP -R18 : GLY -R19 : VAL -R20 : ASN -R21 : VAL -R22 : ILE -R23 : GLY -R24 : LEU -R25 : THR -R26 : ARG -R27 : GLY -R28 : ALA -R29 : ASP -R30 : THR -R31 : ARG -R32 : PHE -R33 : HIS -R34 : HIS -R35 : SER -R36 : GLU -R37 : LYS -R38 : LEU -R39 : ASP -R40 : LYS -R41 : GLY -R42 : GLU -R43 : VAL -R44 : LEU -R45 : ILE -R46 : ALA -R47 : GLN -R48 : PHE -R49 : THR -R50 : GLU -R51 : HIS -R52 : THR -R53 : SER -R54 : ALA -R55 : ILE -R56 : LYS -R57 : VAL -R58 : ARG -R59 : GLY -R60 : LYS -R61 : ALA -R62 : TYR -R63 : ILE -R64 : GLN -R65 : THR -R66 : ARG -R67 : HIS -R68 : GLY -R69 : VAL -R70 : ILE -R71 : GLU -R72 : SER -R73 : GLU -R74 : GLY -S5 : THR -S6 : ASN -S7 : SER -S8 : ASP -S9 : PHE -S10 : VAL -S11 : VAL -S12 : ILE -S13 : LYS -S14 : ALA -S15 : LEU -S16 : GLU -S17 : ASP -S18 : GLY -S19 : VAL -S20 : ASN -S21 : VAL -S22 : ILE -S23 : GLY -S24 : LEU -S25 : THR -S26 : ARG -S27 : GLY -S28 : ALA -S29 : ASP -S30 : THR -S31 : ARG -S32 : PHE -S33 : HIS -S34 : HIS -S35 : SER -S36 : GLU -S37 : LYS -S38 : LEU -S39 : ASP -S40 : LYS -S41 : GLY -S42 : GLU -S43 : VAL -S44 : LEU -S45 : ILE -S46 : ALA -S47 : GLN -S48 : PHE -S49 : THR -S50 : GLU -S51 : HIS -S52 : THR -S53 : SER -S54 : ALA -S55 : ILE -S56 : LYS -S57 : VAL -S58 : ARG -S59 : GLY -S60 : LYS -S61 : ALA -S62 : TYR -S63 : ILE -S64 : GLN -S65 : THR -S66 : ARG -S67 : HIS -S68 : GLY -S69 : VAL -S70 : ILE -S71 : GLU -S72 : SER -S73 : GLU -S74 : GLY -T5 : THR -T6 : ASN -T7 : SER -T8 : ASP -T9 : PHE -T10 : VAL -T11 : VAL -T12 : ILE -T13 : LYS -T14 : ALA -T15 : LEU -T16 : GLU -T17 : ASP -T18 : GLY -T19 : VAL -T20 : ASN -T21 : VAL -T22 : ILE -T23 : GLY -T24 : LEU -T25 : THR -T26 : ARG -T27 : GLY -T28 : ALA -T29 : ASP -T30 : THR -T31 : ARG -T32 : PHE -T33 : HIS -T34 : HIS -T35 : SER -T36 : GLU -T37 : LYS -T38 : LEU -T39 : ASP -T40 : LYS -T41 : GLY -T42 : GLU -T43 : VAL -T44 : LEU -T45 : ILE -T46 : ALA -T47 : GLN -T48 : PHE -T49 : THR -T50 : GLU -T51 : HIS -T52 : THR -T53 : SER -T54 : ALA -T55 : ILE -T56 : LYS -T57 : VAL -T58 : ARG -T59 : GLY -T60 : LYS -T61 : ALA -T62 : TYR -T63 : ILE -T64 : GLN -T65 : THR -T66 : ARG -T67 : HIS -T68 : GLY -T69 : VAL -T70 : ILE -T71 : GLU -T72 : SER -T73 : GLU -T74 : GLY -U5 : THR -U6 : ASN -U7 : SER -U8 : ASP -U9 : PHE -U10 : VAL -U11 : VAL -U12 : ILE -U13 : LYS -U14 : ALA -U15 : LEU -U16 : GLU -U17 : ASP -U18 : GLY -U19 : VAL -U20 : ASN -U21 : VAL -U22 : ILE -U23 : GLY -U24 : LEU -U25 : THR -U26 : ARG -U27 : GLY -U28 : ALA -U29 : ASP -U30 : THR -U31 : ARG -U32 : PHE -U33 : HIS -U34 : HIS -U35 : SER -U36 : GLU -U37 : LYS -U38 : LEU -U39 : ASP -U40 : LYS -U41 : GLY -U42 : GLU -U43 : VAL -U44 : LEU -U45 : ILE -U46 : ALA -U47 : GLN -U48 : PHE -U49 : THR -U50 : GLU -U51 : HIS -U52 : THR -U53 : SER -U54 : ALA -U55 : ILE -U56 : LYS -U57 : VAL -U58 : ARG -U59 : GLY -U60 : LYS -U61 : ALA -U62 : TYR -U63 : ILE -U64 : GLN -U65 : THR -U66 : ARG -U67 : HIS -U68 : GLY -U69 : VAL -U70 : ILE -U71 : GLU -U72 : SER -U73 : GLU -U74 : GLY -V5 : THR -V6 : ASN -V7 : SER -V8 : ASP -V9 : PHE -V10 : VAL -V11 : VAL -V12 : ILE -V13 : LYS -V14 : ALA -V15 : LEU -V16 : GLU -V17 : ASP -V18 : GLY -V19 : VAL -V20 : ASN -V21 : VAL -V22 : ILE -V23 : GLY -V24 : LEU -V25 : THR -V26 : ARG -V27 : GLY -V28 : ALA -V29 : ASP -V30 : THR -V31 : ARG -V32 : PHE -V33 : HIS -V34 : HIS -V35 : SER -V36 : GLU -V37 : LYS -V38 : LEU -V39 : ASP -V40 : LYS -V41 : GLY -V42 : GLU -V43 : VAL -V44 : LEU -V45 : ILE -V46 : ALA -V47 : GLN -V48 : PHE -V49 : THR -V50 : GLU -V51 : HIS -V52 : THR -V53 : SER -V54 : ALA -V55 : ILE -V56 : LYS -V57 : VAL -V58 : ARG -V59 : GLY -V60 : LYS -V61 : ALA -V62 : TYR -V63 : ILE -V64 : GLN -V65 : THR -V66 : ARG -V67 : HIS -V68 : GLY -V69 : VAL -V70 : ILE -V71 : GLU -V72 : SER -V73 : GLU -V74 : GLY -A81 : TRP -A181 : TRP -B81 : TRP -C81 : TRP -D81 : TRP -E81 : TRP -F81 : TRP -G81 : TRP -H81 : TRP -I81 : TRP -J81 : TRP -K81 : TRP -L81 : TRP -M81 : TRP -N81 : TRP -O81 : TRP -P81 : TRP -Q81 : TRP -R81 : TRP -S81 : TRP -T81 : TRP -U81 : TRP -V81 : TRP -W437 : HOH -W562 : HOH -W566 : HOH -W569 : HOH -W610 : HOH -W614 : HOH -W644 : HOH -W689 : HOH -W695 : HOH -W710 : HOH -W719 : HOH -W730 : HOH -W737 : HOH -W748 : HOH -W751 : HOH -W757 : HOH -W758 : HOH -W778 : HOH -W793 : HOH -W810 : HOH -W833 : HOH -W859 : HOH -W864 : HOH -W886 : HOH -W899 : HOH -W909 : HOH -W912 : HOH -W918 : HOH -W927 : HOH -W935 : HOH -W949 : HOH -W954 : HOH -W961 : HOH -W963 : HOH -W966 : HOH -W972 : HOH -W1055 : HOH -W1084 : HOH -W1093 : HOH -W1094 : HOH -W1097 : HOH -W1110 : HOH -W1118 : HOH -W1127 : HOH -W1135 : HOH -W1137 : HOH -W1141 : HOH -W1156 : HOH -W1172 : HOH -W1178 : HOH -W1186 : HOH -W1212 : HOH -W1230 : HOH -W1252 : HOH -W1263 : HOH -A182 : HOH -A183 : HOH -A184 : HOH -A185 : HOH -A186 : HOH -A187 : HOH -A188 : HOH -A189 : HOH -A190 : HOH -A191 : HOH -A192 : HOH -A193 : HOH -A194 : HOH -A195 : HOH -A196 : HOH -A197 : HOH -A198 : HOH -A199 : HOH -A200 : HOH -A201 : HOH -A202 : HOH -A203 : HOH -A204 : HOH -A205 : HOH -A206 : HOH -A207 : HOH -A208 : HOH -A209 : HOH -A210 : HOH -A211 : HOH -A212 : HOH -A213 : HOH -A214 : HOH -A215 : HOH -A216 : HOH -A217 : HOH -A218 : HOH -A219 : HOH -A220 : HOH -A221 : HOH -A222 : HOH -A223 : HOH -A224 : HOH -A225 : HOH -A226 : HOH -A227 : HOH -A228 : HOH -A229 : HOH -A230 : HOH -A231 : HOH -A232 : HOH -A233 : HOH -A234 : HOH -A235 : HOH -A236 : HOH -A237 : HOH -A238 : HOH -A239 : HOH -A240 : HOH -A241 : HOH -A242 : HOH -A243 : HOH -A244 : HOH -A245 : HOH -A246 : HOH -A247 : HOH -A248 : HOH -A249 : HOH -A250 : HOH -A251 : HOH -A252 : HOH -B82 : HOH -B83 : HOH -B84 : HOH -B85 : HOH -B86 : HOH -B87 : HOH -B88 : HOH -B89 : HOH -B90 : HOH -B91 : HOH -B92 : HOH -B93 : HOH -B94 : HOH -B95 : HOH -B96 : HOH -B97 : HOH -B98 : HOH -B99 : HOH -B100 : HOH -B101 : HOH -B102 : HOH -B103 : HOH -B104 : HOH -B105 : HOH -B106 : HOH -B107 : HOH -B108 : HOH -B109 : HOH -B110 : HOH -B111 : HOH -B112 : HOH -B113 : HOH -B114 : HOH -B115 : HOH -B116 : HOH -B117 : HOH -B118 : HOH -B119 : HOH -B120 : HOH -B121 : HOH -B122 : HOH -B123 : HOH -B124 : HOH -B125 : HOH -B126 : HOH -B127 : HOH -B128 : HOH -B129 : HOH -B130 : HOH -B131 : HOH -B132 : HOH -B133 : HOH -B134 : HOH -B135 : HOH -C82 : HOH -C83 : HOH -C84 : HOH -C85 : HOH -C86 : HOH -C87 : HOH -C88 : HOH -C89 : HOH -C90 : HOH -C91 : HOH -C92 : HOH -C93 : HOH -C94 : HOH -C95 : HOH -C96 : HOH -C97 : HOH -C98 : HOH -C99 : HOH -C100 : HOH -C101 : HOH -C102 : HOH -C103 : HOH -C104 : HOH -C105 : HOH -C106 : HOH -C107 : HOH -C108 : HOH -C109 : HOH -C110 : HOH -C111 : HOH -C112 : HOH -C113 : HOH -C114 : HOH -C115 : HOH -C116 : HOH -C117 : HOH -C118 : HOH -C119 : HOH -C120 : HOH -C121 : HOH -C122 : HOH -C123 : HOH -C124 : HOH -C125 : HOH -C126 : HOH -C127 : HOH -C128 : HOH -C129 : HOH -C130 : HOH -C131 : HOH -C132 : HOH -C133 : HOH -C134 : HOH -C135 : HOH -C136 : HOH -C137 : HOH -C138 : HOH -C139 : HOH -C140 : HOH -C141 : HOH -C142 : HOH -C143 : HOH -C144 : HOH -C145 : HOH -C146 : HOH -C147 : HOH -C148 : HOH -C149 : HOH -C150 : HOH -C151 : HOH -C152 : HOH -C153 : HOH -C154 : HOH -C155 : HOH -C156 : HOH -C157 : HOH -C158 : HOH -C159 : HOH -C160 : HOH -C161 : HOH -C162 : HOH -D82 : HOH -D83 : HOH -D84 : HOH -D85 : HOH -D86 : HOH -D87 : HOH -D88 : HOH -D89 : HOH -D90 : HOH -D91 : HOH -D92 : HOH -D93 : HOH -D94 : HOH -D95 : HOH -D96 : HOH -D97 : HOH -D98 : HOH -D99 : HOH -D100 : HOH -D101 : HOH -D102 : HOH -D103 : HOH -D104 : HOH -D105 : HOH -D106 : HOH -D107 : HOH -D108 : HOH -D109 : HOH -D110 : HOH -D111 : HOH -D112 : HOH -D113 : HOH -D114 : HOH -D115 : HOH -D116 : HOH -D117 : HOH -D118 : HOH -D119 : HOH -D120 : HOH -D121 : HOH -D122 : HOH -D123 : HOH -D124 : HOH -D125 : HOH -D126 : HOH -D127 : HOH -D128 : HOH -D129 : HOH -D130 : HOH -D131 : HOH -D132 : HOH -D133 : HOH -D134 : HOH -D135 : HOH -D136 : HOH -D137 : HOH -D138 : HOH -D139 : HOH -D140 : HOH -D141 : HOH -D142 : HOH -D143 : HOH -D144 : HOH -D145 : HOH -D146 : HOH -D147 : HOH -D148 : HOH -D149 : HOH -D150 : HOH -D151 : HOH -D152 : HOH -D153 : HOH -D154 : HOH -E82 : HOH -E83 : HOH -E84 : HOH -E85 : HOH -E86 : HOH -E87 : HOH -E88 : HOH -E89 : HOH -E90 : HOH -E91 : HOH -E92 : HOH -E93 : HOH -E94 : HOH -E95 : HOH -E96 : HOH -E97 : HOH -E98 : HOH -E99 : HOH -E100 : HOH -E101 : HOH -E102 : HOH -E103 : HOH -E104 : HOH -E105 : HOH -E106 : HOH -E107 : HOH -E108 : HOH -E109 : HOH -E110 : HOH -E111 : HOH -E112 : HOH -E113 : HOH -E114 : HOH -E115 : HOH -E116 : HOH -E117 : HOH -E118 : HOH -E119 : HOH -E120 : HOH -E121 : HOH -E122 : HOH -E123 : HOH -E124 : HOH -E125 : HOH -E126 : HOH -E127 : HOH -E128 : HOH -E129 : HOH -E130 : HOH -E131 : HOH -E132 : HOH -E133 : HOH -E134 : HOH -E135 : HOH -E136 : HOH -E137 : HOH -E138 : HOH -E139 : HOH -E140 : HOH -E141 : HOH -E142 : HOH -E143 : HOH -E144 : HOH -E145 : HOH -E146 : HOH -E147 : HOH -E148 : HOH -E149 : HOH -E150 : HOH -F82 : HOH -F83 : HOH -F84 : HOH -F85 : HOH -F86 : HOH -F87 : HOH -F88 : HOH -F89 : HOH -F90 : HOH -F91 : HOH -F92 : HOH -F93 : HOH -F94 : HOH -F95 : HOH -F96 : HOH -F97 : HOH -F98 : HOH -F99 : HOH -F100 : HOH -F101 : HOH -F102 : HOH -F103 : HOH -F104 : HOH -F105 : HOH -F106 : HOH -F107 : HOH -F108 : HOH -F109 : HOH -F110 : HOH -F111 : HOH -F112 : HOH -F113 : HOH -F114 : HOH -F115 : HOH -F116 : HOH -F117 : HOH -F118 : HOH -F119 : HOH -F120 : HOH -F121 : HOH -F122 : HOH -F123 : HOH -F124 : HOH -F125 : HOH -F126 : HOH -F127 : HOH -F128 : HOH -F129 : HOH -F130 : HOH -F131 : HOH -F132 : HOH -F133 : HOH -F134 : HOH -F135 : HOH -F136 : HOH -F137 : HOH -F138 : HOH -F139 : HOH -F140 : HOH -F141 : HOH -F142 : HOH -F143 : HOH -F144 : HOH -F145 : HOH -F146 : HOH -F147 : HOH -F148 : HOH -G82 : HOH -G83 : HOH -G84 : HOH -G85 : HOH -G86 : HOH -G87 : HOH -G88 : HOH -G89 : HOH -G90 : HOH -G91 : HOH -G92 : HOH -G93 : HOH -G94 : HOH -G95 : HOH -G96 : HOH -G97 : HOH -G98 : HOH -G99 : HOH -G100 : HOH -G101 : HOH -G102 : HOH -G103 : HOH -G104 : HOH -G105 : HOH -G106 : HOH -G107 : HOH -G108 : HOH -G109 : HOH -G110 : HOH -G111 : HOH -G112 : HOH -G113 : HOH -G114 : HOH -G115 : HOH -G116 : HOH -G117 : HOH -G118 : HOH -G119 : HOH -G120 : HOH -G121 : HOH -G122 : HOH -G123 : HOH -G124 : HOH -G125 : HOH -G126 : HOH -G127 : HOH -G128 : HOH -G129 : HOH -G130 : HOH -G131 : HOH -G132 : HOH -G133 : HOH -G134 : HOH -G135 : HOH -G136 : HOH -G137 : HOH -G138 : HOH -G139 : HOH -G140 : HOH -G141 : HOH -G142 : HOH -G143 : HOH -G144 : HOH -G145 : HOH -G146 : HOH -G147 : HOH -G148 : HOH -G149 : HOH -G150 : HOH -H82 : HOH -H83 : HOH -H84 : HOH -H85 : HOH -H86 : HOH -H87 : HOH -H88 : HOH -H89 : HOH -H90 : HOH -H91 : HOH -H92 : HOH -H93 : HOH -H94 : HOH -H95 : HOH -H96 : HOH -H97 : HOH -H98 : HOH -H99 : HOH -H100 : HOH -H101 : HOH -H102 : HOH -H103 : HOH -H104 : HOH -H105 : HOH -H106 : HOH -H107 : HOH -H108 : HOH -H109 : HOH -H110 : HOH -H111 : HOH -H112 : HOH -H113 : HOH -H114 : HOH -H115 : HOH -H116 : HOH -H117 : HOH -H118 : HOH -H119 : HOH -H120 : HOH -H121 : HOH -H122 : HOH -H123 : HOH -H124 : HOH -H125 : HOH -H126 : HOH -H127 : HOH -H128 : HOH -H129 : HOH -H130 : HOH -H131 : HOH -H132 : HOH -H133 : HOH -H134 : HOH -H135 : HOH -H136 : HOH -H137 : HOH -H138 : HOH -H139 : HOH -I82 : HOH -I83 : HOH -I84 : HOH -I85 : HOH -I86 : HOH -I87 : HOH -I88 : HOH -I89 : HOH -I90 : HOH -I91 : HOH -I92 : HOH -I93 : HOH -I94 : HOH -I95 : HOH -I96 : HOH -I97 : HOH -I98 : HOH -I99 : HOH -I100 : HOH -I101 : HOH -I102 : HOH -I103 : HOH -I104 : HOH -I105 : HOH -I106 : HOH -I107 : HOH -I108 : HOH -I109 : HOH -I110 : HOH -I111 : HOH -I112 : HOH -I113 : HOH -I114 : HOH -I115 : HOH -I116 : HOH -I117 : HOH -I118 : HOH -I119 : HOH -I120 : HOH -I121 : HOH -I122 : HOH -I123 : HOH -I124 : HOH -I125 : HOH -I126 : HOH -I127 : HOH -I128 : HOH -I129 : HOH -I130 : HOH -I131 : HOH -I132 : HOH -I133 : HOH -I134 : HOH -I135 : HOH -I136 : HOH -I137 : HOH -I138 : HOH -I139 : HOH -I140 : HOH -I141 : HOH -J82 : HOH -J83 : HOH -J84 : HOH -J85 : HOH -J86 : HOH -J87 : HOH -J88 : HOH -J89 : HOH -J90 : HOH -J91 : HOH -J92 : HOH -J93 : HOH -J94 : HOH -J95 : HOH -J96 : HOH -J97 : HOH -J98 : HOH -J99 : HOH -J100 : HOH -J101 : HOH -J102 : HOH -J103 : HOH -J104 : HOH -J105 : HOH -J106 : HOH -J107 : HOH -J108 : HOH -J109 : HOH -J110 : HOH -J111 : HOH -J112 : HOH -J113 : HOH -J114 : HOH -J115 : HOH -J116 : HOH -J117 : HOH -J118 : HOH -J119 : HOH -J120 : HOH -J121 : HOH -J122 : HOH -J123 : HOH -J124 : HOH -J125 : HOH -K82 : HOH -K83 : HOH -K84 : HOH -K85 : HOH -K86 : HOH -K87 : HOH -K88 : HOH -K89 : HOH -K90 : HOH -K91 : HOH -K92 : HOH -K93 : HOH -K94 : HOH -K95 : HOH -K96 : HOH -K97 : HOH -K98 : HOH -K99 : HOH -K100 : HOH -K101 : HOH -K102 : HOH -K103 : HOH -K104 : HOH -K105 : HOH -K106 : HOH -K107 : HOH -K108 : HOH -K109 : HOH -K110 : HOH -K111 : HOH -K112 : HOH -K113 : HOH -K114 : HOH -K115 : HOH -K116 : HOH -K117 : HOH -K118 : HOH -K119 : HOH -K120 : HOH -K121 : HOH -K122 : HOH -K123 : HOH -K124 : HOH -K125 : HOH -K126 : HOH -K127 : HOH -K128 : HOH -K129 : HOH -K130 : HOH -K131 : HOH -K132 : HOH -K133 : HOH -L82 : HOH -L83 : HOH -L84 : HOH -L85 : HOH -L86 : HOH -L87 : HOH -L88 : HOH -L89 : HOH -L90 : HOH -L91 : HOH -L92 : HOH -L93 : HOH -L94 : HOH -L95 : HOH -L96 : HOH -L97 : HOH -L98 : HOH -L99 : HOH -L100 : HOH -L101 : HOH -L102 : HOH -L103 : HOH -L104 : HOH -L105 : HOH -L106 : HOH -L107 : HOH -L108 : HOH -L109 : HOH -L110 : HOH -L111 : HOH -L112 : HOH -M82 : HOH -M83 : HOH -M84 : HOH -M85 : HOH -M86 : HOH -M87 : HOH -M88 : HOH -M89 : HOH -M90 : HOH -M91 : HOH -M92 : HOH -M93 : HOH -M94 : HOH -M95 : HOH -M96 : HOH -M97 : HOH -M98 : HOH -M99 : HOH -M100 : HOH -M101 : HOH -M102 : HOH -M103 : HOH -M104 : HOH -M105 : HOH -M106 : HOH -M107 : HOH -M108 : HOH -M109 : HOH -M110 : HOH -M111 : HOH -M112 : HOH -M113 : HOH -M114 : HOH -M115 : HOH -M116 : HOH -M117 : HOH -M118 : HOH -M119 : HOH -M120 : HOH -M121 : HOH -M122 : HOH -M123 : HOH -M124 : HOH -M125 : HOH -N82 : HOH -N83 : HOH -N84 : HOH -N85 : HOH -N86 : HOH -N87 : HOH -N88 : HOH -N89 : HOH -N90 : HOH -N91 : HOH -N92 : HOH -N93 : HOH -N94 : HOH -N95 : HOH -N96 : HOH -N97 : HOH -N98 : HOH -N99 : HOH -N100 : HOH -N101 : HOH -N102 : HOH -N103 : HOH -N104 : HOH -N105 : HOH -N106 : HOH -N107 : HOH -N108 : HOH -N109 : HOH -N110 : HOH -N111 : HOH -N112 : HOH -N113 : HOH -N114 : HOH -N115 : HOH -N116 : HOH -N117 : HOH -N118 : HOH -N119 : HOH -N120 : HOH -N121 : HOH -N122 : HOH -N123 : HOH -N124 : HOH -N125 : HOH -N126 : HOH -N127 : HOH -O82 : HOH -O83 : HOH -O84 : HOH -O85 : HOH -O86 : HOH -O87 : HOH -O88 : HOH -O89 : HOH -O90 : HOH -O91 : HOH -O92 : HOH -O93 : HOH -O94 : HOH -O95 : HOH -O96 : HOH -O97 : HOH -O98 : HOH -O99 : HOH -O100 : HOH -O101 : HOH -O102 : HOH -O103 : HOH -O104 : HOH -O105 : HOH -O106 : HOH -O107 : HOH -O108 : HOH -O109 : HOH -O110 : HOH -O111 : HOH -O112 : HOH -O113 : HOH -O114 : HOH -O115 : HOH -O116 : HOH -O117 : HOH -O118 : HOH -O119 : HOH -O120 : HOH -O121 : HOH -O122 : HOH -O123 : HOH -O124 : HOH -O125 : HOH -O126 : HOH -O127 : HOH -O128 : HOH -O129 : HOH -O130 : HOH -O131 : HOH -O132 : HOH -O133 : HOH -O134 : HOH -O135 : HOH -O136 : HOH -P82 : HOH -P83 : HOH -P84 : HOH -P85 : HOH -P86 : HOH -P87 : HOH -P88 : HOH -P89 : HOH -P90 : HOH -P91 : HOH -P92 : HOH -P93 : HOH -P94 : HOH -P95 : HOH -P96 : HOH -P97 : HOH -P98 : HOH -P99 : HOH -P100 : HOH -P101 : HOH -P102 : HOH -P103 : HOH -P104 : HOH -P105 : HOH -P106 : HOH -P107 : HOH -P108 : HOH -P109 : HOH -P110 : HOH -P111 : HOH -P112 : HOH -P113 : HOH -P114 : HOH -P115 : HOH -P116 : HOH -P117 : HOH -P118 : HOH -P119 : HOH -P120 : HOH -P121 : HOH -P122 : HOH -Q82 : HOH -Q83 : HOH -Q84 : HOH -Q85 : HOH -Q86 : HOH -Q87 : HOH -Q88 : HOH -Q89 : HOH -Q90 : HOH -Q91 : HOH -Q92 : HOH -Q93 : HOH -Q94 : HOH -Q95 : HOH -Q96 : HOH -Q97 : HOH -Q98 : HOH -Q99 : HOH -Q100 : HOH -Q101 : HOH -Q102 : HOH -Q103 : HOH -Q104 : HOH -Q105 : HOH -Q106 : HOH -Q107 : HOH -Q108 : HOH -Q109 : HOH -Q110 : HOH -Q111 : HOH -Q112 : HOH -Q113 : HOH -Q114 : HOH -Q115 : HOH -Q116 : HOH -Q117 : HOH -Q118 : HOH -Q119 : HOH -Q120 : HOH -Q121 : HOH -Q122 : HOH -Q123 : HOH -Q124 : HOH -Q125 : HOH -Q126 : HOH -Q127 : HOH -R82 : HOH -R83 : HOH -R84 : HOH -R85 : HOH -R86 : HOH -R87 : HOH -R88 : HOH -R89 : HOH -R90 : HOH -R91 : HOH -R92 : HOH -R93 : HOH -R94 : HOH -R95 : HOH -R96 : HOH -R97 : HOH -R98 : HOH -R99 : HOH -R100 : HOH -R101 : HOH -R102 : HOH -R103 : HOH -R104 : HOH -R105 : HOH -R106 : HOH -R107 : HOH -R108 : HOH -R109 : HOH -R110 : HOH -R111 : HOH -R112 : HOH -R113 : HOH -R114 : HOH -R115 : HOH -R116 : HOH -R117 : HOH -R118 : HOH -R119 : HOH -R120 : HOH -R121 : HOH -R122 : HOH -R123 : HOH -R124 : HOH -R125 : HOH -R126 : HOH -R127 : HOH -R128 : HOH -R129 : HOH -R130 : HOH -R131 : HOH -R132 : HOH -R133 : HOH -R134 : HOH -R135 : HOH -R136 : HOH -R137 : HOH -R138 : HOH -R139 : HOH -R140 : HOH -S82 : HOH -S83 : HOH -S84 : HOH -S85 : HOH -S86 : HOH -S87 : HOH -S88 : HOH -S89 : HOH -S90 : HOH -S91 : HOH -S92 : HOH -S93 : HOH -S94 : HOH -S95 : HOH -S96 : HOH -S97 : HOH -S98 : HOH -S99 : HOH -S100 : HOH -S101 : HOH -S102 : HOH -S103 : HOH -S104 : HOH -S105 : HOH -S106 : HOH -S107 : HOH -S108 : HOH -S109 : HOH -S110 : HOH -S111 : HOH -S112 : HOH -S113 : HOH -S114 : HOH -S115 : HOH -S116 : HOH -S117 : HOH -S118 : HOH -S119 : HOH -S120 : HOH -S121 : HOH -S122 : HOH -S123 : HOH -S124 : HOH -S125 : HOH -S126 : HOH -T89 : HOH -T91 : HOH -T113 : HOH -T145 : HOH -T154 : HOH -T190 : HOH -T214 : HOH -T227 : HOH -T238 : HOH -T280 : HOH -T294 : HOH -T304 : HOH -T328 : HOH -T353 : HOH -T358 : HOH -T393 : HOH -T409 : HOH -T466 : HOH -T485 : HOH -T620 : HOH -T625 : HOH -T658 : HOH -T659 : HOH -T664 : HOH -T772 : HOH -T779 : HOH -T807 : HOH -T862 : HOH -T937 : HOH -T978 : HOH -T986 : HOH -T998 : HOH -T1019 : HOH -T1040 : HOH -T1050 : HOH -T1068 : HOH -T1098 : HOH -T1124 : HOH -T1144 : HOH -T1155 : HOH -T1165 : HOH -T1185 : HOH -T1209 : HOH -T1215 : HOH -T1249 : HOH -T1253 : HOH -T1261 : HOH -U82 : HOH -U83 : HOH -U84 : HOH -U85 : HOH -U86 : HOH -U87 : HOH -U88 : HOH -U89 : HOH -U90 : HOH -U91 : HOH -U92 : HOH -U93 : HOH -U94 : HOH -U95 : HOH -U96 : HOH -U97 : HOH -U98 : HOH -U99 : HOH -U100 : HOH -U101 : HOH -U102 : HOH -U103 : HOH -U104 : HOH -U105 : HOH -U106 : HOH -U107 : HOH -U108 : HOH -U109 : HOH -U110 : HOH -U111 : HOH -U112 : HOH -U113 : HOH -U114 : HOH -U115 : HOH -U116 : HOH -U117 : HOH -U118 : HOH -U119 : HOH -U120 : HOH -U121 : HOH -U122 : HOH -U123 : HOH -U124 : HOH -U125 : HOH -U126 : HOH -U127 : HOH -U128 : HOH -U129 : HOH -U130 : HOH -U131 : HOH -V82 : HOH -V83 : HOH -V84 : HOH -V85 : HOH -V86 : HOH -V87 : HOH -V88 : HOH -V89 : HOH -V90 : HOH -V91 : HOH -V92 : HOH -V93 : HOH -V94 : HOH -V95 : HOH -V96 : HOH -V97 : HOH -V98 : HOH -V99 : HOH -V100 : HOH -V101 : HOH -V102 : HOH -V103 : HOH -V104 : HOH -V105 : HOH -V106 : HOH -V107 : HOH -V108 : HOH -V109 : HOH -V110 : HOH -V111 : HOH -V112 : HOH -V113 : HOH -V114 : HOH -V115 : HOH -V116 : HOH -V117 : HOH -V118 : HOH -V119 : HOH -V120 : HOH -V121 : HOH -V122 : HOH -V123 : HOH -V124 : HOH -V125 : HOH -V126 : HOH -V127 : HOH -V128 : HOH -Adjacent stackings ---------------------------------------------- -W101-W155 : adjacent_3p downward -W102-W103 : adjacent_5p upward -W105-W106 : adjacent_5p upward -W107-W108 : adjacent_5p upward -W110-W111 : adjacent_5p upward -W112-W113 : adjacent_5p upward -W115-W116 : adjacent_5p upward -W117-W118 : adjacent_5p upward -W120-W121 : adjacent_5p upward -W122-W123 : adjacent_5p upward -W125-W126 : adjacent_5p upward -W127-W128 : adjacent_5p upward -W130-W131 : adjacent_5p upward -W132-W133 : adjacent_5p upward -W135-W136 : adjacent_5p upward -W137-W138 : adjacent_5p upward -W140-W141 : adjacent_5p upward -W142-W143 : adjacent_5p upward -W145-W146 : adjacent_5p upward -W147-W148 : adjacent_5p upward -W150-W151 : adjacent_5p upward -W152-W153 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 22 -Number of adjacent stackings = 22 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ diff --git a/MCdata/1cgm_MC b/MCdata/1cgm_MC deleted file mode 100644 index be66502cffb5204d08f3ff287abb03f3aaa694dc..0000000000000000000000000000000000000000 --- a/MCdata/1cgm_MC +++ /dev/null @@ -1,176 +0,0 @@ -Residue conformations ------------------------------------------- -I1 : G C3p_exo anti -I2 : A O4p_endo anti -I3 : A C2p_exo syn -E0 : ACE -E1 : ALA -E2 : TYR -E3 : ASN -E4 : PRO -E5 : ILE -E6 : THR -E7 : PRO -E8 : SER -E9 : LYS -E10 : LEU -E11 : ILE -E12 : ALA -E13 : PHE -E14 : SER -E15 : ALA -E16 : SER -E17 : TYR -E18 : VAL -E19 : PRO -E20 : VAL -E21 : ARG -E22 : THR -E23 : LEU -E24 : LEU -E25 : ASN -E26 : PHE -E27 : LEU -E28 : VAL -E29 : ALA -E30 : SER -E31 : GLN -E32 : GLY -E33 : THR -E34 : ALA -E35 : PHE -E36 : GLN -E37 : THR -E38 : GLN -E39 : ALA -E40 : GLY -E41 : ARG -E42 : ASP -E43 : SER -E44 : PHE -E45 : ARG -E46 : GLU -E47 : SER -E48 : LEU -E49 : SER -E50 : ALA -E51 : LEU -E52 : PRO -E53 : SER -E54 : SER -E55 : VAL -E56 : VAL -E57 : ASP -E58 : ILE -E59 : ASN -E60 : SER -E61 : ARG -E62 : PHE -E63 : PRO -E64 : ASP -E65 : ALA -E66 : GLY -E67 : PHE -E68 : TYR -E69 : ALA -E70 : PHE -E71 : LEU -E72 : ASN -E73 : GLY -E74 : PRO -E75 : VAL -E76 : LEU -E77 : ARG -E78 : PRO -E79 : ILE -E80 : PHE -E81 : VAL -E82 : SER -E83 : LEU -E84 : LEU -E85 : SER -E86 : SER -E87 : THR -E88 : ASP -E89 : THR -E90 : ARG -E91 : ASN -E92 : ARG -E93 : VAL -E94 : ILE -E95 : GLU -E96 : VAL -E97 : VAL -E98 : ASP -E99 : PRO -E100 : SER -E101 : ASN -E102 : PRO -E103 : THR -E104 : THR -E105 : ALA -E106 : GLU -E107 : SER -E108 : LEU -E109 : ASN -E110 : ALA -E111 : VAL -E112 : LYS -E113 : ARG -E114 : THR -E115 : ASP -E116 : ASP -E117 : ALA -E118 : SER -E119 : THR -E120 : ALA -E121 : ALA -E122 : ARG -E123 : ALA -E124 : GLU -E125 : ILE -E126 : ASP -E127 : ASN -E128 : LEU -E129 : ILE -E130 : GLU -E131 : SER -E132 : ILE -E133 : SER -E134 : LYS -E135 : GLY -E136 : PHE -E137 : ASP -E138 : VAL -E139 : TYR -E140 : ASP -E141 : ARG -E142 : ALA -E143 : SER -E144 : PHE -E145 : GLU -E146 : ALA -E147 : ALA -E148 : PHE -E149 : SER -E150 : VAL -E151 : VAL -E152 : TRP -E153 : SER -E154 : GLU -E155 : ALA -E156 : THR -E157 : THR -E158 : SER -E159 : LYS -E160 : ALA -E171 : HOH -E172 : HOH -E173 : HOH -E174 : HOH -E175 : HOH -Adjacent stackings ---------------------------------------------- -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 0 -Number of adjacent stackings = 0 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ diff --git a/MCdata/1cq5_MC b/MCdata/1cq5_MC deleted file mode 100644 index 0b34aa6a1848dbc3a65538866a63ce11ec127e7e..0000000000000000000000000000000000000000 --- a/MCdata/1cq5_MC +++ /dev/null @@ -1,111 +0,0 @@ -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : U C3p_endo anti -A7 : U C1p_exo anti -A8 : A C2p_exo anti -A9 : C C3p_endo anti -A10 : C C2p_endo anti -A11 : A C3p_exo syn -A12 : G C3p_endo anti -A13 : G C3p_endo anti -A14 : U C3p_endo anti -A15 : C C3p_endo anti -A16 : A C3p_endo anti -A17 : G C2p_endo anti -A18 : G C3p_endo anti -A19 : U C3p_endo anti -A20 : C C3p_endo anti -A21 : C C3p_endo anti -A22 : G C3p_endo anti -A23 : G C3p_endo anti -A24 : A C3p_endo anti -A25 : A C3p_endo anti -A26 : G C2p_exo anti -A27 : G C2p_exo anti -A28 : A C3p_endo anti -A29 : A C3p_endo anti -A30 : G C3p_endo anti -A31 : C C3p_endo anti -A32 : A C3p_endo anti -A33 : G C3p_endo anti -A34 : C C3p_endo anti -A35 : C C3p_endo anti -A36 : A C3p_endo anti -A37 : A C3p_endo anti -A38 : G C3p_endo anti -A39 : G C3p_endo anti -A40 : C C3p_endo anti -A41 : G C3p_endo anti -A42 : C C3p_endo anti -A43 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A7-A8 : adjacent_5p outward -A11-A12 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A24-A25 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A28-A29 : adjacent_5p upward -A29-A30 : adjacent_5p upward -A32-A33 : adjacent_5p upward -A33-A34 : adjacent_5p upward -A34-A35 : adjacent_5p upward -A35-A36 : adjacent_5p upward -A37-A38 : adjacent_5p upward -A38-A39 : adjacent_5p upward -A39-A40 : adjacent_5p upward -A40-A41 : adjacent_5p upward -A41-A42 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A41 : outward -A9-A37 : outward -A16-A32 : outward -Number of stackings = 34 -Number of adjacent stackings = 31 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -A1-A43 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A42 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A41 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A40 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A39 : U-G Ws/Ww pairing antiparallel cis XXVIII -A6-A38 : U-G Ww/Hw pairing antiparallel trans one_hbond -A8-A38 : A-G O2'/Ww pairing -A9-A36 : C-A Bh/O2' pairing -A9-A38 : C-G O2P/Bs pairing -A10-A11 : C-A O2'/Hh adjacent_5p pairing -A11-A36 : A-A Hw/Ss pairing antiparallel trans one_hbond 41 -A12-A35 : G-C Ww/Ww pairing antiparallel cis XIX -A13-A34 : G-C Ww/Ww pairing antiparallel cis XIX -A14-A33 : U-G Ws/Ww pairing antiparallel cis XXVIII -A15-A31 : C-C Wh/Ww pairing antiparallel cis one_hbond 131 -A15-A32 : C-A Ss/Hw O2'/Bh pairing antiparallel trans one_hbond 77 -A16-A30 : A-G O2P/Ww O2P/Bs pairing -A17-A31 : G-C Ww/O2P pairing -A18-A29 : G-A Ww/Ww pairing antiparallel cis VIII -A18-A30 : G-G Bs/O2' pairing -A19-A28 : U-A Ww/Ww pairing antiparallel cis XX -A20-A27 : C-G Ww/Ww pairing antiparallel cis XIX -A21-A26 : C-G Ww/Ww pairing antiparallel cis XIX -A22-A24 : G-A O2'/Bh pairing -A22-A25 : G-A Sw/Hh Ww/O2P Bs/O2P pairing antiparallel trans one_hbond -A30-A31 : G-C O2P/Bh adjacent_5p pairing -A36-A37 : A-A O2'/C8 adjacent_5p pairing diff --git a/MCdata/1cql_MC b/MCdata/1cql_MC deleted file mode 100644 index bc0e41e2a5c3891eef66490ff1590aa6d6b8e95c..0000000000000000000000000000000000000000 --- a/MCdata/1cql_MC +++ /dev/null @@ -1,1085 +0,0 @@ -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : U C3p_endo anti -A7 : U C1p_exo anti -A8 : A C3p_exo anti -A9 : C C3p_endo syn -A10 : C O4p_endo anti -A11 : A C2p_endo syn -A12 : G C3p_endo anti -A13 : G C3p_endo anti -A14 : U C3p_endo anti -A15 : C C3p_endo anti -A16 : A C3p_endo anti -A17 : G C1p_exo anti -A18 : G C3p_endo anti -A19 : U C3p_endo anti -A20 : C C3p_endo anti -A21 : C C3p_endo anti -A22 : G C3p_endo anti -A23 : G C3p_endo anti -A24 : A C3p_endo anti -A25 : A C3p_endo anti -A26 : G C2p_exo anti -A27 : G C3p_endo anti -A28 : A C3p_endo anti -A29 : A C3p_endo anti -A30 : G C3p_endo anti -A31 : C C3p_endo anti -A32 : A C3p_endo anti -A33 : G C3p_endo anti -A34 : C C3p_endo anti -A35 : C C3p_endo anti -A36 : A C3p_endo anti -A37 : A C3p_endo anti -A38 : G C3p_endo anti -A39 : G C3p_endo anti -A40 : C C3p_endo anti -A41 : G C3p_endo anti -A42 : C C3p_endo anti -A43 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A7-A8 : adjacent_5p outward -A8-A9 : adjacent_5p upward pairing -A9-A10 : adjacent_5p inward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A24-A25 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A28-A29 : adjacent_5p upward -A29-A30 : adjacent_5p upward -A32-A33 : adjacent_5p upward -A33-A34 : adjacent_5p upward -A34-A35 : adjacent_5p upward -A35-A36 : adjacent_5p upward -A38-A39 : adjacent_5p upward -A39-A40 : adjacent_5p upward -A40-A41 : adjacent_5p upward -A41-A42 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A41 : outward -A12-A36 : outward -A16-A32 : outward -Number of stackings = 35 -Number of adjacent stackings = 32 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -A1-A43 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A42 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A41 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A40 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A39 : U-G Ws/Ww pairing antiparallel cis XXVIII -A6-A38 : U-G Ws/Ww pairing antiparallel cis XXVIII -A8-A9 : A-C O2'/Hh adjacent_5p upward pairing -A9-A11 : C-A Hw/Hh pairing antiparallel trans one_hbond 68 -A9-A37 : C-A O2'/Bh pairing -A9-A38 : C-G O2P/Bs pairing -A10-A11 : C-A O2'/C8 adjacent_5p pairing -A10-A36 : C-A Bh/O2' pairing -A11-A36 : A-A Hw/Ss pairing antiparallel trans one_hbond 41 -A12-A35 : G-C Ww/Ww pairing antiparallel cis XIX -A13-A34 : G-C Ww/Ww pairing antiparallel cis XIX -A14-A33 : U-G Ws/Ww pairing antiparallel cis XXVIII -A15-A31 : C-C Wh/Ww pairing antiparallel cis one_hbond 131 -A15-A32 : C-A O2'/Bh pairing -A16-A30 : A-G O2P/Ww O2P/Bs pairing -A17-A31 : G-C Ww/O2P pairing -A18-A29 : G-A Ww/Ww pairing antiparallel cis VIII -A18-A30 : G-G Bs/O2' pairing -A19-A28 : U-A Ww/Ww pairing antiparallel cis XX -A20-A27 : C-G Ww/Ww pairing antiparallel cis XIX -A21-A26 : C-G Ww/Ww pairing antiparallel cis XIX -A22-A24 : G-A O2'/Bh pairing -A22-A25 : G-A Sw/Hh Ww/O2P Bs/O2P pairing antiparallel trans one_hbond -A30-A31 : G-C O2P/Bh adjacent_5p pairing -A36-A37 : A-A O2'/C8 adjacent_5p pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : U C3p_endo anti -A7 : U C2p_endo anti -A8 : A C1p_endo anti -A9 : C C3p_endo syn -A10 : C C1p_exo anti -A11 : A C3p_exo syn -A12 : G C3p_endo anti -A13 : G C3p_endo anti -A14 : U C3p_endo anti -A15 : C C3p_endo anti -A16 : A C3p_endo anti -A17 : G C1p_exo anti -A18 : G C3p_endo anti -A19 : U C3p_endo anti -A20 : C C3p_endo anti -A21 : C C3p_endo anti -A22 : G C3p_endo anti -A23 : G C3p_endo anti -A24 : A C3p_endo anti -A25 : A C3p_endo anti -A26 : G C2p_exo anti -A27 : G C2p_exo anti -A28 : A C3p_endo anti -A29 : A C3p_endo anti -A30 : G C3p_endo anti -A31 : C C3p_endo anti -A32 : A C3p_endo anti -A33 : G C3p_endo anti -A34 : C C3p_endo anti -A35 : C C3p_endo anti -A36 : A C3p_endo anti -A37 : A C3p_endo anti -A38 : G C3p_endo anti -A39 : G C3p_endo anti -A40 : C C3p_endo anti -A41 : G C3p_endo anti -A42 : C C3p_endo anti -A43 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A7-A8 : adjacent_5p outward pairing -A8-A9 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A24-A25 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A28-A29 : adjacent_5p upward -A29-A30 : adjacent_5p upward -A30-A31 : adjacent_5p upward pairing -A32-A33 : adjacent_5p upward -A33-A34 : adjacent_5p upward -A34-A35 : adjacent_5p upward -A35-A36 : adjacent_5p upward -A38-A39 : adjacent_5p upward -A39-A40 : adjacent_5p upward -A40-A41 : adjacent_5p upward -A41-A42 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A41 : outward -A16-A32 : outward -Number of stackings = 34 -Number of adjacent stackings = 32 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A1-A43 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A42 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A41 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A40 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A39 : U-G Ws/Ww pairing antiparallel cis XXVIII -A6-A38 : U-G Ww/Hw pairing antiparallel trans one_hbond -A7-A8 : U-A O2'/Hh adjacent_5p outward pairing -A8-A38 : A-G O2'/Ww pairing -A9-A37 : C-A O2'/Bh pairing -A9-A38 : C-G O2P/Bs pairing -A10-A36 : C-A Bh/O2' pairing -A11-A36 : A-A Hw/Ss pairing antiparallel trans one_hbond 41 -A12-A35 : G-C Ww/Ww pairing antiparallel cis XIX -A13-A34 : G-C Ww/Ww pairing antiparallel cis XIX -A14-A33 : U-G Ws/Ww pairing antiparallel cis XXVIII -A15-A31 : C-C Wh/Ww pairing antiparallel cis one_hbond 131 -A15-A32 : C-A Ss/Hw O2'/Bh pairing antiparallel trans one_hbond 77 -A16-A29 : A-A O2P/Bh pairing -A16-A30 : A-G O2P/Ww O2P/Ww O2P/Bs pairing -A17-A31 : G-C Ww/O2P pairing -A18-A29 : G-A Ww/Ww pairing antiparallel cis VIII -A18-A30 : G-G Bs/O2' pairing -A19-A28 : U-A Ww/Ww pairing antiparallel cis XX -A20-A27 : C-G Ww/Ww pairing antiparallel cis XIX -A21-A26 : C-G Ww/Ww pairing antiparallel cis XIX -A22-A24 : G-A O2'/Bh pairing -A22-A25 : G-A Sw/Hh Ww/O2P Bs/O2P pairing antiparallel trans one_hbond -A30-A31 : G-C O2P/Bh adjacent_5p upward pairing -A36-A37 : A-A O2'/C8 adjacent_5p pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : U C2p_exo anti -A7 : U C2p_endo anti -A8 : A C3p_endo anti -A9 : C C3p_endo anti -A10 : C C1p_exo anti -A11 : A C3p_exo syn -A12 : G C3p_endo anti -A13 : G C3p_endo anti -A14 : U C3p_endo anti -A15 : C C3p_endo anti -A16 : A C3p_endo anti -A17 : G C1p_exo anti -A18 : G C3p_endo anti -A19 : U C3p_endo anti -A20 : C C3p_endo anti -A21 : C C3p_endo anti -A22 : G C3p_endo anti -A23 : G C3p_endo anti -A24 : A C3p_endo anti -A25 : A C3p_endo anti -A26 : G C2p_exo anti -A27 : G C2p_exo anti -A28 : A C3p_endo anti -A29 : A C3p_endo anti -A30 : G C3p_endo anti -A31 : C C3p_endo anti -A32 : A C3p_endo anti -A33 : G C3p_endo anti -A34 : C C3p_endo anti -A35 : C C3p_endo anti -A36 : A C3p_endo anti -A37 : A C3p_endo anti -A38 : G C3p_endo anti -A39 : G C3p_endo anti -A40 : C C3p_endo anti -A41 : G C3p_endo anti -A42 : C C3p_endo anti -A43 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A7-A8 : adjacent_5p outward -A8-A9 : adjacent_5p upward pairing -A11-A12 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A24-A25 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A28-A29 : adjacent_5p upward -A29-A30 : adjacent_5p upward -A32-A33 : adjacent_5p upward -A33-A34 : adjacent_5p upward -A34-A35 : adjacent_5p upward -A35-A36 : adjacent_5p upward -A38-A39 : adjacent_5p upward -A39-A40 : adjacent_5p upward -A40-A41 : adjacent_5p upward -A41-A42 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A41 : outward -A16-A32 : outward -Number of stackings = 33 -Number of adjacent stackings = 31 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A1-A43 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A42 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A41 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A40 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A39 : U-G Ws/Ww pairing antiparallel cis XXVIII -A8-A9 : A-C O2'/Hh adjacent_5p upward pairing -A8-A38 : A-G O2'/Ww pairing -A9-A37 : C-A Ww/C8 O2'/Bh pairing antiparallel trans one_hbond -A9-A38 : C-G O2P/Bs pairing -A10-A11 : C-A O2'/Hh adjacent_5p pairing -A11-A36 : A-A Hw/Ss pairing antiparallel trans one_hbond 41 -A12-A35 : G-C Ww/Ww pairing antiparallel cis XIX -A13-A34 : G-C Ww/Ww pairing antiparallel cis XIX -A14-A33 : U-G Ws/Ww pairing antiparallel cis XXVIII -A15-A31 : C-C Wh/Ww pairing antiparallel cis one_hbond 131 -A15-A32 : C-A O2'/Bh pairing -A16-A30 : A-G O2P/Ww O2P/Bs pairing -A18-A29 : G-A Ww/Ww pairing antiparallel cis VIII -A18-A30 : G-G Bs/O2' pairing -A19-A28 : U-A Ww/Ww pairing antiparallel cis XX -A20-A27 : C-G Ww/Ww pairing antiparallel cis XIX -A21-A26 : C-G Ww/Ww pairing antiparallel cis XIX -A22-A24 : G-A O2'/Bh pairing -A22-A25 : G-A Sw/Hh Ww/O2P Bs/O2P pairing antiparallel trans one_hbond -A30-A31 : G-C O2P/Bh adjacent_5p pairing -A36-A37 : A-A O2'/C8 adjacent_5p pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : U C3p_endo anti -A7 : U C2p_endo anti -A8 : A C3p_exo anti -A9 : C C3p_endo syn -A10 : C C1p_exo anti -A11 : A C2p_endo syn -A12 : G C3p_endo anti -A13 : G C3p_endo anti -A14 : U C3p_endo anti -A15 : C C3p_endo anti -A16 : A C3p_endo anti -A17 : G O4p_endo anti -A18 : G C3p_endo anti -A19 : U C3p_endo anti -A20 : C C3p_endo anti -A21 : C C3p_endo anti -A22 : G C3p_endo anti -A23 : G C3p_endo anti -A24 : A C3p_endo anti -A25 : A C4p_exo anti -A26 : G C2p_exo anti -A27 : G C2p_exo anti -A28 : A C3p_endo anti -A29 : A C3p_endo anti -A30 : G C3p_endo anti -A31 : C C3p_endo anti -A32 : A C3p_endo anti -A33 : G C3p_endo anti -A34 : C C3p_endo anti -A35 : C C3p_endo anti -A36 : A C3p_endo anti -A37 : A C3p_endo anti -A38 : G C3p_endo anti -A39 : G C3p_endo anti -A40 : C C3p_endo anti -A41 : G C3p_endo anti -A42 : C C3p_endo anti -A43 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A7-A8 : adjacent_5p outward -A8-A9 : adjacent_5p upward pairing -A11-A12 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A24-A25 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A28-A29 : adjacent_5p upward -A29-A30 : adjacent_5p upward -A32-A33 : adjacent_5p upward -A33-A34 : adjacent_5p upward -A37-A38 : adjacent_5p upward -A38-A39 : adjacent_5p upward -A39-A40 : adjacent_5p upward -A41-A42 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A41 : outward -A15-A30 : inward -A16-A32 : outward -Number of stackings = 32 -Number of adjacent stackings = 29 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -A1-A43 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A42 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A41 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A40 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A39 : U-G Ws/Ww pairing antiparallel cis XXVIII -A6-A38 : U-G Ww/Bh pairing antiparallel trans one_hbond -A8-A9 : A-C O2'/Hh adjacent_5p upward pairing -A9-A36 : C-A Bh/O2' pairing -A9-A37 : C-A Ww/C8 O2'/Bh pairing antiparallel trans one_hbond -A9-A38 : C-G O2P/Ww O2P/Bs pairing -A10-A36 : C-A Bh/O2' pairing -A12-A35 : G-C Ww/Ww pairing antiparallel cis XIX -A13-A34 : G-C Ww/Ww pairing antiparallel cis XIX -A14-A33 : U-G Ws/Ww pairing antiparallel cis XXVIII -A15-A31 : C-C Wh/Ww pairing antiparallel cis one_hbond 131 -A15-A32 : C-A Ss/Hw O2'/Bh pairing antiparallel trans one_hbond 77 -A16-A30 : A-G O2P/Ww O2P/Bs pairing -A17-A31 : G-C Ww/O2P pairing -A18-A29 : G-A Ww/Ww pairing antiparallel cis VIII -A18-A30 : G-G Bs/O2' pairing -A19-A28 : U-A Ww/Ww pairing antiparallel cis XX -A20-A27 : C-G Ww/Ww pairing antiparallel cis XIX -A21-A26 : C-G Ww/Ww pairing antiparallel cis XIX -A22-A24 : G-A O2'/Bh pairing -A22-A25 : G-A Sw/Hh pairing antiparallel trans one_hbond -A30-A31 : G-C O2P/Bh adjacent_5p pairing -A36-A37 : A-A O2'/C8 adjacent_5p pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : U C3p_endo anti -A7 : U C2p_endo syn -A8 : A C3p_exo anti -A9 : C C3p_endo anti -A10 : C C1p_exo anti -A11 : A C2p_endo anti -A12 : G C3p_endo anti -A13 : G C3p_endo anti -A14 : U C3p_endo anti -A15 : C C3p_endo anti -A16 : A C3p_endo anti -A17 : G O4p_endo anti -A18 : G C3p_endo anti -A19 : U C3p_endo anti -A20 : C C3p_endo anti -A21 : C C3p_endo anti -A22 : G C3p_endo anti -A23 : G C3p_endo anti -A24 : A C3p_endo anti -A25 : A C3p_endo anti -A26 : G C2p_exo anti -A27 : G C2p_exo anti -A28 : A C3p_endo anti -A29 : A C3p_endo anti -A30 : G C3p_endo anti -A31 : C C3p_endo anti -A32 : A C3p_endo anti -A33 : G C3p_endo anti -A34 : C C3p_endo anti -A35 : C C3p_endo anti -A36 : A C3p_endo anti -A37 : A C3p_endo anti -A38 : G C3p_endo anti -A39 : G C3p_endo anti -A40 : C C3p_endo anti -A41 : G C3p_endo anti -A42 : C C3p_endo anti -A43 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A7-A8 : adjacent_5p upward pairing -A8-A9 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A24-A25 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A28-A29 : adjacent_5p upward -A29-A30 : adjacent_5p upward -A32-A33 : adjacent_5p upward -A33-A34 : adjacent_5p upward -A35-A36 : adjacent_5p upward -A37-A38 : adjacent_5p upward -A38-A39 : adjacent_5p upward -A39-A40 : adjacent_5p upward -A40-A41 : adjacent_5p upward -A41-A42 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A41 : outward -A16-A32 : outward -Number of stackings = 33 -Number of adjacent stackings = 31 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A1-A43 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A42 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A41 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A40 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A39 : U-G Ws/Ww pairing antiparallel cis XXVIII -A6-A7 : U-U O2'/Hh adjacent_5p pairing -A6-A38 : U-G Ws/Ww pairing antiparallel cis XXVIII -A7-A8 : U-A O2'/Hh adjacent_5p upward pairing -A7-A9 : U-C Ww/O2P pairing -A7-A37 : U-A Wh/Hw pairing antiparallel trans one_hbond 52 -A10-A11 : C-A O2'/Hh adjacent_5p pairing -A10-A36 : C-A Bh/O2' pairing -A11-A36 : A-A Hw/Ss pairing antiparallel trans one_hbond 41 -A12-A35 : G-C Ww/Ww pairing antiparallel cis XIX -A13-A34 : G-C Ww/Ww pairing antiparallel cis XIX -A14-A33 : U-G Ws/Ww pairing antiparallel cis XXVIII -A15-A31 : C-C Wh/Ww pairing antiparallel cis one_hbond 131 -A15-A32 : C-A Ss/Hw O2'/Bh pairing antiparallel trans one_hbond 77 -A16-A30 : A-G O2P/Ww O2P/Bs pairing -A17-A31 : G-C Ww/O2P pairing -A18-A29 : G-A Ww/Ww pairing antiparallel cis VIII -A18-A30 : G-G Bs/O2' pairing -A19-A28 : U-A Ww/Ww pairing antiparallel cis XX -A20-A27 : C-G Ww/Ww pairing antiparallel cis XIX -A21-A26 : C-G Ww/Ww pairing antiparallel cis XIX -A22-A24 : G-A O2'/Hh pairing -A22-A25 : G-A Sw/Hh Ww/O2P Bs/O2P pairing antiparallel trans one_hbond -A30-A31 : G-C O2P/Bh adjacent_5p pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : U C3p_endo anti -A7 : U C2p_endo syn -A8 : A C3p_exo anti -A9 : C C3p_endo anti -A10 : C C2p_endo anti -A11 : A C3p_endo anti -A12 : G C3p_endo anti -A13 : G C3p_endo anti -A14 : U C3p_endo anti -A15 : C C3p_endo anti -A16 : A C3p_endo anti -A17 : G O4p_endo anti -A18 : G C3p_endo anti -A19 : U C3p_endo anti -A20 : C C3p_endo anti -A21 : C C3p_endo anti -A22 : G C3p_endo anti -A23 : G C3p_endo anti -A24 : A C3p_endo anti -A25 : A C3p_endo anti -A26 : G C2p_exo anti -A27 : G C2p_exo anti -A28 : A C3p_endo anti -A29 : A C3p_endo anti -A30 : G C3p_endo anti -A31 : C C3p_endo anti -A32 : A C3p_endo anti -A33 : G C3p_endo anti -A34 : C C3p_endo anti -A35 : C C3p_endo anti -A36 : A C3p_endo anti -A37 : A C3p_endo anti -A38 : G C3p_endo anti -A39 : G C3p_endo anti -A40 : C C3p_endo anti -A41 : G C3p_endo anti -A42 : C C3p_endo anti -A43 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A24-A25 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A28-A29 : adjacent_5p upward -A29-A30 : adjacent_5p upward -A32-A33 : adjacent_5p upward -A33-A34 : adjacent_5p upward -A37-A38 : adjacent_5p upward -A38-A39 : adjacent_5p upward -A39-A40 : adjacent_5p upward -A40-A41 : adjacent_5p upward -A41-A42 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A41 : outward -A16-A32 : outward -Number of stackings = 31 -Number of adjacent stackings = 29 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A1-A43 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A42 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A41 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A40 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A39 : U-G Ws/Ww pairing antiparallel cis XXVIII -A6-A38 : U-G Ww/Hw pairing antiparallel trans one_hbond -A7-A8 : U-A O2'/Hh adjacent_5p pairing -A7-A9 : U-C Ww/O2P pairing -A9-A36 : C-A Ww/Ww pairing antiparallel cis 71 -A9-A38 : C-G O2P/Bs pairing -A12-A35 : G-C Ww/Ww pairing antiparallel cis XIX -A13-A34 : G-C Ww/Ww pairing antiparallel cis XIX -A14-A33 : U-G Ws/Ww pairing antiparallel cis XXVIII -A15-A31 : C-C Wh/Ww pairing antiparallel cis one_hbond 137 -A15-A32 : C-A Ss/Hw O2'/Bh pairing antiparallel trans one_hbond 77 -A16-A30 : A-G O2P/Ww O2P/Bs pairing -A17-A31 : G-C Ww/O2P pairing -A18-A29 : G-A Ww/Ww pairing antiparallel cis VIII -A18-A30 : G-G Bs/O2' pairing -A19-A28 : U-A Ww/Ww pairing antiparallel cis XX -A20-A27 : C-G Ww/Ww pairing antiparallel cis XIX -A21-A26 : C-G Ww/Ww pairing antiparallel cis XIX -A22-A24 : G-A O2'/Bh O2'/Hh pairing -A22-A25 : G-A Sw/Hh Ww/O2P Bs/O2P pairing antiparallel trans one_hbond -A30-A31 : G-C O2P/Bh adjacent_5p pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : U C3p_endo anti -A7 : U C1p_exo syn -A8 : A C3p_exo anti -A9 : C C3p_endo anti -A10 : C C2p_endo anti -A11 : A C3p_endo anti -A12 : G C3p_endo anti -A13 : G C3p_endo anti -A14 : U C3p_endo anti -A15 : C C3p_endo anti -A16 : A C3p_endo anti -A17 : G O4p_endo anti -A18 : G C3p_endo anti -A19 : U C3p_endo anti -A20 : C C3p_endo anti -A21 : C C3p_endo anti -A22 : G C3p_endo anti -A23 : G C3p_endo anti -A24 : A C3p_endo anti -A25 : A C4p_exo anti -A26 : G C2p_exo anti -A27 : G C3p_endo anti -A28 : A C3p_endo anti -A29 : A C3p_endo anti -A30 : G C3p_endo anti -A31 : C C3p_endo anti -A32 : A C3p_endo anti -A33 : G C3p_endo anti -A34 : C C3p_endo anti -A35 : C C3p_endo anti -A36 : A C3p_endo anti -A37 : A C3p_endo anti -A38 : G C3p_endo anti -A39 : G C3p_endo anti -A40 : C C3p_endo anti -A41 : G C3p_endo anti -A42 : C C3p_endo anti -A43 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A24-A25 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A28-A29 : adjacent_5p upward -A29-A30 : adjacent_5p upward -A32-A33 : adjacent_5p upward -A33-A34 : adjacent_5p upward -A37-A38 : adjacent_5p upward pairing parallel trans one_hbond -A38-A39 : adjacent_5p upward -A39-A40 : adjacent_5p upward -A41-A42 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A41 : outward -A16-A32 : outward -Number of stackings = 31 -Number of adjacent stackings = 29 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A1-A43 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A42 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A41 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A40 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A39 : U-G Ws/Ww pairing antiparallel cis XXVIII -A6-A38 : U-G Ww/Bh pairing antiparallel trans one_hbond -A7-A38 : U-G Ws/Ws pairing antiparallel cis one_hbond -A9-A36 : C-A Ww/Ww pairing antiparallel cis 71 -A12-A35 : G-C Ww/Ww pairing antiparallel cis XIX -A13-A34 : G-C Ww/Ww pairing antiparallel cis XIX -A14-A33 : U-G Ws/Ww pairing antiparallel cis XXVIII -A15-A31 : C-C Wh/Ww pairing antiparallel cis one_hbond 131 -A15-A32 : C-A Ss/Hw O2'/Bh pairing antiparallel trans one_hbond 77 -A16-A30 : A-G O2P/Ww O2P/Bs pairing -A18-A29 : G-A Ww/Ww pairing antiparallel cis VIII -A18-A30 : G-G Bs/O2' pairing -A19-A28 : U-A Ww/Ww pairing antiparallel cis XX -A20-A27 : C-G Ww/Ww pairing antiparallel cis XIX -A21-A26 : C-G Ww/Ww pairing antiparallel cis XIX -A22-A24 : G-A O2'/Bh O2'/Hh Ww/O2P pairing -A22-A25 : G-A Sw/Hh pairing antiparallel trans one_hbond -A30-A31 : G-C O2P/Bh adjacent_5p pairing -A37-A38 : A-G Hw/Ss adjacent_5p upward pairing parallel trans one_hbond -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : U C3p_endo anti -A7 : U C2p_endo anti -A8 : A C2p_endo anti -A9 : C C3p_endo anti -A10 : C C2p_endo syn -A11 : A C3p_endo anti -A12 : G C3p_endo anti -A13 : G C3p_endo anti -A14 : U C3p_endo anti -A15 : C C3p_endo anti -A16 : A C3p_endo anti -A17 : G C1p_exo anti -A18 : G C3p_endo anti -A19 : U C3p_endo anti -A20 : C C3p_endo anti -A21 : C C3p_endo anti -A22 : G C3p_endo anti -A23 : G C3p_endo anti -A24 : A C3p_endo anti -A25 : A C3p_endo anti -A26 : G C2p_exo anti -A27 : G C2p_exo anti -A28 : A C3p_endo anti -A29 : A C3p_endo anti -A30 : G C3p_endo anti -A31 : C C3p_endo anti -A32 : A C3p_endo anti -A33 : G C3p_endo anti -A34 : C C3p_endo anti -A35 : C C3p_endo anti -A36 : A C3p_endo anti -A37 : A C3p_endo anti -A38 : G C3p_endo anti -A39 : G C3p_endo anti -A40 : C C3p_endo anti -A41 : G C3p_endo anti -A42 : C C3p_endo anti -A43 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A24-A25 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A28-A29 : adjacent_5p upward -A29-A30 : adjacent_5p upward -A32-A33 : adjacent_5p upward -A33-A34 : adjacent_5p upward -A35-A36 : adjacent_5p upward -A37-A38 : adjacent_5p upward -A38-A39 : adjacent_5p upward -A39-A40 : adjacent_5p upward -A41-A42 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A41 : outward -A9-A37 : outward -A16-A32 : outward -Number of stackings = 30 -Number of adjacent stackings = 27 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -A1-A43 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A42 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A41 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A40 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A39 : U-G Ws/Ww pairing antiparallel cis XXVIII -A8-A37 : A-A Bh/O2P pairing -A10-A36 : C-A O2'/Ww pairing -A11-A36 : A-A O2P/Ww O2P/Bh pairing -A12-A35 : G-C Ww/Ww pairing antiparallel cis XIX -A13-A34 : G-C Ww/Ww pairing antiparallel cis XIX -A14-A33 : U-G Ws/Ww pairing antiparallel cis XXVIII -A15-A31 : C-C Wh/Ww pairing antiparallel cis one_hbond 131 -A15-A32 : C-A Ss/Hw O2'/Bh pairing antiparallel trans one_hbond 77 -A16-A30 : A-G O2P/Ww O2P/Bs pairing -A17-A31 : G-C Ww/O2P pairing -A18-A29 : G-A Ww/Ww pairing antiparallel cis VIII -A18-A30 : G-G Bs/O2' pairing -A19-A28 : U-A Ww/Ww pairing antiparallel cis XX -A20-A27 : C-G Ww/Ww pairing antiparallel cis XIX -A21-A26 : C-G Ww/Ww pairing antiparallel cis XIX -A22-A25 : G-A Ws/Hh pairing antiparallel trans one_hbond 54 -A30-A31 : G-C O2P/Bh adjacent_5p pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : U C3p_endo anti -A7 : U C2p_endo anti -A8 : A C3p_exo anti -A9 : C C3p_endo syn -A10 : C C1p_exo anti -A11 : A C3p_exo syn -A12 : G C3p_endo anti -A13 : G C3p_endo anti -A14 : U C3p_endo anti -A15 : C C3p_endo anti -A16 : A C3p_endo anti -A17 : G O4p_endo anti -A18 : G C3p_endo anti -A19 : U C3p_endo anti -A20 : C C3p_endo anti -A21 : C C3p_endo anti -A22 : G C3p_endo anti -A23 : G C3p_endo anti -A24 : A C3p_endo anti -A25 : A C3p_endo anti -A26 : G C2p_exo anti -A27 : G C2p_exo anti -A28 : A C3p_endo anti -A29 : A C3p_endo anti -A30 : G C3p_endo anti -A31 : C C3p_endo anti -A32 : A C3p_endo anti -A33 : G C3p_endo anti -A34 : C C3p_endo anti -A35 : C C3p_endo anti -A36 : A C3p_endo anti -A37 : A C3p_endo anti -A38 : G C3p_endo anti -A39 : G C3p_endo anti -A40 : C C3p_endo anti -A41 : G C3p_endo anti -A42 : C C3p_endo anti -A43 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A7-A8 : adjacent_5p outward -A8-A9 : adjacent_5p upward pairing -A11-A12 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A24-A25 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A28-A29 : adjacent_5p upward -A29-A30 : adjacent_5p upward -A30-A31 : adjacent_5p upward pairing -A32-A33 : adjacent_5p upward -A33-A34 : adjacent_5p upward -A37-A38 : adjacent_5p upward -A38-A39 : adjacent_5p upward -A39-A40 : adjacent_5p upward -A40-A41 : adjacent_5p upward -A41-A42 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A41 : outward -A16-A32 : outward -Number of stackings = 33 -Number of adjacent stackings = 31 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A1-A43 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A42 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A41 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A40 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A39 : U-G Ws/Ww pairing antiparallel cis XXVIII -A6-A38 : U-G Ww/Hw pairing antiparallel trans one_hbond -A8-A9 : A-C O2'/Hh adjacent_5p upward pairing -A9-A37 : C-A O2'/Bh pairing -A9-A38 : C-G O2P/Ww O2P/Bs pairing -A10-A11 : C-A O2'/Hh adjacent_5p pairing -A10-A36 : C-A Bh/O2' pairing -A11-A36 : A-A Hw/Ss pairing antiparallel trans one_hbond 41 -A12-A35 : G-C Ww/Ww pairing antiparallel cis XIX -A13-A34 : G-C Ww/Ww pairing antiparallel cis XIX -A14-A33 : U-G Ws/Ww pairing antiparallel cis XXVIII -A15-A31 : C-C Wh/Ww pairing antiparallel cis one_hbond 131 -A15-A32 : C-A Ss/Hw O2'/Bh pairing antiparallel trans one_hbond 77 -A16-A30 : A-G O2P/Ww O2P/Bs pairing -A17-A31 : G-C Ww/O2P pairing -A18-A29 : G-A Ww/Ww pairing antiparallel cis VIII -A18-A30 : G-G Bs/O2' pairing -A19-A28 : U-A Ww/Ww pairing antiparallel cis XX -A20-A27 : C-G Ww/Ww pairing antiparallel cis XIX -A21-A26 : C-G Ww/Ww pairing antiparallel cis XIX -A22-A24 : G-A O2'/Bh O2'/Hh pairing -A22-A25 : G-A Sw/Hh Ww/O2P Bs/O2P pairing antiparallel trans one_hbond -A30-A31 : G-C O2P/Bh adjacent_5p upward pairing -A36-A37 : A-A O2'/C8 adjacent_5p pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : C C3p_endo anti -A4 : G C3p_endo anti -A5 : U C3p_endo anti -A6 : U C3p_endo anti -A7 : U C2p_endo anti -A8 : A C3p_exo anti -A9 : C C3p_endo syn -A10 : C C2p_endo anti -A11 : A C2p_endo syn -A12 : G C3p_endo anti -A13 : G C3p_endo anti -A14 : U C3p_endo anti -A15 : C C3p_endo anti -A16 : A C3p_endo anti -A17 : G C1p_exo anti -A18 : G C3p_endo anti -A19 : U C3p_endo anti -A20 : C C3p_endo anti -A21 : C C3p_endo anti -A22 : G C3p_endo anti -A23 : G C3p_endo anti -A24 : A C3p_endo anti -A25 : A C3p_endo anti -A26 : G C2p_exo anti -A27 : G C3p_endo anti -A28 : A C3p_endo anti -A29 : A C3p_endo anti -A30 : G C3p_endo anti -A31 : C C3p_endo anti -A32 : A C3p_endo anti -A33 : G C3p_endo anti -A34 : C C3p_endo anti -A35 : C C3p_endo anti -A36 : A C3p_endo anti -A37 : A C3p_endo anti -A38 : G C3p_endo anti -A39 : G C3p_endo anti -A40 : C C3p_endo anti -A41 : G C3p_endo anti -A42 : C C3p_endo anti -A43 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A7-A8 : adjacent_5p outward -A11-A12 : adjacent_5p upward pairing -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A24-A25 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A28-A29 : adjacent_5p upward -A29-A30 : adjacent_5p upward -A32-A33 : adjacent_5p upward -A33-A34 : adjacent_5p upward -A38-A39 : adjacent_5p upward -A39-A40 : adjacent_5p upward -A40-A41 : adjacent_5p upward -A41-A42 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A41 : outward -A16-A32 : outward -Number of stackings = 29 -Number of adjacent stackings = 27 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A1-A43 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A42 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A41 : C-G Ww/Ww pairing antiparallel cis XIX -A4-A40 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A39 : U-G Ws/Ww pairing antiparallel cis XXVIII -A6-A38 : U-G Ws/Ww pairing antiparallel cis XXVIII -A8-A9 : A-C O2'/Hh adjacent_5p pairing -A8-A11 : A-A Bh/O2P pairing -A9-A37 : C-A O2'/Bh pairing -A9-A38 : C-G O2P/Bs pairing -A10-A36 : C-A O2'/Ww pairing -A10-A37 : C-A O2P/Bh pairing -A11-A12 : A-G O2'/Hh adjacent_5p upward pairing -A12-A35 : G-C Ww/Ww pairing antiparallel cis XIX -A13-A34 : G-C Ww/Ww pairing antiparallel cis XIX -A14-A33 : U-G Ws/Ww pairing antiparallel cis XXVIII -A15-A31 : C-C Wh/Ww pairing antiparallel cis one_hbond 131 -A15-A32 : C-A Ss/Hw O2'/Bh pairing antiparallel trans one_hbond 77 -A16-A30 : A-G O2P/Ww pairing -A17-A31 : G-C Ww/O2P pairing -A18-A29 : G-A Ww/Ww pairing antiparallel cis VIII -A18-A30 : G-G Bs/O2' pairing -A19-A28 : U-A Ww/Ww pairing antiparallel cis XX -A20-A27 : C-G Ww/Ww pairing antiparallel cis XIX -A21-A26 : C-G Ww/Ww pairing antiparallel cis XIX -A22-A25 : G-A Ws/Hh pairing antiparallel trans one_hbond 54 -A30-A31 : G-C O2P/Bh adjacent_5p pairing diff --git a/MCdata/1csl_MC b/MCdata/1csl_MC deleted file mode 100644 index 437af90fec262bd0a4d905c31f4d1c8d465f5d0d..0000000000000000000000000000000000000000 --- a/MCdata/1csl_MC +++ /dev/null @@ -1,216 +0,0 @@ -Residue conformations ------------------------------------------- -A43 : A C3p_endo anti -A44 : A C3p_endo anti -A45 : C C3p_endo anti -A46 : G C3p_endo anti -A47 : G C3p_endo anti -A48 : G C3p_endo anti -A49 : C C3p_endo anti -A50 : G C3p_endo anti -A51 : C C3p_endo anti -A52 : A C3p_endo anti -A53 : G C3p_endo anti -A54 : A C3p_endo anti -A55 : A C3p_endo anti -B64 : U C3p_endo anti -B65 : C C3p_endo anti -B66 : U C3p_endo anti -B67 : G C3p_endo anti -B68 : A C3p_endo anti -B69 : C C3p_endo anti -B70 : G C3p_endo anti -B71 : G C2p_endo syn -B72 : U C2p_endo anti -B73 : A C3p_endo anti -B74 : C C3p_endo anti -B75 : G C3p_endo anti -B76 : U C3p_endo anti -B77 : U C3p_endo anti -B78 : U C3p_endo anti -A85 : HOH -A87 : HOH -A90 : HOH -A93 : HOH -A95 : HOH -A96 : HOH -A97 : HOH -A99 : HOH -A102 : HOH -A107 : HOH -A108 : HOH -A110 : HOH -A113 : HOH -A116 : HOH -A118 : HOH -A119 : HOH -A121 : HOH -A126 : HOH -A131 : HOH -A134 : HOH -A141 : HOH -A142 : HOH -A144 : HOH -A145 : HOH -A146 : HOH -A149 : HOH -A150 : HOH -A151 : HOH -A154 : HOH -A157 : HOH -A204 : HOH -A205 : HOH -A206 : HOH -A207 : HOH -A208 : HOH -A209 : HOH -A210 : HOH -A212 : HOH -A213 : HOH -A214 : HOH -A215 : HOH -A216 : HOH -A218 : HOH -A220 : HOH -A221 : HOH -A229 : HOH -A239 : HOH -A249 : HOH -A250 : HOH -A254 : HOH -A259 : HOH -A260 : HOH -A262 : HOH -A263 : HOH -A264 : HOH -A267 : HOH -A270 : HOH -A271 : HOH -A272 : HOH -A274 : HOH -A275 : HOH -B79 : HOH -B80 : HOH -B81 : HOH -B82 : HOH -B83 : HOH -B84 : HOH -B86 : HOH -B88 : HOH -B89 : HOH -B91 : HOH -B92 : HOH -B94 : HOH -B98 : HOH -B100 : HOH -B101 : HOH -B103 : HOH -B104 : HOH -B105 : HOH -B106 : HOH -B109 : HOH -B111 : HOH -B112 : HOH -B114 : HOH -B115 : HOH -B120 : HOH -B122 : HOH -B123 : HOH -B128 : HOH -B129 : HOH -B130 : HOH -B133 : HOH -B136 : HOH -B137 : HOH -B139 : HOH -B140 : HOH -B147 : HOH -B148 : HOH -B152 : HOH -B153 : HOH -B156 : HOH -B158 : HOH -B159 : HOH -B201 : HOH -B203 : HOH -B211 : HOH -B222 : HOH -B223 : HOH -B224 : HOH -B225 : HOH -B226 : HOH -B227 : HOH -B228 : HOH -B230 : HOH -B231 : HOH -B232 : HOH -B233 : HOH -B234 : HOH -B235 : HOH -B236 : HOH -B237 : HOH -B238 : HOH -B240 : HOH -B241 : HOH -B242 : HOH -B243 : HOH -B244 : HOH -B245 : HOH -B246 : HOH -B247 : HOH -B248 : HOH -B251 : HOH -B252 : HOH -B253 : HOH -B255 : HOH -B256 : HOH -B257 : HOH -B258 : HOH -B261 : HOH -B265 : HOH -B266 : HOH -B268 : HOH -B269 : HOH -B273 : HOH -Adjacent stackings ---------------------------------------------- -A43-A44 : adjacent_5p upward -A44-A45 : adjacent_5p upward -A45-A46 : adjacent_5p upward -A46-A47 : adjacent_5p upward -A47-A48 : adjacent_5p upward -A48-A49 : adjacent_5p upward -A49-A50 : adjacent_5p upward -A50-A51 : adjacent_5p upward -A51-A52 : adjacent_5p upward -A52-A53 : adjacent_5p upward -A53-A54 : adjacent_5p upward -A54-A55 : adjacent_5p upward -B64-B65 : adjacent_5p upward -B65-B66 : adjacent_5p upward -B66-B67 : adjacent_5p upward -B69-B70 : adjacent_5p upward -B70-B71 : adjacent_5p inward -B73-B74 : adjacent_5p upward -B74-B75 : adjacent_5p upward -B75-B76 : adjacent_5p upward -B76-B77 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A46-B75 : outward -A50-B70 : outward -A52-B67 : outward -B67-B69 : upward -B71-B73 : outward -Number of stackings = 26 -Number of adjacent stackings = 21 -Number of non adjacent stackings = 5 -Base-pairs ------------------------------------------------------ -A44-B76 : A-U Ww/Ww pairing antiparallel cis XX -A45-B75 : C-G Ww/Ww pairing antiparallel cis XIX -A46-B74 : G-C Ww/Ww pairing antiparallel cis XIX -A47-B73 : G-A Ww/Ww pairing antiparallel cis VIII -A48-B71 : G-G Ww/Hh pairing parallel cis VI -A49-B70 : C-G Ww/Ww pairing antiparallel cis XIX -A50-B69 : G-C Ww/Ww pairing antiparallel cis XIX -A51-B67 : C-G Ww/Ww pairing antiparallel cis XIX -A52-B66 : A-U Ww/Ww pairing antiparallel cis XX -A53-B65 : G-C Ww/Ww pairing antiparallel cis XIX -A54-B64 : A-U Ww/Ww pairing antiparallel cis XX diff --git a/MCdata/1cvj_MC b/MCdata/1cvj_MC deleted file mode 100644 index ebf61778382548bf84e82eeb4bff910b52c1b5bb..0000000000000000000000000000000000000000 --- a/MCdata/1cvj_MC +++ /dev/null @@ -1,1393 +0,0 @@ -Residue conformations ------------------------------------------- -M1 : A C3p_endo anti -M2 : A C2p_endo anti -M3 : A C2p_endo anti -M4 : A C3p_endo anti -M5 : A C1p_exo anti -M6 : A C2p_endo anti -M7 : A C2p_endo anti -M8 : A C2p_endo anti -M9 : A C3p_endo anti -N1 : A C2p_endo anti -N2 : A C4p_exo anti -N3 : A C1p_exo anti -N4 : A C1p_exo anti -N5 : A C2p_endo anti -N6 : A C2p_endo syn -N7 : A C3p_endo anti -O1 : A C2p_endo anti -O2 : A C3p_endo anti -O3 : A C2p_endo anti -O4 : A C2p_endo anti -O5 : A C2p_endo anti -O6 : A C2p_endo syn -O7 : A C3p_endo anti -P1 : A C2p_endo anti -P2 : A C3p_endo anti -P3 : A C1p_exo anti -P4 : A C2p_endo anti -P5 : A C2p_endo anti -P6 : A C2p_endo syn -P7 : A C3p_endo anti -Q1 : A C2p_endo anti -Q2 : A C2p_endo anti -Q3 : A C3p_endo anti -Q4 : A C1p_exo anti -Q5 : A C2p_endo anti -Q6 : A C2p_endo anti -Q7 : A C2p_endo syn -Q8 : A C3p_endo anti -R1 : A C2p_endo anti -R2 : A C3p_endo anti -R3 : A C3p_exo anti -R4 : A C1p_exo anti -R5 : A C2p_endo anti -R6 : A C2p_endo syn -R7 : A C3p_endo anti -S1 : A C2p_endo anti -S2 : A C3p_endo anti -S3 : A C1p_exo anti -S4 : A C2p_endo anti -S5 : A C2p_endo anti -S6 : A C2p_endo syn -S7 : A C3p_endo anti -T1 : A C2p_endo anti -T2 : A C4p_exo anti -T3 : A C2p_endo anti -T4 : A C2p_endo anti -T5 : A C2p_endo anti -T6 : A C2p_endo anti -T7 : A C3p_endo anti -A11 : ALA -A12 : SER -A13 : LEU -A14 : TYR -A15 : VAL -A16 : GLY -A17 : ASP -A18 : LEU -A19 : HIS -A20 : PRO -A21 : ASP -A22 : VAL -A23 : THR -A24 : GLU -A25 : ALA -A26 : MET -A27 : LEU -A28 : TYR -A29 : GLU -A30 : LYS -A31 : PHE -A32 : SER -A33 : PRO -A34 : ALA -A35 : GLY -A36 : PRO -A37 : ILE -A38 : LEU -A39 : SER -A40 : ILE -A41 : ARG -A42 : VAL -A43 : CYS -A44 : ARG -A45 : ASP -A46 : MET -A47 : ILE -A48 : THR -A49 : ARG -A50 : ARG -A51 : SER -A52 : LEU -A53 : GLY -A54 : TYR -A55 : ALA -A56 : TYR -A57 : VAL -A58 : ASN -A59 : PHE -A60 : GLN -A61 : GLN -A62 : PRO -A63 : ALA -A64 : ASP -A65 : ALA -A66 : GLU -A67 : ARG -A68 : ALA -A69 : LEU -A70 : ASP -A71 : THR -A72 : MET -A73 : ASN -A74 : PHE -A75 : ASP -A76 : VAL -A77 : ILE -A78 : LYS -A79 : GLY -A80 : LYS -A81 : PRO -A82 : VAL -A83 : ARG -A84 : ILE -A85 : MET -A86 : TRP -A87 : SER -A88 : GLN -A89 : ARG -A90 : ASP -A91 : PRO -A92 : SER -A93 : LEU -A94 : ARG -A95 : LYS -A96 : SER -A97 : GLY -A98 : VAL -A99 : GLY -A100 : ASN -A101 : ILE -A102 : PHE -A103 : ILE -A104 : LYS -A105 : ASN -A106 : LEU -A107 : ASP -A108 : LYS -A109 : SER -A110 : ILE -A111 : ASP -A112 : ASN -A113 : LYS -A114 : ALA -A115 : LEU -A116 : TYR -A117 : ASP -A118 : THR -A119 : PHE -A120 : SER -A121 : ALA -A122 : PHE -A123 : GLY -A124 : ASN -A125 : ILE -A126 : LEU -A127 : SER -A128 : CYS -A129 : LYS -A130 : VAL -A131 : VAL -A132 : CYS -A133 : ASP -A134 : GLU -A135 : ASN -A136 : GLY -A137 : SER -A138 : LYS -A139 : GLY -A140 : TYR -A141 : GLY -A142 : PHE -A143 : VAL -A144 : HIS -A145 : PHE -A146 : GLU -A147 : THR -A148 : GLN -A149 : GLU -A150 : ALA -A151 : ALA -A152 : GLU -A153 : ARG -A154 : ALA -A155 : ILE -A156 : GLU -A157 : LYS -A158 : MET -A159 : ASN -A160 : GLY -A161 : MET -A162 : LEU -A163 : LEU -A164 : ASN -A165 : ASP -A166 : ARG -A167 : LYS -A168 : VAL -A169 : PHE -A170 : VAL -A171 : GLY -A172 : ARG -A173 : PHE -A174 : LYS -A175 : SER -A176 : ARG -A177 : LYS -A178 : GLU -A179 : ARG -B11 : ALA -B12 : SER -B13 : LEU -B14 : TYR -B15 : VAL -B16 : GLY -B17 : ASP -B18 : LEU -B19 : HIS -B20 : PRO -B21 : ASP -B22 : VAL -B23 : THR -B24 : GLU -B25 : ALA -B26 : MET -B27 : LEU -B28 : TYR -B29 : GLU -B30 : LYS -B31 : PHE -B32 : SER -B33 : PRO -B34 : ALA -B35 : GLY -B36 : PRO -B37 : ILE -B38 : LEU -B39 : SER -B40 : ILE -B41 : ARG -B42 : VAL -B43 : CYS -B44 : ARG -B45 : ASP -B46 : MET -B47 : ILE -B48 : THR -B49 : ARG -B50 : ARG -B51 : SER -B52 : LEU -B53 : GLY -B54 : TYR -B55 : ALA -B56 : TYR -B57 : VAL -B58 : ASN -B59 : PHE -B60 : GLN -B61 : GLN -B62 : PRO -B63 : ALA -B64 : ASP -B65 : ALA -B66 : GLU -B67 : ARG -B68 : ALA -B69 : LEU -B70 : ASP -B71 : THR -B72 : MET -B73 : ASN -B74 : PHE -B75 : ASP -B76 : VAL -B77 : ILE -B78 : LYS -B79 : GLY -B80 : LYS -B81 : PRO -B82 : VAL -B83 : ARG -B84 : ILE -B85 : MET -B86 : TRP -B87 : SER -B88 : GLN -B89 : ARG -B90 : ASP -B91 : PRO -B92 : SER -B93 : LEU -B94 : ARG -B95 : LYS -B96 : SER -B97 : GLY -B98 : VAL -B99 : GLY -B100 : ASN -B101 : ILE -B102 : PHE -B103 : ILE -B104 : LYS -B105 : ASN -B106 : LEU -B107 : ASP -B108 : LYS -B109 : SER -B110 : ILE -B111 : ASP -B112 : ASN -B113 : LYS -B114 : ALA -B115 : LEU -B116 : TYR -B117 : ASP -B118 : THR -B119 : PHE -B120 : SER -B121 : ALA -B122 : PHE -B123 : GLY -B124 : ASN -B125 : ILE -B126 : LEU -B127 : SER -B128 : CYS -B129 : LYS -B130 : VAL -B131 : VAL -B132 : CYS -B137 : SER -B138 : LYS -B139 : GLY -B140 : TYR -B141 : GLY -B142 : PHE -B143 : VAL -B144 : HIS -B145 : PHE -B146 : GLU -B147 : THR -B148 : GLN -B149 : GLU -B150 : ALA -B151 : ALA -B152 : GLU -B153 : ARG -B154 : ALA -B155 : ILE -B156 : GLU -B157 : LYS -B158 : MET -B159 : ASN -B170 : VAL -B171 : GLY -B172 : ARG -B173 : PHE -B174 : LYS -B175 : SER -C11 : ALA -C12 : SER -C13 : LEU -C14 : TYR -C15 : VAL -C16 : GLY -C17 : ASP -C18 : LEU -C19 : HIS -C20 : PRO -C21 : ASP -C22 : VAL -C23 : THR -C24 : GLU -C25 : ALA -C26 : MET -C27 : LEU -C28 : TYR -C29 : GLU -C30 : LYS -C31 : PHE -C32 : SER -C33 : PRO -C34 : ALA -C35 : GLY -C36 : PRO -C37 : ILE -C38 : LEU -C39 : SER -C40 : ILE -C41 : ARG -C42 : VAL -C43 : CYS -C44 : ARG -C45 : ASP -C46 : MET -C47 : ILE -C48 : THR -C49 : ARG -C50 : ARG -C51 : SER -C52 : LEU -C53 : GLY -C54 : TYR -C55 : ALA -C56 : TYR -C57 : VAL -C58 : ASN -C59 : PHE -C60 : GLN -C61 : GLN -C62 : PRO -C63 : ALA -C64 : ASP -C65 : ALA -C66 : GLU -C67 : ARG -C68 : ALA -C69 : LEU -C70 : ASP -C71 : THR -C72 : MET -C73 : ASN -C74 : PHE -C75 : ASP -C76 : VAL -C77 : ILE -C78 : LYS -C79 : GLY -C80 : LYS -C81 : PRO -C82 : VAL -C83 : ARG -C84 : ILE -C85 : MET -C86 : TRP -C87 : SER -C88 : GLN -C89 : ARG -C90 : ASP -C91 : PRO -C92 : SER -C93 : LEU -C94 : ARG -C95 : LYS -C96 : SER -C97 : GLY -C98 : VAL -C99 : GLY -C100 : ASN -C101 : ILE -C102 : PHE -C103 : ILE -C104 : LYS -C105 : ASN -C106 : LEU -C107 : ASP -C108 : LYS -C109 : SER -C110 : ILE -C111 : ASP -C112 : ASN -C113 : LYS -C114 : ALA -C115 : LEU -C116 : TYR -C117 : ASP -C118 : THR -C119 : PHE -C120 : SER -C121 : ALA -C122 : PHE -C123 : GLY -C124 : ASN -C125 : ILE -C126 : LEU -C127 : SER -C128 : CYS -C129 : LYS -C130 : VAL -C131 : VAL -C132 : CYS -C133 : ASP -C134 : GLU -C135 : ASN -C136 : GLY -C137 : SER -C138 : LYS -C139 : GLY -C140 : TYR -C141 : GLY -C142 : PHE -C143 : VAL -C144 : HIS -C145 : PHE -C146 : GLU -C147 : THR -C148 : GLN -C149 : GLU -C150 : ALA -C151 : ALA -C152 : GLU -C153 : ARG -C154 : ALA -C155 : ILE -C156 : GLU -C157 : LYS -C158 : MET -C159 : ASN -C160 : GLY -C161 : MET -C162 : LEU -C163 : LEU -C164 : ASN -C165 : ASP -C166 : ARG -C167 : LYS -C168 : VAL -C169 : PHE -C170 : VAL -C171 : GLY -C172 : ARG -C173 : PHE -C174 : LYS -C175 : SER -C176 : ARG -C177 : LYS -C178 : GLU -D11 : ALA -D12 : SER -D13 : LEU -D14 : TYR -D15 : VAL -D16 : GLY -D17 : ASP -D18 : LEU -D19 : HIS -D20 : PRO -D21 : ASP -D22 : VAL -D23 : THR -D24 : GLU -D25 : ALA -D26 : MET -D27 : LEU -D28 : TYR -D29 : GLU -D30 : LYS -D31 : PHE -D32 : SER -D33 : PRO -D34 : ALA -D35 : GLY -D36 : PRO -D37 : ILE -D38 : LEU -D39 : SER -D40 : ILE -D41 : ARG -D42 : VAL -D43 : CYS -D44 : ARG -D45 : ASP -D46 : MET -D47 : ILE -D48 : THR -D49 : ARG -D50 : ARG -D51 : SER -D52 : LEU -D53 : GLY -D54 : TYR -D55 : ALA -D56 : TYR -D57 : VAL -D58 : ASN -D59 : PHE -D60 : GLN -D61 : GLN -D62 : PRO -D63 : ALA -D64 : ASP -D65 : ALA -D66 : GLU -D67 : ARG -D68 : ALA -D69 : LEU -D70 : ASP -D71 : THR -D72 : MET -D73 : ASN -D74 : PHE -D75 : ASP -D76 : VAL -D77 : ILE -D78 : LYS -D79 : GLY -D80 : LYS -D81 : PRO -D82 : VAL -D83 : ARG -D84 : ILE -D85 : MET -D86 : TRP -D87 : SER -D88 : GLN -D89 : ARG -D90 : ASP -D91 : PRO -D92 : SER -D93 : LEU -D94 : ARG -D95 : LYS -D96 : SER -D97 : GLY -D98 : VAL -D99 : GLY -D100 : ASN -D101 : ILE -D102 : PHE -D103 : ILE -D104 : LYS -D105 : ASN -D106 : LEU -D107 : ASP -D108 : LYS -D109 : SER -D110 : ILE -D111 : ASP -D112 : ASN -D113 : LYS -D114 : ALA -D115 : LEU -D116 : TYR -D117 : ASP -D118 : THR -D119 : PHE -D120 : SER -D121 : ALA -D122 : PHE -D123 : GLY -D124 : ASN -D125 : ILE -D126 : LEU -D127 : SER -D128 : CYS -D129 : LYS -D130 : VAL -D131 : VAL -D132 : CYS -D137 : SER -D138 : LYS -D139 : GLY -D140 : TYR -D141 : GLY -D142 : PHE -D143 : VAL -D144 : HIS -D145 : PHE -D146 : GLU -D147 : THR -D148 : GLN -D149 : GLU -D150 : ALA -D151 : ALA -D152 : GLU -D153 : ARG -D154 : ALA -D155 : ILE -D156 : GLU -D157 : LYS -D158 : MET -D159 : ASN -D160 : GLY -D161 : MET -D162 : LEU -D163 : LEU -D164 : ASN -D165 : ASP -D166 : ARG -D167 : LYS -D168 : VAL -D169 : PHE -D170 : VAL -D171 : GLY -D172 : ARG -D173 : PHE -D174 : LYS -D175 : SER -E11 : ALA -E12 : SER -E13 : LEU -E14 : TYR -E15 : VAL -E16 : GLY -E17 : ASP -E18 : LEU -E19 : HIS -E20 : PRO -E21 : ASP -E22 : VAL -E23 : THR -E24 : GLU -E25 : ALA -E26 : MET -E27 : LEU -E28 : TYR -E29 : GLU -E30 : LYS -E31 : PHE -E32 : SER -E33 : PRO -E34 : ALA -E35 : GLY -E36 : PRO -E37 : ILE -E38 : LEU -E39 : SER -E40 : ILE -E41 : ARG -E42 : VAL -E43 : CYS -E44 : ARG -E45 : ASP -E46 : MET -E47 : ILE -E48 : THR -E49 : ARG -E50 : ARG -E51 : SER -E52 : LEU -E53 : GLY -E54 : TYR -E55 : ALA -E56 : TYR -E57 : VAL -E58 : ASN -E59 : PHE -E60 : GLN -E61 : GLN -E62 : PRO -E63 : ALA -E64 : ASP -E65 : ALA -E66 : GLU -E67 : ARG -E68 : ALA -E69 : LEU -E70 : ASP -E71 : THR -E72 : MET -E73 : ASN -E74 : PHE -E75 : ASP -E76 : VAL -E77 : ILE -E78 : LYS -E79 : GLY -E80 : LYS -E81 : PRO -E82 : VAL -E83 : ARG -E84 : ILE -E85 : MET -E86 : TRP -E87 : SER -E88 : GLN -E89 : ARG -E90 : ASP -E91 : PRO -E92 : SER -E93 : LEU -E94 : ARG -E95 : LYS -E96 : SER -E97 : GLY -E98 : VAL -E99 : GLY -E100 : ASN -E101 : ILE -E102 : PHE -E103 : ILE -E104 : LYS -E105 : ASN -E106 : LEU -E107 : ASP -E108 : LYS -E109 : SER -E110 : ILE -E111 : ASP -E112 : ASN -E113 : LYS -E114 : ALA -E115 : LEU -E116 : TYR -E117 : ASP -E118 : THR -E119 : PHE -E120 : SER -E121 : ALA -E122 : PHE -E123 : GLY -E124 : ASN -E125 : ILE -E126 : LEU -E127 : SER -E128 : CYS -E129 : LYS -E130 : VAL -E131 : VAL -E132 : CYS -E133 : ASP -E134 : GLU -E135 : ASN -E136 : GLY -E137 : SER -E138 : LYS -E139 : GLY -E140 : TYR -E141 : GLY -E142 : PHE -E143 : VAL -E144 : HIS -E145 : PHE -E146 : GLU -E147 : THR -E148 : GLN -E149 : GLU -E150 : ALA -E151 : ALA -E152 : GLU -E153 : ARG -E154 : ALA -E155 : ILE -E156 : GLU -E157 : LYS -E158 : MET -E159 : ASN -E160 : GLY -E161 : MET -E162 : LEU -E163 : LEU -E164 : ASN -E165 : ASP -E166 : ARG -E167 : LYS -E168 : VAL -E169 : PHE -E170 : VAL -E171 : GLY -E172 : ARG -E173 : PHE -E174 : LYS -E175 : SER -E176 : ARG -E177 : LYS -E178 : GLU -F11 : ALA -F12 : SER -F13 : LEU -F14 : TYR -F15 : VAL -F16 : GLY -F17 : ASP -F18 : LEU -F19 : HIS -F20 : PRO -F21 : ASP -F22 : VAL -F23 : THR -F24 : GLU -F25 : ALA -F26 : MET -F27 : LEU -F28 : TYR -F29 : GLU -F30 : LYS -F31 : PHE -F32 : SER -F33 : PRO -F34 : ALA -F35 : GLY -F36 : PRO -F37 : ILE -F38 : LEU -F39 : SER -F40 : ILE -F41 : ARG -F42 : VAL -F43 : CYS -F44 : ARG -F45 : ASP -F46 : MET -F47 : ILE -F48 : THR -F49 : ARG -F50 : ARG -F51 : SER -F52 : LEU -F53 : GLY -F54 : TYR -F55 : ALA -F56 : TYR -F57 : VAL -F58 : ASN -F59 : PHE -F60 : GLN -F61 : GLN -F62 : PRO -F63 : ALA -F64 : ASP -F65 : ALA -F66 : GLU -F67 : ARG -F68 : ALA -F69 : LEU -F70 : ASP -F71 : THR -F72 : MET -F73 : ASN -F74 : PHE -F75 : ASP -F76 : VAL -F77 : ILE -F78 : LYS -F79 : GLY -F80 : LYS -F81 : PRO -F82 : VAL -F83 : ARG -F84 : ILE -F85 : MET -F86 : TRP -F87 : SER -F88 : GLN -F89 : ARG -F90 : ASP -F91 : PRO -F92 : SER -F93 : LEU -F94 : ARG -F95 : LYS -F96 : SER -F97 : GLY -F98 : VAL -F99 : GLY -F100 : ASN -F101 : ILE -F112 : ASN -F113 : LYS -F114 : ALA -F115 : LEU -F116 : TYR -F117 : ASP -F118 : THR -F119 : PHE -F120 : SER -F121 : ALA -F122 : PHE -F123 : GLY -F124 : ASN -F125 : ILE -F126 : LEU -F127 : SER -F128 : CYS -F129 : LYS -F130 : VAL -F131 : VAL -F132 : CYS -F137 : SER -F138 : LYS -F139 : GLY -F140 : TYR -F141 : GLY -F142 : PHE -F143 : VAL -F144 : HIS -F145 : PHE -F146 : GLU -F147 : THR -F148 : GLN -F149 : GLU -F168 : VAL -F169 : PHE -F170 : VAL -F171 : GLY -F172 : ARG -F173 : PHE -G11 : ALA -G12 : SER -G13 : LEU -G14 : TYR -G15 : VAL -G16 : GLY -G17 : ASP -G18 : LEU -G19 : HIS -G20 : PRO -G21 : ASP -G22 : VAL -G23 : THR -G24 : GLU -G25 : ALA -G26 : MET -G27 : LEU -G28 : TYR -G29 : GLU -G30 : LYS -G31 : PHE -G32 : SER -G33 : PRO -G34 : ALA -G35 : GLY -G36 : PRO -G37 : ILE -G38 : LEU -G39 : SER -G40 : ILE -G41 : ARG -G42 : VAL -G43 : CYS -G44 : ARG -G45 : ASP -G46 : MET -G47 : ILE -G48 : THR -G49 : ARG -G50 : ARG -G51 : SER -G52 : LEU -G53 : GLY -G54 : TYR -G55 : ALA -G56 : TYR -G57 : VAL -G58 : ASN -G59 : PHE -G60 : GLN -G61 : GLN -G62 : PRO -G63 : ALA -G64 : ASP -G65 : ALA -G66 : GLU -G67 : ARG -G68 : ALA -G69 : LEU -G70 : ASP -G71 : THR -G72 : MET -G73 : ASN -G74 : PHE -G75 : ASP -G76 : VAL -G77 : ILE -G78 : LYS -G79 : GLY -G80 : LYS -G81 : PRO -G82 : VAL -G83 : ARG -G84 : ILE -G85 : MET -G86 : TRP -G87 : SER -G88 : GLN -G89 : ARG -G90 : ASP -G91 : PRO -G92 : SER -G93 : LEU -G94 : ARG -G95 : LYS -G96 : SER -G97 : GLY -G98 : VAL -G99 : GLY -G100 : ASN -G101 : ILE -G102 : PHE -G103 : ILE -G104 : LYS -G105 : ASN -G106 : LEU -G107 : ASP -G108 : LYS -G109 : SER -G110 : ILE -G111 : ASP -G112 : ASN -G113 : LYS -G114 : ALA -G115 : LEU -G116 : TYR -G117 : ASP -G118 : THR -G119 : PHE -G120 : SER -G121 : ALA -G122 : PHE -G123 : GLY -G124 : ASN -G125 : ILE -G126 : LEU -G127 : SER -G128 : CYS -G129 : LYS -G130 : VAL -G131 : VAL -G132 : CYS -G133 : ASP -G134 : GLU -G135 : ASN -G136 : GLY -G137 : SER -G138 : LYS -G139 : GLY -G140 : TYR -G141 : GLY -G142 : PHE -G143 : VAL -G144 : HIS -G145 : PHE -G146 : GLU -G147 : THR -G148 : GLN -G149 : GLU -G150 : ALA -G151 : ALA -G152 : GLU -G153 : ARG -G154 : ALA -G155 : ILE -G156 : GLU -G157 : LYS -G158 : MET -G159 : ASN -G160 : GLY -G161 : MET -G162 : LEU -G163 : LEU -G164 : ASN -G165 : ASP -G166 : ARG -G167 : LYS -G168 : VAL -G169 : PHE -G170 : VAL -G171 : GLY -G172 : ARG -G173 : PHE -G174 : LYS -G175 : SER -H11 : ALA -H12 : SER -H13 : LEU -H14 : TYR -H15 : VAL -H16 : GLY -H17 : ASP -H18 : LEU -H19 : HIS -H20 : PRO -H21 : ASP -H22 : VAL -H23 : THR -H24 : GLU -H25 : ALA -H26 : MET -H27 : LEU -H28 : TYR -H29 : GLU -H30 : LYS -H31 : PHE -H32 : SER -H33 : PRO -H34 : ALA -H35 : GLY -H36 : PRO -H37 : ILE -H38 : LEU -H39 : SER -H40 : ILE -H41 : ARG -H42 : VAL -H43 : CYS -H44 : ARG -H45 : ASP -H46 : MET -H47 : ILE -H48 : THR -H49 : ARG -H50 : ARG -H51 : SER -H52 : LEU -H53 : GLY -H54 : TYR -H55 : ALA -H56 : TYR -H57 : VAL -H58 : ASN -H59 : PHE -H60 : GLN -H61 : GLN -H62 : PRO -H63 : ALA -H64 : ASP -H65 : ALA -H66 : GLU -H67 : ARG -H68 : ALA -H69 : LEU -H70 : ASP -H71 : THR -H72 : MET -H73 : ASN -H74 : PHE -H75 : ASP -H76 : VAL -H77 : ILE -H78 : LYS -H79 : GLY -H80 : LYS -H81 : PRO -H82 : VAL -H83 : ARG -H84 : ILE -H85 : MET -H86 : TRP -H87 : SER -H88 : GLN -H89 : ARG -H90 : ASP -H91 : PRO -H92 : SER -H93 : LEU -H94 : ARG -H95 : LYS -H96 : SER -H97 : GLY -H98 : VAL -H99 : GLY -H100 : ASN -H101 : ILE -H102 : PHE -H103 : ILE -H113 : LYS -H114 : ALA -H115 : LEU -H116 : TYR -H117 : ASP -H118 : THR -H119 : PHE -H120 : SER -H121 : ALA -H122 : PHE -H123 : GLY -H124 : ASN -H125 : ILE -H126 : LEU -H127 : SER -H128 : CYS -H129 : LYS -H130 : VAL -H131 : VAL -H132 : CYS -H137 : SER -H138 : LYS -H139 : GLY -H140 : TYR -H141 : GLY -H142 : PHE -H143 : VAL -H144 : HIS -H145 : PHE -H146 : GLU -H147 : THR -H148 : GLN -H149 : GLU -H150 : ALA -H151 : ALA -H152 : GLU -H173 : PHE -H174 : LYS -H175 : SER -N992 : A C3p_endo anti -O993 : A C3p_endo anti -Q995 : A C3p_endo anti -S997 : A C3p_endo anti -A991 : A C3p_endo anti -D994 : A C3p_endo anti -F996 : A C3p_endo anti -H998 : A C3p_endo anti -N104 : HOH -N145 : HOH -O130 : HOH -O135 : HOH -P149 : HOH -Q137 : HOH -Q139 : HOH -Q144 : HOH -T118 : HOH -T152 : HOH -A992 : HOH -A993 : HOH -A994 : HOH -A995 : HOH -A996 : HOH -A997 : HOH -A998 : HOH -B191 : HOH -B192 : HOH -B193 : HOH -B194 : HOH -B195 : HOH -C191 : HOH -C192 : HOH -C193 : HOH -C194 : HOH -C195 : HOH -C196 : HOH -C197 : HOH -D995 : HOH -D996 : HOH -D997 : HOH -E191 : HOH -E192 : HOH -E193 : HOH -E194 : HOH -E195 : HOH -E196 : HOH -E197 : HOH -E198 : HOH -E199 : HOH -E200 : HOH -E201 : HOH -F997 : HOH -F998 : HOH -F999 : HOH -G191 : HOH -G192 : HOH -H999 : HOH -H1000 : HOH -H1001 : HOH -H1002 : HOH -H1003 : HOH -Adjacent stackings ---------------------------------------------- -M1-M2 : adjacent_5p upward -M4-M5 : adjacent_5p upward -N2-N3 : adjacent_5p upward -O2-O3 : adjacent_5p upward -P2-P3 : adjacent_5p upward -Q3-Q4 : adjacent_5p upward -R2-R3 : adjacent_5p upward -S2-S3 : adjacent_5p upward -T2-T3 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A991-M8 : inward -D994-P6 : inward -F996-R6 : inward -H998-T6 : inward -M7-P5 : outward -N5-Q6 : outward -N6-N992 : inward -O5-R5 : outward -O6-O993 : inward -Q7-Q995 : inward -S5-T5 : outward -S6-S997 : inward -Number of stackings = 21 -Number of adjacent stackings = 9 -Number of non adjacent stackings = 12 -Base-pairs ------------------------------------------------------ diff --git a/MCdata/1cwp_MC b/MCdata/1cwp_MC deleted file mode 100644 index 86a35093bac04a6f4ca611a21f1272d487ee9f2b..0000000000000000000000000000000000000000 --- a/MCdata/1cwp_MC +++ /dev/null @@ -1,501 +0,0 @@ -Residue conformations ------------------------------------------- -A42 : LYS -A43 : ALA -A44 : ILE -A45 : LYS -A46 : ALA -A47 : TRP -A48 : THR -A49 : GLY -A50 : TYR -A51 : SER -A52 : VAL -A53 : SER -A54 : LYS -A55 : TRP -A56 : THR -A57 : ALA -A58 : SER -A59 : CYS -A60 : ALA -A61 : ALA -A62 : ALA -A63 : GLU -A64 : ALA -A65 : LYS -A66 : VAL -A67 : THR -A68 : SER -A69 : ALA -A70 : ILE -A71 : THR -A72 : ILE -A73 : SER -A74 : LEU -A75 : PRO -A76 : ASN -A77 : GLU -A78 : LEU -A79 : SER -A80 : SER -A81 : GLU -A82 : ARG -A83 : ASN -A84 : LYS -A85 : GLN -A86 : LEU -A87 : LYS -A88 : VAL -A89 : GLY -A90 : ARG -A91 : VAL -A92 : LEU -A93 : LEU -A94 : TRP -A95 : LEU -A96 : GLY -A97 : LEU -A98 : LEU -A99 : PRO -A100 : SER -A101 : VAL -A102 : SER -A103 : GLY -A104 : THR -A105 : VAL -A106 : LYS -A107 : SER -A108 : CYS -A109 : VAL -A110 : THR -A111 : GLU -A112 : THR -A113 : GLN -A114 : THR -A115 : THR -A116 : ALA -A117 : ALA -A118 : ALA -A119 : SER -A120 : PHE -A121 : GLN -A122 : VAL -A123 : ALA -A124 : LEU -A125 : ALA -A126 : VAL -A127 : ALA -A128 : ASP -A129 : ASN -A130 : SER -A131 : LYS -A132 : ASP -A133 : VAL -A134 : VAL -A135 : ALA -A136 : ALA -A137 : MET -A138 : TYR -A139 : PRO -A140 : GLU -A141 : ALA -A142 : PHE -A143 : LYS -A144 : GLY -A145 : ILE -A146 : THR -A147 : LEU -A148 : GLU -A149 : GLN -A150 : LEU -A151 : ALA -A152 : ALA -A153 : ASP -A154 : LEU -A155 : THR -A156 : ILE -A157 : TYR -A158 : LEU -A159 : TYR -A160 : SER -A161 : SER -A162 : ALA -A163 : ALA -A164 : LEU -A165 : THR -A166 : GLU -A167 : GLY -A168 : ASP -A169 : VAL -A170 : ILE -A171 : VAL -A172 : HIS -A173 : LEU -A174 : GLU -A175 : VAL -A176 : GLU -A177 : HIS -A178 : VAL -A179 : ARG -A180 : PRO -A181 : THR -A182 : PHE -A183 : ASP -A184 : ASP -A185 : SER -A186 : PHE -A187 : THR -A188 : PRO -A189 : VAL -A190 : TYR -B27 : VAL -B28 : VAL -B29 : GLN -B30 : PRO -B31 : VAL -B32 : ILE -B33 : VAL -B34 : GLU -B35 : PRO -B36 : ILE -B37 : ALA -B38 : SER -B39 : GLY -B40 : GLN -B41 : GLY -B42 : LYS -B43 : ALA -B44 : ILE -B45 : LYS -B46 : ALA -B47 : TRP -B48 : THR -B49 : GLY -B50 : TYR -B51 : SER -B52 : VAL -B53 : SER -B54 : LYS -B55 : TRP -B56 : THR -B57 : ALA -B58 : SER -B59 : CYS -B60 : ALA -B61 : ALA -B62 : ALA -B63 : GLU -B64 : ALA -B65 : LYS -B66 : VAL -B67 : THR -B68 : SER -B69 : ALA -B70 : ILE -B71 : THR -B72 : ILE -B73 : SER -B74 : LEU -B75 : PRO -B76 : ASN -B77 : GLU -B78 : LEU -B79 : SER -B80 : SER -B81 : GLU -B82 : ARG -B83 : ASN -B84 : LYS -B85 : GLN -B86 : LEU -B87 : LYS -B88 : VAL -B89 : GLY -B90 : ARG -B91 : VAL -B92 : LEU -B93 : LEU -B94 : TRP -B95 : LEU -B96 : GLY -B97 : LEU -B98 : LEU -B99 : PRO -B100 : SER -B101 : VAL -B102 : SER -B103 : GLY -B104 : THR -B105 : VAL -B106 : LYS -B107 : SER -B108 : CYS -B109 : VAL -B110 : THR -B111 : GLU -B112 : THR -B113 : GLN -B114 : THR -B115 : THR -B116 : ALA -B117 : ALA -B118 : ALA -B119 : SER -B120 : PHE -B121 : GLN -B122 : VAL -B123 : ALA -B124 : LEU -B125 : ALA -B126 : VAL -B127 : ALA -B128 : ASP -B129 : ASN -B130 : SER -B131 : LYS -B132 : ASP -B133 : VAL -B134 : VAL -B135 : ALA -B136 : ALA -B137 : MET -B138 : TYR -B139 : PRO -B140 : GLU -B141 : ALA -B142 : PHE -B143 : LYS -B144 : GLY -B145 : ILE -B146 : THR -B147 : LEU -B148 : GLU -B149 : GLN -B150 : LEU -B151 : ALA -B152 : ALA -B153 : ASP -B154 : LEU -B155 : THR -B156 : ILE -B157 : TYR -B158 : LEU -B159 : TYR -B160 : SER -B161 : SER -B162 : ALA -B163 : ALA -B164 : LEU -B165 : THR -B166 : GLU -B167 : GLY -B168 : ASP -B169 : VAL -B170 : ILE -B171 : VAL -B172 : HIS -B173 : LEU -B174 : GLU -B175 : VAL -B176 : GLU -B177 : HIS -B178 : VAL -B179 : ARG -B180 : PRO -B181 : THR -B182 : PHE -B183 : ASP -B184 : ASP -B185 : SER -B186 : PHE -B187 : THR -B188 : PRO -B189 : VAL -B190 : TYR -C27 : VAL -C28 : VAL -C29 : GLN -C30 : PRO -C31 : VAL -C32 : ILE -C33 : VAL -C34 : GLU -C35 : PRO -C36 : ILE -C37 : ALA -C38 : SER -C39 : GLY -C40 : GLN -C41 : GLY -C42 : LYS -C43 : ALA -C44 : ILE -C45 : LYS -C46 : ALA -C47 : TRP -C48 : THR -C49 : GLY -C50 : TYR -C51 : SER -C52 : VAL -C53 : SER -C54 : LYS -C55 : TRP -C56 : THR -C57 : ALA -C58 : SER -C59 : CYS -C60 : ALA -C61 : ALA -C62 : ALA -C63 : GLU -C64 : ALA -C65 : LYS -C66 : VAL -C67 : THR -C68 : SER -C69 : ALA -C70 : ILE -C71 : THR -C72 : ILE -C73 : SER -C74 : LEU -C75 : PRO -C76 : ASN -C77 : GLU -C78 : LEU -C79 : SER -C80 : SER -C81 : GLU -C82 : ARG -C83 : ASN -C84 : LYS -C85 : GLN -C86 : LEU -C87 : LYS -C88 : VAL -C89 : GLY -C90 : ARG -C91 : VAL -C92 : LEU -C93 : LEU -C94 : TRP -C95 : LEU -C96 : GLY -C97 : LEU -C98 : LEU -C99 : PRO -C100 : SER -C101 : VAL -C102 : SER -C103 : GLY -C104 : THR -C105 : VAL -C106 : LYS -C107 : SER -C108 : CYS -C109 : VAL -C110 : THR -C111 : GLU -C112 : THR -C113 : GLN -C114 : THR -C115 : THR -C116 : ALA -C117 : ALA -C118 : ALA -C119 : SER -C120 : PHE -C121 : GLN -C122 : VAL -C123 : ALA -C124 : LEU -C125 : ALA -C126 : VAL -C127 : ALA -C128 : ASP -C129 : ASN -C130 : SER -C131 : LYS -C132 : ASP -C133 : VAL -C134 : VAL -C135 : ALA -C136 : ALA -C137 : MET -C138 : TYR -C139 : PRO -C140 : GLU -C141 : ALA -C142 : PHE -C143 : LYS -C144 : GLY -C145 : ILE -C146 : THR -C147 : LEU -C148 : GLU -C149 : GLN -C150 : LEU -C151 : ALA -C152 : ALA -C153 : ASP -C154 : LEU -C155 : THR -C156 : ILE -C157 : TYR -C158 : LEU -C159 : TYR -C160 : SER -C161 : SER -C162 : ALA -C163 : ALA -C164 : LEU -C165 : THR -C166 : GLU -C167 : GLY -C168 : ASP -C169 : VAL -C170 : ILE -C171 : VAL -C172 : HIS -C173 : LEU -C174 : GLU -C175 : VAL -C176 : GLU -C177 : HIS -C178 : VAL -C179 : ARG -C180 : PRO -C181 : THR -C182 : PHE -C183 : ASP -C184 : ASP -C185 : SER -C186 : PHE -C187 : THR -C188 : PRO -C189 : VAL -C190 : TYR -D201 : A C3p_endo syn -D202 : U C3p_endo anti -D203 : A C3p_endo anti -D204 : U C3p_endo anti -E201 : A C3p_endo syn -E202 : U C3p_endo anti -F201 : A C3p_endo syn -F202 : U C3p_endo anti -F203 : A C3p_endo anti -F204 : U C3p_endo anti -Adjacent stackings ---------------------------------------------- -D201-D202 : adjacent_5p outward -D202-D203 : adjacent_5p upward -D203-D204 : adjacent_5p upward -E201-E202 : adjacent_5p outward -F201-F202 : adjacent_5p outward -F202-F203 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 6 -Number of adjacent stackings = 6 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -F203-F204 : A-U O2'/Hh adjacent_5p pairing diff --git a/MCdata/1cx5_MC b/MCdata/1cx5_MC deleted file mode 100644 index 733f6377a0cbd9300c78cdb220ef9fe9cc5aa980..0000000000000000000000000000000000000000 --- a/MCdata/1cx5_MC +++ /dev/null @@ -1,63 +0,0 @@ -Residue conformations ------------------------------------------- -A1 : C O4p_endo anti -A2 : G C2p_endo anti -A3 : C C1p_exo syn -A4 : G O4p_endo anti -A5 : T C4p_exo anti -A6 : T C3p_endo anti -A7 : MMT -A8 : T C2p_endo anti -A9 : G C1p_exo anti -A10 : C C1p_exo anti -A11 : G C1p_exo anti -A12 : C C1p_exo anti -B101 : G C4p_exo anti -B102 : C C3p_endo anti -B103 : G C3p_endo anti -B104 : C C4p_exo anti -B105 : A C3p_endo anti -B106 : A C2p_exo anti -B107 : A C3p_endo anti -B108 : A C3p_endo anti -B109 : C C3p_endo anti -B110 : G C3p_endo anti -B111 : C C3p_endo anti -B112 : G C3p_endo anti -Adjacent stackings ---------------------------------------------- -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -B101-B102 : adjacent_5p upward -B102-B103 : adjacent_5p upward -B103-B104 : adjacent_5p upward -B105-B106 : adjacent_5p upward -B106-B107 : adjacent_5p upward -B107-B108 : adjacent_5p upward -B108-B109 : adjacent_5p upward -B109-B110 : adjacent_5p upward -B110-B111 : adjacent_5p upward -B111-B112 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-B110 : outward -A11-B103 : outward -Number of stackings = 20 -Number of adjacent stackings = 18 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A1-B112 : C-G Ww/Ww pairing antiparallel cis XIX -A2-B111 : G-C Ww/Ww pairing antiparallel cis XIX -A3-B110 : C-G Ww/Ww pairing antiparallel cis XIX -A4-B109 : G-C Ww/Ww pairing antiparallel cis XIX -A5-B108 : T-A Ww/Ww pairing antiparallel cis -A6-B107 : T-A Ww/Ww pairing antiparallel cis one_hbond -A7-B106 : MMT-A pairing antiparallel one_hbond -A8-B105 : T-A Ww/Ww pairing antiparallel cis -A9-B104 : G-C Ww/Ww pairing antiparallel cis XIX -A10-B103 : C-G Ww/Ww pairing antiparallel cis XIX -A11-B102 : G-C Ww/Ww pairing antiparallel cis XIX -A12-B101 : C-G Ww/Ww pairing antiparallel cis XIX diff --git a/MCdata/1d0t_MC b/MCdata/1d0t_MC deleted file mode 100644 index 55803c7d0236c0ceb868a9e5525c22e035eda76e..0000000000000000000000000000000000000000 --- a/MCdata/1d0t_MC +++ /dev/null @@ -1,423 +0,0 @@ -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : G C3p_endo anti -A4 : SRA -A5 : U C3p_endo anti -A6 : C C3p_endo anti -A7 : SRA -A8 : C C3p_endo anti -A9 : C C3p_endo anti -A10 : SRA -A11 : U C3p_exo anti -A12 : U C3p_exo anti -A13 : SRA -A14 : G C3p_endo anti -A15 : G C3p_endo anti -A16 : G C3p_endo anti -A17 : SRA -A18 : U C3p_endo anti -A19 : C C3p_endo anti -A20 : U C3p_endo anti -A21 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A20-A21 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 8 -Number of adjacent stackings = 8 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-A21 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A20 : G-U Ww/Ws pairing antiparallel cis XXVIII -A3-A19 : G-C Ww/Ww pairing antiparallel cis XIX -A6-A16 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A15 : C-G Ww/Ww pairing antiparallel cis XIX -A9-A14 : C-G Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : G C3p_endo anti -A4 : SRA -A5 : U C3p_endo anti -A6 : C C3p_endo anti -A7 : SRA -A8 : C C3p_endo anti -A9 : C C3p_endo anti -A10 : SRA -A11 : U C3p_exo anti -A12 : U C3p_exo anti -A13 : SRA -A14 : G C3p_endo anti -A15 : G C3p_endo anti -A16 : G C3p_endo anti -A17 : SRA -A18 : U C3p_endo anti -A19 : C C3p_endo anti -A20 : U C3p_endo anti -A21 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A19-A20 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 6 -Number of adjacent stackings = 6 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-A21 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A20 : G-U Ww/Ws pairing antiparallel cis XXVIII -A3-A19 : G-C Ww/Ww pairing antiparallel cis XIX -A6-A16 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A15 : C-G Ww/Ww pairing antiparallel cis XIX -A9-A14 : C-G Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : G C3p_endo anti -A4 : SRA -A5 : U C3p_endo anti -A6 : C C3p_endo anti -A7 : SRA -A8 : C C3p_endo anti -A9 : C C3p_endo anti -A10 : SRA -A11 : U C3p_exo anti -A12 : U C3p_exo anti -A13 : SRA -A14 : G C3p_endo anti -A15 : G C3p_endo anti -A16 : G C3p_endo anti -A17 : SRA -A18 : U C3p_endo anti -A19 : C C3p_endo anti -A20 : U C3p_endo anti -A21 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A20-A21 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 9 -Number of adjacent stackings = 9 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-A21 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A20 : G-U Ww/Ws pairing antiparallel cis XXVIII -A3-A19 : G-C Ww/Ww pairing antiparallel cis XIX -A6-A16 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A15 : C-G Ww/Ww pairing antiparallel cis XIX -A9-A14 : C-G Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : G C3p_endo anti -A4 : SRA -A5 : U C3p_endo anti -A6 : C C3p_endo anti -A7 : SRA -A8 : C C3p_endo anti -A9 : C C3p_endo anti -A10 : SRA -A11 : U C3p_exo anti -A12 : U C3p_exo anti -A13 : SRA -A14 : G C3p_endo anti -A15 : G C3p_endo anti -A16 : G C3p_endo anti -A17 : SRA -A18 : U C3p_endo anti -A19 : C C3p_endo anti -A20 : U C3p_endo anti -A21 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A20-A21 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 8 -Number of adjacent stackings = 8 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-A21 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A20 : G-U Ww/Ws pairing antiparallel cis XXVIII -A3-A19 : G-C Ww/Ww pairing antiparallel cis XIX -A6-A16 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A15 : C-G Ww/Ww pairing antiparallel cis XIX -A9-A14 : C-G Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : G C3p_endo anti -A4 : SRA -A5 : U C3p_endo anti -A6 : C C3p_endo anti -A7 : SRA -A8 : C C3p_endo anti -A9 : C C3p_endo anti -A10 : SRA -A11 : U C3p_exo anti -A12 : U C3p_exo anti -A13 : SRA -A14 : G C3p_endo anti -A15 : G C3p_endo anti -A16 : G C3p_endo anti -A17 : SRA -A18 : U C3p_endo anti -A19 : C C3p_endo anti -A20 : U C3p_endo anti -A21 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A20-A21 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 8 -Number of adjacent stackings = 8 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-A21 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A20 : G-U Ww/Ws pairing antiparallel cis XXVIII -A3-A19 : G-C Ww/Ww pairing antiparallel cis XIX -A6-A16 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A15 : C-G Ww/Ww pairing antiparallel cis XIX -A9-A14 : C-G Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : G C3p_endo anti -A4 : SRA -A5 : U C3p_endo anti -A6 : C C3p_endo anti -A7 : SRA -A8 : C C3p_endo anti -A9 : C C3p_endo anti -A10 : SRA -A11 : U C3p_exo anti -A12 : U C3p_exo anti -A13 : SRA -A14 : G C3p_endo anti -A15 : G C3p_endo anti -A16 : G C3p_endo anti -A17 : SRA -A18 : U C3p_endo anti -A19 : C C3p_endo anti -A20 : U C3p_endo anti -A21 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A20-A21 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 8 -Number of adjacent stackings = 8 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-A21 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A20 : G-U Ww/Ws pairing antiparallel cis XXVIII -A3-A19 : G-C Ww/Ww pairing antiparallel cis XIX -A6-A16 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A15 : C-G Ww/Ww pairing antiparallel cis XIX -A9-A14 : C-G Ww/Ww pairing antiparallel cis XIX -A11-A12 : U-U O2'/Hh adjacent_5p pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : G C3p_endo anti -A4 : SRA -A5 : U C3p_endo anti -A6 : C C3p_endo anti -A7 : SRA -A8 : C C3p_endo anti -A9 : C C3p_endo anti -A10 : SRA -A11 : U C3p_exo anti -A12 : U C3p_exo anti -A13 : SRA -A14 : G C3p_endo anti -A15 : G C3p_endo anti -A16 : G C3p_endo anti -A17 : SRA -A18 : U C3p_endo anti -A19 : C C3p_endo anti -A20 : U C3p_endo anti -A21 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A20-A21 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 8 -Number of adjacent stackings = 8 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-A21 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A20 : G-U Ww/Ws pairing antiparallel cis XXVIII -A3-A19 : G-C Ww/Ww pairing antiparallel cis XIX -A6-A16 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A15 : C-G Ww/Ww pairing antiparallel cis XIX -A9-A14 : C-G Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : G C3p_endo anti -A4 : SRA -A5 : U C3p_endo anti -A6 : C C3p_endo anti -A7 : SRA -A8 : C C3p_endo anti -A9 : C C3p_endo anti -A10 : SRA -A11 : U C3p_exo anti -A12 : U C3p_exo anti -A13 : SRA -A14 : G C3p_endo anti -A15 : G C3p_endo anti -A16 : G C3p_endo anti -A17 : SRA -A18 : U C3p_endo anti -A19 : C C3p_endo anti -A20 : U C3p_endo anti -A21 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A20-A21 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 8 -Number of adjacent stackings = 8 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-A21 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A20 : G-U Ww/Ws pairing antiparallel cis XXVIII -A3-A19 : G-C Ww/Ww pairing antiparallel cis XIX -A6-A16 : C-G Ww/Ww pairing antiparallel cis XIX -A7-A14 : SRA-G pairing parallel one_hbond -A8-A15 : C-G Ww/Ww pairing antiparallel cis XIX -A9-A14 : C-G Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : G C3p_endo anti -A4 : SRA -A5 : U C3p_endo anti -A6 : C C3p_endo anti -A7 : SRA -A8 : C C3p_endo anti -A9 : C C3p_endo anti -A10 : SRA -A11 : U C3p_exo anti -A12 : U C3p_exo anti -A13 : SRA -A14 : G C3p_endo anti -A15 : G C3p_endo anti -A16 : G C3p_endo anti -A17 : SRA -A18 : U C3p_endo anti -A19 : C C3p_endo anti -A20 : U C3p_endo anti -A21 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A20-A21 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 8 -Number of adjacent stackings = 8 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-A21 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A20 : G-U Ww/Ws pairing antiparallel cis XXVIII -A3-A19 : G-C Ww/Ww pairing antiparallel cis XIX -A6-A16 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A15 : C-G Ww/Ww pairing antiparallel cis XIX -A9-A14 : C-G Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : G C3p_endo anti -A4 : SRA -A5 : U C3p_endo anti -A6 : C C3p_endo anti -A7 : SRA -A8 : C C3p_endo anti -A9 : C C3p_endo anti -A10 : SRA -A11 : U C3p_exo anti -A12 : U C3p_exo anti -A13 : SRA -A14 : G C3p_endo anti -A15 : G C3p_endo anti -A16 : G C3p_endo anti -A17 : SRA -A18 : U C3p_endo anti -A19 : C C3p_endo anti -A20 : U C3p_endo anti -A21 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A20-A21 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A8-A16 : outward -Number of stackings = 10 -Number of adjacent stackings = 9 -Number of non adjacent stackings = 1 -Base-pairs ------------------------------------------------------ -A1-A21 : G-C Ww/Ww pairing antiparallel cis 130 -A2-A20 : G-U Wh/Ws pairing antiparallel cis one_hbond -A3-A19 : G-C Ww/Ww pairing antiparallel cis XIX -A6-A16 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A15 : C-G Ww/Ww pairing antiparallel cis XIX -A9-A14 : C-G Ww/Ww pairing antiparallel cis XIX diff --git a/MCdata/1d0u_MC b/MCdata/1d0u_MC deleted file mode 100644 index 8626fbe24ab03def2230b49f1f0b47f05477dba1..0000000000000000000000000000000000000000 --- a/MCdata/1d0u_MC +++ /dev/null @@ -1,1232 +0,0 @@ -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : G C3p_endo anti -A4 : A C3p_endo anti -A5 : U C3p_endo anti -A6 : C C3p_endo anti -A7 : A C3p_endo anti -A8 : C C3p_endo anti -A9 : C C3p_endo anti -A10 : A C3p_endo anti -A11 : U C3p_exo anti -A12 : U C3p_exo anti -A13 : A C2p_endo anti -A14 : G C3p_endo anti -A15 : G C3p_endo anti -A16 : G C3p_endo anti -A17 : A C3p_endo anti -A18 : U C3p_endo anti -A19 : C C3p_endo anti -A20 : U C3p_endo anti -A21 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A20-A21 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 17 -Number of adjacent stackings = 17 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-A21 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A20 : G-U Ww/Ws pairing antiparallel cis XXVIII -A3-A19 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A18 : A-U Ww/Ww pairing antiparallel cis XX -A5-A17 : U-A Ww/Ww pairing antiparallel cis XX -A6-A16 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A15 : C-G Ww/Ww pairing antiparallel cis XIX -A9-A14 : C-G Ww/Ww pairing antiparallel cis XIX -A10-A14 : A-G O2'/Bs pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : G C3p_endo anti -A4 : A C3p_endo anti -A5 : U C3p_endo anti -A6 : C C3p_endo anti -A7 : A C3p_exo anti -A8 : C C3p_endo anti -A9 : C C3p_endo anti -A10 : A C3p_endo anti -A11 : U C3p_exo anti -A12 : U C3p_exo anti -A13 : A C2p_endo anti -A14 : G C3p_endo anti -A15 : G C3p_endo anti -A16 : G C3p_endo anti -A17 : A C3p_endo anti -A18 : U C3p_endo anti -A19 : C C3p_endo anti -A20 : U C3p_endo anti -A21 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A20-A21 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 17 -Number of adjacent stackings = 17 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-A21 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A20 : G-U Ww/Ws pairing antiparallel cis XXVIII -A3-A19 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A18 : A-U Ww/Ww pairing antiparallel cis XX -A5-A17 : U-A Ww/Ww pairing antiparallel cis XX -A6-A16 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A15 : C-G Ww/Ww pairing antiparallel cis XIX -A9-A14 : C-G Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : G C3p_endo anti -A4 : A C3p_endo anti -A5 : U C3p_endo anti -A6 : C C3p_endo anti -A7 : A C3p_endo anti -A8 : C C3p_endo anti -A9 : C C3p_endo anti -A10 : A C3p_endo anti -A11 : U C3p_exo anti -A12 : U C3p_exo anti -A13 : A C1p_exo anti -A14 : G C3p_endo anti -A15 : G C3p_endo anti -A16 : G C3p_endo anti -A17 : A C3p_endo anti -A18 : U C3p_endo anti -A19 : C C3p_endo anti -A20 : U C3p_endo anti -A21 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A20-A21 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 17 -Number of adjacent stackings = 17 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-A21 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A20 : G-U Ww/Ws pairing antiparallel cis XXVIII -A3-A19 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A18 : A-U Ww/Ww pairing antiparallel cis XX -A5-A17 : U-A Ww/Ww pairing antiparallel cis XX -A6-A16 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A15 : C-G Ww/Ww pairing antiparallel cis XIX -A9-A14 : C-G Ww/Ww pairing antiparallel cis XIX -A10-A14 : A-G O2'/Bs pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : G C3p_endo anti -A4 : A C3p_endo anti -A5 : U C3p_endo anti -A6 : C C3p_endo anti -A7 : A C3p_endo anti -A8 : C C3p_endo anti -A9 : C C3p_endo anti -A10 : A C3p_endo anti -A11 : U C3p_exo anti -A12 : U C3p_exo anti -A13 : A C1p_exo anti -A14 : G C3p_endo anti -A15 : G C3p_endo anti -A16 : G C3p_endo anti -A17 : A C3p_endo anti -A18 : U C3p_endo anti -A19 : C C3p_endo anti -A20 : U C3p_endo anti -A21 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A19-A20 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 17 -Number of adjacent stackings = 17 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-A21 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A20 : G-U Ww/Ws pairing antiparallel cis XXVIII -A3-A19 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A18 : A-U Ww/Ww pairing antiparallel cis XX -A5-A17 : U-A Ww/Ww pairing antiparallel cis XX -A6-A16 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A15 : C-G Ww/Ww pairing antiparallel cis XIX -A9-A14 : C-G Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : G C3p_endo anti -A4 : A C3p_endo anti -A5 : U C3p_endo anti -A6 : C C3p_endo anti -A7 : A C3p_endo anti -A8 : C C3p_endo anti -A9 : C C3p_endo anti -A10 : A C3p_endo anti -A11 : U C3p_exo anti -A12 : U C3p_exo anti -A13 : A C1p_exo anti -A14 : G C3p_endo anti -A15 : G C3p_endo anti -A16 : G C3p_endo anti -A17 : A C3p_endo anti -A18 : U C3p_endo anti -A19 : C C3p_endo anti -A20 : U C3p_endo anti -A21 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A20-A21 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 17 -Number of adjacent stackings = 17 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-A21 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A20 : G-U Ww/Ws pairing antiparallel cis XXVIII -A3-A19 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A18 : A-U Ww/Ww pairing antiparallel cis XX -A5-A17 : U-A Ww/Ww pairing antiparallel cis XX -A6-A16 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A15 : C-G Ww/Ww pairing antiparallel cis XIX -A9-A14 : C-G Ww/Ww pairing antiparallel cis XIX -A10-A14 : A-G O2'/Bs pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : G C3p_endo anti -A4 : A C3p_endo anti -A5 : U C3p_endo anti -A6 : C C3p_endo anti -A7 : A C3p_endo anti -A8 : C C3p_endo anti -A9 : C C3p_endo anti -A10 : A C3p_endo anti -A11 : U C3p_exo anti -A12 : U C3p_exo anti -A13 : A C2p_endo anti -A14 : G C3p_endo anti -A15 : G C3p_endo anti -A16 : G C3p_endo anti -A17 : A C3p_endo anti -A18 : U C3p_endo anti -A19 : C C3p_endo anti -A20 : U C3p_endo anti -A21 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A20-A21 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 16 -Number of adjacent stackings = 16 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-A21 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A20 : G-U Ww/Ws pairing antiparallel cis XXVIII -A3-A19 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A18 : A-U Ww/Ww pairing antiparallel cis XX -A5-A17 : U-A Ww/Ww pairing antiparallel cis XX -A6-A16 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A15 : C-G Ww/Ww pairing antiparallel cis XIX -A9-A14 : C-G Ww/Ww pairing antiparallel cis XIX -A10-A13 : A-A Bs/Ww pairing antiparallel cis one_hbond -A10-A14 : A-G O2'/Bs pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : G C3p_endo anti -A4 : A C3p_endo anti -A5 : U C3p_endo anti -A6 : C C3p_endo anti -A7 : A C3p_endo anti -A8 : C C3p_endo anti -A9 : C C3p_endo anti -A10 : A C3p_endo anti -A11 : U C3p_exo anti -A12 : U C3p_exo anti -A13 : A C1p_exo anti -A14 : G C3p_endo anti -A15 : G C3p_endo anti -A16 : G C3p_endo anti -A17 : A C3p_endo anti -A18 : U C3p_endo anti -A19 : C C3p_endo anti -A20 : U C3p_endo anti -A21 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A20-A21 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 17 -Number of adjacent stackings = 17 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-A21 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A20 : G-U Ww/Ws pairing antiparallel cis XXVIII -A3-A19 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A18 : A-U Ww/Ww pairing antiparallel cis XX -A5-A17 : U-A Ww/Ww pairing antiparallel cis XX -A6-A16 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A15 : C-G Ww/Ww pairing antiparallel cis XIX -A9-A14 : C-G Ww/Ww pairing antiparallel cis XIX -A10-A13 : A-A Bs/Ww pairing antiparallel cis one_hbond -A10-A14 : A-G O2'/Bs pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : G C3p_endo anti -A4 : A C3p_endo anti -A5 : U C3p_endo anti -A6 : C C3p_endo anti -A7 : A C3p_endo anti -A8 : C C3p_endo anti -A9 : C C3p_endo anti -A10 : A C3p_endo anti -A11 : U C3p_exo anti -A12 : U C3p_exo anti -A13 : A C2p_endo anti -A14 : G C3p_endo anti -A15 : G C3p_endo anti -A16 : G C3p_endo anti -A17 : A C3p_endo anti -A18 : U C3p_endo anti -A19 : C C3p_endo anti -A20 : U C3p_endo anti -A21 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A20-A21 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 17 -Number of adjacent stackings = 17 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-A21 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A20 : G-U Ww/Ws pairing antiparallel cis XXVIII -A3-A19 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A18 : A-U Ww/Ww pairing antiparallel cis XX -A5-A17 : U-A Ww/Ww pairing antiparallel cis XX -A6-A16 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A15 : C-G Ww/Ww pairing antiparallel cis XIX -A9-A14 : C-G Ww/Ww pairing antiparallel cis XIX -A10-A13 : A-A Bs/Ww pairing antiparallel cis one_hbond -A10-A14 : A-G O2'/Bs pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : G C3p_endo anti -A4 : A C3p_endo anti -A5 : U C3p_endo anti -A6 : C C3p_endo anti -A7 : A C3p_endo anti -A8 : C C3p_endo anti -A9 : C C3p_endo anti -A10 : A C3p_endo anti -A11 : U C3p_exo anti -A12 : U C3p_exo anti -A13 : A C2p_endo anti -A14 : G C3p_endo anti -A15 : G C3p_endo anti -A16 : G C3p_endo anti -A17 : A C3p_endo anti -A18 : U C3p_endo anti -A19 : C C3p_endo anti -A20 : U C3p_endo anti -A21 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A20-A21 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 16 -Number of adjacent stackings = 16 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-A21 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A20 : G-U Ww/Ws pairing antiparallel cis XXVIII -A3-A19 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A18 : A-U Ww/Ww pairing antiparallel cis XX -A5-A17 : U-A Ww/Ww pairing antiparallel cis XX -A6-A16 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A15 : C-G Ww/Ww pairing antiparallel cis XIX -A9-A14 : C-G Ww/Ww pairing antiparallel cis XIX -A10-A13 : A-A Bs/Ww pairing antiparallel cis one_hbond -A10-A14 : A-G O2'/Bs pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : G C3p_endo anti -A4 : A C3p_endo anti -A5 : U C3p_endo anti -A6 : C C3p_endo anti -A7 : A C3p_endo anti -A8 : C C3p_endo anti -A9 : C C3p_endo anti -A10 : A C3p_endo anti -A11 : U C3p_exo anti -A12 : U C3p_exo anti -A13 : A C1p_exo anti -A14 : G C3p_endo anti -A15 : G C3p_endo anti -A16 : G C3p_endo anti -A17 : A C3p_endo anti -A18 : U C3p_endo anti -A19 : C C3p_endo anti -A20 : U C3p_endo anti -A21 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A20-A21 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 17 -Number of adjacent stackings = 17 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-A21 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A20 : G-U Ww/Ws pairing antiparallel cis XXVIII -A3-A19 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A18 : A-U Ww/Ww pairing antiparallel cis XX -A5-A17 : U-A Ww/Ww pairing antiparallel cis XX -A6-A16 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A15 : C-G Ww/Ww pairing antiparallel cis XIX -A9-A14 : C-G Ww/Ww pairing antiparallel cis XIX -A10-A13 : A-A Bs/Ww pairing antiparallel cis one_hbond -A10-A14 : A-G O2'/Bs pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : G C3p_endo anti -A4 : A C3p_endo anti -A5 : U C3p_endo anti -A6 : C C3p_endo anti -A7 : A C3p_endo anti -A8 : C C3p_endo anti -A9 : C C3p_endo anti -A10 : A C3p_endo anti -A11 : U C3p_exo anti -A12 : U C3p_exo anti -A13 : A C2p_endo anti -A14 : G C3p_endo anti -A15 : G C3p_endo anti -A16 : G C3p_endo anti -A17 : A C3p_endo anti -A18 : U C3p_endo anti -A19 : C C3p_endo anti -A20 : U C3p_endo anti -A21 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A20-A21 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A7-A16 : outward -Number of stackings = 18 -Number of adjacent stackings = 17 -Number of non adjacent stackings = 1 -Base-pairs ------------------------------------------------------ -A1-A21 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A20 : G-U Ww/Ws pairing antiparallel cis XXVIII -A3-A19 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A18 : A-U Ww/Ww pairing antiparallel cis XX -A5-A17 : U-A Ww/Ww pairing antiparallel cis XX -A6-A16 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A15 : C-G Ww/Ww pairing antiparallel cis XIX -A9-A14 : C-G Ww/Ww pairing antiparallel cis XIX -A10-A13 : A-A Bs/Ww pairing antiparallel cis one_hbond -A10-A14 : A-G O2'/Bs pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : G C3p_endo anti -A4 : A C3p_endo anti -A5 : U C3p_endo anti -A6 : C C3p_endo anti -A7 : A C3p_endo anti -A8 : C C3p_endo anti -A9 : C C3p_endo anti -A10 : A C3p_endo anti -A11 : U C3p_exo anti -A12 : U C3p_exo anti -A13 : A C2p_endo anti -A14 : G C3p_endo anti -A15 : G C3p_endo anti -A16 : G C3p_endo anti -A17 : A C3p_endo anti -A18 : U C3p_endo anti -A19 : C C3p_endo anti -A20 : U C3p_endo anti -A21 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A20-A21 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 17 -Number of adjacent stackings = 17 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-A21 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A20 : G-U Ww/Ws pairing antiparallel cis XXVIII -A3-A19 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A18 : A-U Ww/Ww pairing antiparallel cis XX -A5-A17 : U-A Ww/Ww pairing antiparallel cis XX -A6-A16 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A15 : C-G Ww/Ww pairing antiparallel cis XIX -A9-A14 : C-G Ww/Ww pairing antiparallel cis XIX -A10-A14 : A-G O2'/Bs pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : G C3p_endo anti -A4 : A C3p_endo anti -A5 : U C3p_endo anti -A6 : C C3p_endo anti -A7 : A C3p_exo anti -A8 : C C3p_endo anti -A9 : C C3p_endo anti -A10 : A C3p_endo anti -A11 : U C3p_exo anti -A12 : U C3p_exo anti -A13 : A C3p_exo anti -A14 : G C3p_endo anti -A15 : G C3p_endo anti -A16 : G C3p_endo anti -A17 : A C3p_endo anti -A18 : U C3p_endo anti -A19 : C C3p_endo anti -A20 : U C3p_endo anti -A21 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A20-A21 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 15 -Number of adjacent stackings = 15 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-A21 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A20 : G-U Ww/Ws pairing antiparallel cis XXVIII -A3-A19 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A18 : A-U Ww/Ww pairing antiparallel cis XX -A5-A17 : U-A Ww/Ww pairing antiparallel cis XX -A6-A16 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A15 : C-G Ww/Ww pairing antiparallel cis XIX -A9-A14 : C-G Ww/Ww pairing antiparallel cis XIX -A12-A13 : U-A O2P/Hh adjacent_5p pairing -A13-A14 : A-G O2'/Hh adjacent_5p pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : G C3p_endo anti -A4 : A C3p_endo anti -A5 : U C3p_endo anti -A6 : C C3p_endo anti -A7 : A C3p_exo anti -A8 : C C3p_endo anti -A9 : C C3p_endo anti -A10 : A C3p_endo anti -A11 : U C3p_exo anti -A12 : U C3p_exo anti -A13 : A C2p_exo anti -A14 : G C3p_endo anti -A15 : G C3p_endo anti -A16 : G C3p_endo anti -A17 : A C3p_endo anti -A18 : U C3p_endo anti -A19 : C C3p_endo anti -A20 : U C3p_endo anti -A21 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A19-A20 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 16 -Number of adjacent stackings = 16 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-A21 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A20 : G-U Ww/Ws pairing antiparallel cis XXVIII -A3-A19 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A18 : A-U Ww/Ww pairing antiparallel cis XX -A5-A17 : U-A Ww/Ww pairing antiparallel cis XX -A6-A16 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A15 : C-G Ww/Ww pairing antiparallel cis XIX -A9-A14 : C-G Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : G C3p_endo anti -A4 : A C3p_endo anti -A5 : U C3p_endo anti -A6 : C C3p_endo anti -A7 : A C3p_exo anti -A8 : C C3p_endo anti -A9 : C C3p_endo anti -A10 : A C3p_endo anti -A11 : U C3p_exo anti -A12 : U C3p_exo anti -A13 : A C1p_exo anti -A14 : G C3p_endo anti -A15 : G C3p_endo anti -A16 : G C3p_endo anti -A17 : A C3p_endo anti -A18 : U C3p_endo anti -A19 : C C3p_endo anti -A20 : U C3p_endo anti -A21 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A20-A21 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 16 -Number of adjacent stackings = 16 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-A21 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A20 : G-U Ww/Ws pairing antiparallel cis XXVIII -A3-A19 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A18 : A-U Ww/Ww pairing antiparallel cis XX -A5-A17 : U-A Ww/Ww pairing antiparallel cis XX -A6-A16 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A15 : C-G Ww/Ww pairing antiparallel cis XIX -A9-A14 : C-G Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : G C3p_endo anti -A4 : A C3p_endo anti -A5 : U C3p_endo anti -A6 : C C3p_endo anti -A7 : A C3p_exo anti -A8 : C C3p_endo anti -A9 : C C3p_endo anti -A10 : A C3p_endo anti -A11 : U C3p_exo anti -A12 : U C3p_exo anti -A13 : A C1p_exo anti -A14 : G C3p_endo anti -A15 : G C3p_endo anti -A16 : G C3p_endo anti -A17 : A C3p_endo anti -A18 : U C3p_endo anti -A19 : C C3p_endo anti -A20 : U C3p_endo anti -A21 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A20-A21 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 15 -Number of adjacent stackings = 15 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-A21 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A20 : G-U Ww/Ws pairing antiparallel cis XXVIII -A3-A19 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A18 : A-U Ww/Ww pairing antiparallel cis XX -A5-A17 : U-A Ww/Ww pairing antiparallel cis XX -A6-A16 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A15 : C-G Ww/Ww pairing antiparallel cis XIX -A9-A14 : C-G Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : G C3p_endo anti -A4 : A C3p_endo anti -A5 : U C3p_endo anti -A6 : C C3p_endo anti -A7 : A C3p_exo anti -A8 : C C3p_endo anti -A9 : C C3p_endo anti -A10 : A C3p_endo anti -A11 : U C3p_exo anti -A12 : U C3p_exo anti -A13 : A C1p_exo anti -A14 : G C3p_endo anti -A15 : G C3p_endo anti -A16 : G C3p_endo anti -A17 : A C3p_endo anti -A18 : U C3p_endo anti -A19 : C C3p_endo anti -A20 : U C3p_endo anti -A21 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A20-A21 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 17 -Number of adjacent stackings = 17 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-A21 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A20 : G-U Ww/Ws pairing antiparallel cis XXVIII -A3-A19 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A18 : A-U Ww/Ww pairing antiparallel cis XX -A5-A17 : U-A Ww/Ww pairing antiparallel cis XX -A6-A16 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A15 : C-G Ww/Ww pairing antiparallel cis XIX -A9-A14 : C-G Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : G C3p_endo anti -A4 : A C3p_endo anti -A5 : U C3p_endo anti -A6 : C C3p_endo anti -A7 : A C3p_exo anti -A8 : C C3p_endo anti -A9 : C C3p_endo anti -A10 : A C3p_endo anti -A11 : U C3p_exo anti -A12 : U C3p_exo anti -A13 : A C1p_exo anti -A14 : G C3p_endo anti -A15 : G C3p_endo anti -A16 : G C3p_endo anti -A17 : A C3p_endo anti -A18 : U C3p_endo anti -A19 : C C3p_endo anti -A20 : U C3p_endo anti -A21 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A20-A21 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 17 -Number of adjacent stackings = 17 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-A21 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A20 : G-U Ww/Ws pairing antiparallel cis XXVIII -A3-A19 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A18 : A-U Ww/Ww pairing antiparallel cis XX -A5-A17 : U-A Ww/Ww pairing antiparallel cis XX -A6-A16 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A15 : C-G Ww/Ww pairing antiparallel cis XIX -A9-A14 : C-G Ww/Ww pairing antiparallel cis XIX -A10-A13 : A-A Bs/Ww pairing antiparallel cis one_hbond -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : G C3p_endo anti -A4 : A C3p_endo anti -A5 : U C3p_endo anti -A6 : C C3p_endo anti -A7 : A C3p_exo anti -A8 : C C3p_endo anti -A9 : C C3p_endo anti -A10 : A C3p_endo anti -A11 : U C3p_exo anti -A12 : U C3p_exo anti -A13 : A C2p_endo anti -A14 : G C3p_endo anti -A15 : G C3p_endo anti -A16 : G C3p_endo anti -A17 : A C3p_endo anti -A18 : U C3p_endo anti -A19 : C C3p_endo anti -A20 : U C3p_endo anti -A21 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A20-A21 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 16 -Number of adjacent stackings = 16 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-A21 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A20 : G-U Ww/Ws pairing antiparallel cis XXVIII -A3-A19 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A18 : A-U Ww/Ww pairing antiparallel cis XX -A5-A17 : U-A Ww/Ww pairing antiparallel cis XX -A6-A16 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A15 : C-G Ww/Ww pairing antiparallel cis XIX -A9-A14 : C-G Ww/Ww pairing antiparallel cis XIX -A10-A14 : A-G O2'/Bs pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : G C3p_endo anti -A4 : A C3p_endo anti -A5 : U C3p_endo anti -A6 : C C3p_endo anti -A7 : A C3p_exo anti -A8 : C C3p_endo anti -A9 : C C3p_endo anti -A10 : A C3p_endo anti -A11 : U C3p_exo anti -A12 : U C3p_exo anti -A13 : A C2p_endo anti -A14 : G C3p_endo anti -A15 : G C3p_endo anti -A16 : G C3p_endo anti -A17 : A C3p_endo anti -A18 : U C3p_endo anti -A19 : C C3p_endo anti -A20 : U C3p_endo anti -A21 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A20-A21 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 16 -Number of adjacent stackings = 16 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-A21 : G-C Ww/Ww pairing antiparallel cis 130 -A2-A20 : G-U Ww/Ws pairing antiparallel cis XXVIII -A3-A19 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A18 : A-U Ww/Ww pairing antiparallel cis XX -A5-A17 : U-A Ww/Ww pairing antiparallel cis XX -A6-A16 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A15 : C-G Ww/Ww pairing antiparallel cis XIX -A9-A14 : C-G Ww/Ww pairing antiparallel cis XIX -A10-A13 : A-A Bs/Ww pairing antiparallel cis one_hbond -A10-A14 : A-G O2'/Bs pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : G C3p_endo anti -A4 : A C3p_endo anti -A5 : U C3p_endo anti -A6 : C C3p_endo anti -A7 : A C3p_exo anti -A8 : C C3p_endo anti -A9 : C C3p_endo anti -A10 : A C3p_endo anti -A11 : U C3p_exo anti -A12 : U C3p_exo anti -A13 : A C2p_endo anti -A14 : G C3p_endo anti -A15 : G C3p_endo anti -A16 : G C3p_endo anti -A17 : A C3p_endo anti -A18 : U C3p_endo anti -A19 : C C3p_endo anti -A20 : U C3p_endo anti -A21 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A19-A20 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 16 -Number of adjacent stackings = 16 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-A21 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A20 : G-U Ww/Ws pairing antiparallel cis XXVIII -A3-A19 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A18 : A-U Ww/Ww pairing antiparallel cis XX -A5-A17 : U-A Ww/Ww pairing antiparallel cis XX -A6-A16 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A15 : C-G Ww/Ww pairing antiparallel cis XIX -A9-A14 : C-G Ww/Ww pairing antiparallel cis XIX -A10-A14 : A-G O2'/Bs pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : G C3p_endo anti -A4 : A C3p_endo anti -A5 : U C3p_endo anti -A6 : C C3p_endo anti -A7 : A C3p_exo anti -A8 : C C3p_endo anti -A9 : C C3p_endo anti -A10 : A C3p_endo anti -A11 : U C3p_exo anti -A12 : U C3p_exo anti -A13 : A C2p_endo anti -A14 : G C3p_endo anti -A15 : G C3p_endo anti -A16 : G C3p_endo anti -A17 : A C3p_endo anti -A18 : U C3p_endo anti -A19 : C C3p_endo anti -A20 : U C3p_endo anti -A21 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A20-A21 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 16 -Number of adjacent stackings = 16 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-A21 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A20 : G-U Ww/Ws pairing antiparallel cis XXVIII -A3-A19 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A18 : A-U Ww/Ww pairing antiparallel cis XX -A5-A17 : U-A Ww/Ww pairing antiparallel cis XX -A6-A16 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A15 : C-G Ww/Ww pairing antiparallel cis XIX -A9-A14 : C-G Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : G C3p_endo anti -A4 : A C3p_endo anti -A5 : U C3p_endo anti -A6 : C C3p_endo anti -A7 : A C3p_exo anti -A8 : C C3p_endo anti -A9 : C C3p_endo anti -A10 : A C3p_endo anti -A11 : U C3p_exo anti -A12 : U C3p_exo anti -A13 : A C2p_endo anti -A14 : G C3p_endo anti -A15 : G C3p_endo anti -A16 : G C3p_endo anti -A17 : A C3p_endo anti -A18 : U C3p_endo anti -A19 : C C3p_endo anti -A20 : U C3p_endo anti -A21 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A20-A21 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 16 -Number of adjacent stackings = 16 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-A21 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A20 : G-U Ww/Ws pairing antiparallel cis XXVIII -A3-A19 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A18 : A-U Ww/Ww pairing antiparallel cis XX -A5-A17 : U-A Ww/Ww pairing antiparallel cis XX -A6-A16 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A15 : C-G Ww/Ww pairing antiparallel cis XIX -A9-A14 : C-G Ww/Ww pairing antiparallel cis XIX -A10-A13 : A-A Bs/Ww pairing antiparallel cis one_hbond -A10-A14 : A-G O2'/Bs pairing diff --git a/MCdata/1d4r_MC b/MCdata/1d4r_MC deleted file mode 100644 index 8bc606d8f7d547e3748f6b4a302ffea3cc2e964d..0000000000000000000000000000000000000000 --- a/MCdata/1d4r_MC +++ /dev/null @@ -1,314 +0,0 @@ -Residue conformations ------------------------------------------- -A1 : GDP -A2 : G C3p_endo anti -A3 : U C3p_endo anti -A4 : G C3p_endo anti -A5 : A C3p_endo anti -A6 : C C3p_endo anti -A7 : C C3p_endo anti -A8 : U C2p_exo anti -A9 : C C3p_endo anti -A10 : C C3p_endo anti -A11 : C C3p_endo anti -A12 : G C2p_exo anti -A13 : G C3p_endo anti -A14 : G C3p_endo anti -A15 : A C3p_endo anti -A16 : G C3p_endo anti -A17 : C C3p_endo anti -A18 : G C3p_endo anti -A19 : G C3p_endo anti -A20 : G C3p_endo anti -A21 : G C2p_exo anti -A22 : G C3p_endo anti -A23 : A C1p_endo anti -A24 : C C3p_endo anti -A25 : C C3p_endo anti -A26 : A C3p_endo anti -A27 : C C3p_endo anti -A28 : U C3p_endo anti -A29 : A23 -B1 : GDP -B2 : G C3p_endo anti -B3 : U C3p_endo anti -B4 : G C3p_endo anti -B5 : A C3p_endo anti -B6 : C C3p_endo anti -B7 : C C3p_endo anti -B8 : U C3p_endo anti -B9 : C C3p_endo anti -B10 : C C3p_endo anti -B11 : C C3p_endo anti -B12 : G C3p_endo anti -B13 : G C3p_endo anti -B14 : G C3p_endo anti -B15 : A C3p_endo anti -B16 : G C2p_exo anti -B17 : C C3p_endo anti -B18 : G C3p_endo anti -B19 : G C3p_endo anti -B20 : G C3p_endo anti -B21 : G C2p_exo anti -B22 : G C3p_endo anti -B23 : A C2p_exo anti -B24 : C C3p_endo anti -B25 : C C3p_endo anti -B26 : A C3p_endo anti -B27 : C C3p_endo anti -B28 : U C3p_endo anti -B29 : A unknown unknown -C1 : GDP -C2 : G C3p_endo anti -C3 : U C3p_endo anti -C4 : G C3p_endo anti -C5 : A C3p_endo anti -C6 : C C3p_endo anti -C7 : C C3p_endo anti -C8 : U C3p_endo anti -C9 : C C3p_endo anti -C10 : C C3p_endo anti -C11 : C C3p_endo anti -C12 : G C3p_endo anti -C13 : G C3p_endo anti -C14 : G C3p_endo anti -C15 : A C3p_endo anti -C16 : G C3p_endo anti -C17 : C C3p_endo anti -C18 : G C3p_endo anti -C19 : G C3p_endo anti -C20 : G C3p_endo anti -C21 : G C2p_exo anti -C22 : G C3p_endo anti -C23 : A C1p_endo anti -C24 : C C3p_endo anti -C25 : C C3p_endo anti -C26 : A C3p_endo anti -C27 : C C3p_endo anti -C28 : U C3p_endo anti -C29 : A unknown unknown -A304 : MG -A305 : MG -B302 : MG -B303 : MG -C301 : MG -A101 : HOH -A109 : HOH -A110 : HOH -A111 : HOH -A112 : HOH -A115 : HOH -A116 : HOH -A121 : HOH -A123 : HOH -A126 : HOH -A127 : HOH -A128 : HOH -A129 : HOH -A131 : HOH -A132 : HOH -A133 : HOH -A134 : HOH -A136 : HOH -A139 : HOH -A141 : HOH -A145 : HOH -A147 : HOH -A150 : HOH -A158 : HOH -A161 : HOH -A165 : HOH -A170 : HOH -A173 : HOH -A175 : HOH -A176 : HOH -A181 : HOH -A182 : HOH -A184 : HOH -A185 : HOH -A186 : HOH -A189 : HOH -A193 : HOH -A195 : HOH -A196 : HOH -A200 : HOH -A201 : HOH -A203 : HOH -A205 : HOH -A315 : HOH -A316 : HOH -A317 : HOH -A318 : HOH -A319 : HOH -A320 : HOH -A321 : HOH -A322 : HOH -B103 : HOH -B104 : HOH -B106 : HOH -B108 : HOH -B113 : HOH -B117 : HOH -B118 : HOH -B125 : HOH -B130 : HOH -B140 : HOH -B142 : HOH -B144 : HOH -B146 : HOH -B148 : HOH -B149 : HOH -B151 : HOH -B153 : HOH -B157 : HOH -B163 : HOH -B166 : HOH -B167 : HOH -B169 : HOH -B172 : HOH -B174 : HOH -B179 : HOH -B180 : HOH -B191 : HOH -B192 : HOH -B197 : HOH -B199 : HOH -B204 : HOH -B310 : HOH -B311 : HOH -B312 : HOH -B313 : HOH -B314 : HOH -C102 : HOH -C105 : HOH -C107 : HOH -C114 : HOH -C119 : HOH -C120 : HOH -C122 : HOH -C124 : HOH -C135 : HOH -C137 : HOH -C138 : HOH -C143 : HOH -C152 : HOH -C154 : HOH -C155 : HOH -C156 : HOH -C159 : HOH -C160 : HOH -C162 : HOH -C164 : HOH -C168 : HOH -C171 : HOH -C177 : HOH -C178 : HOH -C183 : HOH -C187 : HOH -C188 : HOH -C190 : HOH -C194 : HOH -C198 : HOH -C202 : HOH -C306 : HOH -C307 : HOH -C308 : HOH -C309 : HOH -Adjacent stackings ---------------------------------------------- -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A22-A23 : adjacent_5p upward -A23-A24 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A27-A28 : adjacent_5p upward -B2-B3 : adjacent_5p upward -B3-B4 : adjacent_5p upward -B4-B5 : adjacent_5p upward -B5-B6 : adjacent_5p upward -B7-B8 : adjacent_5p upward -B10-B11 : adjacent_5p upward -B13-B14 : adjacent_5p upward -B14-B15 : adjacent_5p upward -B15-B16 : adjacent_5p upward -B16-B17 : adjacent_5p upward -B18-B19 : adjacent_5p upward -B19-B20 : adjacent_5p upward -B20-B21 : adjacent_5p upward -B21-B22 : adjacent_5p upward -B22-B23 : adjacent_5p upward -B23-B24 : adjacent_5p upward -B25-B26 : adjacent_5p upward -B26-B27 : adjacent_5p upward -B27-B28 : adjacent_5p upward -C3-C4 : adjacent_5p upward -C4-C5 : adjacent_5p upward -C5-C6 : adjacent_5p upward -C6-C7 : adjacent_5p upward -C7-C8 : adjacent_5p upward -C9-C10 : adjacent_5p upward -C11-C12 : adjacent_5p upward -C13-C14 : adjacent_5p upward -C14-C15 : adjacent_5p upward -C15-C16 : adjacent_5p upward -C16-C17 : adjacent_5p upward -C17-C18 : adjacent_5p upward -C18-C19 : adjacent_5p upward -C19-C20 : adjacent_5p upward -C20-C21 : adjacent_5p upward -C21-C22 : adjacent_5p upward -C22-C23 : adjacent_5p upward -C23-C24 : adjacent_5p upward -C24-C25 : adjacent_5p upward -C25-C26 : adjacent_5p upward -C26-C27 : adjacent_5p upward -C27-C28 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-B26 : outward -A12-B18 : outward -A18-B12 : outward -A21-B9 : outward -A26-B4 : outward -Number of stackings = 68 -Number of adjacent stackings = 63 -Number of non adjacent stackings = 5 -Base-pairs ------------------------------------------------------ -A2-B27 : G-C Ww/Ww pairing antiparallel cis XIX -A3-B26 : U-A Ww/Ww pairing antiparallel cis XX -A4-B25 : G-C Ww/Ww pairing antiparallel cis XIX -A5-B24 : A-C Wh/Ww pairing antiparallel cis one_hbond 75 -A6-B23 : C-A Wh/Ww pairing antiparallel cis one_hbond 71 -A7-B22 : C-G Ww/Ww pairing antiparallel cis XIX -A8-B21 : U-G Ws/Ww pairing antiparallel cis XXVIII -A9-B20 : C-G Ww/Ww pairing antiparallel cis XIX -A10-B19 : C-G Ww/Ww pairing antiparallel cis XIX -A11-B18 : C-G Ww/Ww pairing antiparallel cis XIX -A12-B17 : G-C Ww/Ww pairing antiparallel cis XIX -A13-B16 : G-G Bh/Ww pairing antiparallel trans 115 -A14-B15 : G-A Wh/Wh pairing antiparallel cis one_hbond -A16-B13 : G-G Ww/Bh pairing antiparallel trans 115 -A17-B12 : C-G Ww/Ww pairing antiparallel cis XIX -A18-B11 : G-C Ww/Ww pairing antiparallel cis XIX -A19-B10 : G-C Ww/Ww pairing antiparallel cis XIX -A20-B9 : G-C Ww/Ww pairing antiparallel cis XIX -A21-B8 : G-U Ww/Ws pairing antiparallel cis XXVIII -A22-B7 : G-C Ww/Ww pairing antiparallel cis XIX -A23-B6 : A-C Wh/Ww pairing antiparallel cis one_hbond 75 -A24-B5 : C-A Ww/Wh pairing antiparallel cis one_hbond 75 -A25-B4 : C-G Ww/Ww pairing antiparallel cis XIX -A26-B3 : A-U Ww/Ww pairing antiparallel cis XX -A27-B2 : C-G Ww/Ww pairing antiparallel cis XIX diff --git a/MCdata/1d6k_MC b/MCdata/1d6k_MC deleted file mode 100644 index f23854dbf9de9d0c88cde118669f6979ed7cfa15..0000000000000000000000000000000000000000 --- a/MCdata/1d6k_MC +++ /dev/null @@ -1,3761 +0,0 @@ -Residue conformations ------------------------------------------- -B267 : G C2p_exo anti -B268 : G C3p_endo anti -B269 : A C3p_endo anti -B270 : C C3p_endo anti -B271 : C C3p_endo anti -B272 : G C3p_endo anti -B273 : A C3p_endo anti -B274 : U C3p_endo anti -B275 : G C3p_endo anti -B276 : G C3p_endo anti -B277 : U C3p_endo anti -B278 : A C3p_endo anti -B279 : G C3p_endo anti -B280 : U C3p_endo anti -B281 : G C2p_exo anti -B282 : U C3p_endo anti -B283 : C C3p_endo anti -B284 : U C3p_endo anti -B285 : U C3p_endo anti -B291 : C C2p_endo anti -B292 : G C2p_endo anti -B293 : G C3p_endo anti -B294 : A C3p_endo anti -B295 : U C3p_endo anti -B296 : G C1p_endo anti -B297 : C C3p_endo anti -B298 : G C3p_endo anti -B299 : A C1p_endo anti -B300 : G C3p_endo anti -B301 : A C3p_endo anti -B302 : G C3p_endo anti -B303 : U C3p_endo anti -B304 : A C3p_endo anti -B305 : G C3p_endo anti -B306 : G C3p_endo anti -B307 : U C3p_endo anti -B308 : C C3p_endo anti -A1 : MET -A2 : PHE -A3 : THR -A4 : ILE -A5 : ASN -A6 : ALA -A7 : GLU -A8 : VAL -A9 : ARG -A10 : LYS -A11 : GLU -A12 : GLN -A13 : GLY -A14 : LYS -A15 : GLY -A16 : ALA -A17 : SER -A18 : ARG -A19 : ARG -A20 : LEU -A21 : ARG -A22 : ALA -A23 : ALA -A24 : ASN -A25 : LYS -A26 : PHE -A27 : PRO -A28 : ALA -A29 : ILE -A30 : ILE -A31 : TYR -A32 : GLY -A33 : GLY -A34 : LYS -A35 : GLU -A36 : ALA -A37 : PRO -A38 : LEU -A39 : ALA -A40 : ILE -A41 : GLU -A42 : LEU -A43 : ASP -A44 : HIS -A45 : ASP -A46 : LYS -A47 : VAL -A48 : MET -A49 : ASN -A50 : MET -A51 : GLN -A52 : ALA -A53 : LYS -A54 : ALA -A55 : GLU -A56 : PHE -A57 : TYR -A58 : SER -A59 : GLU -A60 : VAL -A61 : LEU -A62 : THR -A63 : ILE -A64 : VAL -A65 : VAL -A66 : ASP -A67 : GLY -A68 : LYS -A69 : GLU -A70 : ILE -A71 : LYS -A72 : VAL -A73 : LYS -A74 : ALA -A75 : GLN -A76 : ASP -A77 : VAL -A78 : GLN -A79 : ARG -A80 : HIS -A81 : PRO -A82 : TYR -A83 : LYS -A84 : PRO -A85 : LYS -A86 : LEU -A87 : GLN -A88 : HIS -A89 : ILE -A90 : ASP -A91 : PHE -A92 : VAL -A93 : ARG -A94 : ALA -Adjacent stackings ---------------------------------------------- -B268-B269 : adjacent_5p upward -B269-B270 : adjacent_5p upward -B270-B271 : adjacent_5p upward -B271-B272 : adjacent_5p upward -B273-B274 : adjacent_5p upward -B274-B275 : adjacent_5p upward -B275-B276 : adjacent_5p upward -B276-B277 : adjacent_5p upward -B277-B278 : adjacent_5p upward -B278-B279 : adjacent_5p upward -B279-B280 : adjacent_5p upward -B281-B282 : adjacent_5p upward -B282-B283 : adjacent_5p upward -B283-B284 : adjacent_5p upward -B293-B294 : adjacent_5p upward -B294-B295 : adjacent_5p upward -B296-B297 : adjacent_5p upward -B299-B300 : adjacent_5p upward -B300-B301 : adjacent_5p upward -B301-B302 : adjacent_5p upward -B302-B303 : adjacent_5p upward -B303-B304 : adjacent_5p upward -B304-B305 : adjacent_5p upward -B305-B306 : adjacent_5p upward -B306-B307 : adjacent_5p upward -B307-B308 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -B273-B304 : outward -B278-B299 : outward -B281-B296 : outward -Number of stackings = 29 -Number of adjacent stackings = 26 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -A17-B298 : SER-G pairing one_hbond -A31-B273 : TYR-A pairing one_hbond -A31-B274 : TYR-U pairing one_hbond -B268-B308 : G-C Ww/Ww pairing antiparallel cis XIX -B269-B307 : A-U Ww/Ww pairing antiparallel cis XX -B270-B306 : C-G Ww/Ww pairing antiparallel cis XIX -B271-B305 : C-G Ww/Ww pairing antiparallel cis XIX -B272-B303 : G-U Ww/O2P pairing -B272-B304 : G-A Ss/Hh O2'/Bh pairing antiparallel trans XI -B273-B303 : A-U Hh/Ws pairing antiparallel trans XXIV -B274-B302 : U-G Hw/Ww pairing antiparallel trans one_hbond 91 -B276-B300 : G-G Ww/Bh pairing antiparallel trans 115 -B277-B299 : U-A Ws/Hh pairing antiparallel trans XXIV -B278-B298 : A-G Hh/Ss Bh/O2' pairing antiparallel trans XI -B279-B297 : G-C Ww/Ww pairing antiparallel cis XIX -B280-B296 : U-G Ws/Ww pairing antiparallel cis XXVIII -B281-B295 : G-U Ww/Ws pairing antiparallel cis XXVIII -B282-B294 : U-A Ww/Ww pairing antiparallel cis XX -B283-B293 : C-G Ww/Ww pairing antiparallel cis XIX -B284-B292 : U-G Ss/Ws O2'/Ww pairing parallel trans one_hbond -B285-B291 : U-C O2P/Bh adjacent_5p pairing -Residue conformations ------------------------------------------- -B267 : G C2p_endo anti -B268 : G C2p_exo anti -B269 : A C3p_endo anti -B270 : C C3p_endo anti -B271 : C C3p_endo anti -B272 : G C3p_endo anti -B273 : A C2p_exo anti -B274 : U C4p_exo anti -B275 : G C3p_endo anti -B276 : G C3p_endo anti -B277 : U C3p_endo anti -B278 : A C3p_endo anti -B279 : G C3p_endo anti -B280 : U C3p_endo anti -B281 : G C3p_endo anti -B282 : U C3p_endo anti -B283 : C C3p_endo anti -B284 : U C2p_exo anti -B285 : U C2p_endo anti -B291 : C C2p_endo anti -B292 : G O4p_endo anti -B293 : G C3p_endo anti -B294 : A C3p_endo anti -B295 : U C3p_endo anti -B296 : G C2p_exo anti -B297 : C C3p_endo anti -B298 : G C3p_endo anti -B299 : A C1p_endo anti -B300 : G C3p_endo anti -B301 : A C3p_endo anti -B302 : G C3p_endo anti -B303 : U C3p_endo anti -B304 : A C3p_endo anti -B305 : G C3p_endo anti -B306 : G C3p_endo anti -B307 : U C3p_endo anti -B308 : C C3p_endo anti -A1 : MET -A2 : PHE -A3 : THR -A4 : ILE -A5 : ASN -A6 : ALA -A7 : GLU -A8 : VAL -A9 : ARG -A10 : LYS -A11 : GLU -A12 : GLN -A13 : GLY -A14 : LYS -A15 : GLY -A16 : ALA -A17 : SER -A18 : ARG -A19 : ARG -A20 : LEU -A21 : ARG -A22 : ALA -A23 : ALA -A24 : ASN -A25 : LYS -A26 : PHE -A27 : PRO -A28 : ALA -A29 : ILE -A30 : ILE -A31 : TYR -A32 : GLY -A33 : GLY -A34 : LYS -A35 : GLU -A36 : ALA -A37 : PRO -A38 : LEU -A39 : ALA -A40 : ILE -A41 : GLU -A42 : LEU -A43 : ASP -A44 : HIS -A45 : ASP -A46 : LYS -A47 : VAL -A48 : MET -A49 : ASN -A50 : MET -A51 : GLN -A52 : ALA -A53 : LYS -A54 : ALA -A55 : GLU -A56 : PHE -A57 : TYR -A58 : SER -A59 : GLU -A60 : VAL -A61 : LEU -A62 : THR -A63 : ILE -A64 : VAL -A65 : VAL -A66 : ASP -A67 : GLY -A68 : LYS -A69 : GLU -A70 : ILE -A71 : LYS -A72 : VAL -A73 : LYS -A74 : ALA -A75 : GLN -A76 : ASP -A77 : VAL -A78 : GLN -A79 : ARG -A80 : HIS -A81 : PRO -A82 : TYR -A83 : LYS -A84 : PRO -A85 : LYS -A86 : LEU -A87 : GLN -A88 : HIS -A89 : ILE -A90 : ASP -A91 : PHE -A92 : VAL -A93 : ARG -A94 : ALA -Adjacent stackings ---------------------------------------------- -B268-B269 : adjacent_5p upward -B269-B270 : adjacent_5p upward -B270-B271 : adjacent_5p upward -B271-B272 : adjacent_5p upward -B273-B274 : adjacent_5p upward -B274-B275 : adjacent_5p upward -B275-B276 : adjacent_5p upward -B276-B277 : adjacent_5p upward -B277-B278 : adjacent_5p upward -B278-B279 : adjacent_5p upward -B279-B280 : adjacent_5p upward -B281-B282 : adjacent_5p upward -B282-B283 : adjacent_5p upward -B293-B294 : adjacent_5p upward -B294-B295 : adjacent_5p upward -B296-B297 : adjacent_5p upward -B299-B300 : adjacent_5p upward -B300-B301 : adjacent_5p upward -B301-B302 : adjacent_5p upward -B302-B303 : adjacent_5p upward -B303-B304 : adjacent_5p upward -B304-B305 : adjacent_5p upward -B305-B306 : adjacent_5p upward -B306-B307 : adjacent_5p upward -B307-B308 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -B273-B304 : outward -B278-B299 : outward -B281-B296 : outward -B291-B293 : upward -Number of stackings = 29 -Number of adjacent stackings = 25 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A14-B279 : LYS-G pairing one_hbond -A31-B273 : TYR-A pairing one_hbond -A31-B274 : TYR-U pairing one_hbond -B268-B308 : G-C Ww/Ww pairing antiparallel cis XIX -B269-B307 : A-U Ww/Ww pairing antiparallel cis XX -B270-B306 : C-G Ww/Ww pairing antiparallel cis XIX -B271-B305 : C-G Ww/Ww pairing antiparallel cis XIX -B272-B303 : G-U Ww/O2P pairing -B272-B304 : G-A Ss/Hh O2'/Bh pairing antiparallel trans XI -B273-B303 : A-U Hh/Ws pairing antiparallel trans XXIV -B274-B302 : U-G Hw/Ww pairing antiparallel trans one_hbond 91 -B276-B300 : G-G Ww/Bh pairing antiparallel trans 115 -B277-B299 : U-A Ws/Hh pairing antiparallel trans XXIV -B278-B298 : A-G Hh/Ss Bh/O2' pairing antiparallel trans XI -B279-B297 : G-C Ww/Ww pairing antiparallel cis XIX -B280-B296 : U-G Ws/Ww pairing antiparallel cis XXVIII -B281-B295 : G-U Ww/Ws pairing antiparallel cis XXVIII -B282-B294 : U-A Ww/Ww pairing antiparallel cis XX -B283-B293 : C-G Ww/Ww pairing antiparallel cis XIX -B284-B291 : U-C O2'/Bh pairing -Residue conformations ------------------------------------------- -B267 : G C3p_endo anti -B268 : G C3p_endo anti -B269 : A C3p_endo anti -B270 : C C3p_endo anti -B271 : C C3p_endo anti -B272 : G C3p_endo anti -B273 : A C2p_exo anti -B274 : U C4p_exo anti -B275 : G C3p_endo anti -B276 : G C3p_endo anti -B277 : U C3p_endo anti -B278 : A C3p_endo anti -B279 : G C3p_endo anti -B280 : U C3p_endo anti -B281 : G C3p_endo anti -B282 : U C3p_endo anti -B283 : C C3p_endo anti -B284 : U C3p_endo anti -B285 : U C2p_endo anti -B291 : C C3p_exo anti -B292 : G C1p_endo anti -B293 : G C2p_exo anti -B294 : A C3p_endo anti -B295 : U C3p_endo anti -B296 : G C3p_endo anti -B297 : C C3p_endo anti -B298 : G C3p_endo anti -B299 : A C2p_exo anti -B300 : G C3p_endo anti -B301 : A C3p_endo anti -B302 : G C3p_endo anti -B303 : U C3p_endo anti -B304 : A C3p_endo anti -B305 : G C3p_endo anti -B306 : G C3p_endo anti -B307 : U C3p_endo anti -B308 : C C3p_endo anti -A1 : MET -A2 : PHE -A3 : THR -A4 : ILE -A5 : ASN -A6 : ALA -A7 : GLU -A8 : VAL -A9 : ARG -A10 : LYS -A11 : GLU -A12 : GLN -A13 : GLY -A14 : LYS -A15 : GLY -A16 : ALA -A17 : SER -A18 : ARG -A19 : ARG -A20 : LEU -A21 : ARG -A22 : ALA -A23 : ALA -A24 : ASN -A25 : LYS -A26 : PHE -A27 : PRO -A28 : ALA -A29 : ILE -A30 : ILE -A31 : TYR -A32 : GLY -A33 : GLY -A34 : LYS -A35 : GLU -A36 : ALA -A37 : PRO -A38 : LEU -A39 : ALA -A40 : ILE -A41 : GLU -A42 : LEU -A43 : ASP -A44 : HIS -A45 : ASP -A46 : LYS -A47 : VAL -A48 : MET -A49 : ASN -A50 : MET -A51 : GLN -A52 : ALA -A53 : LYS -A54 : ALA -A55 : GLU -A56 : PHE -A57 : TYR -A58 : SER -A59 : GLU -A60 : VAL -A61 : LEU -A62 : THR -A63 : ILE -A64 : VAL -A65 : VAL -A66 : ASP -A67 : GLY -A68 : LYS -A69 : GLU -A70 : ILE -A71 : LYS -A72 : VAL -A73 : LYS -A74 : ALA -A75 : GLN -A76 : ASP -A77 : VAL -A78 : GLN -A79 : ARG -A80 : HIS -A81 : PRO -A82 : TYR -A83 : LYS -A84 : PRO -A85 : LYS -A86 : LEU -A87 : GLN -A88 : HIS -A89 : ILE -A90 : ASP -A91 : PHE -A92 : VAL -A93 : ARG -A94 : ALA -Adjacent stackings ---------------------------------------------- -B268-B269 : adjacent_5p upward -B269-B270 : adjacent_5p upward -B270-B271 : adjacent_5p upward -B271-B272 : adjacent_5p upward -B273-B274 : adjacent_5p upward -B274-B275 : adjacent_5p upward -B275-B276 : adjacent_5p upward -B276-B277 : adjacent_5p upward -B277-B278 : adjacent_5p upward -B278-B279 : adjacent_5p upward -B279-B280 : adjacent_5p upward -B281-B282 : adjacent_5p upward -B282-B283 : adjacent_5p upward -B283-B284 : adjacent_5p upward -B293-B294 : adjacent_5p upward -B294-B295 : adjacent_5p upward -B296-B297 : adjacent_5p upward -B299-B300 : adjacent_5p upward -B300-B301 : adjacent_5p upward -B301-B302 : adjacent_5p upward -B302-B303 : adjacent_5p upward -B303-B304 : adjacent_5p upward -B304-B305 : adjacent_5p upward -B305-B306 : adjacent_5p upward -B306-B307 : adjacent_5p upward -B307-B308 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -B273-B304 : outward -B278-B299 : outward -B281-B296 : outward -Number of stackings = 29 -Number of adjacent stackings = 26 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -A14-B279 : LYS-G pairing one_hbond -A17-B298 : SER-G pairing one_hbond -A31-B273 : TYR-A pairing one_hbond -B268-B308 : G-C Ww/Ww pairing antiparallel cis XIX -B269-B307 : A-U Ww/Ww pairing antiparallel cis XX -B270-B306 : C-G Ww/Ww pairing antiparallel cis XIX -B271-B305 : C-G Ww/Ww pairing antiparallel cis XIX -B272-B304 : G-A Ss/Hh O2'/Bh pairing antiparallel trans XI -B273-B303 : A-U Hh/Ws pairing antiparallel trans XXIV -B274-B302 : U-G Hw/Ww pairing antiparallel trans one_hbond 91 -B276-B300 : G-G Ww/Bh pairing antiparallel trans one_hbond -B277-B298 : U-G O2P/Ww pairing -B277-B299 : U-A Ws/Hh pairing antiparallel trans XXIV -B278-B298 : A-G Hh/Ss Bh/O2' pairing antiparallel trans XI -B279-B297 : G-C Ww/Ww pairing antiparallel cis XIX -B280-B296 : U-G Ws/Ww pairing antiparallel cis XXVIII -B281-B295 : G-U Ww/Ws pairing antiparallel cis XXVIII -B282-B294 : U-A Ww/Ww pairing antiparallel cis XX -B283-B293 : C-G Ww/Ww pairing antiparallel cis XIX -B284-B292 : U-G Ws/Ws pairing parallel trans one_hbond 87 -B285-B291 : U-C O2P/Bh adjacent_5p pairing -B285-B292 : U-G O2'/Hh pairing -Residue conformations ------------------------------------------- -B267 : G C3p_exo syn -B268 : G C3p_endo anti -B269 : A C3p_endo anti -B270 : C C3p_endo anti -B271 : C C3p_endo anti -B272 : G C3p_endo anti -B273 : A C3p_endo anti -B274 : U C4p_exo anti -B275 : G C3p_endo anti -B276 : G C3p_endo anti -B277 : U C3p_endo anti -B278 : A C3p_endo anti -B279 : G C3p_endo anti -B280 : U C3p_endo anti -B281 : G C3p_endo anti -B282 : U C3p_endo anti -B283 : C C3p_endo anti -B284 : U C3p_endo anti -B285 : U C2p_endo anti -B291 : C C2p_endo anti -B292 : G C3p_exo anti -B293 : G C3p_endo anti -B294 : A C3p_endo anti -B295 : U C3p_endo anti -B296 : G C2p_exo anti -B297 : C C3p_endo anti -B298 : G C3p_endo anti -B299 : A C2p_exo anti -B300 : G C3p_endo anti -B301 : A C3p_endo anti -B302 : G C3p_endo anti -B303 : U C3p_endo anti -B304 : A C3p_endo anti -B305 : G C3p_endo anti -B306 : G C3p_endo anti -B307 : U C3p_endo anti -B308 : C C3p_endo anti -A1 : MET -A2 : PHE -A3 : THR -A4 : ILE -A5 : ASN -A6 : ALA -A7 : GLU -A8 : VAL -A9 : ARG -A10 : LYS -A11 : GLU -A12 : GLN -A13 : GLY -A14 : LYS -A15 : GLY -A16 : ALA -A17 : SER -A18 : ARG -A19 : ARG -A20 : LEU -A21 : ARG -A22 : ALA -A23 : ALA -A24 : ASN -A25 : LYS -A26 : PHE -A27 : PRO -A28 : ALA -A29 : ILE -A30 : ILE -A31 : TYR -A32 : GLY -A33 : GLY -A34 : LYS -A35 : GLU -A36 : ALA -A37 : PRO -A38 : LEU -A39 : ALA -A40 : ILE -A41 : GLU -A42 : LEU -A43 : ASP -A44 : HIS -A45 : ASP -A46 : LYS -A47 : VAL -A48 : MET -A49 : ASN -A50 : MET -A51 : GLN -A52 : ALA -A53 : LYS -A54 : ALA -A55 : GLU -A56 : PHE -A57 : TYR -A58 : SER -A59 : GLU -A60 : VAL -A61 : LEU -A62 : THR -A63 : ILE -A64 : VAL -A65 : VAL -A66 : ASP -A67 : GLY -A68 : LYS -A69 : GLU -A70 : ILE -A71 : LYS -A72 : VAL -A73 : LYS -A74 : ALA -A75 : GLN -A76 : ASP -A77 : VAL -A78 : GLN -A79 : ARG -A80 : HIS -A81 : PRO -A82 : TYR -A83 : LYS -A84 : PRO -A85 : LYS -A86 : LEU -A87 : GLN -A88 : HIS -A89 : ILE -A90 : ASP -A91 : PHE -A92 : VAL -A93 : ARG -A94 : ALA -Adjacent stackings ---------------------------------------------- -B268-B269 : adjacent_5p upward -B269-B270 : adjacent_5p upward -B270-B271 : adjacent_5p upward -B271-B272 : adjacent_5p upward -B273-B274 : adjacent_5p upward -B274-B275 : adjacent_5p upward -B275-B276 : adjacent_5p upward -B276-B277 : adjacent_5p upward -B277-B278 : adjacent_5p upward -B278-B279 : adjacent_5p upward -B279-B280 : adjacent_5p upward -B281-B282 : adjacent_5p upward -B282-B283 : adjacent_5p upward -B283-B284 : adjacent_5p upward -B293-B294 : adjacent_5p upward -B294-B295 : adjacent_5p upward -B296-B297 : adjacent_5p upward -B299-B300 : adjacent_5p upward -B300-B301 : adjacent_5p upward -B301-B302 : adjacent_5p upward -B302-B303 : adjacent_5p upward -B303-B304 : adjacent_5p upward -B304-B305 : adjacent_5p upward -B305-B306 : adjacent_5p upward -B306-B307 : adjacent_5p upward -B307-B308 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -B273-B304 : outward -B278-B299 : outward -B281-B296 : outward -Number of stackings = 29 -Number of adjacent stackings = 26 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -A14-B279 : LYS-G pairing one_hbond -A17-B298 : SER-G pairing one_hbond -A31-B273 : TYR-A pairing one_hbond -A31-B274 : TYR-U pairing one_hbond -B268-B308 : G-C Ww/Ww pairing antiparallel cis XIX -B269-B307 : A-U Ww/Ww pairing antiparallel cis XX -B270-B306 : C-G Ww/Ww pairing antiparallel cis XIX -B271-B305 : C-G Ww/Ww pairing antiparallel cis XIX -B272-B303 : G-U Ww/O2P pairing -B272-B304 : G-A Ss/Hh O2'/Bh pairing antiparallel trans XI -B273-B303 : A-U Hh/Ws pairing antiparallel trans XXIV -B274-B302 : U-G Hw/Ww pairing antiparallel trans one_hbond 91 -B276-B300 : G-G Ww/Bh pairing antiparallel trans 115 -B277-B298 : U-G O2P/Ww pairing -B277-B299 : U-A Ws/Hh pairing antiparallel trans XXIV -B278-B298 : A-G Hh/Ss Bh/O2' pairing antiparallel trans XI -B279-B297 : G-C Ww/Ww pairing antiparallel cis XIX -B280-B296 : U-G Ws/Ww pairing antiparallel cis XXVIII -B281-B295 : G-U Ww/Ws pairing antiparallel cis XXVIII -B282-B294 : U-A Ww/Ww pairing antiparallel cis XX -B283-B293 : C-G Ww/Ww pairing antiparallel cis XIX -B284-B292 : U-G Ws/Ww pairing parallel trans one_hbond 87 -B285-B291 : U-C O2P/Bh adjacent_5p pairing -Residue conformations ------------------------------------------- -B267 : G C3p_endo anti -B268 : G C2p_exo anti -B269 : A C3p_endo anti -B270 : C C3p_endo anti -B271 : C C3p_endo anti -B272 : G C3p_endo anti -B273 : A C2p_exo anti -B274 : U C4p_exo anti -B275 : G C3p_endo anti -B276 : G C3p_endo anti -B277 : U C3p_endo anti -B278 : A C3p_endo anti -B279 : G C3p_endo anti -B280 : U C3p_endo anti -B281 : G C1p_endo anti -B282 : U C3p_endo anti -B283 : C C3p_endo anti -B284 : U C3p_endo anti -B285 : U C3p_exo anti -B291 : C C2p_endo anti -B292 : G O4p_endo anti -B293 : G C3p_endo anti -B294 : A C3p_endo anti -B295 : U C3p_endo anti -B296 : G C3p_endo anti -B297 : C C3p_endo anti -B298 : G C3p_endo anti -B299 : A C2p_exo anti -B300 : G C3p_endo anti -B301 : A C3p_endo anti -B302 : G C3p_endo anti -B303 : U C3p_endo anti -B304 : A C3p_endo anti -B305 : G C3p_endo anti -B306 : G C3p_endo anti -B307 : U C3p_endo anti -B308 : C C3p_endo anti -A1 : MET -A2 : PHE -A3 : THR -A4 : ILE -A5 : ASN -A6 : ALA -A7 : GLU -A8 : VAL -A9 : ARG -A10 : LYS -A11 : GLU -A12 : GLN -A13 : GLY -A14 : LYS -A15 : GLY -A16 : ALA -A17 : SER -A18 : ARG -A19 : ARG -A20 : LEU -A21 : ARG -A22 : ALA -A23 : ALA -A24 : ASN -A25 : LYS -A26 : PHE -A27 : PRO -A28 : ALA -A29 : ILE -A30 : ILE -A31 : TYR -A32 : GLY -A33 : GLY -A34 : LYS -A35 : GLU -A36 : ALA -A37 : PRO -A38 : LEU -A39 : ALA -A40 : ILE -A41 : GLU -A42 : LEU -A43 : ASP -A44 : HIS -A45 : ASP -A46 : LYS -A47 : VAL -A48 : MET -A49 : ASN -A50 : MET -A51 : GLN -A52 : ALA -A53 : LYS -A54 : ALA -A55 : GLU -A56 : PHE -A57 : TYR -A58 : SER -A59 : GLU -A60 : VAL -A61 : LEU -A62 : THR -A63 : ILE -A64 : VAL -A65 : VAL -A66 : ASP -A67 : GLY -A68 : LYS -A69 : GLU -A70 : ILE -A71 : LYS -A72 : VAL -A73 : LYS -A74 : ALA -A75 : GLN -A76 : ASP -A77 : VAL -A78 : GLN -A79 : ARG -A80 : HIS -A81 : PRO -A82 : TYR -A83 : LYS -A84 : PRO -A85 : LYS -A86 : LEU -A87 : GLN -A88 : HIS -A89 : ILE -A90 : ASP -A91 : PHE -A92 : VAL -A93 : ARG -A94 : ALA -Adjacent stackings ---------------------------------------------- -B268-B269 : adjacent_5p upward -B269-B270 : adjacent_5p upward -B270-B271 : adjacent_5p upward -B271-B272 : adjacent_5p upward -B273-B274 : adjacent_5p upward -B274-B275 : adjacent_5p upward -B275-B276 : adjacent_5p upward -B276-B277 : adjacent_5p upward -B277-B278 : adjacent_5p upward -B278-B279 : adjacent_5p upward -B279-B280 : adjacent_5p upward -B281-B282 : adjacent_5p upward -B282-B283 : adjacent_5p upward -B291-B292 : adjacent_5p downward -B293-B294 : adjacent_5p upward -B294-B295 : adjacent_5p upward -B296-B297 : adjacent_5p upward -B299-B300 : adjacent_5p upward -B300-B301 : adjacent_5p upward -B301-B302 : adjacent_5p upward -B302-B303 : adjacent_5p upward -B303-B304 : adjacent_5p upward -B304-B305 : adjacent_5p upward -B305-B306 : adjacent_5p upward -B306-B307 : adjacent_5p upward -B307-B308 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -B273-B304 : outward -B278-B299 : outward -B281-B296 : outward -B291-B293 : upward -Number of stackings = 30 -Number of adjacent stackings = 26 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A14-B279 : LYS-G pairing one_hbond -A17-B298 : SER-G pairing one_hbond -A31-B273 : TYR-A pairing one_hbond -B268-B308 : G-C Ww/Ww pairing antiparallel cis XIX -B269-B307 : A-U Ww/Ww pairing antiparallel cis XX -B270-B306 : C-G Ww/Ww pairing antiparallel cis XIX -B271-B305 : C-G Ww/Ww pairing antiparallel cis XIX -B272-B303 : G-U Ww/O2P pairing -B272-B304 : G-A Ss/Hh O2'/Bh pairing antiparallel trans XI -B273-B303 : A-U Hh/Ws pairing antiparallel trans XXIV -B274-B302 : U-G Hw/Ww pairing antiparallel trans one_hbond 91 -B276-B300 : G-G Ww/Hw pairing antiparallel trans one_hbond -B277-B298 : U-G O2P/Ww pairing -B277-B299 : U-A Ww/Hh pairing antiparallel trans XXIV -B278-B298 : A-G Hh/Ss Bh/O2' pairing antiparallel trans XI -B279-B297 : G-C Ww/Ww pairing antiparallel cis XIX -B280-B296 : U-G Ws/Ww pairing antiparallel cis XXVIII -B281-B295 : G-U Ww/Ws pairing antiparallel cis XXVIII -B282-B294 : U-A Ww/Ww pairing antiparallel cis XX -B283-B293 : C-G Ww/Ww pairing antiparallel cis XIX -B284-B291 : U-C O2'/Bh pairing -Residue conformations ------------------------------------------- -B267 : G C1p_exo syn -B268 : G C3p_endo anti -B269 : A C3p_endo anti -B270 : C C3p_endo anti -B271 : C C3p_endo anti -B272 : G C3p_endo anti -B273 : A C2p_exo anti -B274 : U C4p_exo anti -B275 : G C3p_endo anti -B276 : G C3p_endo anti -B277 : U C3p_endo anti -B278 : A C3p_endo anti -B279 : G C3p_endo anti -B280 : U C3p_endo anti -B281 : G C2p_exo anti -B282 : U C3p_endo anti -B283 : C C3p_endo anti -B284 : U C3p_endo anti -B285 : U C2p_endo anti -B291 : C C2p_endo anti -B292 : G C3p_exo anti -B293 : G C3p_endo anti -B294 : A C3p_endo anti -B295 : U C3p_endo anti -B296 : G C2p_exo anti -B297 : C C3p_endo anti -B298 : G C3p_endo anti -B299 : A C2p_exo anti -B300 : G C3p_endo anti -B301 : A C3p_endo anti -B302 : G C3p_endo anti -B303 : U C3p_endo anti -B304 : A C3p_endo anti -B305 : G C3p_endo anti -B306 : G C3p_endo anti -B307 : U C3p_endo anti -B308 : C C3p_endo anti -A1 : MET -A2 : PHE -A3 : THR -A4 : ILE -A5 : ASN -A6 : ALA -A7 : GLU -A8 : VAL -A9 : ARG -A10 : LYS -A11 : GLU -A12 : GLN -A13 : GLY -A14 : LYS -A15 : GLY -A16 : ALA -A17 : SER -A18 : ARG -A19 : ARG -A20 : LEU -A21 : ARG -A22 : ALA -A23 : ALA -A24 : ASN -A25 : LYS -A26 : PHE -A27 : PRO -A28 : ALA -A29 : ILE -A30 : ILE -A31 : TYR -A32 : GLY -A33 : GLY -A34 : LYS -A35 : GLU -A36 : ALA -A37 : PRO -A38 : LEU -A39 : ALA -A40 : ILE -A41 : GLU -A42 : LEU -A43 : ASP -A44 : HIS -A45 : ASP -A46 : LYS -A47 : VAL -A48 : MET -A49 : ASN -A50 : MET -A51 : GLN -A52 : ALA -A53 : LYS -A54 : ALA -A55 : GLU -A56 : PHE -A57 : TYR -A58 : SER -A59 : GLU -A60 : VAL -A61 : LEU -A62 : THR -A63 : ILE -A64 : VAL -A65 : VAL -A66 : ASP -A67 : GLY -A68 : LYS -A69 : GLU -A70 : ILE -A71 : LYS -A72 : VAL -A73 : LYS -A74 : ALA -A75 : GLN -A76 : ASP -A77 : VAL -A78 : GLN -A79 : ARG -A80 : HIS -A81 : PRO -A82 : TYR -A83 : LYS -A84 : PRO -A85 : LYS -A86 : LEU -A87 : GLN -A88 : HIS -A89 : ILE -A90 : ASP -A91 : PHE -A92 : VAL -A93 : ARG -A94 : ALA -Adjacent stackings ---------------------------------------------- -B268-B269 : adjacent_5p upward -B269-B270 : adjacent_5p upward -B270-B271 : adjacent_5p upward -B271-B272 : adjacent_5p upward -B273-B274 : adjacent_5p upward -B274-B275 : adjacent_5p upward -B275-B276 : adjacent_5p upward -B276-B277 : adjacent_5p upward -B278-B279 : adjacent_5p upward -B279-B280 : adjacent_5p upward -B281-B282 : adjacent_5p upward -B283-B284 : adjacent_5p upward -B293-B294 : adjacent_5p upward -B294-B295 : adjacent_5p upward -B296-B297 : adjacent_5p upward -B299-B300 : adjacent_5p upward -B300-B301 : adjacent_5p upward -B301-B302 : adjacent_5p upward -B302-B303 : adjacent_5p upward -B303-B304 : adjacent_5p upward -B304-B305 : adjacent_5p upward -B305-B306 : adjacent_5p upward -B306-B307 : adjacent_5p upward -B307-B308 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -B273-B304 : outward -B278-B299 : outward -B281-B296 : outward -Number of stackings = 27 -Number of adjacent stackings = 24 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -A14-B279 : LYS-G pairing -A31-B274 : TYR-U pairing one_hbond -B268-B308 : G-C Ww/Ww pairing antiparallel cis XIX -B269-B307 : A-U Ww/Ww pairing antiparallel cis XX -B270-B306 : C-G Ww/Ww pairing antiparallel cis XIX -B271-B305 : C-G Ww/Ww pairing antiparallel cis XIX -B272-B303 : G-U Ww/O2P pairing -B272-B304 : G-A Ss/Hh O2'/Bh pairing antiparallel trans XI -B273-B303 : A-U Hh/Ws pairing antiparallel trans XXIV -B274-B302 : U-G Hw/Ww pairing antiparallel trans one_hbond 91 -B276-B300 : G-G Ww/Hw pairing antiparallel trans one_hbond -B277-B299 : U-A Ws/Hh pairing antiparallel trans XXIV -B278-B298 : A-G Hh/Ss O2P/Bs Bh/O2' pairing antiparallel trans one_hbond -B279-B297 : G-C Ww/Ww pairing antiparallel cis XIX -B280-B296 : U-G Ws/Ww pairing antiparallel cis XXVIII -B281-B295 : G-U Ww/Ws pairing antiparallel cis XXVIII -B282-B294 : U-A Ww/Ww pairing antiparallel cis XX -B283-B293 : C-G Ww/Ww pairing antiparallel cis XIX -B284-B292 : U-G Ws/Ws pairing parallel trans one_hbond 87 -B285-B291 : U-C O2P/Bh adjacent_5p pairing -Residue conformations ------------------------------------------- -B267 : G C2p_endo anti -B268 : G C3p_endo anti -B269 : A C3p_endo anti -B270 : C C3p_endo anti -B271 : C C3p_endo anti -B272 : G C3p_endo anti -B273 : A C2p_exo anti -B274 : U C4p_exo anti -B275 : G C3p_endo anti -B276 : G C3p_endo anti -B277 : U C3p_endo anti -B278 : A C3p_endo anti -B279 : G C3p_endo anti -B280 : U C3p_endo anti -B281 : G C2p_exo anti -B282 : U C3p_endo anti -B283 : C C3p_endo anti -B284 : U C3p_endo anti -B285 : U C2p_endo anti -B291 : C C3p_exo anti -B292 : G C1p_endo anti -B293 : G C2p_exo anti -B294 : A C3p_endo anti -B295 : U C3p_endo anti -B296 : G C1p_endo anti -B297 : C C3p_endo anti -B298 : G C3p_endo anti -B299 : A C2p_exo anti -B300 : G C3p_endo anti -B301 : A C3p_endo anti -B302 : G C3p_endo anti -B303 : U C3p_endo anti -B304 : A C3p_endo anti -B305 : G C3p_endo anti -B306 : G C3p_endo anti -B307 : U C3p_endo anti -B308 : C C3p_endo anti -A1 : MET -A2 : PHE -A3 : THR -A4 : ILE -A5 : ASN -A6 : ALA -A7 : GLU -A8 : VAL -A9 : ARG -A10 : LYS -A11 : GLU -A12 : GLN -A13 : GLY -A14 : LYS -A15 : GLY -A16 : ALA -A17 : SER -A18 : ARG -A19 : ARG -A20 : LEU -A21 : ARG -A22 : ALA -A23 : ALA -A24 : ASN -A25 : LYS -A26 : PHE -A27 : PRO -A28 : ALA -A29 : ILE -A30 : ILE -A31 : TYR -A32 : GLY -A33 : GLY -A34 : LYS -A35 : GLU -A36 : ALA -A37 : PRO -A38 : LEU -A39 : ALA -A40 : ILE -A41 : GLU -A42 : LEU -A43 : ASP -A44 : HIS -A45 : ASP -A46 : LYS -A47 : VAL -A48 : MET -A49 : ASN -A50 : MET -A51 : GLN -A52 : ALA -A53 : LYS -A54 : ALA -A55 : GLU -A56 : PHE -A57 : TYR -A58 : SER -A59 : GLU -A60 : VAL -A61 : LEU -A62 : THR -A63 : ILE -A64 : VAL -A65 : VAL -A66 : ASP -A67 : GLY -A68 : LYS -A69 : GLU -A70 : ILE -A71 : LYS -A72 : VAL -A73 : LYS -A74 : ALA -A75 : GLN -A76 : ASP -A77 : VAL -A78 : GLN -A79 : ARG -A80 : HIS -A81 : PRO -A82 : TYR -A83 : LYS -A84 : PRO -A85 : LYS -A86 : LEU -A87 : GLN -A88 : HIS -A89 : ILE -A90 : ASP -A91 : PHE -A92 : VAL -A93 : ARG -A94 : ALA -Adjacent stackings ---------------------------------------------- -B268-B269 : adjacent_5p upward -B269-B270 : adjacent_5p upward -B270-B271 : adjacent_5p upward -B271-B272 : adjacent_5p upward -B273-B274 : adjacent_5p upward -B274-B275 : adjacent_5p upward -B275-B276 : adjacent_5p upward -B276-B277 : adjacent_5p upward -B277-B278 : adjacent_5p upward -B278-B279 : adjacent_5p upward -B279-B280 : adjacent_5p upward -B281-B282 : adjacent_5p upward -B282-B283 : adjacent_5p upward -B283-B284 : adjacent_5p upward -B293-B294 : adjacent_5p upward -B294-B295 : adjacent_5p upward -B296-B297 : adjacent_5p upward -B299-B300 : adjacent_5p upward -B300-B301 : adjacent_5p upward -B301-B302 : adjacent_5p upward -B302-B303 : adjacent_5p upward -B303-B304 : adjacent_5p upward -B304-B305 : adjacent_5p upward -B305-B306 : adjacent_5p upward -B306-B307 : adjacent_5p upward -B307-B308 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -B273-B304 : outward -B278-B299 : outward -B281-B296 : outward -Number of stackings = 29 -Number of adjacent stackings = 26 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -A14-B279 : LYS-G pairing one_hbond -A17-B298 : SER-G pairing one_hbond -A31-B273 : TYR-A pairing one_hbond -A31-B274 : TYR-U pairing one_hbond -B268-B308 : G-C Ww/Ww pairing antiparallel cis XIX -B269-B307 : A-U Ww/Ww pairing antiparallel cis XX -B270-B306 : C-G Ww/Ww pairing antiparallel cis XIX -B271-B305 : C-G Ww/Ww pairing antiparallel cis XIX -B272-B303 : G-U Ww/O2P pairing -B272-B304 : G-A Ss/Hh O2'/Bh pairing antiparallel trans XI -B273-B303 : A-U Hh/Ws pairing antiparallel trans XXIV -B274-B302 : U-G Hw/Ww pairing antiparallel trans one_hbond 91 -B276-B300 : G-G Ww/Bh pairing antiparallel trans 115 -B277-B299 : U-A Ws/Hh pairing antiparallel trans XXIV -B278-B298 : A-G Hh/Ss Bh/O2' pairing antiparallel trans XI -B279-B297 : G-C Ww/Ww pairing antiparallel cis XIX -B280-B296 : U-G Ws/Ww pairing antiparallel cis XXVIII -B281-B295 : G-U Ww/Ws pairing antiparallel cis XXVIII -B282-B294 : U-A Ww/Ww pairing antiparallel cis XX -B283-B293 : C-G Ww/Ww pairing antiparallel cis XIX -B284-B292 : U-G Ws/Ws pairing parallel trans one_hbond 87 -B285-B291 : U-C O2P/Bh adjacent_5p pairing -B285-B292 : U-G O2'/Hh pairing -Residue conformations ------------------------------------------- -B267 : G C3p_exo anti -B268 : G C2p_exo anti -B269 : A C3p_endo anti -B270 : C C3p_endo anti -B271 : C C3p_endo anti -B272 : G C3p_endo anti -B273 : A C2p_exo anti -B274 : U C3p_endo anti -B275 : G C3p_endo anti -B276 : G C3p_endo anti -B277 : U C3p_endo anti -B278 : A C3p_endo anti -B279 : G C3p_endo anti -B280 : U C3p_endo anti -B281 : G C1p_endo anti -B282 : U C3p_endo anti -B283 : C C3p_endo anti -B284 : U C3p_endo anti -B285 : U C3p_endo anti -B291 : C C2p_endo anti -B292 : G C3p_endo anti -B293 : G C2p_exo anti -B294 : A C3p_endo anti -B295 : U C3p_endo anti -B296 : G C2p_exo anti -B297 : C C3p_endo anti -B298 : G C3p_endo anti -B299 : A C2p_exo anti -B300 : G C3p_endo anti -B301 : A C3p_endo anti -B302 : G C3p_endo anti -B303 : U C3p_endo anti -B304 : A C3p_endo anti -B305 : G C3p_endo anti -B306 : G C3p_endo anti -B307 : U C3p_endo anti -B308 : C C3p_endo anti -A1 : MET -A2 : PHE -A3 : THR -A4 : ILE -A5 : ASN -A6 : ALA -A7 : GLU -A8 : VAL -A9 : ARG -A10 : LYS -A11 : GLU -A12 : GLN -A13 : GLY -A14 : LYS -A15 : GLY -A16 : ALA -A17 : SER -A18 : ARG -A19 : ARG -A20 : LEU -A21 : ARG -A22 : ALA -A23 : ALA -A24 : ASN -A25 : LYS -A26 : PHE -A27 : PRO -A28 : ALA -A29 : ILE -A30 : ILE -A31 : TYR -A32 : GLY -A33 : GLY -A34 : LYS -A35 : GLU -A36 : ALA -A37 : PRO -A38 : LEU -A39 : ALA -A40 : ILE -A41 : GLU -A42 : LEU -A43 : ASP -A44 : HIS -A45 : ASP -A46 : LYS -A47 : VAL -A48 : MET -A49 : ASN -A50 : MET -A51 : GLN -A52 : ALA -A53 : LYS -A54 : ALA -A55 : GLU -A56 : PHE -A57 : TYR -A58 : SER -A59 : GLU -A60 : VAL -A61 : LEU -A62 : THR -A63 : ILE -A64 : VAL -A65 : VAL -A66 : ASP -A67 : GLY -A68 : LYS -A69 : GLU -A70 : ILE -A71 : LYS -A72 : VAL -A73 : LYS -A74 : ALA -A75 : GLN -A76 : ASP -A77 : VAL -A78 : GLN -A79 : ARG -A80 : HIS -A81 : PRO -A82 : TYR -A83 : LYS -A84 : PRO -A85 : LYS -A86 : LEU -A87 : GLN -A88 : HIS -A89 : ILE -A90 : ASP -A91 : PHE -A92 : VAL -A93 : ARG -A94 : ALA -Adjacent stackings ---------------------------------------------- -B268-B269 : adjacent_5p upward -B269-B270 : adjacent_5p upward -B270-B271 : adjacent_5p upward -B271-B272 : adjacent_5p upward -B273-B274 : adjacent_5p upward -B274-B275 : adjacent_5p upward -B275-B276 : adjacent_5p upward -B276-B277 : adjacent_5p upward -B277-B278 : adjacent_5p upward -B278-B279 : adjacent_5p upward -B279-B280 : adjacent_5p upward -B281-B282 : adjacent_5p upward -B282-B283 : adjacent_5p upward -B283-B284 : adjacent_5p upward -B293-B294 : adjacent_5p upward -B294-B295 : adjacent_5p upward -B296-B297 : adjacent_5p upward -B297-B298 : adjacent_5p upward -B299-B300 : adjacent_5p upward -B300-B301 : adjacent_5p upward -B301-B302 : adjacent_5p upward -B302-B303 : adjacent_5p upward -B303-B304 : adjacent_5p upward -B304-B305 : adjacent_5p upward -B305-B306 : adjacent_5p upward -B306-B307 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -B273-B304 : outward -B278-B299 : outward -B281-B296 : outward -Number of stackings = 29 -Number of adjacent stackings = 26 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -A17-B298 : SER-G pairing one_hbond -A31-B273 : TYR-A pairing one_hbond -A31-B274 : TYR-U pairing one_hbond -B268-B308 : G-C Ww/Ww pairing antiparallel cis XIX -B269-B307 : A-U Ww/Ww pairing antiparallel cis XX -B270-B306 : C-G Ww/Ww pairing antiparallel cis XIX -B271-B305 : C-G Ww/Ww pairing antiparallel cis XIX -B272-B303 : G-U Ww/O2P pairing -B272-B304 : G-A Ss/Hh O2'/Bh pairing antiparallel trans XI -B273-B303 : A-U Hh/Ws pairing antiparallel trans XXIV -B274-B302 : U-G Hw/Ww pairing antiparallel trans one_hbond 91 -B276-B300 : G-G Ww/Bh pairing antiparallel trans 115 -B277-B299 : U-A Ws/Hh pairing antiparallel trans XXIV -B278-B298 : A-G Hh/Ss O2P/Bs Bh/O2' pairing antiparallel trans XI -B279-B297 : G-C Ww/Ww pairing antiparallel cis XIX -B280-B296 : U-G Ws/Ww pairing antiparallel cis XXVIII -B281-B295 : G-U Ww/Ws pairing antiparallel cis XXVIII -B282-B294 : U-A Ww/Ww pairing antiparallel cis XX -B283-B293 : C-G Ww/Ww pairing antiparallel cis XIX -B285-B291 : U-C O2P/Bh adjacent_5p pairing -Residue conformations ------------------------------------------- -B267 : G C2p_endo syn -B268 : G C3p_endo anti -B269 : A C3p_endo anti -B270 : C C3p_endo anti -B271 : C C3p_endo anti -B272 : G C3p_endo anti -B273 : A C3p_endo anti -B274 : U C4p_exo anti -B275 : G C3p_endo anti -B276 : G C3p_endo anti -B277 : U C3p_endo anti -B278 : A C3p_endo anti -B279 : G C3p_endo anti -B280 : U C3p_endo anti -B281 : G C3p_endo anti -B282 : U C3p_endo anti -B283 : C C3p_endo anti -B284 : U C3p_endo anti -B285 : U C2p_endo anti -B291 : C C1p_exo anti -B292 : G C2p_endo anti -B293 : G C2p_exo anti -B294 : A C3p_endo anti -B295 : U C3p_endo anti -B296 : G C3p_endo anti -B297 : C C3p_endo anti -B298 : G C3p_endo anti -B299 : A C1p_endo anti -B300 : G C3p_endo anti -B301 : A C3p_endo anti -B302 : G C3p_endo anti -B303 : U C3p_endo anti -B304 : A C3p_endo anti -B305 : G C3p_endo anti -B306 : G C3p_endo anti -B307 : U C3p_endo anti -B308 : C C4p_exo anti -A1 : MET -A2 : PHE -A3 : THR -A4 : ILE -A5 : ASN -A6 : ALA -A7 : GLU -A8 : VAL -A9 : ARG -A10 : LYS -A11 : GLU -A12 : GLN -A13 : GLY -A14 : LYS -A15 : GLY -A16 : ALA -A17 : SER -A18 : ARG -A19 : ARG -A20 : LEU -A21 : ARG -A22 : ALA -A23 : ALA -A24 : ASN -A25 : LYS -A26 : PHE -A27 : PRO -A28 : ALA -A29 : ILE -A30 : ILE -A31 : TYR -A32 : GLY -A33 : GLY -A34 : LYS -A35 : GLU -A36 : ALA -A37 : PRO -A38 : LEU -A39 : ALA -A40 : ILE -A41 : GLU -A42 : LEU -A43 : ASP -A44 : HIS -A45 : ASP -A46 : LYS -A47 : VAL -A48 : MET -A49 : ASN -A50 : MET -A51 : GLN -A52 : ALA -A53 : LYS -A54 : ALA -A55 : GLU -A56 : PHE -A57 : TYR -A58 : SER -A59 : GLU -A60 : VAL -A61 : LEU -A62 : THR -A63 : ILE -A64 : VAL -A65 : VAL -A66 : ASP -A67 : GLY -A68 : LYS -A69 : GLU -A70 : ILE -A71 : LYS -A72 : VAL -A73 : LYS -A74 : ALA -A75 : GLN -A76 : ASP -A77 : VAL -A78 : GLN -A79 : ARG -A80 : HIS -A81 : PRO -A82 : TYR -A83 : LYS -A84 : PRO -A85 : LYS -A86 : LEU -A87 : GLN -A88 : HIS -A89 : ILE -A90 : ASP -A91 : PHE -A92 : VAL -A93 : ARG -A94 : ALA -Adjacent stackings ---------------------------------------------- -B268-B269 : adjacent_5p upward -B269-B270 : adjacent_5p upward -B270-B271 : adjacent_5p upward -B271-B272 : adjacent_5p upward -B273-B274 : adjacent_5p upward -B274-B275 : adjacent_5p upward -B275-B276 : adjacent_5p upward -B276-B277 : adjacent_5p upward -B277-B278 : adjacent_5p upward -B278-B279 : adjacent_5p upward -B279-B280 : adjacent_5p upward -B281-B282 : adjacent_5p upward -B282-B283 : adjacent_5p upward -B283-B284 : adjacent_5p upward -B293-B294 : adjacent_5p upward -B294-B295 : adjacent_5p upward -B296-B297 : adjacent_5p upward -B299-B300 : adjacent_5p upward -B300-B301 : adjacent_5p upward -B301-B302 : adjacent_5p upward -B302-B303 : adjacent_5p upward -B303-B304 : adjacent_5p upward -B304-B305 : adjacent_5p upward -B305-B306 : adjacent_5p upward -B306-B307 : adjacent_5p upward -B307-B308 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -B273-B304 : outward -B278-B299 : outward -B281-B296 : outward -Number of stackings = 29 -Number of adjacent stackings = 26 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -A14-B279 : LYS-G pairing one_hbond -A31-B273 : TYR-A pairing one_hbond -B268-B308 : G-C Ww/Ww pairing antiparallel cis XIX -B269-B307 : A-U Ww/Ww pairing antiparallel cis XX -B270-B306 : C-G Ww/Ww pairing antiparallel cis XIX -B271-B305 : C-G Ww/Ww pairing antiparallel cis XIX -B272-B303 : G-U Ww/O2P pairing -B272-B304 : G-A Ss/Hh O2'/Bh pairing antiparallel trans XI -B273-B303 : A-U Hh/Ws pairing antiparallel trans XXIV -B274-B302 : U-G Hw/Ww pairing antiparallel trans one_hbond 91 -B276-B300 : G-G Ww/Bh pairing antiparallel trans one_hbond -B277-B299 : U-A Ws/Hh pairing antiparallel trans XXIV -B278-B298 : A-G Hh/Ss Bh/O2' pairing antiparallel trans XI -B279-B297 : G-C Ww/Ww pairing antiparallel cis XIX -B280-B296 : U-G Ws/Ww pairing antiparallel cis XXVIII -B281-B295 : G-U Ww/Ws pairing antiparallel cis XXVIII -B282-B294 : U-A Ww/Ww pairing antiparallel cis XX -B283-B293 : C-G Ww/Ww pairing antiparallel cis XIX -B284-B292 : U-G O2'/Ww pairing -B285-B291 : U-C O2P/Bh adjacent_5p pairing -B292-B293 : G-G O2'/C8 adjacent_5p pairing -Residue conformations ------------------------------------------- -B267 : G C3p_exo anti -B268 : G C2p_exo anti -B269 : A C3p_endo anti -B270 : C C3p_endo anti -B271 : C C3p_endo anti -B272 : G C3p_endo anti -B273 : A C2p_exo anti -B274 : U C4p_exo anti -B275 : G C3p_endo anti -B276 : G C3p_endo anti -B277 : U C3p_endo anti -B278 : A C3p_endo anti -B279 : G C3p_endo anti -B280 : U C3p_endo anti -B281 : G C3p_endo anti -B282 : U C3p_endo anti -B283 : C C3p_endo anti -B284 : U C3p_endo anti -B285 : U C3p_endo anti -B291 : C C2p_endo anti -B292 : G C3p_exo anti -B293 : G C3p_endo anti -B294 : A C3p_endo anti -B295 : U C3p_endo anti -B296 : G C2p_exo anti -B297 : C C3p_endo anti -B298 : G C3p_endo anti -B299 : A C3p_endo anti -B300 : G C3p_endo anti -B301 : A C3p_endo anti -B302 : G C3p_endo anti -B303 : U C3p_endo anti -B304 : A C3p_endo anti -B305 : G C2p_exo anti -B306 : G C3p_endo anti -B307 : U C3p_endo anti -B308 : C C3p_endo anti -A1 : MET -A2 : PHE -A3 : THR -A4 : ILE -A5 : ASN -A6 : ALA -A7 : GLU -A8 : VAL -A9 : ARG -A10 : LYS -A11 : GLU -A12 : GLN -A13 : GLY -A14 : LYS -A15 : GLY -A16 : ALA -A17 : SER -A18 : ARG -A19 : ARG -A20 : LEU -A21 : ARG -A22 : ALA -A23 : ALA -A24 : ASN -A25 : LYS -A26 : PHE -A27 : PRO -A28 : ALA -A29 : ILE -A30 : ILE -A31 : TYR -A32 : GLY -A33 : GLY -A34 : LYS -A35 : GLU -A36 : ALA -A37 : PRO -A38 : LEU -A39 : ALA -A40 : ILE -A41 : GLU -A42 : LEU -A43 : ASP -A44 : HIS -A45 : ASP -A46 : LYS -A47 : VAL -A48 : MET -A49 : ASN -A50 : MET -A51 : GLN -A52 : ALA -A53 : LYS -A54 : ALA -A55 : GLU -A56 : PHE -A57 : TYR -A58 : SER -A59 : GLU -A60 : VAL -A61 : LEU -A62 : THR -A63 : ILE -A64 : VAL -A65 : VAL -A66 : ASP -A67 : GLY -A68 : LYS -A69 : GLU -A70 : ILE -A71 : LYS -A72 : VAL -A73 : LYS -A74 : ALA -A75 : GLN -A76 : ASP -A77 : VAL -A78 : GLN -A79 : ARG -A80 : HIS -A81 : PRO -A82 : TYR -A83 : LYS -A84 : PRO -A85 : LYS -A86 : LEU -A87 : GLN -A88 : HIS -A89 : ILE -A90 : ASP -A91 : PHE -A92 : VAL -A93 : ARG -A94 : ALA -Adjacent stackings ---------------------------------------------- -B268-B269 : adjacent_5p upward -B269-B270 : adjacent_5p upward -B270-B271 : adjacent_5p upward -B271-B272 : adjacent_5p upward -B273-B274 : adjacent_5p upward -B274-B275 : adjacent_5p upward -B275-B276 : adjacent_5p upward -B276-B277 : adjacent_5p upward -B277-B278 : adjacent_5p upward -B278-B279 : adjacent_5p upward -B279-B280 : adjacent_5p upward -B281-B282 : adjacent_5p upward -B282-B283 : adjacent_5p upward -B283-B284 : adjacent_5p upward -B293-B294 : adjacent_5p upward -B294-B295 : adjacent_5p upward -B295-B296 : adjacent_5p upward -B296-B297 : adjacent_5p upward -B299-B300 : adjacent_5p upward -B300-B301 : adjacent_5p upward -B301-B302 : adjacent_5p upward -B302-B303 : adjacent_5p upward -B303-B304 : adjacent_5p upward -B304-B305 : adjacent_5p upward -B305-B306 : adjacent_5p upward -B306-B307 : adjacent_5p upward -B307-B308 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -B273-B304 : outward -B278-B299 : outward -B281-B296 : outward -Number of stackings = 30 -Number of adjacent stackings = 27 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -A14-B279 : LYS-G pairing one_hbond -A31-B273 : TYR-A pairing one_hbond -A88-B275 : HIS-G pairing one_hbond -B267-B272 : G-G Ws/Wh pairing antiparallel cis one_hbond 115 -B268-B308 : G-C Ww/Ww pairing antiparallel cis XIX -B269-B307 : A-U Ww/Ww pairing antiparallel cis XX -B270-B306 : C-G Ww/Ww pairing antiparallel cis XIX -B271-B305 : C-G Ww/Ww pairing antiparallel cis XIX -B272-B304 : G-A Ss/Hh O2'/Bh pairing antiparallel trans XI -B273-B303 : A-U Hh/Ws pairing antiparallel trans XXIV -B274-B302 : U-G Hw/Ww pairing antiparallel trans one_hbond 91 -B276-B300 : G-G Ww/Bh pairing antiparallel trans 115 -B277-B298 : U-G O2P/Ww pairing -B277-B299 : U-A Ws/Hh pairing antiparallel trans XXIV -B278-B298 : A-G Hh/Ss Bh/O2' pairing antiparallel trans XI -B279-B297 : G-C Ww/Ww pairing antiparallel cis XIX -B280-B296 : U-G Ws/Ww pairing antiparallel cis XXVIII -B281-B295 : G-U Ww/Ws pairing antiparallel cis XXVIII -B282-B294 : U-A Ww/Ww pairing antiparallel cis XX -B283-B293 : C-G Ww/Ww pairing antiparallel cis XIX -B284-B292 : U-G Ss/Ws O2'/Ww pairing parallel trans one_hbond -B285-B291 : U-C O2P/Bh adjacent_5p pairing -B292-B293 : G-G O2'/C8 adjacent_5p pairing -Residue conformations ------------------------------------------- -B267 : G C3p_endo anti -B268 : G C3p_endo anti -B269 : A C3p_endo anti -B270 : C C3p_endo anti -B271 : C C3p_endo anti -B272 : G C3p_endo anti -B273 : A C2p_exo anti -B274 : U C3p_endo anti -B275 : G C3p_endo anti -B276 : G C3p_endo anti -B277 : U C3p_endo anti -B278 : A C3p_endo anti -B279 : G C3p_endo anti -B280 : U C3p_endo anti -B281 : G C1p_endo anti -B282 : U C3p_endo anti -B283 : C C3p_endo anti -B284 : U C3p_endo anti -B285 : U C3p_exo anti -B291 : C C2p_endo anti -B292 : G C1p_endo anti -B293 : G C3p_endo anti -B294 : A C3p_endo anti -B295 : U C3p_endo anti -B296 : G C3p_endo anti -B297 : C C3p_endo anti -B298 : G C3p_endo anti -B299 : A C2p_exo anti -B300 : G C3p_endo anti -B301 : A C3p_endo anti -B302 : G C3p_endo anti -B303 : U C3p_endo anti -B304 : A C3p_endo anti -B305 : G C3p_endo anti -B306 : G C3p_endo anti -B307 : U C3p_endo anti -B308 : C C3p_endo anti -A1 : MET -A2 : PHE -A3 : THR -A4 : ILE -A5 : ASN -A6 : ALA -A7 : GLU -A8 : VAL -A9 : ARG -A10 : LYS -A11 : GLU -A12 : GLN -A13 : GLY -A14 : LYS -A15 : GLY -A16 : ALA -A17 : SER -A18 : ARG -A19 : ARG -A20 : LEU -A21 : ARG -A22 : ALA -A23 : ALA -A24 : ASN -A25 : LYS -A26 : PHE -A27 : PRO -A28 : ALA -A29 : ILE -A30 : ILE -A31 : TYR -A32 : GLY -A33 : GLY -A34 : LYS -A35 : GLU -A36 : ALA -A37 : PRO -A38 : LEU -A39 : ALA -A40 : ILE -A41 : GLU -A42 : LEU -A43 : ASP -A44 : HIS -A45 : ASP -A46 : LYS -A47 : VAL -A48 : MET -A49 : ASN -A50 : MET -A51 : GLN -A52 : ALA -A53 : LYS -A54 : ALA -A55 : GLU -A56 : PHE -A57 : TYR -A58 : SER -A59 : GLU -A60 : VAL -A61 : LEU -A62 : THR -A63 : ILE -A64 : VAL -A65 : VAL -A66 : ASP -A67 : GLY -A68 : LYS -A69 : GLU -A70 : ILE -A71 : LYS -A72 : VAL -A73 : LYS -A74 : ALA -A75 : GLN -A76 : ASP -A77 : VAL -A78 : GLN -A79 : ARG -A80 : HIS -A81 : PRO -A82 : TYR -A83 : LYS -A84 : PRO -A85 : LYS -A86 : LEU -A87 : GLN -A88 : HIS -A89 : ILE -A90 : ASP -A91 : PHE -A92 : VAL -A93 : ARG -A94 : ALA -Adjacent stackings ---------------------------------------------- -B268-B269 : adjacent_5p upward -B269-B270 : adjacent_5p upward -B270-B271 : adjacent_5p upward -B271-B272 : adjacent_5p upward -B273-B274 : adjacent_5p upward -B274-B275 : adjacent_5p upward -B275-B276 : adjacent_5p upward -B276-B277 : adjacent_5p upward -B277-B278 : adjacent_5p upward -B278-B279 : adjacent_5p upward -B279-B280 : adjacent_5p upward -B281-B282 : adjacent_5p upward -B282-B283 : adjacent_5p upward -B283-B284 : adjacent_5p upward -B293-B294 : adjacent_5p upward -B294-B295 : adjacent_5p upward -B296-B297 : adjacent_5p upward -B297-B298 : adjacent_5p upward -B299-B300 : adjacent_5p upward -B300-B301 : adjacent_5p upward -B301-B302 : adjacent_5p upward -B302-B303 : adjacent_5p upward -B303-B304 : adjacent_5p upward -B304-B305 : adjacent_5p upward -B305-B306 : adjacent_5p upward -B306-B307 : adjacent_5p upward -B307-B308 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -B273-B304 : outward -B278-B299 : outward -B281-B296 : outward -Number of stackings = 30 -Number of adjacent stackings = 27 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -A14-B280 : LYS-U pairing one_hbond -A17-B298 : SER-G pairing one_hbond -A31-B273 : TYR-A pairing one_hbond -A88-B275 : HIS-G pairing one_hbond -B268-B308 : G-C Ww/Ww pairing antiparallel cis XIX -B269-B307 : A-U Ww/Ww pairing antiparallel cis XX -B270-B306 : C-G Ww/Ww pairing antiparallel cis XIX -B271-B305 : C-G Ww/Ww pairing antiparallel cis XIX -B272-B303 : G-U Ww/O2P pairing -B272-B304 : G-A Ss/Hh O2'/Bh pairing antiparallel trans XI -B273-B303 : A-U Hh/Ws pairing antiparallel trans XXIV -B274-B302 : U-G Hw/Ww pairing antiparallel trans one_hbond 91 -B275-B301 : G-A Wh/Wh pairing antiparallel cis one_hbond -B276-B300 : G-G Ww/Bh pairing antiparallel trans 115 -B277-B299 : U-A Ws/Hh pairing antiparallel trans XXIV -B278-B298 : A-G Hh/Ss Bh/O2' pairing antiparallel trans XI -B279-B297 : G-C Ww/Ww pairing antiparallel cis XIX -B280-B296 : U-G Ws/Ww pairing antiparallel cis XXVIII -B281-B295 : G-U Ww/Ws pairing antiparallel cis XXVIII -B282-B294 : U-A Ww/Ww pairing antiparallel cis XX -B283-B293 : C-G Ww/Ww pairing antiparallel cis XIX -B284-B292 : U-G Bs/Ww pairing parallel trans one_hbond 87 -B285-B291 : U-C O2P/Bh adjacent_5p pairing -Residue conformations ------------------------------------------- -B267 : G C1p_exo anti -B268 : G C3p_endo anti -B269 : A C3p_endo anti -B270 : C C3p_endo anti -B271 : C C3p_endo anti -B272 : G C3p_endo anti -B273 : A C3p_endo anti -B274 : U C4p_exo anti -B275 : G C3p_endo anti -B276 : G C3p_endo anti -B277 : U C3p_endo anti -B278 : A C3p_endo anti -B279 : G C3p_endo anti -B280 : U C3p_endo anti -B281 : G C3p_endo anti -B282 : U C3p_endo anti -B283 : C C3p_endo anti -B284 : U C3p_endo anti -B285 : U C2p_endo anti -B291 : C C3p_exo anti -B292 : G C2p_endo anti -B293 : G C2p_exo anti -B294 : A C3p_endo anti -B295 : U C3p_endo anti -B296 : G C3p_endo anti -B297 : C C3p_endo anti -B298 : G C3p_endo anti -B299 : A C2p_exo anti -B300 : G C3p_endo anti -B301 : A C3p_endo anti -B302 : G C3p_endo anti -B303 : U C3p_endo anti -B304 : A C3p_endo anti -B305 : G C3p_endo anti -B306 : G C3p_endo anti -B307 : U C3p_endo anti -B308 : C C4p_exo anti -A1 : MET -A2 : PHE -A3 : THR -A4 : ILE -A5 : ASN -A6 : ALA -A7 : GLU -A8 : VAL -A9 : ARG -A10 : LYS -A11 : GLU -A12 : GLN -A13 : GLY -A14 : LYS -A15 : GLY -A16 : ALA -A17 : SER -A18 : ARG -A19 : ARG -A20 : LEU -A21 : ARG -A22 : ALA -A23 : ALA -A24 : ASN -A25 : LYS -A26 : PHE -A27 : PRO -A28 : ALA -A29 : ILE -A30 : ILE -A31 : TYR -A32 : GLY -A33 : GLY -A34 : LYS -A35 : GLU -A36 : ALA -A37 : PRO -A38 : LEU -A39 : ALA -A40 : ILE -A41 : GLU -A42 : LEU -A43 : ASP -A44 : HIS -A45 : ASP -A46 : LYS -A47 : VAL -A48 : MET -A49 : ASN -A50 : MET -A51 : GLN -A52 : ALA -A53 : LYS -A54 : ALA -A55 : GLU -A56 : PHE -A57 : TYR -A58 : SER -A59 : GLU -A60 : VAL -A61 : LEU -A62 : THR -A63 : ILE -A64 : VAL -A65 : VAL -A66 : ASP -A67 : GLY -A68 : LYS -A69 : GLU -A70 : ILE -A71 : LYS -A72 : VAL -A73 : LYS -A74 : ALA -A75 : GLN -A76 : ASP -A77 : VAL -A78 : GLN -A79 : ARG -A80 : HIS -A81 : PRO -A82 : TYR -A83 : LYS -A84 : PRO -A85 : LYS -A86 : LEU -A87 : GLN -A88 : HIS -A89 : ILE -A90 : ASP -A91 : PHE -A92 : VAL -A93 : ARG -A94 : ALA -Adjacent stackings ---------------------------------------------- -B268-B269 : adjacent_5p upward -B269-B270 : adjacent_5p upward -B270-B271 : adjacent_5p upward -B271-B272 : adjacent_5p upward -B273-B274 : adjacent_5p upward -B274-B275 : adjacent_5p upward -B275-B276 : adjacent_5p upward -B276-B277 : adjacent_5p upward -B277-B278 : adjacent_5p upward -B278-B279 : adjacent_5p upward -B279-B280 : adjacent_5p upward -B281-B282 : adjacent_5p upward -B282-B283 : adjacent_5p upward -B283-B284 : adjacent_5p upward -B293-B294 : adjacent_5p upward -B294-B295 : adjacent_5p upward -B296-B297 : adjacent_5p upward -B299-B300 : adjacent_5p upward -B300-B301 : adjacent_5p upward -B301-B302 : adjacent_5p upward -B302-B303 : adjacent_5p upward -B304-B305 : adjacent_5p upward -B305-B306 : adjacent_5p upward -B306-B307 : adjacent_5p upward -B307-B308 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -B273-B304 : outward -B278-B299 : outward -B281-B296 : outward -Number of stackings = 28 -Number of adjacent stackings = 25 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -A14-B279 : LYS-G pairing one_hbond -A31-B273 : TYR-A pairing one_hbond -B268-B308 : G-C Ww/Ww pairing antiparallel cis XIX -B269-B307 : A-U Ww/Ww pairing antiparallel cis XX -B270-B306 : C-G Ww/Ww pairing antiparallel cis XIX -B271-B305 : C-G Ww/Ww pairing antiparallel cis XIX -B272-B303 : G-U Ww/O2P pairing -B272-B304 : G-A Ss/Hh O2'/Bh pairing antiparallel trans XI -B273-B303 : A-U Hh/Ws pairing antiparallel trans XXIV -B274-B302 : U-G Hw/Ww pairing antiparallel trans one_hbond 91 -B276-B300 : G-G Ww/Bh pairing antiparallel trans one_hbond -B277-B299 : U-A Ws/Hh pairing antiparallel trans XXIV -B278-B298 : A-G Hh/Ss O2P/Bs Bh/O2' pairing antiparallel trans XI -B279-B297 : G-C Ww/Ww pairing antiparallel cis XIX -B280-B296 : U-G Ws/Ww pairing antiparallel cis XXVIII -B281-B295 : G-U Ww/Ws pairing antiparallel cis XXVIII -B282-B294 : U-A Ww/Ww pairing antiparallel cis XX -B283-B293 : C-G Ww/Ww pairing antiparallel cis XIX -B284-B292 : U-G Ss/Ws O2'/Ww pairing parallel trans one_hbond -B285-B291 : U-C O2P/Bh adjacent_5p pairing -B292-B293 : G-G O2'/C8 adjacent_5p pairing -Residue conformations ------------------------------------------- -B267 : G C4p_endo anti -B268 : G C3p_endo anti -B269 : A C3p_endo anti -B270 : C C3p_endo anti -B271 : C C3p_endo anti -B272 : G C3p_endo anti -B273 : A C3p_endo anti -B274 : U C4p_exo anti -B275 : G C3p_endo anti -B276 : G C3p_endo anti -B277 : U C3p_endo anti -B278 : A C3p_endo anti -B279 : G C3p_endo anti -B280 : U C3p_endo anti -B281 : G C2p_exo anti -B282 : U C3p_endo anti -B283 : C C3p_endo anti -B284 : U C3p_endo anti -B285 : U C2p_endo anti -B291 : C C2p_endo anti -B292 : G C1p_endo anti -B293 : G C3p_endo anti -B294 : A C3p_endo anti -B295 : U C3p_endo anti -B296 : G C3p_endo anti -B297 : C C3p_endo anti -B298 : G C3p_endo anti -B299 : A C2p_exo anti -B300 : G C1p_endo anti -B301 : A C3p_endo anti -B302 : G C3p_endo anti -B303 : U C3p_endo anti -B304 : A C3p_endo anti -B305 : G C3p_endo anti -B306 : G C3p_endo anti -B307 : U C3p_endo anti -B308 : C C3p_endo anti -A1 : MET -A2 : PHE -A3 : THR -A4 : ILE -A5 : ASN -A6 : ALA -A7 : GLU -A8 : VAL -A9 : ARG -A10 : LYS -A11 : GLU -A12 : GLN -A13 : GLY -A14 : LYS -A15 : GLY -A16 : ALA -A17 : SER -A18 : ARG -A19 : ARG -A20 : LEU -A21 : ARG -A22 : ALA -A23 : ALA -A24 : ASN -A25 : LYS -A26 : PHE -A27 : PRO -A28 : ALA -A29 : ILE -A30 : ILE -A31 : TYR -A32 : GLY -A33 : GLY -A34 : LYS -A35 : GLU -A36 : ALA -A37 : PRO -A38 : LEU -A39 : ALA -A40 : ILE -A41 : GLU -A42 : LEU -A43 : ASP -A44 : HIS -A45 : ASP -A46 : LYS -A47 : VAL -A48 : MET -A49 : ASN -A50 : MET -A51 : GLN -A52 : ALA -A53 : LYS -A54 : ALA -A55 : GLU -A56 : PHE -A57 : TYR -A58 : SER -A59 : GLU -A60 : VAL -A61 : LEU -A62 : THR -A63 : ILE -A64 : VAL -A65 : VAL -A66 : ASP -A67 : GLY -A68 : LYS -A69 : GLU -A70 : ILE -A71 : LYS -A72 : VAL -A73 : LYS -A74 : ALA -A75 : GLN -A76 : ASP -A77 : VAL -A78 : GLN -A79 : ARG -A80 : HIS -A81 : PRO -A82 : TYR -A83 : LYS -A84 : PRO -A85 : LYS -A86 : LEU -A87 : GLN -A88 : HIS -A89 : ILE -A90 : ASP -A91 : PHE -A92 : VAL -A93 : ARG -A94 : ALA -Adjacent stackings ---------------------------------------------- -B268-B269 : adjacent_5p upward -B269-B270 : adjacent_5p upward -B270-B271 : adjacent_5p upward -B271-B272 : adjacent_5p upward -B273-B274 : adjacent_5p upward -B274-B275 : adjacent_5p upward -B275-B276 : adjacent_5p upward -B276-B277 : adjacent_5p upward -B277-B278 : adjacent_5p upward -B278-B279 : adjacent_5p upward -B279-B280 : adjacent_5p upward -B281-B282 : adjacent_5p upward -B282-B283 : adjacent_5p upward -B283-B284 : adjacent_5p upward -B293-B294 : adjacent_5p upward -B294-B295 : adjacent_5p upward -B295-B296 : adjacent_5p upward -B296-B297 : adjacent_5p upward -B297-B298 : adjacent_5p upward -B299-B300 : adjacent_5p upward -B300-B301 : adjacent_5p upward -B301-B302 : adjacent_5p upward -B302-B303 : adjacent_5p upward -B303-B304 : adjacent_5p upward -B304-B305 : adjacent_5p upward -B305-B306 : adjacent_5p upward -B306-B307 : adjacent_5p upward -B307-B308 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -B273-B304 : outward -B278-B299 : outward -B281-B296 : outward -Number of stackings = 31 -Number of adjacent stackings = 28 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -A31-B273 : TYR-A pairing one_hbond -A31-B274 : TYR-U pairing one_hbond -B268-B308 : G-C Ww/Ww pairing antiparallel cis XIX -B269-B307 : A-U Ww/Ww pairing antiparallel cis XX -B270-B306 : C-G Ww/Ww pairing antiparallel cis XIX -B271-B305 : C-G Ww/Ww pairing antiparallel cis XIX -B272-B303 : G-U Ww/O2P pairing -B272-B304 : G-A Ss/Hh O2'/Bh pairing antiparallel trans XI -B273-B303 : A-U Hh/Ws pairing antiparallel trans XXIV -B274-B302 : U-G Hw/Ww pairing antiparallel trans one_hbond 91 -B275-B301 : G-A Wh/Wh pairing antiparallel cis one_hbond -B276-B300 : G-G Ww/Hw pairing antiparallel trans one_hbond -B277-B299 : U-A Ws/Hh pairing antiparallel trans XXIV -B278-B298 : A-G Hh/Ss Bh/O2' pairing antiparallel trans XI -B279-B297 : G-C Ww/Ww pairing antiparallel cis XIX -B280-B296 : U-G Ws/Ww pairing antiparallel cis XXVIII -B281-B295 : G-U Ww/Ws pairing antiparallel cis XXVIII -B282-B294 : U-A Ww/Ww pairing antiparallel cis XX -B283-B293 : C-G Ww/Ww pairing antiparallel cis XIX -B284-B292 : U-G Ws/Ws pairing parallel trans one_hbond 87 -B285-B291 : U-C O2P/Bh adjacent_5p pairing -B285-B292 : U-G O2'/Hh pairing -Residue conformations ------------------------------------------- -B267 : G C3p_endo anti -B268 : G O4p_endo anti -B269 : A C3p_endo anti -B270 : C C3p_endo anti -B271 : C C3p_endo anti -B272 : G C3p_endo anti -B273 : A C2p_exo anti -B274 : U C3p_endo anti -B275 : G C3p_endo anti -B276 : G C3p_endo anti -B277 : U C3p_endo anti -B278 : A C3p_endo anti -B279 : G C3p_endo anti -B280 : U C3p_endo anti -B281 : G C4p_exo anti -B282 : U C3p_endo anti -B283 : C C3p_endo anti -B284 : U C3p_endo anti -B285 : U C3p_endo anti -B291 : C C2p_exo anti -B292 : G C3p_exo anti -B293 : G C2p_exo anti -B294 : A C3p_endo anti -B295 : U C3p_endo anti -B296 : G C3p_endo anti -B297 : C C3p_endo anti -B298 : G C3p_endo anti -B299 : A C2p_exo anti -B300 : G C3p_endo anti -B301 : A C3p_endo anti -B302 : G C3p_endo anti -B303 : U C3p_endo anti -B304 : A C3p_endo anti -B305 : G C3p_endo anti -B306 : G C3p_endo anti -B307 : U C3p_endo anti -B308 : C C4p_exo anti -A1 : MET -A2 : PHE -A3 : THR -A4 : ILE -A5 : ASN -A6 : ALA -A7 : GLU -A8 : VAL -A9 : ARG -A10 : LYS -A11 : GLU -A12 : GLN -A13 : GLY -A14 : LYS -A15 : GLY -A16 : ALA -A17 : SER -A18 : ARG -A19 : ARG -A20 : LEU -A21 : ARG -A22 : ALA -A23 : ALA -A24 : ASN -A25 : LYS -A26 : PHE -A27 : PRO -A28 : ALA -A29 : ILE -A30 : ILE -A31 : TYR -A32 : GLY -A33 : GLY -A34 : LYS -A35 : GLU -A36 : ALA -A37 : PRO -A38 : LEU -A39 : ALA -A40 : ILE -A41 : GLU -A42 : LEU -A43 : ASP -A44 : HIS -A45 : ASP -A46 : LYS -A47 : VAL -A48 : MET -A49 : ASN -A50 : MET -A51 : GLN -A52 : ALA -A53 : LYS -A54 : ALA -A55 : GLU -A56 : PHE -A57 : TYR -A58 : SER -A59 : GLU -A60 : VAL -A61 : LEU -A62 : THR -A63 : ILE -A64 : VAL -A65 : VAL -A66 : ASP -A67 : GLY -A68 : LYS -A69 : GLU -A70 : ILE -A71 : LYS -A72 : VAL -A73 : LYS -A74 : ALA -A75 : GLN -A76 : ASP -A77 : VAL -A78 : GLN -A79 : ARG -A80 : HIS -A81 : PRO -A82 : TYR -A83 : LYS -A84 : PRO -A85 : LYS -A86 : LEU -A87 : GLN -A88 : HIS -A89 : ILE -A90 : ASP -A91 : PHE -A92 : VAL -A93 : ARG -A94 : ALA -Adjacent stackings ---------------------------------------------- -B268-B269 : adjacent_5p upward -B269-B270 : adjacent_5p upward -B270-B271 : adjacent_5p upward -B271-B272 : adjacent_5p upward -B273-B274 : adjacent_5p upward -B274-B275 : adjacent_5p upward -B275-B276 : adjacent_5p upward -B276-B277 : adjacent_5p upward -B277-B278 : adjacent_5p upward -B278-B279 : adjacent_5p upward -B279-B280 : adjacent_5p upward -B280-B281 : adjacent_5p upward -B281-B282 : adjacent_5p upward -B282-B283 : adjacent_5p upward -B283-B284 : adjacent_5p upward -B293-B294 : adjacent_5p upward -B294-B295 : adjacent_5p upward -B295-B296 : adjacent_5p upward -B296-B297 : adjacent_5p upward -B297-B298 : adjacent_5p upward -B299-B300 : adjacent_5p upward -B300-B301 : adjacent_5p upward -B301-B302 : adjacent_5p upward -B302-B303 : adjacent_5p upward -B303-B304 : adjacent_5p upward -B304-B305 : adjacent_5p upward -B305-B306 : adjacent_5p upward -B306-B307 : adjacent_5p upward -B307-B308 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -B273-B304 : outward -B278-B299 : outward -B281-B296 : outward -Number of stackings = 32 -Number of adjacent stackings = 29 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -A14-B279 : LYS-G pairing one_hbond -A31-B273 : TYR-A pairing one_hbond -B268-B308 : G-C Ww/Ww pairing antiparallel cis XIX -B269-B307 : A-U Ww/Ww pairing antiparallel cis XX -B270-B306 : C-G Ww/Ww pairing antiparallel cis XIX -B271-B305 : C-G Ww/Ww pairing antiparallel cis XIX -B272-B304 : G-A Ss/Hh O2'/Bh pairing antiparallel trans XI -B273-B303 : A-U Hh/Ws pairing antiparallel trans XXIV -B274-B302 : U-G Hw/Ww pairing antiparallel trans one_hbond 91 -B276-B300 : G-G Ww/Bh pairing antiparallel trans 115 -B277-B298 : U-G O2P/Ww pairing -B277-B299 : U-A Ws/Hh pairing antiparallel trans XXIV -B278-B298 : A-G Hh/Ss Bh/O2' pairing antiparallel trans XI -B279-B297 : G-C Ww/Ww pairing antiparallel cis XIX -B280-B296 : U-G Ws/Ww pairing antiparallel cis XXVIII -B281-B295 : G-U Ww/Ws pairing antiparallel cis XXVIII -B282-B294 : U-A Ww/Ww pairing antiparallel cis XX -B283-B293 : C-G Ww/Ww pairing antiparallel cis XIX -B292-B293 : G-G O2'/C8 adjacent_5p pairing -Residue conformations ------------------------------------------- -B267 : G C1p_exo anti -B268 : G C2p_exo anti -B269 : A C3p_endo anti -B270 : C C3p_endo anti -B271 : C C3p_endo anti -B272 : G C3p_endo anti -B273 : A C2p_exo anti -B274 : U C2p_exo anti -B275 : G C3p_endo anti -B276 : G C3p_endo anti -B277 : U C3p_endo anti -B278 : A C3p_endo anti -B279 : G C3p_endo anti -B280 : U C3p_endo anti -B281 : G C2p_exo anti -B282 : U C3p_endo anti -B283 : C C3p_endo anti -B284 : U C2p_exo anti -B285 : U C3p_exo anti -B291 : C C2p_exo anti -B292 : G C2p_endo anti -B293 : G C3p_endo anti -B294 : A C3p_endo anti -B295 : U C3p_endo anti -B296 : G C2p_exo anti -B297 : C C3p_endo anti -B298 : G C3p_endo anti -B299 : A C2p_exo anti -B300 : G C3p_endo anti -B301 : A C2p_exo anti -B302 : G C3p_endo anti -B303 : U C3p_endo anti -B304 : A C3p_endo anti -B305 : G C3p_endo anti -B306 : G C3p_endo anti -B307 : U C3p_endo anti -B308 : C C3p_endo anti -A1 : MET -A2 : PHE -A3 : THR -A4 : ILE -A5 : ASN -A6 : ALA -A7 : GLU -A8 : VAL -A9 : ARG -A10 : LYS -A11 : GLU -A12 : GLN -A13 : GLY -A14 : LYS -A15 : GLY -A16 : ALA -A17 : SER -A18 : ARG -A19 : ARG -A20 : LEU -A21 : ARG -A22 : ALA -A23 : ALA -A24 : ASN -A25 : LYS -A26 : PHE -A27 : PRO -A28 : ALA -A29 : ILE -A30 : ILE -A31 : TYR -A32 : GLY -A33 : GLY -A34 : LYS -A35 : GLU -A36 : ALA -A37 : PRO -A38 : LEU -A39 : ALA -A40 : ILE -A41 : GLU -A42 : LEU -A43 : ASP -A44 : HIS -A45 : ASP -A46 : LYS -A47 : VAL -A48 : MET -A49 : ASN -A50 : MET -A51 : GLN -A52 : ALA -A53 : LYS -A54 : ALA -A55 : GLU -A56 : PHE -A57 : TYR -A58 : SER -A59 : GLU -A60 : VAL -A61 : LEU -A62 : THR -A63 : ILE -A64 : VAL -A65 : VAL -A66 : ASP -A67 : GLY -A68 : LYS -A69 : GLU -A70 : ILE -A71 : LYS -A72 : VAL -A73 : LYS -A74 : ALA -A75 : GLN -A76 : ASP -A77 : VAL -A78 : GLN -A79 : ARG -A80 : HIS -A81 : PRO -A82 : TYR -A83 : LYS -A84 : PRO -A85 : LYS -A86 : LEU -A87 : GLN -A88 : HIS -A89 : ILE -A90 : ASP -A91 : PHE -A92 : VAL -A93 : ARG -A94 : ALA -Adjacent stackings ---------------------------------------------- -B268-B269 : adjacent_5p upward -B269-B270 : adjacent_5p upward -B270-B271 : adjacent_5p upward -B271-B272 : adjacent_5p upward -B273-B274 : adjacent_5p upward -B274-B275 : adjacent_5p upward -B275-B276 : adjacent_5p upward -B276-B277 : adjacent_5p upward -B277-B278 : adjacent_5p upward -B278-B279 : adjacent_5p upward -B279-B280 : adjacent_5p upward -B281-B282 : adjacent_5p upward -B282-B283 : adjacent_5p upward -B293-B294 : adjacent_5p upward -B294-B295 : adjacent_5p upward -B295-B296 : adjacent_5p upward -B296-B297 : adjacent_5p upward -B299-B300 : adjacent_5p upward -B300-B301 : adjacent_5p upward -B301-B302 : adjacent_5p upward -B302-B303 : adjacent_5p upward -B303-B304 : adjacent_5p upward -B304-B305 : adjacent_5p upward -B305-B306 : adjacent_5p upward -B306-B307 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -B273-B304 : outward -B278-B299 : outward -B281-B296 : outward -Number of stackings = 28 -Number of adjacent stackings = 25 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -A17-B298 : SER-G pairing one_hbond -A31-B273 : TYR-A pairing one_hbond -B268-B308 : G-C Ww/Ww pairing antiparallel cis XIX -B269-B307 : A-U Ww/Ww pairing antiparallel cis XX -B270-B306 : C-G Ww/Ww pairing antiparallel cis XIX -B271-B305 : C-G Ww/Ww pairing antiparallel cis XIX -B272-B304 : G-A Ss/Hh O2'/Bh pairing antiparallel trans XI -B273-B303 : A-U Hh/Ws pairing antiparallel trans XXIV -B274-B302 : U-G Hw/Ww pairing antiparallel trans one_hbond 91 -B276-B300 : G-G Ww/Bh pairing antiparallel trans 115 -B277-B298 : U-G O2P/Ww pairing -B277-B299 : U-A Ww/Hh pairing antiparallel trans -B278-B298 : A-G Hh/Ss Bh/O2' pairing antiparallel trans XI -B279-B297 : G-C Ww/Ww pairing antiparallel cis XIX -B280-B296 : U-G Ws/Ww pairing antiparallel cis XXVIII -B281-B295 : G-U Ww/Ws pairing antiparallel cis XXVIII -B282-B294 : U-A Ww/Ww pairing antiparallel cis XX -B283-B285 : C-U Hh/O2P pairing -B283-B293 : C-G Ww/Ww pairing antiparallel cis XIX -B284-B291 : U-C O2'/Bh pairing -Residue conformations ------------------------------------------- -B267 : G C2p_endo anti -B268 : G C3p_endo anti -B269 : A C3p_endo anti -B270 : C C3p_endo anti -B271 : C C3p_endo anti -B272 : G C3p_endo anti -B273 : A C2p_exo anti -B274 : U C4p_exo anti -B275 : G C3p_endo anti -B276 : G C3p_endo anti -B277 : U C3p_endo anti -B278 : A C3p_endo anti -B279 : G C3p_endo anti -B280 : U C3p_endo anti -B281 : G C3p_endo anti -B282 : U C3p_endo anti -B283 : C C3p_endo anti -B284 : U C3p_endo anti -B285 : U C1p_endo syn -B291 : C C4p_endo anti -B292 : G O4p_endo anti -B293 : G C3p_endo anti -B294 : A C3p_endo anti -B295 : U C3p_endo anti -B296 : G C3p_endo anti -B297 : C C3p_endo anti -B298 : G C3p_endo anti -B299 : A C2p_exo anti -B300 : G C3p_endo anti -B301 : A C3p_endo anti -B302 : G C3p_endo anti -B303 : U C3p_endo anti -B304 : A C3p_endo anti -B305 : G C2p_exo anti -B306 : G C3p_endo anti -B307 : U C3p_endo anti -B308 : C C3p_endo anti -A1 : MET -A2 : PHE -A3 : THR -A4 : ILE -A5 : ASN -A6 : ALA -A7 : GLU -A8 : VAL -A9 : ARG -A10 : LYS -A11 : GLU -A12 : GLN -A13 : GLY -A14 : LYS -A15 : GLY -A16 : ALA -A17 : SER -A18 : ARG -A19 : ARG -A20 : LEU -A21 : ARG -A22 : ALA -A23 : ALA -A24 : ASN -A25 : LYS -A26 : PHE -A27 : PRO -A28 : ALA -A29 : ILE -A30 : ILE -A31 : TYR -A32 : GLY -A33 : GLY -A34 : LYS -A35 : GLU -A36 : ALA -A37 : PRO -A38 : LEU -A39 : ALA -A40 : ILE -A41 : GLU -A42 : LEU -A43 : ASP -A44 : HIS -A45 : ASP -A46 : LYS -A47 : VAL -A48 : MET -A49 : ASN -A50 : MET -A51 : GLN -A52 : ALA -A53 : LYS -A54 : ALA -A55 : GLU -A56 : PHE -A57 : TYR -A58 : SER -A59 : GLU -A60 : VAL -A61 : LEU -A62 : THR -A63 : ILE -A64 : VAL -A65 : VAL -A66 : ASP -A67 : GLY -A68 : LYS -A69 : GLU -A70 : ILE -A71 : LYS -A72 : VAL -A73 : LYS -A74 : ALA -A75 : GLN -A76 : ASP -A77 : VAL -A78 : GLN -A79 : ARG -A80 : HIS -A81 : PRO -A82 : TYR -A83 : LYS -A84 : PRO -A85 : LYS -A86 : LEU -A87 : GLN -A88 : HIS -A89 : ILE -A90 : ASP -A91 : PHE -A92 : VAL -A93 : ARG -A94 : ALA -Adjacent stackings ---------------------------------------------- -B268-B269 : adjacent_5p upward -B269-B270 : adjacent_5p upward -B270-B271 : adjacent_5p upward -B271-B272 : adjacent_5p upward -B273-B274 : adjacent_5p upward -B274-B275 : adjacent_5p upward -B275-B276 : adjacent_5p upward -B276-B277 : adjacent_5p upward -B277-B278 : adjacent_5p upward -B278-B279 : adjacent_5p upward -B279-B280 : adjacent_5p upward -B281-B282 : adjacent_5p upward -B282-B283 : adjacent_5p upward -B283-B284 : adjacent_5p upward -B293-B294 : adjacent_5p upward -B294-B295 : adjacent_5p upward -B295-B296 : adjacent_5p upward -B296-B297 : adjacent_5p upward -B297-B298 : adjacent_5p upward -B299-B300 : adjacent_5p upward -B300-B301 : adjacent_5p upward -B301-B302 : adjacent_5p upward -B302-B303 : adjacent_5p upward -B303-B304 : adjacent_5p upward -B304-B305 : adjacent_5p upward -B305-B306 : adjacent_5p upward -B306-B307 : adjacent_5p upward -B307-B308 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -B273-B304 : outward -B278-B299 : outward -B281-B296 : outward -Number of stackings = 31 -Number of adjacent stackings = 28 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -A31-B273 : TYR-A pairing one_hbond -A31-B274 : TYR-U pairing one_hbond -B267-B268 : G-G Bs/O2' Ss/O2' adjacent_5p pairing -B268-B308 : G-C Ww/Ww pairing antiparallel cis XIX -B269-B307 : A-U Ww/Ww pairing antiparallel cis XX -B270-B306 : C-G Ww/Ww pairing antiparallel cis XIX -B271-B305 : C-G Ww/Ww pairing antiparallel cis XIX -B272-B304 : G-A Ss/Hh O2'/Bh pairing antiparallel trans XI -B273-B303 : A-U Hh/Ws pairing antiparallel trans XXIV -B274-B302 : U-G Hw/Ww pairing antiparallel trans one_hbond 91 -B276-B300 : G-G Ww/Bh pairing antiparallel trans 115 -B277-B299 : U-A Ws/Hh pairing antiparallel trans XXIV -B278-B298 : A-G Hh/Ss Bh/O2' pairing antiparallel trans XI -B279-B297 : G-C Ww/Ww pairing antiparallel cis XIX -B280-B296 : U-G Ws/Ww pairing antiparallel cis XXVIII -B281-B295 : G-U Ww/Ws pairing antiparallel cis XXVIII -B282-B294 : U-A Ww/Ww pairing antiparallel cis XX -B283-B293 : C-G Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -B267 : G C2p_exo anti -B268 : G C3p_endo anti -B269 : A C2p_exo anti -B270 : C C3p_endo anti -B271 : C C3p_endo anti -B272 : G C3p_endo anti -B273 : A C2p_exo anti -B274 : U C4p_exo anti -B275 : G C3p_endo anti -B276 : G C3p_endo anti -B277 : U C3p_endo anti -B278 : A C3p_endo anti -B279 : G C3p_endo anti -B280 : U C3p_endo anti -B281 : G C2p_exo anti -B282 : U C3p_endo anti -B283 : C C3p_endo anti -B284 : U C3p_endo anti -B285 : U C2p_endo anti -B291 : C C3p_exo anti -B292 : G C2p_exo anti -B293 : G C2p_exo anti -B294 : A C3p_endo anti -B295 : U C3p_endo anti -B296 : G C2p_exo anti -B297 : C C3p_endo anti -B298 : G C3p_endo anti -B299 : A C1p_endo anti -B300 : G C3p_endo anti -B301 : A C3p_endo anti -B302 : G C3p_endo anti -B303 : U C3p_endo anti -B304 : A C3p_endo anti -B305 : G C2p_exo anti -B306 : G C3p_endo anti -B307 : U C3p_endo anti -B308 : C C3p_endo anti -A1 : MET -A2 : PHE -A3 : THR -A4 : ILE -A5 : ASN -A6 : ALA -A7 : GLU -A8 : VAL -A9 : ARG -A10 : LYS -A11 : GLU -A12 : GLN -A13 : GLY -A14 : LYS -A15 : GLY -A16 : ALA -A17 : SER -A18 : ARG -A19 : ARG -A20 : LEU -A21 : ARG -A22 : ALA -A23 : ALA -A24 : ASN -A25 : LYS -A26 : PHE -A27 : PRO -A28 : ALA -A29 : ILE -A30 : ILE -A31 : TYR -A32 : GLY -A33 : GLY -A34 : LYS -A35 : GLU -A36 : ALA -A37 : PRO -A38 : LEU -A39 : ALA -A40 : ILE -A41 : GLU -A42 : LEU -A43 : ASP -A44 : HIS -A45 : ASP -A46 : LYS -A47 : VAL -A48 : MET -A49 : ASN -A50 : MET -A51 : GLN -A52 : ALA -A53 : LYS -A54 : ALA -A55 : GLU -A56 : PHE -A57 : TYR -A58 : SER -A59 : GLU -A60 : VAL -A61 : LEU -A62 : THR -A63 : ILE -A64 : VAL -A65 : VAL -A66 : ASP -A67 : GLY -A68 : LYS -A69 : GLU -A70 : ILE -A71 : LYS -A72 : VAL -A73 : LYS -A74 : ALA -A75 : GLN -A76 : ASP -A77 : VAL -A78 : GLN -A79 : ARG -A80 : HIS -A81 : PRO -A82 : TYR -A83 : LYS -A84 : PRO -A85 : LYS -A86 : LEU -A87 : GLN -A88 : HIS -A89 : ILE -A90 : ASP -A91 : PHE -A92 : VAL -A93 : ARG -A94 : ALA -Adjacent stackings ---------------------------------------------- -B268-B269 : adjacent_5p upward -B269-B270 : adjacent_5p upward -B270-B271 : adjacent_5p upward -B271-B272 : adjacent_5p upward -B273-B274 : adjacent_5p upward -B274-B275 : adjacent_5p upward -B275-B276 : adjacent_5p upward -B276-B277 : adjacent_5p upward -B277-B278 : adjacent_5p upward -B278-B279 : adjacent_5p upward -B279-B280 : adjacent_5p upward -B281-B282 : adjacent_5p upward -B282-B283 : adjacent_5p upward -B283-B284 : adjacent_5p upward -B291-B292 : adjacent_5p downward -B293-B294 : adjacent_5p upward -B294-B295 : adjacent_5p upward -B296-B297 : adjacent_5p upward -B299-B300 : adjacent_5p upward -B300-B301 : adjacent_5p upward -B301-B302 : adjacent_5p upward -B302-B303 : adjacent_5p upward -B303-B304 : adjacent_5p upward -B304-B305 : adjacent_5p upward -B305-B306 : adjacent_5p upward -B306-B307 : adjacent_5p upward -B307-B308 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -B273-B304 : outward -B278-B299 : outward -B281-B296 : outward -Number of stackings = 30 -Number of adjacent stackings = 27 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -A14-B280 : LYS-U pairing one_hbond -B268-B308 : G-C Ww/Ww pairing antiparallel cis XIX -B269-B307 : A-U Ww/Ww pairing antiparallel cis XX -B270-B306 : C-G Ww/Ww pairing antiparallel cis XIX -B271-B305 : C-G Ww/Ww pairing antiparallel cis XIX -B272-B304 : G-A Ss/Hh O2'/Bh pairing antiparallel trans XI -B273-B303 : A-U Hh/Ws pairing antiparallel trans XXIV -B274-B302 : U-G Hw/Ww pairing antiparallel trans one_hbond 91 -B276-B300 : G-G Ww/Bh pairing antiparallel trans 115 -B277-B299 : U-A Ws/Hh pairing antiparallel trans XXIV -B278-B298 : A-G Hh/Ss Bh/O2' pairing antiparallel trans XI -B279-B297 : G-C Ww/Ww pairing antiparallel cis XIX -B280-B296 : U-G Ws/Ww pairing antiparallel cis XXVIII -B281-B295 : G-U Ww/Ws pairing antiparallel cis XXVIII -B282-B294 : U-A Ww/Ww pairing antiparallel cis XX -B283-B293 : C-G Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -B267 : G C2p_exo anti -B268 : G C3p_endo anti -B269 : A C3p_endo anti -B270 : C C3p_endo anti -B271 : C C3p_endo anti -B272 : G C3p_endo anti -B273 : A C2p_exo anti -B274 : U C4p_exo anti -B275 : G C3p_endo anti -B276 : G C3p_endo anti -B277 : U C3p_endo anti -B278 : A C3p_endo anti -B279 : G C3p_endo anti -B280 : U C3p_endo anti -B281 : G C2p_exo anti -B282 : U C3p_endo anti -B283 : C C3p_endo anti -B284 : U C3p_endo anti -B285 : U C1p_endo anti -B291 : C C3p_exo anti -B292 : G C2p_endo anti -B293 : G C2p_exo anti -B294 : A C3p_endo anti -B295 : U C3p_endo anti -B296 : G C2p_exo anti -B297 : C C3p_endo anti -B298 : G C3p_endo anti -B299 : A C2p_exo anti -B300 : G C3p_endo anti -B301 : A C3p_endo anti -B302 : G C3p_endo anti -B303 : U C3p_endo anti -B304 : A C3p_endo anti -B305 : G C3p_endo anti -B306 : G C3p_endo anti -B307 : U C3p_endo anti -B308 : C C3p_endo anti -A1 : MET -A2 : PHE -A3 : THR -A4 : ILE -A5 : ASN -A6 : ALA -A7 : GLU -A8 : VAL -A9 : ARG -A10 : LYS -A11 : GLU -A12 : GLN -A13 : GLY -A14 : LYS -A15 : GLY -A16 : ALA -A17 : SER -A18 : ARG -A19 : ARG -A20 : LEU -A21 : ARG -A22 : ALA -A23 : ALA -A24 : ASN -A25 : LYS -A26 : PHE -A27 : PRO -A28 : ALA -A29 : ILE -A30 : ILE -A31 : TYR -A32 : GLY -A33 : GLY -A34 : LYS -A35 : GLU -A36 : ALA -A37 : PRO -A38 : LEU -A39 : ALA -A40 : ILE -A41 : GLU -A42 : LEU -A43 : ASP -A44 : HIS -A45 : ASP -A46 : LYS -A47 : VAL -A48 : MET -A49 : ASN -A50 : MET -A51 : GLN -A52 : ALA -A53 : LYS -A54 : ALA -A55 : GLU -A56 : PHE -A57 : TYR -A58 : SER -A59 : GLU -A60 : VAL -A61 : LEU -A62 : THR -A63 : ILE -A64 : VAL -A65 : VAL -A66 : ASP -A67 : GLY -A68 : LYS -A69 : GLU -A70 : ILE -A71 : LYS -A72 : VAL -A73 : LYS -A74 : ALA -A75 : GLN -A76 : ASP -A77 : VAL -A78 : GLN -A79 : ARG -A80 : HIS -A81 : PRO -A82 : TYR -A83 : LYS -A84 : PRO -A85 : LYS -A86 : LEU -A87 : GLN -A88 : HIS -A89 : ILE -A90 : ASP -A91 : PHE -A92 : VAL -A93 : ARG -A94 : ALA -Adjacent stackings ---------------------------------------------- -B268-B269 : adjacent_5p upward -B269-B270 : adjacent_5p upward -B270-B271 : adjacent_5p upward -B271-B272 : adjacent_5p upward -B273-B274 : adjacent_5p upward -B274-B275 : adjacent_5p upward -B275-B276 : adjacent_5p upward -B276-B277 : adjacent_5p upward -B277-B278 : adjacent_5p upward -B278-B279 : adjacent_5p upward -B279-B280 : adjacent_5p upward -B281-B282 : adjacent_5p upward -B282-B283 : adjacent_5p upward -B283-B284 : adjacent_5p upward -B293-B294 : adjacent_5p upward -B294-B295 : adjacent_5p upward -B295-B296 : adjacent_5p upward -B296-B297 : adjacent_5p upward -B299-B300 : adjacent_5p upward -B300-B301 : adjacent_5p upward -B301-B302 : adjacent_5p upward -B302-B303 : adjacent_5p upward -B303-B304 : adjacent_5p upward -B304-B305 : adjacent_5p upward -B305-B306 : adjacent_5p upward -B306-B307 : adjacent_5p upward -B307-B308 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -B273-B304 : outward -B278-B299 : outward -B281-B296 : outward -Number of stackings = 30 -Number of adjacent stackings = 27 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -A14-B279 : LYS-G pairing one_hbond -A37-B274 : PRO-U pairing one_hbond -A88-B275 : HIS-G pairing one_hbond -B268-B308 : G-C Ww/Ww pairing antiparallel cis XIX -B269-B307 : A-U Ww/Ww pairing antiparallel cis XX -B270-B306 : C-G Ww/Ww pairing antiparallel cis XIX -B271-B305 : C-G Ww/Ww pairing antiparallel cis XIX -B272-B303 : G-U Ww/O2P pairing -B272-B304 : G-A Ss/Hh O2'/Bh pairing antiparallel trans XI -B273-B303 : A-U Hh/Ws pairing antiparallel trans XXIV -B274-B302 : U-G Hw/Ww pairing antiparallel trans one_hbond 91 -B275-B301 : G-A Wh/Wh pairing antiparallel cis one_hbond -B276-B300 : G-G Ww/Bh pairing antiparallel trans 115 -B277-B299 : U-A Ws/Hh pairing antiparallel trans XXIV -B278-B298 : A-G Hh/Ss O2P/Bs Bh/O2' pairing antiparallel trans XI -B279-B297 : G-C Ww/Ww pairing antiparallel cis XIX -B280-B296 : U-G Ws/Ww pairing antiparallel cis XXVIII -B281-B295 : G-U Ww/Ws pairing antiparallel cis XXVIII -B282-B294 : U-A Ww/Ww pairing antiparallel cis XX -B283-B293 : C-G Ww/Ww pairing antiparallel cis XIX -B292-B293 : G-G O2'/C8 adjacent_5p pairing -Residue conformations ------------------------------------------- -B267 : G C2p_endo syn -B268 : G C2p_exo anti -B269 : A C3p_endo anti -B270 : C C3p_endo anti -B271 : C C3p_endo anti -B272 : G C3p_endo anti -B273 : A C3p_endo anti -B274 : U C3p_endo anti -B275 : G C3p_endo anti -B276 : G C3p_endo anti -B277 : U C3p_endo anti -B278 : A C3p_endo anti -B279 : G C3p_endo anti -B280 : U C3p_endo anti -B281 : G C2p_exo anti -B282 : U C3p_endo anti -B283 : C C3p_endo anti -B284 : U C3p_endo anti -B285 : U C3p_exo anti -B291 : C C2p_exo anti -B292 : G C3p_exo anti -B293 : G C3p_endo anti -B294 : A C3p_endo anti -B295 : U C3p_endo anti -B296 : G C2p_exo anti -B297 : C C3p_endo anti -B298 : G C3p_endo anti -B299 : A C2p_exo anti -B300 : G C3p_endo anti -B301 : A C3p_endo anti -B302 : G C3p_endo anti -B303 : U C3p_endo anti -B304 : A C3p_endo anti -B305 : G C3p_endo anti -B306 : G C3p_endo anti -B307 : U C3p_endo anti -B308 : C C3p_endo anti -A1 : MET -A2 : PHE -A3 : THR -A4 : ILE -A5 : ASN -A6 : ALA -A7 : GLU -A8 : VAL -A9 : ARG -A10 : LYS -A11 : GLU -A12 : GLN -A13 : GLY -A14 : LYS -A15 : GLY -A16 : ALA -A17 : SER -A18 : ARG -A19 : ARG -A20 : LEU -A21 : ARG -A22 : ALA -A23 : ALA -A24 : ASN -A25 : LYS -A26 : PHE -A27 : PRO -A28 : ALA -A29 : ILE -A30 : ILE -A31 : TYR -A32 : GLY -A33 : GLY -A34 : LYS -A35 : GLU -A36 : ALA -A37 : PRO -A38 : LEU -A39 : ALA -A40 : ILE -A41 : GLU -A42 : LEU -A43 : ASP -A44 : HIS -A45 : ASP -A46 : LYS -A47 : VAL -A48 : MET -A49 : ASN -A50 : MET -A51 : GLN -A52 : ALA -A53 : LYS -A54 : ALA -A55 : GLU -A56 : PHE -A57 : TYR -A58 : SER -A59 : GLU -A60 : VAL -A61 : LEU -A62 : THR -A63 : ILE -A64 : VAL -A65 : VAL -A66 : ASP -A67 : GLY -A68 : LYS -A69 : GLU -A70 : ILE -A71 : LYS -A72 : VAL -A73 : LYS -A74 : ALA -A75 : GLN -A76 : ASP -A77 : VAL -A78 : GLN -A79 : ARG -A80 : HIS -A81 : PRO -A82 : TYR -A83 : LYS -A84 : PRO -A85 : LYS -A86 : LEU -A87 : GLN -A88 : HIS -A89 : ILE -A90 : ASP -A91 : PHE -A92 : VAL -A93 : ARG -A94 : ALA -Adjacent stackings ---------------------------------------------- -B268-B269 : adjacent_5p upward -B269-B270 : adjacent_5p upward -B270-B271 : adjacent_5p upward -B271-B272 : adjacent_5p upward -B273-B274 : adjacent_5p upward -B274-B275 : adjacent_5p upward -B275-B276 : adjacent_5p upward -B276-B277 : adjacent_5p upward -B277-B278 : adjacent_5p upward -B278-B279 : adjacent_5p upward -B279-B280 : adjacent_5p upward -B281-B282 : adjacent_5p upward -B282-B283 : adjacent_5p upward -B293-B294 : adjacent_5p upward -B294-B295 : adjacent_5p upward -B296-B297 : adjacent_5p upward -B299-B300 : adjacent_5p upward -B300-B301 : adjacent_5p upward -B301-B302 : adjacent_5p upward -B302-B303 : adjacent_5p upward -B303-B304 : adjacent_5p upward -B304-B305 : adjacent_5p upward -B305-B306 : adjacent_5p upward -B306-B307 : adjacent_5p upward -B307-B308 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -B273-B304 : outward -B278-B299 : outward -B281-B296 : outward -Number of stackings = 28 -Number of adjacent stackings = 25 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -A14-B279 : LYS-G pairing one_hbond -A17-B298 : SER-G pairing one_hbond -A31-B273 : TYR-A pairing one_hbond -B268-B308 : G-C Ww/Ww pairing antiparallel cis XIX -B269-B307 : A-U Ww/Ww pairing antiparallel cis XX -B270-B306 : C-G Ww/Ww pairing antiparallel cis XIX -B271-B305 : C-G Ww/Ww pairing antiparallel cis XIX -B272-B303 : G-U Ww/O2P pairing -B272-B304 : G-A Ss/Hh O2'/Bh pairing antiparallel trans XI -B273-B303 : A-U Hh/Ws pairing antiparallel trans XXIV -B274-B302 : U-G Hw/Ww pairing antiparallel trans one_hbond 91 -B275-B301 : G-A Hw/Wh pairing antiparallel cis one_hbond 64 -B276-B300 : G-G Ww/Bh pairing antiparallel trans one_hbond -B277-B299 : U-A Ws/Hh pairing antiparallel trans XXIV -B278-B298 : A-G Hh/Ss Bh/O2' pairing antiparallel trans XI -B279-B297 : G-C Ww/Ww pairing antiparallel cis XIX -B280-B296 : U-G Ws/Ww pairing antiparallel cis XXVIII -B281-B295 : G-U Ww/Ws pairing antiparallel cis XXVIII -B282-B294 : U-A Ww/Ww pairing antiparallel cis XX -B283-B285 : C-U Hh/O2P pairing -B283-B293 : C-G Ww/Ww pairing antiparallel cis XIX -B284-B291 : U-C O2'/Bh pairing -B291-B292 : C-G O2P/Bs adjacent_5p pairing -Residue conformations ------------------------------------------- -B267 : G C3p_exo syn -B268 : G C3p_endo anti -B269 : A C3p_endo anti -B270 : C C3p_endo anti -B271 : C C3p_endo anti -B272 : G C2p_exo anti -B273 : A C3p_endo anti -B274 : U C4p_exo anti -B275 : G C3p_endo anti -B276 : G C3p_endo anti -B277 : U C3p_endo anti -B278 : A C3p_endo anti -B279 : G C3p_endo anti -B280 : U C3p_endo anti -B281 : G C2p_exo anti -B282 : U C3p_endo anti -B283 : C C3p_endo anti -B284 : U C3p_endo anti -B285 : U C2p_endo anti -B291 : C C3p_exo anti -B292 : G C2p_exo anti -B293 : G C3p_endo anti -B294 : A C3p_endo anti -B295 : U C3p_endo anti -B296 : G C2p_exo anti -B297 : C C3p_endo anti -B298 : G C3p_endo anti -B299 : A C2p_exo anti -B300 : G C3p_endo anti -B301 : A C3p_endo anti -B302 : G C3p_endo anti -B303 : U C3p_endo anti -B304 : A C3p_endo anti -B305 : G C3p_endo anti -B306 : G C3p_endo anti -B307 : U C3p_endo anti -B308 : C C3p_endo anti -A1 : MET -A2 : PHE -A3 : THR -A4 : ILE -A5 : ASN -A6 : ALA -A7 : GLU -A8 : VAL -A9 : ARG -A10 : LYS -A11 : GLU -A12 : GLN -A13 : GLY -A14 : LYS -A15 : GLY -A16 : ALA -A17 : SER -A18 : ARG -A19 : ARG -A20 : LEU -A21 : ARG -A22 : ALA -A23 : ALA -A24 : ASN -A25 : LYS -A26 : PHE -A27 : PRO -A28 : ALA -A29 : ILE -A30 : ILE -A31 : TYR -A32 : GLY -A33 : GLY -A34 : LYS -A35 : GLU -A36 : ALA -A37 : PRO -A38 : LEU -A39 : ALA -A40 : ILE -A41 : GLU -A42 : LEU -A43 : ASP -A44 : HIS -A45 : ASP -A46 : LYS -A47 : VAL -A48 : MET -A49 : ASN -A50 : MET -A51 : GLN -A52 : ALA -A53 : LYS -A54 : ALA -A55 : GLU -A56 : PHE -A57 : TYR -A58 : SER -A59 : GLU -A60 : VAL -A61 : LEU -A62 : THR -A63 : ILE -A64 : VAL -A65 : VAL -A66 : ASP -A67 : GLY -A68 : LYS -A69 : GLU -A70 : ILE -A71 : LYS -A72 : VAL -A73 : LYS -A74 : ALA -A75 : GLN -A76 : ASP -A77 : VAL -A78 : GLN -A79 : ARG -A80 : HIS -A81 : PRO -A82 : TYR -A83 : LYS -A84 : PRO -A85 : LYS -A86 : LEU -A87 : GLN -A88 : HIS -A89 : ILE -A90 : ASP -A91 : PHE -A92 : VAL -A93 : ARG -A94 : ALA -Adjacent stackings ---------------------------------------------- -B268-B269 : adjacent_5p upward -B269-B270 : adjacent_5p upward -B270-B271 : adjacent_5p upward -B271-B272 : adjacent_5p upward -B273-B274 : adjacent_5p upward -B274-B275 : adjacent_5p upward -B275-B276 : adjacent_5p upward -B276-B277 : adjacent_5p upward -B277-B278 : adjacent_5p upward -B278-B279 : adjacent_5p upward -B279-B280 : adjacent_5p upward -B281-B282 : adjacent_5p upward -B282-B283 : adjacent_5p upward -B283-B284 : adjacent_5p upward -B291-B292 : adjacent_5p downward -B293-B294 : adjacent_5p upward -B294-B295 : adjacent_5p upward -B296-B297 : adjacent_5p upward -B299-B300 : adjacent_5p upward -B300-B301 : adjacent_5p upward -B301-B302 : adjacent_5p upward -B302-B303 : adjacent_5p upward -B303-B304 : adjacent_5p upward -B304-B305 : adjacent_5p upward -B305-B306 : adjacent_5p upward -B306-B307 : adjacent_5p upward -B307-B308 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -B273-B304 : outward -B278-B299 : outward -B281-B296 : outward -Number of stackings = 30 -Number of adjacent stackings = 27 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -A14-B279 : LYS-G pairing one_hbond -A31-B273 : TYR-A pairing one_hbond -B268-B308 : G-C Ww/Ww pairing antiparallel cis XIX -B269-B307 : A-U Ww/Ww pairing antiparallel cis XX -B270-B306 : C-G Ww/Ww pairing antiparallel cis XIX -B271-B305 : C-G Ww/Ww pairing antiparallel cis XIX -B272-B304 : G-A Ss/Hh pairing antiparallel trans XI -B273-B303 : A-U Hh/Ws pairing antiparallel trans XXIV -B276-B300 : G-G Ww/Bh pairing antiparallel trans 115 -B277-B299 : U-A Ws/Hh pairing antiparallel trans XXIV -B278-B298 : A-G Hh/Ss Bh/O2' pairing antiparallel trans XI -B279-B297 : G-C Ww/Ww pairing antiparallel cis XIX -B280-B296 : U-G Ws/Ww pairing antiparallel cis XXVIII -B281-B295 : G-U Ww/Ws pairing antiparallel cis XXVIII -B282-B294 : U-A Ww/Ww pairing antiparallel cis XX -B283-B293 : C-G Ww/Ww pairing antiparallel cis XIX diff --git a/MCdata/1ddl_MC b/MCdata/1ddl_MC deleted file mode 100644 index d39790cabab5c2b513741df9706866cfe69b1eb2..0000000000000000000000000000000000000000 --- a/MCdata/1ddl_MC +++ /dev/null @@ -1,854 +0,0 @@ -Residue conformations ------------------------------------------- -D1 : U C3p_endo anti -D2 : U C3p_endo anti -D3 : U C3p_endo anti -D4 : U C3p_endo anti -D5 : U C3p_endo anti -D6 : U C3p_endo anti -D7 : U C3p_endo anti -E1 : U C3p_endo anti -E2 : U C4p_exo anti -A1 : MET -A2 : GLU -A3 : GLN -A4 : ASP -A5 : LYS -A6 : ILE -A7 : LEU -A8 : ALA -A9 : HIS -A10 : GLN -A11 : ALA -A12 : SER -A13 : LEU -A14 : ASN -A15 : THR -A16 : LYS -A17 : PRO -A18 : SER -A19 : LEU -A20 : LEU -A21 : PRO -A22 : PRO -A23 : PRO -A24 : VAL -A25 : GLY -A26 : ASN -A27 : PRO -A28 : PRO -A29 : PRO -A30 : VAL -A31 : ILE -A32 : SER -A33 : TYR -A34 : PRO -A35 : PHE -A36 : GLN -A37 : ILE -A38 : THR -A39 : LEU -A40 : ALA -A41 : SER -A42 : LEU -A43 : GLY -A44 : THR -A45 : GLU -A46 : ASP -A47 : ALA -A48 : ALA -A49 : ASP -A50 : SER -A51 : VAL -A52 : SER -A53 : ILE -A54 : ALA -A55 : SER -A56 : ASN -A57 : SER -A58 : VAL -A59 : LEU -A60 : ALA -A61 : THR -A62 : TYR -A63 : THR -A64 : ALA -A65 : LEU -A66 : TYR -A67 : ARG -A68 : HIS -A69 : ALA -A70 : GLN -A71 : LEU -A72 : LYS -A73 : HIS -A74 : LEU -A75 : LYS -A76 : ALA -A77 : THR -A78 : ILE -A79 : HIS -A80 : PRO -A81 : THR -A82 : TYR -A83 : MET -A84 : ALA -A85 : PRO -A86 : LYS -A87 : TYR -A88 : PRO -A89 : THR -A90 : SER -A91 : VAL -A92 : ALA -A93 : LEU -A94 : VAL -A95 : TRP -A96 : VAL -A97 : PRO -A98 : ALA -A99 : ASN -A100 : SER -A101 : THR -A102 : ALA -A103 : THR -A104 : SER -A105 : THR -A106 : GLN -A107 : VAL -A108 : LEU -A109 : ASP -A110 : THR -A111 : TYR -A112 : GLY -A113 : GLY -A114 : LEU -A115 : HIS -A116 : PHE -A117 : CYS -A118 : ILE -A119 : GLY -A120 : GLY -A121 : SER -A122 : VAL -A123 : ASN -A124 : SER -A125 : VAL -A126 : LYS -A127 : PRO -A128 : ILE -A129 : ASP -A130 : VAL -A131 : GLU -A132 : ALA -A133 : ASN -A134 : LEU -A135 : THR -A136 : ASN -A137 : LEU -A138 : ASN -A139 : PRO -A140 : ILE -A141 : ILE -A142 : LYS -A143 : ALA -A144 : SER -A145 : THR -A146 : THR -A147 : PHE -A148 : THR -A149 : ASP -A150 : THR -A151 : PRO -A152 : LYS -A153 : LEU -A154 : LEU -A155 : TYR -A156 : TYR -A157 : SER -A158 : LYS -A159 : ALA -A160 : GLN -A161 : ALA -A162 : THR -A163 : ALA -A164 : PRO -A165 : THR -A166 : SER -A167 : PRO -A168 : THR -A169 : CYS -A170 : TYR -A171 : LEU -A172 : THR -A173 : ILE -A174 : GLN -A175 : GLY -A176 : GLN -A177 : ILE -A178 : GLU -A179 : LEU -A180 : SER -A181 : SER -A182 : PRO -A183 : LEU -A184 : LEU -A185 : GLN -A186 : ALA -A187 : SER -A188 : SER -B1 : MET -B2 : GLU -B3 : GLN -B4 : ASP -B5 : LYS -B6 : ILE -B7 : LEU -B8 : ALA -B9 : HIS -B10 : GLN -B11 : ALA -B12 : SER -B13 : LEU -B14 : ASN -B15 : THR -B16 : LYS -B17 : PRO -B18 : SER -B19 : LEU -B20 : LEU -B21 : PRO -B22 : PRO -B23 : PRO -B24 : VAL -B25 : GLY -B26 : ASN -B27 : PRO -B28 : PRO -B29 : PRO -B30 : VAL -B31 : ILE -B32 : SER -B33 : TYR -B34 : PRO -B35 : PHE -B36 : GLN -B37 : ILE -B38 : THR -B39 : LEU -B40 : ALA -B41 : SER -B42 : LEU -B43 : GLY -B44 : THR -B45 : GLU -B46 : ASP -B47 : ALA -B48 : ALA -B49 : ASP -B50 : SER -B51 : VAL -B52 : SER -B53 : ILE -B54 : ALA -B55 : SER -B56 : ASN -B57 : SER -B58 : VAL -B59 : LEU -B60 : ALA -B61 : THR -B62 : TYR -B63 : THR -B64 : ALA -B65 : LEU -B66 : TYR -B67 : ARG -B68 : HIS -B69 : ALA -B70 : GLN -B71 : LEU -B72 : LYS -B73 : HIS -B74 : LEU -B75 : LYS -B76 : ALA -B77 : THR -B78 : ILE -B79 : HIS -B80 : PRO -B81 : THR -B82 : TYR -B83 : MET -B84 : ALA -B85 : PRO -B86 : LYS -B87 : TYR -B88 : PRO -B89 : THR -B90 : SER -B91 : VAL -B92 : ALA -B93 : LEU -B94 : VAL -B95 : TRP -B96 : VAL -B97 : PRO -B98 : ALA -B99 : ASN -B100 : SER -B101 : THR -B102 : ALA -B103 : THR -B104 : SER -B105 : THR -B106 : GLN -B107 : VAL -B108 : LEU -B109 : ASP -B110 : THR -B111 : TYR -B112 : GLY -B113 : GLY -B114 : LEU -B115 : HIS -B116 : PHE -B117 : CYS -B118 : ILE -B119 : GLY -B120 : GLY -B121 : SER -B122 : VAL -B123 : ASN -B124 : SER -B125 : VAL -B126 : LYS -B127 : PRO -B128 : ILE -B129 : ASP -B130 : VAL -B131 : GLU -B132 : ALA -B133 : ASN -B134 : LEU -B135 : THR -B136 : ASN -B137 : LEU -B138 : ASN -B139 : PRO -B140 : ILE -B141 : ILE -B142 : LYS -B143 : ALA -B144 : SER -B145 : THR -B146 : THR -B147 : PHE -B148 : THR -B149 : ASP -B150 : THR -B151 : PRO -B152 : LYS -B153 : LEU -B154 : LEU -B155 : TYR -B156 : TYR -B157 : SER -B158 : LYS -B159 : ALA -B160 : GLN -B161 : ALA -B162 : THR -B163 : ALA -B164 : PRO -B165 : THR -B166 : SER -B167 : PRO -B168 : THR -B169 : CYS -B170 : TYR -B171 : LEU -B172 : THR -B173 : ILE -B174 : GLN -B175 : GLY -B176 : GLN -B177 : ILE -B178 : GLU -B179 : LEU -B180 : SER -B181 : SER -B182 : PRO -B183 : LEU -B184 : LEU -B185 : GLN -B186 : ALA -B187 : SER -B188 : SER -C14 : ASN -C15 : THR -C16 : LYS -C17 : PRO -C18 : SER -C19 : LEU -C20 : LEU -C21 : PRO -C22 : PRO -C23 : PRO -C24 : VAL -C25 : GLY -C26 : ASN -C27 : PRO -C28 : PRO -C29 : PRO -C30 : VAL -C31 : ILE -C32 : SER -C33 : TYR -C34 : PRO -C35 : PHE -C36 : GLN -C37 : ILE -C38 : THR -C39 : LEU -C40 : ALA -C41 : SER -C42 : LEU -C43 : GLY -C44 : THR -C45 : GLU -C46 : ASP -C47 : ALA -C48 : ALA -C49 : ASP -C50 : SER -C51 : VAL -C52 : SER -C53 : ILE -C54 : ALA -C55 : SER -C56 : ASN -C57 : SER -C58 : VAL -C59 : LEU -C60 : ALA -C61 : THR -C62 : TYR -C63 : THR -C64 : ALA -C65 : LEU -C66 : TYR -C67 : ARG -C68 : HIS -C69 : ALA -C70 : GLN -C71 : LEU -C72 : LYS -C73 : HIS -C74 : LEU -C75 : LYS -C76 : ALA -C77 : THR -C78 : ILE -C79 : HIS -C80 : PRO -C81 : THR -C82 : TYR -C83 : MET -C84 : ALA -C85 : PRO -C86 : LYS -C87 : TYR -C88 : PRO -C89 : THR -C90 : SER -C91 : VAL -C92 : ALA -C93 : LEU -C94 : VAL -C95 : TRP -C96 : VAL -C97 : PRO -C98 : ALA -C99 : ASN -C100 : SER -C101 : THR -C102 : ALA -C103 : THR -C104 : SER -C105 : THR -C106 : GLN -C107 : VAL -C108 : LEU -C109 : ASP -C110 : THR -C111 : TYR -C112 : GLY -C113 : GLY -C114 : LEU -C115 : HIS -C116 : PHE -C117 : CYS -C118 : ILE -C119 : GLY -C120 : GLY -C121 : SER -C122 : VAL -C123 : ASN -C124 : SER -C125 : VAL -C126 : LYS -C127 : PRO -C128 : ILE -C129 : ASP -C130 : VAL -C131 : GLU -C132 : ALA -C133 : ASN -C134 : LEU -C135 : THR -C136 : ASN -C137 : LEU -C138 : ASN -C139 : PRO -C140 : ILE -C141 : ILE -C142 : LYS -C143 : ALA -C144 : SER -C145 : THR -C146 : THR -C147 : PHE -C148 : THR -C149 : ASP -C150 : THR -C151 : PRO -C152 : LYS -C153 : LEU -C154 : LEU -C155 : TYR -C156 : TYR -C157 : SER -C158 : LYS -C159 : ALA -C160 : GLN -C161 : ALA -C162 : THR -C163 : ALA -C164 : PRO -C165 : THR -C166 : SER -C167 : PRO -C168 : THR -C169 : CYS -C170 : TYR -C171 : LEU -C172 : THR -C173 : ILE -C174 : GLN -C175 : GLY -C176 : GLN -C177 : ILE -C178 : GLU -C179 : LEU -C180 : SER -C181 : SER -C182 : PRO -C183 : LEU -C184 : LEU -C185 : GLN -C186 : ALA -C187 : SER -C188 : SER -E2801 : HOH -A2002 : HOH -A2003 : HOH -A2101 : HOH -A2102 : HOH -A2103 : HOH -A2104 : HOH -A2105 : HOH -A2106 : HOH -A2107 : HOH -A2108 : HOH -A2109 : HOH -A2110 : HOH -A2111 : HOH -A2112 : HOH -A2113 : HOH -A2114 : HOH -A2115 : HOH -A2116 : HOH -A2117 : HOH -A2118 : HOH -A2119 : HOH -A2120 : HOH -A2121 : HOH -A2122 : HOH -A2123 : HOH -A2124 : HOH -A2125 : HOH -A2126 : HOH -A2127 : HOH -A2128 : HOH -A2129 : HOH -A2130 : HOH -A2131 : HOH -A2132 : HOH -A2133 : HOH -A2134 : HOH -A2135 : HOH -A2136 : HOH -A2137 : HOH -A2138 : HOH -A2139 : HOH -A2140 : HOH -A2141 : HOH -A2142 : HOH -A2143 : HOH -A2144 : HOH -A2145 : HOH -A2146 : HOH -A2147 : HOH -A2148 : HOH -A2149 : HOH -A2150 : HOH -A2151 : HOH -A2152 : HOH -A2153 : HOH -A2154 : HOH -A2155 : HOH -A2156 : HOH -A2157 : HOH -A2158 : HOH -A2159 : HOH -A2160 : HOH -A2161 : HOH -A2162 : HOH -A2163 : HOH -A2164 : HOH -A2165 : HOH -A2167 : HOH -A2168 : HOH -A2169 : HOH -A2170 : HOH -A2171 : HOH -A2172 : HOH -A2173 : HOH -A2174 : HOH -A2175 : HOH -A2176 : HOH -A2177 : HOH -A2178 : HOH -A2179 : HOH -A2180 : HOH -A2181 : HOH -A2182 : HOH -A2183 : HOH -A2184 : HOH -A2185 : HOH -A2241 : HOH -A2258 : HOH -A2260 : HOH -A2268 : HOH -A2403 : HOH -A2404 : HOH -A2405 : HOH -A2406 : HOH -A2407 : HOH -A2408 : HOH -A2409 : HOH -A2415 : HOH -A2416 : HOH -A2419 : HOH -A2420 : HOH -A2421 : HOH -A2501 : HOH -A2502 : HOH -A2802 : HOH -A2803 : HOH -B2001 : HOH -B2004 : HOH -B2166 : HOH -B2201 : HOH -B2202 : HOH -B2203 : HOH -B2204 : HOH -B2205 : HOH -B2206 : HOH -B2207 : HOH -B2208 : HOH -B2209 : HOH -B2210 : HOH -B2211 : HOH -B2212 : HOH -B2213 : HOH -B2214 : HOH -B2215 : HOH -B2216 : HOH -B2217 : HOH -B2218 : HOH -B2219 : HOH -B2220 : HOH -B2221 : HOH -B2222 : HOH -B2223 : HOH -B2224 : HOH -B2225 : HOH -B2226 : HOH -B2227 : HOH -B2228 : HOH -B2229 : HOH -B2230 : HOH -B2231 : HOH -B2232 : HOH -B2233 : HOH -B2234 : HOH -B2235 : HOH -B2236 : HOH -B2237 : HOH -B2238 : HOH -B2239 : HOH -B2240 : HOH -B2242 : HOH -B2243 : HOH -B2244 : HOH -B2245 : HOH -B2246 : HOH -B2247 : HOH -B2248 : HOH -B2249 : HOH -B2250 : HOH -B2251 : HOH -B2252 : HOH -B2253 : HOH -B2254 : HOH -B2255 : HOH -B2256 : HOH -B2257 : HOH -B2259 : HOH -B2261 : HOH -B2262 : HOH -B2263 : HOH -B2264 : HOH -B2266 : HOH -B2267 : HOH -B2269 : HOH -B2270 : HOH -B2271 : HOH -B2360 : HOH -B2401 : HOH -B2402 : HOH -B2410 : HOH -B2411 : HOH -B2412 : HOH -B2413 : HOH -B2414 : HOH -B2417 : HOH -B2601 : HOH -B2603 : HOH -B2604 : HOH -B2606 : HOH -B2607 : HOH -B2608 : HOH -B2609 : HOH -B2610 : HOH -B2611 : HOH -B2612 : HOH -B2615 : HOH -B2616 : HOH -B2617 : HOH -B2618 : HOH -B2619 : HOH -C2005 : HOH -C2006 : HOH -C2265 : HOH -C2301 : HOH -C2302 : HOH -C2303 : HOH -C2304 : HOH -C2305 : HOH -C2306 : HOH -C2307 : HOH -C2308 : HOH -C2309 : HOH -C2310 : HOH -C2311 : HOH -C2312 : HOH -C2313 : HOH -C2314 : HOH -C2315 : HOH -C2316 : HOH -C2317 : HOH -C2318 : HOH -C2319 : HOH -C2320 : HOH -C2321 : HOH -C2322 : HOH -C2323 : HOH -C2324 : HOH -C2325 : HOH -C2326 : HOH -C2327 : HOH -C2328 : HOH -C2329 : HOH -C2330 : HOH -C2331 : HOH -C2332 : HOH -C2333 : HOH -C2334 : HOH -C2335 : HOH -C2336 : HOH -C2337 : HOH -C2338 : HOH -C2339 : HOH -C2340 : HOH -C2341 : HOH -C2342 : HOH -C2343 : HOH -C2344 : HOH -C2345 : HOH -C2346 : HOH -C2347 : HOH -C2348 : HOH -C2349 : HOH -C2350 : HOH -C2351 : HOH -C2352 : HOH -C2353 : HOH -C2354 : HOH -C2355 : HOH -C2356 : HOH -C2357 : HOH -C2358 : HOH -C2359 : HOH -C2361 : HOH -C2362 : HOH -C2363 : HOH -C2364 : HOH -C2365 : HOH -C2366 : HOH -C2367 : HOH -C2368 : HOH -C2369 : HOH -C2418 : HOH -C2503 : HOH -C2504 : HOH -C2602 : HOH -C2605 : HOH -C2613 : HOH -C2614 : HOH -C2620 : HOH -C2621 : HOH -C2701 : HOH -C2702 : HOH -C2703 : HOH -C2704 : HOH -C2901 : HOH -Adjacent stackings ---------------------------------------------- -D5-D6 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 1 -Number of adjacent stackings = 1 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -D1-D2 : U-U Ww/O2' adjacent_5p pairing diff --git a/MCdata/1ddy_MC b/MCdata/1ddy_MC deleted file mode 100644 index 7eb8a6bf3eed18d663fa185a50a64a6a0bab24f1..0000000000000000000000000000000000000000 --- a/MCdata/1ddy_MC +++ /dev/null @@ -1,319 +0,0 @@ -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C2p_exo anti -A3 : A C3p_endo anti -A4 : A C4p_exo anti -A5 : C C3p_endo anti -A6 : C C3p_endo anti -A7 : G C3p_endo anti -A8 : G C3p_endo anti -A9 : U C3p_endo anti -A10 : G C3p_endo anti -A11 : C C4p_exo anti -A12 : G C3p_endo anti -A13 : C C3p_endo anti -A14 : A C2p_endo anti -A15 : U C1p_exo syn -A16 : A C3p_endo anti -A17 : A C3p_endo anti -A18 : C C3p_endo anti -A19 : C C3p_endo anti -A20 : A C3p_endo anti -A21 : C C3p_endo anti -A22 : C C1p_exo anti -A23 : U C2p_endo anti -A24 : C C2p_endo anti -A25 : A C3p_endo anti -A26 : G C2p_endo syn -A27 : U C2p_endo anti -A28 : G C3p_endo anti -A29 : C C3p_endo anti -A30 : G C2p_endo anti -A31 : A C3p_endo anti -A32 : G C3p_endo anti -A33 : C C3p_endo anti -A34 : A C3p_endo anti -A35 : A C3p_endo anti -C201 : G C3p_endo anti -C202 : G C3p_endo anti -C203 : A C3p_endo anti -C204 : A C3p_endo anti -C205 : C C3p_endo anti -C206 : C C3p_endo anti -C207 : G C3p_endo anti -C208 : G C3p_endo anti -C209 : U C3p_endo anti -C210 : G C3p_endo anti -C211 : C C4p_exo anti -C212 : G C3p_endo anti -C213 : C C3p_endo anti -C214 : A C2p_endo anti -C215 : U C2p_endo syn -C216 : A C3p_endo anti -C217 : A C3p_endo anti -C218 : C C3p_endo anti -C219 : C C3p_endo anti -C220 : A C3p_endo anti -C221 : C C3p_endo anti -C222 : C C2p_endo anti -C223 : U C2p_endo anti -C224 : C C4p_exo anti -C225 : A C3p_endo anti -C226 : G C2p_endo syn -C227 : U C2p_endo anti -C228 : G C3p_endo anti -C229 : C C3p_endo anti -C230 : G C2p_endo anti -C231 : A C3p_endo anti -C232 : G C3p_endo anti -C233 : C C3p_endo anti -C234 : A C3p_endo anti -C235 : A C3p_endo anti -E401 : G C3p_endo anti -E402 : G C3p_endo anti -E403 : A C2p_exo anti -E404 : A C3p_endo anti -E405 : C C3p_endo anti -E406 : C C3p_endo anti -E407 : G C3p_endo anti -E408 : G C3p_endo anti -E409 : U C3p_endo anti -E410 : G C3p_endo anti -E411 : C O4p_endo anti -E412 : G C3p_endo anti -E413 : C C3p_endo anti -E414 : A C2p_endo anti -E415 : U C2p_endo syn -E416 : A C2p_exo anti -E417 : A C3p_endo anti -E418 : C C3p_endo anti -E419 : C C3p_endo anti -E420 : A C3p_endo anti -E421 : C C3p_endo anti -E422 : C C2p_endo anti -E423 : U C2p_endo anti -E424 : C C2p_endo anti -E425 : A C3p_endo anti -E426 : G C2p_endo syn -E427 : U C2p_endo anti -E428 : G C3p_endo anti -E429 : C C3p_endo anti -E430 : G C2p_endo anti -E431 : A C3p_endo anti -E432 : G C3p_endo anti -E433 : C C3p_endo anti -E434 : A C3p_endo anti -E435 : A C3p_endo anti -G601 : G C3p_endo anti -G602 : G C3p_endo anti -G603 : A C3p_endo anti -G604 : A C3p_endo anti -G605 : C C3p_endo anti -G606 : C C3p_endo anti -G607 : G C3p_endo anti -G608 : G C3p_endo anti -G609 : U C3p_endo anti -G610 : G C3p_endo anti -G611 : C C4p_exo anti -G612 : G C3p_endo anti -G613 : C C3p_endo anti -G614 : A C2p_endo anti -G615 : U C2p_endo syn -G616 : A C3p_endo anti -G617 : A C3p_endo anti -G618 : C C3p_endo anti -G619 : C C3p_endo anti -G620 : A C3p_endo anti -G621 : C C3p_endo anti -G622 : C C2p_endo anti -G623 : U C1p_exo anti -G624 : C C2p_endo anti -G625 : A C4p_exo anti -G626 : G C2p_endo syn -G627 : U C2p_endo anti -G628 : G C3p_endo anti -G629 : C C3p_endo anti -G630 : G C2p_endo anti -G631 : A C3p_endo anti -G632 : G C3p_endo anti -G633 : C C3p_endo anti -G634 : A C3p_endo anti -G635 : A C3p_endo anti -A101 : B12 -C301 : B12 -E501 : B12 -G701 : B12 -A102 : NME -C302 : NME -E502 : NME -G702 : NME -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p inward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A28-A29 : adjacent_5p upward -A29-A30 : adjacent_5p inward -A31-A32 : adjacent_5p upward -A32-A33 : adjacent_5p upward -A33-A34 : adjacent_5p upward -A34-A35 : adjacent_5p upward -C201-C202 : adjacent_5p upward -C202-C203 : adjacent_5p upward -C203-C204 : adjacent_5p upward -C204-C205 : adjacent_5p upward -C206-C207 : adjacent_5p upward -C207-C208 : adjacent_5p upward -C208-C209 : adjacent_5p upward -C212-C213 : adjacent_5p upward -C213-C214 : adjacent_5p inward -C216-C217 : adjacent_5p upward -C217-C218 : adjacent_5p upward -C218-C219 : adjacent_5p upward -C219-C220 : adjacent_5p upward -C220-C221 : adjacent_5p upward -C228-C229 : adjacent_5p upward -C229-C230 : adjacent_5p inward -C231-C232 : adjacent_5p upward -C232-C233 : adjacent_5p upward -C233-C234 : adjacent_5p upward -C234-C235 : adjacent_5p upward -E401-E402 : adjacent_5p upward -E402-E403 : adjacent_5p upward -E403-E404 : adjacent_5p upward -E404-E405 : adjacent_5p upward -E405-E406 : adjacent_5p upward -E407-E408 : adjacent_5p upward -E408-E409 : adjacent_5p upward -E412-E413 : adjacent_5p upward -E413-E414 : adjacent_5p inward -E416-E417 : adjacent_5p upward -E417-E418 : adjacent_5p upward -E418-E419 : adjacent_5p upward -E419-E420 : adjacent_5p upward -E420-E421 : adjacent_5p upward -E421-E422 : adjacent_5p upward -E428-E429 : adjacent_5p upward -E429-E430 : adjacent_5p inward -E431-E432 : adjacent_5p upward -E432-E433 : adjacent_5p upward -E433-E434 : adjacent_5p upward -E434-E435 : adjacent_5p upward -G601-G602 : adjacent_5p upward -G602-G603 : adjacent_5p upward -G603-G604 : adjacent_5p upward -G604-G605 : adjacent_5p upward -G607-G608 : adjacent_5p upward -G608-G609 : adjacent_5p upward -G612-G613 : adjacent_5p upward -G613-G614 : adjacent_5p inward -G616-G617 : adjacent_5p upward -G617-G618 : adjacent_5p upward -G618-G619 : adjacent_5p upward -G619-G620 : adjacent_5p upward -G620-G621 : adjacent_5p upward -G621-G622 : adjacent_5p upward -G628-G629 : adjacent_5p upward -G629-G630 : adjacent_5p inward -G631-G632 : adjacent_5p upward -G632-G633 : adjacent_5p upward -G633-G634 : adjacent_5p upward -G634-G635 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A10-A15 : inward -A10-A26 : downward -A11-A15 : outward -A12-A34 : outward -A20-A26 : outward -A23-A25 : outward -C210-C215 : inward -C210-C226 : downward -C211-C215 : outward -C212-C234 : outward -C220-C226 : outward -C223-C225 : outward -E410-E415 : inward -E410-E426 : downward -E411-E415 : outward -E420-E426 : outward -E423-E425 : outward -G610-G615 : inward -G610-G626 : downward -G611-G615 : outward -G612-G634 : outward -G620-G626 : outward -G623-G625 : outward -Number of stackings = 104 -Number of adjacent stackings = 81 -Number of non adjacent stackings = 23 -Base-pairs ------------------------------------------------------ -A7-A22 : G-C Ww/Ww pairing antiparallel cis XIX -A8-A21 : G-C Ww/Ww pairing antiparallel cis XIX -A8-A25 : G-A O2'/Ww pairing -A9-A20 : U-A Ww/Ww pairing antiparallel cis XX -A10-A28 : G-G Ww/Hh pairing parallel cis VI -A11-A30 : C-G Ww/Ww pairing antiparallel cis XIX -A12-A33 : G-C Ww/Ww pairing antiparallel cis XIX -A13-A32 : C-G Ww/Ww pairing antiparallel cis XIX -A14-A31 : A-A Ww/Ww pairing parallel trans I -A15-A27 : U-U Hh/Ww pairing antiparallel trans 81 -A15-A29 : U-C Wh/Wh pairing antiparallel cis one_hbond -A17-A29 : A-C Wh/Ws pairing antiparallel cis one_hbond 78 -A18-A28 : C-G Ww/Ww pairing antiparallel cis XIX -A19-A26 : C-G Ww/Ww pairing antiparallel cis XIX -C207-C222 : G-C Ww/Ww pairing antiparallel cis XIX -C208-C221 : G-C Ww/Ww pairing antiparallel cis XIX -C208-C225 : G-A O2'/Ww pairing -C209-C220 : U-A Ww/Ww pairing antiparallel cis XX -C210-C228 : G-G Ww/Hh pairing parallel cis VI -C211-C230 : C-G Ww/Ww pairing antiparallel cis XIX -C212-C233 : G-C Ww/Ww pairing antiparallel cis XIX -C213-C232 : C-G Ww/Ww pairing antiparallel cis XIX -C214-C231 : A-A Ww/Ww pairing parallel trans I -C215-C227 : U-U Hh/Ww pairing antiparallel trans 81 -C215-C229 : U-C Wh/Wh pairing antiparallel cis one_hbond -C217-C229 : A-C Wh/Ws pairing antiparallel cis one_hbond 78 -C218-C228 : C-G Ww/Ww pairing antiparallel cis XIX -C219-C226 : C-G Ww/Ww pairing antiparallel cis XIX -E407-E422 : G-C Ww/Ww pairing antiparallel cis XIX -E408-E421 : G-C Ww/Ww pairing antiparallel cis XIX -E408-E425 : G-A O2'/Ww pairing -E409-E420 : U-A Ww/Ww pairing antiparallel cis XX -E410-E418 : G-C Wh/Wh pairing antiparallel cis one_hbond -E410-E428 : G-G Ww/Hh pairing parallel cis VI -E411-E413 : C-C O2'/Bh pairing -E411-E430 : C-G Ww/Ww pairing antiparallel cis XIX -E412-E433 : G-C Ww/Ww pairing antiparallel cis XIX -E413-E432 : C-G Ww/Ww pairing antiparallel cis XIX -E414-E431 : A-A Ww/Ww pairing parallel trans I -E415-E427 : U-U Hh/Ww pairing antiparallel trans 81 -E415-E429 : U-C Wh/Wh pairing antiparallel cis one_hbond -E417-E429 : A-C Wh/Ws pairing antiparallel cis one_hbond 78 -E418-E428 : C-G Ww/Ww pairing antiparallel cis XIX -E419-E426 : C-G Ww/Ww pairing antiparallel cis XIX -G607-G622 : G-C Ww/Ww pairing antiparallel cis XIX -G608-G621 : G-C Ww/Ww pairing antiparallel cis XIX -G608-G625 : G-A O2'/Ww O2'/Bh pairing -G609-G620 : U-A Ww/Ww pairing antiparallel cis XX -G610-G618 : G-C Wh/Bh pairing antiparallel cis one_hbond 123 -G610-G628 : G-G Ww/Hh pairing parallel cis VI -G611-G630 : C-G Ww/Ww pairing antiparallel cis XIX -G612-G633 : G-C Ww/Ww pairing antiparallel cis XIX -G613-G632 : C-G Ww/Ww pairing antiparallel cis XIX -G614-G631 : A-A Ww/Ww pairing parallel trans one_hbond -G615-G627 : U-U Hh/Ww pairing antiparallel trans 81 -G615-G629 : U-C Wh/Wh pairing antiparallel cis one_hbond -G617-G629 : A-C Wh/Ws pairing antiparallel cis one_hbond 78 -G618-G628 : C-G Ww/Ww pairing antiparallel cis XIX -G619-G626 : C-G Ww/Ww pairing antiparallel cis XIX -G627-G629 : U-C Ws/Hw pairing parallel cis one_hbond 99 diff --git a/MCdata/1dfu_MC b/MCdata/1dfu_MC deleted file mode 100644 index e5e4425d6b908840765523f24f20725e2b27b15a..0000000000000000000000000000000000000000 --- a/MCdata/1dfu_MC +++ /dev/null @@ -1,432 +0,0 @@ -Residue conformations ------------------------------------------- -M91 : C C3p_endo anti -M92 : C C3p_endo anti -M93 : C C3p_endo anti -M94 : A C3p_endo anti -M95 : U C3p_endo anti -M96 : G C3p_endo anti -M97 : C C3p_endo anti -M98 : G C3p_endo anti -M99 : A C2p_exo anti -M100 : G C3p_endo anti -M101 : A C3p_endo anti -M102 : G C3p_endo anti -M103 : U C3p_endo anti -M104 : A C3p_endo anti -M105 : G C3p_endo anti -M106 : G C3p_endo anti -M107 : G C3p_endo anti -M108 : A C3p_endo anti -M109 : C C3p_endo anti -N68 : U C3p_endo anti -N69 : G C4p_exo syn -N70 : C C3p_endo anti -N71 : C C3p_endo anti -N72 : G C3p_endo anti -N73 : A C3p_endo anti -N74 : U C3p_endo anti -N75 : G C3p_endo anti -N76 : G C3p_endo anti -N77 : U C3p_endo anti -N78 : A C3p_endo anti -N79 : G C3p_endo anti -N80 : U C3p_endo anti -N81 : G C3p_endo anti -N82 : U C3p_endo anti -N83 : G C3p_endo anti -N84 : G C3p_endo anti -N85 : G C3p_endo anti -N86 : G C3p_endo anti -P1 : MET -P2 : PHE -P3 : THR -P4 : ILE -P5 : ASN -P6 : ALA -P7 : GLU -P8 : VAL -P9 : ARG -P10 : LYS -P11 : GLU -P12 : GLN -P13 : GLY -P14 : LYS -P15 : GLY -P16 : ALA -P17 : SER -P18 : ARG -P19 : ARG -P20 : LEU -P21 : ARG -P22 : ALA -P23 : ALA -P24 : ASN -P25 : LYS -P26 : PHE -P27 : PRO -P28 : ALA -P29 : ILE -P30 : ILE -P31 : TYR -P32 : GLY -P33 : GLY -P34 : LYS -P35 : GLU -P36 : ALA -P37 : PRO -P38 : LEU -P39 : ALA -P40 : ILE -P41 : GLU -P42 : LEU -P43 : ASP -P44 : HIS -P45 : ASP -P46 : LYS -P47 : VAL -P48 : MET -P49 : ASN -P50 : MET -P51 : GLN -P52 : ALA -P53 : LYS -P54 : ALA -P55 : GLU -P56 : PHE -P57 : TYR -P58 : SER -P59 : GLU -P60 : VAL -P61 : LEU -P62 : THR -P63 : ILE -P64 : VAL -P65 : VAL -P66 : ASP -P67 : GLY -P68 : LYS -P69 : GLU -P70 : ILE -P71 : LYS -P72 : VAL -P73 : LYS -P74 : ALA -P75 : GLN -P76 : ASP -P77 : VAL -P78 : GLN -P79 : ARG -P80 : HIS -P81 : PRO -P82 : TYR -P83 : LYS -P84 : PRO -P85 : LYS -P86 : LEU -P87 : GLN -P88 : HIS -P89 : ILE -P90 : ASP -P91 : PHE -P92 : VAL -P93 : ARG -P94 : ALA -M501 : MG -M502 : MG -M503 : MG -M505 : MG -N504 : MG -M506 : HOH -M507 : HOH -M508 : HOH -M509 : HOH -M510 : HOH -M511 : HOH -M512 : HOH -M513 : HOH -M514 : HOH -M515 : HOH -M516 : HOH -M517 : HOH -M518 : HOH -M519 : HOH -M520 : HOH -M521 : HOH -M522 : HOH -M523 : HOH -M524 : HOH -M525 : HOH -M526 : HOH -M527 : HOH -M528 : HOH -M529 : HOH -M530 : HOH -M531 : HOH -M532 : HOH -M533 : HOH -M534 : HOH -M535 : HOH -M536 : HOH -M537 : HOH -M538 : HOH -M539 : HOH -M540 : HOH -M541 : HOH -M542 : HOH -M543 : HOH -M544 : HOH -M545 : HOH -M546 : HOH -M547 : HOH -M548 : HOH -M549 : HOH -M550 : HOH -M551 : HOH -M552 : HOH -M553 : HOH -M554 : HOH -M555 : HOH -M556 : HOH -M557 : HOH -M558 : HOH -M559 : HOH -M560 : HOH -M561 : HOH -M562 : HOH -M563 : HOH -M564 : HOH -M565 : HOH -M566 : HOH -M567 : HOH -M568 : HOH -M569 : HOH -M570 : HOH -M571 : HOH -M572 : HOH -M573 : HOH -M574 : HOH -M575 : HOH -M576 : HOH -M577 : HOH -M578 : HOH -M579 : HOH -M580 : HOH -M581 : HOH -M582 : HOH -M583 : HOH -M584 : HOH -M585 : HOH -M586 : HOH -M587 : HOH -M588 : HOH -M589 : HOH -M590 : HOH -M591 : HOH -M592 : HOH -N505 : HOH -N506 : HOH -N507 : HOH -N508 : HOH -N509 : HOH -N510 : HOH -N511 : HOH -N512 : HOH -N513 : HOH -N514 : HOH -N515 : HOH -N516 : HOH -N517 : HOH -N518 : HOH -N519 : HOH -N520 : HOH -N521 : HOH -N522 : HOH -N523 : HOH -N524 : HOH -N525 : HOH -N526 : HOH -N527 : HOH -N528 : HOH -N529 : HOH -N530 : HOH -N531 : HOH -N532 : HOH -N533 : HOH -N534 : HOH -N535 : HOH -N536 : HOH -N537 : HOH -N538 : HOH -N539 : HOH -N540 : HOH -N541 : HOH -N542 : HOH -N543 : HOH -N544 : HOH -N545 : HOH -N546 : HOH -N547 : HOH -N548 : HOH -N549 : HOH -N550 : HOH -N551 : HOH -N552 : HOH -N553 : HOH -N554 : HOH -N555 : HOH -N556 : HOH -N557 : HOH -N558 : HOH -N559 : HOH -N560 : HOH -N561 : HOH -N562 : HOH -N563 : HOH -N564 : HOH -N565 : HOH -N566 : HOH -N567 : HOH -N568 : HOH -N569 : HOH -N570 : HOH -N571 : HOH -N572 : HOH -N573 : HOH -N574 : HOH -N575 : HOH -N576 : HOH -N577 : HOH -N578 : HOH -N579 : HOH -P95 : HOH -P96 : HOH -P97 : HOH -P98 : HOH -P99 : HOH -P100 : HOH -P101 : HOH -P102 : HOH -P103 : HOH -P104 : HOH -P105 : HOH -P106 : HOH -P107 : HOH -P108 : HOH -P109 : HOH -P110 : HOH -P111 : HOH -P112 : HOH -P113 : HOH -P114 : HOH -P115 : HOH -P116 : HOH -P117 : HOH -P118 : HOH -P119 : HOH -P120 : HOH -P121 : HOH -P122 : HOH -P123 : HOH -P124 : HOH -P125 : HOH -P126 : HOH -P127 : HOH -P128 : HOH -P129 : HOH -P130 : HOH -P131 : HOH -P132 : HOH -P133 : HOH -P134 : HOH -P135 : HOH -P136 : HOH -P137 : HOH -P138 : HOH -P139 : HOH -P140 : HOH -P141 : HOH -P142 : HOH -P143 : HOH -P144 : HOH -P145 : HOH -P146 : HOH -P147 : HOH -P148 : HOH -P149 : HOH -P150 : HOH -P151 : HOH -P152 : HOH -P153 : HOH -P154 : HOH -P155 : HOH -P156 : HOH -P157 : HOH -P158 : HOH -P159 : HOH -P160 : HOH -P161 : HOH -P162 : HOH -P163 : HOH -P164 : HOH -P165 : HOH -P166 : HOH -P167 : HOH -P168 : HOH -P169 : HOH -P170 : HOH -P171 : HOH -P172 : HOH -P173 : HOH -P174 : HOH -Adjacent stackings ---------------------------------------------- -M93-M94 : adjacent_5p upward -M94-M95 : adjacent_5p upward -M96-M97 : adjacent_5p upward -M97-M98 : adjacent_5p upward -M99-M100 : adjacent_5p upward -M100-M101 : adjacent_5p upward -M101-M102 : adjacent_5p upward -M102-M103 : adjacent_5p upward -M103-M104 : adjacent_5p upward -M104-M105 : adjacent_5p upward -M105-M106 : adjacent_5p upward -M106-M107 : adjacent_5p upward -N71-N72 : adjacent_5p upward -N73-N74 : adjacent_5p upward -N74-N75 : adjacent_5p upward -N75-N76 : adjacent_5p upward -N76-N77 : adjacent_5p upward -N78-N79 : adjacent_5p upward -N79-N80 : adjacent_5p upward -N81-N82 : adjacent_5p upward -N82-N83 : adjacent_5p upward -N83-N84 : adjacent_5p upward -N84-N85 : adjacent_5p upward -N85-N86 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -M94-N83 : outward -M96-N81 : outward -M99-N78 : outward -M104-N73 : outward -Number of stackings = 28 -Number of adjacent stackings = 24 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -M91-N85 : C-G Ww/Ww pairing antiparallel cis XIX -M92-N84 : C-G Ww/Ww pairing antiparallel cis XIX -M93-N83 : C-G Ww/Ww pairing antiparallel cis XIX -M94-N82 : A-U Ww/Ww pairing antiparallel cis XX -M95-N81 : U-G Ws/Ww pairing antiparallel cis XXVIII -M96-N80 : G-U Ww/Ws pairing antiparallel cis XXVIII -M97-N79 : C-G Ww/Ww pairing antiparallel cis XIX -M98-N78 : G-A Ss/Hh O2'/Bh pairing antiparallel trans XI -M99-N77 : A-U Hh/Ws pairing antiparallel trans XXIV -M100-N76 : G-G Bh/Ww pairing antiparallel trans 115 -M101-N75 : A-G Wh/Wh pairing antiparallel cis one_hbond -M102-N74 : G-U Ww/Bh pairing antiparallel trans 91 -M103-N73 : U-A Ws/Hh pairing antiparallel trans XXIV -M104-N72 : A-G Hh/Ss Bh/O2' pairing antiparallel trans XI -M105-N71 : G-C Ww/Ww pairing antiparallel cis XIX -M106-N70 : G-C Ww/Ww pairing antiparallel cis XIX -M108-M109 : A-C O2P/Bh adjacent_5p pairing -N68-N69 : U-G O2'/Bs O2'/Ss adjacent_5p pairing diff --git a/MCdata/1di2_MC b/MCdata/1di2_MC deleted file mode 100644 index 2ec790b6824731013861ccbd6a9f87e14ee8417c..0000000000000000000000000000000000000000 --- a/MCdata/1di2_MC +++ /dev/null @@ -1,577 +0,0 @@ -Residue conformations ------------------------------------------- -C1 : G C3p_endo anti -C2 : G C3p_endo anti -C3 : C C3p_endo anti -C4 : G C3p_endo anti -C5 : C C3p_endo anti -C6 : G C3p_endo anti -C7 : C C3p_endo anti -C8 : G C3p_endo anti -C9 : C C3p_endo anti -C10 : C C3p_endo anti -D11 : G C3p_endo anti -D12 : G C3p_endo anti -D13 : C C3p_endo anti -D14 : G C3p_endo anti -D15 : C C3p_endo anti -D16 : G C3p_endo anti -D17 : C C3p_endo anti -D18 : G C3p_endo anti -D19 : C C3p_endo anti -D20 : C C3p_endo anti -E21 : G C3p_endo anti -E22 : G C3p_endo anti -E23 : C C3p_endo anti -E24 : G C3p_endo anti -E25 : C C3p_endo anti -E26 : G C3p_endo anti -E27 : C C3p_endo anti -E28 : G C3p_endo anti -E29 : C C3p_endo anti -E30 : C C3p_endo anti -G41 : G C3p_endo anti -G42 : G C3p_endo anti -G43 : C C3p_endo anti -G44 : G C3p_endo anti -G45 : C C3p_endo anti -G46 : G C3p_endo anti -G47 : C C3p_endo anti -G48 : G C3p_endo anti -G49 : C C3p_endo anti -G50 : C C3p_endo anti -A112 : MET -A113 : PRO -A114 : VAL -A115 : GLY -A116 : SER -A117 : LEU -A118 : GLN -A119 : GLU -A120 : LEU -A121 : ALA -A122 : VAL -A123 : GLN -A124 : LYS -A125 : GLY -A126 : TRP -A127 : ARG -A128 : LEU -A129 : PRO -A130 : GLU -A131 : TYR -A132 : THR -A133 : VAL -A134 : ALA -A135 : GLN -A136 : GLU -A137 : SER -A138 : GLY -A139 : PRO -A140 : PRO -A141 : HIS -A142 : LYS -A143 : ARG -A144 : GLU -A145 : PHE -A146 : THR -A147 : ILE -A148 : THR -A149 : CYS -A150 : ARG -A151 : VAL -A152 : GLU -A153 : THR -A154 : PHE -A155 : VAL -A156 : GLU -A157 : THR -A158 : GLY -A159 : SER -A160 : GLY -A161 : THR -A162 : SER -A163 : LYS -A164 : GLN -A165 : VAL -A166 : ALA -A167 : LYS -A168 : ARG -A169 : VAL -A170 : ALA -A171 : ALA -A172 : GLU -A173 : LYS -A174 : LEU -A175 : LEU -A176 : THR -A177 : LYS -A178 : PHE -A179 : LYS -A180 : THR -B112 : MET -B113 : PRO -B114 : VAL -B115 : GLY -B116 : SER -B117 : LEU -B118 : GLN -B119 : GLU -B120 : LEU -B121 : ALA -B122 : VAL -B123 : GLN -B124 : LYS -B125 : GLY -B126 : TRP -B127 : ARG -B128 : LEU -B129 : PRO -B130 : GLU -B131 : TYR -B132 : THR -B133 : VAL -B134 : ALA -B135 : GLN -B145 : PHE -B146 : THR -B147 : ILE -B148 : THR -B149 : CYS -B150 : ARG -B151 : VAL -B152 : GLU -B153 : THR -B154 : PHE -B155 : VAL -B156 : GLU -B157 : THR -B158 : GLY -B159 : SER -B160 : GLY -B161 : THR -B162 : SER -B163 : LYS -B164 : GLN -B165 : VAL -B166 : ALA -B167 : LYS -B168 : ARG -B169 : VAL -B170 : ALA -B171 : ALA -B172 : GLU -B173 : LYS -B174 : LEU -B175 : LEU -B176 : THR -B177 : LYS -B178 : PHE -B179 : LYS -B180 : THR -C11 : HOH -C12 : HOH -C13 : HOH -C14 : HOH -C15 : HOH -C16 : HOH -C17 : HOH -C18 : HOH -C19 : HOH -C20 : HOH -C21 : HOH -C22 : HOH -C23 : HOH -C24 : HOH -C25 : HOH -C26 : HOH -C27 : HOH -C28 : HOH -C29 : HOH -C30 : HOH -C31 : HOH -C32 : HOH -C33 : HOH -C34 : HOH -C35 : HOH -C36 : HOH -C37 : HOH -C38 : HOH -C39 : HOH -C40 : HOH -C41 : HOH -C42 : HOH -C43 : HOH -C44 : HOH -C45 : HOH -C46 : HOH -C47 : HOH -C48 : HOH -C49 : HOH -C50 : HOH -C51 : HOH -C52 : HOH -C53 : HOH -C54 : HOH -C55 : HOH -C56 : HOH -C57 : HOH -C58 : HOH -C59 : HOH -C60 : HOH -C61 : HOH -C62 : HOH -C63 : HOH -C64 : HOH -C65 : HOH -C66 : HOH -C67 : HOH -C68 : HOH -C69 : HOH -C70 : HOH -C71 : HOH -C72 : HOH -C73 : HOH -D21 : HOH -D22 : HOH -D23 : HOH -D24 : HOH -D25 : HOH -D26 : HOH -D27 : HOH -D28 : HOH -D29 : HOH -D30 : HOH -D31 : HOH -D32 : HOH -D33 : HOH -D34 : HOH -D35 : HOH -D36 : HOH -D37 : HOH -D38 : HOH -D39 : HOH -D40 : HOH -D41 : HOH -D42 : HOH -D43 : HOH -D44 : HOH -D45 : HOH -D46 : HOH -D47 : HOH -D48 : HOH -D49 : HOH -D50 : HOH -D51 : HOH -D52 : HOH -D53 : HOH -D54 : HOH -D55 : HOH -D56 : HOH -D57 : HOH -D58 : HOH -D59 : HOH -D60 : HOH -D61 : HOH -D62 : HOH -D63 : HOH -D64 : HOH -D65 : HOH -D66 : HOH -D67 : HOH -D68 : HOH -D69 : HOH -D70 : HOH -D71 : HOH -D72 : HOH -D73 : HOH -D74 : HOH -D75 : HOH -D76 : HOH -D77 : HOH -D78 : HOH -D79 : HOH -D80 : HOH -D81 : HOH -D82 : HOH -D83 : HOH -E31 : HOH -E32 : HOH -E33 : HOH -E34 : HOH -E35 : HOH -E36 : HOH -E37 : HOH -E38 : HOH -E39 : HOH -E40 : HOH -E41 : HOH -E42 : HOH -E43 : HOH -E44 : HOH -E45 : HOH -E46 : HOH -E47 : HOH -E48 : HOH -E49 : HOH -E50 : HOH -E51 : HOH -E52 : HOH -E53 : HOH -E54 : HOH -E55 : HOH -E56 : HOH -E57 : HOH -E58 : HOH -E59 : HOH -E60 : HOH -E61 : HOH -E62 : HOH -E63 : HOH -E64 : HOH -E65 : HOH -E66 : HOH -E67 : HOH -E68 : HOH -E69 : HOH -E70 : HOH -E71 : HOH -E72 : HOH -E73 : HOH -E74 : HOH -E75 : HOH -E76 : HOH -E77 : HOH -E78 : HOH -E79 : HOH -E80 : HOH -E81 : HOH -E82 : HOH -A181 : HOH -A182 : HOH -A183 : HOH -A184 : HOH -A185 : HOH -A186 : HOH -A187 : HOH -A188 : HOH -A189 : HOH -A190 : HOH -A191 : HOH -A192 : HOH -A193 : HOH -A194 : HOH -A195 : HOH -A196 : HOH -A197 : HOH -A198 : HOH -A199 : HOH -A200 : HOH -A201 : HOH -A202 : HOH -A203 : HOH -A204 : HOH -A205 : HOH -A206 : HOH -A207 : HOH -A208 : HOH -A209 : HOH -A210 : HOH -A211 : HOH -A212 : HOH -A213 : HOH -A214 : HOH -A215 : HOH -A216 : HOH -A217 : HOH -A218 : HOH -A219 : HOH -A220 : HOH -A221 : HOH -A222 : HOH -A223 : HOH -A224 : HOH -A225 : HOH -A226 : HOH -A227 : HOH -A228 : HOH -A229 : HOH -A230 : HOH -A231 : HOH -A232 : HOH -A233 : HOH -A234 : HOH -A235 : HOH -A236 : HOH -A237 : HOH -A238 : HOH -A239 : HOH -A240 : HOH -A241 : HOH -A242 : HOH -A243 : HOH -A244 : HOH -A245 : HOH -A246 : HOH -A247 : HOH -A248 : HOH -A249 : HOH -A250 : HOH -A251 : HOH -A252 : HOH -A253 : HOH -A254 : HOH -A255 : HOH -A256 : HOH -A257 : HOH -A258 : HOH -A259 : HOH -A260 : HOH -A261 : HOH -A262 : HOH -A263 : HOH -A264 : HOH -A265 : HOH -A266 : HOH -A267 : HOH -A268 : HOH -A269 : HOH -A270 : HOH -A271 : HOH -A272 : HOH -A273 : HOH -A274 : HOH -A275 : HOH -A276 : HOH -A277 : HOH -B181 : HOH -B182 : HOH -B183 : HOH -B184 : HOH -B185 : HOH -B186 : HOH -B187 : HOH -B188 : HOH -B189 : HOH -B190 : HOH -B191 : HOH -B192 : HOH -B193 : HOH -B194 : HOH -B195 : HOH -B196 : HOH -B197 : HOH -B198 : HOH -B199 : HOH -B200 : HOH -B201 : HOH -B202 : HOH -B203 : HOH -B204 : HOH -B205 : HOH -B206 : HOH -B207 : HOH -B208 : HOH -B209 : HOH -B210 : HOH -B211 : HOH -B212 : HOH -B213 : HOH -B214 : HOH -B215 : HOH -B216 : HOH -B217 : HOH -B218 : HOH -B219 : HOH -B220 : HOH -B221 : HOH -B222 : HOH -B223 : HOH -B224 : HOH -B225 : HOH -B226 : HOH -B227 : HOH -B228 : HOH -B229 : HOH -B230 : HOH -B231 : HOH -B232 : HOH -B233 : HOH -B234 : HOH -B235 : HOH -B236 : HOH -B237 : HOH -B238 : HOH -B239 : HOH -B240 : HOH -B241 : HOH -B242 : HOH -B243 : HOH -B244 : HOH -B245 : HOH -B246 : HOH -B247 : HOH -B248 : HOH -B249 : HOH -B250 : HOH -B251 : HOH -B252 : HOH -B253 : HOH -B254 : HOH -B255 : HOH -B256 : HOH -B257 : HOH -B258 : HOH -B259 : HOH -B260 : HOH -B261 : HOH -B262 : HOH -B263 : HOH -B264 : HOH -Adjacent stackings ---------------------------------------------- -C1-C2 : adjacent_5p upward -C2-C3 : adjacent_5p upward -C3-C4 : adjacent_5p upward -C4-C5 : adjacent_5p upward -C6-C7 : adjacent_5p upward -C8-C9 : adjacent_5p upward -C9-C10 : adjacent_5p upward -D11-D12 : adjacent_5p upward -D12-D13 : adjacent_5p upward -D13-D14 : adjacent_5p upward -D14-D15 : adjacent_5p upward -D16-D17 : adjacent_5p upward -D18-D19 : adjacent_5p upward -D19-D20 : adjacent_5p upward -E21-E22 : adjacent_5p upward -E22-E23 : adjacent_5p upward -E23-E24 : adjacent_5p upward -E24-E25 : adjacent_5p upward -E25-E26 : adjacent_5p upward -E26-E27 : adjacent_5p upward -E28-E29 : adjacent_5p upward -E29-E30 : adjacent_5p upward -G41-G42 : adjacent_5p upward -G42-G43 : adjacent_5p upward -G44-G45 : adjacent_5p upward -G45-G46 : adjacent_5p upward -G46-G47 : adjacent_5p upward -G48-G49 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -C4-D18 : outward -C6-D16 : outward -C8-D14 : outward -D11-G41 : outward -Number of stackings = 32 -Number of adjacent stackings = 28 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -C1-D20 : G-C Ww/Ww pairing antiparallel cis XIX -C2-D19 : G-C Ww/Ww pairing antiparallel cis XIX -C3-D18 : C-G Ww/Ww pairing antiparallel cis XIX -C4-D17 : G-C Ww/Ww pairing antiparallel cis XIX -C5-D16 : C-G Ww/Ww pairing antiparallel cis XIX -C6-D15 : G-C Ww/Ww pairing antiparallel cis XIX -C7-D14 : C-G Ww/Ww pairing antiparallel cis XIX -C8-D13 : G-C Ww/Ww pairing antiparallel cis XIX -C9-D12 : C-G Ww/Ww pairing antiparallel cis XIX -C10-D11 : C-G Ww/Ww pairing antiparallel cis XIX diff --git a/MCdata/1dk1_MC b/MCdata/1dk1_MC deleted file mode 100644 index 8a68ee16efeb3971a30afdd26ff7535a06506693..0000000000000000000000000000000000000000 --- a/MCdata/1dk1_MC +++ /dev/null @@ -1,255 +0,0 @@ -Residue conformations ------------------------------------------- -B1 : G C3p_endo anti -B2 : G C3p_endo anti -B3 : G C3p_endo anti -B4 : C C3p_endo anti -B5 : G C3p_exo anti -B6 : G C3p_endo anti -B7 : C C3p_endo anti -B8 : C C3p_endo anti -B9 : U C3p_endo anti -B10 : U C2p_endo anti -B11 : C C2p_endo anti -B12 : G C3p_endo syn -B13 : G C3p_endo anti -B14 : G C2p_exo anti -B15 : C C4p_exo anti -B16 : U C4p_exo anti -B17 : A C3p_exo anti -B18 : G C3p_endo anti -B19 : A C3p_endo anti -B20 : C C3p_endo anti -B21 : G C3p_endo anti -B22 : G C3p_endo anti -B23 : U C3p_endo anti -B24 : G C3p_endo anti -B25 : G C3p_endo anti -B26 : G C3p_endo anti -B27 : A C3p_endo anti -B28 : G C4p_endo anti -B29 : A C2p_endo anti -B30 : G C3p_endo anti -B31 : G C3p_endo anti -B32 : C C3p_endo anti -B33 : U C3p_endo anti -B34 : U C2p_endo syn -B35 : C C2p_endo anti -B36 : G C3p_endo anti -B37 : G C2p_exo anti -B38 : C C3p_endo anti -B39 : U C3p_endo anti -B40 : G C3p_endo anti -B41 : G C3p_endo anti -B42 : U C3p_endo anti -B43 : C C3p_endo anti -B44 : C C2p_exo anti -B45 : A C3p_endo anti -B46 : C C2p_endo anti -B47 : C C2p_endo syn -B48 : C C3p_endo anti -B49 : G C3p_endo anti -B50 : U C3p_endo anti -B51 : G C2p_endo anti -B52 : A C2p_endo anti -B53 : C C3p_endo syn -B54 : G C3p_endo anti -B55 : C C3p_endo anti -B56 : U C3p_endo anti -B57 : C C2p_exo anti -A101 : PRO -A102 : ILE -A103 : THR -A104 : LYS -A105 : GLU -A106 : GLU -A107 : LYS -A108 : GLN -A109 : LYS -A110 : VAL -A111 : MSE -A112 : GLN -A113 : GLU -A114 : PHE -A115 : ALA -A116 : ARG -A117 : PHE -A118 : PRO -A119 : GLY -A120 : ASP -A121 : THR -A122 : GLY -A123 : SER -A124 : THR -A125 : GLU -A126 : VAL -A127 : GLN -A128 : VAL -A129 : ALA -A130 : LEU -A131 : LEU -A132 : THR -A133 : LEU -A134 : ARG -A135 : ILE -A136 : ASN -A137 : ARG -A138 : LEU -A139 : SER -A140 : GLU -A141 : HIS -A142 : LEU -A143 : LYS -A144 : VAL -A145 : HIS -A146 : LYS -A147 : LYS -A148 : ASP -A149 : HIS -A150 : HIS -A151 : SER -A152 : HIS -A153 : ARG -A154 : GLY -A155 : LEU -A156 : LEU -A157 : MSE -A158 : MSE -A159 : VAL -A160 : GLY -A161 : GLN -A162 : ARG -A163 : ARG -A164 : ARG -A165 : LEU -A166 : LEU -A167 : ARG -A168 : TYR -A169 : LEU -A170 : GLN -A171 : ARG -A172 : GLU -A173 : ASP -A174 : PRO -A175 : GLU -A176 : ARG -A177 : TYR -A178 : ARG -A179 : MSE -A180 : LEU -A181 : ILE -A182 : GLU -A183 : LYS -A184 : LEU -A185 : GLY -A186 : ILE -B200 : MG -B201 : MG -B202 : MG -B203 : MG -B204 : MG -B205 : MG -B206 : MG -B208 : MG -B209 : MG -B210 : NA -B211 : NA -A213 : K -B301 : HOH -B305 : HOH -B307 : HOH -B308 : HOH -B309 : HOH -B310 : HOH -B311 : HOH -B313 : HOH -B314 : HOH -B315 : HOH -B316 : HOH -B317 : HOH -B318 : HOH -B319 : HOH -B322 : HOH -B323 : HOH -B324 : HOH -A300 : HOH -A302 : HOH -A303 : HOH -A304 : HOH -A306 : HOH -A312 : HOH -A320 : HOH -A321 : HOH -Adjacent stackings ---------------------------------------------- -B1-B2 : adjacent_5p upward -B2-B3 : adjacent_5p upward -B3-B4 : adjacent_5p upward -B6-B7 : adjacent_5p upward -B7-B8 : adjacent_5p upward -B8-B9 : adjacent_5p upward -B13-B14 : adjacent_5p upward -B14-B15 : adjacent_5p upward -B15-B16 : adjacent_5p upward -B18-B19 : adjacent_5p upward -B19-B20 : adjacent_5p upward -B21-B22 : adjacent_5p upward -B22-B23 : adjacent_5p upward -B23-B24 : adjacent_5p upward -B24-B25 : adjacent_5p upward -B25-B26 : adjacent_5p upward -B26-B27 : adjacent_5p upward -B27-B28 : adjacent_5p upward -B30-B31 : adjacent_5p upward -B31-B32 : adjacent_5p upward -B32-B33 : adjacent_5p upward -B37-B38 : adjacent_5p upward -B38-B39 : adjacent_5p upward -B40-B41 : adjacent_5p upward -B41-B42 : adjacent_5p upward -B44-B45 : adjacent_5p upward -B45-B46 : adjacent_5p upward -B49-B50 : adjacent_5p upward -B50-B51 : adjacent_5p upward -B54-B55 : adjacent_5p upward -B55-B56 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -B2-B57 : outward -B5-B54 : outward -B6-B52 : downward pairing -B8-B14 : outward -B9-B11 : upward -B16-B51 : inward -B18-B52 : outward -B21-B49 : outward -B24-B45 : outward -B30-B40 : outward -Number of stackings = 41 -Number of adjacent stackings = 31 -Number of non adjacent stackings = 10 -Base-pairs ------------------------------------------------------ -B1-B57 : G-C Ww/Ww pairing antiparallel cis XIX -B2-B56 : G-U Ww/Ws pairing antiparallel cis XXVIII -B3-B55 : G-C Ww/Ww pairing antiparallel cis XIX -B4-B54 : C-G Ww/Ww pairing antiparallel cis XIX -B5-B53 : G-C Ww/O2P Bs/O2P pairing -B6-B15 : G-C Ww/Ww pairing antiparallel cis XIX -B6-B52 : G-A Hh/O2' downward pairing -B7-B14 : C-G Ww/Ww pairing antiparallel cis XIX -B8-B13 : C-G Ww/Ww pairing antiparallel cis XIX -B9-B12 : U-G Bs/Ww pairing parallel trans 87 -B10-B11 : U-C O2P/Bh adjacent_5p pairing -B16-B52 : U-A Ww/Hh pairing antiparallel trans XXIV -B18-B51 : G-G Hw/Sw pairing antiparallel trans one_hbond 112 -B18-B53 : G-C Ww/Ww pairing antiparallel cis XIX -B19-B50 : A-U Ww/Ww pairing antiparallel cis XX -B20-B49 : C-G Ww/Ww pairing antiparallel cis XIX -B21-B48 : G-C Ww/Ww pairing antiparallel cis XIX -B22-B46 : G-C Ww/Ww pairing antiparallel cis XIX -B23-B45 : U-A Ww/Ww pairing antiparallel cis XX -B24-B44 : G-C Ww/Ww pairing antiparallel cis XIX -B25-B43 : G-C Ww/Ww pairing antiparallel cis XIX -B26-B42 : G-U Ww/Ws pairing antiparallel cis XXVIII -B27-B41 : A-G Ww/Ww pairing antiparallel cis VIII -B30-B39 : G-U Ww/Ws pairing antiparallel cis XXVIII -B31-B38 : G-C Ww/Ww pairing antiparallel cis XIX -B32-B37 : C-G Ww/Ww pairing antiparallel cis XIX -B34-B35 : U-C O2P/Bh adjacent_5p pairing diff --git a/MCdata/1dqf_MC b/MCdata/1dqf_MC deleted file mode 100644 index eed45dcdbd3f6355bd4de05927512b0b9e83d1c1..0000000000000000000000000000000000000000 --- a/MCdata/1dqf_MC +++ /dev/null @@ -1,92 +0,0 @@ -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : C C3p_endo anti -A3 : C C3p_endo anti -A4 : A C3p_endo anti -A5 : C C3p_endo anti -A6 : C C3p_endo anti -A7 : C C3p_endo anti -A8 : U C3p_endo anti -A9 : G C3p_endo anti -B10 : C C3p_endo anti -B11 : A C3p_endo anti -B12 : G C3p_endo anti -B13 : G C3p_endo anti -B14 : G C3p_endo anti -B15 : U C3p_endo anti -B16 : C C3p_endo anti -B17 : G C3p_endo anti -B18 : G C3p_endo anti -B19 : C C3p_endo anti -B201 : CA -B202 : CA -A102 : HOH -A113 : HOH -A114 : HOH -A115 : HOH -A123 : HOH -A124 : HOH -A125 : HOH -A127 : HOH -A128 : HOH -A132 : HOH -A134 : HOH -A137 : HOH -B101 : HOH -B103 : HOH -B104 : HOH -B105 : HOH -B106 : HOH -B107 : HOH -B108 : HOH -B109 : HOH -B110 : HOH -B111 : HOH -B112 : HOH -B116 : HOH -B117 : HOH -B118 : HOH -B119 : HOH -B120 : HOH -B121 : HOH -B122 : HOH -B126 : HOH -B129 : HOH -B130 : HOH -B131 : HOH -B133 : HOH -B135 : HOH -B136 : HOH -B138 : HOH -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -B10-B11 : adjacent_5p upward -B11-B12 : adjacent_5p upward -B12-B13 : adjacent_5p upward -B13-B14 : adjacent_5p upward -B14-B15 : adjacent_5p upward -B17-B18 : adjacent_5p upward -B18-B19 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-B17 : outward -A9-B11 : outward -Number of stackings = 17 -Number of adjacent stackings = 15 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A1-B19 : G-C Ww/Ww pairing antiparallel cis XIX -A2-B18 : C-G Ww/Ww pairing antiparallel cis XIX -A3-B17 : C-G Ww/Ww pairing antiparallel cis XIX -A4-B15 : A-U Ww/Ww pairing antiparallel cis XX -A5-B14 : C-G Ww/Ww pairing antiparallel cis XIX -A6-B13 : C-G Ww/Ww pairing antiparallel cis XIX -A7-B12 : C-G Ww/Ww pairing antiparallel cis XIX -A8-B11 : U-A Ww/Ww pairing antiparallel cis XX -A9-B10 : G-C Ww/Ww pairing antiparallel cis XIX diff --git a/MCdata/1dqh_MC b/MCdata/1dqh_MC deleted file mode 100644 index 5c1201ee911e95b9bca04bb40998790ef29a4234..0000000000000000000000000000000000000000 --- a/MCdata/1dqh_MC +++ /dev/null @@ -1,109 +0,0 @@ -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : C C3p_endo anti -A3 : C C3p_endo anti -A4 : A C3p_endo anti -A5 : C C3p_endo anti -A6 : C C3p_endo anti -A7 : C C3p_endo anti -A8 : U C3p_endo anti -A9 : G C3p_endo anti -B10 : C C3p_endo anti -B11 : A C3p_endo anti -B12 : G C3p_endo anti -B13 : G C3p_endo anti -B14 : G C3p_endo anti -B15 : U C3p_endo anti -B16 : C C3p_endo anti -B17 : G C3p_endo anti -B18 : G C3p_endo anti -B19 : C C3p_endo anti -A103 : HOH -A107 : HOH -A108 : HOH -A124 : HOH -A126 : HOH -A127 : HOH -A131 : HOH -A132 : HOH -A133 : HOH -A135 : HOH -A140 : HOH -A141 : HOH -A142 : HOH -A145 : HOH -A151 : HOH -A153 : HOH -A155 : HOH -A156 : HOH -B100 : HOH -B101 : HOH -B102 : HOH -B104 : HOH -B105 : HOH -B106 : HOH -B109 : HOH -B110 : HOH -B111 : HOH -B112 : HOH -B113 : HOH -B114 : HOH -B115 : HOH -B116 : HOH -B117 : HOH -B118 : HOH -B119 : HOH -B120 : HOH -B121 : HOH -B122 : HOH -B123 : HOH -B125 : HOH -B128 : HOH -B129 : HOH -B130 : HOH -B134 : HOH -B136 : HOH -B137 : HOH -B138 : HOH -B139 : HOH -B143 : HOH -B144 : HOH -B146 : HOH -B147 : HOH -B148 : HOH -B149 : HOH -B150 : HOH -B152 : HOH -B154 : HOH -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -B10-B11 : adjacent_5p upward -B11-B12 : adjacent_5p upward -B12-B13 : adjacent_5p upward -B13-B14 : adjacent_5p upward -B14-B15 : adjacent_5p upward -B17-B18 : adjacent_5p upward -B18-B19 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-B17 : outward -A9-B11 : outward -Number of stackings = 17 -Number of adjacent stackings = 15 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A1-B19 : G-C Ww/Ww pairing antiparallel cis XIX -A2-B18 : C-G Ww/Ww pairing antiparallel cis XIX -A3-B17 : C-G Ww/Ww pairing antiparallel cis XIX -A4-B15 : A-U Ww/Ww pairing antiparallel cis XX -A5-B14 : C-G Ww/Ww pairing antiparallel cis XIX -A6-B13 : C-G Ww/Ww pairing antiparallel cis XIX -A7-B12 : C-G Ww/Ww pairing antiparallel cis XIX -A8-B11 : U-A Ww/Ww pairing antiparallel cis XX -A9-B10 : G-C Ww/Ww pairing antiparallel cis XIX diff --git a/MCdata/1drr_MC b/MCdata/1drr_MC deleted file mode 100644 index f88a9fddc825166cce6cc8c4096280830e59b81c..0000000000000000000000000000000000000000 --- a/MCdata/1drr_MC +++ /dev/null @@ -1,485 +0,0 @@ -Residue conformations ------------------------------------------- -A1 : G C1p_exo anti -A2 : A C1p_exo anti -A3 : A C1p_exo anti -A4 : G C3p_endo anti -A5 : A C1p_exo anti -A6 : G C1p_exo anti -A7 : A C3p_endo anti -A8 : A C3p_endo anti -A9 : G C3p_endo anti -A10 : C C1p_exo anti -B1 : G C3p_endo anti -B2 : C C2p_exo anti -B3 : U C3p_endo anti -B4 : U C2p_exo anti -B5 : C C3p_endo anti -B6 : U C3p_endo anti -B7 : C C3p_endo anti -B8 : U C3p_endo anti -B9 : U C3p_endo anti -B10 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -B1-B2 : adjacent_5p upward -B8-B9 : adjacent_5p upward -B9-B10 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A9-B3 : outward -Number of stackings = 13 -Number of adjacent stackings = 12 -Number of non adjacent stackings = 1 -Base-pairs ------------------------------------------------------ -A1-B10 : G-C Ww/Ww pairing antiparallel cis XIX -A2-B9 : A-U Ww/Ww pairing antiparallel cis XX -A3-B8 : A-U Ww/Ww pairing antiparallel cis XX -A4-B7 : G-C Ww/Ww pairing antiparallel cis XIX -A5-B6 : A-U Ww/Ww pairing antiparallel cis XX -A6-B5 : G-C Ww/Ww pairing antiparallel cis XIX -A7-B4 : A-U Ww/Ww pairing antiparallel cis XX -A8-B3 : A-U Ww/Ww pairing antiparallel cis XX -A9-B2 : G-C Ww/Ww pairing antiparallel cis XIX -A10-B1 : C-G Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -A1 : G C1p_exo anti -A2 : A C1p_exo anti -A3 : A C1p_exo anti -A4 : G C1p_exo anti -A5 : A C1p_exo anti -A6 : G C1p_exo anti -A7 : A C1p_exo anti -A8 : A C1p_exo anti -A9 : G C1p_exo anti -A10 : C C1p_exo anti -B1 : G C3p_endo anti -B2 : C C3p_endo anti -B3 : U C3p_endo anti -B4 : U C2p_exo anti -B5 : C C3p_endo anti -B6 : U C2p_exo anti -B7 : C C2p_exo anti -B8 : U C2p_exo anti -B9 : U C3p_endo anti -B10 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -B1-B2 : adjacent_5p upward -B3-B4 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 11 -Number of adjacent stackings = 11 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-B10 : G-C Ww/Ww pairing antiparallel cis XIX -A2-B9 : A-U Ww/Ww pairing antiparallel cis XX -A3-B8 : A-U Ww/Ww pairing antiparallel cis XX -A4-B7 : G-C Ww/Ww pairing antiparallel cis XIX -A5-B6 : A-U Ww/Ww pairing antiparallel cis XX -A6-B5 : G-C Ww/Ww pairing antiparallel cis XIX -A7-B4 : A-U Ww/Ww pairing antiparallel cis XX -A8-B3 : A-U Ww/Ww pairing antiparallel cis XX -A9-B2 : G-C Ww/Ww pairing antiparallel cis XIX -A10-B1 : C-G Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -A1 : G C1p_exo anti -A2 : A C1p_exo anti -A3 : A C3p_endo anti -A4 : G C1p_exo anti -A5 : A C1p_exo anti -A6 : G C3p_endo anti -A7 : A C1p_exo anti -A8 : A C1p_exo anti -A9 : G C1p_exo anti -A10 : C C1p_exo anti -B1 : G O4p_endo anti -B2 : C C3p_endo anti -B3 : U C2p_exo anti -B4 : U C3p_endo anti -B5 : C C3p_endo anti -B6 : U C3p_endo anti -B7 : C C3p_endo anti -B8 : U C2p_exo anti -B9 : U C3p_endo anti -B10 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -B1-B2 : adjacent_5p upward -B4-B5 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 11 -Number of adjacent stackings = 11 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-B10 : G-C Ww/Ww pairing antiparallel cis XIX -A2-B9 : A-U Ww/Ww pairing antiparallel cis XX -A3-B8 : A-U Ww/Ww pairing antiparallel cis XX -A4-B7 : G-C Ww/Ww pairing antiparallel cis XIX -A5-B6 : A-U Ww/Ww pairing antiparallel cis XX -A6-B5 : G-C Ww/Ww pairing antiparallel cis XIX -A7-B4 : A-U Ww/Ww pairing antiparallel cis XX -A8-B3 : A-U Ww/Ww pairing antiparallel cis XX -A9-B2 : G-C Ww/Ww pairing antiparallel cis XIX -A10-B1 : C-G Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -A1 : G C1p_exo anti -A2 : A C1p_exo anti -A3 : A C1p_exo anti -A4 : G C1p_exo anti -A5 : A C1p_exo anti -A6 : G C1p_exo anti -A7 : A C1p_exo anti -A8 : A C1p_exo anti -A9 : G C1p_exo anti -A10 : C C1p_exo anti -B1 : G C3p_endo anti -B2 : C C3p_endo anti -B3 : U C3p_endo anti -B4 : U C2p_exo anti -B5 : C C3p_endo anti -B6 : U C3p_endo anti -B7 : C C2p_exo anti -B8 : U C3p_endo anti -B9 : U C3p_endo anti -B10 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -B1-B2 : adjacent_5p upward -B3-B4 : adjacent_5p upward -B9-B10 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 12 -Number of adjacent stackings = 12 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-B10 : G-C Ww/Ww pairing antiparallel cis XIX -A2-B9 : A-U Ww/Ww pairing antiparallel cis XX -A3-B8 : A-U Ww/Ww pairing antiparallel cis XX -A4-B7 : G-C Ww/Ww pairing antiparallel cis XIX -A5-B6 : A-U Ww/Ww pairing antiparallel cis XX -A6-B5 : G-C Ww/Ww pairing antiparallel cis XIX -A7-B4 : A-U Ww/Ww pairing antiparallel cis XX -A8-B3 : A-U Ww/Ww pairing antiparallel cis XX -A9-B2 : G-C Ww/Ww pairing antiparallel cis XIX -A10-B1 : C-G Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -A1 : G C1p_exo anti -A2 : A C1p_exo anti -A3 : A C1p_exo anti -A4 : G C1p_exo anti -A5 : A C1p_exo anti -A6 : G C1p_exo anti -A7 : A C3p_endo anti -A8 : A C1p_exo anti -A9 : G C3p_endo anti -A10 : C C1p_exo anti -B1 : G C3p_endo anti -B2 : C C3p_endo anti -B3 : U C3p_endo anti -B4 : U C2p_exo anti -B5 : C C3p_endo anti -B6 : U C3p_endo anti -B7 : C C2p_exo anti -B8 : U C3p_endo anti -B9 : U C3p_endo anti -B10 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -B1-B2 : adjacent_5p upward -B6-B7 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 11 -Number of adjacent stackings = 11 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-B10 : G-C Ww/Ww pairing antiparallel cis XIX -A2-B9 : A-U Ww/Ww pairing antiparallel cis XX -A3-B8 : A-U Ww/Ww pairing antiparallel cis XX -A4-B7 : G-C Ww/Ww pairing antiparallel cis XIX -A5-B6 : A-U Ww/Ww pairing antiparallel cis XX -A6-B5 : G-C Ww/Ww pairing antiparallel cis XIX -A7-B4 : A-U Ww/Ww pairing antiparallel cis XX -A8-B3 : A-U Ww/Ww pairing antiparallel cis XX -A9-B2 : G-C Ww/Ww pairing antiparallel cis XIX -A10-B1 : C-G Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : A C1p_exo anti -A3 : A C1p_exo anti -A4 : G C1p_exo anti -A5 : A C1p_exo anti -A6 : G C1p_exo anti -A7 : A C1p_exo anti -A8 : A C1p_exo anti -A9 : G C1p_exo anti -A10 : C C1p_exo anti -B1 : G C3p_endo anti -B2 : C C2p_exo anti -B3 : U C3p_endo anti -B4 : U C3p_endo anti -B5 : C C2p_exo anti -B6 : U C3p_endo anti -B7 : C C2p_exo anti -B8 : U C3p_endo anti -B9 : U C3p_endo anti -B10 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -B1-B2 : adjacent_5p upward -B3-B4 : adjacent_5p upward -B4-B5 : adjacent_5p upward -B9-B10 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 13 -Number of adjacent stackings = 13 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-B10 : G-C Ww/Ww pairing antiparallel cis XIX -A2-B9 : A-U Ww/Ww pairing antiparallel cis XX -A3-B8 : A-U Ww/Ww pairing antiparallel cis XX -A4-B7 : G-C Ww/Ww pairing antiparallel cis XIX -A5-B6 : A-U Ww/Ww pairing antiparallel cis XX -A6-B5 : G-C Ww/Ww pairing antiparallel cis XIX -A7-B4 : A-U Ww/Ww pairing antiparallel cis XX -A8-B3 : A-U Ww/Ww pairing antiparallel cis XX -A9-B2 : G-C Ww/Ww pairing antiparallel cis XIX -A10-B1 : C-G Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -A1 : G C1p_exo anti -A2 : A C1p_exo anti -A3 : A C1p_exo anti -A4 : G C1p_exo anti -A5 : A C3p_endo anti -A6 : G C1p_exo anti -A7 : A C1p_exo anti -A8 : A C1p_exo anti -A9 : G C3p_endo anti -A10 : C C3p_endo anti -B1 : G C3p_endo anti -B2 : C C2p_exo anti -B3 : U C3p_endo anti -B4 : U C3p_endo anti -B5 : C C3p_endo anti -B6 : U C2p_exo anti -B7 : C C3p_endo anti -B8 : U C2p_exo anti -B9 : U C3p_endo anti -B10 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -B1-B2 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 10 -Number of adjacent stackings = 10 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-B10 : G-C Ww/Ww pairing antiparallel cis XIX -A2-B9 : A-U Ww/Ww pairing antiparallel cis XX -A3-B8 : A-U Ww/Ww pairing antiparallel cis XX -A4-B7 : G-C Ww/Ww pairing antiparallel cis XIX -A5-B6 : A-U Ww/Ww pairing antiparallel cis XX -A6-B5 : G-C Ww/Ww pairing antiparallel cis XIX -A7-B4 : A-U Ww/Ww pairing antiparallel cis XX -A8-B3 : A-U Ww/Ww pairing antiparallel cis XX -A9-B2 : G-C Ww/Ww pairing antiparallel cis XIX -A10-B1 : C-G Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : A C1p_exo anti -A3 : A C1p_exo anti -A4 : G C1p_exo anti -A5 : A C1p_exo anti -A6 : G C1p_exo anti -A7 : A C1p_exo anti -A8 : A C3p_endo anti -A9 : G C1p_exo anti -A10 : C C1p_exo anti -B1 : G C3p_endo anti -B2 : C C3p_endo anti -B3 : U C3p_endo anti -B4 : U C2p_exo anti -B5 : C C3p_endo anti -B6 : U C3p_endo anti -B7 : C C3p_endo anti -B8 : U C3p_endo anti -B9 : U C3p_endo anti -B10 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -B1-B2 : adjacent_5p upward -B5-B6 : adjacent_5p upward -B6-B7 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 12 -Number of adjacent stackings = 12 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-B10 : G-C Ww/Ww pairing antiparallel cis XIX -A2-B9 : A-U Ww/Ww pairing antiparallel cis XX -A3-B8 : A-U Ww/Ww pairing antiparallel cis XX -A4-B7 : G-C Ww/Ww pairing antiparallel cis XIX -A5-B6 : A-U Ww/Ww pairing antiparallel cis XX -A6-B5 : G-C Ww/Ww pairing antiparallel cis XIX -A7-B4 : A-U Ww/Ww pairing antiparallel cis XX -A8-B3 : A-U Ww/Ww pairing antiparallel cis XX -A9-B2 : G-C Ww/Ww pairing antiparallel cis XIX -A10-B1 : C-G Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -A1 : G C1p_exo anti -A2 : A C1p_exo anti -A3 : A C1p_exo anti -A4 : G C1p_exo anti -A5 : A C1p_exo anti -A6 : G C1p_exo anti -A7 : A C1p_exo anti -A8 : A C1p_exo anti -A9 : G C1p_exo anti -A10 : C C1p_exo anti -B1 : G C3p_endo anti -B2 : C C3p_endo anti -B3 : U C2p_exo anti -B4 : U C3p_endo anti -B5 : C C2p_exo anti -B6 : U C2p_exo anti -B7 : C C3p_endo anti -B8 : U C2p_exo anti -B9 : U C3p_endo anti -B10 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -B1-B2 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 10 -Number of adjacent stackings = 10 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-B10 : G-C Ww/Ww pairing antiparallel cis XIX -A2-B9 : A-U Ww/Ww pairing antiparallel cis XX -A3-B8 : A-U Ww/Ww pairing antiparallel cis XX -A4-B7 : G-C Ww/Ww pairing antiparallel cis XIX -A5-B6 : A-U Ww/Ww pairing antiparallel cis XX -A6-B5 : G-C Ww/Ww pairing antiparallel cis XIX -A7-B4 : A-U Ww/Ww pairing antiparallel cis XX -A8-B3 : A-U Ww/Ww pairing antiparallel cis XX -A9-B2 : G-C Ww/Ww pairing antiparallel cis XIX -A10-B1 : C-G Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -A1 : G C1p_exo anti -A2 : A C1p_exo anti -A3 : A C1p_exo anti -A4 : G C1p_exo anti -A5 : A C3p_endo anti -A6 : G C1p_exo anti -A7 : A C1p_exo anti -A8 : A C1p_exo anti -A9 : G C1p_exo anti -A10 : C C3p_endo anti -B1 : G C4p_exo anti -B2 : C C3p_endo anti -B3 : U C3p_endo anti -B4 : U C3p_endo anti -B5 : C C3p_endo anti -B6 : U C3p_endo anti -B7 : C C3p_endo anti -B8 : U C3p_endo anti -B9 : U C3p_endo anti -B10 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -B1-B2 : adjacent_5p upward -B3-B4 : adjacent_5p upward -B9-B10 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 12 -Number of adjacent stackings = 12 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-B10 : G-C Ww/Ww pairing antiparallel cis XIX -A2-B9 : A-U Ww/Ww pairing antiparallel cis XX -A3-B8 : A-U Ww/Ww pairing antiparallel cis XX -A4-B7 : G-C Ww/Ww pairing antiparallel cis XIX -A5-B6 : A-U Ww/Ww pairing antiparallel cis XX -A6-B5 : G-C Ww/Ww pairing antiparallel cis XIX -A7-B4 : A-U Ww/Ww pairing antiparallel cis XX -A8-B3 : A-U Ww/Ww pairing antiparallel cis XX -A9-B2 : G-C Ww/Ww pairing antiparallel cis XIX -A10-B1 : C-G Ww/Ww pairing antiparallel cis XIX diff --git a/MCdata/1drz_MC b/MCdata/1drz_MC deleted file mode 100644 index d66d6a07363faa9a2e63c2b63201d2995239f75b..0000000000000000000000000000000000000000 --- a/MCdata/1drz_MC +++ /dev/null @@ -1,284 +0,0 @@ -Residue conformations ------------------------------------------- -B101 : G C3p_endo anti -B102 : G C3p_endo anti -B103 : C C3p_endo anti -B104 : C C3p_endo anti -B105 : G C3p_endo anti -B106 : G C3p_endo anti -B107 : C C3p_endo anti -B108 : A C3p_endo anti -B109 : U C3p_endo anti -B110 : G C3p_endo anti -B111 : G C3p_endo anti -B112 : U C3p_endo anti -B113 : C C3p_endo anti -B114 : C C3p_endo anti -B115 : C C3p_endo anti -B116 : A C3p_endo anti -B117 : G C3p_endo anti -B118 : C C3p_endo anti -B119 : C C3p_endo anti -B120 : U C4p_exo anti -B121 : C C3p_endo anti -B122 : C C3p_exo anti -B123 : U C3p_endo anti -B124 : C C4p_exo anti -B125 : G C3p_endo syn -B126 : C C3p_endo anti -B127 : U C3p_endo anti -B128 : G C3p_endo anti -B129 : G C3p_endo anti -B130 : C C3p_endo anti -B131 : G C3p_endo anti -B132 : C C3p_endo anti -B133 : C C3p_endo anti -B134 : G C3p_endo anti -B135 : G C3p_endo anti -B136 : C C3p_endo anti -B137 : U C3p_endo anti -B138 : G C3p_endo anti -B139 : G C3p_endo anti -B140 : G C3p_endo anti -B141 : C C3p_exo anti -B142 : A C3p_endo anti -B143 : A C3p_endo anti -B144 : C C3p_endo anti -B145 : A C3p_endo anti -B146 : C C3p_endo anti -B147 : C C3p_endo anti -B148 : A C3p_endo anti -B149 : U C3p_endo anti -B150 : U C2p_endo anti -B151 : G C3p_endo anti -B152 : C C2p_endo anti -B153 : A C3p_endo anti -B154 : C C3p_endo anti -B155 : U C3p_exo anti -B156 : C C3p_endo anti -B157 : C C3p_endo anti -B158 : G C2p_exo anti -B159 : G C3p_endo anti -B160 : U C3p_endo anti -B161 : G C3p_endo anti -B162 : G C3p_exo anti -B163 : C C3p_exo anti -B164 : G C3p_exo anti -B165 : A C3p_endo anti -B166 : A C3p_endo anti -B167 : U C3p_exo anti -B168 : G C3p_endo anti -B169 : G C3p_endo anti -B170 : G C3p_endo anti -B171 : A C3p_endo anti -B172 : C C3p_endo anti -A4 : PRO -A5 : GLU -A6 : THR -A7 : ARG -A8 : PRO -A9 : ASN -A10 : HIS -A11 : THR -A12 : ILE -A13 : TYR -A14 : ILE -A15 : ASN -A16 : ASN -A17 : LEU -A18 : ASN -A19 : GLU -A20 : LYS -A21 : ILE -A22 : LYS -A23 : LYS -A24 : ASP -A25 : GLU -A26 : LEU -A27 : LYS -A28 : LYS -A29 : SER -A30 : LEU -A31 : HIS -A32 : ALA -A33 : ILE -A34 : PHE -A35 : SER -A36 : ARG -A37 : PHE -A38 : GLY -A39 : GLN -A40 : ILE -A41 : LEU -A42 : ASP -A43 : ILE -A44 : LEU -A45 : VAL -A46 : SER -A47 : ARG -A48 : SER -A49 : LEU -A50 : LYS -A51 : MSE -A52 : ARG -A53 : GLY -A54 : GLN -A55 : ALA -A56 : PHE -A57 : VAL -A58 : ILE -A59 : PHE -A60 : LYS -A61 : GLU -A62 : VAL -A63 : SER -A64 : SER -A65 : ALA -A66 : THR -A67 : ASN -A68 : ALA -A69 : LEU -A70 : ARG -A71 : SER -A72 : MSE -A73 : GLN -A74 : GLY -A75 : PHE -A76 : PRO -A77 : PHE -A78 : TYR -A79 : ASP -A80 : LYS -A81 : PRO -A82 : MSE -A83 : ARG -A84 : ILE -A85 : GLN -A86 : TYR -A87 : ALA -A88 : LYS -A89 : THR -A90 : ASP -A91 : SER -A92 : ASP -A93 : ILE -A94 : ILE -A95 : ALA -A96 : LYS -A97 : MSE -A98 : LYS -B401 : MG -B402 : MG -B403 : MG -A404 : SO4 -A405 : SO4 -B305 : HOH -B308 : HOH -B309 : HOH -B310 : HOH -B316 : HOH -B317 : HOH -B318 : HOH -B319 : HOH -A301 : HOH -A302 : HOH -A303 : HOH -A304 : HOH -A306 : HOH -A307 : HOH -A311 : HOH -A312 : HOH -A313 : HOH -A314 : HOH -A315 : HOH -Adjacent stackings ---------------------------------------------- -B101-B102 : adjacent_5p upward -B102-B103 : adjacent_5p upward -B103-B104 : adjacent_5p upward -B105-B106 : adjacent_5p upward -B106-B107 : adjacent_5p upward -B107-B108 : adjacent_5p upward -B108-B109 : adjacent_5p upward -B110-B111 : adjacent_5p upward -B111-B112 : adjacent_5p upward -B112-B113 : adjacent_5p upward -B114-B115 : adjacent_5p upward -B115-B116 : adjacent_5p upward -B116-B117 : adjacent_5p upward -B117-B118 : adjacent_5p upward -B118-B119 : adjacent_5p upward -B119-B120 : adjacent_5p upward -B128-B129 : adjacent_5p upward -B129-B130 : adjacent_5p upward -B131-B132 : adjacent_5p upward -B132-B133 : adjacent_5p upward -B134-B135 : adjacent_5p upward -B135-B136 : adjacent_5p upward -B136-B137 : adjacent_5p upward -B138-B139 : adjacent_5p upward -B139-B140 : adjacent_5p upward -B140-B141 : adjacent_5p upward -B142-B143 : adjacent_5p upward -B143-B144 : adjacent_5p upward -B144-B145 : adjacent_5p upward -B145-B146 : adjacent_5p upward -B146-B147 : adjacent_5p upward -B147-B148 : adjacent_5p upward -B148-B149 : adjacent_5p upward -B153-B154 : adjacent_5p upward -B156-B157 : adjacent_5p upward -B158-B159 : adjacent_5p upward -B159-B160 : adjacent_5p upward -B160-B161 : adjacent_5p upward -B161-B162 : adjacent_5p upward -B165-B166 : adjacent_5p upward -B168-B169 : adjacent_5p upward -B169-B170 : adjacent_5p upward -B170-B171 : adjacent_5p upward -B171-B172 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -B101-B138 : outward -B105-B134 : outward -B108-B131 : outward -B116-B168 : outward -B120-B124 : upward -B121-B162 : downward -B125-B128 : outward -B145-B161 : outward -B163-B165 : outward -Number of stackings = 53 -Number of adjacent stackings = 44 -Number of non adjacent stackings = 9 -Base-pairs ------------------------------------------------------ -B101-B137 : G-U Ww/Ws pairing antiparallel cis XXVIII -B102-B136 : G-C Ww/Ww pairing antiparallel cis XIX -B103-B135 : C-G Ww/Ww pairing antiparallel cis XIX -B104-B134 : C-G Ww/Ww pairing antiparallel cis XIX -B105-B133 : G-C Ww/Ww pairing antiparallel cis XIX -B106-B132 : G-C Ww/Ww pairing antiparallel cis XIX -B107-B131 : C-G Ww/Ww pairing antiparallel cis XIX -B111-B172 : G-C Ww/Ww pairing antiparallel cis XIX -B112-B171 : U-A Ww/Ww pairing antiparallel cis XX -B113-B170 : C-G Ww/Ww pairing antiparallel cis XIX -B114-B169 : C-G Ww/Ww pairing antiparallel cis XIX -B115-B168 : C-G Ww/Ww pairing antiparallel cis XIX -B116-B167 : A-U Ww/Ww pairing antiparallel cis XX -B117-B130 : G-C Ww/Ww pairing antiparallel cis XIX -B118-B129 : C-G Ww/Ww pairing antiparallel cis XIX -B119-B128 : C-G Ww/Ww pairing antiparallel cis XIX -B119-B165 : C-A O2'/Ss pairing -B120-B163 : U-C O2'/Bh pairing -B121-B139 : C-G Ww/Ww pairing antiparallel cis XIX -B121-B142 : C-A O2'/Ww pairing -B122-B138 : C-G Ww/Ww pairing antiparallel cis XIX -B122-B163 : C-C O2P/Bh pairing -B129-B166 : G-A Sw/Ss O2'/Ww pairing parallel trans one_hbond 57 -B140-B142 : G-A O2'/Hh pairing -B140-B162 : G-G Ws/Hw pairing antiparallel trans one_hbond -B141-B161 : C-G Wh/Hh pairing antiparallel trans one_hbond 117 -B143-B162 : A-G Ww/Ww pairing antiparallel cis VIII -B144-B161 : C-G Ww/Ww pairing antiparallel cis XIX -B145-B160 : A-U Ww/Ww pairing antiparallel cis XX -B146-B159 : C-G Ww/Ww pairing antiparallel cis XIX -B147-B158 : C-G Ww/Ww pairing antiparallel cis XIX -B155-B156 : U-C Bs/Hh adjacent_5p pairing parallel cis 99 -B155-B157 : U-C O2'/Bh pairing diff --git a/MCdata/1duh_MC b/MCdata/1duh_MC deleted file mode 100644 index ab26eb360291b2a9917c6f55b6ad2175a877d911..0000000000000000000000000000000000000000 --- a/MCdata/1duh_MC +++ /dev/null @@ -1,93 +0,0 @@ -Residue conformations ------------------------------------------- -A31 : C C3p_endo anti -A32 : U C3p_endo anti -A33 : C C3p_endo anti -A34 : U C3p_endo anti -A35 : G C3p_endo anti -A36 : U C3p_endo anti -A37 : U C3p_endo anti -A38 : U C3p_endo anti -A39 : A C3p_endo anti -A40 : C C3p_endo anti -A41 : C C2p_endo anti -A42 : A C2p_endo syn -A43 : G C3p_endo anti -A44 : G C3p_endo anti -A45 : U C3p_endo anti -A46 : C C3p_endo anti -A47 : A C3p_endo anti -A48 : G C3p_endo anti -A49 : G C3p_endo anti -A50 : U C3p_endo anti -A51 : C C3p_endo anti -A52 : C C3p_endo anti -A53 : G C3p_endo anti -A54 : G C2p_endo anti -A55 : A C3p_endo anti -A56 : A C3p_endo anti -A57 : G C3p_endo anti -A58 : G C3p_endo anti -A59 : A C3p_endo anti -A60 : A C3p_endo anti -A61 : G C3p_endo anti -A62 : C C3p_endo anti -A63 : A C3p_endo anti -A64 : G C3p_endo anti -A65 : C C3p_endo anti -A66 : C C3p_endo anti -A67 : A C3p_endo anti -A68 : A C3p_endo anti -A69 : G C3p_endo anti -A70 : G C3p_endo anti -A71 : C C3p_endo anti -A72 : A C3p_endo anti -A73 : G C3p_endo anti -A74 : A C3p_endo anti -A75 : PGP -A1 : LU -A2 : MG -A3 : SO4 -A4 : SO4 -A101 : HOH -A102 : HOH -A103 : HOH -A104 : HOH -A105 : HOH -A106 : HOH -Adjacent stackings ---------------------------------------------- -A31-A32 : adjacent_5p upward -A34-A35 : adjacent_5p upward -A35-A36 : adjacent_5p upward -A39-A40 : adjacent_5p upward -A43-A44 : adjacent_5p upward -A44-A45 : adjacent_5p upward -A45-A46 : adjacent_5p upward -A47-A48 : adjacent_5p upward -A48-A49 : adjacent_5p upward -A49-A50 : adjacent_5p upward -A50-A51 : adjacent_5p upward -A51-A52 : adjacent_5p upward -A52-A53 : adjacent_5p upward -A53-A54 : adjacent_5p upward -A55-A56 : adjacent_5p upward -A56-A57 : adjacent_5p upward -A57-A58 : adjacent_5p upward -A58-A59 : adjacent_5p upward -A59-A60 : adjacent_5p upward -A60-A61 : adjacent_5p upward -A62-A63 : adjacent_5p upward -A63-A64 : adjacent_5p upward -A64-A65 : adjacent_5p upward -A66-A67 : adjacent_5p upward -A67-A68 : adjacent_5p upward -A68-A69 : adjacent_5p upward -A69-A70 : adjacent_5p upward -A70-A71 : adjacent_5p upward -A72-A73 : adjacent_5p upward -A73-A74 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A40-A42 : inward -Number of stackings = 31 -Number of adjacent stackings = 30 -Number of non adjacent stackings = 1 -Base-pairs ------------------------------------------------------ diff --git a/MCdata/1dul_MC b/MCdata/1dul_MC deleted file mode 100644 index d83bbd7a008a64dc67368bcc0d41ea5813b162bf..0000000000000000000000000000000000000000 --- a/MCdata/1dul_MC +++ /dev/null @@ -1,497 +0,0 @@ -Residue conformations ------------------------------------------- -B130 : G C3p_endo anti -B131 : G C3p_endo anti -B132 : C C3p_endo anti -B133 : U C3p_endo anti -B134 : C C3p_endo anti -B135 : U C3p_endo anti -B136 : G C3p_endo anti -B137 : U C3p_endo anti -B138 : U C3p_endo anti -B139 : U C3p_endo anti -B140 : A C3p_endo anti -B141 : C C3p_endo anti -B142 : C C3p_endo anti -B143 : A C3p_exo anti -B144 : G C3p_endo anti -B145 : G C3p_endo anti -B146 : U C3p_endo anti -B147 : C C3p_endo anti -B148 : A C3p_endo anti -B149 : G C3p_endo anti -B150 : G C3p_endo anti -B151 : U C3p_endo anti -B152 : C C3p_endo anti -B153 : C C3p_endo anti -B154 : G C3p_endo anti -B155 : A C3p_endo anti -B156 : A C3p_endo anti -B157 : A C3p_endo anti -B158 : G C3p_endo anti -B159 : G C2p_exo anti -B160 : A C3p_endo anti -B161 : A C3p_endo anti -B162 : G C3p_endo anti -B163 : C C3p_endo anti -B164 : A C3p_endo anti -B165 : G C3p_endo anti -B166 : C C3p_endo anti -B167 : C C3p_endo anti -B168 : A C3p_endo anti -B169 : A C3p_endo anti -B170 : G C3p_endo anti -B171 : G C3p_endo anti -B172 : C C3p_endo anti -B173 : A C3p_endo anti -B174 : G C3p_endo anti -B175 : A C3p_endo anti -B176 : G C3p_endo anti -B177 : C C3p_endo anti -B178 : CCC -A1 : PHE -A2 : ASP -A3 : LEU -A4 : ASN -A5 : ASP -A6 : PHE -A7 : LEU -A8 : GLU -A9 : GLN -A23 : LYS -A24 : VAL -A25 : LEU -A26 : VAL -A27 : ARG -A28 : MSE -A29 : GLU -A30 : ALA -A31 : ILE -A32 : ILE -A33 : ASN -A34 : SER -A35 : MSE -A36 : THR -A37 : MSE -A38 : LYS -A39 : GLU -A40 : ARG -A41 : ALA -A42 : LYS -A43 : PRO -A44 : GLU -A45 : ILE -A46 : ILE -A47 : LYS -A48 : GLY -A49 : SER -A50 : ARG -A51 : LYS -A52 : ARG -A53 : ARG -A54 : ILE -A55 : ALA -A56 : ALA -A57 : GLY -A58 : SER -A59 : GLY -A60 : MSE -A61 : GLN -A62 : VAL -A63 : GLN -A64 : ASP -A65 : VAL -A66 : ASN -A67 : ARG -A68 : LEU -A69 : LEU -A70 : LYS -A71 : GLN -A72 : PHE -A73 : ASP -A74 : ASP -A75 : MSE -A76 : GLN -A77 : ARG -A78 : MSE -A79 : MSE -A80 : LYS -A81 : LYS -A82 : MSE -B701 : K -B702 : K -B703 : K -B704 : MG -B705 : MG -B706 : MG -B707 : MG -B801 : HOH -B802 : HOH -B803 : HOH -B804 : HOH -B805 : HOH -B806 : HOH -B807 : HOH -B808 : HOH -B809 : HOH -B810 : HOH -B811 : HOH -B812 : HOH -B813 : HOH -B814 : HOH -B815 : HOH -B816 : HOH -B817 : HOH -B818 : HOH -B819 : HOH -B820 : HOH -B821 : HOH -B822 : HOH -B823 : HOH -B824 : HOH -B825 : HOH -B826 : HOH -B827 : HOH -B828 : HOH -B829 : HOH -B830 : HOH -B831 : HOH -B832 : HOH -B833 : HOH -B834 : HOH -B835 : HOH -B836 : HOH -B837 : HOH -B838 : HOH -B839 : HOH -B840 : HOH -B841 : HOH -B842 : HOH -B843 : HOH -B844 : HOH -B845 : HOH -B846 : HOH -B847 : HOH -B848 : HOH -B849 : HOH -B850 : HOH -B851 : HOH -B852 : HOH -B853 : HOH -B854 : HOH -B855 : HOH -B856 : HOH -B857 : HOH -B858 : HOH -B859 : HOH -B860 : HOH -B861 : HOH -B862 : HOH -B863 : HOH -B864 : HOH -B865 : HOH -B866 : HOH -B867 : HOH -B868 : HOH -B869 : HOH -B870 : HOH -B871 : HOH -B872 : HOH -B873 : HOH -B874 : HOH -B875 : HOH -B876 : HOH -B877 : HOH -B878 : HOH -B879 : HOH -B880 : HOH -B881 : HOH -B882 : HOH -B883 : HOH -B884 : HOH -B885 : HOH -B886 : HOH -B887 : HOH -B888 : HOH -B889 : HOH -B890 : HOH -B891 : HOH -B892 : HOH -B893 : HOH -B894 : HOH -B895 : HOH -B896 : HOH -B897 : HOH -B898 : HOH -B899 : HOH -B900 : HOH -B901 : HOH -B902 : HOH -B903 : HOH -B904 : HOH -B905 : HOH -B906 : HOH -B907 : HOH -B908 : HOH -B909 : HOH -B910 : HOH -B911 : HOH -B912 : HOH -B913 : HOH -B914 : HOH -B915 : HOH -B916 : HOH -B917 : HOH -B918 : HOH -B919 : HOH -B920 : HOH -B921 : HOH -B922 : HOH -B923 : HOH -B924 : HOH -B925 : HOH -B926 : HOH -B927 : HOH -B928 : HOH -B929 : HOH -B930 : HOH -B931 : HOH -B932 : HOH -B933 : HOH -B934 : HOH -B935 : HOH -B936 : HOH -B937 : HOH -B938 : HOH -B939 : HOH -B940 : HOH -B941 : HOH -B942 : HOH -B943 : HOH -B944 : HOH -B945 : HOH -B946 : HOH -B947 : HOH -B948 : HOH -B949 : HOH -B950 : HOH -B951 : HOH -B952 : HOH -B953 : HOH -B954 : HOH -B955 : HOH -B956 : HOH -B957 : HOH -B958 : HOH -B959 : HOH -B960 : HOH -B961 : HOH -B962 : HOH -B963 : HOH -B964 : HOH -B965 : HOH -B966 : HOH -B967 : HOH -B968 : HOH -B969 : HOH -B970 : HOH -B971 : HOH -B972 : HOH -B973 : HOH -B974 : HOH -B975 : HOH -B976 : HOH -B977 : HOH -B978 : HOH -B979 : HOH -B980 : HOH -B981 : HOH -B982 : HOH -B983 : HOH -B984 : HOH -B985 : HOH -B986 : HOH -B987 : HOH -B988 : HOH -B989 : HOH -B990 : HOH -B991 : HOH -B992 : HOH -B993 : HOH -B994 : HOH -B995 : HOH -B996 : HOH -B997 : HOH -B998 : HOH -B999 : HOH -B1000 : HOH -B1001 : HOH -B1002 : HOH -B1003 : HOH -B1004 : HOH -B1005 : HOH -B1006 : HOH -B1007 : HOH -B1008 : HOH -B1009 : HOH -B1010 : HOH -B1011 : HOH -B1012 : HOH -B1013 : HOH -B1014 : HOH -B1015 : HOH -B1016 : HOH -B1017 : HOH -B1018 : HOH -B1019 : HOH -B1020 : HOH -B1021 : HOH -B1022 : HOH -B1023 : HOH -B1024 : HOH -B1025 : HOH -B1026 : HOH -B1027 : HOH -B1028 : HOH -B1029 : HOH -B1030 : HOH -B1031 : HOH -B1032 : HOH -B1033 : HOH -B1034 : HOH -B1035 : HOH -B1036 : HOH -B1037 : HOH -B1038 : HOH -B1039 : HOH -B1040 : HOH -B1041 : HOH -B1042 : HOH -B1043 : HOH -B1044 : HOH -B1045 : HOH -B1046 : HOH -B1047 : HOH -A101 : HOH -A102 : HOH -A103 : HOH -A104 : HOH -A105 : HOH -A106 : HOH -A107 : HOH -A108 : HOH -A109 : HOH -A110 : HOH -A111 : HOH -A112 : HOH -A113 : HOH -A114 : HOH -A115 : HOH -A116 : HOH -A117 : HOH -A118 : HOH -A119 : HOH -A120 : HOH -A121 : HOH -A122 : HOH -A123 : HOH -A124 : HOH -A125 : HOH -A126 : HOH -A127 : HOH -A128 : HOH -A129 : HOH -A130 : HOH -A131 : HOH -A132 : HOH -A133 : HOH -A134 : HOH -A135 : HOH -A136 : HOH -A137 : HOH -A138 : HOH -A139 : HOH -A140 : HOH -A141 : HOH -A142 : HOH -A143 : HOH -A144 : HOH -A145 : HOH -A146 : HOH -A147 : HOH -A148 : HOH -A149 : HOH -A150 : HOH -A151 : HOH -A152 : HOH -Adjacent stackings ---------------------------------------------- -B130-B131 : adjacent_5p upward -B131-B132 : adjacent_5p upward -B132-B133 : adjacent_5p upward -B133-B134 : adjacent_5p upward -B134-B135 : adjacent_5p upward -B136-B137 : adjacent_5p upward -B137-B138 : adjacent_5p upward -B138-B139 : adjacent_5p upward -B140-B141 : adjacent_5p upward -B141-B142 : adjacent_5p upward -B144-B145 : adjacent_5p upward -B145-B146 : adjacent_5p upward -B146-B147 : adjacent_5p upward -B148-B149 : adjacent_5p upward -B149-B150 : adjacent_5p upward -B150-B151 : adjacent_5p upward -B151-B152 : adjacent_5p upward -B153-B154 : adjacent_5p upward -B155-B156 : adjacent_5p upward -B156-B157 : adjacent_5p upward -B158-B159 : adjacent_5p upward -B159-B160 : adjacent_5p upward -B160-B161 : adjacent_5p upward -B161-B162 : adjacent_5p upward -B163-B164 : adjacent_5p upward -B164-B165 : adjacent_5p upward -B165-B166 : adjacent_5p upward -B166-B167 : adjacent_5p upward -B167-B168 : adjacent_5p upward -B168-B169 : adjacent_5p upward -B169-B170 : adjacent_5p upward -B170-B171 : adjacent_5p upward -B171-B172 : adjacent_5p upward -B172-B173 : adjacent_5p upward -B173-B174 : adjacent_5p upward -B174-B175 : adjacent_5p upward -B175-B176 : adjacent_5p upward -B176-B177 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -B136-B173 : outward -B144-B168 : outward -B147-B162 : inward -B148-B164 : outward -B154-B158 : outward -Number of stackings = 43 -Number of adjacent stackings = 38 -Number of non adjacent stackings = 5 -Base-pairs ------------------------------------------------------ -B131-B177 : G-C Ww/Ww pairing antiparallel cis XIX -B132-B176 : C-G Ww/Ww pairing antiparallel cis XIX -B133-B175 : U-A Ww/Ww pairing antiparallel cis XX -B134-B174 : C-G Ww/Ww pairing antiparallel cis XIX -B135-B173 : U-A Ww/Ww pairing antiparallel cis XX -B136-B172 : G-C Ww/Ww pairing antiparallel cis XIX -B137-B171 : U-G Ws/Ww pairing antiparallel cis XXVIII -B138-B170 : U-G Ws/Ww pairing antiparallel cis XXVIII -B139-B169 : U-A Ww/Ww pairing antiparallel cis XX -B144-B167 : G-C Ww/Ww pairing antiparallel cis XIX -B145-B166 : G-C Ww/Ww pairing antiparallel cis XIX -B146-B165 : U-G Ws/Ww pairing antiparallel cis XXVIII -B147-B163 : C-C Bh/O2P pairing -B147-B164 : C-A Ss/Hw O2'/Bh pairing antiparallel trans one_hbond 77 -B148-B162 : A-G O2P/Ww O2P/Bs pairing -B148-B163 : A-C Hh/Ww pairing antiparallel trans XXV -B149-B162 : G-G Hw/Sw pairing antiparallel trans one_hbond 112 -B150-B161 : G-A Ww/Ww pairing antiparallel cis VIII -B151-B160 : U-A Ww/Ww pairing antiparallel cis XX -B152-B159 : C-G Ww/Ww pairing antiparallel cis XIX -B153-B158 : C-G Ww/Ww pairing antiparallel cis XIX -B154-B156 : G-A O2'/Hh pairing -B154-B157 : G-A Ss/Hh Bs/O2P pairing antiparallel trans one_hbond diff --git a/MCdata/1duq_MC b/MCdata/1duq_MC deleted file mode 100644 index c4c88060b544e1684855d9186b1d031fd6c50977..0000000000000000000000000000000000000000 --- a/MCdata/1duq_MC +++ /dev/null @@ -1,334 +0,0 @@ -Residue conformations ------------------------------------------- -A101 : G C3p_endo anti -A102 : C C3p_endo anti -A103 : U C3p_endo anti -A104 : G C3p_endo anti -A105 : G C3p_endo anti -A106 : G C3p_endo anti -A107 : C C3p_endo anti -A108 : G C3p_endo anti -A109 : C C3p_endo anti -A110 : A C3p_endo anti -A111 : G C3p_endo anti -A112 : G C3p_endo anti -B117 : C C3p_endo anti -B118 : C C3p_endo anti -B119 : U C3p_endo anti -B120 : G C3p_endo anti -B121 : A C3p_endo anti -B122 : C C3p_endo anti -B123 : G C3p_endo anti -B124 : G C1p_exo syn -B125 : U C3p_endo anti -B126 : A C3p_endo anti -B127 : C C3p_endo anti -B128 : A C3p_endo anti -B129 : G C3p_endo anti -B130 : C C3p_endo anti -C201 : G C3p_endo anti -C202 : C C3p_endo anti -C203 : U C3p_endo anti -C204 : G C3p_endo anti -C205 : G C3p_endo anti -C206 : G C3p_endo anti -C207 : C C3p_endo anti -C208 : G C3p_endo anti -C209 : C C3p_endo anti -C210 : A C3p_endo anti -C211 : G C3p_endo anti -C212 : G C3p_endo anti -D217 : C C3p_endo anti -D218 : C C3p_endo anti -D219 : U C3p_endo anti -D220 : G C3p_endo anti -D221 : A C3p_endo anti -D222 : C C3p_endo anti -D223 : G C3p_endo anti -D224 : G C4p_exo syn -D225 : U C4p_exo anti -D226 : A C3p_endo anti -D227 : C C3p_endo anti -D228 : A C3p_endo anti -D229 : G C3p_endo anti -D230 : C C3p_endo anti -E301 : G C3p_endo anti -E302 : C C3p_endo anti -E303 : U C3p_endo anti -E304 : G C3p_endo anti -E305 : G C3p_endo anti -E306 : G C3p_endo anti -E307 : C C3p_endo anti -E308 : G C3p_endo anti -E309 : C C3p_endo anti -E310 : A C3p_endo anti -E311 : G C3p_endo anti -E312 : G C3p_endo anti -F317 : C C3p_endo anti -F318 : C C3p_endo anti -F319 : U C3p_endo anti -F320 : G C3p_endo anti -F321 : A C3p_endo anti -F322 : C C3p_endo anti -F323 : G C3p_endo anti -F324 : G C1p_exo syn -F325 : U C4p_exo anti -F326 : A C3p_endo anti -F327 : C C3p_endo anti -F328 : A C3p_endo anti -F329 : G C3p_endo anti -F330 : C C3p_endo anti -G401 : G C3p_endo anti -G402 : C C3p_endo anti -G403 : U C3p_endo anti -G404 : G C3p_endo anti -G405 : G C3p_endo anti -G406 : G C3p_endo anti -G407 : C C3p_endo anti -G408 : G C3p_endo anti -G409 : C C3p_endo anti -G410 : A C3p_endo anti -G411 : G C3p_endo anti -G412 : G C3p_endo anti -H417 : C C3p_endo anti -H418 : C C3p_endo anti -H419 : U C3p_endo anti -H420 : G C3p_endo anti -H421 : A C3p_endo anti -H422 : C C3p_endo anti -H423 : G C3p_endo anti -H424 : G C4p_exo syn -H425 : U C4p_exo anti -H426 : A C3p_endo anti -H427 : C C3p_endo anti -H428 : A C3p_endo anti -H429 : G C3p_endo anti -H430 : C C3p_endo anti -B911 : NA -C904 : NA -C906 : NA -C913 : NA -D901 : NA -E912 : NA -G905 : NA -G914 : NA -H902 : NA -H903 : NA -A506 : HOH -A508 : HOH -A509 : HOH -A516 : HOH -A538 : HOH -A541 : HOH -A548 : HOH -A603 : HOH -A605 : HOH -A611 : HOH -A619 : HOH -B502 : HOH -B503 : HOH -B505 : HOH -B510 : HOH -B520 : HOH -B522 : HOH -B525 : HOH -B526 : HOH -B530 : HOH -B531 : HOH -B533 : HOH -B535 : HOH -B543 : HOH -B546 : HOH -B606 : HOH -B617 : HOH -B624 : HOH -B625 : HOH -C528 : HOH -C532 : HOH -C540 : HOH -C631 : HOH -C633 : HOH -C637 : HOH -D514 : HOH -D517 : HOH -D523 : HOH -D542 : HOH -D547 : HOH -D601 : HOH -D612 : HOH -D616 : HOH -D620 : HOH -D623 : HOH -D628 : HOH -E507 : HOH -E518 : HOH -E521 : HOH -E545 : HOH -E607 : HOH -E610 : HOH -E613 : HOH -F504 : HOH -F511 : HOH -F524 : HOH -F527 : HOH -F529 : HOH -F536 : HOH -F537 : HOH -F539 : HOH -F544 : HOH -F614 : HOH -F621 : HOH -F626 : HOH -F630 : HOH -G512 : HOH -G519 : HOH -G608 : HOH -G618 : HOH -G622 : HOH -G627 : HOH -G632 : HOH -G635 : HOH -G636 : HOH -H513 : HOH -H515 : HOH -H534 : HOH -H602 : HOH -H604 : HOH -H609 : HOH -H615 : HOH -H629 : HOH -Adjacent stackings ---------------------------------------------- -A101-A102 : adjacent_5p upward -A102-A103 : adjacent_5p upward -A103-A104 : adjacent_5p upward -A104-A105 : adjacent_5p upward -A105-A106 : adjacent_5p upward -A106-A107 : adjacent_5p upward -A107-A108 : adjacent_5p upward -A108-A109 : adjacent_5p upward -A110-A111 : adjacent_5p upward -A111-A112 : adjacent_5p upward -B117-B118 : adjacent_5p upward -B123-B124 : adjacent_5p inward -B126-B127 : adjacent_5p upward -B128-B129 : adjacent_5p upward -B129-B130 : adjacent_5p upward -C201-C202 : adjacent_5p upward -C202-C203 : adjacent_5p upward -C203-C204 : adjacent_5p upward -C204-C205 : adjacent_5p upward -C205-C206 : adjacent_5p upward -C206-C207 : adjacent_5p upward -C208-C209 : adjacent_5p upward -C210-C211 : adjacent_5p upward -C211-C212 : adjacent_5p upward -D217-D218 : adjacent_5p upward -D218-D219 : adjacent_5p upward -D219-D220 : adjacent_5p upward -D223-D224 : adjacent_5p inward -D228-D229 : adjacent_5p upward -D229-D230 : adjacent_5p upward -E301-E302 : adjacent_5p upward -E303-E304 : adjacent_5p upward -E304-E305 : adjacent_5p upward -E305-E306 : adjacent_5p upward -E306-E307 : adjacent_5p upward -E307-E308 : adjacent_5p upward -E308-E309 : adjacent_5p upward -E310-E311 : adjacent_5p upward -E311-E312 : adjacent_5p upward -F317-F318 : adjacent_5p upward -F323-F324 : adjacent_5p inward -F326-F327 : adjacent_5p upward -F328-F329 : adjacent_5p upward -F329-F330 : adjacent_5p upward -G401-G402 : adjacent_5p upward -G402-G403 : adjacent_5p upward -G403-G404 : adjacent_5p upward -G404-G405 : adjacent_5p upward -G405-G406 : adjacent_5p upward -G406-G407 : adjacent_5p upward -G407-G408 : adjacent_5p upward -G408-G409 : adjacent_5p upward -G410-G411 : adjacent_5p upward -G411-G412 : adjacent_5p upward -H417-H418 : adjacent_5p upward -H418-H419 : adjacent_5p upward -H419-H420 : adjacent_5p upward -H423-H424 : adjacent_5p inward -H427-H428 : adjacent_5p upward -H428-H429 : adjacent_5p upward -H429-H430 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A104-B128 : outward -A108-B123 : outward -A110-B120 : outward -A112-C201 : upward -B117-D230 : downward -B120-B122 : upward -B124-B126 : outward -C208-D223 : outward -C210-D220 : outward -D220-D222 : upward -D224-D226 : outward -E304-F328 : outward -E308-F323 : outward -E310-F320 : outward -E312-G401 : upward -F317-H430 : downward -F320-F322 : upward -F324-F326 : outward -G408-H423 : outward -G410-H420 : outward -H420-H422 : upward -H424-H426 : outward -Number of stackings = 83 -Number of adjacent stackings = 61 -Number of non adjacent stackings = 22 -Base-pairs ------------------------------------------------------ -A101-B130 : G-C Ww/Ww pairing antiparallel cis XIX -A102-B129 : C-G Ww/Ww pairing antiparallel cis XIX -A103-B128 : U-A Ww/Ww pairing antiparallel cis XX -A104-B127 : G-C Ww/Ww pairing antiparallel cis XIX -A105-B126 : G-A Ww/Ww pairing antiparallel cis VIII -A106-B124 : G-G Ww/Hh pairing parallel cis VI -A107-B123 : C-G Ww/Ww pairing antiparallel cis XIX -A108-B122 : G-C Ww/Ww pairing antiparallel cis XIX -A109-B120 : C-G Ww/Ww pairing antiparallel cis XIX -A110-B119 : A-U Ww/Ww pairing antiparallel cis XX -A111-B118 : G-C Ww/Ww pairing antiparallel cis XIX -A112-B117 : G-C Ww/Ww pairing antiparallel cis XIX -C202-D229 : C-G Ww/Ww pairing antiparallel cis 130 -C203-D228 : U-A Ww/Ww pairing antiparallel cis XX -C204-D227 : G-C Ww/Ww pairing antiparallel cis XIX -C205-D226 : G-A Wh/Bs pairing antiparallel cis one_hbond -C206-D224 : G-G Ww/Hh pairing parallel cis VI -C207-D223 : C-G Ww/Ww pairing antiparallel cis XIX -C208-D222 : G-C Ww/Ww pairing antiparallel cis XIX -C209-D220 : C-G Ww/Ww pairing antiparallel cis XIX -C210-D219 : A-U Ww/Ww pairing antiparallel cis XX -C211-D218 : G-C Ww/Ww pairing antiparallel cis XIX -C212-D217 : G-C Ww/Ww pairing antiparallel cis XIX -D225-G408 : U-G Wh/Sw pairing antiparallel cis one_hbond -E301-F330 : G-C Ww/Ww pairing antiparallel cis XIX -E302-F329 : C-G Ww/Ww pairing antiparallel cis XIX -E303-F328 : U-A Ww/Ww pairing antiparallel cis XX -E304-F327 : G-C Ww/Ww pairing antiparallel cis XIX -E305-F326 : G-A Ww/Ww pairing antiparallel cis VIII -E306-F324 : G-G Ww/Hh pairing parallel cis VI -E307-F323 : C-G Ww/Ww pairing antiparallel cis XIX -E308-F322 : G-C Ww/Ww pairing antiparallel cis XIX -E309-F320 : C-G Ww/Ww pairing antiparallel cis XIX -E310-F319 : A-U Ww/Ww pairing antiparallel cis XX -E311-F318 : G-C Ww/Ww pairing antiparallel cis XIX -E312-F317 : G-C Ww/Ww pairing antiparallel cis XIX -G402-H429 : C-G Ww/Ww pairing antiparallel cis XIX -G403-H428 : U-A Ww/Ww pairing antiparallel cis XX -G404-H427 : G-C Ww/Ww pairing antiparallel cis XIX -G405-H426 : G-A Wh/Bs pairing antiparallel cis one_hbond -G406-H424 : G-G Ww/Hh pairing parallel cis VI -G407-H423 : C-G Ww/Ww pairing antiparallel cis XIX -G408-H422 : G-C Ww/Ww pairing antiparallel cis XIX -G409-H420 : C-G Ww/Ww pairing antiparallel cis XIX -G410-H419 : A-U Ww/Ww pairing antiparallel cis XX -G411-H418 : G-C Ww/Ww pairing antiparallel cis XIX -G412-H417 : G-C Ww/Ww pairing antiparallel cis XIX diff --git a/MCdata/1dv4_MC b/MCdata/1dv4_MC deleted file mode 100644 index e7cad7240cc3961070fb8498e538c5d79ec8f7f2..0000000000000000000000000000000000000000 --- a/MCdata/1dv4_MC +++ /dev/null @@ -1,650 +0,0 @@ -Residue conformations ------------------------------------------- -A1 : N -A2 : N -A3 : N -A4 : N -A5 : N -A6 : N -A7 : N -A8 : N -A9 : N -A10 : N -A11 : N -A12 : N -A13 : N -A14 : N -A15 : N -A16 : N -A17 : N -A18 : N -A19 : N -A20 : N -A21 : N -A22 : N -A23 : N -A24 : N -A25 : N -A26 : N -A27 : N -A28 : N -A29 : N -A30 : N -A31 : N -A32 : N -A33 : N -A34 : N -A35 : N -A36 : N -A37 : N -A38 : N -A39 : N -A40 : N -A41 : N -A42 : N -A43 : N -A44 : N -A45 : N -A46 : N -A47 : N -A48 : N -A49 : N -A50 : N -A51 : N -A52 : N -A53 : N -A54 : N -A55 : N -A56 : N -A57 : N -A58 : N -A59 : N -A60 : N -A61 : N -A62 : N -A63 : N -A64 : N -A65 : N -A66 : N -A67 : N -A68 : N -A69 : N -A70 : N -A71 : N -A72 : N -A73 : N -A74 : N -A75 : N -A76 : N -A77 : N -A78 : N -A79 : N -A80 : N -A81 : N -A82 : N -A83 : N -A84 : N -A85 : N -A86 : N -A87 : N -A88 : N -A89 : N -A90 : N -A91 : N -A92 : N -A93 : N -A94 : N -A95 : N -A96 : N -A97 : N -A98 : N -A99 : N -A100 : N -A101 : N -A102 : N -A103 : N -A104 : N -A105 : N -A106 : N -A107 : N -A108 : N -A109 : N -A110 : N -A111 : N -A112 : N -A113 : N -A114 : N -A115 : N -A116 : N -A117 : N -A118 : N -A119 : N -A120 : N -A121 : N -A122 : N -A123 : N -A124 : N -A125 : N -A126 : N -A127 : N -A128 : N -A129 : N -A130 : N -A131 : N -A132 : N -A133 : N -A134 : N -A135 : N -A136 : N -A137 : N -A138 : N -A139 : N -A140 : N -A141 : N -A142 : N -A143 : N -A144 : N -A145 : N -A146 : N -A147 : N -A148 : N -A149 : N -A150 : N -A151 : N -A152 : N -A153 : N -A154 : N -A155 : N -A156 : N -A157 : N -A158 : N -A159 : N -A160 : N -A161 : N -A162 : N -A163 : N -A164 : N -A165 : N -A166 : N -A167 : N -A168 : N -A169 : N -A170 : N -A171 : N -A172 : N -A173 : N -A174 : N -A175 : N -A176 : N -A177 : N -A178 : N -A179 : N -A180 : N -A181 : N -A182 : N -A183 : N -A184 : N -A185 : N -A186 : N -A187 : N -A188 : N -A189 : N -A190 : N -A191 : N -A193 : N -A194 : N -A195 : N -A196 : N -A197 : N -A198 : N -A199 : N -A200 : N -A201 : N -A202 : N -A203 : N -A204 : N -A205 : N -A206 : N -A207 : N -A208 : N -A209 : N -A210 : N -A211 : N -A212 : N -A213 : N -A214 : N -A215 : N -A216 : N -A217 : N -A218 : N -A219 : N -A220 : N -A221 : N -A222 : N -A223 : N -A224 : N -A225 : N -A226 : N -A227 : N -A228 : N -A229 : N -A230 : N -A231 : N -A232 : N -A233 : N -A234 : N -A235 : N -A236 : N -A237 : N -A238 : N -A239 : N -A240 : N -A241 : N -A242 : N -A243 : N -A244 : N -A245 : N -A246 : N -A247 : N -A248 : N -A249 : N -A250 : N -A251 : N -A252 : N -A253 : N -A254 : N -A255 : N -A256 : N -A257 : N -A258 : N -A259 : N -A260 : N -A261 : N -A262 : N -A263 : N -A264 : N -A265 : N -A266 : N -A267 : N -A268 : N -A269 : N -A270 : N -A271 : N -A272 : N -A273 : N -A274 : N -A275 : N -A276 : N -A277 : N -A278 : N -A279 : N -A280 : N -A281 : N -A282 : N -A283 : N -A284 : N -A285 : N -A286 : N -A287 : N -A288 : N -A289 : N -A290 : N -A291 : N -A292 : N -A293 : N -A294 : N -A295 : N -A296 : N -A297 : N -A298 : N -A299 : N -A300 : N -A301 : N -A302 : N -A303 : N -A304 : N -A305 : N -A306 : N -A307 : N -A308 : N -A309 : N -A310 : N -A311 : N -A312 : N -A313 : N -A314 : N -A315 : N -A316 : N -A317 : N -A318 : N -A319 : N -A320 : N -A321 : N -A322 : N -A323 : N -A324 : N -A325 : N -A326 : N -A327 : N -A328 : N -A329 : N -A330 : N -A331 : N -A332 : N -A333 : N -A334 : N -A335 : N -A336 : N -A337 : N -A338 : N -A339 : N -A340 : N -A341 : N -A342 : N -A343 : N -A344 : N -A345 : N -A346 : N -A347 : N -A348 : N -A350 : N -A351 : N -A352 : N -A353 : N -A354 : N -A355 : N -A356 : N -A357 : N -A358 : N -A359 : N -A360 : N -A361 : N -A362 : N -A363 : N -A364 : N -E24 : ILE -E25 : ASN -E26 : PRO -E27 : ASN -E28 : LYS -E29 : LEU -E30 : GLU -E31 : LEU -E32 : GLU -E33 : GLU -E34 : ARG -E35 : VAL -E36 : VAL -E37 : ALA -E38 : VAL -E39 : ASN -E40 : ARG -E41 : VAL -E42 : ALA -E43 : LYS -E44 : VAL -E45 : VAL -E46 : LYS -E47 : GLY -E48 : GLY -E49 : ARG -E50 : ARG -E51 : LEU -E52 : ARG -E53 : PHE -E54 : SER -E55 : ALA -E56 : LEU -E57 : VAL -E58 : VAL -E59 : VAL -E60 : GLY -E61 : ASP -E62 : LYS -E63 : ASN -E64 : GLY -E65 : HIS -E66 : VAL -E67 : GLY -E68 : PHE -E69 : GLY -E70 : THR -E71 : GLY -E72 : LYS -E73 : ALA -E74 : GLN -E75 : GLU -E76 : VAL -E77 : PRO -E78 : GLU -E79 : ALA -E80 : ILE -E81 : ARG -E82 : LYS -E83 : ALA -E84 : ILE -E85 : GLU -E86 : ASP -E87 : ALA -E88 : LYS -E89 : LYS -E90 : ASN -E91 : LEU -E92 : ILE -E93 : GLU -E94 : VAL -E95 : PRO -E96 : ILE -E97 : VAL -E98 : GLY -E99 : THR -E100 : THR -E101 : ILE -E102 : PRO -E103 : HIS -E104 : GLU -E105 : VAL -E106 : ILE -E107 : GLY -E108 : HIS -E109 : PHE -E110 : GLY -E111 : ALA -E112 : GLY -E113 : GLU -E114 : ILE -E115 : ILE -E116 : LEU -E117 : LYS -E118 : PRO -E119 : ALA -E120 : SER -E121 : GLU -E122 : GLY -E123 : THR -E124 : GLY -E125 : VAL -E126 : ILE -E127 : ALA -E128 : GLY -E129 : GLY -E130 : PRO -E131 : ALA -E132 : ARG -E133 : ALA -E134 : VAL -E135 : LEU -E136 : GLU -E137 : LEU -E138 : ALA -E139 : GLY -E140 : ILE -E141 : SER -E142 : ASP -E143 : ILE -E144 : LEU -E145 : SER -E146 : LYS -E147 : SER -E148 : ILE -E149 : GLY -E150 : SER -E151 : ASN -E152 : THR -E153 : PRO -E154 : ILE -E155 : ASN -E156 : MET -E157 : VAL -E158 : ARG -E159 : ALA -E160 : THR -E161 : PHE -E162 : ASP -E163 : GLY -E164 : LEU -E165 : LYS -E166 : GLN -E167 : LEU -E168 : LYS -G12 : LEU -G13 : GLN -G14 : PRO -G15 : ASP -G16 : LEU -G17 : VAL -G18 : TYR -G19 : GLY -G20 : ASP -G21 : VAL -G22 : LEU -G23 : VAL -G24 : THR -G25 : ALA -G26 : PHE -G27 : ILE -G28 : ASN -G29 : LYS -G30 : ILE -G31 : MET -G32 : ARG -G33 : ASP -G34 : GLY -G35 : LYS -G36 : LYS -G37 : ASN -G38 : LEU -G39 : ALA -G40 : ALA -G41 : ARG -G42 : ILE -G43 : PHE -G44 : TYR -G45 : ASP -G46 : ALA -G47 : CYS -G48 : LYS -G49 : ILE -G50 : ILE -G51 : GLN -G52 : GLU -G53 : LYS -G54 : THR -G55 : GLY -G56 : GLN -G57 : GLU -G58 : PRO -G59 : LEU -G60 : LYS -G61 : VAL -G62 : PHE -G63 : LYS -G64 : GLN -G65 : ALA -G66 : VAL -G67 : GLU -G68 : ASN -G69 : VAL -G70 : LYS -G71 : PRO -G72 : ARG -G73 : MET -G74 : GLU -G75 : VAL -G76 : ARG -G77 : SER -G78 : ARG -G79 : ARG -G80 : VAL -G81 : GLY -G82 : GLY -G83 : ALA -G84 : ASN -G85 : TYR -G86 : GLN -G87 : VAL -G88 : PRO -G89 : MET -G90 : GLU -G91 : VAL -G92 : SER -G93 : PRO -G94 : ARG -G95 : ARG -G96 : GLN -G97 : GLN -G98 : SER -G99 : LEU -G100 : ALA -G101 : LEU -G102 : ARG -G103 : TRP -G104 : LEU -G105 : VAL -G106 : GLN -G107 : ALA -G108 : ALA -G109 : ASN -G110 : GLN -G111 : ARG -G112 : PRO -G113 : GLU -G114 : ARG -G115 : ARG -G116 : ALA -G117 : ALA -G118 : VAL -G119 : ARG -G120 : ILE -G121 : ALA -G122 : HIS -G123 : GLU -G124 : LEU -G125 : MET -G126 : ASP -G127 : ALA -G128 : ALA -G129 : GLU -G130 : GLY -G131 : LYS -G132 : GLY -G133 : GLY -G134 : ALA -G135 : VAL -G136 : LYS -G137 : LYS -G138 : LYS -G139 : GLU -G140 : ASP -G141 : VAL -G142 : GLU -G143 : ARG -G144 : MET -G145 : ALA -G146 : GLU -E1 : WO2 -Adjacent stackings ---------------------------------------------- -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 0 -Number of adjacent stackings = 0 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ diff --git a/MCdata/1dz5_MC b/MCdata/1dz5_MC deleted file mode 100644 index 2898a069d16d3d52f1d9f287089e080881c4c8c2..0000000000000000000000000000000000000000 --- a/MCdata/1dz5_MC +++ /dev/null @@ -1,3903 +0,0 @@ -Residue conformations ------------------------------------------- -A1 : ALA -A2 : VAL -A3 : PRO -A4 : GLU -A5 : THR -A6 : ARG -A7 : PRO -A8 : ASN -A9 : HIS -A10 : THR -A11 : ILE -A12 : TYR -A13 : ILE -A14 : ASN -A15 : ASN -A16 : LEU -A17 : ASN -A18 : GLU -A19 : LYS -A20 : ILE -A21 : LYS -A22 : LYS -A23 : ASP -A24 : GLU -A25 : LEU -A26 : LYS -A27 : LYS -A28 : SER -A29 : LEU -A30 : HIS -A31 : ALA -A32 : ILE -A33 : PHE -A34 : SER -A35 : ARG -A36 : PHE -A37 : GLY -A38 : GLN -A39 : ILE -A40 : LEU -A41 : ASP -A42 : ILE -A43 : LEU -A44 : VAL -A45 : SER -A46 : ARG -A47 : SER -A48 : LEU -A49 : LYS -A50 : MET -A51 : ARG -A52 : GLY -A53 : GLN -A54 : ALA -A55 : PHE -A56 : VAL -A57 : ILE -A58 : PHE -A59 : LYS -A60 : GLU -A61 : VAL -A62 : SER -A63 : SER -A64 : ALA -A65 : THR -A66 : ASN -A67 : ALA -A68 : LEU -A69 : ARG -A70 : SER -A71 : MET -A72 : GLN -A73 : GLY -A74 : PHE -A75 : PRO -A76 : PHE -A77 : TYR -A78 : ASP -A79 : LYS -A80 : PRO -A81 : MET -A82 : ARG -A83 : ILE -A84 : GLN -A85 : TYR -A86 : ALA -A87 : LYS -A88 : THR -A89 : ASP -A90 : SER -A91 : ASP -A92 : ILE -A93 : ILE -A94 : ALA -A95 : LYS -A96 : MET -A97 : LYS -A98 : GLY -A99 : THR -A100 : PHE -A101 : VAL -B1 : ALA -B2 : VAL -B3 : PRO -B4 : GLU -B5 : THR -B6 : ARG -B7 : PRO -B8 : ASN -B9 : HIS -B10 : THR -B11 : ILE -B12 : TYR -B13 : ILE -B14 : ASN -B15 : ASN -B16 : LEU -B17 : ASN -B18 : GLU -B19 : LYS -B20 : ILE -B21 : LYS -B22 : LYS -B23 : ASP -B24 : GLU -B25 : LEU -B26 : LYS -B27 : LYS -B28 : SER -B29 : LEU -B30 : HIS -B31 : ALA -B32 : ILE -B33 : PHE -B34 : SER -B35 : ARG -B36 : PHE -B37 : GLY -B38 : GLN -B39 : ILE -B40 : LEU -B41 : ASP -B42 : ILE -B43 : LEU -B44 : VAL -B45 : SER -B46 : ARG -B47 : SER -B48 : LEU -B49 : LYS -B50 : MET -B51 : ARG -B52 : GLY -B53 : GLN -B54 : ALA -B55 : PHE -B56 : VAL -B57 : ILE -B58 : PHE -B59 : LYS -B60 : GLU -B61 : VAL -B62 : SER -B63 : SER -B64 : ALA -B65 : THR -B66 : ASN -B67 : ALA -B68 : LEU -B69 : ARG -B70 : SER -B71 : MET -B72 : GLN -B73 : GLY -B74 : PHE -B75 : PRO -B76 : PHE -B77 : TYR -B78 : ASP -B79 : LYS -B80 : PRO -B81 : MET -B82 : ARG -B83 : ILE -B84 : GLN -B85 : TYR -B86 : ALA -B87 : LYS -B88 : THR -B89 : ASP -B90 : SER -B91 : ASP -B92 : ILE -B93 : ILE -B94 : ALA -B95 : LYS -B96 : MET -B97 : LYS -B98 : GLY -B99 : THR -B100 : PHE -B101 : VAL -C8 : G C2p_exo anti -C9 : A C2p_exo anti -C10 : G C2p_exo anti -C11 : A C2p_exo anti -C12 : C C3p_endo anti -C13 : A C2p_exo anti -C14 : U C2p_exo anti -C15 : U C2p_endo anti -C16 : G C2p_exo anti -C17 : C C1p_exo anti -C18 : A C3p_endo anti -C19 : C C2p_exo anti -C20 : C C2p_exo anti -C21 : C C2p_exo anti -C22 : G C3p_endo anti -C23 : G C2p_exo anti -C24 : A C3p_endo anti -C25 : G C3p_endo anti -C26 : U C3p_endo anti -C27 : C C3p_endo anti -C28 : U C3p_endo anti -C29 : C C2p_exo anti -D34 : G C2p_exo anti -D35 : A C2p_exo anti -D36 : G C2p_exo anti -D37 : A C2p_exo anti -D38 : C C3p_endo anti -D39 : A C2p_exo anti -D40 : U C2p_exo anti -D41 : U C2p_endo anti -D42 : G C2p_exo anti -D43 : C C1p_exo anti -D44 : A C3p_endo anti -D45 : C C2p_exo anti -D46 : C C2p_exo anti -D47 : C C2p_exo anti -D48 : G C3p_endo anti -D49 : G C2p_exo anti -D50 : A C3p_endo anti -D51 : G C3p_endo anti -D52 : U C3p_endo anti -D53 : C C3p_endo anti -D54 : U C3p_endo anti -D55 : C C2p_exo anti -Adjacent stackings ---------------------------------------------- -C8-C9 : adjacent_5p upward -C9-C10 : adjacent_5p upward -C10-C11 : adjacent_5p upward -C11-C12 : adjacent_5p upward -C12-C13 : adjacent_5p upward -C13-C14 : adjacent_5p upward -C18-C19 : adjacent_5p upward -C20-C21 : adjacent_5p upward -C22-C23 : adjacent_5p upward -C23-C24 : adjacent_5p upward -C25-C26 : adjacent_5p upward -C26-C27 : adjacent_5p upward -C27-C28 : adjacent_5p upward -D34-D35 : adjacent_5p upward -D35-D36 : adjacent_5p upward -D36-D37 : adjacent_5p upward -D37-D38 : adjacent_5p upward -D38-D39 : adjacent_5p upward -D39-D40 : adjacent_5p upward -D44-D45 : adjacent_5p upward -D46-D47 : adjacent_5p upward -D48-D49 : adjacent_5p upward -D49-D50 : adjacent_5p upward -D51-D52 : adjacent_5p upward -D52-D53 : adjacent_5p upward -D53-D54 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -C13-D51 : outward -C22-D48 : outward -C25-D39 : outward -Number of stackings = 29 -Number of adjacent stackings = 26 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -A88-D43 : THR-C pairing one_hbond -B88-C17 : THR-C pairing one_hbond -C8-D55 : G-C Ww/Ww pairing antiparallel cis XIX -C9-D54 : A-U Ww/Ww pairing antiparallel cis XX -C10-D53 : G-C Ww/Ww pairing antiparallel cis XIX -C11-D52 : A-U Ww/Ww pairing antiparallel cis XX -C12-D51 : C-G Ww/Ww pairing antiparallel cis XIX -C19-C20 : C-C O2P/Hh adjacent_5p pairing -C20-D49 : C-G Ww/Ww pairing antiparallel cis XIX -C21-D48 : C-G Ww/Ww pairing antiparallel cis XIX -C22-D47 : G-C Ww/Ww pairing antiparallel cis XIX -C23-D46 : G-C Ww/Ww pairing antiparallel cis XIX -C25-D38 : G-C Ww/Ww pairing antiparallel cis XIX -C26-D37 : U-A Ww/Ww pairing antiparallel cis XX -C27-D36 : C-G Ww/Ww pairing antiparallel cis XIX -C28-D35 : U-A Ww/Ww pairing antiparallel cis XX -C29-D34 : C-G Ww/Ww pairing antiparallel cis XIX -D45-D46 : C-C O2P/Hh adjacent_5p pairing -Residue conformations ------------------------------------------- -A1 : ALA -A2 : VAL -A3 : PRO -A4 : GLU -A5 : THR -A6 : ARG -A7 : PRO -A8 : ASN -A9 : HIS -A10 : THR -A11 : ILE -A12 : TYR -A13 : ILE -A14 : ASN -A15 : ASN -A16 : LEU -A17 : ASN -A18 : GLU -A19 : LYS -A20 : ILE -A21 : LYS -A22 : LYS -A23 : ASP -A24 : GLU -A25 : LEU -A26 : LYS -A27 : LYS -A28 : SER -A29 : LEU -A30 : HIS -A31 : ALA -A32 : ILE -A33 : PHE -A34 : SER -A35 : ARG -A36 : PHE -A37 : GLY -A38 : GLN -A39 : ILE -A40 : LEU -A41 : ASP -A42 : ILE -A43 : LEU -A44 : VAL -A45 : SER -A46 : ARG -A47 : SER -A48 : LEU -A49 : LYS -A50 : MET -A51 : ARG -A52 : GLY -A53 : GLN -A54 : ALA -A55 : PHE -A56 : VAL -A57 : ILE -A58 : PHE -A59 : LYS -A60 : GLU -A61 : VAL -A62 : SER -A63 : SER -A64 : ALA -A65 : THR -A66 : ASN -A67 : ALA -A68 : LEU -A69 : ARG -A70 : SER -A71 : MET -A72 : GLN -A73 : GLY -A74 : PHE -A75 : PRO -A76 : PHE -A77 : TYR -A78 : ASP -A79 : LYS -A80 : PRO -A81 : MET -A82 : ARG -A83 : ILE -A84 : GLN -A85 : TYR -A86 : ALA -A87 : LYS -A88 : THR -A89 : ASP -A90 : SER -A91 : ASP -A92 : ILE -A93 : ILE -A94 : ALA -A95 : LYS -A96 : MET -A97 : LYS -A98 : GLY -A99 : THR -A100 : PHE -A101 : VAL -B1 : ALA -B2 : VAL -B3 : PRO -B4 : GLU -B5 : THR -B6 : ARG -B7 : PRO -B8 : ASN -B9 : HIS -B10 : THR -B11 : ILE -B12 : TYR -B13 : ILE -B14 : ASN -B15 : ASN -B16 : LEU -B17 : ASN -B18 : GLU -B19 : LYS -B20 : ILE -B21 : LYS -B22 : LYS -B23 : ASP -B24 : GLU -B25 : LEU -B26 : LYS -B27 : LYS -B28 : SER -B29 : LEU -B30 : HIS -B31 : ALA -B32 : ILE -B33 : PHE -B34 : SER -B35 : ARG -B36 : PHE -B37 : GLY -B38 : GLN -B39 : ILE -B40 : LEU -B41 : ASP -B42 : ILE -B43 : LEU -B44 : VAL -B45 : SER -B46 : ARG -B47 : SER -B48 : LEU -B49 : LYS -B50 : MET -B51 : ARG -B52 : GLY -B53 : GLN -B54 : ALA -B55 : PHE -B56 : VAL -B57 : ILE -B58 : PHE -B59 : LYS -B60 : GLU -B61 : VAL -B62 : SER -B63 : SER -B64 : ALA -B65 : THR -B66 : ASN -B67 : ALA -B68 : LEU -B69 : ARG -B70 : SER -B71 : MET -B72 : GLN -B73 : GLY -B74 : PHE -B75 : PRO -B76 : PHE -B77 : TYR -B78 : ASP -B79 : LYS -B80 : PRO -B81 : MET -B82 : ARG -B83 : ILE -B84 : GLN -B85 : TYR -B86 : ALA -B87 : LYS -B88 : THR -B89 : ASP -B90 : SER -B91 : ASP -B92 : ILE -B93 : ILE -B94 : ALA -B95 : LYS -B96 : MET -B97 : LYS -B98 : GLY -B99 : THR -B100 : PHE -B101 : VAL -C8 : G C2p_exo anti -C9 : A C2p_exo anti -C10 : G C2p_exo anti -C11 : A C3p_endo anti -C12 : C C3p_endo anti -C13 : A C2p_exo anti -C14 : U C2p_exo anti -C15 : U C2p_endo anti -C16 : G C2p_exo anti -C17 : C C1p_exo anti -C18 : A C1p_exo anti -C19 : C C2p_exo anti -C20 : C C2p_exo anti -C21 : C C2p_exo anti -C22 : G C3p_endo anti -C23 : G C2p_exo anti -C24 : A C3p_endo anti -C25 : G C3p_endo anti -C26 : U C3p_endo anti -C27 : C C3p_endo anti -C28 : U C3p_endo anti -C29 : C C2p_exo anti -D34 : G C2p_exo anti -D35 : A C2p_exo anti -D36 : G C2p_exo anti -D37 : A C3p_endo anti -D38 : C C3p_endo anti -D39 : A C2p_exo anti -D40 : U C2p_exo anti -D41 : U C2p_endo anti -D42 : G C2p_exo anti -D43 : C C1p_exo anti -D44 : A C1p_exo anti -D45 : C C2p_exo anti -D46 : C C2p_exo anti -D47 : C C2p_exo anti -D48 : G C3p_endo anti -D49 : G C2p_exo anti -D50 : A C3p_endo anti -D51 : G C3p_endo anti -D52 : U C3p_endo anti -D53 : C C3p_endo anti -D54 : U C3p_endo anti -D55 : C C2p_exo anti -Adjacent stackings ---------------------------------------------- -C8-C9 : adjacent_5p upward -C9-C10 : adjacent_5p upward -C10-C11 : adjacent_5p upward -C11-C12 : adjacent_5p upward -C12-C13 : adjacent_5p upward -C13-C14 : adjacent_5p upward -C18-C19 : adjacent_5p upward pairing -C20-C21 : adjacent_5p upward -C22-C23 : adjacent_5p upward -C23-C24 : adjacent_5p upward -C25-C26 : adjacent_5p upward -C27-C28 : adjacent_5p upward -D34-D35 : adjacent_5p upward -D35-D36 : adjacent_5p upward -D36-D37 : adjacent_5p upward -D37-D38 : adjacent_5p upward -D38-D39 : adjacent_5p upward -D39-D40 : adjacent_5p upward -D44-D45 : adjacent_5p upward pairing -D46-D47 : adjacent_5p upward -D48-D49 : adjacent_5p upward -D49-D50 : adjacent_5p upward -D51-D52 : adjacent_5p upward -D53-D54 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -C13-D51 : outward -C22-D48 : outward -C25-D39 : outward -Number of stackings = 27 -Number of adjacent stackings = 24 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -A14-D42 : ASN-G pairing one_hbond -B14-C16 : ASN-G pairing one_hbond -C8-D55 : G-C Ww/Ww pairing antiparallel cis XIX -C9-D54 : A-U Ww/Ww pairing antiparallel cis XX -C10-D53 : G-C Ww/Ww pairing antiparallel cis XIX -C11-D52 : A-U Ww/Ww pairing antiparallel cis XX -C12-D51 : C-G Ww/Ww pairing antiparallel cis XIX -C18-C19 : A-C O2'/Hh adjacent_5p upward pairing -C19-D50 : C-A O2P/Ww pairing -C20-D49 : C-G Ww/Ww pairing antiparallel cis XIX -C21-D48 : C-G Ww/Ww pairing antiparallel cis XIX -C22-D47 : G-C Ww/Ww pairing antiparallel cis XIX -C23-D46 : G-C Ww/Ww pairing antiparallel cis XIX -C24-D45 : A-C Ww/O2P pairing -C25-D38 : G-C Ww/Ww pairing antiparallel cis XIX -C26-D37 : U-A Ww/Ww pairing antiparallel cis XX -C27-D36 : C-G Ww/Ww pairing antiparallel cis XIX -C28-D35 : U-A Ww/Ww pairing antiparallel cis XX -C29-D34 : C-G Ww/Ww pairing antiparallel cis XIX -D44-D45 : A-C O2'/Hh adjacent_5p upward pairing -Residue conformations ------------------------------------------- -A1 : ALA -A2 : VAL -A3 : PRO -A4 : GLU -A5 : THR -A6 : ARG -A7 : PRO -A8 : ASN -A9 : HIS -A10 : THR -A11 : ILE -A12 : TYR -A13 : ILE -A14 : ASN -A15 : ASN -A16 : LEU -A17 : ASN -A18 : GLU -A19 : LYS -A20 : ILE -A21 : LYS -A22 : LYS -A23 : ASP -A24 : GLU -A25 : LEU -A26 : LYS -A27 : LYS -A28 : SER -A29 : LEU -A30 : HIS -A31 : ALA -A32 : ILE -A33 : PHE -A34 : SER -A35 : ARG -A36 : PHE -A37 : GLY -A38 : GLN -A39 : ILE -A40 : LEU -A41 : ASP -A42 : ILE -A43 : LEU -A44 : VAL -A45 : SER -A46 : ARG -A47 : SER -A48 : LEU -A49 : LYS -A50 : MET -A51 : ARG -A52 : GLY -A53 : GLN -A54 : ALA -A55 : PHE -A56 : VAL -A57 : ILE -A58 : PHE -A59 : LYS -A60 : GLU -A61 : VAL -A62 : SER -A63 : SER -A64 : ALA -A65 : THR -A66 : ASN -A67 : ALA -A68 : LEU -A69 : ARG -A70 : SER -A71 : MET -A72 : GLN -A73 : GLY -A74 : PHE -A75 : PRO -A76 : PHE -A77 : TYR -A78 : ASP -A79 : LYS -A80 : PRO -A81 : MET -A82 : ARG -A83 : ILE -A84 : GLN -A85 : TYR -A86 : ALA -A87 : LYS -A88 : THR -A89 : ASP -A90 : SER -A91 : ASP -A92 : ILE -A93 : ILE -A94 : ALA -A95 : LYS -A96 : MET -A97 : LYS -A98 : GLY -A99 : THR -A100 : PHE -A101 : VAL -B1 : ALA -B2 : VAL -B3 : PRO -B4 : GLU -B5 : THR -B6 : ARG -B7 : PRO -B8 : ASN -B9 : HIS -B10 : THR -B11 : ILE -B12 : TYR -B13 : ILE -B14 : ASN -B15 : ASN -B16 : LEU -B17 : ASN -B18 : GLU -B19 : LYS -B20 : ILE -B21 : LYS -B22 : LYS -B23 : ASP -B24 : GLU -B25 : LEU -B26 : LYS -B27 : LYS -B28 : SER -B29 : LEU -B30 : HIS -B31 : ALA -B32 : ILE -B33 : PHE -B34 : SER -B35 : ARG -B36 : PHE -B37 : GLY -B38 : GLN -B39 : ILE -B40 : LEU -B41 : ASP -B42 : ILE -B43 : LEU -B44 : VAL -B45 : SER -B46 : ARG -B47 : SER -B48 : LEU -B49 : LYS -B50 : MET -B51 : ARG -B52 : GLY -B53 : GLN -B54 : ALA -B55 : PHE -B56 : VAL -B57 : ILE -B58 : PHE -B59 : LYS -B60 : GLU -B61 : VAL -B62 : SER -B63 : SER -B64 : ALA -B65 : THR -B66 : ASN -B67 : ALA -B68 : LEU -B69 : ARG -B70 : SER -B71 : MET -B72 : GLN -B73 : GLY -B74 : PHE -B75 : PRO -B76 : PHE -B77 : TYR -B78 : ASP -B79 : LYS -B80 : PRO -B81 : MET -B82 : ARG -B83 : ILE -B84 : GLN -B85 : TYR -B86 : ALA -B87 : LYS -B88 : THR -B89 : ASP -B90 : SER -B91 : ASP -B92 : ILE -B93 : ILE -B94 : ALA -B95 : LYS -B96 : MET -B97 : LYS -B98 : GLY -B99 : THR -B100 : PHE -B101 : VAL -C8 : G C2p_exo anti -C9 : A C2p_exo anti -C10 : G C2p_exo anti -C11 : A C2p_exo anti -C12 : C C3p_endo anti -C13 : A C2p_exo anti -C14 : U C2p_exo anti -C15 : U C2p_endo anti -C16 : G C2p_exo anti -C17 : C C1p_exo anti -C18 : A C2p_exo anti -C19 : C C2p_exo anti -C20 : C C2p_exo anti -C21 : C C2p_exo anti -C22 : G C3p_endo anti -C23 : G C2p_exo anti -C24 : A C3p_endo anti -C25 : G C3p_endo anti -C26 : U C2p_exo anti -C27 : C C3p_endo anti -C28 : U C3p_endo anti -C29 : C C2p_exo anti -D34 : G C2p_exo anti -D35 : A C2p_exo anti -D36 : G C2p_exo anti -D37 : A C2p_exo anti -D38 : C C3p_endo anti -D39 : A C2p_exo anti -D40 : U C2p_exo anti -D41 : U C2p_endo anti -D42 : G C2p_exo anti -D43 : C C1p_exo anti -D44 : A C2p_exo anti -D45 : C C2p_exo anti -D46 : C C2p_exo anti -D47 : C C2p_exo anti -D48 : G C3p_endo anti -D49 : G C2p_exo anti -D50 : A C3p_endo anti -D51 : G C3p_endo anti -D52 : U C2p_exo anti -D53 : C C3p_endo anti -D54 : U C3p_endo anti -D55 : C C2p_exo anti -Adjacent stackings ---------------------------------------------- -C9-C10 : adjacent_5p upward -C10-C11 : adjacent_5p upward -C11-C12 : adjacent_5p upward -C12-C13 : adjacent_5p upward -C13-C14 : adjacent_5p upward -C18-C19 : adjacent_5p upward -C20-C21 : adjacent_5p upward -C21-C22 : adjacent_5p upward -C22-C23 : adjacent_5p upward -C23-C24 : adjacent_5p upward -C25-C26 : adjacent_5p upward -C26-C27 : adjacent_5p upward -C27-C28 : adjacent_5p upward -D35-D36 : adjacent_5p upward -D36-D37 : adjacent_5p upward -D37-D38 : adjacent_5p upward -D38-D39 : adjacent_5p upward -D39-D40 : adjacent_5p upward -D44-D45 : adjacent_5p upward -D46-D47 : adjacent_5p upward -D47-D48 : adjacent_5p upward -D48-D49 : adjacent_5p upward -D49-D50 : adjacent_5p upward -D51-D52 : adjacent_5p upward -D52-D53 : adjacent_5p upward -D53-D54 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -C13-D51 : outward -C22-D48 : outward -C25-D39 : outward -Number of stackings = 29 -Number of adjacent stackings = 26 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -A51-D40 : ARG-U pairing one_hbond -B51-C14 : ARG-U pairing one_hbond -C8-D55 : G-C Ww/Ww pairing antiparallel cis XIX -C9-D54 : A-U Ww/Ww pairing antiparallel cis XX -C10-D53 : G-C Ww/Ww pairing antiparallel cis XIX -C11-D52 : A-U Ww/Ww pairing antiparallel cis XX -C12-D51 : C-G Ww/Ww pairing antiparallel cis XIX -C19-C20 : C-C O2P/Hh adjacent_5p pairing -C20-D49 : C-G Ww/Ww pairing antiparallel cis XIX -C21-D48 : C-G Ww/Ww pairing antiparallel cis XIX -C22-D47 : G-C Ww/Ww pairing antiparallel cis XIX -C23-D46 : G-C Ww/Ww pairing antiparallel cis XIX -C25-D38 : G-C Ww/Ww pairing antiparallel cis XIX -C26-D37 : U-A Ww/Ww pairing antiparallel cis XX -C27-D36 : C-G Ww/Ww pairing antiparallel cis XIX -C28-D35 : U-A Ww/Ww pairing antiparallel cis XX -C29-D34 : C-G Ww/Ww pairing antiparallel cis XIX -D45-D46 : C-C O2P/Hh adjacent_5p pairing -Residue conformations ------------------------------------------- -A1 : ALA -A2 : VAL -A3 : PRO -A4 : GLU -A5 : THR -A6 : ARG -A7 : PRO -A8 : ASN -A9 : HIS -A10 : THR -A11 : ILE -A12 : TYR -A13 : ILE -A14 : ASN -A15 : ASN -A16 : LEU -A17 : ASN -A18 : GLU -A19 : LYS -A20 : ILE -A21 : LYS -A22 : LYS -A23 : ASP -A24 : GLU -A25 : LEU -A26 : LYS -A27 : LYS -A28 : SER -A29 : LEU -A30 : HIS -A31 : ALA -A32 : ILE -A33 : PHE -A34 : SER -A35 : ARG -A36 : PHE -A37 : GLY -A38 : GLN -A39 : ILE -A40 : LEU -A41 : ASP -A42 : ILE -A43 : LEU -A44 : VAL -A45 : SER -A46 : ARG -A47 : SER -A48 : LEU -A49 : LYS -A50 : MET -A51 : ARG -A52 : GLY -A53 : GLN -A54 : ALA -A55 : PHE -A56 : VAL -A57 : ILE -A58 : PHE -A59 : LYS -A60 : GLU -A61 : VAL -A62 : SER -A63 : SER -A64 : ALA -A65 : THR -A66 : ASN -A67 : ALA -A68 : LEU -A69 : ARG -A70 : SER -A71 : MET -A72 : GLN -A73 : GLY -A74 : PHE -A75 : PRO -A76 : PHE -A77 : TYR -A78 : ASP -A79 : LYS -A80 : PRO -A81 : MET -A82 : ARG -A83 : ILE -A84 : GLN -A85 : TYR -A86 : ALA -A87 : LYS -A88 : THR -A89 : ASP -A90 : SER -A91 : ASP -A92 : ILE -A93 : ILE -A94 : ALA -A95 : LYS -A96 : MET -A97 : LYS -A98 : GLY -A99 : THR -A100 : PHE -A101 : VAL -B1 : ALA -B2 : VAL -B3 : PRO -B4 : GLU -B5 : THR -B6 : ARG -B7 : PRO -B8 : ASN -B9 : HIS -B10 : THR -B11 : ILE -B12 : TYR -B13 : ILE -B14 : ASN -B15 : ASN -B16 : LEU -B17 : ASN -B18 : GLU -B19 : LYS -B20 : ILE -B21 : LYS -B22 : LYS -B23 : ASP -B24 : GLU -B25 : LEU -B26 : LYS -B27 : LYS -B28 : SER -B29 : LEU -B30 : HIS -B31 : ALA -B32 : ILE -B33 : PHE -B34 : SER -B35 : ARG -B36 : PHE -B37 : GLY -B38 : GLN -B39 : ILE -B40 : LEU -B41 : ASP -B42 : ILE -B43 : LEU -B44 : VAL -B45 : SER -B46 : ARG -B47 : SER -B48 : LEU -B49 : LYS -B50 : MET -B51 : ARG -B52 : GLY -B53 : GLN -B54 : ALA -B55 : PHE -B56 : VAL -B57 : ILE -B58 : PHE -B59 : LYS -B60 : GLU -B61 : VAL -B62 : SER -B63 : SER -B64 : ALA -B65 : THR -B66 : ASN -B67 : ALA -B68 : LEU -B69 : ARG -B70 : SER -B71 : MET -B72 : GLN -B73 : GLY -B74 : PHE -B75 : PRO -B76 : PHE -B77 : TYR -B78 : ASP -B79 : LYS -B80 : PRO -B81 : MET -B82 : ARG -B83 : ILE -B84 : GLN -B85 : TYR -B86 : ALA -B87 : LYS -B88 : THR -B89 : ASP -B90 : SER -B91 : ASP -B92 : ILE -B93 : ILE -B94 : ALA -B95 : LYS -B96 : MET -B97 : LYS -B98 : GLY -B99 : THR -B100 : PHE -B101 : VAL -C8 : G C2p_exo anti -C9 : A C2p_exo anti -C10 : G C3p_endo anti -C11 : A C2p_exo anti -C12 : C C3p_endo anti -C13 : A O4p_endo anti -C14 : U C4p_exo anti -C15 : U C1p_exo anti -C16 : G C2p_exo anti -C17 : C C1p_exo anti -C18 : A C4p_exo anti -C19 : C C2p_exo anti -C20 : C C2p_exo anti -C21 : C C2p_exo anti -C22 : G C2p_exo anti -C23 : G C3p_endo anti -C24 : A C3p_endo anti -C25 : G C2p_exo anti -C26 : U C3p_endo anti -C27 : C C3p_endo anti -C28 : U C3p_endo anti -C29 : C C2p_exo anti -D34 : G C2p_exo anti -D35 : A C2p_exo anti -D36 : G C3p_endo anti -D37 : A C2p_exo anti -D38 : C C3p_endo anti -D39 : A O4p_endo anti -D40 : U C4p_exo anti -D41 : U C1p_exo anti -D42 : G C2p_exo anti -D43 : C C1p_exo anti -D44 : A C4p_exo anti -D45 : C C2p_exo anti -D46 : C C2p_exo anti -D47 : C C2p_exo anti -D48 : G C2p_exo anti -D49 : G C3p_endo anti -D50 : A C3p_endo anti -D51 : G C2p_exo anti -D52 : U C3p_endo anti -D53 : C C3p_endo anti -D54 : U C3p_endo anti -D55 : C C2p_exo anti -Adjacent stackings ---------------------------------------------- -C8-C9 : adjacent_5p upward -C9-C10 : adjacent_5p upward -C10-C11 : adjacent_5p upward -C11-C12 : adjacent_5p upward -C13-C14 : adjacent_5p upward -C18-C19 : adjacent_5p upward -C20-C21 : adjacent_5p upward -C22-C23 : adjacent_5p upward -C23-C24 : adjacent_5p upward -C25-C26 : adjacent_5p upward -C26-C27 : adjacent_5p upward -C27-C28 : adjacent_5p upward -D34-D35 : adjacent_5p upward -D35-D36 : adjacent_5p upward -D36-D37 : adjacent_5p upward -D37-D38 : adjacent_5p upward -D39-D40 : adjacent_5p upward -D44-D45 : adjacent_5p upward -D46-D47 : adjacent_5p upward -D48-D49 : adjacent_5p upward -D49-D50 : adjacent_5p upward -D51-D52 : adjacent_5p upward -D52-D53 : adjacent_5p upward -D53-D54 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -C13-D51 : outward -C22-D48 : outward -C25-D39 : outward -Number of stackings = 27 -Number of adjacent stackings = 24 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -C8-D55 : G-C Ww/Ww pairing antiparallel cis XIX -C9-D54 : A-U Ww/Ww pairing antiparallel cis XX -C10-D53 : G-C Ww/Ww pairing antiparallel cis XIX -C11-D52 : A-U Ww/Ww pairing antiparallel cis XX -C12-D51 : C-G Ww/Ww pairing antiparallel cis XIX -C14-C16 : U-G O2'/Bs O2'/Ss pairing -C19-C20 : C-C O2P/Hh adjacent_5p pairing -C20-D49 : C-G Ww/Ww pairing antiparallel cis XIX -C21-D48 : C-G Ww/Ww pairing antiparallel cis XIX -C22-D47 : G-C Ww/Ww pairing antiparallel cis XIX -C23-D46 : G-C Ww/Ww pairing antiparallel cis XIX -C25-D38 : G-C Ww/Ww pairing antiparallel cis XIX -C26-D37 : U-A Ww/Ww pairing antiparallel cis XX -C27-D36 : C-G Ww/Ww pairing antiparallel cis XIX -C28-D35 : U-A Ww/Ww pairing antiparallel cis XX -C29-D34 : C-G Ww/Ww pairing antiparallel cis XIX -D40-D42 : U-G O2'/Bs O2'/Ss pairing -D45-D46 : C-C O2P/Hh adjacent_5p pairing -Residue conformations ------------------------------------------- -A1 : ALA -A2 : VAL -A3 : PRO -A4 : GLU -A5 : THR -A6 : ARG -A7 : PRO -A8 : ASN -A9 : HIS -A10 : THR -A11 : ILE -A12 : TYR -A13 : ILE -A14 : ASN -A15 : ASN -A16 : LEU -A17 : ASN -A18 : GLU -A19 : LYS -A20 : ILE -A21 : LYS -A22 : LYS -A23 : ASP -A24 : GLU -A25 : LEU -A26 : LYS -A27 : LYS -A28 : SER -A29 : LEU -A30 : HIS -A31 : ALA -A32 : ILE -A33 : PHE -A34 : SER -A35 : ARG -A36 : PHE -A37 : GLY -A38 : GLN -A39 : ILE -A40 : LEU -A41 : ASP -A42 : ILE -A43 : LEU -A44 : VAL -A45 : SER -A46 : ARG -A47 : SER -A48 : LEU -A49 : LYS -A50 : MET -A51 : ARG -A52 : GLY -A53 : GLN -A54 : ALA -A55 : PHE -A56 : VAL -A57 : ILE -A58 : PHE -A59 : LYS -A60 : GLU -A61 : VAL -A62 : SER -A63 : SER -A64 : ALA -A65 : THR -A66 : ASN -A67 : ALA -A68 : LEU -A69 : ARG -A70 : SER -A71 : MET -A72 : GLN -A73 : GLY -A74 : PHE -A75 : PRO -A76 : PHE -A77 : TYR -A78 : ASP -A79 : LYS -A80 : PRO -A81 : MET -A82 : ARG -A83 : ILE -A84 : GLN -A85 : TYR -A86 : ALA -A87 : LYS -A88 : THR -A89 : ASP -A90 : SER -A91 : ASP -A92 : ILE -A93 : ILE -A94 : ALA -A95 : LYS -A96 : MET -A97 : LYS -A98 : GLY -A99 : THR -A100 : PHE -A101 : VAL -B1 : ALA -B2 : VAL -B3 : PRO -B4 : GLU -B5 : THR -B6 : ARG -B7 : PRO -B8 : ASN -B9 : HIS -B10 : THR -B11 : ILE -B12 : TYR -B13 : ILE -B14 : ASN -B15 : ASN -B16 : LEU -B17 : ASN -B18 : GLU -B19 : LYS -B20 : ILE -B21 : LYS -B22 : LYS -B23 : ASP -B24 : GLU -B25 : LEU -B26 : LYS -B27 : LYS -B28 : SER -B29 : LEU -B30 : HIS -B31 : ALA -B32 : ILE -B33 : PHE -B34 : SER -B35 : ARG -B36 : PHE -B37 : GLY -B38 : GLN -B39 : ILE -B40 : LEU -B41 : ASP -B42 : ILE -B43 : LEU -B44 : VAL -B45 : SER -B46 : ARG -B47 : SER -B48 : LEU -B49 : LYS -B50 : MET -B51 : ARG -B52 : GLY -B53 : GLN -B54 : ALA -B55 : PHE -B56 : VAL -B57 : ILE -B58 : PHE -B59 : LYS -B60 : GLU -B61 : VAL -B62 : SER -B63 : SER -B64 : ALA -B65 : THR -B66 : ASN -B67 : ALA -B68 : LEU -B69 : ARG -B70 : SER -B71 : MET -B72 : GLN -B73 : GLY -B74 : PHE -B75 : PRO -B76 : PHE -B77 : TYR -B78 : ASP -B79 : LYS -B80 : PRO -B81 : MET -B82 : ARG -B83 : ILE -B84 : GLN -B85 : TYR -B86 : ALA -B87 : LYS -B88 : THR -B89 : ASP -B90 : SER -B91 : ASP -B92 : ILE -B93 : ILE -B94 : ALA -B95 : LYS -B96 : MET -B97 : LYS -B98 : GLY -B99 : THR -B100 : PHE -B101 : VAL -C8 : G C2p_exo anti -C9 : A C2p_exo anti -C10 : G C2p_exo anti -C11 : A C2p_exo anti -C12 : C C3p_endo anti -C13 : A C2p_exo anti -C14 : U C2p_exo anti -C15 : U C2p_endo anti -C16 : G C2p_exo anti -C17 : C C1p_exo syn -C18 : A C2p_exo anti -C19 : C C2p_exo anti -C20 : C C2p_exo anti -C21 : C C2p_exo anti -C22 : G C3p_endo anti -C23 : G C2p_exo anti -C24 : A C2p_exo anti -C25 : G C2p_exo anti -C26 : U C2p_exo anti -C27 : C C3p_endo anti -C28 : U C3p_endo anti -C29 : C C2p_exo anti -D34 : G C2p_exo anti -D35 : A C2p_exo anti -D36 : G C2p_exo anti -D37 : A C2p_exo anti -D38 : C C3p_endo anti -D39 : A C2p_exo anti -D40 : U C2p_exo anti -D41 : U C2p_endo anti -D42 : G C2p_exo anti -D43 : C C1p_exo syn -D44 : A C2p_exo anti -D45 : C C2p_exo anti -D46 : C C2p_exo anti -D47 : C C2p_exo anti -D48 : G C3p_endo anti -D49 : G C2p_exo anti -D50 : A C2p_exo anti -D51 : G C2p_exo anti -D52 : U C2p_exo anti -D53 : C C3p_endo anti -D54 : U C3p_endo anti -D55 : C C2p_exo anti -Adjacent stackings ---------------------------------------------- -C8-C9 : adjacent_5p upward -C9-C10 : adjacent_5p upward -C10-C11 : adjacent_5p upward -C11-C12 : adjacent_5p upward -C13-C14 : adjacent_5p upward -C20-C21 : adjacent_5p upward -C22-C23 : adjacent_5p upward -C23-C24 : adjacent_5p upward -C26-C27 : adjacent_5p upward -C27-C28 : adjacent_5p upward -D34-D35 : adjacent_5p upward -D35-D36 : adjacent_5p upward -D36-D37 : adjacent_5p upward -D37-D38 : adjacent_5p upward -D39-D40 : adjacent_5p upward -D46-D47 : adjacent_5p upward -D48-D49 : adjacent_5p upward -D49-D50 : adjacent_5p upward -D52-D53 : adjacent_5p upward -D53-D54 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -C13-D51 : outward -C22-D48 : outward -C25-D39 : outward -Number of stackings = 23 -Number of adjacent stackings = 20 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -A45-C24 : SER-A pairing one_hbond -A91-D45 : ASP-C pairing one_hbond -B45-D50 : SER-A pairing one_hbond -B91-C19 : ASP-C pairing one_hbond -C8-D55 : G-C Ww/Ww pairing antiparallel cis XIX -C9-D54 : A-U Ww/Ww pairing antiparallel cis XX -C10-D53 : G-C Ww/Ww pairing antiparallel cis XIX -C11-D52 : A-U Ww/Ww pairing antiparallel cis XX -C12-D51 : C-G Ww/Ww pairing antiparallel cis XIX -C19-C20 : C-C O2P/Hh adjacent_5p pairing -C20-D49 : C-G Ww/Ww pairing antiparallel cis XIX -C21-D48 : C-G Ww/Ww pairing antiparallel cis XIX -C22-D47 : G-C Ww/Ww pairing antiparallel cis XIX -C23-D46 : G-C Ww/Ww pairing antiparallel cis XIX -C25-D38 : G-C Ww/Ww pairing antiparallel cis XIX -C26-D37 : U-A Ww/Ww pairing antiparallel cis XX -C27-D36 : C-G Ww/Ww pairing antiparallel cis XIX -C28-D35 : U-A Ww/Ww pairing antiparallel cis XX -C29-D34 : C-G Ww/Ww pairing antiparallel cis XIX -D45-D46 : C-C O2P/Hh adjacent_5p pairing -Residue conformations ------------------------------------------- -A1 : ALA -A2 : VAL -A3 : PRO -A4 : GLU -A5 : THR -A6 : ARG -A7 : PRO -A8 : ASN -A9 : HIS -A10 : THR -A11 : ILE -A12 : TYR -A13 : ILE -A14 : ASN -A15 : ASN -A16 : LEU -A17 : ASN -A18 : GLU -A19 : LYS -A20 : ILE -A21 : LYS -A22 : LYS -A23 : ASP -A24 : GLU -A25 : LEU -A26 : LYS -A27 : LYS -A28 : SER -A29 : LEU -A30 : HIS -A31 : ALA -A32 : ILE -A33 : PHE -A34 : SER -A35 : ARG -A36 : PHE -A37 : GLY -A38 : GLN -A39 : ILE -A40 : LEU -A41 : ASP -A42 : ILE -A43 : LEU -A44 : VAL -A45 : SER -A46 : ARG -A47 : SER -A48 : LEU -A49 : LYS -A50 : MET -A51 : ARG -A52 : GLY -A53 : GLN -A54 : ALA -A55 : PHE -A56 : VAL -A57 : ILE -A58 : PHE -A59 : LYS -A60 : GLU -A61 : VAL -A62 : SER -A63 : SER -A64 : ALA -A65 : THR -A66 : ASN -A67 : ALA -A68 : LEU -A69 : ARG -A70 : SER -A71 : MET -A72 : GLN -A73 : GLY -A74 : PHE -A75 : PRO -A76 : PHE -A77 : TYR -A78 : ASP -A79 : LYS -A80 : PRO -A81 : MET -A82 : ARG -A83 : ILE -A84 : GLN -A85 : TYR -A86 : ALA -A87 : LYS -A88 : THR -A89 : ASP -A90 : SER -A91 : ASP -A92 : ILE -A93 : ILE -A94 : ALA -A95 : LYS -A96 : MET -A97 : LYS -A98 : GLY -A99 : THR -A100 : PHE -A101 : VAL -B1 : ALA -B2 : VAL -B3 : PRO -B4 : GLU -B5 : THR -B6 : ARG -B7 : PRO -B8 : ASN -B9 : HIS -B10 : THR -B11 : ILE -B12 : TYR -B13 : ILE -B14 : ASN -B15 : ASN -B16 : LEU -B17 : ASN -B18 : GLU -B19 : LYS -B20 : ILE -B21 : LYS -B22 : LYS -B23 : ASP -B24 : GLU -B25 : LEU -B26 : LYS -B27 : LYS -B28 : SER -B29 : LEU -B30 : HIS -B31 : ALA -B32 : ILE -B33 : PHE -B34 : SER -B35 : ARG -B36 : PHE -B37 : GLY -B38 : GLN -B39 : ILE -B40 : LEU -B41 : ASP -B42 : ILE -B43 : LEU -B44 : VAL -B45 : SER -B46 : ARG -B47 : SER -B48 : LEU -B49 : LYS -B50 : MET -B51 : ARG -B52 : GLY -B53 : GLN -B54 : ALA -B55 : PHE -B56 : VAL -B57 : ILE -B58 : PHE -B59 : LYS -B60 : GLU -B61 : VAL -B62 : SER -B63 : SER -B64 : ALA -B65 : THR -B66 : ASN -B67 : ALA -B68 : LEU -B69 : ARG -B70 : SER -B71 : MET -B72 : GLN -B73 : GLY -B74 : PHE -B75 : PRO -B76 : PHE -B77 : TYR -B78 : ASP -B79 : LYS -B80 : PRO -B81 : MET -B82 : ARG -B83 : ILE -B84 : GLN -B85 : TYR -B86 : ALA -B87 : LYS -B88 : THR -B89 : ASP -B90 : SER -B91 : ASP -B92 : ILE -B93 : ILE -B94 : ALA -B95 : LYS -B96 : MET -B97 : LYS -B98 : GLY -B99 : THR -B100 : PHE -B101 : VAL -C8 : G C2p_exo anti -C9 : A C2p_exo anti -C10 : G C3p_endo anti -C11 : A C3p_endo anti -C12 : C C3p_endo anti -C13 : A C3p_endo anti -C14 : U C2p_exo anti -C15 : U C1p_exo anti -C16 : G C1p_endo anti -C17 : C C1p_exo anti -C18 : A C1p_exo anti -C19 : C C3p_endo anti -C20 : C C2p_exo anti -C21 : C C2p_exo anti -C22 : G C2p_exo anti -C23 : G C2p_exo anti -C24 : A C3p_endo anti -C25 : G C3p_endo anti -C26 : U C3p_endo anti -C27 : C C3p_endo anti -C28 : U C3p_endo anti -C29 : C C2p_exo anti -D34 : G C2p_exo anti -D35 : A C2p_exo anti -D36 : G C3p_endo anti -D37 : A C3p_endo anti -D38 : C C3p_endo anti -D39 : A C3p_endo anti -D40 : U C2p_exo anti -D41 : U C1p_exo anti -D42 : G C1p_endo anti -D43 : C C1p_exo anti -D44 : A C1p_exo anti -D45 : C C3p_endo anti -D46 : C C2p_exo anti -D47 : C C2p_exo anti -D48 : G C2p_exo anti -D49 : G C2p_exo anti -D50 : A C3p_endo anti -D51 : G C3p_endo anti -D52 : U C3p_endo anti -D53 : C C3p_endo anti -D54 : U C3p_endo anti -D55 : C C2p_exo anti -Adjacent stackings ---------------------------------------------- -C8-C9 : adjacent_5p upward -C9-C10 : adjacent_5p upward -C10-C11 : adjacent_5p upward -C11-C12 : adjacent_5p upward -C13-C14 : adjacent_5p upward -C18-C19 : adjacent_5p upward -C20-C21 : adjacent_5p upward -C22-C23 : adjacent_5p upward -C23-C24 : adjacent_5p upward -C25-C26 : adjacent_5p upward -C26-C27 : adjacent_5p upward -C27-C28 : adjacent_5p upward -D34-D35 : adjacent_5p upward -D35-D36 : adjacent_5p upward -D36-D37 : adjacent_5p upward -D37-D38 : adjacent_5p upward -D39-D40 : adjacent_5p upward -D44-D45 : adjacent_5p upward -D46-D47 : adjacent_5p upward -D48-D49 : adjacent_5p upward -D49-D50 : adjacent_5p upward -D51-D52 : adjacent_5p upward -D52-D53 : adjacent_5p upward -D53-D54 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -C13-D51 : outward -C22-D48 : outward -C25-D39 : outward -Number of stackings = 27 -Number of adjacent stackings = 24 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -C8-D55 : G-C Ww/Ww pairing antiparallel cis XIX -C9-D54 : A-U Ww/Ww pairing antiparallel cis XX -C10-D53 : G-C Ww/Ww pairing antiparallel cis XIX -C11-D52 : A-U Ww/Ww pairing antiparallel cis XX -C12-D51 : C-G Ww/Ww pairing antiparallel cis -C19-C20 : C-C O2P/Bh O2P/Hh adjacent_5p pairing -C19-D50 : C-A O2P/Ww pairing -C20-D49 : C-G Ww/Ww pairing antiparallel cis XIX -C21-D48 : C-G Ww/Ww pairing antiparallel cis XIX -C22-D47 : G-C Ww/Ww pairing antiparallel cis XIX -C23-D46 : G-C Ww/Ww pairing antiparallel cis XIX -C24-D45 : A-C Ww/O2P pairing -C25-D38 : G-C Ww/Ww pairing antiparallel cis -C26-D37 : U-A Ww/Ww pairing antiparallel cis XX -C27-D36 : C-G Ww/Ww pairing antiparallel cis XIX -C28-D35 : U-A Ww/Ww pairing antiparallel cis XX -C29-D34 : C-G Ww/Ww pairing antiparallel cis XIX -D45-D46 : C-C O2P/Bh O2P/Hh adjacent_5p pairing -Residue conformations ------------------------------------------- -A1 : ALA -A2 : VAL -A3 : PRO -A4 : GLU -A5 : THR -A6 : ARG -A7 : PRO -A8 : ASN -A9 : HIS -A10 : THR -A11 : ILE -A12 : TYR -A13 : ILE -A14 : ASN -A15 : ASN -A16 : LEU -A17 : ASN -A18 : GLU -A19 : LYS -A20 : ILE -A21 : LYS -A22 : LYS -A23 : ASP -A24 : GLU -A25 : LEU -A26 : LYS -A27 : LYS -A28 : SER -A29 : LEU -A30 : HIS -A31 : ALA -A32 : ILE -A33 : PHE -A34 : SER -A35 : ARG -A36 : PHE -A37 : GLY -A38 : GLN -A39 : ILE -A40 : LEU -A41 : ASP -A42 : ILE -A43 : LEU -A44 : VAL -A45 : SER -A46 : ARG -A47 : SER -A48 : LEU -A49 : LYS -A50 : MET -A51 : ARG -A52 : GLY -A53 : GLN -A54 : ALA -A55 : PHE -A56 : VAL -A57 : ILE -A58 : PHE -A59 : LYS -A60 : GLU -A61 : VAL -A62 : SER -A63 : SER -A64 : ALA -A65 : THR -A66 : ASN -A67 : ALA -A68 : LEU -A69 : ARG -A70 : SER -A71 : MET -A72 : GLN -A73 : GLY -A74 : PHE -A75 : PRO -A76 : PHE -A77 : TYR -A78 : ASP -A79 : LYS -A80 : PRO -A81 : MET -A82 : ARG -A83 : ILE -A84 : GLN -A85 : TYR -A86 : ALA -A87 : LYS -A88 : THR -A89 : ASP -A90 : SER -A91 : ASP -A92 : ILE -A93 : ILE -A94 : ALA -A95 : LYS -A96 : MET -A97 : LYS -A98 : GLY -A99 : THR -A100 : PHE -A101 : VAL -B1 : ALA -B2 : VAL -B3 : PRO -B4 : GLU -B5 : THR -B6 : ARG -B7 : PRO -B8 : ASN -B9 : HIS -B10 : THR -B11 : ILE -B12 : TYR -B13 : ILE -B14 : ASN -B15 : ASN -B16 : LEU -B17 : ASN -B18 : GLU -B19 : LYS -B20 : ILE -B21 : LYS -B22 : LYS -B23 : ASP -B24 : GLU -B25 : LEU -B26 : LYS -B27 : LYS -B28 : SER -B29 : LEU -B30 : HIS -B31 : ALA -B32 : ILE -B33 : PHE -B34 : SER -B35 : ARG -B36 : PHE -B37 : GLY -B38 : GLN -B39 : ILE -B40 : LEU -B41 : ASP -B42 : ILE -B43 : LEU -B44 : VAL -B45 : SER -B46 : ARG -B47 : SER -B48 : LEU -B49 : LYS -B50 : MET -B51 : ARG -B52 : GLY -B53 : GLN -B54 : ALA -B55 : PHE -B56 : VAL -B57 : ILE -B58 : PHE -B59 : LYS -B60 : GLU -B61 : VAL -B62 : SER -B63 : SER -B64 : ALA -B65 : THR -B66 : ASN -B67 : ALA -B68 : LEU -B69 : ARG -B70 : SER -B71 : MET -B72 : GLN -B73 : GLY -B74 : PHE -B75 : PRO -B76 : PHE -B77 : TYR -B78 : ASP -B79 : LYS -B80 : PRO -B81 : MET -B82 : ARG -B83 : ILE -B84 : GLN -B85 : TYR -B86 : ALA -B87 : LYS -B88 : THR -B89 : ASP -B90 : SER -B91 : ASP -B92 : ILE -B93 : ILE -B94 : ALA -B95 : LYS -B96 : MET -B97 : LYS -B98 : GLY -B99 : THR -B100 : PHE -B101 : VAL -C8 : G C2p_exo anti -C9 : A C2p_exo anti -C10 : G C2p_exo anti -C11 : A C2p_exo anti -C12 : C C3p_endo anti -C13 : A C2p_exo anti -C14 : U C2p_exo anti -C15 : U C2p_endo anti -C16 : G C2p_exo anti -C17 : C C1p_exo anti -C18 : A C3p_endo anti -C19 : C C2p_exo anti -C20 : C C2p_exo anti -C21 : C C2p_exo anti -C22 : G C2p_exo anti -C23 : G C2p_exo anti -C24 : A C3p_endo anti -C25 : G O4p_endo anti -C26 : U C3p_endo anti -C27 : C C3p_endo anti -C28 : U C3p_endo anti -C29 : C C2p_exo anti -D34 : G C2p_exo anti -D35 : A C2p_exo anti -D36 : G C2p_exo anti -D37 : A C2p_exo anti -D38 : C C3p_endo anti -D39 : A C2p_exo anti -D40 : U C2p_exo anti -D41 : U C2p_endo anti -D42 : G C2p_exo anti -D43 : C C1p_exo anti -D44 : A C3p_endo anti -D45 : C C2p_exo anti -D46 : C C2p_exo anti -D47 : C C2p_exo anti -D48 : G C2p_exo anti -D49 : G C2p_exo anti -D50 : A C3p_endo anti -D51 : G O4p_endo anti -D52 : U C3p_endo anti -D53 : C C3p_endo anti -D54 : U C3p_endo anti -D55 : C C2p_exo anti -Adjacent stackings ---------------------------------------------- -C9-C10 : adjacent_5p upward -C10-C11 : adjacent_5p upward -C11-C12 : adjacent_5p upward -C12-C13 : adjacent_5p upward -C13-C14 : adjacent_5p upward -C18-C19 : adjacent_5p upward -C20-C21 : adjacent_5p upward -C21-C22 : adjacent_5p upward -C22-C23 : adjacent_5p upward -C23-C24 : adjacent_5p upward -C26-C27 : adjacent_5p upward -C27-C28 : adjacent_5p upward -D35-D36 : adjacent_5p upward -D36-D37 : adjacent_5p upward -D37-D38 : adjacent_5p upward -D38-D39 : adjacent_5p upward -D39-D40 : adjacent_5p upward -D44-D45 : adjacent_5p upward -D46-D47 : adjacent_5p upward -D47-D48 : adjacent_5p upward -D48-D49 : adjacent_5p upward -D49-D50 : adjacent_5p upward -D52-D53 : adjacent_5p upward -D53-D54 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -C13-D51 : outward -C22-D48 : outward -C25-D39 : outward -Number of stackings = 27 -Number of adjacent stackings = 24 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -C8-D55 : G-C Ww/Ww pairing antiparallel cis XIX -C9-D54 : A-U Ww/Ww pairing antiparallel cis XX -C10-D53 : G-C Ww/Ww pairing antiparallel cis XIX -C11-D52 : A-U Ww/Ww pairing antiparallel cis XX -C12-D51 : C-G Ww/Ww pairing antiparallel cis XIX -C19-C20 : C-C O2P/Hh adjacent_5p pairing -C20-D49 : C-G Ww/Ww pairing antiparallel cis XIX -C21-D48 : C-G Ww/Ww pairing antiparallel cis XIX -C22-D47 : G-C Ww/Ww pairing antiparallel cis XIX -C23-D46 : G-C Ww/Ww pairing antiparallel cis XIX -C25-D38 : G-C Ww/Ww pairing antiparallel cis XIX -C26-D37 : U-A Ww/Ww pairing antiparallel cis XX -C27-D36 : C-G Ww/Ww pairing antiparallel cis XIX -C28-D35 : U-A Ww/Ww pairing antiparallel cis XX -C29-D34 : C-G Ww/Ww pairing antiparallel cis XIX -D45-D46 : C-C O2P/Hh adjacent_5p pairing -Residue conformations ------------------------------------------- -A1 : ALA -A2 : VAL -A3 : PRO -A4 : GLU -A5 : THR -A6 : ARG -A7 : PRO -A8 : ASN -A9 : HIS -A10 : THR -A11 : ILE -A12 : TYR -A13 : ILE -A14 : ASN -A15 : ASN -A16 : LEU -A17 : ASN -A18 : GLU -A19 : LYS -A20 : ILE -A21 : LYS -A22 : LYS -A23 : ASP -A24 : GLU -A25 : LEU -A26 : LYS -A27 : LYS -A28 : SER -A29 : LEU -A30 : HIS -A31 : ALA -A32 : ILE -A33 : PHE -A34 : SER -A35 : ARG -A36 : PHE -A37 : GLY -A38 : GLN -A39 : ILE -A40 : LEU -A41 : ASP -A42 : ILE -A43 : LEU -A44 : VAL -A45 : SER -A46 : ARG -A47 : SER -A48 : LEU -A49 : LYS -A50 : MET -A51 : ARG -A52 : GLY -A53 : GLN -A54 : ALA -A55 : PHE -A56 : VAL -A57 : ILE -A58 : PHE -A59 : LYS -A60 : GLU -A61 : VAL -A62 : SER -A63 : SER -A64 : ALA -A65 : THR -A66 : ASN -A67 : ALA -A68 : LEU -A69 : ARG -A70 : SER -A71 : MET -A72 : GLN -A73 : GLY -A74 : PHE -A75 : PRO -A76 : PHE -A77 : TYR -A78 : ASP -A79 : LYS -A80 : PRO -A81 : MET -A82 : ARG -A83 : ILE -A84 : GLN -A85 : TYR -A86 : ALA -A87 : LYS -A88 : THR -A89 : ASP -A90 : SER -A91 : ASP -A92 : ILE -A93 : ILE -A94 : ALA -A95 : LYS -A96 : MET -A97 : LYS -A98 : GLY -A99 : THR -A100 : PHE -A101 : VAL -B1 : ALA -B2 : VAL -B3 : PRO -B4 : GLU -B5 : THR -B6 : ARG -B7 : PRO -B8 : ASN -B9 : HIS -B10 : THR -B11 : ILE -B12 : TYR -B13 : ILE -B14 : ASN -B15 : ASN -B16 : LEU -B17 : ASN -B18 : GLU -B19 : LYS -B20 : ILE -B21 : LYS -B22 : LYS -B23 : ASP -B24 : GLU -B25 : LEU -B26 : LYS -B27 : LYS -B28 : SER -B29 : LEU -B30 : HIS -B31 : ALA -B32 : ILE -B33 : PHE -B34 : SER -B35 : ARG -B36 : PHE -B37 : GLY -B38 : GLN -B39 : ILE -B40 : LEU -B41 : ASP -B42 : ILE -B43 : LEU -B44 : VAL -B45 : SER -B46 : ARG -B47 : SER -B48 : LEU -B49 : LYS -B50 : MET -B51 : ARG -B52 : GLY -B53 : GLN -B54 : ALA -B55 : PHE -B56 : VAL -B57 : ILE -B58 : PHE -B59 : LYS -B60 : GLU -B61 : VAL -B62 : SER -B63 : SER -B64 : ALA -B65 : THR -B66 : ASN -B67 : ALA -B68 : LEU -B69 : ARG -B70 : SER -B71 : MET -B72 : GLN -B73 : GLY -B74 : PHE -B75 : PRO -B76 : PHE -B77 : TYR -B78 : ASP -B79 : LYS -B80 : PRO -B81 : MET -B82 : ARG -B83 : ILE -B84 : GLN -B85 : TYR -B86 : ALA -B87 : LYS -B88 : THR -B89 : ASP -B90 : SER -B91 : ASP -B92 : ILE -B93 : ILE -B94 : ALA -B95 : LYS -B96 : MET -B97 : LYS -B98 : GLY -B99 : THR -B100 : PHE -B101 : VAL -C8 : G C2p_exo anti -C9 : A C2p_exo anti -C10 : G C3p_endo anti -C11 : A C3p_endo anti -C12 : C C3p_endo anti -C13 : A C3p_endo anti -C14 : U C2p_exo anti -C15 : U C2p_endo anti -C16 : G C3p_exo anti -C17 : C C1p_exo syn -C18 : A C3p_endo anti -C19 : C C2p_exo anti -C20 : C C2p_exo anti -C21 : C C2p_exo anti -C22 : G C2p_exo anti -C23 : G C2p_exo anti -C24 : A C3p_endo anti -C25 : G C2p_exo anti -C26 : U C3p_endo anti -C27 : C C3p_endo anti -C28 : U C3p_endo anti -C29 : C C2p_exo anti -D34 : G C2p_exo anti -D35 : A C2p_exo anti -D36 : G C3p_endo anti -D37 : A C3p_endo anti -D38 : C C3p_endo anti -D39 : A C3p_endo anti -D40 : U C2p_exo anti -D41 : U C2p_endo anti -D42 : G C3p_exo anti -D43 : C C1p_exo syn -D44 : A C3p_endo anti -D45 : C C2p_exo anti -D46 : C C2p_exo anti -D47 : C C2p_exo anti -D48 : G C2p_exo anti -D49 : G C2p_exo anti -D50 : A C3p_endo anti -D51 : G C2p_exo anti -D52 : U C3p_endo anti -D53 : C C3p_endo anti -D54 : U C3p_endo anti -D55 : C C2p_exo anti -Adjacent stackings ---------------------------------------------- -C8-C9 : adjacent_5p upward -C9-C10 : adjacent_5p upward -C10-C11 : adjacent_5p upward -C11-C12 : adjacent_5p upward -C12-C13 : adjacent_5p upward -C13-C14 : adjacent_5p upward -C18-C19 : adjacent_5p upward pairing -C20-C21 : adjacent_5p upward -C22-C23 : adjacent_5p upward -C23-C24 : adjacent_5p upward -C25-C26 : adjacent_5p upward -C26-C27 : adjacent_5p upward -C27-C28 : adjacent_5p upward -D34-D35 : adjacent_5p upward -D35-D36 : adjacent_5p upward -D36-D37 : adjacent_5p upward -D37-D38 : adjacent_5p upward -D38-D39 : adjacent_5p upward -D39-D40 : adjacent_5p upward -D44-D45 : adjacent_5p upward pairing -D46-D47 : adjacent_5p upward -D48-D49 : adjacent_5p upward -D49-D50 : adjacent_5p upward -D51-D52 : adjacent_5p upward -D52-D53 : adjacent_5p upward -D53-D54 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -C13-D51 : outward -C22-D48 : outward -C25-D39 : outward -Number of stackings = 29 -Number of adjacent stackings = 26 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -A15-D41 : ASN-U pairing one_hbond -B15-C15 : ASN-U pairing one_hbond -C8-D55 : G-C Ww/Ww pairing antiparallel cis XIX -C9-D54 : A-U Ww/Ww pairing antiparallel cis XX -C10-D53 : G-C Ww/Ww pairing antiparallel cis XIX -C11-D52 : A-U Ww/Ww pairing antiparallel cis XX -C12-D51 : C-G Ww/Ww pairing antiparallel cis XIX -C18-C19 : A-C O2P/Bh adjacent_5p upward pairing -C19-C20 : C-C O2P/Hh adjacent_5p pairing -C19-D50 : C-A O2P/Ww pairing -C20-D49 : C-G Ww/Ww pairing antiparallel cis XIX -C21-D48 : C-G Ww/Ww pairing antiparallel cis XIX -C22-D47 : G-C Ww/Ww pairing antiparallel cis XIX -C23-D46 : G-C Ww/Ww pairing antiparallel cis XIX -C24-D45 : A-C Ww/O2P pairing -C25-D38 : G-C Ww/Ww pairing antiparallel cis XIX -C26-D37 : U-A Ww/Ww pairing antiparallel cis XX -C27-D36 : C-G Ww/Ww pairing antiparallel cis XIX -C28-D35 : U-A Ww/Ww pairing antiparallel cis XX -C29-D34 : C-G Ww/Ww pairing antiparallel cis XIX -D44-D45 : A-C O2P/Bh adjacent_5p upward pairing -D45-D46 : C-C O2P/Hh adjacent_5p pairing -Residue conformations ------------------------------------------- -A1 : ALA -A2 : VAL -A3 : PRO -A4 : GLU -A5 : THR -A6 : ARG -A7 : PRO -A8 : ASN -A9 : HIS -A10 : THR -A11 : ILE -A12 : TYR -A13 : ILE -A14 : ASN -A15 : ASN -A16 : LEU -A17 : ASN -A18 : GLU -A19 : LYS -A20 : ILE -A21 : LYS -A22 : LYS -A23 : ASP -A24 : GLU -A25 : LEU -A26 : LYS -A27 : LYS -A28 : SER -A29 : LEU -A30 : HIS -A31 : ALA -A32 : ILE -A33 : PHE -A34 : SER -A35 : ARG -A36 : PHE -A37 : GLY -A38 : GLN -A39 : ILE -A40 : LEU -A41 : ASP -A42 : ILE -A43 : LEU -A44 : VAL -A45 : SER -A46 : ARG -A47 : SER -A48 : LEU -A49 : LYS -A50 : MET -A51 : ARG -A52 : GLY -A53 : GLN -A54 : ALA -A55 : PHE -A56 : VAL -A57 : ILE -A58 : PHE -A59 : LYS -A60 : GLU -A61 : VAL -A62 : SER -A63 : SER -A64 : ALA -A65 : THR -A66 : ASN -A67 : ALA -A68 : LEU -A69 : ARG -A70 : SER -A71 : MET -A72 : GLN -A73 : GLY -A74 : PHE -A75 : PRO -A76 : PHE -A77 : TYR -A78 : ASP -A79 : LYS -A80 : PRO -A81 : MET -A82 : ARG -A83 : ILE -A84 : GLN -A85 : TYR -A86 : ALA -A87 : LYS -A88 : THR -A89 : ASP -A90 : SER -A91 : ASP -A92 : ILE -A93 : ILE -A94 : ALA -A95 : LYS -A96 : MET -A97 : LYS -A98 : GLY -A99 : THR -A100 : PHE -A101 : VAL -B1 : ALA -B2 : VAL -B3 : PRO -B4 : GLU -B5 : THR -B6 : ARG -B7 : PRO -B8 : ASN -B9 : HIS -B10 : THR -B11 : ILE -B12 : TYR -B13 : ILE -B14 : ASN -B15 : ASN -B16 : LEU -B17 : ASN -B18 : GLU -B19 : LYS -B20 : ILE -B21 : LYS -B22 : LYS -B23 : ASP -B24 : GLU -B25 : LEU -B26 : LYS -B27 : LYS -B28 : SER -B29 : LEU -B30 : HIS -B31 : ALA -B32 : ILE -B33 : PHE -B34 : SER -B35 : ARG -B36 : PHE -B37 : GLY -B38 : GLN -B39 : ILE -B40 : LEU -B41 : ASP -B42 : ILE -B43 : LEU -B44 : VAL -B45 : SER -B46 : ARG -B47 : SER -B48 : LEU -B49 : LYS -B50 : MET -B51 : ARG -B52 : GLY -B53 : GLN -B54 : ALA -B55 : PHE -B56 : VAL -B57 : ILE -B58 : PHE -B59 : LYS -B60 : GLU -B61 : VAL -B62 : SER -B63 : SER -B64 : ALA -B65 : THR -B66 : ASN -B67 : ALA -B68 : LEU -B69 : ARG -B70 : SER -B71 : MET -B72 : GLN -B73 : GLY -B74 : PHE -B75 : PRO -B76 : PHE -B77 : TYR -B78 : ASP -B79 : LYS -B80 : PRO -B81 : MET -B82 : ARG -B83 : ILE -B84 : GLN -B85 : TYR -B86 : ALA -B87 : LYS -B88 : THR -B89 : ASP -B90 : SER -B91 : ASP -B92 : ILE -B93 : ILE -B94 : ALA -B95 : LYS -B96 : MET -B97 : LYS -B98 : GLY -B99 : THR -B100 : PHE -B101 : VAL -C8 : G C2p_exo anti -C9 : A C2p_exo anti -C10 : G C3p_endo anti -C11 : A C3p_endo anti -C12 : C C3p_endo anti -C13 : A C2p_exo anti -C14 : U C2p_exo anti -C15 : U C1p_exo anti -C16 : G C1p_endo syn -C17 : C C1p_exo syn -C18 : A C1p_exo anti -C19 : C C2p_exo anti -C20 : C C2p_exo anti -C21 : C C2p_exo anti -C22 : G C2p_exo anti -C23 : G C2p_exo anti -C24 : A C3p_endo anti -C25 : G C4p_exo anti -C26 : U C3p_endo anti -C27 : C C3p_endo anti -C28 : U C3p_endo anti -C29 : C C2p_exo anti -D34 : G C2p_exo anti -D35 : A C2p_exo anti -D36 : G C3p_endo anti -D37 : A C3p_endo anti -D38 : C C3p_endo anti -D39 : A C2p_exo anti -D40 : U C2p_exo anti -D41 : U C1p_exo anti -D42 : G C1p_endo syn -D43 : C C1p_exo syn -D44 : A C1p_exo anti -D45 : C C2p_exo anti -D46 : C C2p_exo anti -D47 : C C2p_exo anti -D48 : G C2p_exo anti -D49 : G C2p_exo anti -D50 : A C3p_endo anti -D51 : G C4p_exo anti -D52 : U C3p_endo anti -D53 : C C3p_endo anti -D54 : U C3p_endo anti -D55 : C C2p_exo anti -Adjacent stackings ---------------------------------------------- -C8-C9 : adjacent_5p upward -C9-C10 : adjacent_5p upward -C10-C11 : adjacent_5p upward -C11-C12 : adjacent_5p upward -C12-C13 : adjacent_5p upward -C13-C14 : adjacent_5p upward -C18-C19 : adjacent_5p upward -C20-C21 : adjacent_5p upward -C22-C23 : adjacent_5p upward -C23-C24 : adjacent_5p upward -C26-C27 : adjacent_5p upward -C27-C28 : adjacent_5p upward -D34-D35 : adjacent_5p upward -D35-D36 : adjacent_5p upward -D36-D37 : adjacent_5p upward -D37-D38 : adjacent_5p upward -D38-D39 : adjacent_5p upward -D39-D40 : adjacent_5p upward -D44-D45 : adjacent_5p upward -D46-D47 : adjacent_5p upward -D48-D49 : adjacent_5p upward -D49-D50 : adjacent_5p upward -D52-D53 : adjacent_5p upward -D53-D54 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -C13-D51 : outward -C22-D48 : outward -C25-D39 : outward -Number of stackings = 27 -Number of adjacent stackings = 24 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -A12-D43 : TYR-C pairing one_hbond -B12-C17 : TYR-C pairing one_hbond -B79-C15 : LYS-U pairing one_hbond -C8-D55 : G-C Ww/Ww pairing antiparallel cis XIX -C9-D54 : A-U Ww/Ww pairing antiparallel cis XX -C10-D53 : G-C Ww/Ww pairing antiparallel cis XIX -C11-D52 : A-U Ww/Ww pairing antiparallel cis XX -C12-D51 : C-G Ww/Ww pairing antiparallel cis XIX -C19-D50 : C-A O2P/Ww pairing -C20-D49 : C-G Ww/Ww pairing antiparallel cis XIX -C21-D48 : C-G Ww/Ww pairing antiparallel cis XIX -C22-D47 : G-C Ww/Ww pairing antiparallel cis XIX -C23-D46 : G-C Ww/Ww pairing antiparallel cis XIX -C24-D45 : A-C Ww/O2P pairing -C25-D38 : G-C Ww/Ww pairing antiparallel cis XIX -C26-D37 : U-A Ww/Ww pairing antiparallel cis XX -C27-D36 : C-G Ww/Ww pairing antiparallel cis XIX -C28-D35 : U-A Ww/Ww pairing antiparallel cis XX -C29-D34 : C-G Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -A1 : ALA -A2 : VAL -A3 : PRO -A4 : GLU -A5 : THR -A6 : ARG -A7 : PRO -A8 : ASN -A9 : HIS -A10 : THR -A11 : ILE -A12 : TYR -A13 : ILE -A14 : ASN -A15 : ASN -A16 : LEU -A17 : ASN -A18 : GLU -A19 : LYS -A20 : ILE -A21 : LYS -A22 : LYS -A23 : ASP -A24 : GLU -A25 : LEU -A26 : LYS -A27 : LYS -A28 : SER -A29 : LEU -A30 : HIS -A31 : ALA -A32 : ILE -A33 : PHE -A34 : SER -A35 : ARG -A36 : PHE -A37 : GLY -A38 : GLN -A39 : ILE -A40 : LEU -A41 : ASP -A42 : ILE -A43 : LEU -A44 : VAL -A45 : SER -A46 : ARG -A47 : SER -A48 : LEU -A49 : LYS -A50 : MET -A51 : ARG -A52 : GLY -A53 : GLN -A54 : ALA -A55 : PHE -A56 : VAL -A57 : ILE -A58 : PHE -A59 : LYS -A60 : GLU -A61 : VAL -A62 : SER -A63 : SER -A64 : ALA -A65 : THR -A66 : ASN -A67 : ALA -A68 : LEU -A69 : ARG -A70 : SER -A71 : MET -A72 : GLN -A73 : GLY -A74 : PHE -A75 : PRO -A76 : PHE -A77 : TYR -A78 : ASP -A79 : LYS -A80 : PRO -A81 : MET -A82 : ARG -A83 : ILE -A84 : GLN -A85 : TYR -A86 : ALA -A87 : LYS -A88 : THR -A89 : ASP -A90 : SER -A91 : ASP -A92 : ILE -A93 : ILE -A94 : ALA -A95 : LYS -A96 : MET -A97 : LYS -A98 : GLY -A99 : THR -A100 : PHE -A101 : VAL -B1 : ALA -B2 : VAL -B3 : PRO -B4 : GLU -B5 : THR -B6 : ARG -B7 : PRO -B8 : ASN -B9 : HIS -B10 : THR -B11 : ILE -B12 : TYR -B13 : ILE -B14 : ASN -B15 : ASN -B16 : LEU -B17 : ASN -B18 : GLU -B19 : LYS -B20 : ILE -B21 : LYS -B22 : LYS -B23 : ASP -B24 : GLU -B25 : LEU -B26 : LYS -B27 : LYS -B28 : SER -B29 : LEU -B30 : HIS -B31 : ALA -B32 : ILE -B33 : PHE -B34 : SER -B35 : ARG -B36 : PHE -B37 : GLY -B38 : GLN -B39 : ILE -B40 : LEU -B41 : ASP -B42 : ILE -B43 : LEU -B44 : VAL -B45 : SER -B46 : ARG -B47 : SER -B48 : LEU -B49 : LYS -B50 : MET -B51 : ARG -B52 : GLY -B53 : GLN -B54 : ALA -B55 : PHE -B56 : VAL -B57 : ILE -B58 : PHE -B59 : LYS -B60 : GLU -B61 : VAL -B62 : SER -B63 : SER -B64 : ALA -B65 : THR -B66 : ASN -B67 : ALA -B68 : LEU -B69 : ARG -B70 : SER -B71 : MET -B72 : GLN -B73 : GLY -B74 : PHE -B75 : PRO -B76 : PHE -B77 : TYR -B78 : ASP -B79 : LYS -B80 : PRO -B81 : MET -B82 : ARG -B83 : ILE -B84 : GLN -B85 : TYR -B86 : ALA -B87 : LYS -B88 : THR -B89 : ASP -B90 : SER -B91 : ASP -B92 : ILE -B93 : ILE -B94 : ALA -B95 : LYS -B96 : MET -B97 : LYS -B98 : GLY -B99 : THR -B100 : PHE -B101 : VAL -C8 : G C2p_exo anti -C9 : A C2p_exo anti -C10 : G C2p_exo anti -C11 : A C2p_exo anti -C12 : C C3p_endo anti -C13 : A C2p_exo anti -C14 : U C2p_exo anti -C15 : U C3p_exo anti -C16 : G C1p_endo anti -C17 : C C1p_exo syn -C18 : A C2p_exo anti -C19 : C C2p_exo anti -C20 : C C2p_exo anti -C21 : C C2p_exo anti -C22 : G C2p_exo anti -C23 : G C2p_exo anti -C24 : A C3p_endo anti -C25 : G C4p_exo anti -C26 : U C3p_endo anti -C27 : C C3p_endo anti -C28 : U C3p_endo anti -C29 : C C2p_exo anti -D34 : G C2p_exo anti -D35 : A C2p_exo anti -D36 : G C2p_exo anti -D37 : A C2p_exo anti -D38 : C C3p_endo anti -D39 : A C2p_exo anti -D40 : U C2p_exo anti -D41 : U C3p_exo anti -D42 : G C1p_endo anti -D43 : C C1p_exo syn -D44 : A C2p_exo anti -D45 : C C2p_exo anti -D46 : C C2p_exo anti -D47 : C C2p_exo anti -D48 : G C2p_exo anti -D49 : G C2p_exo anti -D50 : A C3p_endo anti -D51 : G C4p_exo anti -D52 : U C3p_endo anti -D53 : C C3p_endo anti -D54 : U C3p_endo anti -D55 : C C2p_exo anti -Adjacent stackings ---------------------------------------------- -C8-C9 : adjacent_5p upward -C9-C10 : adjacent_5p upward -C10-C11 : adjacent_5p upward -C11-C12 : adjacent_5p upward -C13-C14 : adjacent_5p upward -C18-C19 : adjacent_5p upward -C20-C21 : adjacent_5p upward -C21-C22 : adjacent_5p upward -C22-C23 : adjacent_5p upward -C23-C24 : adjacent_5p upward -C26-C27 : adjacent_5p upward -C27-C28 : adjacent_5p upward -D34-D35 : adjacent_5p upward -D35-D36 : adjacent_5p upward -D36-D37 : adjacent_5p upward -D37-D38 : adjacent_5p upward -D39-D40 : adjacent_5p upward -D44-D45 : adjacent_5p upward -D46-D47 : adjacent_5p upward -D47-D48 : adjacent_5p upward -D48-D49 : adjacent_5p upward -D49-D50 : adjacent_5p upward -D52-D53 : adjacent_5p upward -D53-D54 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -C13-D51 : outward -C22-D48 : outward -C25-D39 : outward -Number of stackings = 27 -Number of adjacent stackings = 24 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -A91-D45 : ASP-C pairing one_hbond -B91-C19 : ASP-C pairing one_hbond -C8-D55 : G-C Ww/Ww pairing antiparallel cis XIX -C9-D54 : A-U Ww/Ww pairing antiparallel cis XX -C10-D53 : G-C Ww/Ww pairing antiparallel cis XIX -C11-D52 : A-U Ww/Ww pairing antiparallel cis XX -C12-D51 : C-G Ww/Ww pairing antiparallel cis XIX -C19-C20 : C-C O2P/Ww O2P/Bh O2P/Hh adjacent_5p pairing -C19-D50 : C-A O2P/Ww pairing -C20-D49 : C-G Ww/Ww pairing antiparallel cis XIX -C20-D50 : C-A Ws/Bs pairing antiparallel cis one_hbond -C21-D48 : C-G Ww/Ww pairing antiparallel cis XIX -C22-D47 : G-C Ww/Ww pairing antiparallel cis XIX -C23-D46 : G-C Ww/Ww pairing antiparallel cis XIX -C24-D45 : A-C Ww/O2P pairing -C24-D46 : A-C Bs/Ws pairing antiparallel cis one_hbond -C25-D38 : G-C Ww/Ww pairing antiparallel cis XIX -C26-D37 : U-A Ww/Ww pairing antiparallel cis XX -C27-D36 : C-G Ww/Ww pairing antiparallel cis XIX -C28-D35 : U-A Ww/Ww pairing antiparallel cis XX -C29-D34 : C-G Ww/Ww pairing antiparallel cis XIX -D45-D46 : C-C O2P/Ww O2P/Bh O2P/Hh adjacent_5p pairing -Residue conformations ------------------------------------------- -A1 : ALA -A2 : VAL -A3 : PRO -A4 : GLU -A5 : THR -A6 : ARG -A7 : PRO -A8 : ASN -A9 : HIS -A10 : THR -A11 : ILE -A12 : TYR -A13 : ILE -A14 : ASN -A15 : ASN -A16 : LEU -A17 : ASN -A18 : GLU -A19 : LYS -A20 : ILE -A21 : LYS -A22 : LYS -A23 : ASP -A24 : GLU -A25 : LEU -A26 : LYS -A27 : LYS -A28 : SER -A29 : LEU -A30 : HIS -A31 : ALA -A32 : ILE -A33 : PHE -A34 : SER -A35 : ARG -A36 : PHE -A37 : GLY -A38 : GLN -A39 : ILE -A40 : LEU -A41 : ASP -A42 : ILE -A43 : LEU -A44 : VAL -A45 : SER -A46 : ARG -A47 : SER -A48 : LEU -A49 : LYS -A50 : MET -A51 : ARG -A52 : GLY -A53 : GLN -A54 : ALA -A55 : PHE -A56 : VAL -A57 : ILE -A58 : PHE -A59 : LYS -A60 : GLU -A61 : VAL -A62 : SER -A63 : SER -A64 : ALA -A65 : THR -A66 : ASN -A67 : ALA -A68 : LEU -A69 : ARG -A70 : SER -A71 : MET -A72 : GLN -A73 : GLY -A74 : PHE -A75 : PRO -A76 : PHE -A77 : TYR -A78 : ASP -A79 : LYS -A80 : PRO -A81 : MET -A82 : ARG -A83 : ILE -A84 : GLN -A85 : TYR -A86 : ALA -A87 : LYS -A88 : THR -A89 : ASP -A90 : SER -A91 : ASP -A92 : ILE -A93 : ILE -A94 : ALA -A95 : LYS -A96 : MET -A97 : LYS -A98 : GLY -A99 : THR -A100 : PHE -A101 : VAL -B1 : ALA -B2 : VAL -B3 : PRO -B4 : GLU -B5 : THR -B6 : ARG -B7 : PRO -B8 : ASN -B9 : HIS -B10 : THR -B11 : ILE -B12 : TYR -B13 : ILE -B14 : ASN -B15 : ASN -B16 : LEU -B17 : ASN -B18 : GLU -B19 : LYS -B20 : ILE -B21 : LYS -B22 : LYS -B23 : ASP -B24 : GLU -B25 : LEU -B26 : LYS -B27 : LYS -B28 : SER -B29 : LEU -B30 : HIS -B31 : ALA -B32 : ILE -B33 : PHE -B34 : SER -B35 : ARG -B36 : PHE -B37 : GLY -B38 : GLN -B39 : ILE -B40 : LEU -B41 : ASP -B42 : ILE -B43 : LEU -B44 : VAL -B45 : SER -B46 : ARG -B47 : SER -B48 : LEU -B49 : LYS -B50 : MET -B51 : ARG -B52 : GLY -B53 : GLN -B54 : ALA -B55 : PHE -B56 : VAL -B57 : ILE -B58 : PHE -B59 : LYS -B60 : GLU -B61 : VAL -B62 : SER -B63 : SER -B64 : ALA -B65 : THR -B66 : ASN -B67 : ALA -B68 : LEU -B69 : ARG -B70 : SER -B71 : MET -B72 : GLN -B73 : GLY -B74 : PHE -B75 : PRO -B76 : PHE -B77 : TYR -B78 : ASP -B79 : LYS -B80 : PRO -B81 : MET -B82 : ARG -B83 : ILE -B84 : GLN -B85 : TYR -B86 : ALA -B87 : LYS -B88 : THR -B89 : ASP -B90 : SER -B91 : ASP -B92 : ILE -B93 : ILE -B94 : ALA -B95 : LYS -B96 : MET -B97 : LYS -B98 : GLY -B99 : THR -B100 : PHE -B101 : VAL -C8 : G C2p_exo anti -C9 : A C2p_exo anti -C10 : G C2p_exo anti -C11 : A C2p_exo anti -C12 : C C3p_endo anti -C13 : A C2p_exo anti -C14 : U C3p_endo anti -C15 : U C3p_exo anti -C16 : G C1p_endo anti -C17 : C C1p_exo anti -C18 : A C1p_endo anti -C19 : C C2p_exo anti -C20 : C C2p_exo anti -C21 : C C2p_exo anti -C22 : G C2p_exo anti -C23 : G C2p_exo anti -C24 : A C2p_exo anti -C25 : G C4p_exo anti -C26 : U C2p_exo anti -C27 : C C3p_endo anti -C28 : U C3p_endo anti -C29 : C C2p_exo anti -D34 : G C2p_exo anti -D35 : A C2p_exo anti -D36 : G C2p_exo anti -D37 : A C2p_exo anti -D38 : C C3p_endo anti -D39 : A C2p_exo anti -D40 : U C3p_endo anti -D41 : U C3p_exo anti -D42 : G C1p_endo anti -D43 : C C1p_exo anti -D44 : A C1p_endo anti -D45 : C C2p_exo anti -D46 : C C2p_exo anti -D47 : C C2p_exo anti -D48 : G C2p_exo anti -D49 : G C2p_exo anti -D50 : A C2p_exo anti -D51 : G C4p_exo anti -D52 : U C2p_exo anti -D53 : C C3p_endo anti -D54 : U C3p_endo anti -D55 : C C2p_exo anti -Adjacent stackings ---------------------------------------------- -C8-C9 : adjacent_5p upward -C9-C10 : adjacent_5p upward -C10-C11 : adjacent_5p upward -C11-C12 : adjacent_5p upward -C12-C13 : adjacent_5p upward -C13-C14 : adjacent_5p upward -C18-C19 : adjacent_5p upward -C20-C21 : adjacent_5p upward -C21-C22 : adjacent_5p upward -C22-C23 : adjacent_5p upward -C23-C24 : adjacent_5p upward -C26-C27 : adjacent_5p upward -C27-C28 : adjacent_5p upward -D34-D35 : adjacent_5p upward -D35-D36 : adjacent_5p upward -D36-D37 : adjacent_5p upward -D37-D38 : adjacent_5p upward -D38-D39 : adjacent_5p upward -D39-D40 : adjacent_5p upward -D44-D45 : adjacent_5p upward -D46-D47 : adjacent_5p upward -D47-D48 : adjacent_5p upward -D48-D49 : adjacent_5p upward -D49-D50 : adjacent_5p upward -D52-D53 : adjacent_5p upward -D53-D54 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -C13-D51 : outward -C25-D39 : outward -Number of stackings = 28 -Number of adjacent stackings = 26 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -C8-D55 : G-C Ww/Ww pairing antiparallel cis XIX -C9-D54 : A-U Ww/Ww pairing antiparallel cis XX -C10-D53 : G-C Ww/Ww pairing antiparallel cis XIX -C11-D52 : A-U Ww/Ww pairing antiparallel cis XX -C12-D51 : C-G Ww/Ww pairing antiparallel cis XIX -C14-C16 : U-G O2'/Bs pairing -C17-C18 : C-A O2'/Hh adjacent_5p pairing -C19-C20 : C-C O2P/Ww adjacent_5p pairing -C19-D50 : C-A O2P/Ww O2P/Bh pairing -C20-D49 : C-G Ww/Ww pairing antiparallel cis XIX -C20-D50 : C-A Ws/Bs pairing antiparallel cis one_hbond -C21-D48 : C-G Ww/Ww pairing antiparallel cis XIX -C22-D47 : G-C Ww/Ww pairing antiparallel cis XIX -C23-D46 : G-C Ww/Ww pairing antiparallel cis XIX -C24-D45 : A-C Ww/O2P Bh/O2P pairing -C24-D46 : A-C Bs/Ws pairing antiparallel cis one_hbond -C25-D38 : G-C Ww/Ww pairing antiparallel cis XIX -C26-D37 : U-A Ww/Ww pairing antiparallel cis XX -C27-D36 : C-G Ww/Ww pairing antiparallel cis XIX -C28-D35 : U-A Ww/Ww pairing antiparallel cis XX -C29-D34 : C-G Ww/Ww pairing antiparallel cis XIX -D40-D42 : U-G O2'/Bs pairing -D43-D44 : C-A O2'/Hh adjacent_5p pairing -D45-D46 : C-C O2P/Ww adjacent_5p pairing -Residue conformations ------------------------------------------- -A1 : ALA -A2 : VAL -A3 : PRO -A4 : GLU -A5 : THR -A6 : ARG -A7 : PRO -A8 : ASN -A9 : HIS -A10 : THR -A11 : ILE -A12 : TYR -A13 : ILE -A14 : ASN -A15 : ASN -A16 : LEU -A17 : ASN -A18 : GLU -A19 : LYS -A20 : ILE -A21 : LYS -A22 : LYS -A23 : ASP -A24 : GLU -A25 : LEU -A26 : LYS -A27 : LYS -A28 : SER -A29 : LEU -A30 : HIS -A31 : ALA -A32 : ILE -A33 : PHE -A34 : SER -A35 : ARG -A36 : PHE -A37 : GLY -A38 : GLN -A39 : ILE -A40 : LEU -A41 : ASP -A42 : ILE -A43 : LEU -A44 : VAL -A45 : SER -A46 : ARG -A47 : SER -A48 : LEU -A49 : LYS -A50 : MET -A51 : ARG -A52 : GLY -A53 : GLN -A54 : ALA -A55 : PHE -A56 : VAL -A57 : ILE -A58 : PHE -A59 : LYS -A60 : GLU -A61 : VAL -A62 : SER -A63 : SER -A64 : ALA -A65 : THR -A66 : ASN -A67 : ALA -A68 : LEU -A69 : ARG -A70 : SER -A71 : MET -A72 : GLN -A73 : GLY -A74 : PHE -A75 : PRO -A76 : PHE -A77 : TYR -A78 : ASP -A79 : LYS -A80 : PRO -A81 : MET -A82 : ARG -A83 : ILE -A84 : GLN -A85 : TYR -A86 : ALA -A87 : LYS -A88 : THR -A89 : ASP -A90 : SER -A91 : ASP -A92 : ILE -A93 : ILE -A94 : ALA -A95 : LYS -A96 : MET -A97 : LYS -A98 : GLY -A99 : THR -A100 : PHE -A101 : VAL -B1 : ALA -B2 : VAL -B3 : PRO -B4 : GLU -B5 : THR -B6 : ARG -B7 : PRO -B8 : ASN -B9 : HIS -B10 : THR -B11 : ILE -B12 : TYR -B13 : ILE -B14 : ASN -B15 : ASN -B16 : LEU -B17 : ASN -B18 : GLU -B19 : LYS -B20 : ILE -B21 : LYS -B22 : LYS -B23 : ASP -B24 : GLU -B25 : LEU -B26 : LYS -B27 : LYS -B28 : SER -B29 : LEU -B30 : HIS -B31 : ALA -B32 : ILE -B33 : PHE -B34 : SER -B35 : ARG -B36 : PHE -B37 : GLY -B38 : GLN -B39 : ILE -B40 : LEU -B41 : ASP -B42 : ILE -B43 : LEU -B44 : VAL -B45 : SER -B46 : ARG -B47 : SER -B48 : LEU -B49 : LYS -B50 : MET -B51 : ARG -B52 : GLY -B53 : GLN -B54 : ALA -B55 : PHE -B56 : VAL -B57 : ILE -B58 : PHE -B59 : LYS -B60 : GLU -B61 : VAL -B62 : SER -B63 : SER -B64 : ALA -B65 : THR -B66 : ASN -B67 : ALA -B68 : LEU -B69 : ARG -B70 : SER -B71 : MET -B72 : GLN -B73 : GLY -B74 : PHE -B75 : PRO -B76 : PHE -B77 : TYR -B78 : ASP -B79 : LYS -B80 : PRO -B81 : MET -B82 : ARG -B83 : ILE -B84 : GLN -B85 : TYR -B86 : ALA -B87 : LYS -B88 : THR -B89 : ASP -B90 : SER -B91 : ASP -B92 : ILE -B93 : ILE -B94 : ALA -B95 : LYS -B96 : MET -B97 : LYS -B98 : GLY -B99 : THR -B100 : PHE -B101 : VAL -C8 : G C2p_exo anti -C9 : A C2p_exo anti -C10 : G C3p_endo anti -C11 : A C3p_endo anti -C12 : C C3p_endo anti -C13 : A C3p_endo anti -C14 : U C2p_exo anti -C15 : U C3p_exo anti -C16 : G C1p_endo syn -C17 : C C1p_exo anti -C18 : A C2p_exo anti -C19 : C C2p_exo anti -C20 : C C2p_exo anti -C21 : C C2p_exo anti -C22 : G C3p_endo anti -C23 : G C3p_endo anti -C24 : A C3p_endo anti -C25 : G C4p_exo anti -C26 : U C3p_endo anti -C27 : C C3p_endo anti -C28 : U C3p_endo anti -C29 : C C2p_exo anti -D34 : G C2p_exo anti -D35 : A C2p_exo anti -D36 : G C3p_endo anti -D37 : A C3p_endo anti -D38 : C C3p_endo anti -D39 : A C3p_endo anti -D40 : U C2p_exo anti -D41 : U C3p_exo anti -D42 : G C1p_endo syn -D43 : C C1p_exo anti -D44 : A C2p_exo anti -D45 : C C2p_exo anti -D46 : C C2p_exo anti -D47 : C C2p_exo anti -D48 : G C3p_endo anti -D49 : G C3p_endo anti -D50 : A C3p_endo anti -D51 : G C4p_exo anti -D52 : U C3p_endo anti -D53 : C C3p_endo anti -D54 : U C3p_endo anti -D55 : C C2p_exo anti -Adjacent stackings ---------------------------------------------- -C8-C9 : adjacent_5p upward -C9-C10 : adjacent_5p upward -C10-C11 : adjacent_5p upward -C11-C12 : adjacent_5p upward -C12-C13 : adjacent_5p upward -C18-C19 : adjacent_5p upward -C20-C21 : adjacent_5p upward -C21-C22 : adjacent_5p upward -C22-C23 : adjacent_5p upward -C23-C24 : adjacent_5p upward -C25-C26 : adjacent_5p upward -C26-C27 : adjacent_5p upward -C27-C28 : adjacent_5p upward -D34-D35 : adjacent_5p upward -D35-D36 : adjacent_5p upward -D36-D37 : adjacent_5p upward -D37-D38 : adjacent_5p upward -D38-D39 : adjacent_5p upward -D44-D45 : adjacent_5p upward -D46-D47 : adjacent_5p upward -D47-D48 : adjacent_5p upward -D48-D49 : adjacent_5p upward -D49-D50 : adjacent_5p upward -D51-D52 : adjacent_5p upward -D52-D53 : adjacent_5p upward -D53-D54 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -C13-D51 : outward -C22-D48 : outward -C25-D39 : outward -Number of stackings = 29 -Number of adjacent stackings = 26 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -A12-D43 : TYR-C pairing one_hbond -A14-D42 : ASN-G pairing one_hbond -A55-D43 : PHE-C pairing one_hbond -A79-D41 : LYS-U pairing one_hbond -B12-C17 : TYR-C pairing one_hbond -B14-C16 : ASN-G pairing one_hbond -B55-C17 : PHE-C pairing one_hbond -B79-C15 : LYS-U pairing one_hbond -C8-D55 : G-C Ww/Ww pairing antiparallel cis XIX -C9-D54 : A-U Ww/Ww pairing antiparallel cis XX -C10-D53 : G-C Ww/Ww pairing antiparallel cis XIX -C11-D52 : A-U Ww/Ww pairing antiparallel cis XX -C12-D51 : C-G Ww/Ww pairing antiparallel cis XIX -C17-C18 : C-A O2'/Hh adjacent_5p pairing -C19-C20 : C-C O2P/Hh adjacent_5p pairing -C20-D49 : C-G Ww/Ww pairing antiparallel cis XIX -C21-D48 : C-G Ww/Ww pairing antiparallel cis XIX -C22-D47 : G-C Ww/Ww pairing antiparallel cis XIX -C23-D46 : G-C Ww/Ww pairing antiparallel cis XIX -C25-D38 : G-C Ww/Ww pairing antiparallel cis XIX -C26-D37 : U-A Ww/Ww pairing antiparallel cis XX -C27-D36 : C-G Ww/Ww pairing antiparallel cis XIX -C28-D35 : U-A Ww/Ww pairing antiparallel cis XX -C29-D34 : C-G Ww/Ww pairing antiparallel cis XIX -D43-D44 : C-A O2'/Hh adjacent_5p pairing -D45-D46 : C-C O2P/Hh adjacent_5p pairing -Residue conformations ------------------------------------------- -A1 : ALA -A2 : VAL -A3 : PRO -A4 : GLU -A5 : THR -A6 : ARG -A7 : PRO -A8 : ASN -A9 : HIS -A10 : THR -A11 : ILE -A12 : TYR -A13 : ILE -A14 : ASN -A15 : ASN -A16 : LEU -A17 : ASN -A18 : GLU -A19 : LYS -A20 : ILE -A21 : LYS -A22 : LYS -A23 : ASP -A24 : GLU -A25 : LEU -A26 : LYS -A27 : LYS -A28 : SER -A29 : LEU -A30 : HIS -A31 : ALA -A32 : ILE -A33 : PHE -A34 : SER -A35 : ARG -A36 : PHE -A37 : GLY -A38 : GLN -A39 : ILE -A40 : LEU -A41 : ASP -A42 : ILE -A43 : LEU -A44 : VAL -A45 : SER -A46 : ARG -A47 : SER -A48 : LEU -A49 : LYS -A50 : MET -A51 : ARG -A52 : GLY -A53 : GLN -A54 : ALA -A55 : PHE -A56 : VAL -A57 : ILE -A58 : PHE -A59 : LYS -A60 : GLU -A61 : VAL -A62 : SER -A63 : SER -A64 : ALA -A65 : THR -A66 : ASN -A67 : ALA -A68 : LEU -A69 : ARG -A70 : SER -A71 : MET -A72 : GLN -A73 : GLY -A74 : PHE -A75 : PRO -A76 : PHE -A77 : TYR -A78 : ASP -A79 : LYS -A80 : PRO -A81 : MET -A82 : ARG -A83 : ILE -A84 : GLN -A85 : TYR -A86 : ALA -A87 : LYS -A88 : THR -A89 : ASP -A90 : SER -A91 : ASP -A92 : ILE -A93 : ILE -A94 : ALA -A95 : LYS -A96 : MET -A97 : LYS -A98 : GLY -A99 : THR -A100 : PHE -A101 : VAL -B1 : ALA -B2 : VAL -B3 : PRO -B4 : GLU -B5 : THR -B6 : ARG -B7 : PRO -B8 : ASN -B9 : HIS -B10 : THR -B11 : ILE -B12 : TYR -B13 : ILE -B14 : ASN -B15 : ASN -B16 : LEU -B17 : ASN -B18 : GLU -B19 : LYS -B20 : ILE -B21 : LYS -B22 : LYS -B23 : ASP -B24 : GLU -B25 : LEU -B26 : LYS -B27 : LYS -B28 : SER -B29 : LEU -B30 : HIS -B31 : ALA -B32 : ILE -B33 : PHE -B34 : SER -B35 : ARG -B36 : PHE -B37 : GLY -B38 : GLN -B39 : ILE -B40 : LEU -B41 : ASP -B42 : ILE -B43 : LEU -B44 : VAL -B45 : SER -B46 : ARG -B47 : SER -B48 : LEU -B49 : LYS -B50 : MET -B51 : ARG -B52 : GLY -B53 : GLN -B54 : ALA -B55 : PHE -B56 : VAL -B57 : ILE -B58 : PHE -B59 : LYS -B60 : GLU -B61 : VAL -B62 : SER -B63 : SER -B64 : ALA -B65 : THR -B66 : ASN -B67 : ALA -B68 : LEU -B69 : ARG -B70 : SER -B71 : MET -B72 : GLN -B73 : GLY -B74 : PHE -B75 : PRO -B76 : PHE -B77 : TYR -B78 : ASP -B79 : LYS -B80 : PRO -B81 : MET -B82 : ARG -B83 : ILE -B84 : GLN -B85 : TYR -B86 : ALA -B87 : LYS -B88 : THR -B89 : ASP -B90 : SER -B91 : ASP -B92 : ILE -B93 : ILE -B94 : ALA -B95 : LYS -B96 : MET -B97 : LYS -B98 : GLY -B99 : THR -B100 : PHE -B101 : VAL -C8 : G C2p_exo anti -C9 : A C2p_exo anti -C10 : G C3p_endo anti -C11 : A C3p_endo anti -C12 : C C3p_endo anti -C13 : A C3p_endo anti -C14 : U C2p_exo anti -C15 : U C3p_exo anti -C16 : G C2p_exo syn -C17 : C C1p_exo anti -C18 : A C2p_exo anti -C19 : C C2p_exo anti -C20 : C C2p_exo anti -C21 : C C2p_exo anti -C22 : G C2p_exo anti -C23 : G C2p_exo anti -C24 : A C3p_endo anti -C25 : G C4p_exo anti -C26 : U C3p_endo anti -C27 : C C3p_endo anti -C28 : U C3p_endo anti -C29 : C C2p_exo anti -D34 : G C2p_exo anti -D35 : A C2p_exo anti -D36 : G C3p_endo anti -D37 : A C3p_endo anti -D38 : C C3p_endo anti -D39 : A C3p_endo anti -D40 : U C2p_exo anti -D41 : U C3p_exo anti -D42 : G C2p_exo syn -D43 : C C1p_exo anti -D44 : A C2p_exo anti -D45 : C C2p_exo anti -D46 : C C2p_exo anti -D47 : C C2p_exo anti -D48 : G C2p_exo anti -D49 : G C2p_exo anti -D50 : A C3p_endo anti -D51 : G C4p_exo anti -D52 : U C3p_endo anti -D53 : C C3p_endo anti -D54 : U C3p_endo anti -D55 : C C2p_exo anti -Adjacent stackings ---------------------------------------------- -C8-C9 : adjacent_5p upward -C9-C10 : adjacent_5p upward -C10-C11 : adjacent_5p upward -C11-C12 : adjacent_5p upward -C13-C14 : adjacent_5p upward -C18-C19 : adjacent_5p upward -C20-C21 : adjacent_5p upward -C21-C22 : adjacent_5p upward -C22-C23 : adjacent_5p upward -C23-C24 : adjacent_5p upward -C25-C26 : adjacent_5p upward -C26-C27 : adjacent_5p upward -C27-C28 : adjacent_5p upward -D34-D35 : adjacent_5p upward -D35-D36 : adjacent_5p upward -D36-D37 : adjacent_5p upward -D37-D38 : adjacent_5p upward -D39-D40 : adjacent_5p upward -D44-D45 : adjacent_5p upward -D46-D47 : adjacent_5p upward -D47-D48 : adjacent_5p upward -D48-D49 : adjacent_5p upward -D49-D50 : adjacent_5p upward -D51-D52 : adjacent_5p upward -D52-D53 : adjacent_5p upward -D53-D54 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -C13-D51 : outward -C25-D39 : outward -Number of stackings = 28 -Number of adjacent stackings = 26 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -C8-D55 : G-C Ww/Ww pairing antiparallel cis XIX -C9-D54 : A-U Ww/Ww pairing antiparallel cis XX -C10-D53 : G-C Ww/Ww pairing antiparallel cis XIX -C11-D52 : A-U Ww/Ww pairing antiparallel cis XX -C12-D51 : C-G Ww/Ww pairing antiparallel cis XIX -C19-C20 : C-C O2P/Hh adjacent_5p pairing -C20-D49 : C-G Ww/Ww pairing antiparallel cis XIX -C21-D48 : C-G Ww/Ww pairing antiparallel cis XIX -C22-D47 : G-C Ww/Ww pairing antiparallel cis XIX -C23-D46 : G-C Ww/Ww pairing antiparallel cis XIX -C25-D38 : G-C Ww/Ww pairing antiparallel cis XIX -C26-D37 : U-A Ww/Ww pairing antiparallel cis XX -C27-D36 : C-G Ww/Ww pairing antiparallel cis XIX -C28-D35 : U-A Ww/Ww pairing antiparallel cis XX -C29-D34 : C-G Ww/Ww pairing antiparallel cis XIX -D45-D46 : C-C O2P/Hh adjacent_5p pairing diff --git a/MCdata/1e4p_MC b/MCdata/1e4p_MC deleted file mode 100644 index 6e2ab604bf6e174a01de31a9ca7be2d88f25c3f6..0000000000000000000000000000000000000000 --- a/MCdata/1e4p_MC +++ /dev/null @@ -1,1153 +0,0 @@ -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : U C3p_endo anti -A3 : G C2p_exo anti -A4 : C C3p_endo anti -A5 : G C3p_endo anti -A6 : A C3p_endo anti -A7 : A C3p_endo anti -A8 : G C3p_endo anti -A9 : A C3p_endo anti -A10 : C C3p_endo anti -A11 : G C3p_endo anti -A12 : A C2p_exo anti -A13 : A C3p_endo anti -A14 : A C3p_endo anti -A15 : G C3p_endo anti -A16 : U C3p_endo anti -A17 : C C3p_endo anti -A18 : C C3p_endo anti -A19 : G C2p_endo anti -A20 : A C3p_endo anti -A21 : G C2p_exo anti -A22 : C C3p_endo anti -A23 : G C2p_exo anti -A24 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A23-A24 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A6-A20 : outward -Number of stackings = 17 -Number of adjacent stackings = 16 -Number of non adjacent stackings = 1 -Base-pairs ------------------------------------------------------ -A1-A24 : G-C Ww/Ww pairing antiparallel cis -A2-A23 : U-G Ws/Ww pairing antiparallel cis XXVIII -A3-A22 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A21 : C-G Ww/Ww pairing antiparallel cis XIX -A5-A20 : G-A Ss/Hh pairing antiparallel trans XI -A6-A19 : A-G Hh/Sw pairing antiparallel trans one_hbond -A7-A18 : A-C Wh/Ww pairing antiparallel cis one_hbond 75 -A8-A17 : G-C Ww/Ww pairing antiparallel cis XIX -A9-A16 : A-U Ww/Ww pairing antiparallel cis XX -A10-A15 : C-G Ww/Ww pairing antiparallel cis XIX -A11-A13 : G-A Ss/O2P pairing -A11-A14 : G-A O2'/Bh Bs/O2P pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : U C3p_endo anti -A3 : G C2p_exo anti -A4 : C C3p_endo anti -A5 : G C3p_endo anti -A6 : A C3p_endo anti -A7 : A C3p_endo anti -A8 : G C3p_endo anti -A9 : A C3p_endo anti -A10 : C C3p_endo anti -A11 : G C3p_endo anti -A12 : A C2p_exo anti -A13 : A C3p_endo anti -A14 : A C3p_endo anti -A15 : G C3p_endo anti -A16 : U C3p_endo anti -A17 : C C3p_endo anti -A18 : C C3p_endo anti -A19 : G C2p_endo anti -A20 : A C3p_endo anti -A21 : G C2p_exo anti -A22 : C C3p_endo anti -A23 : G C2p_exo anti -A24 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A23-A24 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A5-A19 : inward pairing -A6-A20 : outward -Number of stackings = 16 -Number of adjacent stackings = 14 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A1-A24 : G-C Ww/Ww pairing antiparallel cis -A2-A3 : U-G O2'/Hh adjacent_5p pairing -A2-A23 : U-G Ws/Ww pairing antiparallel cis XXVIII -A3-A22 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A21 : C-G Ww/Ww pairing antiparallel cis XIX -A5-A19 : G-G Bs/O2' inward pairing -A5-A20 : G-A O2'/Bh pairing -A8-A17 : G-C Ww/Ww pairing antiparallel cis XIX -A9-A16 : A-U Ww/Ww pairing antiparallel cis XX -A10-A15 : C-G Ww/Ww pairing antiparallel cis XIX -A11-A13 : G-A O2'/Hh pairing -Residue conformations ------------------------------------------- -A1 : G O4p_endo anti -A2 : U C3p_endo anti -A3 : G C3p_endo anti -A4 : C C3p_endo anti -A5 : G C3p_endo anti -A6 : A C3p_endo anti -A7 : A C3p_endo anti -A8 : G C3p_endo anti -A9 : A C3p_endo anti -A10 : C C3p_endo anti -A11 : G C3p_endo anti -A12 : A C3p_endo anti -A13 : A C3p_endo anti -A14 : A C3p_endo anti -A15 : G C3p_endo anti -A16 : U C3p_endo anti -A17 : C C3p_endo anti -A18 : C C3p_endo anti -A19 : G C2p_endo anti -A20 : A C3p_endo anti -A21 : G C2p_exo anti -A22 : C C3p_endo anti -A23 : G C2p_exo anti -A24 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A23-A24 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A5-A19 : inward -A6-A20 : outward -Number of stackings = 17 -Number of adjacent stackings = 15 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A1-A24 : G-C Ww/Ww pairing antiparallel cis one_hbond -A2-A23 : U-G Ws/Ww pairing antiparallel cis XXVIII -A3-A22 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A21 : C-G Ww/Ww pairing antiparallel cis XIX -A5-A20 : G-A Ss/Hh pairing antiparallel trans one_hbond -A7-A18 : A-C Wh/Ww pairing antiparallel cis one_hbond 78 -A8-A17 : G-C Ww/Ww pairing antiparallel cis XIX -A9-A16 : A-U Ww/Ww pairing antiparallel cis XX -A10-A15 : C-G Ww/Ww pairing antiparallel cis XIX -A11-A14 : G-A Sw/Hh Ww/O2P Bs/O2P pairing antiparallel trans one_hbond -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : U C3p_endo anti -A3 : G C2p_exo anti -A4 : C C3p_endo anti -A5 : G C3p_endo anti -A6 : A C3p_endo anti -A7 : A C3p_endo anti -A8 : G C3p_endo anti -A9 : A C3p_endo anti -A10 : C C3p_endo anti -A11 : G C3p_endo anti -A12 : A C2p_exo anti -A13 : A C3p_endo anti -A14 : A C3p_endo anti -A15 : G C3p_endo anti -A16 : U C3p_endo anti -A17 : C C3p_endo anti -A18 : C C3p_endo anti -A19 : G C2p_endo anti -A20 : A C3p_endo anti -A21 : G C3p_endo anti -A22 : C C3p_endo anti -A23 : G C2p_exo anti -A24 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A23-A24 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A5-A19 : inward pairing -A6-A20 : outward -Number of stackings = 15 -Number of adjacent stackings = 13 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A2-A23 : U-G Ws/Ww pairing antiparallel cis XXVIII -A3-A22 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A21 : C-G Ww/Ww pairing antiparallel cis XIX -A5-A19 : G-G Bs/O2' inward pairing -A5-A20 : G-A Ss/Hh pairing antiparallel trans one_hbond -A8-A17 : G-C Ww/Ww pairing antiparallel cis XIX -A9-A16 : A-U Ww/Ww pairing antiparallel cis XX -A10-A15 : C-G Ww/Ww pairing antiparallel cis XIX -A11-A13 : G-A Hh/O2P pairing -A11-A14 : G-A Sw/Hh Ww/O2P Bs/O2P pairing antiparallel trans one_hbond -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : U C3p_endo anti -A3 : G C2p_exo anti -A4 : C C3p_endo anti -A5 : G C3p_endo anti -A6 : A C3p_endo anti -A7 : A C3p_endo anti -A8 : G C3p_endo anti -A9 : A C3p_endo anti -A10 : C C3p_endo anti -A11 : G C3p_endo anti -A12 : A C3p_endo anti -A13 : A C3p_endo anti -A14 : A C3p_endo anti -A15 : G C3p_endo anti -A16 : U C3p_endo anti -A17 : C C3p_endo anti -A18 : C C3p_endo anti -A19 : G C2p_endo anti -A20 : A C3p_endo anti -A21 : G C3p_endo anti -A22 : C C3p_endo anti -A23 : G C2p_exo anti -A24 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A23-A24 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A5-A19 : inward -A6-A20 : outward -Number of stackings = 18 -Number of adjacent stackings = 16 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A1-A24 : G-C Ww/Ww pairing antiparallel cis one_hbond -A2-A23 : U-G Ws/Ww pairing antiparallel cis XXVIII -A3-A22 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A21 : C-G Ww/Ww pairing antiparallel cis XIX -A5-A20 : G-A Ss/Hh pairing antiparallel trans XI -A8-A17 : G-C Ww/Ww pairing antiparallel cis XIX -A9-A16 : A-U Ww/Ww pairing antiparallel cis XX -A10-A15 : C-G Ww/Ww pairing antiparallel cis XIX -A11-A13 : G-A Hh/O2P pairing -A11-A14 : G-A Sw/Hh Ww/O2P Bs/O2P pairing antiparallel trans one_hbond -Residue conformations ------------------------------------------- -A1 : G C4p_exo anti -A2 : U C3p_endo anti -A3 : G C3p_endo anti -A4 : C C3p_endo anti -A5 : G C3p_endo anti -A6 : A C3p_endo anti -A7 : A C3p_endo anti -A8 : G C3p_endo anti -A9 : A C3p_endo anti -A10 : C C3p_endo anti -A11 : G C3p_endo anti -A12 : A C2p_exo anti -A13 : A C3p_endo anti -A14 : A C3p_endo anti -A15 : G C3p_endo anti -A16 : U C3p_endo anti -A17 : C C3p_endo anti -A18 : C C3p_endo anti -A19 : G C2p_endo anti -A20 : A C3p_endo anti -A21 : G C3p_endo anti -A22 : C C3p_endo anti -A23 : G C2p_exo anti -A24 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A23-A24 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A6-A20 : outward -Number of stackings = 17 -Number of adjacent stackings = 16 -Number of non adjacent stackings = 1 -Base-pairs ------------------------------------------------------ -A1-A24 : G-C Ww/Ww pairing antiparallel cis -A2-A23 : U-G Ws/Ww pairing antiparallel cis XXVIII -A3-A22 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A21 : C-G Ww/Ww pairing antiparallel cis XIX -A5-A20 : G-A Ss/Hh pairing antiparallel trans XI -A8-A17 : G-C Ww/Ww pairing antiparallel cis XIX -A9-A16 : A-U Ww/Ww pairing antiparallel cis XX -A10-A15 : C-G Ww/Ww pairing antiparallel cis XIX -A11-A13 : G-A Ss/O2P pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : U C3p_endo anti -A3 : G C3p_endo anti -A4 : C C3p_endo anti -A5 : G C3p_endo anti -A6 : A C3p_endo anti -A7 : A C3p_endo anti -A8 : G C2p_exo anti -A9 : A C3p_endo anti -A10 : C C3p_endo anti -A11 : G C3p_endo anti -A12 : A C2p_exo anti -A13 : A C3p_endo anti -A14 : A C3p_endo anti -A15 : G C3p_endo anti -A16 : U C3p_endo anti -A17 : C C3p_endo anti -A18 : C C3p_endo anti -A19 : G C2p_endo anti -A20 : A C3p_endo anti -A21 : G C3p_endo anti -A22 : C C3p_endo anti -A23 : G C2p_exo anti -A24 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A4-A5 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A23-A24 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A5-A19 : inward -A6-A20 : outward -Number of stackings = 14 -Number of adjacent stackings = 12 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A1-A24 : G-C Ww/Ww pairing antiparallel cis -A2-A23 : U-G Ws/Ww pairing antiparallel cis XXVIII -A3-A22 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A21 : C-G Ww/Ww pairing antiparallel cis XIX -A6-A19 : A-G Hh/Sw pairing antiparallel trans one_hbond -A8-A17 : G-C Ww/Ww pairing antiparallel cis XIX -A9-A16 : A-U Ww/Ww pairing antiparallel cis XX -A10-A15 : C-G Ww/Ww pairing antiparallel cis XIX -A11-A13 : G-A Ss/O2P pairing -A11-A14 : G-A Bs/O2P pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : U C3p_endo anti -A3 : G C2p_exo anti -A4 : C C3p_endo anti -A5 : G C4p_exo anti -A6 : A C3p_endo anti -A7 : A C3p_endo anti -A8 : G C3p_endo anti -A9 : A C3p_endo anti -A10 : C C3p_endo anti -A11 : G C3p_endo anti -A12 : A C2p_exo anti -A13 : A C3p_endo anti -A14 : A C3p_endo anti -A15 : G C3p_endo anti -A16 : U C3p_endo anti -A17 : C C3p_endo anti -A18 : C C3p_endo anti -A19 : G C2p_endo anti -A20 : A C3p_endo anti -A21 : G C3p_endo anti -A22 : C C3p_endo anti -A23 : G C2p_exo anti -A24 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A23-A24 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A6-A20 : outward -Number of stackings = 17 -Number of adjacent stackings = 16 -Number of non adjacent stackings = 1 -Base-pairs ------------------------------------------------------ -A2-A3 : U-G O2'/Hh adjacent_5p pairing -A2-A23 : U-G Ws/Ww pairing antiparallel cis XXVIII -A3-A22 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A21 : C-G Ww/Ww pairing antiparallel cis XIX -A5-A20 : G-A Ss/Hh O2'/Bh pairing antiparallel trans XI -A7-A18 : A-C Wh/Ww pairing antiparallel cis one_hbond 75 -A8-A17 : G-C Ww/Ww pairing antiparallel cis XIX -A9-A16 : A-U Ww/Ww pairing antiparallel cis XX -A10-A15 : C-G Ww/Ww pairing antiparallel cis XIX -A11-A13 : G-A Ss/O2P pairing -A14-A15 : A-G O2P/Hh adjacent_5p pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : U C3p_endo anti -A3 : G C3p_endo anti -A4 : C C3p_endo anti -A5 : G C3p_endo anti -A6 : A C3p_endo anti -A7 : A C3p_endo anti -A8 : G C3p_endo anti -A9 : A C3p_endo anti -A10 : C C3p_endo anti -A11 : G C3p_endo anti -A12 : A C2p_exo anti -A13 : A C3p_endo anti -A14 : A C3p_endo anti -A15 : G C3p_endo anti -A16 : U C3p_endo anti -A17 : C C3p_endo anti -A18 : C C3p_endo anti -A19 : G C2p_endo anti -A20 : A C3p_endo anti -A21 : G C3p_endo anti -A22 : C C3p_endo anti -A23 : G C2p_exo anti -A24 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A4-A5 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A23-A24 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A5-A19 : inward pairing -A6-A20 : outward -Number of stackings = 14 -Number of adjacent stackings = 12 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A1-A24 : G-C Ww/Ww pairing antiparallel cis one_hbond -A2-A23 : U-G Ws/Ww pairing antiparallel cis XXVIII -A3-A22 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A21 : C-G Ww/Ww pairing antiparallel cis XIX -A5-A19 : G-G Bs/O2' inward pairing -A5-A20 : G-A Ss/Hh pairing antiparallel trans one_hbond -A6-A19 : A-G Hh/Sw pairing antiparallel trans one_hbond -A8-A17 : G-C Ww/Ww pairing antiparallel cis XIX -A9-A16 : A-U Ww/Ww pairing antiparallel cis XX -A10-A15 : C-G Ww/Ww pairing antiparallel cis XIX -A11-A13 : G-A Ss/O2P pairing -A11-A14 : G-A Bs/O2P pairing -A19-A20 : G-A O2'/Hh adjacent_5p pairing -Residue conformations ------------------------------------------- -A1 : G C2p_exo anti -A2 : U C3p_endo anti -A3 : G C2p_exo anti -A4 : C C3p_endo anti -A5 : G C4p_exo anti -A6 : A C3p_endo anti -A7 : A C3p_endo anti -A8 : G C3p_endo anti -A9 : A C3p_endo anti -A10 : C C3p_endo anti -A11 : G C3p_endo anti -A12 : A C3p_endo anti -A13 : A C3p_endo anti -A14 : A C3p_endo anti -A15 : G C3p_endo anti -A16 : U C3p_endo anti -A17 : C C3p_endo anti -A18 : C C3p_endo anti -A19 : G C2p_endo anti -A20 : A C3p_endo anti -A21 : G C3p_endo anti -A22 : C C3p_endo anti -A23 : G C2p_exo anti -A24 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A23-A24 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A5-A19 : inward -A6-A20 : outward -Number of stackings = 17 -Number of adjacent stackings = 15 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A1-A24 : G-C Ww/Ww pairing antiparallel cis -A2-A3 : U-G O2'/Hh adjacent_5p pairing -A2-A23 : U-G Ws/Ww pairing antiparallel cis XXVIII -A3-A22 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A21 : C-G Ww/Ww pairing antiparallel cis XIX -A5-A20 : G-A O2'/Bh pairing -A7-A18 : A-C Wh/Ww pairing antiparallel cis one_hbond 75 -A8-A17 : G-C Ww/Ww pairing antiparallel cis XIX -A9-A16 : A-U Ww/Ww pairing antiparallel cis XX -A10-A15 : C-G Ww/Ww pairing antiparallel cis XIX -A11-A13 : G-A O2'/Hh pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : U C3p_endo anti -A3 : G C3p_endo anti -A4 : C C3p_endo anti -A5 : G C3p_endo anti -A6 : A C3p_endo anti -A7 : A C3p_endo anti -A8 : G C3p_endo anti -A9 : A C3p_endo anti -A10 : C C3p_endo anti -A11 : G C3p_endo anti -A12 : A C3p_endo anti -A13 : A C3p_endo anti -A14 : A C3p_endo anti -A15 : G C3p_endo anti -A16 : U C3p_endo anti -A17 : C C3p_endo anti -A18 : C C3p_endo anti -A19 : G C2p_endo anti -A20 : A C3p_endo anti -A21 : G C3p_endo anti -A22 : C C3p_endo anti -A23 : G C2p_exo anti -A24 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A23-A24 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A6-A20 : outward -A11-A15 : outward -Number of stackings = 15 -Number of adjacent stackings = 13 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A1-A24 : G-C Ww/Ww pairing antiparallel cis one_hbond -A2-A23 : U-G Ws/Ww pairing antiparallel cis XXVIII -A3-A22 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A21 : C-G Ww/Ww pairing antiparallel cis XIX -A5-A20 : G-A Ss/Hh pairing antiparallel trans one_hbond -A6-A19 : A-G Hh/Sw pairing antiparallel trans one_hbond -A8-A17 : G-C Ww/Ww pairing antiparallel cis XIX -A9-A16 : A-U Ww/Ww pairing antiparallel cis XX -A10-A15 : C-G Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -A1 : G C2p_exo anti -A2 : U C3p_endo anti -A3 : G C2p_exo anti -A4 : C C3p_endo anti -A5 : G C3p_endo anti -A6 : A C3p_endo anti -A7 : A C3p_endo anti -A8 : G C2p_exo anti -A9 : A C3p_endo anti -A10 : C C3p_endo anti -A11 : G C3p_endo anti -A12 : A C2p_exo anti -A13 : A C3p_endo anti -A14 : A C3p_endo anti -A15 : G C3p_endo anti -A16 : U C3p_endo anti -A17 : C C3p_endo anti -A18 : C C3p_endo anti -A19 : G C1p_exo anti -A20 : A C3p_endo anti -A21 : G C3p_endo anti -A22 : C C3p_endo anti -A23 : G C2p_exo anti -A24 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A23-A24 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A5-A19 : inward pairing -A6-A20 : outward -Number of stackings = 15 -Number of adjacent stackings = 13 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A1-A24 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A23 : U-G Ws/Ww pairing antiparallel cis XXVIII -A3-A22 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A21 : C-G Ww/Ww pairing antiparallel cis XIX -A5-A19 : G-G Bs/O2' inward pairing -A5-A20 : G-A Ss/Hh pairing antiparallel trans XI -A6-A19 : A-G Hh/Sw pairing antiparallel trans one_hbond -A7-A18 : A-C Bs/Ws pairing antiparallel cis one_hbond -A8-A17 : G-C Ww/Ww pairing antiparallel cis XIX -A9-A16 : A-U Ww/Ww pairing antiparallel cis XX -A10-A15 : C-G Ww/Ww pairing antiparallel cis XIX -A11-A13 : G-A O2'/Hh pairing -Residue conformations ------------------------------------------- -A1 : G C2p_exo anti -A2 : U C3p_endo anti -A3 : G C3p_endo anti -A4 : C C3p_endo anti -A5 : G C3p_endo anti -A6 : A C3p_endo anti -A7 : A C3p_endo anti -A8 : G C3p_endo anti -A9 : A C3p_endo anti -A10 : C C3p_endo anti -A11 : G C3p_endo anti -A12 : A C3p_endo anti -A13 : A C3p_endo anti -A14 : A C3p_endo anti -A15 : G C3p_endo anti -A16 : U C3p_endo anti -A17 : C C3p_endo anti -A18 : C C3p_endo anti -A19 : G C2p_endo anti -A20 : A C3p_endo anti -A21 : G C3p_endo anti -A22 : C C3p_endo anti -A23 : G C2p_exo anti -A24 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A4-A5 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A23-A24 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A5-A19 : inward pairing -A6-A20 : outward -Number of stackings = 16 -Number of adjacent stackings = 14 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A2-A23 : U-G Ws/Ww pairing antiparallel cis XXVIII -A3-A22 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A21 : C-G Ww/Ww pairing antiparallel cis XIX -A5-A19 : G-G Bs/O2' inward pairing -A5-A20 : G-A Sw/Hh pairing antiparallel trans one_hbond -A7-A18 : A-C Wh/Ww pairing antiparallel cis one_hbond 75 -A8-A17 : G-C Ww/Ww pairing antiparallel cis XIX -A9-A16 : A-U Ww/Ww pairing antiparallel cis XX -A10-A15 : C-G Ww/Ww pairing antiparallel cis XIX -A11-A13 : G-A Ss/O2P pairing -A11-A14 : G-A Bs/O2P pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : U C3p_endo anti -A3 : G C3p_endo anti -A4 : C C3p_endo anti -A5 : G C3p_endo anti -A6 : A C3p_endo anti -A7 : A C3p_endo anti -A8 : G C3p_endo anti -A9 : A C3p_endo anti -A10 : C C3p_endo anti -A11 : G C3p_endo anti -A12 : A C2p_exo anti -A13 : A C3p_endo anti -A14 : A C3p_endo anti -A15 : G C3p_endo anti -A16 : U C3p_endo anti -A17 : C C3p_endo anti -A18 : C C3p_endo anti -A19 : G C2p_endo anti -A20 : A C3p_endo anti -A21 : G C3p_endo anti -A22 : C C3p_endo anti -A23 : G C2p_exo anti -A24 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A4-A5 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A23-A24 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A5-A19 : inward -A6-A20 : outward -Number of stackings = 18 -Number of adjacent stackings = 16 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A1-A24 : G-C Ww/Ww pairing antiparallel cis -A2-A23 : U-G Ws/Ww pairing antiparallel cis XXVIII -A3-A22 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A21 : C-G Ww/Ww pairing antiparallel cis XIX -A5-A20 : G-A Sw/Hh pairing antiparallel trans one_hbond -A7-A18 : A-C Wh/Ww pairing antiparallel cis one_hbond 75 -A8-A17 : G-C Ww/Ww pairing antiparallel cis XIX -A9-A16 : A-U Ww/Ww pairing antiparallel cis XX -A10-A15 : C-G Ww/Ww pairing antiparallel cis XIX -A11-A13 : G-A Ss/O2P pairing -A11-A14 : G-A Bs/O2P pairing -Residue conformations ------------------------------------------- -A1 : G C4p_exo anti -A2 : U C3p_endo anti -A3 : G C3p_endo anti -A4 : C C3p_endo anti -A5 : G C3p_endo anti -A6 : A C3p_endo anti -A7 : A C3p_endo anti -A8 : G C3p_endo anti -A9 : A C3p_endo anti -A10 : C C3p_endo anti -A11 : G C3p_endo anti -A12 : A C2p_exo anti -A13 : A C3p_endo anti -A14 : A C3p_endo anti -A15 : G C3p_endo anti -A16 : U C3p_endo anti -A17 : C C3p_endo anti -A18 : C C3p_endo anti -A19 : G C2p_endo anti -A20 : A C3p_endo anti -A21 : G C3p_endo anti -A22 : C C3p_endo anti -A23 : G C2p_exo anti -A24 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A4-A5 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A23-A24 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A5-A19 : inward pairing -A6-A20 : outward -Number of stackings = 15 -Number of adjacent stackings = 13 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A1-A24 : G-C Ww/Ww pairing antiparallel cis -A2-A23 : U-G Ws/Ww pairing antiparallel cis XXVIII -A3-A22 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A21 : C-G Ww/Ww pairing antiparallel cis XIX -A5-A19 : G-G Bs/O2' inward pairing -A5-A20 : G-A Ss/Hh pairing antiparallel trans one_hbond -A7-A18 : A-C Wh/Ww pairing antiparallel cis one_hbond 75 -A8-A17 : G-C Ww/Ww pairing antiparallel cis XIX -A9-A16 : A-U Ww/Ww pairing antiparallel cis XX -A10-A15 : C-G Ww/Ww pairing antiparallel cis XIX -Residue conformations ------------------------------------------- -A1 : G O4p_endo anti -A2 : U C3p_endo anti -A3 : G C2p_exo anti -A4 : C C3p_endo anti -A5 : G C3p_endo anti -A6 : A C3p_endo anti -A7 : A C3p_endo anti -A8 : G C3p_endo anti -A9 : A C3p_endo anti -A10 : C C3p_endo anti -A11 : G C3p_endo anti -A12 : A C3p_endo anti -A13 : A C3p_endo anti -A14 : A C3p_endo anti -A15 : G C3p_endo anti -A16 : U C3p_endo anti -A17 : C C3p_endo anti -A18 : C C3p_endo anti -A19 : G C2p_endo anti -A20 : A C3p_endo anti -A21 : G C3p_endo anti -A22 : C C3p_endo anti -A23 : G C2p_exo anti -A24 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A23-A24 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A5-A19 : inward pairing -A6-A20 : outward -Number of stackings = 17 -Number of adjacent stackings = 15 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A1-A24 : G-C Ww/Ww pairing antiparallel cis -A2-A23 : U-G Ws/Ww pairing antiparallel cis XXVIII -A3-A22 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A21 : C-G Ww/Ww pairing antiparallel cis XIX -A5-A19 : G-G Bs/O2' inward pairing -A5-A20 : G-A Sw/Hh pairing antiparallel trans one_hbond -A6-A19 : A-G Hh/Sw pairing antiparallel trans one_hbond -A7-A18 : A-C Wh/Ww pairing antiparallel cis one_hbond 75 -A8-A17 : G-C Ww/Ww pairing antiparallel cis XIX -A9-A16 : A-U Ww/Ww pairing antiparallel cis XX -A10-A15 : C-G Ww/Ww pairing antiparallel cis XIX -A11-A14 : G-A Sw/Hh pairing antiparallel trans one_hbond -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : U C3p_endo anti -A3 : G C3p_endo anti -A4 : C C3p_endo anti -A5 : G C3p_endo anti -A6 : A C3p_endo anti -A7 : A C3p_endo anti -A8 : G C3p_endo anti -A9 : A C3p_endo anti -A10 : C C3p_endo anti -A11 : G C3p_endo anti -A12 : A C2p_exo anti -A13 : A C3p_endo anti -A14 : A C3p_endo anti -A15 : G C3p_endo anti -A16 : U C3p_endo anti -A17 : C C3p_endo anti -A18 : C C3p_endo anti -A19 : G C2p_endo anti -A20 : A C3p_endo anti -A21 : G C3p_endo anti -A22 : C C3p_endo anti -A23 : G C2p_exo anti -A24 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A23-A24 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A5-A19 : inward -A6-A20 : outward -Number of stackings = 18 -Number of adjacent stackings = 16 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A1-A24 : G-C Ww/Ww pairing antiparallel cis one_hbond -A2-A23 : U-G Ws/Ww pairing antiparallel cis XXVIII -A3-A22 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A21 : C-G Ww/Ww pairing antiparallel cis XIX -A5-A20 : G-A Sw/Hh pairing antiparallel trans one_hbond -A6-A19 : A-G Hh/Sw pairing antiparallel trans one_hbond -A8-A17 : G-C Ww/Ww pairing antiparallel cis XIX -A9-A16 : A-U Ww/Ww pairing antiparallel cis XX -A10-A15 : C-G Ww/Ww pairing antiparallel cis XIX -A11-A14 : G-A Bs/O2P pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : U C3p_endo anti -A3 : G C2p_exo anti -A4 : C C3p_endo anti -A5 : G C3p_endo anti -A6 : A C3p_endo anti -A7 : A C3p_endo anti -A8 : G C3p_endo anti -A9 : A C3p_endo anti -A10 : C C3p_endo anti -A11 : G C3p_endo anti -A12 : A C2p_exo anti -A13 : A C3p_endo anti -A14 : A C3p_endo anti -A15 : G C3p_endo anti -A16 : U C3p_endo anti -A17 : C C3p_endo anti -A18 : C C3p_endo anti -A19 : G C2p_endo anti -A20 : A C3p_endo anti -A21 : G C3p_endo anti -A22 : C C3p_endo anti -A23 : G C2p_exo anti -A24 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A23-A24 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A5-A19 : inward -A6-A20 : outward -Number of stackings = 17 -Number of adjacent stackings = 15 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A1-A24 : G-C Ww/Ww pairing antiparallel cis -A2-A23 : U-G Ws/Ww pairing antiparallel cis XXVIII -A3-A22 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A21 : C-G Ww/Ww pairing antiparallel cis XIX -A5-A20 : G-A Ss/Hh pairing antiparallel trans XI -A7-A18 : A-C Wh/Ws pairing antiparallel cis one_hbond 78 -A8-A17 : G-C Ww/Ww pairing antiparallel cis XIX -A9-A16 : A-U Ww/Ww pairing antiparallel cis XX -A10-A15 : C-G Ww/Ww pairing antiparallel cis XIX -A11-A14 : G-A Bs/O2P pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : U C3p_endo anti -A3 : G C3p_endo anti -A4 : C C3p_endo anti -A5 : G C3p_endo anti -A6 : A C3p_endo anti -A7 : A C3p_endo anti -A8 : G C3p_endo anti -A9 : A C3p_endo anti -A10 : C C3p_endo anti -A11 : G C3p_endo anti -A12 : A C2p_exo anti -A13 : A C3p_endo anti -A14 : A C3p_endo anti -A15 : G C3p_endo anti -A16 : U C3p_endo anti -A17 : C C3p_endo anti -A18 : C C3p_endo anti -A19 : G C2p_endo anti -A20 : A C3p_endo anti -A21 : G C3p_endo anti -A22 : C C3p_endo anti -A23 : G C2p_exo anti -A24 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A4-A5 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A23-A24 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 13 -Number of adjacent stackings = 13 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-A24 : G-C Ww/Ww pairing antiparallel cis -A2-A23 : U-G Ws/Ww pairing antiparallel cis XXVIII -A3-A22 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A21 : C-G Ww/Ww pairing antiparallel cis XIX -A5-A6 : G-A O2'/C8 adjacent_5p pairing -A5-A20 : G-A Ss/Hh pairing antiparallel trans XI -A8-A17 : G-C Ww/Ww pairing antiparallel cis XIX -A9-A16 : A-U Ww/Ww pairing antiparallel cis XX -A10-A15 : C-G Ww/Ww pairing antiparallel cis XIX -A11-A13 : G-A Ss/O2P pairing -A11-A14 : G-A Bs/O2P pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : U C3p_endo anti -A3 : G C3p_endo anti -A4 : C C3p_endo anti -A5 : G C3p_endo anti -A6 : A C3p_endo anti -A7 : A C3p_endo anti -A8 : G C3p_endo anti -A9 : A C2p_exo anti -A10 : C C3p_endo anti -A11 : G C3p_endo anti -A12 : A C3p_endo anti -A13 : A C3p_endo anti -A14 : A C3p_endo anti -A15 : G C3p_endo anti -A16 : U C3p_endo anti -A17 : C C3p_endo anti -A18 : C C3p_endo anti -A19 : G C2p_endo anti -A20 : A C3p_endo anti -A21 : G C3p_endo anti -A22 : C C3p_endo anti -A23 : G C2p_exo anti -A24 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A23-A24 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A5-A19 : inward -A6-A20 : outward -Number of stackings = 15 -Number of adjacent stackings = 13 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A1-A24 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A23 : U-G Ws/Ww pairing antiparallel cis XXVIII -A3-A22 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A21 : C-G Ww/Ww pairing antiparallel cis XIX -A7-A18 : A-C Wh/Ws pairing antiparallel cis one_hbond 78 -A8-A17 : G-C Ww/Ww pairing antiparallel cis XIX -A9-A16 : A-U Ww/Ww pairing antiparallel cis XX -A10-A15 : C-G Ww/Ww pairing antiparallel cis XIX -A11-A13 : G-A Ss/O2P pairing diff --git a/MCdata/1e7k_MC b/MCdata/1e7k_MC deleted file mode 100644 index 67fc7bbfc34214bb31f703277f58a357d6cbe883..0000000000000000000000000000000000000000 --- a/MCdata/1e7k_MC +++ /dev/null @@ -1,332 +0,0 @@ -Residue conformations ------------------------------------------- -A4 : ALA -A5 : ASP -A6 : VAL -A7 : ASN -A8 : PRO -A9 : LYS -A10 : ALA -A11 : TYR -A12 : PRO -A13 : LEU -A14 : ALA -A15 : ASP -A16 : ALA -A17 : HIS -A18 : LEU -A19 : THR -A20 : LYS -A21 : LYS -A22 : LEU -A23 : LEU -A24 : ASP -A25 : LEU -A26 : VAL -A27 : GLN -A28 : GLN -A29 : SER -A30 : CYS -A31 : ASN -A32 : TYR -A33 : LYS -A34 : GLN -A35 : LEU -A36 : ARG -A37 : LYS -A38 : GLY -A39 : ALA -A40 : ASN -A41 : GLU -A42 : ALA -A43 : THR -A44 : LYS -A45 : THR -A46 : LEU -A47 : ASN -A48 : ARG -A49 : GLY -A50 : ILE -A51 : SER -A52 : GLU -A53 : PHE -A54 : ILE -A55 : VAL -A56 : MET -A57 : ALA -A58 : ALA -A59 : ASP -A60 : ALA -A61 : GLU -A62 : PRO -A63 : LEU -A64 : GLU -A65 : ILE -A66 : ILE -A67 : LEU -A68 : HIS -A69 : LEU -A70 : PRO -A71 : LEU -A72 : LEU -A73 : CYS -A74 : GLU -A75 : ASP -A76 : LYS -A77 : ASN -A78 : VAL -A79 : PRO -A80 : TYR -A81 : VAL -A82 : PHE -A83 : VAL -A84 : ARG -A85 : SER -A86 : LYS -A87 : GLN -A88 : ALA -A89 : LEU -A90 : GLY -A91 : ARG -A92 : ALA -A93 : CYS -A94 : GLY -A95 : VAL -A96 : SER -A97 : ARG -A98 : PRO -A99 : VAL -A100 : ILE -A101 : ALA -A102 : CYS -A103 : SER -A104 : VAL -A105 : THR -A106 : ILE -A107 : LYS -A108 : GLU -A109 : GLY -A110 : SER -A111 : GLN -A112 : LEU -A113 : LYS -A114 : GLN -A115 : GLN -A116 : ILE -A117 : GLN -A118 : SER -A119 : ILE -A120 : GLN -A121 : GLN -A122 : SER -A123 : ILE -A124 : GLU -A125 : ARG -A126 : LEU -A127 : LEU -A128 : VAL -B6 : VAL -B7 : ASN -B8 : PRO -B9 : LYS -B10 : ALA -B11 : TYR -B12 : PRO -B13 : LEU -B14 : ALA -B15 : ASP -B16 : ALA -B17 : HIS -B18 : LEU -B19 : THR -B20 : LYS -B21 : LYS -B22 : LEU -B23 : LEU -B24 : ASP -B25 : LEU -B26 : VAL -B27 : GLN -B28 : GLN -B29 : SER -B30 : CYS -B31 : ASN -B32 : TYR -B33 : LYS -B34 : GLN -B35 : LEU -B36 : ARG -B37 : LYS -B38 : GLY -B39 : ALA -B40 : ASN -B41 : GLU -B42 : ALA -B43 : THR -B44 : LYS -B45 : THR -B46 : LEU -B47 : ASN -B48 : ARG -B49 : GLY -B50 : ILE -B51 : SER -B52 : GLU -B53 : PHE -B54 : ILE -B55 : VAL -B56 : MET -B57 : ALA -B58 : ALA -B59 : ASP -B60 : ALA -B61 : GLU -B62 : PRO -B63 : LEU -B64 : GLU -B65 : ILE -B66 : ILE -B67 : LEU -B68 : HIS -B69 : LEU -B70 : PRO -B71 : LEU -B72 : LEU -B73 : CYS -B74 : GLU -B75 : ASP -B76 : LYS -B77 : ASN -B78 : VAL -B79 : PRO -B80 : TYR -B81 : VAL -B82 : PHE -B83 : VAL -B84 : ARG -B85 : SER -B86 : LYS -B87 : GLN -B88 : ALA -B89 : LEU -B90 : GLY -B91 : ARG -B92 : ALA -B93 : CYS -B94 : GLY -B95 : VAL -B96 : SER -B97 : ARG -B98 : PRO -B99 : VAL -B100 : ILE -B101 : ALA -B102 : CYS -B103 : SER -B104 : VAL -B105 : THR -B106 : ILE -B107 : LYS -B108 : GLU -B109 : GLY -B110 : SER -B111 : GLN -B112 : LEU -B113 : LYS -B114 : GLN -B115 : GLN -B116 : ILE -B117 : GLN -B118 : SER -B119 : ILE -B120 : GLN -B121 : GLN -B122 : SER -B123 : ILE -B124 : GLU -B125 : ARG -B126 : LEU -B127 : LEU -B128 : VAL -C26 : G C2p_exo anti -C27 : C C3p_endo anti -C28 : C C3p_endo anti -C29 : A C3p_endo anti -C30 : A C2p_endo syn -C31 : U C2p_endo anti -C32 : G C2p_endo anti -C33 : A C4p_exo anti -C34 : G C2p_endo anti -C35 : G C2p_exo anti -C41 : C C3p_endo anti -C42 : C C3p_endo anti -C43 : G C2p_endo anti -C44 : A C2p_endo anti -C45 : G C3p_endo anti -C46 : G C3p_endo anti -C47 : C C3p_endo anti -D26 : G C3p_endo anti -D27 : C C3p_endo anti -D28 : C C3p_endo anti -D29 : A C3p_endo anti -D30 : A C2p_endo syn -D31 : U C2p_endo anti -D32 : G C2p_endo anti -D33 : A C4p_exo anti -D34 : G C2p_endo anti -D35 : G C3p_endo anti -D41 : C C3p_endo anti -D42 : C C3p_endo anti -D43 : G O4p_endo anti -D44 : A C2p_endo anti -D45 : G C3p_endo anti -D46 : G C3p_endo anti -D47 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -C26-C27 : adjacent_5p upward -C27-C28 : adjacent_5p upward -C28-C29 : adjacent_5p upward -C33-C34 : adjacent_5p upward -C34-C35 : adjacent_5p upward -C41-C42 : adjacent_5p upward -C42-C43 : adjacent_5p upward -C45-C46 : adjacent_5p upward -C46-C47 : adjacent_5p upward -D26-D27 : adjacent_5p upward -D28-D29 : adjacent_5p upward -D33-D34 : adjacent_5p upward -D34-D35 : adjacent_5p upward -D41-D42 : adjacent_5p upward -D42-D43 : adjacent_5p upward -D45-D46 : adjacent_5p upward -D46-D47 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -C30-C44 : inward pairing -C33-C44 : outward -D30-D44 : inward pairing -D32-D43 : inward pairing -D33-D44 : outward -Number of stackings = 22 -Number of adjacent stackings = 17 -Number of non adjacent stackings = 5 -Base-pairs ------------------------------------------------------ -C26-C47 : G-C Ww/Ww pairing antiparallel cis XIX -C27-C46 : C-G Ww/Ww pairing antiparallel cis XIX -C28-C45 : C-G Ww/Ww pairing antiparallel cis XIX -C29-C44 : A-A O2'/Ww pairing -C30-C44 : A-A Bh/O2' inward pairing -C32-C44 : G-A Ss/Hh pairing antiparallel trans XI -C33-C43 : A-G Hh/Ss pairing antiparallel trans XI -C33-C45 : A-G O2'/Bs O2'/Ss Ss/O2' pairing -C34-C42 : G-C Ww/Ww pairing antiparallel cis XIX -C35-C41 : G-C Ww/Ww pairing antiparallel cis XIX -D26-D47 : G-C Ww/Ww pairing antiparallel cis XIX -D27-D46 : C-G Ww/Ww pairing antiparallel cis XIX -D28-D45 : C-G Ww/Ww pairing antiparallel cis XIX -D29-D44 : A-A O2'/Ww pairing -D30-D44 : A-A Bh/O2' inward pairing -D32-D43 : G-G Bs/O2' inward pairing -D32-D44 : G-A Ss/Hh pairing antiparallel trans XI -D33-D43 : A-G Hh/Ss pairing antiparallel trans XI -D33-D45 : A-G O2'/Ss pairing -D34-D42 : G-C Ww/Ww pairing antiparallel cis XIX -D35-D41 : G-C Ww/Ww pairing antiparallel cis XIX diff --git a/MCdata/1e8o_MC b/MCdata/1e8o_MC deleted file mode 100644 index d1e940ffcc4fc814d0cc8a508ecb4116a3bc7206..0000000000000000000000000000000000000000 --- a/MCdata/1e8o_MC +++ /dev/null @@ -1,434 +0,0 @@ -Residue conformations ------------------------------------------- -A2 : PRO -A3 : GLN -A4 : TYR -A5 : GLN -A6 : THR -A7 : TRP -A8 : GLU -A9 : GLU -A10 : PHE -A11 : SER -A12 : ARG -A13 : ALA -A14 : ALA -A15 : GLU -A16 : LYS -A17 : LEU -A18 : TYR -A19 : LEU -A20 : ALA -A21 : ASP -A22 : PRO -A23 : MET -A24 : LYS -A25 : ALA -A26 : ARG -A27 : VAL -A28 : VAL -A29 : LEU -A30 : LYS -A31 : TYR -A32 : ARG -A33 : HIS -A34 : SER -A35 : ASP -A36 : GLY -A37 : ASN -A38 : LEU -A39 : CYS -A40 : VAL -A41 : LYS -A42 : VAL -A43 : THR -A44 : ASP -A45 : ASP -A46 : LEU -A47 : VAL -A48 : CYS -A49 : LEU -A50 : VAL -A51 : TYR -A52 : LYS -A53 : THR -A54 : ASP -A55 : GLN -A56 : ALA -A57 : GLN -A58 : ASP -A59 : VAL -A60 : LYS -A61 : LYS -A62 : ILE -A63 : GLU -A64 : LYS -A65 : PHE -A66 : HIS -A67 : SER -A68 : GLN -A69 : LEU -A70 : MET -A71 : ARG -A72 : LEU -A73 : MET -A74 : VAL -A75 : ALA -B2 : VAL -B3 : LEU -B4 : LEU -B5 : GLU -B6 : SER -B7 : GLU -B8 : GLN -B9 : PHE -B10 : LEU -B11 : THR -B12 : GLU -B13 : LEU -B14 : THR -B15 : ARG -B16 : LEU -B17 : PHE -B18 : GLN -B19 : LYS -B20 : CYS -B21 : ARG -B22 : THR -B23 : SER -B24 : GLY -B25 : SER -B26 : VAL -B27 : TYR -B28 : ILE -B29 : THR -B30 : LEU -B31 : LYS -B32 : LYS -B33 : TYR -B34 : ASP -B54 : ASN -B55 : LYS -B56 : CYS -B57 : LEU -B58 : LEU -B59 : ARG -B60 : ALA -B61 : THR -B62 : ASP -B63 : GLY -B64 : LYS -B65 : LYS -B66 : LYS -B67 : ILE -B68 : SER -B69 : THR -B70 : VAL -B71 : VAL -B72 : SER -B73 : SER -B74 : LYS -B75 : GLU -B76 : VAL -B77 : ASN -B78 : LYS -B79 : PHE -B80 : GLN -B81 : MET -B82 : ALA -B83 : TYR -B84 : SER -B85 : ASN -B86 : LEU -B87 : LEU -B88 : ARG -B89 : ALA -B90 : ASN -B91 : MET -B92 : ASP -B93 : GLY -B94 : LEU -B95 : LYS -C5 : GLN -C6 : THR -C7 : TRP -C8 : GLU -C9 : GLU -C10 : PHE -C11 : SER -C12 : ARG -C13 : ALA -C14 : ALA -C15 : GLU -C16 : LYS -C17 : LEU -C18 : TYR -C19 : LEU -C20 : ALA -C21 : ASP -C22 : PRO -C23 : MET -C24 : LYS -C25 : ALA -C26 : ARG -C27 : VAL -C28 : VAL -C29 : LEU -C30 : LYS -C31 : TYR -C32 : ARG -C33 : HIS -C34 : SER -C35 : ASP -C36 : GLY -C37 : ASN -C38 : LEU -C39 : CYS -C40 : VAL -C41 : LYS -C42 : VAL -C43 : THR -C44 : ASP -C45 : ASP -C46 : LEU -C47 : VAL -C48 : CYS -C49 : LEU -C50 : VAL -C51 : TYR -C52 : LYS -C53 : THR -C54 : ASP -C55 : GLN -C56 : ALA -C57 : GLN -C58 : ASP -C59 : VAL -C60 : LYS -C61 : LYS -C62 : ILE -C63 : GLU -C64 : LYS -C65 : PHE -C66 : HIS -C67 : SER -C68 : GLN -C69 : LEU -C70 : MET -C71 : ARG -C72 : LEU -C73 : MET -C74 : VAL -C75 : ALA -D2 : VAL -D3 : LEU -D4 : LEU -D5 : GLU -D6 : SER -D7 : GLU -D8 : GLN -D9 : PHE -D10 : LEU -D11 : THR -D12 : GLU -D13 : LEU -D14 : THR -D15 : ARG -D16 : LEU -D17 : PHE -D18 : GLN -D19 : LYS -D20 : CYS -D21 : ARG -D22 : THR -D23 : SER -D24 : GLY -D25 : SER -D26 : VAL -D27 : TYR -D28 : ILE -D29 : THR -D30 : LEU -D31 : LYS -D32 : LYS -D33 : TYR -D34 : ASP -D35 : GLY -D54 : ASN -D55 : LYS -D56 : CYS -D57 : LEU -D58 : LEU -D59 : ARG -D60 : ALA -D61 : THR -D62 : ASP -D63 : GLY -D64 : LYS -D65 : LYS -D66 : LYS -D67 : ILE -D68 : SER -D69 : THR -D70 : VAL -D71 : VAL -D72 : SER -D73 : SER -D74 : LYS -D75 : GLU -D76 : VAL -D77 : ASN -D78 : LYS -D79 : PHE -D80 : GLN -D81 : MET -D82 : ALA -D83 : TYR -D84 : SER -D85 : ASN -D86 : LEU -D87 : LEU -D88 : ARG -D89 : ALA -D90 : ASN -D91 : MET -D92 : ASP -D93 : GLY -D94 : LEU -D95 : LYS -E99 : GDP -E100 : G C3p_endo anti -E101 : G C3p_endo anti -E102 : C C3p_endo anti -E103 : C C3p_endo anti -E104 : G C3p_endo anti -E105 : G C3p_endo anti -E106 : G C3p_endo anti -E107 : C C3p_endo anti -E108 : G C3p_endo anti -E109 : C C3p_endo anti -E110 : G C3p_endo anti -E111 : G C3p_endo anti -E112 : U C3p_endo anti -E113 : G C3p_endo anti -E114 : G C3p_endo anti -E115 : C C3p_endo anti -E116 : G C3p_endo anti -E117 : C C3p_endo anti -E118 : G C3p_endo anti -E119 : C C3p_endo anti -E120 : G C3p_endo anti -E121 : C C3p_endo anti -E122 : C C3p_endo anti -E123 : U C3p_endo anti -E124 : G C3p_endo anti -E125 : U C3p_endo anti -E126 : A C3p_endo anti -E127 : G C3p_endo anti -E128 : U C3p_exo anti -E129 : C C3p_endo anti -E130 : C C3p_endo anti -E131 : C C3p_endo anti -E132 : A C2p_endo anti -E133 : G C3p_endo anti -E134 : C C3p_endo anti -E135 : U C2p_endo anti -E136 : A C3p_exo anti -E137 : C C3p_endo syn -E138 : U C3p_exo anti -E139 : C C3p_exo anti -E140 : G C3p_endo anti -E141 : G C3p_endo anti -E142 : G C3p_endo anti -E143 : A C3p_endo anti -E144 : G C3p_endo anti -E145 : G C3p_endo anti -E146 : C C3p_endo anti -E147 : U C3p_endo anti -E148 : C C4p_endo anti -A1076 : SO4 -B1002 : SO4 -E1149 : SO4 -A2001 : HOH -B2001 : HOH -B2002 : HOH -C2001 : HOH -D2001 : HOH -D2002 : HOH -D2003 : HOH -E2001 : HOH -E2002 : HOH -E2003 : HOH -E2004 : HOH -E2005 : HOH -E2006 : HOH -E2007 : HOH -E2008 : HOH -E2009 : HOH -E2010 : HOH -E2011 : HOH -E2012 : HOH -E2013 : HOH -E2014 : HOH -E2015 : HOH -Adjacent stackings ---------------------------------------------- -E100-E101 : adjacent_5p upward -E101-E102 : adjacent_5p upward -E104-E105 : adjacent_5p upward -E105-E106 : adjacent_5p upward -E106-E107 : adjacent_5p upward -E108-E109 : adjacent_5p upward -E110-E111 : adjacent_5p upward -E111-E112 : adjacent_5p upward -E113-E114 : adjacent_5p upward -E114-E115 : adjacent_5p upward -E115-E116 : adjacent_5p upward -E118-E119 : adjacent_5p upward -E120-E121 : adjacent_5p upward -E122-E123 : adjacent_5p upward -E124-E125 : adjacent_5p upward -E126-E127 : adjacent_5p upward -E129-E130 : adjacent_5p upward -E131-E132 : adjacent_5p upward -E133-E134 : adjacent_5p upward -E134-E135 : adjacent_5p upward -E140-E141 : adjacent_5p upward -E141-E142 : adjacent_5p upward -E142-E143 : adjacent_5p upward -E143-E144 : adjacent_5p upward -E144-E145 : adjacent_5p upward -E145-E146 : adjacent_5p upward -E146-E147 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -E104-E124 : outward -E108-E120 : outward -E110-E118 : outward -E113-E136 : outward -E132-E140 : outward -Number of stackings = 32 -Number of adjacent stackings = 27 -Number of non adjacent stackings = 5 -Base-pairs ------------------------------------------------------ -E100-E147 : G-U Ww/Ws pairing antiparallel cis XXVIII -E101-E146 : G-C Ww/Ww pairing antiparallel cis XIX -E102-E145 : C-G Ww/Ww pairing antiparallel cis XIX -E103-E144 : C-G Ww/Ww pairing antiparallel cis XIX -E104-E123 : G-U Ww/Ws pairing antiparallel cis one_hbond -E105-E122 : G-C Ww/Ww pairing antiparallel cis XIX -E106-E121 : G-C Ww/Ww pairing antiparallel cis XIX -E107-E120 : C-G Ww/Ww pairing antiparallel cis XIX -E108-E119 : G-C Ww/Ww pairing antiparallel cis XIX -E109-E118 : C-G Ww/Ww pairing antiparallel cis XIX -E110-E117 : G-C Ww/Ww pairing antiparallel cis XIX -E111-E116 : G-G Bs/Hh pairing antiparallel trans 34 -E112-E114 : U-G O2'/Hh pairing -E112-E115 : U-C Ww/O2P pairing -E113-E137 : G-C Ww/Ww pairing antiparallel cis XIX -E114-E134 : G-C Ww/Ww pairing antiparallel cis XIX -E115-E133 : C-G Ww/Ww pairing antiparallel cis XIX -E116-E132 : G-A O2'/Ww pairing -E125-E127 : U-G O2'/Hh pairing -E128-E143 : U-A Ww/Ww pairing antiparallel cis XX -E129-E142 : C-G Ww/Ww pairing antiparallel cis XIX -E130-E141 : C-G Ww/Ww pairing antiparallel cis XIX -E131-E140 : C-G Ww/Ww pairing antiparallel cis XIX -E133-E140 : G-G O2'/Ss pairing diff --git a/MCdata/1e8s_MC b/MCdata/1e8s_MC deleted file mode 100644 index 3a4fdeaeb58d41887949f309bdd4f0c0512c6fb1..0000000000000000000000000000000000000000 --- a/MCdata/1e8s_MC +++ /dev/null @@ -1,242 +0,0 @@ -Residue conformations ------------------------------------------- -A5 : GLN -A6 : THR -A7 : TRP -A8 : GLU -A9 : GLU -A10 : PHE -A11 : SER -A12 : ARG -A13 : ALA -A14 : ALA -A15 : GLU -A16 : LYS -A17 : LEU -A18 : TYR -A19 : LEU -A20 : ALA -A21 : ASP -A22 : PRO -A23 : MET -A24 : LYS -A25 : ALA -A26 : ARG -A27 : VAL -A28 : VAL -A29 : LEU -A30 : LYS -A31 : TYR -A32 : ARG -A33 : HIS -A34 : SER -A35 : ASP -A36 : GLY -A37 : ASN -A38 : LEU -A39 : CYS -A40 : VAL -A41 : LYS -A42 : VAL -A43 : THR -A44 : ASP -A45 : ASP -A46 : LEU -A47 : VAL -A48 : CYS -A49 : LEU -A50 : VAL -A51 : TYR -A52 : LYS -A53 : THR -A54 : ASP -A55 : GLN -A56 : ALA -A57 : GLN -A58 : ASP -A59 : VAL -A60 : LYS -A61 : LYS -A62 : ILE -A63 : GLU -A64 : LYS -A65 : PHE -A66 : HIS -A67 : SER -A68 : GLN -A69 : LEU -A70 : MET -A71 : ARG -A72 : LEU -A73 : MET -A74 : VAL -A75 : ALA -B2 : VAL -B3 : LEU -B4 : LEU -B5 : GLU -B6 : SER -B7 : GLU -B8 : GLN -B9 : PHE -B10 : LEU -B11 : THR -B12 : GLU -B13 : LEU -B14 : THR -B15 : ARG -B16 : LEU -B17 : PHE -B18 : GLN -B19 : LYS -B20 : CYS -B21 : ARG -B22 : THR -B23 : SER -B24 : GLY -B25 : SER -B26 : VAL -B27 : TYR -B28 : ILE -B29 : THR -B30 : LEU -B31 : LYS -B32 : LYS -B33 : TYR -B34 : ASP -B35 : GLY -B54 : ASN -B55 : LYS -B56 : CYS -B57 : LEU -B58 : LEU -B59 : ARG -B60 : ALA -B61 : THR -B62 : ASP -B63 : GLY -B64 : LYS -B65 : LYS -B66 : LYS -B67 : ILE -B68 : SER -B69 : THR -B70 : VAL -B71 : VAL -B72 : SER -B73 : SER -B74 : LYS -B75 : GLU -B76 : VAL -B77 : ASN -B78 : LYS -B79 : PHE -B80 : GLN -B81 : MET -B82 : ALA -B83 : TYR -B84 : SER -B85 : ASN -B86 : LEU -B87 : LEU -B88 : ARG -B89 : ALA -B90 : ASN -B91 : MET -B92 : ASP -B93 : GLY -B94 : LEU -B95 : LYS -C380 : G unknown unknown -C381 : C unknown unknown -C382 : U unknown unknown -C383 : A unknown unknown -C384 : G unknown unknown -C385 : C unknown unknown -C386 : G unknown unknown -C387 : A unknown unknown -C388 : G unknown unknown -C389 : A unknown unknown -C390 : C unknown unknown -C391 : C unknown unknown -C392 : C unknown unknown -C393 : C unknown unknown -C394 : G unknown unknown -C395 : U unknown unknown -C396 : C unknown unknown -C397 : U unknown unknown -C398 : C unknown unknown -C399 : U unknown unknown -C101 : G unknown unknown -C102 : C unknown unknown -C103 : C unknown unknown -C104 : G unknown unknown -C105 : G unknown unknown -C106 : G unknown unknown -C107 : C unknown unknown -C108 : G unknown unknown -C109 : C unknown unknown -C110 : G unknown unknown -C111 : G unknown unknown -C112 : U unknown unknown -C113 : G unknown unknown -C114 : G unknown unknown -C115 : C unknown unknown -C116 : G unknown unknown -C117 : C unknown unknown -C118 : G unknown unknown -C119 : C unknown unknown -C120 : G unknown unknown -C121 : C unknown unknown -C122 : C unknown unknown -C123 : U unknown unknown -C124 : G unknown unknown -C125 : U unknown unknown -C126 : A unknown unknown -C127 : G unknown unknown -C128 : U unknown unknown -C129 : C unknown unknown -C130 : C unknown unknown -C131 : C unknown unknown -C132 : A unknown unknown -C133 : G unknown unknown -C134 : C unknown unknown -C135 : U unknown unknown -C136 : A unknown unknown -C137 : C unknown unknown -C138 : U unknown unknown -C139 : C unknown unknown -C140 : G unknown unknown -C141 : G unknown unknown -C142 : G unknown unknown -C143 : A unknown unknown -C144 : G unknown unknown -C145 : G unknown unknown -C146 : C unknown unknown -C147 : U unknown unknown -C148 : G unknown unknown -C149 : A unknown unknown -C150 : G unknown unknown -C151 : G unknown unknown -C152 : U unknown unknown -C153 : G unknown unknown -C154 : G unknown unknown -C155 : G unknown unknown -C156 : A unknown unknown -C157 : G unknown unknown -C158 : G unknown unknown -C159 : A unknown unknown -C160 : U unknown unknown -C161 : C unknown unknown -C162 : G unknown unknown -C163 : C unknown unknown -C164 : U unknown unknown -C165 : A unknown unknown -C166 : G unknown unknown -C1001 : EU3 -C1002 : EU3 -Adjacent stackings ---------------------------------------------- -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 0 -Number of adjacent stackings = 0 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ diff --git a/MCdata/1e95_MC b/MCdata/1e95_MC deleted file mode 100644 index 41c244a603f5f3473bdf2d5768748260ef9b2b2a..0000000000000000000000000000000000000000 --- a/MCdata/1e95_MC +++ /dev/null @@ -1,1214 +0,0 @@ -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : C C3p_endo anti -A3 : G C3p_endo anti -A4 : G C3p_endo anti -A5 : C C3p_endo anti -A6 : C C3p_endo anti -A7 : A C2p_endo anti -A8 : G C3p_endo anti -A9 : C C3p_endo anti -A10 : U C3p_endo anti -A11 : C C3p_endo anti -A12 : C C3p_endo anti -A13 : A C3p_endo anti -A14 : G C3p_endo anti -A15 : G C3p_endo anti -A16 : C C3p_endo anti -A17 : C C3p_endo anti -A18 : G C3p_endo anti -A19 : C C1p_exo anti -A20 : C C2p_endo anti -A21 : A C3p_endo anti -A22 : A C4p_exo anti -A23 : A O4p_endo anti -A24 : C C2p_endo anti -A25 : A C3p_endo anti -A26 : A C3p_endo anti -A27 : U C3p_endo anti -A28 : A C2p_endo anti -A29 : U C3p_endo anti -A30 : G C3p_endo anti -A31 : G C4p_exo anti -A32 : A C3p_endo anti -A33 : G C3p_endo anti -A34 : C C3p_endo anti -A35 : A C3p_endo anti -A36 : C C4p_exo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A29-A30 : adjacent_5p upward -A30-A31 : adjacent_5p upward -A31-A32 : adjacent_5p upward -A32-A33 : adjacent_5p upward -A33-A34 : adjacent_5p upward -A35-A36 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A3-A18 : outward -A8-A35 : outward -A23-A25 : upward -Number of stackings = 21 -Number of adjacent stackings = 18 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -A1-A19 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A18 : C-G Ww/Ww pairing antiparallel cis XIX -A3-A17 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A16 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A15 : C-G Ww/Ww pairing antiparallel cis XIX -A5-A26 : C-A O2'/Bh pairing -A6-A14 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A34 : G-C Ww/Ww pairing antiparallel cis XIX -A9-A33 : C-G Ww/Ww pairing antiparallel cis XIX -A10-A32 : U-A Ww/Ww pairing antiparallel cis XX -A11-A31 : C-G Ww/Ww pairing antiparallel cis XIX -A12-A30 : C-G Ww/Ww pairing antiparallel cis XIX -A13-A29 : A-U Wh/Bh pairing antiparallel cis one_hbond 48 -A16-A26 : C-A Ss/Bs pairing antiparallel cis one_hbond -A18-A21 : G-A Sw/Ww pairing antiparallel cis one_hbond 55 -A18-A22 : G-A O2'/Ww pairing -A22-A23 : A-A O2'/C8 adjacent_5p pairing -A27-A28 : U-A O2'/Hh adjacent_5p pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : C C3p_endo anti -A3 : G C3p_endo anti -A4 : G C3p_endo anti -A5 : C C3p_endo anti -A6 : C C3p_endo anti -A7 : A C2p_endo anti -A8 : G C3p_endo anti -A9 : C C3p_endo anti -A10 : U C3p_endo anti -A11 : C C3p_endo anti -A12 : C C3p_endo anti -A13 : A C3p_endo anti -A14 : G C3p_endo anti -A15 : G C3p_endo anti -A16 : C C3p_endo anti -A17 : C C3p_endo anti -A18 : G C3p_endo anti -A19 : C C2p_endo anti -A20 : C C2p_endo anti -A21 : A C3p_endo anti -A22 : A C4p_exo anti -A23 : A O4p_endo anti -A24 : C C2p_endo anti -A25 : A C3p_endo anti -A26 : A C3p_endo anti -A27 : U C3p_endo anti -A28 : A C2p_endo anti -A29 : U C3p_endo anti -A30 : G C3p_endo anti -A31 : G C4p_exo anti -A32 : A C3p_endo anti -A33 : G C3p_endo anti -A34 : C C3p_endo anti -A35 : A C3p_endo anti -A36 : C C4p_exo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A21-A22 : adjacent_5p upward pairing -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A29-A30 : adjacent_5p upward -A30-A31 : adjacent_5p upward -A31-A32 : adjacent_5p upward -A32-A33 : adjacent_5p upward -A33-A34 : adjacent_5p upward -A35-A36 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A3-A18 : outward -A8-A35 : outward -A23-A25 : upward pairing -Number of stackings = 21 -Number of adjacent stackings = 18 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -A1-A19 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A18 : C-G Ww/Ww pairing antiparallel cis XIX -A3-A17 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A16 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A15 : C-G Ww/Ww pairing antiparallel cis XIX -A5-A26 : C-A O2'/Bh pairing -A6-A14 : C-G Ww/Ww pairing antiparallel cis XIX -A7-A30 : A-G Ww/O2P pairing -A8-A34 : G-C Ww/Ww pairing antiparallel cis XIX -A9-A33 : C-G Ww/Ww pairing antiparallel cis XIX -A10-A32 : U-A Ww/Ww pairing antiparallel cis XX -A11-A31 : C-G Ww/Ww pairing antiparallel cis XIX -A12-A30 : C-G Ww/Ww pairing antiparallel cis XIX -A13-A29 : A-U Wh/Bh pairing antiparallel cis one_hbond -A14-A28 : G-A O2'/Ww pairing -A16-A26 : C-A Ss/Bs pairing antiparallel cis one_hbond -A18-A21 : G-A Sw/Ww pairing antiparallel cis one_hbond 55 -A21-A22 : A-A O2'/C8 adjacent_5p upward pairing -A22-A23 : A-A O2'/C8 adjacent_5p pairing -A23-A25 : A-A O2'/Hh upward pairing -A27-A28 : U-A O2'/Hh adjacent_5p pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : C C3p_endo anti -A3 : G C4p_exo anti -A4 : G C3p_endo anti -A5 : C C3p_endo anti -A6 : C C3p_endo anti -A7 : A C2p_endo anti -A8 : G C3p_endo anti -A9 : C C3p_endo anti -A10 : U C3p_endo anti -A11 : C C3p_endo anti -A12 : C C3p_endo anti -A13 : A C3p_endo anti -A14 : G C3p_endo anti -A15 : G C3p_endo anti -A16 : C C3p_endo anti -A17 : C C3p_endo anti -A18 : G C3p_endo anti -A19 : C C2p_endo anti -A20 : C C2p_endo anti -A21 : A C3p_endo anti -A22 : A C4p_exo anti -A23 : A O4p_endo anti -A24 : C C3p_exo anti -A25 : A C3p_endo anti -A26 : A C3p_endo anti -A27 : U C3p_endo anti -A28 : A C2p_endo anti -A29 : U C3p_endo anti -A30 : G C3p_endo anti -A31 : G C4p_exo anti -A32 : A C3p_endo anti -A33 : G C3p_endo anti -A34 : C C3p_endo anti -A35 : A C3p_endo anti -A36 : C C4p_exo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A29-A30 : adjacent_5p upward -A30-A31 : adjacent_5p upward -A31-A32 : adjacent_5p upward -A32-A33 : adjacent_5p upward -A33-A34 : adjacent_5p upward -A35-A36 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A3-A18 : outward -A8-A35 : outward -Number of stackings = 19 -Number of adjacent stackings = 17 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A1-A19 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A18 : C-G Ww/Ww pairing antiparallel cis XIX -A3-A17 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A16 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A15 : C-G Ww/Ww pairing antiparallel cis XIX -A5-A26 : C-A O2'/Bh pairing -A6-A14 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A34 : G-C Ww/Ww pairing antiparallel cis XIX -A9-A33 : C-G Ww/Ww pairing antiparallel cis XIX -A10-A32 : U-A Ww/Ww pairing antiparallel cis XX -A11-A31 : C-G Ww/Ww pairing antiparallel cis XIX -A12-A30 : C-G Ww/Ww pairing antiparallel cis XIX -A13-A29 : A-U Wh/Bh pairing antiparallel cis one_hbond -A16-A26 : C-A Ss/Bs pairing antiparallel cis one_hbond -A18-A21 : G-A Sw/Ww pairing antiparallel cis one_hbond 55 -A21-A22 : A-A O2'/C8 adjacent_5p pairing -A22-A23 : A-A O2'/C8 adjacent_5p pairing -A27-A28 : U-A O2'/Hh adjacent_5p pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : C C3p_endo anti -A3 : G C4p_exo anti -A4 : G C3p_endo anti -A5 : C C3p_endo anti -A6 : C C3p_endo anti -A7 : A C2p_endo anti -A8 : G C3p_endo anti -A9 : C C3p_endo anti -A10 : U C3p_endo anti -A11 : C C3p_endo anti -A12 : C C3p_endo anti -A13 : A C3p_endo anti -A14 : G C3p_endo anti -A15 : G C3p_endo anti -A16 : C C3p_endo anti -A17 : C C3p_endo anti -A18 : G C3p_endo anti -A19 : C C1p_exo anti -A20 : C C2p_endo anti -A21 : A C3p_endo anti -A22 : A O4p_endo anti -A23 : A O4p_endo anti -A24 : C C3p_exo anti -A25 : A C3p_endo anti -A26 : A C3p_endo anti -A27 : U C3p_endo anti -A28 : A C2p_endo anti -A29 : U C3p_endo anti -A30 : G C3p_endo anti -A31 : G C3p_endo anti -A32 : A C3p_endo anti -A33 : G C3p_endo anti -A34 : C C3p_endo anti -A35 : A C3p_endo anti -A36 : C C4p_exo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A29-A30 : adjacent_5p upward -A30-A31 : adjacent_5p upward -A31-A32 : adjacent_5p upward -A32-A33 : adjacent_5p upward -A33-A34 : adjacent_5p upward -A35-A36 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A3-A18 : outward -A8-A35 : outward -Number of stackings = 21 -Number of adjacent stackings = 19 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A1-A19 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A18 : C-G Ww/Ww pairing antiparallel cis XIX -A3-A17 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A16 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A15 : C-G Ww/Ww pairing antiparallel cis XIX -A6-A14 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A34 : G-C Ww/Ww pairing antiparallel cis XIX -A9-A33 : C-G Ww/Ww pairing antiparallel cis XIX -A10-A32 : U-A Ww/Ww pairing antiparallel cis XX -A11-A31 : C-G Ww/Ww pairing antiparallel cis XIX -A12-A30 : C-G Ww/Ww pairing antiparallel cis XIX -A13-A29 : A-U Wh/Bh pairing antiparallel cis one_hbond 48 -A15-A27 : G-U Sw/Ws pairing antiparallel cis one_hbond 85 -A16-A26 : C-A Ss/Bs pairing antiparallel cis one_hbond -A18-A22 : G-A O2'/Ww pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : C C3p_endo anti -A3 : G C3p_endo anti -A4 : G C3p_endo anti -A5 : C C3p_endo anti -A6 : C C3p_endo anti -A7 : A C2p_endo anti -A8 : G C3p_endo anti -A9 : C C3p_endo anti -A10 : U C3p_endo anti -A11 : C C3p_endo anti -A12 : C C3p_endo anti -A13 : A C3p_endo anti -A14 : G C3p_endo anti -A15 : G C4p_exo anti -A16 : C C3p_endo anti -A17 : C C3p_endo anti -A18 : G C3p_endo anti -A19 : C C1p_exo anti -A20 : C C2p_endo anti -A21 : A C3p_endo anti -A22 : A O4p_endo anti -A23 : A O4p_endo anti -A24 : C C3p_exo anti -A25 : A C3p_endo anti -A26 : A C3p_endo anti -A27 : U C3p_endo anti -A28 : A C2p_endo anti -A29 : U C3p_endo anti -A30 : G C3p_endo anti -A31 : G C4p_exo anti -A32 : A C3p_endo anti -A33 : G C3p_endo anti -A34 : C C3p_endo anti -A35 : A C3p_endo anti -A36 : C C4p_exo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A22-A23 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A29-A30 : adjacent_5p upward -A30-A31 : adjacent_5p upward -A31-A32 : adjacent_5p upward -A32-A33 : adjacent_5p upward -A33-A34 : adjacent_5p upward -A34-A35 : adjacent_5p upward -A35-A36 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A3-A18 : outward -A8-A35 : outward -A23-A25 : upward pairing -Number of stackings = 22 -Number of adjacent stackings = 19 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -A1-A19 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A18 : C-G Ww/Ww pairing antiparallel cis XIX -A3-A17 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A16 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A15 : C-G Ww/Ww pairing antiparallel cis XIX -A6-A14 : C-G Ww/Ww pairing antiparallel cis XIX -A7-A30 : A-G Ww/O2P pairing -A8-A34 : G-C Ww/Ww pairing antiparallel cis XIX -A9-A33 : C-G Ww/Ww pairing antiparallel cis XIX -A10-A32 : U-A Ww/Ww pairing antiparallel cis XX -A11-A31 : C-G Ww/Ww pairing antiparallel cis XIX -A12-A30 : C-G Ww/Ww pairing antiparallel cis XIX -A13-A29 : A-U Wh/Bh pairing antiparallel cis one_hbond -A14-A28 : G-A O2'/Ww pairing -A18-A21 : G-A Sw/Ww pairing antiparallel cis one_hbond 55 -A18-A22 : G-A Ss/Wh O2'/Ww pairing antiparallel cis one_hbond 63 -A23-A25 : A-A O2'/Hh upward pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : C C3p_endo anti -A3 : G C4p_exo anti -A4 : G C3p_endo anti -A5 : C C3p_endo anti -A6 : C C3p_endo anti -A7 : A C2p_endo anti -A8 : G C3p_endo anti -A9 : C C3p_endo anti -A10 : U C3p_endo anti -A11 : C C3p_endo anti -A12 : C C3p_endo anti -A13 : A C3p_endo anti -A14 : G C3p_endo anti -A15 : G C3p_endo anti -A16 : C C3p_endo anti -A17 : C C3p_endo anti -A18 : G C3p_endo anti -A19 : C C1p_exo anti -A20 : C C2p_endo anti -A21 : A C3p_endo anti -A22 : A C4p_exo anti -A23 : A O4p_endo anti -A24 : C C3p_exo anti -A25 : A C3p_endo anti -A26 : A C3p_endo anti -A27 : U C3p_endo anti -A28 : A C2p_endo anti -A29 : U C3p_endo anti -A30 : G C3p_endo anti -A31 : G C3p_endo anti -A32 : A C3p_endo anti -A33 : G C3p_endo anti -A34 : C C3p_endo anti -A35 : A C3p_endo anti -A36 : C C4p_exo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A29-A30 : adjacent_5p upward -A30-A31 : adjacent_5p upward -A31-A32 : adjacent_5p upward -A32-A33 : adjacent_5p upward -A33-A34 : adjacent_5p upward -A35-A36 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A3-A18 : outward -A8-A35 : outward -Number of stackings = 18 -Number of adjacent stackings = 16 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A1-A19 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A18 : C-G Ww/Ww pairing antiparallel cis XIX -A3-A17 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A16 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A15 : C-G Ww/Ww pairing antiparallel cis XIX -A6-A14 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A34 : G-C Ww/Ww pairing antiparallel cis XIX -A9-A33 : C-G Ww/Ww pairing antiparallel cis XIX -A10-A32 : U-A Ww/Ww pairing antiparallel cis XX -A11-A31 : C-G Ww/Ww pairing antiparallel cis XIX -A12-A30 : C-G Ww/Ww pairing antiparallel cis XIX -A13-A29 : A-U Wh/Bh pairing antiparallel cis one_hbond 48 -A14-A28 : G-A O2'/Ww pairing -A16-A26 : C-A Ss/Bs pairing antiparallel cis one_hbond -A21-A22 : A-A O2'/C8 adjacent_5p pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : C C3p_endo anti -A3 : G C3p_endo anti -A4 : G C3p_endo anti -A5 : C C3p_endo anti -A6 : C C3p_endo anti -A7 : A C2p_endo anti -A8 : G C3p_endo anti -A9 : C C3p_endo anti -A10 : U C3p_endo anti -A11 : C C3p_endo anti -A12 : C C3p_endo anti -A13 : A C3p_endo anti -A14 : G C3p_endo anti -A15 : G C3p_endo anti -A16 : C C3p_endo anti -A17 : C C3p_endo anti -A18 : G C3p_endo anti -A19 : C C2p_endo anti -A20 : C C2p_endo anti -A21 : A C3p_endo anti -A22 : A C4p_exo anti -A23 : A O4p_endo anti -A24 : C C3p_exo anti -A25 : A C3p_endo anti -A26 : A C3p_endo anti -A27 : U C3p_endo anti -A28 : A C2p_endo anti -A29 : U C3p_endo anti -A30 : G C3p_endo anti -A31 : G C4p_exo anti -A32 : A C3p_endo anti -A33 : G C3p_endo anti -A34 : C C4p_exo anti -A35 : A C2p_exo anti -A36 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A29-A30 : adjacent_5p upward -A30-A31 : adjacent_5p upward -A31-A32 : adjacent_5p upward -A32-A33 : adjacent_5p upward -A33-A34 : adjacent_5p upward -A35-A36 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A3-A18 : outward -A8-A35 : outward -A23-A25 : upward pairing -Number of stackings = 21 -Number of adjacent stackings = 18 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -A1-A19 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A18 : C-G Ww/Ww pairing antiparallel cis XIX -A3-A17 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A16 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A15 : C-G Ww/Ww pairing antiparallel cis XIX -A6-A14 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A34 : G-C Ww/Ww pairing antiparallel cis XIX -A9-A33 : C-G Ww/Ww pairing antiparallel cis XIX -A10-A32 : U-A Ww/Ww pairing antiparallel cis XX -A11-A31 : C-G Ww/Ww pairing antiparallel cis XIX -A12-A30 : C-G Ww/Ww pairing antiparallel cis XIX -A13-A29 : A-U Wh/Bh pairing antiparallel cis one_hbond 48 -A14-A28 : G-A O2'/Ww O2'/Bh pairing -A15-A27 : G-U Sw/Ws pairing antiparallel cis one_hbond 85 -A18-A21 : G-A Sw/Ww pairing antiparallel cis one_hbond 55 -A21-A22 : A-A O2'/C8 adjacent_5p pairing -A22-A23 : A-A O2'/C8 adjacent_5p pairing -A23-A25 : A-A O2'/Hh upward pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : C C3p_endo anti -A3 : G C3p_endo anti -A4 : G C3p_endo anti -A5 : C C3p_endo anti -A6 : C C3p_endo anti -A7 : A C2p_endo anti -A8 : G C3p_endo anti -A9 : C C3p_endo anti -A10 : U C3p_endo anti -A11 : C C3p_endo anti -A12 : C C3p_endo anti -A13 : A C3p_endo anti -A14 : G C3p_endo anti -A15 : G C3p_endo anti -A16 : C C3p_endo anti -A17 : C C3p_endo anti -A18 : G C3p_endo anti -A19 : C C2p_endo anti -A20 : C C2p_endo anti -A21 : A C3p_endo anti -A22 : A C4p_exo anti -A23 : A C1p_exo anti -A24 : C C3p_exo anti -A25 : A C3p_endo anti -A26 : A C3p_endo anti -A27 : U C3p_endo anti -A28 : A C2p_endo anti -A29 : U C3p_endo anti -A30 : G C3p_endo anti -A31 : G C4p_exo anti -A32 : A C3p_endo anti -A33 : G C3p_endo anti -A34 : C C3p_endo anti -A35 : A C3p_endo anti -A36 : C C4p_exo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A21-A22 : adjacent_5p upward pairing -A22-A23 : adjacent_5p upward pairing -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A29-A30 : adjacent_5p upward -A30-A31 : adjacent_5p upward -A31-A32 : adjacent_5p upward -A32-A33 : adjacent_5p upward -A33-A34 : adjacent_5p upward -A35-A36 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A3-A18 : outward -A8-A35 : outward -A23-A25 : upward pairing -Number of stackings = 22 -Number of adjacent stackings = 19 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -A1-A19 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A18 : C-G Ww/Ww pairing antiparallel cis XIX -A3-A17 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A16 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A15 : C-G Ww/Ww pairing antiparallel cis XIX -A6-A14 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A34 : G-C Ww/Ww pairing antiparallel cis XIX -A9-A33 : C-G Ww/Ww pairing antiparallel cis XIX -A10-A32 : U-A Ww/Ww pairing antiparallel cis XX -A11-A31 : C-G Ww/Ww pairing antiparallel cis XIX -A12-A30 : C-G Ww/Ww pairing antiparallel cis XIX -A13-A29 : A-U Ww/Wh pairing antiparallel cis one_hbond -A14-A28 : G-A O2'/Ww pairing -A18-A21 : G-A Sw/Ww pairing antiparallel cis one_hbond 55 -A21-A22 : A-A O2'/C8 adjacent_5p upward pairing -A22-A23 : A-A O2'/C8 adjacent_5p upward pairing -A23-A25 : A-A O2'/Hh upward pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : C C3p_endo anti -A3 : G C4p_exo anti -A4 : G C3p_endo anti -A5 : C C3p_endo anti -A6 : C C3p_endo anti -A7 : A C2p_endo anti -A8 : G C3p_endo anti -A9 : C C3p_endo anti -A10 : U C3p_endo anti -A11 : C C3p_endo anti -A12 : C C3p_endo anti -A13 : A C3p_endo anti -A14 : G C3p_endo anti -A15 : G C3p_endo anti -A16 : C C3p_endo anti -A17 : C C3p_endo anti -A18 : G C3p_endo anti -A19 : C C2p_endo anti -A20 : C C2p_endo anti -A21 : A C3p_endo anti -A22 : A C4p_exo anti -A23 : A C3p_endo anti -A24 : C C3p_exo syn -A25 : A C3p_endo anti -A26 : A C2p_exo anti -A27 : U C3p_endo anti -A28 : A C2p_endo anti -A29 : U C3p_endo anti -A30 : G C3p_endo anti -A31 : G C3p_endo anti -A32 : A C3p_endo anti -A33 : G C3p_endo anti -A34 : C C3p_endo anti -A35 : A C3p_endo anti -A36 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A29-A30 : adjacent_5p upward -A30-A31 : adjacent_5p upward -A31-A32 : adjacent_5p upward -A32-A33 : adjacent_5p upward -A33-A34 : adjacent_5p upward -A35-A36 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A3-A18 : outward -A8-A35 : outward -A23-A25 : upward -Number of stackings = 19 -Number of adjacent stackings = 16 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -A1-A19 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A18 : C-G Ww/Ww pairing antiparallel cis XIX -A3-A17 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A16 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A15 : C-G Ww/Ww pairing antiparallel cis XIX -A6-A14 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A34 : G-C Ww/Ww pairing antiparallel cis XIX -A9-A33 : C-G Ww/Ww pairing antiparallel cis XIX -A10-A32 : U-A Ww/Ww pairing antiparallel cis XX -A11-A31 : C-G Ww/Ww pairing antiparallel cis XIX -A12-A30 : C-G Ww/Ww pairing antiparallel cis XIX -A13-A29 : A-U Wh/Hw pairing antiparallel cis one_hbond 48 -A15-A27 : G-U Sw/Ws pairing antiparallel cis one_hbond 85 -A16-A26 : C-A Ss/Bs pairing antiparallel cis one_hbond -A21-A22 : A-A O2'/C8 adjacent_5p pairing -A22-A23 : A-A O2'/C8 adjacent_5p pairing -A23-A24 : A-C O2P/Bh adjacent_5p pairing -A27-A28 : U-A O2'/Hh adjacent_5p pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : C C3p_endo anti -A3 : G C4p_exo anti -A4 : G C3p_endo anti -A5 : C C3p_endo anti -A6 : C C3p_endo anti -A7 : A C2p_endo anti -A8 : G C3p_endo anti -A9 : C C3p_endo anti -A10 : U C3p_endo anti -A11 : C C3p_endo anti -A12 : C C3p_endo anti -A13 : A C3p_endo anti -A14 : G C3p_endo anti -A15 : G C3p_endo anti -A16 : C C3p_endo anti -A17 : C C3p_endo anti -A18 : G C3p_endo anti -A19 : C C1p_exo anti -A20 : C C2p_endo anti -A21 : A C3p_endo anti -A22 : A C4p_exo anti -A23 : A C3p_endo anti -A24 : C C3p_exo syn -A25 : A C2p_exo anti -A26 : A C2p_exo anti -A27 : U C3p_endo anti -A28 : A C2p_endo anti -A29 : U C3p_endo anti -A30 : G C3p_endo anti -A31 : G C4p_exo anti -A32 : A C3p_endo anti -A33 : G C3p_endo anti -A34 : C C4p_exo anti -A35 : A C3p_endo anti -A36 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A22-A23 : adjacent_5p upward pairing -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A29-A30 : adjacent_5p upward -A30-A31 : adjacent_5p upward -A31-A32 : adjacent_5p upward -A32-A33 : adjacent_5p upward -A33-A34 : adjacent_5p upward -A35-A36 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A3-A18 : outward -A8-A35 : outward -A23-A25 : upward -Number of stackings = 21 -Number of adjacent stackings = 18 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -A1-A19 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A18 : C-G Ww/Ww pairing antiparallel cis XIX -A3-A17 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A16 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A15 : C-G Ww/Ww pairing antiparallel cis XIX -A5-A26 : C-A O2'/Bh pairing -A6-A14 : C-G Ww/Ww pairing antiparallel cis XIX -A7-A30 : A-G Ww/O2P pairing -A8-A34 : G-C Ww/Ww pairing antiparallel cis XIX -A9-A33 : C-G Ww/Ww pairing antiparallel cis XIX -A10-A32 : U-A Ww/Ww pairing antiparallel cis XX -A11-A31 : C-G Ww/Ww pairing antiparallel cis XIX -A12-A30 : C-G Ww/Ww pairing antiparallel cis XIX -A13-A29 : A-U Wh/Bh pairing antiparallel cis one_hbond -A14-A28 : G-A O2'/Ww pairing -A15-A27 : G-U Sw/Ws pairing antiparallel cis one_hbond 85 -A16-A26 : C-A Ss/Bs pairing antiparallel cis one_hbond -A18-A21 : G-A Sw/Ww pairing antiparallel cis one_hbond 55 -A18-A22 : G-A Ss/Wh O2'/Ww pairing antiparallel cis one_hbond 63 -A22-A23 : A-A O2'/C8 adjacent_5p upward pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : C C3p_endo anti -A3 : G C4p_exo anti -A4 : G C3p_endo anti -A5 : C C3p_endo anti -A6 : C C3p_endo anti -A7 : A C2p_endo anti -A8 : G C3p_endo anti -A9 : C C3p_endo anti -A10 : U C3p_endo anti -A11 : C C3p_endo anti -A12 : C C3p_endo anti -A13 : A C3p_endo anti -A14 : G C3p_endo anti -A15 : G C3p_endo anti -A16 : C C3p_endo anti -A17 : C C3p_endo anti -A18 : G C3p_endo anti -A19 : C C1p_exo anti -A20 : C C2p_endo anti -A21 : A C3p_endo anti -A22 : A O4p_endo anti -A23 : A C3p_endo anti -A24 : C C3p_exo syn -A25 : A C3p_endo anti -A26 : A C2p_exo anti -A27 : U C3p_endo anti -A28 : A C2p_endo anti -A29 : U C3p_endo anti -A30 : G C3p_endo anti -A31 : G C4p_exo anti -A32 : A C3p_endo anti -A33 : G C3p_endo anti -A34 : C C3p_endo anti -A35 : A C3p_endo anti -A36 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A22-A23 : adjacent_5p upward pairing -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A29-A30 : adjacent_5p upward -A30-A31 : adjacent_5p upward -A31-A32 : adjacent_5p upward -A32-A33 : adjacent_5p upward -A33-A34 : adjacent_5p upward -A35-A36 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A3-A18 : outward -A8-A35 : outward -A23-A25 : upward -Number of stackings = 21 -Number of adjacent stackings = 18 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -A1-A19 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A18 : C-G Ww/Ww pairing antiparallel cis XIX -A3-A17 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A16 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A15 : C-G Ww/Ww pairing antiparallel cis XIX -A6-A14 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A34 : G-C Ww/Ww pairing antiparallel cis XIX -A9-A33 : C-G Ww/Ww pairing antiparallel cis XIX -A10-A32 : U-A Ww/Ww pairing antiparallel cis XX -A11-A31 : C-G Ww/Ww pairing antiparallel cis XIX -A12-A30 : C-G Ww/Ww pairing antiparallel cis XIX -A13-A29 : A-U Wh/Bh pairing antiparallel cis one_hbond -A14-A28 : G-A O2'/Ww pairing -A15-A27 : G-U Sw/Ws pairing antiparallel cis one_hbond 85 -A16-A26 : C-A Ss/Bs pairing antiparallel cis one_hbond -A22-A23 : A-A O2'/C8 adjacent_5p upward pairing -A23-A24 : A-C O2P/Bh adjacent_5p pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : C C3p_endo anti -A3 : G C3p_endo anti -A4 : G C3p_endo anti -A5 : C C3p_endo anti -A6 : C C3p_endo anti -A7 : A C2p_endo anti -A8 : G C3p_endo anti -A9 : C C3p_endo anti -A10 : U C3p_endo anti -A11 : C C3p_endo anti -A12 : C C3p_endo anti -A13 : A C3p_endo anti -A14 : G C3p_endo anti -A15 : G C3p_endo anti -A16 : C C3p_endo anti -A17 : C C3p_endo anti -A18 : G C3p_endo anti -A19 : C C2p_endo anti -A20 : C C2p_endo anti -A21 : A C3p_endo anti -A22 : A C3p_endo anti -A23 : A O4p_endo anti -A24 : C C3p_exo anti -A25 : A C3p_endo anti -A26 : A C3p_endo anti -A27 : U C3p_endo anti -A28 : A C2p_endo anti -A29 : U C3p_endo anti -A30 : G C3p_endo anti -A31 : G C4p_exo anti -A32 : A C3p_endo anti -A33 : G C3p_endo anti -A34 : C C3p_endo anti -A35 : A C3p_endo anti -A36 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A21-A22 : adjacent_5p upward pairing -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A29-A30 : adjacent_5p upward -A30-A31 : adjacent_5p upward -A31-A32 : adjacent_5p upward -A32-A33 : adjacent_5p upward -A33-A34 : adjacent_5p upward -A35-A36 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A3-A18 : outward -A8-A35 : outward -Number of stackings = 19 -Number of adjacent stackings = 17 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A1-A19 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A18 : C-G Ww/Ww pairing antiparallel cis XIX -A3-A17 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A16 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A15 : C-G Ww/Ww pairing antiparallel cis XIX -A6-A14 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A34 : G-C Ww/Ww pairing antiparallel cis XIX -A9-A33 : C-G Ww/Ww pairing antiparallel cis XIX -A10-A32 : U-A Ww/Ww pairing antiparallel cis XX -A11-A31 : C-G Ww/Ww pairing antiparallel cis XIX -A12-A30 : C-G Ww/Ww pairing antiparallel cis XIX -A13-A29 : A-U Wh/Bh pairing antiparallel cis one_hbond 48 -A18-A21 : G-A Sw/Ww pairing antiparallel cis one_hbond 55 -A21-A22 : A-A O2'/C8 adjacent_5p upward pairing -A22-A23 : A-A O2'/C8 adjacent_5p pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : C C3p_endo anti -A3 : G C4p_exo anti -A4 : G C3p_endo anti -A5 : C C3p_endo anti -A6 : C C3p_endo anti -A7 : A C2p_endo anti -A8 : G C3p_endo anti -A9 : C C3p_endo anti -A10 : U C3p_endo anti -A11 : C C3p_endo anti -A12 : C C3p_endo anti -A13 : A C3p_endo anti -A14 : G C3p_endo anti -A15 : G C3p_endo anti -A16 : C C3p_endo anti -A17 : C C3p_endo anti -A18 : G C3p_endo anti -A19 : C C2p_endo anti -A20 : C C2p_endo anti -A21 : A C3p_endo anti -A22 : A C4p_exo anti -A23 : A C3p_endo anti -A24 : C C2p_endo syn -A25 : A C3p_endo anti -A26 : A C2p_exo anti -A27 : U C3p_endo anti -A28 : A C2p_endo anti -A29 : U C3p_endo anti -A30 : G C3p_endo anti -A31 : G C4p_exo anti -A32 : A C3p_endo anti -A33 : G C3p_endo anti -A34 : C C3p_endo anti -A35 : A C3p_endo anti -A36 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A21-A22 : adjacent_5p upward pairing -A26-A27 : adjacent_5p upward -A29-A30 : adjacent_5p upward -A30-A31 : adjacent_5p upward -A31-A32 : adjacent_5p upward -A32-A33 : adjacent_5p upward -A33-A34 : adjacent_5p upward -A35-A36 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A3-A18 : outward -A8-A35 : outward -A23-A25 : upward -Number of stackings = 20 -Number of adjacent stackings = 17 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -A1-A19 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A18 : C-G Ww/Ww pairing antiparallel cis XIX -A3-A17 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A16 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A15 : C-G Ww/Ww pairing antiparallel cis XIX -A6-A14 : C-G Ww/Ww pairing antiparallel cis XIX -A7-A31 : A-G Wh/Bh pairing parallel cis one_hbond 66 -A8-A34 : G-C Ww/Ww pairing antiparallel cis XIX -A9-A33 : C-G Ww/Ww pairing antiparallel cis XIX -A10-A32 : U-A Ww/Ww pairing antiparallel cis XX -A11-A31 : C-G Ww/Ww pairing antiparallel cis XIX -A12-A30 : C-G Ww/Ww pairing antiparallel cis XIX -A13-A29 : A-U Wh/Bh pairing antiparallel cis one_hbond 48 -A14-A28 : G-A O2'/Ww pairing -A15-A27 : G-U Sw/Ws pairing antiparallel cis one_hbond 85 -A16-A26 : C-A Ss/Bs pairing antiparallel cis one_hbond -A18-A21 : G-A Sw/Ww pairing antiparallel cis one_hbond 55 -A21-A22 : A-A O2'/C8 adjacent_5p upward pairing -A27-A28 : U-A O2'/Hh adjacent_5p pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : C C3p_endo anti -A3 : G C3p_endo anti -A4 : G C3p_endo anti -A5 : C C3p_endo anti -A6 : C C3p_endo anti -A7 : A C2p_endo anti -A8 : G C3p_endo anti -A9 : C C3p_endo anti -A10 : U C3p_endo anti -A11 : C C3p_endo anti -A12 : C C3p_endo anti -A13 : A C3p_endo anti -A14 : G C3p_endo anti -A15 : G C4p_exo anti -A16 : C C3p_endo anti -A17 : C C3p_endo anti -A18 : G C3p_endo anti -A19 : C C1p_exo anti -A20 : C C2p_endo anti -A21 : A C3p_endo anti -A22 : A C4p_exo anti -A23 : A O4p_endo anti -A24 : C C3p_exo anti -A25 : A C3p_endo anti -A26 : A C3p_endo anti -A27 : U C3p_endo anti -A28 : A C2p_endo anti -A29 : U C3p_endo anti -A30 : G C3p_endo anti -A31 : G C4p_exo anti -A32 : A C3p_endo anti -A33 : G C3p_endo anti -A34 : C C3p_endo anti -A35 : A C3p_endo anti -A36 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A21-A22 : adjacent_5p upward pairing -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A29-A30 : adjacent_5p upward -A30-A31 : adjacent_5p upward -A31-A32 : adjacent_5p upward -A32-A33 : adjacent_5p upward -A33-A34 : adjacent_5p upward -A35-A36 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A3-A18 : outward -A8-A35 : outward -Number of stackings = 23 -Number of adjacent stackings = 21 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A1-A19 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A18 : C-G Ww/Ww pairing antiparallel cis XIX -A3-A17 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A16 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A15 : C-G Ww/Ww pairing antiparallel cis XIX -A6-A14 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A34 : G-C Ww/Ww pairing antiparallel cis XIX -A9-A33 : C-G Ww/Ww pairing antiparallel cis XIX -A10-A32 : U-A Ww/Ww pairing antiparallel cis XX -A11-A31 : C-G Ww/Ww pairing antiparallel cis XIX -A12-A30 : C-G Ww/Ww pairing antiparallel cis XIX -A13-A29 : A-U Wh/Bh pairing antiparallel cis one_hbond 48 -A14-A28 : G-A O2'/Ww pairing -A18-A21 : G-A Sw/Ww pairing antiparallel cis one_hbond 55 -A21-A22 : A-A O2'/C8 adjacent_5p upward pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : C C3p_endo anti -A3 : G C3p_endo anti -A4 : G C3p_endo anti -A5 : C C3p_endo anti -A6 : C C3p_endo anti -A7 : A C2p_endo anti -A8 : G C3p_endo anti -A9 : C C3p_endo anti -A10 : U C3p_endo anti -A11 : C C3p_endo anti -A12 : C C3p_endo anti -A13 : A C3p_endo anti -A14 : G C3p_endo anti -A15 : G C4p_exo anti -A16 : C C3p_endo anti -A17 : C C3p_endo anti -A18 : G C3p_endo anti -A19 : C C1p_exo anti -A20 : C C2p_endo anti -A21 : A C3p_endo anti -A22 : A O4p_endo anti -A23 : A O4p_endo anti -A24 : C C3p_exo anti -A25 : A C3p_endo anti -A26 : A C3p_endo anti -A27 : U C3p_endo anti -A28 : A C2p_endo anti -A29 : U C3p_endo anti -A30 : G C3p_endo anti -A31 : G C4p_exo anti -A32 : A C3p_endo anti -A33 : G C3p_endo anti -A34 : C C4p_exo anti -A35 : A C3p_endo anti -A36 : C C4p_exo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A22-A23 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A29-A30 : adjacent_5p upward -A30-A31 : adjacent_5p upward -A31-A32 : adjacent_5p upward -A32-A33 : adjacent_5p upward -A33-A34 : adjacent_5p upward -A35-A36 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A3-A18 : outward -A8-A35 : outward -Number of stackings = 22 -Number of adjacent stackings = 20 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A1-A19 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A18 : C-G Ww/Ww pairing antiparallel cis XIX -A3-A17 : G-C Ww/Ww pairing antiparallel cis XIX -A4-A16 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A15 : C-G Ww/Ww pairing antiparallel cis XIX -A6-A14 : C-G Ww/Ww pairing antiparallel cis XIX -A7-A30 : A-G Ww/O2P pairing -A8-A34 : G-C Ww/Ww pairing antiparallel cis XIX -A9-A33 : C-G Ww/Ww pairing antiparallel cis XIX -A10-A32 : U-A Ww/Ww pairing antiparallel cis XX -A11-A31 : C-G Ww/Ww pairing antiparallel cis XIX -A12-A30 : C-G Ww/Ww pairing antiparallel cis XIX -A13-A29 : A-U Wh/Bh pairing antiparallel cis one_hbond -A14-A28 : G-A O2'/Ww pairing -A18-A22 : G-A O2'/Ww pairing -A23-A25 : A-A O2'/Hh pairing diff --git a/MCdata/1ebq_MC b/MCdata/1ebq_MC deleted file mode 100644 index 531275f58a5bddf994e9fd870b74022e8ab8746e..0000000000000000000000000000000000000000 --- a/MCdata/1ebq_MC +++ /dev/null @@ -1,376 +0,0 @@ -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : U C3p_endo anti -A4 : G C3p_endo anti -A5 : G C3p_endo anti -A6 : G C3p_endo anti -A7 : C C3p_endo anti -A8 : G C3p_endo anti -A9 : C C3p_endo anti -A10 : A C3p_endo anti -A11 : G C3p_endo anti -A12 : C C3p_endo anti -A13 : U C2p_exo anti -A14 : U C2p_endo anti -A15 : C C2p_endo anti -A16 : G C3p_endo syn -A17 : G C3p_endo anti -A18 : C C3p_endo anti -A19 : U C3p_endo anti -A20 : G C3p_endo anti -A21 : C C3p_endo anti -A22 : G C3p_endo anti -A23 : G C2p_endo anti -A24 : U C3p_exo anti -A25 : A C2p_exo anti -A26 : C C3p_endo anti -A27 : A C3p_endo anti -A28 : C C3p_endo anti -A29 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A15-A16 : adjacent_5p inward pairing -A16-A17 : adjacent_5p outward -A17-A18 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A28-A29 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A27 : outward -A10-A20 : outward -A23-A25 : outward pairing -Number of stackings = 23 -Number of adjacent stackings = 20 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -A1-A29 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A28 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A27 : U-A Ww/Ww pairing antiparallel cis XX -A4-A26 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A25 : G-A Ww/Ww pairing antiparallel cis VIII -A6-A23 : G-G Ww/Ww pairing parallel trans III -A7-A22 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A21 : G-C Ww/Ww pairing antiparallel cis XIX -A9-A20 : C-G Ww/Ww pairing antiparallel cis XIX -A10-A19 : A-U Ww/Ww pairing antiparallel cis XX -A11-A18 : G-C Ww/Ww pairing antiparallel cis XIX -A12-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A13-A14 : U-U O2P/Ww adjacent_5p pairing -A13-A15 : U-C O2'/Bh pairing -A13-A16 : U-G Bs/Ww pairing parallel trans one_hbond -A15-A16 : C-G O2'/Bs O2'/Ss O2P/Bs adjacent_5p inward pairing -A23-A25 : G-A O2'/Hh outward pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : U C3p_endo anti -A4 : G C3p_endo anti -A5 : G C2p_endo anti -A6 : G O4p_endo anti -A7 : C C3p_endo anti -A8 : G C3p_endo anti -A9 : C C3p_endo anti -A10 : A C3p_endo anti -A11 : G C3p_endo anti -A12 : C C3p_endo anti -A13 : U C2p_exo anti -A14 : U C2p_endo anti -A15 : C C3p_exo anti -A16 : G C3p_endo syn -A17 : G C2p_exo anti -A18 : C C3p_endo anti -A19 : U C3p_endo anti -A20 : G C3p_endo anti -A21 : C C3p_endo anti -A22 : G C3p_endo anti -A23 : G C2p_endo syn -A24 : U C3p_exo anti -A25 : A C2p_exo anti -A26 : C C3p_endo anti -A27 : A C3p_endo anti -A28 : C C3p_endo anti -A29 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A15-A16 : adjacent_5p inward -A16-A17 : adjacent_5p outward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A28-A29 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A27 : outward -A10-A20 : outward -A23-A25 : outward pairing -Number of stackings = 25 -Number of adjacent stackings = 22 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -A1-A29 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A28 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A27 : U-A Ww/Ww pairing antiparallel cis XX -A4-A26 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A25 : G-A Ww/Ww pairing antiparallel cis VIII -A6-A23 : G-G Ww/Ww pairing parallel trans III -A7-A22 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A21 : G-C Ww/Ww pairing antiparallel cis XIX -A9-A20 : C-G Ww/Ww pairing antiparallel cis XIX -A10-A19 : A-U Ww/Ww pairing antiparallel cis XX -A11-A18 : G-C Ww/Ww pairing antiparallel cis XIX -A12-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A13-A14 : U-U O2P/Ww adjacent_5p pairing -A13-A16 : U-G Bs/Ww pairing parallel trans one_hbond -A23-A25 : G-A O2'/Hh outward pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : U C3p_endo anti -A4 : G C3p_endo anti -A5 : G C1p_exo anti -A6 : G O4p_endo anti -A7 : C C3p_endo anti -A8 : G C3p_endo anti -A9 : C C3p_endo anti -A10 : A C3p_endo anti -A11 : G C3p_endo anti -A12 : C C3p_endo anti -A13 : U C2p_exo anti -A14 : U C2p_endo anti -A15 : C C3p_exo anti -A16 : G C3p_endo syn -A17 : G C3p_endo anti -A18 : C C3p_endo anti -A19 : U C3p_endo anti -A20 : G C3p_endo anti -A21 : C C3p_endo anti -A22 : G C3p_endo anti -A23 : G C2p_endo syn -A24 : U C3p_exo anti -A25 : A C2p_exo anti -A26 : C C3p_endo anti -A27 : A C3p_endo anti -A28 : C C3p_endo anti -A29 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A16-A17 : adjacent_5p outward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A28-A29 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A27 : outward -A8-A22 : outward -A10-A20 : outward -A23-A25 : outward -Number of stackings = 25 -Number of adjacent stackings = 21 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A1-A29 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A28 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A27 : U-A Ww/Ww pairing antiparallel cis XX -A4-A26 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A6 : G-G O2'/Hh adjacent_5p pairing -A5-A25 : G-A Ww/Ww pairing antiparallel cis VIII -A6-A23 : G-G Ww/Ww pairing parallel trans III -A7-A22 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A21 : G-C Ww/Ww pairing antiparallel cis XIX -A9-A20 : C-G Ww/Ww pairing antiparallel cis XIX -A10-A19 : A-U Ww/Ww pairing antiparallel cis XX -A11-A18 : G-C Ww/Ww pairing antiparallel cis XIX -A12-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A13-A16 : U-G Bs/Ww pairing parallel trans 87 -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : U C3p_endo anti -A4 : G C3p_endo anti -A5 : G C2p_exo anti -A6 : G C4p_exo anti -A7 : C C3p_endo anti -A8 : G C3p_endo anti -A9 : C C3p_endo anti -A10 : A C3p_endo anti -A11 : G C3p_endo anti -A12 : C C3p_endo anti -A13 : U C2p_exo anti -A14 : U C3p_exo anti -A15 : C C3p_exo anti -A16 : G C3p_endo syn -A17 : G C3p_endo anti -A18 : C C3p_endo anti -A19 : U C3p_endo anti -A20 : G C3p_endo anti -A21 : C C3p_endo anti -A22 : G C3p_endo anti -A23 : G C2p_endo anti -A24 : U C3p_exo anti -A25 : A C1p_endo anti -A26 : C C3p_endo anti -A27 : A C3p_endo anti -A28 : C C3p_endo anti -A29 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A16-A17 : adjacent_5p outward -A17-A18 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A28-A29 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A27 : outward -A8-A22 : outward -A10-A20 : outward -A23-A25 : outward -Number of stackings = 23 -Number of adjacent stackings = 19 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A1-A29 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A28 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A27 : U-A Ww/Ww pairing antiparallel cis XX -A4-A26 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A25 : G-A Ww/Ww pairing antiparallel cis VIII -A6-A23 : G-G Ww/Ww pairing parallel trans III -A7-A22 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A21 : G-C Ww/Ww pairing antiparallel cis XIX -A9-A20 : C-G Ww/Ww pairing antiparallel cis XIX -A10-A19 : A-U Ww/Ww pairing antiparallel cis XX -A11-A18 : G-C Ww/Ww pairing antiparallel cis XIX -A12-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A13-A16 : U-G Bs/Ww pairing parallel trans one_hbond -A15-A16 : C-G O2'/Ss adjacent_5p pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : U C3p_endo anti -A4 : G C3p_endo anti -A5 : G C1p_endo anti -A6 : G O4p_endo anti -A7 : C C2p_exo anti -A8 : G C3p_endo anti -A9 : C C3p_endo anti -A10 : A C3p_endo anti -A11 : G C3p_endo anti -A12 : C C3p_endo anti -A13 : U C2p_exo anti -A14 : U C3p_exo anti -A15 : C C2p_endo anti -A16 : G C3p_endo syn -A17 : G C2p_exo anti -A18 : C C3p_endo anti -A19 : U C3p_endo anti -A20 : G C3p_endo anti -A21 : C C3p_endo anti -A22 : G C3p_endo anti -A23 : G C2p_endo syn -A24 : U C3p_exo anti -A25 : A C1p_endo anti -A26 : C C3p_endo anti -A27 : A C3p_endo anti -A28 : C C3p_endo anti -A29 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A15-A16 : adjacent_5p inward -A16-A17 : adjacent_5p outward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A28-A29 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A27 : outward -A8-A22 : outward -A10-A20 : outward -A23-A25 : outward -Number of stackings = 26 -Number of adjacent stackings = 22 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A1-A29 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A28 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A27 : U-A Ww/Ww pairing antiparallel cis XX -A4-A26 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A25 : G-A Ww/Ww pairing antiparallel cis VIII -A6-A23 : G-G Ww/Ww pairing parallel trans III -A7-A22 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A21 : G-C Ww/Ww pairing antiparallel cis XIX -A9-A20 : C-G Ww/Ww pairing antiparallel cis XIX -A10-A19 : A-U Ww/Ww pairing antiparallel cis XX -A11-A18 : G-C Ww/Ww pairing antiparallel cis XIX -A12-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A13-A14 : U-U O2P/Hh O2P/Ww adjacent_5p pairing -A13-A16 : U-G Bs/Ww pairing parallel trans one_hbond diff --git a/MCdata/1ebr_MC b/MCdata/1ebr_MC deleted file mode 100644 index 1c801f08baf44668cbe7b7e69d21a14ea1ddce5a..0000000000000000000000000000000000000000 --- a/MCdata/1ebr_MC +++ /dev/null @@ -1,385 +0,0 @@ -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : U C3p_endo anti -A4 : G C3p_endo anti -A5 : G C3p_exo anti -A6 : G O4p_endo anti -A7 : C C3p_endo anti -A8 : G C2p_exo anti -A9 : C C3p_endo anti -A10 : A C3p_endo anti -A11 : G C3p_endo anti -A12 : C C3p_endo anti -A13 : U C2p_exo anti -A14 : U C3p_exo anti -A15 : C C3p_exo anti -A16 : G C3p_endo syn -A17 : G C3p_endo anti -A18 : C C3p_endo anti -A19 : U C3p_endo anti -A20 : G C4p_exo anti -A21 : A C3p_exo syn -A22 : C O4p_endo anti -A23 : G C3p_endo anti -A24 : G C3p_exo syn -A25 : U C2p_endo anti -A26 : A C4p_exo anti -A27 : C C3p_endo anti -A28 : A C3p_endo anti -A29 : C C3p_endo anti -A30 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A8-A9 : adjacent_5p upward pairing -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A16-A17 : adjacent_5p outward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A22-A23 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A28-A29 : adjacent_5p upward -A29-A30 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A28 : outward -A13-A15 : upward -A24-A26 : outward pairing -Number of stackings = 20 -Number of adjacent stackings = 17 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -A1-A30 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A29 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A28 : U-A Ww/Ww pairing antiparallel cis XX -A4-A27 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A6 : G-G O2'/Hh adjacent_5p pairing -A5-A26 : G-A Ww/Ww pairing antiparallel cis VIII -A6-A7 : G-C O2P/Bh adjacent_5p pairing -A6-A24 : G-G Ww/Ww pairing parallel trans III -A7-A23 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A9 : G-C O2P/Bh adjacent_5p upward pairing -A8-A22 : G-C Ww/Ww pairing antiparallel cis XIX -A9-A20 : C-G Ww/Ww pairing antiparallel cis XIX -A10-A19 : A-U Ww/Ww pairing antiparallel cis XX -A11-A18 : G-C Ww/Ww pairing antiparallel cis XIX -A12-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A13-A16 : U-G Bs/Ww pairing parallel trans one_hbond -A14-A16 : U-G O2'/Hh pairing -A20-A22 : G-C O2'/Bh pairing -A23-A24 : G-G O2'/Bs adjacent_5p pairing -A24-A26 : G-A O2'/Hh outward pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : U C3p_endo anti -A4 : G C3p_endo anti -A5 : G C3p_exo anti -A6 : G O4p_endo anti -A7 : C C4p_exo anti -A8 : G C2p_exo anti -A9 : C C3p_endo anti -A10 : A C3p_endo anti -A11 : G C3p_endo anti -A12 : C C3p_endo anti -A13 : U C3p_endo anti -A14 : U C2p_endo anti -A15 : C C3p_exo anti -A16 : G C2p_exo syn -A17 : G C3p_endo anti -A18 : C C3p_endo anti -A19 : U C3p_endo anti -A20 : G O4p_endo anti -A21 : A C2p_endo syn -A22 : C O4p_endo anti -A23 : G O4p_endo anti -A24 : G C3p_exo anti -A25 : U C3p_exo anti -A26 : A O4p_endo anti -A27 : C C3p_endo anti -A28 : A C3p_endo anti -A29 : C C3p_endo anti -A30 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A5-A6 : adjacent_5p upward pairing -A8-A9 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A16-A17 : adjacent_5p outward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A22-A23 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A28-A29 : adjacent_5p upward -A29-A30 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A28 : outward -A10-A20 : outward -A13-A15 : upward -A24-A26 : outward -Number of stackings = 20 -Number of adjacent stackings = 16 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A1-A30 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A29 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A28 : U-A Ww/Ww pairing antiparallel cis XX -A4-A27 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A6 : G-G O2'/Hh adjacent_5p upward pairing -A5-A7 : G-C O2'/Bh pairing -A5-A26 : G-A Ww/Ww pairing antiparallel cis VIII -A6-A24 : G-G Ww/Ww pairing parallel trans III -A7-A23 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A22 : G-C Ww/Ww pairing antiparallel cis XIX -A9-A20 : C-G Ww/Ww pairing antiparallel cis XIX -A10-A19 : A-U Ww/Ww pairing antiparallel cis XX -A11-A18 : G-C Ww/Ww pairing antiparallel cis XIX -A12-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A13-A16 : U-G Ws/Ws pairing parallel trans one_hbond 87 -A14-A15 : U-C O2P/Bh adjacent_5p pairing -A14-A16 : U-G O2'/Ww pairing -A19-A21 : U-A Bs/Hw pairing parallel cis one_hbond 47 -A20-A22 : G-C O2'/Bh pairing -A24-A25 : G-U O2'/Hh adjacent_5p pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : U C3p_endo anti -A4 : G C3p_endo anti -A5 : G C3p_exo anti -A6 : G C3p_endo anti -A7 : C C1p_exo anti -A8 : G C1p_exo anti -A9 : C C3p_endo anti -A10 : A C3p_endo anti -A11 : G C3p_endo anti -A12 : C C3p_endo anti -A13 : U C2p_exo anti -A14 : U C2p_endo anti -A15 : C C2p_endo syn -A16 : G C2p_exo syn -A17 : G C3p_endo anti -A18 : C C3p_endo anti -A19 : U C3p_endo anti -A20 : G C4p_exo anti -A21 : A C3p_exo syn -A22 : C C1p_exo anti -A23 : G C4p_exo anti -A24 : G C2p_endo syn -A25 : U C3p_exo anti -A26 : A C2p_exo anti -A27 : C C3p_endo anti -A28 : A C3p_endo anti -A29 : C C3p_endo anti -A30 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward pairing -A7-A8 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A15-A16 : adjacent_5p inward pairing -A16-A17 : adjacent_5p outward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A22-A23 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A28-A29 : adjacent_5p upward -A29-A30 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A28 : outward -A24-A26 : outward pairing -Number of stackings = 23 -Number of adjacent stackings = 21 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -A1-A30 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A29 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A25 : U-U Hw/Ww pairing antiparallel trans one_hbond 81 -A3-A28 : U-A Ww/Ww pairing antiparallel cis XX -A4-A27 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A6 : G-G O2'/Hh adjacent_5p upward pairing -A5-A7 : G-C O2'/Bh pairing -A5-A26 : G-A Ww/Ww pairing antiparallel cis VIII -A6-A24 : G-G Ww/Ww pairing parallel trans III -A7-A23 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A9 : G-C O2'/Hh adjacent_5p pairing -A8-A22 : G-C Ww/Ww pairing antiparallel cis XIX -A9-A20 : C-G Ww/Ww pairing antiparallel cis XIX -A10-A19 : A-U Ww/Ww pairing antiparallel cis XX -A11-A18 : G-C Ww/Ww pairing antiparallel cis XIX -A12-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A13-A16 : U-G Bs/Ww pairing parallel trans 87 -A14-A15 : U-C O2P/Bh adjacent_5p pairing -A15-A16 : C-G O2'/Bs adjacent_5p inward pairing -A23-A24 : G-G O2'/Bs O2'/Ss adjacent_5p pairing -A24-A26 : G-A O2'/Hh outward pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : U C3p_endo anti -A4 : G C3p_endo anti -A5 : G C2p_endo syn -A6 : G C4p_exo anti -A7 : C C3p_endo anti -A8 : G C3p_endo anti -A9 : C C3p_endo anti -A10 : A C3p_endo anti -A11 : G C3p_endo anti -A12 : C C3p_endo anti -A13 : U C3p_endo anti -A14 : U C3p_exo anti -A15 : C C2p_endo syn -A16 : G C3p_endo syn -A17 : G C3p_endo anti -A18 : C C2p_exo anti -A19 : U C3p_endo anti -A20 : G O4p_endo anti -A21 : A C2p_endo syn -A22 : C O4p_endo anti -A23 : G O4p_endo anti -A24 : G C3p_exo syn -A25 : U C2p_endo anti -A26 : A C1p_exo anti -A27 : C C3p_endo anti -A28 : A C3p_endo anti -A29 : C C3p_endo anti -A30 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A5-A6 : adjacent_5p upward pairing -A6-A7 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A15-A16 : adjacent_5p inward pairing -A16-A17 : adjacent_5p outward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A22-A23 : adjacent_5p upward -A28-A29 : adjacent_5p upward -A29-A30 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A28 : outward -A10-A20 : outward -A24-A26 : outward pairing -Number of stackings = 20 -Number of adjacent stackings = 17 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -A1-A30 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A29 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A28 : U-A Ww/Ww pairing antiparallel cis XX -A4-A27 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A6 : G-G O2'/Hh adjacent_5p upward pairing -A5-A26 : G-A Ww/Ww pairing antiparallel cis VIII -A6-A24 : G-G Ww/Ww pairing parallel trans III -A7-A23 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A22 : G-C Ww/Ww pairing antiparallel cis XIX -A9-A20 : C-G Ww/Ww pairing antiparallel cis XIX -A10-A19 : A-U Ww/Ww pairing antiparallel cis XX -A11-A18 : G-C Ww/Ww pairing antiparallel cis XIX -A12-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A13-A15 : U-C Ws/Hh Ww/O2' pairing antiparallel trans one_hbond -A14-A15 : U-C O2'/Hh adjacent_5p pairing -A15-A16 : C-G O2'/Bs adjacent_5p inward pairing -A24-A26 : G-A O2'/Hh outward pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : U C3p_endo anti -A4 : G C3p_endo anti -A5 : G C3p_exo anti -A6 : G O4p_endo anti -A7 : C C4p_exo anti -A8 : G C2p_exo anti -A9 : C C3p_endo anti -A10 : A C3p_endo anti -A11 : G C3p_endo anti -A12 : C C3p_endo anti -A13 : U C3p_endo anti -A14 : U C3p_exo anti -A15 : C C3p_exo syn -A16 : G C3p_endo syn -A17 : G C3p_endo anti -A18 : C C3p_endo anti -A19 : U C3p_endo anti -A20 : G O4p_endo anti -A21 : A C2p_endo anti -A22 : C C4p_exo anti -A23 : G C4p_exo anti -A24 : G C3p_exo syn -A25 : U C2p_endo anti -A26 : A C3p_endo anti -A27 : C C3p_endo anti -A28 : A C3p_endo anti -A29 : C C3p_endo anti -A30 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward pairing -A8-A9 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A15-A16 : adjacent_5p inward pairing -A16-A17 : adjacent_5p outward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A22-A23 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A28-A29 : adjacent_5p upward -A29-A30 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A28 : outward -Number of stackings = 21 -Number of adjacent stackings = 20 -Number of non adjacent stackings = 1 -Base-pairs ------------------------------------------------------ -A1-A30 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A29 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A28 : U-A Ww/Ww pairing antiparallel cis XX -A4-A27 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A6 : G-G O2'/Hh O2'/C8 adjacent_5p upward pairing -A5-A26 : G-A Ww/Ww pairing antiparallel cis VIII -A6-A24 : G-G Ww/Ww pairing parallel trans III -A7-A8 : C-G O2'/C8 adjacent_5p pairing -A7-A23 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A22 : G-C Ww/Ww pairing antiparallel cis XIX -A9-A20 : C-G Ww/Ww pairing antiparallel cis XIX -A10-A19 : A-U Ww/Ww pairing antiparallel cis XX -A11-A18 : G-C Ww/Ww pairing antiparallel cis XIX -A12-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A13-A16 : U-G Bs/Ww pairing parallel trans 87 -A15-A16 : C-G O2'/Bs O2'/Ss adjacent_5p inward pairing -A19-A21 : U-A Ss/Hw pairing antiparallel trans one_hbond 45 -A20-A22 : G-C O2'/Bh pairing diff --git a/MCdata/1ebs_MC b/MCdata/1ebs_MC deleted file mode 100644 index 536768133fd79002352cb280dd1deef4e4321118..0000000000000000000000000000000000000000 --- a/MCdata/1ebs_MC +++ /dev/null @@ -1,383 +0,0 @@ -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : U C3p_endo anti -A4 : G C4p_exo anti -A5 : G C1p_exo anti -A6 : G C3p_endo anti -A7 : C C3p_endo anti -A8 : G C3p_endo anti -A9 : C C3p_endo anti -A10 : A C3p_endo anti -A11 : G C3p_endo anti -A12 : C C3p_endo anti -A13 : U C3p_endo anti -A14 : U C3p_exo anti -A15 : C C2p_endo anti -A16 : G C3p_endo syn -A17 : G C2p_exo anti -A18 : C C3p_endo anti -A19 : U C3p_endo anti -A20 : G C3p_endo anti -A21 : C C3p_endo anti -A22 : G C3p_endo anti -A23 : G C2p_endo anti -A24 : U C3p_exo anti -A25 : A O4p_endo anti -A26 : C C4p_exo anti -A27 : A C3p_endo anti -A28 : C C3p_endo anti -A29 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A16-A17 : adjacent_5p outward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A22-A23 : adjacent_5p inward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A28-A29 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A27 : outward -A10-A20 : outward -A23-A25 : outward -Number of stackings = 25 -Number of adjacent stackings = 22 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -A1-A29 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A28 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A27 : U-A Ww/Ww pairing antiparallel cis XX -A4-A26 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A25 : G-A Ww/Ww pairing antiparallel cis VIII -A6-A23 : G-G Ww/Ww pairing parallel trans III -A7-A22 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A21 : G-C Ww/Ww pairing antiparallel cis XIX -A9-A20 : C-G Ww/Ww pairing antiparallel cis XIX -A10-A19 : A-U Ww/Ww pairing antiparallel cis XX -A11-A18 : G-C Ww/Ww pairing antiparallel cis XIX -A12-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A13-A15 : U-C Ww/O2P pairing -A13-A16 : U-G Bs/Ww pairing parallel trans 87 -A15-A16 : C-G O2'/Ss adjacent_5p pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : U C3p_endo anti -A4 : G C4p_exo anti -A5 : G C1p_exo anti -A6 : G C3p_endo anti -A7 : C C3p_endo anti -A8 : G C3p_endo anti -A9 : C C3p_endo anti -A10 : A C3p_endo anti -A11 : G C3p_endo anti -A12 : C C3p_endo anti -A13 : U C3p_endo anti -A14 : U C3p_exo anti -A15 : C C3p_exo anti -A16 : G C3p_endo syn -A17 : G C2p_exo anti -A18 : C C3p_endo anti -A19 : U C3p_endo anti -A20 : G C3p_endo anti -A21 : C C3p_endo anti -A22 : G C3p_endo anti -A23 : G C2p_endo anti -A24 : U C3p_exo anti -A25 : A C3p_endo anti -A26 : C C3p_endo anti -A27 : A C3p_endo anti -A28 : C C3p_endo anti -A29 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A16-A17 : adjacent_5p outward -A17-A18 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A22-A23 : adjacent_5p inward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A28-A29 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A27 : outward -A8-A22 : outward -A10-A20 : outward -A13-A15 : upward -Number of stackings = 24 -Number of adjacent stackings = 20 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A1-A29 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A28 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A27 : U-A Ww/Ww pairing antiparallel cis XX -A4-A26 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A25 : G-A Ww/Ww pairing antiparallel cis VIII -A6-A23 : G-G Ww/Ww pairing parallel trans III -A7-A22 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A21 : G-C Ww/Ww pairing antiparallel cis XIX -A9-A20 : C-G Ww/Ww pairing antiparallel cis XIX -A10-A19 : A-U Ww/Ww pairing antiparallel cis XX -A11-A18 : G-C Ww/Ww pairing antiparallel cis XIX -A12-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A13-A16 : U-G Bs/Ww pairing parallel trans one_hbond -A14-A15 : U-C O2P/Bh adjacent_5p pairing -A14-A16 : U-G O2'/Hh pairing -A23-A25 : G-A C8/O2' pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : U C3p_endo anti -A4 : G C4p_exo anti -A5 : G O4p_endo anti -A6 : G C3p_endo anti -A7 : C C3p_endo anti -A8 : G C3p_endo anti -A9 : C C3p_endo anti -A10 : A C3p_endo anti -A11 : G C3p_endo anti -A12 : C C3p_endo anti -A13 : U C3p_endo anti -A14 : U C3p_exo anti -A15 : C C2p_endo anti -A16 : G C3p_endo syn -A17 : G C2p_exo anti -A18 : C C3p_endo anti -A19 : U C3p_endo anti -A20 : G C3p_endo anti -A21 : C C3p_endo anti -A22 : G C3p_endo anti -A23 : G C3p_exo anti -A24 : U C3p_exo anti -A25 : A C3p_exo anti -A26 : C C4p_exo anti -A27 : A C3p_endo anti -A28 : C C3p_endo anti -A29 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A15-A16 : adjacent_5p inward pairing -A16-A17 : adjacent_5p outward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A22-A23 : adjacent_5p inward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A28-A29 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A27 : outward -A8-A22 : outward -A10-A20 : outward -Number of stackings = 25 -Number of adjacent stackings = 22 -Number of non adjacent stackings = 3 -Base-pairs ------------------------------------------------------ -A1-A29 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A28 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A27 : U-A Ww/Ww pairing antiparallel cis XX -A4-A26 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A25 : G-A Ww/Ww pairing antiparallel cis VIII -A6-A23 : G-G Ww/Ww pairing parallel trans III -A7-A22 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A21 : G-C Ww/Ww pairing antiparallel cis XIX -A9-A20 : C-G Ww/Ww pairing antiparallel cis XIX -A10-A19 : A-U Ww/Ww pairing antiparallel cis XX -A11-A18 : G-C Ww/Ww pairing antiparallel cis XIX -A12-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A13-A15 : U-C O2'/Bh pairing -A13-A16 : U-G Bs/Ww pairing parallel trans 87 -A14-A15 : U-C O2'/Hh adjacent_5p pairing -A15-A16 : C-G O2'/Bs adjacent_5p inward pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : U C3p_endo anti -A4 : G C2p_endo anti -A5 : G C1p_exo anti -A6 : G C1p_exo anti -A7 : C C3p_endo anti -A8 : G C3p_endo anti -A9 : C C3p_endo anti -A10 : A C3p_endo anti -A11 : G C3p_endo anti -A12 : C C3p_endo anti -A13 : U C3p_endo anti -A14 : U C2p_endo syn -A15 : C C3p_exo anti -A16 : G C3p_endo syn -A17 : G C2p_exo anti -A18 : C C3p_endo anti -A19 : U C3p_endo anti -A20 : G C3p_endo anti -A21 : C C3p_endo anti -A22 : G C3p_endo anti -A23 : G C2p_endo anti -A24 : U C3p_exo anti -A25 : A C1p_exo anti -A26 : C C4p_exo anti -A27 : A C3p_endo anti -A28 : C C3p_endo anti -A29 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward pairing -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A16-A17 : adjacent_5p outward -A17-A18 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A22-A23 : adjacent_5p inward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A28-A29 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A27 : outward -A10-A20 : outward -A13-A15 : upward -A23-A25 : outward -Number of stackings = 25 -Number of adjacent stackings = 21 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A1-A29 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A28 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A27 : U-A Ww/Ww pairing antiparallel cis XX -A4-A5 : G-G O2'/C8 adjacent_5p upward pairing -A4-A26 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A25 : G-A Ww/Ww pairing antiparallel cis VIII -A6-A23 : G-G Ww/Ww pairing parallel trans III -A7-A22 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A21 : G-C Ww/Ww pairing antiparallel cis XIX -A9-A20 : C-G Ww/Ww pairing antiparallel cis XIX -A10-A19 : A-U Ww/Ww pairing antiparallel cis XX -A11-A18 : G-C Ww/Ww pairing antiparallel cis XIX -A12-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A13-A16 : U-G Bs/Ww pairing parallel trans one_hbond -A14-A15 : U-C O2P/Bh adjacent_5p pairing -A14-A16 : U-G O2'/Hh pairing -Residue conformations ------------------------------------------- -A1 : G C3p_endo anti -A2 : G C3p_endo anti -A3 : U C3p_endo anti -A4 : G C3p_endo anti -A5 : G C3p_endo anti -A6 : G C4p_exo anti -A7 : C C3p_endo anti -A8 : G C3p_endo anti -A9 : C C3p_endo anti -A10 : A C3p_endo anti -A11 : G C3p_endo anti -A12 : C C3p_endo anti -A13 : U C2p_exo anti -A14 : U C2p_endo anti -A15 : C C3p_exo anti -A16 : G C3p_endo syn -A17 : G C3p_endo anti -A18 : C C3p_endo anti -A19 : U C3p_endo anti -A20 : G C3p_endo anti -A21 : C C3p_endo anti -A22 : G C3p_endo anti -A23 : G C2p_endo anti -A24 : U C3p_exo anti -A25 : A C2p_endo anti -A26 : C C4p_exo anti -A27 : A C3p_endo anti -A28 : C C3p_endo anti -A29 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A16-A17 : adjacent_5p outward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A19-A20 : adjacent_5p upward -A20-A21 : adjacent_5p upward -A21-A22 : adjacent_5p upward -A22-A23 : adjacent_5p inward -A25-A26 : adjacent_5p upward -A26-A27 : adjacent_5p upward -A27-A28 : adjacent_5p upward -A28-A29 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A4-A27 : outward -A8-A22 : outward -A10-A20 : outward -A23-A25 : outward -Number of stackings = 27 -Number of adjacent stackings = 23 -Number of non adjacent stackings = 4 -Base-pairs ------------------------------------------------------ -A1-A29 : G-C Ww/Ww pairing antiparallel cis XIX -A2-A28 : G-C Ww/Ww pairing antiparallel cis XIX -A3-A27 : U-A Ww/Ww pairing antiparallel cis XX -A4-A26 : G-C Ww/Ww pairing antiparallel cis XIX -A5-A25 : G-A Ww/Ww pairing antiparallel cis VIII -A6-A23 : G-G Ww/Ww pairing parallel trans III -A7-A22 : C-G Ww/Ww pairing antiparallel cis XIX -A8-A21 : G-C Ww/Ww pairing antiparallel cis XIX -A9-A20 : C-G Ww/Ww pairing antiparallel cis XIX -A10-A19 : A-U Ww/Ww pairing antiparallel cis XX -A11-A18 : G-C Ww/Ww pairing antiparallel cis XIX -A12-A17 : C-G Ww/Ww pairing antiparallel cis XIX -A13-A16 : U-G Ws/Ww pairing parallel trans one_hbond -A14-A16 : U-G Hh/Hw pairing antiparallel cis one_hbond diff --git a/MCdata/1ec6_MC b/MCdata/1ec6_MC deleted file mode 100644 index 125f1aebc47e95fd00accd5ecc31755cddb5bfa2..0000000000000000000000000000000000000000 --- a/MCdata/1ec6_MC +++ /dev/null @@ -1,427 +0,0 @@ -Residue conformations ------------------------------------------- -C1 : G C3p_endo anti -C2 : A C3p_endo anti -C3 : G C2p_exo anti -C4 : G C3p_endo anti -C5 : A C3p_endo anti -C6 : C C3p_endo anti -C7 : C C3p_endo anti -C8 : U O4p_endo anti -C9 : A C3p_endo anti -C10 : G O4p_endo syn -C11 : A O4p_endo anti -C12 : U C4p_exo anti -C13 : C O4p_endo anti -C14 : A C3p_endo anti -C15 : C C3p_endo anti -C16 : C C3p_endo anti -C17 : C C3p_endo anti -C18 : C C3p_endo anti -C19 : U C3p_endo anti -C20 : C C2p_exo anti -D1 : G C3p_endo anti -D2 : A C3p_endo anti -D3 : G C2p_exo anti -D4 : G C3p_endo anti -D5 : A C3p_endo anti -D6 : C C3p_endo anti -D7 : C C2p_exo anti -D8 : U C2p_exo anti -D9 : A C3p_endo anti -D10 : G C3p_endo anti -D11 : A C4p_exo syn -D12 : U C4p_exo anti -D13 : C O4p_endo anti -D14 : A C3p_endo anti -D15 : C C3p_endo anti -D16 : C C3p_endo anti -D17 : C C3p_endo anti -D18 : C C3p_endo anti -D19 : U C3p_endo anti -D20 : C C3p_endo anti -A4 : MET -A5 : LYS -A6 : GLU -A7 : LEU -A8 : VAL -A9 : GLU -A10 : ILE -A11 : ALA -A12 : VAL -A13 : PRO -A14 : GLU -A15 : ASN -A16 : LEU -A17 : VAL -A18 : GLY -A19 : ALA -A20 : ILE -A21 : LEU -A22 : GLY -A23 : LYS -A24 : GLY -A25 : GLY -A26 : LYS -A27 : THR -A28 : LEU -A29 : VAL -A30 : GLU -A31 : TYR -A32 : GLN -A33 : GLU -A34 : LEU -A35 : THR -A36 : GLY -A37 : ALA -A38 : ARG -A39 : ILE -A40 : GLN -A41 : ILE -A42 : SER -A43 : LYS -A44 : LYS -A45 : GLY -A46 : GLU -A47 : PHE -A48 : LEU -A49 : PRO -A50 : GLY -A51 : THR -A52 : ARG -A53 : ASN -A54 : ARG -A55 : ARG -A56 : VAL -A57 : THR -A58 : ILE -A59 : THR -A60 : GLY -A61 : SER -A62 : PRO -A63 : ALA -A64 : ALA -A65 : THR -A66 : GLN -A67 : ALA -A68 : ALA -A69 : GLN -A70 : TYR -A71 : LEU -A72 : ILE -A73 : SER -A74 : GLN -A75 : ARG -A76 : VAL -A77 : THR -A78 : TYR -A79 : GLU -A80 : GLN -A81 : GLY -A82 : VAL -A83 : ARG -A84 : ALA -A85 : SER -A86 : ASN -A87 : PRO -A88 : GLN -A89 : LYS -A90 : VAL -B4 : MET -B5 : LYS -B6 : GLU -B7 : LEU -B8 : VAL -B9 : GLU -B10 : ILE -B11 : ALA -B12 : VAL -B13 : PRO -B14 : GLU -B15 : ASN -B16 : LEU -B17 : VAL -B18 : GLY -B19 : ALA -B20 : ILE -B21 : LEU -B22 : GLY -B23 : LYS -B24 : GLY -B25 : GLY -B26 : LYS -B27 : THR -B28 : LEU -B29 : VAL -B30 : GLU -B31 : TYR -B32 : GLN -B33 : GLU -B34 : LEU -B35 : THR -B36 : GLY -B37 : ALA -B38 : ARG -B39 : ILE -B40 : GLN -B41 : ILE -B42 : SER -B43 : LYS -B44 : LYS -B45 : GLY -B46 : GLU -B47 : PHE -B48 : LEU -B49 : PRO -B50 : GLY -B51 : THR -B52 : ARG -B53 : ASN -B54 : ARG -B55 : ARG -B56 : VAL -B57 : THR -B58 : ILE -B59 : THR -B60 : GLY -B61 : SER -B62 : PRO -B63 : ALA -B64 : ALA -B65 : THR -B66 : GLN -B67 : ALA -B68 : ALA -B69 : GLN -B70 : TYR -B71 : LEU -B72 : ILE -B73 : SER -B74 : GLN -B75 : ARG -B76 : VAL -B77 : THR -B78 : TYR -B79 : GLU -B80 : GLN -B81 : GLY -B82 : VAL -B83 : ARG -B84 : ALA -B85 : SER -B86 : ASN -B87 : PRO -C21 : HOH -C22 : HOH -C23 : HOH -C24 : HOH -C25 : HOH -C26 : HOH -C27 : HOH -C28 : HOH -C29 : HOH -C30 : HOH -C31 : HOH -C32 : HOH -C33 : HOH -C34 : HOH -C35 : HOH -C36 : HOH -C37 : HOH -C38 : HOH -C39 : HOH -C40 : HOH -C41 : HOH -C42 : HOH -C43 : HOH -C44 : HOH -C45 : HOH -C46 : HOH -D21 : HOH -D22 : HOH -D23 : HOH -D24 : HOH -D25 : HOH -D26 : HOH -D27 : HOH -D28 : HOH -D29 : HOH -D30 : HOH -D31 : HOH -D32 : HOH -D33 : HOH -D34 : HOH -D35 : HOH -D36 : HOH -D37 : HOH -D38 : HOH -D39 : HOH -D40 : HOH -D41 : HOH -D42 : HOH -D43 : HOH -D44 : HOH -D45 : HOH -D46 : HOH -D47 : HOH -D48 : HOH -D49 : HOH -A91 : HOH -A92 : HOH -A93 : HOH -A94 : HOH -A95 : HOH -A96 : HOH -A97 : HOH -A98 : HOH -A99 : HOH -A100 : HOH -A101 : HOH -A102 : HOH -A103 : HOH -A104 : HOH -A105 : HOH -A106 : HOH -A107 : HOH -A108 : HOH -A109 : HOH -A110 : HOH -A111 : HOH -A112 : HOH -A113 : HOH -A114 : HOH -A115 : HOH -A116 : HOH -A117 : HOH -A118 : HOH -A119 : HOH -A120 : HOH -A121 : HOH -A122 : HOH -A123 : HOH -A124 : HOH -A125 : HOH -A126 : HOH -A127 : HOH -A128 : HOH -A129 : HOH -A130 : HOH -A131 : HOH -A132 : HOH -A133 : HOH -A134 : HOH -A135 : HOH -A136 : HOH -A137 : HOH -A138 : HOH -A139 : HOH -A140 : HOH -A141 : HOH -A142 : HOH -A143 : HOH -A144 : HOH -A145 : HOH -B91 : HOH -B92 : HOH -B93 : HOH -B94 : HOH -B95 : HOH -B96 : HOH -B97 : HOH -B98 : HOH -B99 : HOH -B100 : HOH -B101 : HOH -B102 : HOH -B103 : HOH -B104 : HOH -B105 : HOH -B106 : HOH -B107 : HOH -B108 : HOH -B109 : HOH -B110 : HOH -B111 : HOH -B112 : HOH -B113 : HOH -B114 : HOH -B115 : HOH -B116 : HOH -B117 : HOH -B118 : HOH -B119 : HOH -B120 : HOH -B121 : HOH -B122 : HOH -B123 : HOH -B124 : HOH -B125 : HOH -B126 : HOH -B127 : HOH -B128 : HOH -B129 : HOH -B130 : HOH -B131 : HOH -B132 : HOH -B133 : HOH -B134 : HOH -B135 : HOH -B136 : HOH -B137 : HOH -B138 : HOH -B139 : HOH -B140 : HOH -B141 : HOH -B142 : HOH -B143 : HOH -B144 : HOH -B145 : HOH -B146 : HOH -B147 : HOH -B148 : HOH -B149 : HOH -B150 : HOH -Adjacent stackings ---------------------------------------------- -C1-C2 : adjacent_5p upward -C2-C3 : adjacent_5p upward -C3-C4 : adjacent_5p upward -C4-C5 : adjacent_5p upward -C5-C6 : adjacent_5p upward -C14-C15 : adjacent_5p upward -C15-C16 : adjacent_5p upward -C16-C17 : adjacent_5p upward -C17-C18 : adjacent_5p upward -C18-C19 : adjacent_5p upward -C19-C20 : adjacent_5p upward -D1-D2 : adjacent_5p upward -D2-D3 : adjacent_5p upward -D3-D4 : adjacent_5p upward -D4-D5 : adjacent_5p upward -D5-D6 : adjacent_5p upward -D6-D7 : adjacent_5p upward -D9-D10 : adjacent_5p upward -D14-D15 : adjacent_5p upward -D15-D16 : adjacent_5p upward -D16-D17 : adjacent_5p upward -D17-D18 : adjacent_5p upward -D19-D20 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -C4-C18 : outward -C7-C9 : upward -Number of stackings = 25 -Number of adjacent stackings = 23 -Number of non adjacent stackings = 2 -Base-pairs ------------------------------------------------------ -C1-C20 : G-C Ww/Ww pairing antiparallel cis XIX -C2-C19 : A-U Ww/Ww pairing antiparallel cis XX -C3-C18 : G-C Ww/Ww pairing antiparallel cis XIX -C4-C17 : G-C Ww/Ww pairing antiparallel cis XIX -C5-C14 : A-A Bh/O2P pairing -C5-C16 : A-C Ww/Wh pairing antiparallel cis one_hbond 71 -C7-C10 : C-G Bs/Ww pairing parallel trans 129 -C8-C10 : U-G O2'/Hh pairing -C12-C13 : U-C O2P/Bh adjacent_5p pairing -D1-D20 : G-C Ww/Ww pairing antiparallel cis XIX -D2-D19 : A-U Ww/Ww pairing antiparallel cis XX -D3-D18 : G-C Ww/Ww pairing antiparallel cis XIX -D4-D17 : G-C Ww/Ww pairing antiparallel cis XIX -D13-D14 : C-A O2'/Hh adjacent_5p pairing diff --git a/MCdata/1efo_MC b/MCdata/1efo_MC deleted file mode 100644 index 94b18d181e0dd28f54a749b697f03eed0fbc1e5a..0000000000000000000000000000000000000000 --- a/MCdata/1efo_MC +++ /dev/null @@ -1,72 +0,0 @@ -Residue conformations ------------------------------------------- -A1 : C C3p_endo anti -A2 : T C3p_endo anti -A3 : C C3p_endo anti -A4 : C C3p_endo anti -A5 : T C3p_endo anti -A6 : C C3p_endo anti -A7 : T C3p_endo anti -A8 : T C4p_exo anti -A9 : C C4p_exo anti -B10 : G C3p_endo anti -B11 : A C3p_endo anti -B12 : A C3p_endo anti -B13 : G C3p_endo anti -B14 : A C3p_endo anti -B15 : G C3p_endo anti -B16 : A C3p_endo anti -B17 : G C3p_endo anti -B18 : A C3p_endo anti -B19 : G C3p_endo anti -A103 : HOH -A106 : HOH -A113 : HOH -A117 : HOH -A118 : HOH -A120 : HOH -A121 : HOH -B101 : HOH -B102 : HOH -B104 : HOH -B105 : HOH -B107 : HOH -B108 : HOH -B109 : HOH -B110 : HOH -B111 : HOH -B112 : HOH -B114 : HOH -B115 : HOH -B116 : HOH -B119 : HOH -B122 : HOH -B123 : HOH -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A8-A9 : adjacent_5p upward -B10-B11 : adjacent_5p upward -B11-B12 : adjacent_5p upward -B12-B13 : adjacent_5p upward -B13-B14 : adjacent_5p upward -B14-B15 : adjacent_5p upward -B17-B18 : adjacent_5p upward -B18-B19 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -B15-B17 : upward -Number of stackings = 14 -Number of adjacent stackings = 13 -Number of non adjacent stackings = 1 -Base-pairs ------------------------------------------------------ -A1-B19 : C-G Ww/Ww pairing antiparallel cis XIX -A2-B18 : T-A Ww/Ww pairing antiparallel cis -A3-B17 : C-G Ww/Ww pairing antiparallel cis XIX -A4-B15 : C-G Ww/Ww pairing antiparallel cis XIX -A5-B14 : T-A Ww/Ww pairing antiparallel cis -A6-B13 : C-G Ww/Ww pairing antiparallel cis XIX -A7-B12 : T-A Ww/Ww pairing antiparallel cis -A8-B11 : T-A Ww/Ww pairing antiparallel cis -A9-B10 : C-G Ww/Ww pairing antiparallel cis XIX diff --git a/MCdata/1efs_MC b/MCdata/1efs_MC deleted file mode 100644 index 0e73c6df0e2642a2dbd1444c3883b0a7e6bfbd3d..0000000000000000000000000000000000000000 --- a/MCdata/1efs_MC +++ /dev/null @@ -1,681 +0,0 @@ -Residue conformations ------------------------------------------- -A1 : G C2p_endo anti -A2 : A C2p_endo anti -A3 : G C2p_endo anti -A4 : A C2p_endo anti -A5 : G C2p_endo anti -A6 : G C2p_endo anti -A7 : A O4p_endo anti -A8 : A C2p_endo anti -A9 : G C2p_endo anti -A10 : A C2p_endo anti -A11 : G C2p_endo anti -A12 : A C1p_exo anti -A13 : A C3p_endo anti -B26 : U C3p_endo anti -B25 : U C3p_endo anti -B24 : C C3p_endo anti -B23 : U C3p_endo anti -B22 : C C3p_endo anti -B21 : U C3p_endo anti -B20 : U C3p_endo anti -B19 : C C3p_endo anti -B18 : C C3p_endo anti -B17 : U C3p_endo anti -B16 : C C3p_endo anti -B15 : U C3p_endo anti -B14 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A12-A13 : adjacent_5p upward -B14-B15 : adjacent_3p downward -B15-B16 : adjacent_3p downward -B16-B17 : adjacent_3p downward -B17-B18 : adjacent_3p downward -B18-B19 : adjacent_3p downward -B19-B20 : adjacent_3p downward -B20-B21 : adjacent_3p downward -B22-B23 : adjacent_3p downward -B23-B24 : adjacent_3p downward -B24-B25 : adjacent_3p downward -B25-B26 : adjacent_3p downward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 23 -Number of adjacent stackings = 23 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-B14 : G-C Ww/Ww pairing antiparallel cis XIX -A2-B15 : A-U Ww/Ww pairing antiparallel cis XX -A3-B16 : G-C Ww/Ww pairing antiparallel cis XIX -A4-B17 : A-U Ww/Ww pairing antiparallel cis XX -A5-B18 : G-C Ww/Ww pairing antiparallel cis XIX -A6-B19 : G-C Ww/Ww pairing antiparallel cis XIX -A7-B20 : A-U Ww/Ww pairing antiparallel cis XX -A8-B21 : A-U Ww/Ww pairing antiparallel cis XX -A9-B22 : G-C Ww/Ww pairing antiparallel cis XIX -A10-B23 : A-U Ww/Ww pairing antiparallel cis XX -A11-B24 : G-C Ww/Ww pairing antiparallel cis XIX -A12-B25 : A-U Ww/Ww pairing antiparallel cis XX -A13-B26 : A-U Ww/Ww pairing antiparallel cis XX -Residue conformations ------------------------------------------- -A1 : G C2p_endo anti -A2 : A C2p_endo anti -A3 : G C2p_endo anti -A4 : A C1p_exo anti -A5 : G C2p_endo anti -A6 : G C2p_endo anti -A7 : A O4p_endo anti -A8 : A C2p_endo anti -A9 : G C2p_endo syn -A10 : A C1p_exo syn -A11 : G C1p_exo anti -A12 : A C1p_exo syn -A13 : A C3p_endo anti -B26 : U C3p_endo anti -B25 : U C3p_endo anti -B24 : C C3p_endo anti -B23 : U C3p_endo anti -B22 : C C3p_endo anti -B21 : U C3p_endo anti -B20 : U C3p_endo anti -B19 : C C3p_endo anti -B18 : C C3p_endo anti -B17 : U C3p_endo anti -B16 : C C3p_endo anti -B15 : U C3p_endo anti -B14 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A12-A13 : adjacent_5p upward -B14-B15 : adjacent_3p downward -B15-B16 : adjacent_3p downward -B17-B18 : adjacent_3p downward -B18-B19 : adjacent_3p downward -B19-B20 : adjacent_3p downward -B20-B21 : adjacent_3p downward -B21-B22 : adjacent_3p downward -B23-B24 : adjacent_3p downward -B25-B26 : adjacent_3p downward -Non-Adjacent stackings ------------------------------------------ -A4-B16 : outward -Number of stackings = 21 -Number of adjacent stackings = 20 -Number of non adjacent stackings = 1 -Base-pairs ------------------------------------------------------ -A1-B14 : G-C Ww/Ww pairing antiparallel cis one_hbond -A2-B15 : A-U Ww/Ww pairing antiparallel cis XX -A3-B16 : G-C Ww/Ww pairing antiparallel cis XIX -A4-B17 : A-U Ww/Ww pairing antiparallel cis XX -A5-B18 : G-C Ww/Ww pairing antiparallel cis XIX -A6-B19 : G-C Ww/Ww pairing antiparallel cis XIX -A7-B20 : A-U Ww/Ww pairing antiparallel cis XX -A8-B21 : A-U Ww/Ww pairing antiparallel cis XX -A9-B22 : G-C Ww/Ww pairing antiparallel cis XIX -A10-B23 : A-U Ww/Ww pairing antiparallel cis XX -A11-B24 : G-C Ww/Ww pairing antiparallel cis XIX -A12-B25 : A-U Ww/Ww pairing antiparallel cis XX -A13-B26 : A-U Ww/Ww pairing antiparallel cis XX -Residue conformations ------------------------------------------- -A1 : G C2p_endo anti -A2 : A C2p_endo anti -A3 : G C2p_endo anti -A4 : A C2p_endo anti -A5 : G C2p_endo anti -A6 : G C2p_endo anti -A7 : A O4p_endo anti -A8 : A C2p_endo anti -A9 : G C2p_endo anti -A10 : A C2p_endo anti -A11 : G C2p_endo anti -A12 : A C1p_exo anti -A13 : A C2p_endo anti -B26 : U C3p_endo anti -B25 : U C3p_endo anti -B24 : C C3p_endo anti -B23 : U C3p_endo anti -B22 : C C3p_endo anti -B21 : U C3p_endo anti -B20 : U C3p_endo anti -B19 : C C3p_endo anti -B18 : C C3p_endo anti -B17 : U C3p_endo anti -B16 : C C3p_endo anti -B15 : U C3p_endo anti -B14 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A12-A13 : adjacent_5p upward -B15-B16 : adjacent_3p downward -B16-B17 : adjacent_3p downward -B17-B18 : adjacent_3p downward -B19-B20 : adjacent_3p downward -B20-B21 : adjacent_3p downward -B22-B23 : adjacent_3p downward -B23-B24 : adjacent_3p downward -B24-B25 : adjacent_3p downward -B25-B26 : adjacent_3p downward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 21 -Number of adjacent stackings = 21 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-B14 : G-C Ww/Ww pairing antiparallel cis XIX -A2-B15 : A-U Ww/Ww pairing antiparallel cis XX -A3-B16 : G-C Ww/Ww pairing antiparallel cis XIX -A4-B17 : A-U Ww/Ww pairing antiparallel cis XX -A5-B18 : G-C Ww/Ww pairing antiparallel cis XIX -A6-B19 : G-C Ww/Ww pairing antiparallel cis XIX -A7-B20 : A-U Ww/Ww pairing antiparallel cis XX -A8-B21 : A-U Ww/Ww pairing antiparallel cis XX -A9-B22 : G-C Ww/Ww pairing antiparallel cis XIX -A10-B23 : A-U Ww/Ww pairing antiparallel cis XX -A11-B24 : G-C Ww/Ww pairing antiparallel cis XIX -A12-B25 : A-U Ww/Ww pairing antiparallel cis XX -A13-B26 : A-U Ww/Ww pairing antiparallel cis XX -Residue conformations ------------------------------------------- -A1 : G C2p_endo anti -A2 : A C2p_endo syn -A3 : G C2p_endo anti -A4 : A C2p_endo anti -A5 : G C2p_endo anti -A6 : G C2p_endo anti -A7 : A O4p_endo anti -A8 : A C2p_endo anti -A9 : G C2p_endo anti -A10 : A C1p_exo anti -A11 : G C2p_endo anti -A12 : A C1p_exo syn -A13 : A C2p_endo anti -B26 : U C3p_endo anti -B25 : U C3p_endo anti -B24 : C C3p_endo anti -B23 : U C3p_endo anti -B22 : C C3p_endo anti -B21 : U C3p_endo anti -B20 : U C3p_endo anti -B19 : C C3p_endo anti -B18 : C C3p_endo anti -B17 : U C3p_endo anti -B16 : C C3p_endo anti -B15 : U C3p_endo anti -B14 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A12-A13 : adjacent_5p upward -B15-B16 : adjacent_3p downward -B16-B17 : adjacent_3p downward -B17-B18 : adjacent_3p downward -B18-B19 : adjacent_3p downward -B19-B20 : adjacent_3p downward -B20-B21 : adjacent_3p downward -B21-B22 : adjacent_3p downward -B22-B23 : adjacent_3p downward -B23-B24 : adjacent_3p downward -B24-B25 : adjacent_3p downward -B25-B26 : adjacent_3p downward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 23 -Number of adjacent stackings = 23 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-B14 : G-C Ww/Ww pairing antiparallel cis XIX -A2-B15 : A-U Ww/Ww pairing antiparallel cis XX -A3-B16 : G-C Ww/Ww pairing antiparallel cis XIX -A4-B17 : A-U Ww/Ww pairing antiparallel cis XX -A5-B18 : G-C Ww/Ww pairing antiparallel cis XIX -A6-B19 : G-C Ww/Ww pairing antiparallel cis XIX -A7-B20 : A-U Ww/Ww pairing antiparallel cis XX -A8-B21 : A-U Ww/Ww pairing antiparallel cis XX -A9-B22 : G-C Ww/Ww pairing antiparallel cis XIX -A10-B23 : A-U Ww/Ww pairing antiparallel cis XX -A11-B24 : G-C Ww/Ww pairing antiparallel cis XIX -A12-B25 : A-U Ww/Ww pairing antiparallel cis XX -A13-B26 : A-U Ww/Ww pairing antiparallel cis XX -Residue conformations ------------------------------------------- -A1 : G C2p_endo anti -A2 : A C2p_endo syn -A3 : G C2p_endo anti -A4 : A C2p_endo anti -A5 : G C2p_endo anti -A6 : G C2p_endo anti -A7 : A O4p_endo anti -A8 : A C2p_endo anti -A9 : G C2p_endo anti -A10 : A C2p_endo anti -A11 : G C1p_exo anti -A12 : A C2p_endo syn -A13 : A C3p_exo anti -B26 : U C3p_endo anti -B25 : U C3p_endo anti -B24 : C C3p_endo anti -B23 : U C3p_endo anti -B22 : C C3p_endo anti -B21 : U C3p_endo anti -B20 : U C3p_endo anti -B19 : C C3p_endo anti -B18 : C C3p_endo anti -B17 : U C3p_endo anti -B16 : C C3p_endo anti -B15 : U C3p_endo anti -B14 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A12-A13 : adjacent_5p upward -B15-B16 : adjacent_3p downward -B16-B17 : adjacent_3p downward -B17-B18 : adjacent_3p downward -B18-B19 : adjacent_3p downward -B19-B20 : adjacent_3p downward -B20-B21 : adjacent_3p downward -B21-B22 : adjacent_3p downward -B22-B23 : adjacent_3p downward -B23-B24 : adjacent_3p downward -B24-B25 : adjacent_3p downward -B25-B26 : adjacent_3p downward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 22 -Number of adjacent stackings = 22 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-B14 : G-C Ww/Ww pairing antiparallel cis XIX -A2-B15 : A-U Ww/Ww pairing antiparallel cis XX -A3-B16 : G-C Ww/Ww pairing antiparallel cis XIX -A4-B17 : A-U Ww/Ww pairing antiparallel cis XX -A5-B18 : G-C Ww/Ww pairing antiparallel cis XIX -A6-B19 : G-C Ww/Ww pairing antiparallel cis XIX -A7-B20 : A-U Ww/Ww pairing antiparallel cis XX -A8-B21 : A-U Ww/Ww pairing antiparallel cis XX -A9-B22 : G-C Ww/Ww pairing antiparallel cis XIX -A10-B23 : A-U Ww/Ww pairing antiparallel cis XX -A11-B24 : G-C Ww/Ww pairing antiparallel cis XIX -A12-B25 : A-U Ww/Ww pairing antiparallel cis XX -A13-B26 : A-U Ww/Ww pairing antiparallel cis XX -Residue conformations ------------------------------------------- -A1 : G C2p_endo anti -A2 : A C2p_endo anti -A3 : G C2p_endo anti -A4 : A C2p_endo anti -A5 : G C2p_endo anti -A6 : G C2p_endo anti -A7 : A O4p_endo anti -A8 : A C2p_endo anti -A9 : G C2p_endo anti -A10 : A C1p_exo anti -A11 : G C2p_endo anti -A12 : A C1p_exo anti -A13 : A C3p_endo anti -B26 : U C3p_endo anti -B25 : U C3p_endo anti -B24 : C C3p_endo anti -B23 : U C3p_endo anti -B22 : C C3p_endo anti -B21 : U C3p_endo anti -B20 : U C3p_endo anti -B19 : C C3p_endo anti -B18 : C C3p_endo anti -B17 : U C3p_endo anti -B16 : C C3p_endo anti -B15 : U C3p_endo anti -B14 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A12-A13 : adjacent_5p upward -B14-B15 : adjacent_3p downward -B15-B16 : adjacent_3p downward -B16-B17 : adjacent_3p downward -B17-B18 : adjacent_3p downward -B18-B19 : adjacent_3p downward -B19-B20 : adjacent_3p downward -B20-B21 : adjacent_3p downward -B21-B22 : adjacent_3p downward -B22-B23 : adjacent_3p downward -B23-B24 : adjacent_3p downward -B24-B25 : adjacent_3p downward -B25-B26 : adjacent_3p downward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 24 -Number of adjacent stackings = 24 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-B14 : G-C Ww/Ww pairing antiparallel cis XIX -A2-B15 : A-U Ww/Ww pairing antiparallel cis XX -A3-B16 : G-C Ww/Ww pairing antiparallel cis XIX -A4-B17 : A-U Ww/Ww pairing antiparallel cis XX -A5-B18 : G-C Ww/Ww pairing antiparallel cis XIX -A6-B19 : G-C Ww/Ww pairing antiparallel cis XIX -A7-B20 : A-U Ww/Ww pairing antiparallel cis XX -A8-B21 : A-U Ww/Ww pairing antiparallel cis XX -A9-B22 : G-C Ww/Ww pairing antiparallel cis XIX -A10-B23 : A-U Ww/Ww pairing antiparallel cis XX -A11-B24 : G-C Ww/Ww pairing antiparallel cis XIX -A12-B25 : A-U Ww/Ww pairing antiparallel cis XX -A13-B26 : A-U Ww/Ww pairing antiparallel cis XX -Residue conformations ------------------------------------------- -A1 : G C2p_endo anti -A2 : A C2p_endo syn -A3 : G C2p_endo anti -A4 : A C2p_endo anti -A5 : G C2p_endo anti -A6 : G C2p_endo anti -A7 : A O4p_endo anti -A8 : A C2p_endo anti -A9 : G C2p_endo anti -A10 : A C2p_endo anti -A11 : G C2p_endo anti -A12 : A C2p_endo anti -A13 : A C3p_endo anti -B26 : U C3p_endo anti -B25 : U C3p_endo anti -B24 : C C3p_endo anti -B23 : U C3p_endo anti -B22 : C C3p_endo anti -B21 : U C3p_endo anti -B20 : U C3p_endo anti -B19 : C C3p_endo anti -B18 : C C3p_endo anti -B17 : U C3p_endo anti -B16 : C C3p_endo anti -B15 : U C3p_endo anti -B14 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A12-A13 : adjacent_5p upward -B15-B16 : adjacent_3p downward -B16-B17 : adjacent_3p downward -B17-B18 : adjacent_3p downward -B18-B19 : adjacent_3p downward -B19-B20 : adjacent_3p downward -B20-B21 : adjacent_3p downward -B21-B22 : adjacent_3p downward -B23-B24 : adjacent_3p downward -B24-B25 : adjacent_3p downward -B25-B26 : adjacent_3p downward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 22 -Number of adjacent stackings = 22 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-B14 : G-C Ww/Ww pairing antiparallel cis XIX -A2-B15 : A-U Ww/Ww pairing antiparallel cis XX -A3-B16 : G-C Ww/Ww pairing antiparallel cis XIX -A4-B17 : A-U Ww/Ww pairing antiparallel cis XX -A5-B18 : G-C Ww/Ww pairing antiparallel cis XIX -A6-B19 : G-C Ww/Ww pairing antiparallel cis XIX -A7-B20 : A-U Ww/Ww pairing antiparallel cis XX -A8-B21 : A-U Ww/Ww pairing antiparallel cis XX -A9-B22 : G-C Ww/Ww pairing antiparallel cis XIX -A10-B23 : A-U Ww/Ww pairing antiparallel cis XX -A11-B24 : G-C Ww/Ww pairing antiparallel cis XIX -A12-B25 : A-U Ww/Ww pairing antiparallel cis XX -A13-B26 : A-U Ww/Ww pairing antiparallel cis XX -Residue conformations ------------------------------------------- -A1 : G C2p_endo anti -A2 : A C2p_endo anti -A3 : G C2p_endo anti -A4 : A C2p_endo anti -A5 : G C2p_endo anti -A6 : G C2p_endo anti -A7 : A O4p_endo anti -A8 : A C2p_endo anti -A9 : G C2p_endo anti -A10 : A C2p_endo anti -A11 : G C2p_endo anti -A12 : A C2p_endo anti -A13 : A C2p_endo anti -B26 : U C3p_endo anti -B25 : U C3p_endo anti -B24 : C C3p_endo anti -B23 : U C3p_endo anti -B22 : C C3p_endo anti -B21 : U C3p_endo anti -B20 : U C3p_endo anti -B19 : C C3p_endo anti -B18 : C C3p_endo anti -B17 : U C3p_endo anti -B16 : C C3p_endo anti -B15 : U C3p_endo anti -B14 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A12-A13 : adjacent_5p upward -B14-B15 : adjacent_3p downward -B15-B16 : adjacent_3p downward -B16-B17 : adjacent_3p downward -B17-B18 : adjacent_3p downward -B18-B19 : adjacent_3p downward -B19-B20 : adjacent_3p downward -B20-B21 : adjacent_3p downward -B21-B22 : adjacent_3p downward -B22-B23 : adjacent_3p downward -B23-B24 : adjacent_3p downward -B24-B25 : adjacent_3p downward -B25-B26 : adjacent_3p downward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 24 -Number of adjacent stackings = 24 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-B14 : G-C Ww/Ww pairing antiparallel cis XIX -A2-B15 : A-U Ww/Ww pairing antiparallel cis XX -A3-B16 : G-C Ww/Ww pairing antiparallel cis XIX -A4-B17 : A-U Ww/Ww pairing antiparallel cis XX -A5-B18 : G-C Ww/Ww pairing antiparallel cis XIX -A6-B19 : G-C Ww/Ww pairing antiparallel cis XIX -A7-B20 : A-U Ww/Ww pairing antiparallel cis XX -A8-B21 : A-U Ww/Ww pairing antiparallel cis XX -A9-B22 : G-C Ww/Ww pairing antiparallel cis XIX -A10-B23 : A-U Ww/Ww pairing antiparallel cis XX -A11-B24 : G-C Ww/Ww pairing antiparallel cis XIX -A12-B25 : A-U Ww/Ww pairing antiparallel cis XX -A13-B26 : A-U Ww/Ww pairing antiparallel cis XX -Residue conformations ------------------------------------------- -A1 : G C2p_endo anti -A2 : A C2p_endo anti -A3 : G C2p_endo anti -A4 : A C2p_endo anti -A5 : G C2p_endo anti -A6 : G C2p_endo anti -A7 : A O4p_endo anti -A8 : A C2p_endo anti -A9 : G C3p_exo syn -A10 : A C2p_endo syn -A11 : G C3p_exo anti -A12 : A C2p_endo syn -A13 : A C3p_exo anti -B26 : U C3p_endo anti -B25 : U C3p_endo anti -B24 : C C3p_endo anti -B23 : U C3p_endo anti -B22 : C C3p_endo anti -B21 : U C3p_endo anti -B20 : U C3p_endo anti -B19 : C C3p_endo anti -B18 : C C3p_endo anti -B17 : U C3p_endo anti -B16 : C C3p_endo anti -B15 : U C3p_endo anti -B14 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A12-A13 : adjacent_5p upward -B15-B16 : adjacent_3p downward -B16-B17 : adjacent_3p downward -B17-B18 : adjacent_3p downward -B18-B19 : adjacent_3p downward -B19-B20 : adjacent_3p downward -B20-B21 : adjacent_3p downward -B22-B23 : adjacent_3p downward -B23-B24 : adjacent_3p downward -B24-B25 : adjacent_3p downward -B25-B26 : adjacent_3p downward -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 21 -Number of adjacent stackings = 21 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ -A1-B14 : G-C Ww/Ww pairing antiparallel cis XIX -A2-B15 : A-U Ww/Ww pairing antiparallel cis XX -A3-B16 : G-C Ww/Ww pairing antiparallel cis XIX -A4-B17 : A-U Ww/Ww pairing antiparallel cis XX -A5-B18 : G-C Ww/Ww pairing antiparallel cis XIX -A6-B19 : G-C Ww/Ww pairing antiparallel cis XIX -A7-B20 : A-U Ww/Ww pairing antiparallel cis XX -A8-B21 : A-U Ww/Ww pairing antiparallel cis XX -A9-B22 : G-C Ww/Ww pairing antiparallel cis XIX -A10-B23 : A-U Ww/Ww pairing antiparallel cis XX -A11-B24 : G-C Ww/Ww pairing antiparallel cis XIX -A12-B25 : A-U Ww/Ww pairing antiparallel cis XX -A13-B26 : A-U Ww/Ww pairing antiparallel cis XX -Residue conformations ------------------------------------------- -A1 : G C2p_endo anti -A2 : A C2p_endo anti -A3 : G C2p_endo anti -A4 : A C2p_endo syn -A5 : G C2p_endo anti -A6 : G C2p_endo anti -A7 : A O4p_endo anti -A8 : A C2p_endo anti -A9 : G C3p_exo anti -A10 : A C2p_endo syn -A11 : G C2p_endo anti -A12 : A C1p_exo anti -A13 : A C2p_endo anti -B26 : U C3p_endo anti -B25 : U C3p_endo anti -B24 : C C3p_endo anti -B23 : U C3p_endo anti -B22 : C C2p_exo anti -B21 : U C3p_endo anti -B20 : U C3p_endo anti -B19 : C C3p_endo anti -B18 : C C3p_endo anti -B17 : U C3p_endo anti -B16 : C C3p_endo anti -B15 : U C3p_endo anti -B14 : C C3p_endo anti -Adjacent stackings ---------------------------------------------- -A1-A2 : adjacent_5p upward -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A12-A13 : adjacent_5p upward -B14-B15 : adjacent_3p downward -B15-B16 : adjacent_3p downward -B16-B17 : adjacent_3p downward -B17-B18 : adjacent_3p downward -B18-B19 : adjacent_3p downward -B19-B20 : adjacent_3p downward -B20-B21 : adjacent_3p downward -B23-B24 : adjacent_3p downward -B25-B26 : adjacent_3p downward -Non-Adjacent stackings ------------------------------------------ -A4-B16 : outward -Number of stackings = 20 -Number of adjacent stackings = 19 -Number of non adjacent stackings = 1 -Base-pairs ------------------------------------------------------ -A2-B15 : A-U Ww/Ww pairing antiparallel cis XX -A3-B16 : G-C Ww/Ww pairing antiparallel cis XIX -A4-B17 : A-U Ww/Ww pairing antiparallel cis XX -A5-B18 : G-C Ww/Ww pairing antiparallel cis XIX -A6-B19 : G-C Ww/Ww pairing antiparallel cis -A7-B20 : A-U Ww/Ww pairing antiparallel cis XX -A8-B21 : A-U Ww/Ww pairing antiparallel cis XX -A9-B22 : G-C Wh/Wh pairing antiparallel cis one_hbond -A10-B22 : A-C Bs/Ws pairing antiparallel cis one_hbond -A10-B23 : A-U Ww/Ww pairing antiparallel cis XX -A11-B24 : G-C Ww/Ww pairing antiparallel cis XIX -A12-B25 : A-U Ww/Ww pairing antiparallel cis XX -A13-B26 : A-U Ww/Ww pairing antiparallel cis XX diff --git a/MCdata/1efw_MC b/MCdata/1efw_MC deleted file mode 100644 index aea26de7d8510ec0b9c2008cef0efdabce95c860..0000000000000000000000000000000000000000 --- a/MCdata/1efw_MC +++ /dev/null @@ -1,1567 +0,0 @@ -Residue conformations ------------------------------------------- -C1 : G C3p_endo anti -C2 : G C3p_endo anti -C3 : A C3p_endo anti -C4 : G C3p_endo anti -C5 : C C3p_endo anti -C6 : G C3p_endo anti -C7 : G C1p_exo anti -C8 : 4SU -C9 : A C2p_endo anti -C10 : G C3p_endo anti -C11 : U C3p_endo anti -C12 : U C3p_endo anti -C13 : C C3p_endo anti -C14 : A C3p_endo anti -C15 : G C3p_endo anti -C16 : H2U -C17 : C C3p_exo syn -C18 : G C2p_endo anti -C19 : G C2p_endo anti -C20 : H2U -C20.A : H2U -C21 : A C3p_endo anti -C22 : G C3p_endo anti -C23 : A C3p_endo anti -C24 : A C3p_endo anti -C25 : U C3p_endo anti -C26 : A C3p_endo anti -C27 : C C3p_endo anti -C28 : C C3p_endo anti -C29 : U C3p_endo anti -C30 : G C3p_endo anti -C31 : C C3p_endo anti -C32 : C C3p_endo anti -C33 : U C2p_endo anti -C34 : QUO -C35 : U C3p_endo anti -C36 : C C3p_endo anti -C37 : 2MA -C38 : C C3p_endo anti -C39 : G C3p_endo anti -C40 : C C3p_endo anti -C41 : A C3p_endo anti -C42 : G C3p_endo anti -C43 : G C3p_endo anti -C44 : G C3p_endo anti -C45 : G C3p_endo anti -C46 : G7M -C47 : U C3p_endo anti -C48 : C C3p_endo anti -C49 : G C3p_endo anti -C50 : C C3p_endo anti -C51 : G C3p_endo anti -C52 : G C3p_endo anti -C53 : G C3p_endo anti -C54 : 5MU -C55 : PSU -C56 : C C3p_endo anti -C57 : G C3p_endo anti -C58 : A C2p_endo syn -C59 : G C3p_endo anti -C60 : U C2p_endo anti -C61 : C C3p_endo anti -C62 : C C3p_endo anti -C63 : C C3p_endo anti -C64 : G C3p_endo anti -C65 : PSU -C66 : C C3p_endo anti -C67 : C C3p_endo anti -C68 : G C3p_endo anti -C69 : U C3p_endo anti -C70 : U C3p_endo anti -C71 : C C3p_endo anti -C72 : C C3p_endo anti -D1 : G C3p_endo anti -D2 : G C3p_endo anti -D3 : A C3p_endo anti -D4 : G C3p_endo anti -D5 : C C3p_endo anti -D6 : G C3p_endo anti -D7 : G C2p_endo anti -D8 : 4SU -D9 : A C3p_exo anti -D10 : G C3p_endo anti -D11 : U C3p_endo anti -D12 : U C3p_endo anti -D13 : C C3p_endo anti -D14 : A C3p_endo anti -D15 : G C3p_endo anti -D16 : H2U -D17 : C C2p_endo syn -D18 : G C2p_endo anti -D19 : G C2p_endo syn -D20 : H2U -D20.A : H2U -D21 : A C3p_endo anti -D22 : G C3p_endo anti -D23 : A C3p_endo anti -D24 : A C3p_endo anti -D25 : U C3p_endo anti -D26 : A C3p_endo anti -D27 : C C3p_endo anti -D28 : C C3p_endo anti -D29 : U C3p_endo anti -D30 : G C3p_endo anti -D31 : C C3p_endo anti -D32 : C C3p_endo anti -D33 : U C2p_endo anti -D34 : QUO -D35 : U C3p_endo anti -D36 : C C3p_endo anti -D37 : 2MA -D38 : C C3p_endo anti -D39 : G C3p_endo anti -D40 : C C3p_endo anti -D41 : A C3p_endo anti -D42 : G C3p_endo anti -D43 : G C3p_endo anti -D44 : G C3p_endo anti -D45 : G C3p_endo anti -D46 : G7M -D47 : U C3p_exo syn -D48 : C C3p_endo anti -D49 : G C3p_endo anti -D50 : C C3p_endo anti -D51 : G C3p_endo anti -D52 : G C3p_endo anti -D53 : G C3p_endo anti -D54 : 5MU -D55 : PSU -D56 : C C3p_endo anti -D57 : G C3p_endo anti -D58 : A C2p_endo syn -D59 : G C3p_endo anti -D60 : U C2p_endo anti -D61 : C C3p_endo anti -D62 : C C3p_endo anti -D63 : C C3p_endo anti -D64 : G C3p_endo anti -D65 : PSU -D66 : C C3p_endo anti -D67 : C C3p_endo anti -D68 : G C4p_exo anti -D69 : U C3p_endo anti -D70 : U C3p_endo anti -D71 : C C3p_endo anti -D72 : C C3p_endo anti -A1 : MET -A2 : ARG -A3 : ARG -A4 : THR -A5 : HIS -A6 : TYR -A7 : ALA -A8 : GLY -A9 : SER -A10 : LEU -A11 : ARG -A12 : GLU -A13 : THR -A14 : HIS -A15 : VAL -A16 : GLY -A17 : GLU -A18 : GLU -A19 : VAL -A20 : VAL -A21 : LEU -A22 : GLU -A23 : GLY -A24 : TRP -A25 : VAL -A26 : ASN -A27 : ARG -A28 : ARG -A29 : ARG -A30 : ASP -A31 : LEU -A32 : GLY -A33 : GLY -A34 : LEU -A35 : ILE -A36 : PHE -A37 : LEU -A38 : ASP -A39 : LEU -A40 : ARG -A41 : ASP -A42 : ARG -A43 : GLU -A44 : GLY -A45 : LEU -A46 : VAL -A47 : GLN -A48 : LEU -A49 : VAL -A50 : ALA -A51 : HIS -A52 : PRO -A53 : ALA -A54 : SER -A55 : PRO -A56 : ALA -A57 : TYR -A58 : ALA -A59 : THR -A60 : ALA -A61 : GLU -A62 : ARG -A63 : VAL -A64 : ARG -A65 : PRO -A66 : GLU -A67 : TRP -A68 : VAL -A69 : VAL -A70 : ARG -A71 : ALA -A72 : LYS -A73 : GLY -A74 : LEU -A75 : VAL -A76 : ARG -A77 : LEU -A78 : ARG -A79 : PRO -A80 : GLU -A81 : PRO -A82 : ASN -A83 : PRO -A84 : ARG -A85 : LEU -A86 : ALA -A87 : THR -A88 : GLY -A89 : ARG -A90 : VAL -A91 : GLU -A92 : VAL -A93 : GLU -A94 : LEU -A95 : SER -A96 : ALA -A97 : LEU -A98 : GLU -A99 : VAL -A100 : LEU -A101 : ALA -A102 : GLU -A103 : ALA -A104 : LYS -A105 : THR -A106 : PRO -A107 : PRO -A108 : PHE -A109 : PRO -A110 : VAL -A111 : ASP -A112 : ALA -A113 : GLY -A114 : TRP -A115 : ARG -A116 : GLY -A117 : GLU -A118 : GLU -A119 : GLU -A120 : LYS -A121 : GLU -A122 : ALA -A123 : SER -A124 : GLU -A125 : GLU -A126 : LEU -A127 : ARG -A128 : LEU -A129 : LYS -A130 : TYR -A131 : ARG -A132 : TYR -A133 : LEU -A134 : ASP -A135 : LEU -A136 : ARG -A137 : ARG -A138 : ARG -A139 : ARG -A140 : MET -A141 : GLN -A142 : GLU -A143 : ASN -A144 : LEU -A145 : ARG -A146 : LEU -A147 : ARG -A148 : HIS -A149 : ARG -A150 : VAL -A151 : ILE -A152 : LYS -A153 : ALA -A154 : ILE -A155 : TRP -A156 : ASP -A157 : PHE -A158 : LEU -A159 : ASP -A160 : ARG -A161 : GLU -A162 : GLY -A163 : PHE -A164 : VAL -A165 : GLN -A166 : VAL -A167 : GLU -A168 : THR -A169 : PRO -A170 : PHE -A171 : LEU -A172 : THR -A173 : LYS -A174 : SER -A175 : THR -A176 : PRO -A177 : GLU -A178 : GLY -A179 : ALA -A180 : ARG -A181 : ASP -A182 : PHE -A183 : LEU -A184 : VAL -A185 : PRO -A186 : TYR -A187 : ARG -A188 : HIS -A189 : GLU -A190 : PRO -A191 : GLY -A192 : LEU -A193 : PHE -A194 : TYR -A195 : ALA -A196 : LEU -A197 : PRO -A198 : GLN -A199 : SER -A200 : PRO -A201 : GLN -A202 : LEU -A203 : PHE -A204 : LYS -A205 : GLN -A206 : MET -A207 : LEU -A208 : MET -A209 : VAL -A210 : ALA -A211 : GLY -A212 : LEU -A213 : ASP -A214 : ARG -A215 : TYR -A216 : PHE -A217 : GLN -A218 : ILE -A219 : ALA -A220 : ARG -A221 : CYS -A222 : PHE -A223 : ARG -A224 : ASP -A225 : GLU -A226 : ASP -A227 : LEU -A228 : ARG -A229 : ALA -A230 : ASP -A231 : ARG -A232 : GLN -A233 : PRO -A234 : ASP -A235 : PHE -A236 : THR -A237 : GLN -A238 : LEU -A239 : ASP -A240 : LEU -A241 : GLU -A242 : MET -A243 : SER -A244 : PHE -A245 : VAL -A246 : GLU -A247 : VAL -A248 : GLU -A249 : ASP -A250 : VAL -A251 : LEU -A252 : GLU -A253 : LEU -A254 : ASN -A255 : GLU -A256 : ARG -A257 : LEU -A258 : MET -A259 : ALA -A260 : HIS -A261 : VAL -A262 : PHE -A263 : ARG -A264 : GLU -A265 : ALA -A266 : LEU -A267 : GLY -A268 : VAL -A269 : GLU -A270 : LEU -A271 : PRO -A272 : LEU -A273 : PRO -A274 : PHE -A275 : PRO -A276 : ARG -A277 : LEU -A278 : SER -A279 : TYR -A280 : GLU -A281 : GLU -A282 : ALA -A283 : MET -A284 : GLU -A285 : ARG -A286 : TYR -A287 : GLY -A288 : SER -A289 : ASP -A290 : LYS -A291 : PRO -A292 : ASP -A293 : LEU -A294 : ARG -A295 : PHE -A296 : GLY -A297 : LEU -A298 : GLU -A299 : LEU -A300 : LYS -A301 : GLU -A302 : VAL -A303 : GLY -A304 : PRO -A305 : LEU -A306 : PHE -A307 : ARG -A308 : GLN -A309 : SER -A310 : GLY -A311 : PHE -A312 : ARG -A313 : VAL -A314 : PHE -A315 : GLN -A316 : GLU -A317 : ALA -A318 : GLU -A319 : SER -A320 : VAL -A321 : LYS -A322 : ALA -A323 : LEU -A324 : ALA -A325 : LEU -A326 : PRO -A327 : LYS -A328 : ALA -A329 : LEU -A330 : SER -A331 : ARG -A332 : LYS -A333 : GLU -A334 : VAL -A335 : ALA -A336 : GLU -A337 : LEU -A338 : GLU -A339 : GLU -A340 : VAL -A341 : ALA -A342 : LYS -A343 : ARG -A344 : HIS -A345 : LYS -A346 : ALA -A347 : GLN -A348 : GLY -A349 : LEU -A350 : ALA -A351 : TRP -A352 : ALA -A353 : ARG -A354 : VAL -A355 : GLU -A356 : GLU -A357 : GLY -A358 : GLY -A359 : PHE -A360 : SER -A361 : GLY -A362 : GLY -A363 : VAL -A364 : ALA -A365 : LYS -A366 : PHE -A367 : LEU -A368 : GLU -A369 : PRO -A370 : VAL -A371 : ARG -A372 : GLU -A373 : ALA -A374 : LEU -A375 : LEU -A376 : GLN -A377 : ALA -A378 : THR -A379 : GLU -A380 : ALA -A381 : ARG -A382 : PRO -A383 : GLY -A384 : ASP -A385 : THR -A386 : LEU -A387 : LEU -A388 : PHE -A389 : VAL -A390 : ALA -A391 : GLY -A392 : PRO -A393 : ARG -A394 : LYS -A395 : VAL -A396 : ALA -A397 : ALA -A398 : THR -A399 : ALA -A400 : LEU -A401 : GLY -A402 : ALA -A403 : VAL -A404 : ARG -A405 : LEU -A406 : ARG -A407 : ALA -A408 : ALA -A409 : ASP -A410 : LEU -A411 : LEU -A412 : GLY -A413 : LEU -A414 : LYS -A415 : ARG -A416 : GLU -A417 : GLY -A418 : PHE -A419 : ARG -A420 : PHE -A421 : LEU -A422 : TRP -A423 : VAL -A424 : VAL -A425 : ASP -A426 : PHE -A427 : PRO -A428 : LEU -A429 : LEU -A430 : GLU -A431 : TRP -A432 : ASP -A433 : GLU -A434 : GLU -A435 : GLU -A436 : GLU -A437 : ALA -A438 : TRP -A439 : THR -A440 : TYR -A441 : MET -A442 : HIS -A443 : HIS -A444 : PRO -A445 : PHE -A446 : THR -A447 : SER -A448 : PRO -A449 : HIS -A450 : PRO -A451 : GLU -A452 : ASP -A453 : LEU -A454 : PRO -A455 : LEU -A456 : LEU -A457 : GLU -A458 : LYS -A459 : ASP -A460 : PRO -A461 : GLY -A462 : ARG -A463 : VAL -A464 : ARG -A465 : ALA -A466 : LEU -A467 : ALA -A468 : TYR -A469 : ASP -A470 : LEU -A471 : VAL -A472 : LEU -A473 : ASN -A474 : GLY -A475 : VAL -A476 : GLU -A477 : VAL -A478 : GLY -A479 : GLY -A480 : GLY -A481 : SER -A482 : ILE -A483 : ARG -A484 : ILE -A485 : HIS -A486 : ASP -A487 : PRO -A488 : ARG -A489 : LEU -A490 : GLN -A491 : ALA -A492 : ARG -A493 : VAL -A494 : PHE -A495 : ARG -A496 : LEU -A497 : LEU -A498 : GLY -A499 : ILE -A500 : GLY -A501 : GLU -A502 : GLU -A503 : GLU -A504 : GLN -A505 : ARG -A506 : GLU -A507 : LYS -A508 : PHE -A509 : GLY -A510 : PHE -A511 : PHE -A512 : LEU -A513 : GLU -A514 : ALA -A515 : LEU -A516 : GLU -A517 : TYR -A518 : GLY -A519 : ALA -A520 : PRO -A521 : PRO -A522 : HIS -A523 : GLY -A524 : GLY -A525 : ILE -A526 : ALA -A527 : TRP -A528 : GLY -A529 : LEU -A530 : ASP -A531 : ARG -A532 : LEU -A533 : LEU -A534 : ALA -A535 : LEU -A536 : MET -A537 : THR -A538 : GLY -A539 : SER -A540 : PRO -A541 : SER -A542 : ILE -A543 : ARG -A544 : GLU -A545 : VAL -A546 : ILE -A547 : ALA -A548 : PHE -A549 : PRO -A550 : LYS -A551 : ASN -A552 : LYS -A553 : GLU -A554 : GLY -A555 : LYS -A556 : ASP -A557 : PRO -A558 : LEU -A559 : THR -A560 : GLY -A561 : ALA -A562 : PRO -A563 : SER -A564 : PRO -A565 : VAL -A566 : PRO -A567 : GLU -A568 : GLU -A569 : GLN -A570 : LEU -A571 : ARG -A572 : GLU -A573 : LEU -A574 : GLY -A575 : LEU -A576 : MET -A577 : VAL -A578 : VAL -A579 : ARG -A580 : PRO -B1 : MET -B2 : ARG -B3 : ARG -B4 : THR -B5 : HIS -B6 : TYR -B7 : ALA -B8 : GLY -B9 : SER -B10 : LEU -B11 : ARG -B12 : GLU -B13 : THR -B14 : HIS -B15 : VAL -B16 : GLY -B17 : GLU -B18 : GLU -B19 : VAL -B20 : VAL -B21 : LEU -B22 : GLU -B23 : GLY -B24 : TRP -B25 : VAL -B26 : ASN -B27 : ARG -B28 : ARG -B29 : ARG -B30 : ASP -B31 : LEU -B32 : GLY -B33 : GLY -B34 : LEU -B35 : ILE -B36 : PHE -B37 : LEU -B38 : ASP -B39 : LEU -B40 : ARG -B41 : ASP -B42 : ARG -B43 : GLU -B44 : GLY -B45 : LEU -B46 : VAL -B47 : GLN -B48 : LEU -B49 : VAL -B50 : ALA -B51 : HIS -B52 : PRO -B53 : ALA -B54 : SER -B55 : PRO -B56 : ALA -B57 : TYR -B58 : ALA -B59 : THR -B60 : ALA -B61 : GLU -B62 : ARG -B63 : VAL -B64 : ARG -B65 : PRO -B66 : GLU -B67 : TRP -B68 : VAL -B69 : VAL -B70 : ARG -B71 : ALA -B72 : LYS -B73 : GLY -B74 : LEU -B75 : VAL -B76 : ARG -B77 : LEU -B78 : ARG -B79 : PRO -B80 : GLU -B81 : PRO -B82 : ASN -B83 : PRO -B84 : ARG -B85 : LEU -B86 : ALA -B87 : THR -B88 : GLY -B89 : ARG -B90 : VAL -B91 : GLU -B92 : VAL -B93 : GLU -B94 : LEU -B95 : SER -B96 : ALA -B97 : LEU -B98 : GLU -B99 : VAL -B100 : LEU -B101 : ALA -B102 : GLU -B103 : ALA -B104 : LYS -B105 : THR -B106 : PRO -B107 : PRO -B108 : PHE -B109 : PRO -B110 : VAL -B111 : ASP -B112 : ALA -B113 : GLY -B114 : TRP -B115 : ARG -B116 : GLY -B117 : GLU -B118 : GLU -B119 : GLU -B120 : LYS -B121 : GLU -B122 : ALA -B123 : SER -B124 : GLU -B125 : GLU -B126 : LEU -B127 : ARG -B128 : LEU -B129 : LYS -B130 : TYR -B131 : ARG -B132 : TYR -B133 : LEU -B134 : ASP -B135 : LEU -B136 : ARG -B137 : ARG -B138 : ARG -B139 : ARG -B140 : MET -B141 : GLN -B142 : GLU -B143 : ASN -B144 : LEU -B145 : ARG -B146 : LEU -B147 : ARG -B148 : HIS -B149 : ARG -B150 : VAL -B151 : ILE -B152 : LYS -B153 : ALA -B154 : ILE -B155 : TRP -B156 : ASP -B157 : PHE -B158 : LEU -B159 : ASP -B160 : ARG -B161 : GLU -B162 : GLY -B163 : PHE -B164 : VAL -B165 : GLN -B166 : VAL -B167 : GLU -B168 : THR -B169 : PRO -B170 : PHE -B171 : LEU -B172 : THR -B173 : LYS -B174 : SER -B175 : THR -B176 : PRO -B177 : GLU -B178 : GLY -B179 : ALA -B180 : ARG -B181 : ASP -B182 : PHE -B183 : LEU -B184 : VAL -B185 : PRO -B186 : TYR -B187 : ARG -B188 : HIS -B189 : GLU -B190 : PRO -B191 : GLY -B192 : LEU -B193 : PHE -B194 : TYR -B195 : ALA -B196 : LEU -B197 : PRO -B198 : GLN -B199 : SER -B200 : PRO -B201 : GLN -B202 : LEU -B203 : PHE -B204 : LYS -B205 : GLN -B206 : MET -B207 : LEU -B208 : MET -B209 : VAL -B210 : ALA -B211 : GLY -B212 : LEU -B213 : ASP -B214 : ARG -B215 : TYR -B216 : PHE -B217 : GLN -B218 : ILE -B219 : ALA -B220 : ARG -B221 : CYS -B222 : PHE -B223 : ARG -B224 : ASP -B225 : GLU -B226 : ASP -B227 : LEU -B228 : ARG -B229 : ALA -B230 : ASP -B231 : ARG -B232 : GLN -B233 : PRO -B234 : ASP -B235 : PHE -B236 : THR -B237 : GLN -B238 : LEU -B239 : ASP -B240 : LEU -B241 : GLU -B242 : MET -B243 : SER -B244 : PHE -B245 : VAL -B246 : GLU -B247 : VAL -B248 : GLU -B249 : ASP -B250 : VAL -B251 : LEU -B252 : GLU -B253 : LEU -B254 : ASN -B255 : GLU -B256 : ARG -B257 : LEU -B258 : MET -B259 : ALA -B260 : HIS -B261 : VAL -B262 : PHE -B263 : ARG -B264 : GLU -B265 : ALA -B266 : LEU -B267 : GLY -B268 : VAL -B269 : GLU -B270 : LEU -B271 : PRO -B272 : LEU -B273 : PRO -B274 : PHE -B275 : PRO -B276 : ARG -B277 : LEU -B278 : SER -B279 : TYR -B280 : GLU -B281 : GLU -B282 : ALA -B283 : MET -B284 : GLU -B285 : ARG -B286 : TYR -B287 : GLY -B288 : SER -B289 : ASP -B290 : LYS -B291 : PRO -B292 : ASP -B293 : LEU -B294 : ARG -B295 : PHE -B296 : GLY -B297 : LEU -B298 : GLU -B299 : LEU -B300 : LYS -B301 : GLU -B302 : VAL -B303 : GLY -B304 : PRO -B305 : LEU -B306 : PHE -B307 : ARG -B308 : GLN -B309 : SER -B310 : GLY -B311 : PHE -B312 : ARG -B313 : VAL -B314 : PHE -B315 : GLN -B316 : GLU -B317 : ALA -B318 : GLU -B319 : SER -B320 : VAL -B321 : LYS -B322 : ALA -B323 : LEU -B324 : ALA -B325 : LEU -B326 : PRO -B327 : LYS -B328 : ALA -B329 : LEU -B330 : SER -B331 : ARG -B332 : LYS -B333 : GLU -B334 : VAL -B335 : ALA -B336 : GLU -B337 : LEU -B338 : GLU -B339 : GLU -B340 : VAL -B341 : ALA -B342 : LYS -B343 : ARG -B344 : HIS -B345 : LYS -B346 : ALA -B347 : GLN -B348 : GLY -B349 : LEU -B350 : ALA -B351 : TRP -B352 : ALA -B353 : ARG -B354 : VAL -B355 : GLU -B356 : GLU -B357 : GLY -B358 : GLY -B359 : PHE -B360 : SER -B361 : GLY -B362 : GLY -B363 : VAL -B364 : ALA -B365 : LYS -B366 : PHE -B367 : LEU -B368 : GLU -B369 : PRO -B370 : VAL -B371 : ARG -B372 : GLU -B373 : ALA -B374 : LEU -B375 : LEU -B376 : GLN -B377 : ALA -B378 : THR -B379 : GLU -B380 : ALA -B381 : ARG -B382 : PRO -B383 : GLY -B384 : ASP -B385 : THR -B386 : LEU -B387 : LEU -B388 : PHE -B389 : VAL -B390 : ALA -B391 : GLY -B392 : PRO -B393 : ARG -B394 : LYS -B395 : VAL -B396 : ALA -B397 : ALA -B398 : THR -B399 : ALA -B400 : LEU -B401 : GLY -B402 : ALA -B403 : VAL -B404 : ARG -B405 : LEU -B406 : ARG -B407 : ALA -B408 : ALA -B409 : ASP -B410 : LEU -B411 : LEU -B412 : GLY -B413 : LEU -B414 : LYS -B415 : ARG -B416 : GLU -B417 : GLY -B418 : PHE -B419 : ARG -B420 : PHE -B421 : LEU -B422 : TRP -B423 : VAL -B424 : VAL -B425 : ASP -B426 : PHE -B427 : PRO -B428 : LEU -B429 : LEU -B430 : GLU -B431 : TRP -B432 : ASP -B433 : GLU -B434 : GLU -B435 : GLU -B436 : GLU -B437 : ALA -B438 : TRP -B439 : THR -B440 : TYR -B441 : MET -B442 : HIS -B443 : HIS -B444 : PRO -B445 : PHE -B446 : THR -B447 : SER -B448 : PRO -B449 : HIS -B450 : PRO -B451 : GLU -B452 : ASP -B453 : LEU -B454 : PRO -B455 : LEU -B456 : LEU -B457 : GLU -B458 : LYS -B459 : ASP -B460 : PRO -B461 : GLY -B462 : ARG -B463 : VAL -B464 : ARG -B465 : ALA -B466 : LEU -B467 : ALA -B468 : TYR -B469 : ASP -B470 : LEU -B471 : VAL -B472 : LEU -B473 : ASN -B474 : GLY -B475 : VAL -B476 : GLU -B477 : VAL -B478 : GLY -B479 : GLY -B480 : GLY -B481 : SER -B482 : ILE -B483 : ARG -B484 : ILE -B485 : HIS -B486 : ASP -B487 : PRO -B488 : ARG -B489 : LEU -B490 : GLN -B491 : ALA -B492 : ARG -B493 : VAL -B494 : PHE -B495 : ARG -B496 : LEU -B497 : LEU -B498 : GLY -B499 : ILE -B500 : GLY -B501 : GLU -B502 : GLU -B503 : GLU -B504 : GLN -B505 : ARG -B506 : GLU -B507 : LYS -B508 : PHE -B509 : GLY -B510 : PHE -B511 : PHE -B512 : LEU -B513 : GLU -B514 : ALA -B515 : LEU -B516 : GLU -B517 : TYR -B518 : GLY -B519 : ALA -B520 : PRO -B521 : PRO -B522 : HIS -B523 : GLY -B524 : GLY -B525 : ILE -B526 : ALA -B527 : TRP -B528 : GLY -B529 : LEU -B530 : ASP -B531 : ARG -B532 : LEU -B533 : LEU -B534 : ALA -B535 : LEU -B536 : MET -B537 : THR -B538 : GLY -B539 : SER -B540 : PRO -B541 : SER -B542 : ILE -B543 : ARG -B544 : GLU -B545 : VAL -B546 : ILE -B547 : ALA -B548 : PHE -B549 : PRO -B550 : LYS -B551 : ASN -B552 : LYS -B553 : GLU -B554 : GLY -B555 : LYS -B556 : ASP -B557 : PRO -B558 : LEU -B559 : THR -B560 : GLY -B561 : ALA -B562 : PRO -B563 : SER -B564 : PRO -B565 : VAL -B566 : PRO -B567 : GLU -B568 : GLU -B569 : GLN -B570 : LEU -B571 : ARG -B572 : GLU -B573 : LEU -B574 : GLY -B575 : LEU -B576 : MET -B577 : VAL -B578 : VAL -B579 : ARG -B580 : PRO -C2011 : HOH -C2020 : HOH -C2033 : HOH -C2034 : HOH -C2038 : HOH -C2044 : HOH -C2046 : HOH -C2049 : HOH -C2060 : HOH -C2069 : HOH -C2076 : HOH -C2078 : HOH -D2005 : HOH -D2008 : HOH -D2021 : HOH -D2027 : HOH -D2047 : HOH -D2051 : HOH -D2067 : HOH -D2080 : HOH -D2088 : HOH -D2091 : HOH -A2003 : HOH -A2004 : HOH -A2010 : HOH -A2012 : HOH -A2013 : HOH -A2014 : HOH -A2015 : HOH -A2016 : HOH -A2017 : HOH -A2018 : HOH -A2019 : HOH -A2022 : HOH -A2024 : HOH -A2025 : HOH -A2026 : HOH -A2031 : HOH -A2032 : HOH -A2035 : HOH -A2036 : HOH -A2040 : HOH -A2041 : HOH -A2042 : HOH -A2048 : HOH -A2052 : HOH -A2054 : HOH -A2057 : HOH -A2058 : HOH -A2061 : HOH -A2062 : HOH -A2063 : HOH -A2064 : HOH -A2065 : HOH -A2072 : HOH -A2073 : HOH -A2074 : HOH -A2075 : HOH -A2079 : HOH -A2082 : HOH -A2083 : HOH -A2087 : HOH -A2089 : HOH -A2093 : HOH -A2096 : HOH -B2001 : HOH -B2002 : HOH -B2006 : HOH -B2007 : HOH -B2009 : HOH -B2023 : HOH -B2028 : HOH -B2029 : HOH -B2030 : HOH -B2037 : HOH -B2039 : HOH -B2043 : HOH -B2045 : HOH -B2050 : HOH -B2053 : HOH -B2055 : HOH -B2056 : HOH -B2059 : HOH -B2066 : HOH -B2068 : HOH -B2070 : HOH -B2071 : HOH -B2077 : HOH -B2081 : HOH -B2084 : HOH -B2085 : HOH -B2086 : HOH -B2090 : HOH -B2092 : HOH -B2094 : HOH -B2095 : HOH -Adjacent stackings ---------------------------------------------- -C1-C2 : adjacent_5p upward -C2-C3 : adjacent_5p upward -C3-C4 : adjacent_5p upward -C4-C5 : adjacent_5p upward -C5-C6 : adjacent_5p upward -C6-C7 : adjacent_5p upward -C10-C11 : adjacent_5p upward -C12-C13 : adjacent_5p upward -C14-C15 : adjacent_5p upward -C22-C23 : adjacent_5p upward -C23-C24 : adjacent_5p upward -C24-C25 : adjacent_5p upward -C25-C26 : adjacent_5p upward -C26-C27 : adjacent_5p upward -C27-C28 : adjacent_5p upward -C30-C31 : adjacent_5p upward -C31-C32 : adjacent_5p upward -C35-C36 : adjacent_5p upward -C38-C39 : adjacent_5p upward -C39-C40 : adjacent_5p upward -C41-C42 : adjacent_5p upward -C42-C43 : adjacent_5p upward -C43-C44 : adjacent_5p upward -C44-C45 : adjacent_5p upward -C49-C50 : adjacent_5p upward -C51-C52 : adjacent_5p upward -C52-C53 : adjacent_5p upward -C56-C57 : adjacent_5p upward -C59-C60 : adjacent_5p upward -C62-C63 : adjacent_5p upward -C66-C67 : adjacent_5p upward -C68-C69 : adjacent_5p upward -C71-C72 : adjacent_5p upward -D1-D2 : adjacent_5p upward -D2-D3 : adjacent_5p upward -D3-D4 : adjacent_5p upward -D4-D5 : adjacent_5p upward -D6-D7 : adjacent_5p upward -D10-D11 : adjacent_5p upward -D11-D12 : adjacent_5p upward -D12-D13 : adjacent_5p upward -D14-D15 : adjacent_5p upward -D22-D23 : adjacent_5p upward -D23-D24 : adjacent_5p upward -D24-D25 : adjacent_5p upward -D25-D26 : adjacent_5p upward -D26-D27 : adjacent_5p upward -D27-D28 : adjacent_5p upward -D30-D31 : adjacent_5p upward -D31-D32 : adjacent_5p upward -D35-D36 : adjacent_5p upward -D38-D39 : adjacent_5p upward -D39-D40 : adjacent_5p upward -D40-D41 : adjacent_5p upward -D41-D42 : adjacent_5p upward -D42-D43 : adjacent_5p upward -D43-D44 : adjacent_5p upward -D44-D45 : adjacent_5p upward -D49-D50 : adjacent_5p upward -D51-D52 : adjacent_5p upward -D52-D53 : adjacent_5p upward -D56-D57 : adjacent_5p upward -D59-D60 : adjacent_5p upward -D62-D63 : adjacent_5p upward -D63-D64 : adjacent_5p upward -D66-D67 : adjacent_5p upward -D68-D69 : adjacent_5p upward -D69-D70 : adjacent_5p upward -D71-D72 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -C6-C68 : outward -C7-C49 : upward -C9-C45 : inward pairing -C14-C22 : outward -C15-C59 : upward -C18-C57 : inward pairing -C18-C58 : outward -C19-C57 : outward -C21-C48 : outward -C30-C41 : outward -C51-C64 : outward -C53-C62 : outward -C58-C61 : upward -D6-D68 : outward -D7-D49 : upward -D9-D45 : inward pairing -D14-D22 : outward -D15-D59 : upward -D18-D57 : inward pairing -D18-D58 : outward -D19-D57 : outward -D21-D48 : outward -D30-D41 : outward -D51-D64 : outward -D58-D61 : upward -Number of stackings = 94 -Number of adjacent stackings = 69 -Number of non adjacent stackings = 25 -Base-pairs ------------------------------------------------------ -C2-C71 : G-C Ws/Ww pairing antiparallel cis one_hbond -C3-C70 : A-U Ww/Ww pairing antiparallel cis XX -C4-C69 : G-U Ww/Ws pairing antiparallel cis XXVIII -C5-C68 : C-G Ww/Ww pairing antiparallel cis 130 -C6-C67 : G-C Ww/Ww pairing antiparallel cis XIX -C7-C66 : G-C Ww/Ww pairing antiparallel cis XIX -C9-C10 : A-G O2'/Hh adjacent_5p pairing -C9-C23 : A-A Hh/Hh pairing parallel trans II -C9-C45 : A-G O2'/Bs inward pairing -C10-C25 : G-U Ww/Ws pairing antiparallel cis XXVIII -C10-C45 : G-G Hh/Bs pairing parallel cis 33 -C11-C24 : U-A Ws/Ww pairing antiparallel cis -C12-C23 : U-A Ww/Ww pairing antiparallel cis XX -C13-C22 : C-G Ww/Ww pairing antiparallel cis one_hbond 130 -C14-C21 : A-A Wh/Ss pairing antiparallel cis one_hbond 40 -C15-C48 : G-C Ww/Ww pairing parallel trans XXII -C18-C57 : G-G O2'/Ww O2'/Bs inward pairing -C19-C56 : G-C Ww/Ww pairing antiparallel cis XIX -C21-C22 : A-G O2'/Hh O2'/C8 adjacent_5p pairing -C26-C44 : A-G Ww/Ww pairing antiparallel cis one_hbond -C27-C43 : C-G Ww/Ww pairing antiparallel cis XIX -C28-C42 : C-G Ww/Ww pairing antiparallel cis XIX -C29-C41 : U-A Ww/Ww pairing antiparallel cis XX -C30-C40 : G-C Ww/Ww pairing antiparallel cis XIX -C31-C39 : C-G Ww/Ww pairing antiparallel cis XIX -C32-C38 : C-C Ww/Wh pairing antiparallel cis one_hbond 137 -C50-C64 : C-G Ww/Ww pairing antiparallel cis XIX -C51-C63 : G-C Ww/Ww pairing antiparallel cis XIX -C52-C62 : G-C Ww/Ww pairing antiparallel cis XIX -C53-C61 : G-C Ww/Ww pairing antiparallel cis XIX -C60-C61 : U-C O2P/Bh adjacent_5p pairing -D1-D72 : G-C Ww/Ws pairing antiparallel cis one_hbond 130 -D2-D71 : G-C Ws/Ww pairing antiparallel cis one_hbond -D3-D70 : A-U Ww/Ws pairing antiparallel cis -D4-D69 : G-U Ww/Ws pairing antiparallel cis XXVIII -D5-D68 : C-G Ww/Ww pairing antiparallel cis XIX -D6-D67 : G-C Ww/Ww pairing antiparallel cis -D7-D66 : G-C Ww/Ww pairing antiparallel cis XIX -D9-D10 : A-G O2'/Hh adjacent_5p pairing -D9-D13 : A-C O2P/Bh pairing -D9-D23 : A-A Hh/Hh pairing parallel trans II -D9-D45 : A-G O2'/Bs inward pairing -D10-D25 : G-U Ww/Ws pairing antiparallel cis XXVIII -D10-D45 : G-G Hh/Sw pairing parallel cis one_hbond 109 -D11-D24 : U-A Ww/Ww pairing antiparallel cis XX -D12-D23 : U-A Ww/Ww pairing antiparallel cis XX -D13-D22 : C-G Ww/Ww pairing antiparallel cis XIX -D14-D21 : A-A Wh/Ss Ww/O2' pairing antiparallel cis one_hbond 40 -D15-D48 : G-C Ww/Ww pairing parallel trans XXII -D18-D57 : G-G O2'/Bs inward pairing -D19-D56 : G-C Ww/Ww pairing antiparallel cis XIX -D21-D22 : A-G O2'/C8 adjacent_5p pairing -D26-D44 : A-G Ww/Ww pairing antiparallel cis VIII -D27-D43 : C-G Ww/Ww pairing antiparallel cis XIX -D28-D42 : C-G Ww/Ww pairing antiparallel cis XIX -D29-D41 : U-A Ww/Ww pairing antiparallel cis XX -D30-D40 : G-C Ww/Ww pairing antiparallel cis XIX -D31-D39 : C-G Ww/Ww pairing antiparallel cis XIX -D32-D38 : C-C Ws/Wh pairing antiparallel cis one_hbond 137 -D50-D64 : C-G Ww/Ww pairing antiparallel cis XIX -D51-D63 : G-C Ww/Ww pairing antiparallel cis XIX -D52-D62 : G-C Ww/Ww pairing antiparallel cis XIX -D53-D61 : G-C Ww/Ww pairing antiparallel cis XIX -D60-D61 : U-C O2P/Bh O2P/Bh adjacent_5p pairing diff --git a/MCdata/1eg0_MC b/MCdata/1eg0_MC deleted file mode 100644 index 61628d28b61bed6530ef6727cbc228233a87b897..0000000000000000000000000000000000000000 --- a/MCdata/1eg0_MC +++ /dev/null @@ -1,1665 +0,0 @@ -Residue conformations ------------------------------------------- -I1 : N -I2 : N -I3 : N -I4 : N -I5 : N -I6 : N -I7 : N -I8 : N -I9 : N -I10 : N -I11 : N -I12 : N -I13 : N -I14 : N -I15 : N -I16 : N -I17 : N -I18 : N -I19 : N -I20 : N -I21 : N -I22 : N -I23 : N -I24 : N -I25 : N -I26 : N -I27 : N -I28 : N -I29 : N -I30 : N -I31 : N -I32 : N -I33 : N -L1 : C unknown unknown -L2 : U unknown unknown -L3 : G unknown unknown -L4 : G unknown unknown -L5 : G unknown unknown -L6 : A unknown unknown -L7 : U unknown unknown -L8 : G unknown unknown -L9 : U unknown unknown -L10 : U unknown unknown -L11 : G unknown unknown -L12 : G unknown unknown -L13 : C unknown unknown -L14 : U unknown unknown -L15 : U unknown unknown -L16 : A unknown unknown -L17 : G unknown unknown -L18 : A unknown unknown -L19 : A unknown unknown -L20 : G unknown unknown -L21 : C unknown unknown -L22 : A unknown unknown -L23 : G unknown unknown -L24 : C unknown unknown -L25 : C unknown unknown -L26 : A unknown unknown -L27 : U unknown unknown -L28 : C unknown unknown -L29 : A unknown unknown -L30 : U unknown unknown -L31 : U unknown unknown -L32 : U unknown unknown -L33 : A unknown unknown -L34 : A unknown unknown -L35 : A unknown unknown -L36 : G unknown unknown -L37 : A unknown unknown -L38 : G unknown unknown -L39 : U unknown unknown -L40 : G unknown unknown -L41 : C unknown unknown -L42 : G unknown unknown -L43 : U unknown unknown -L44 : A unknown unknown -L45 : A unknown unknown -L46 : C unknown unknown -L47 : A unknown unknown -L48 : G unknown unknown -L49 : C unknown unknown -L50 : U unknown unknown -L51 : C unknown unknown -L52 : A unknown unknown -L53 : C unknown unknown -L54 : C unknown unknown -L55 : A unknown unknown -L56 : G unknown unknown -L57 : C unknown unknown -M1 : G unknown unknown -M2 : C unknown unknown -M3 : U unknown unknown -M4 : C unknown unknown -M5 : C unknown unknown -M6 : U unknown unknown -M7 : A unknown unknown -M8 : G unknown unknown -M9 : U unknown unknown -M10 : A unknown unknown -M11 : C unknown unknown -M12 : G unknown unknown -M13 : A unknown unknown -M14 : G unknown unknown -M15 : A unknown unknown -M16 : G unknown unknown -M17 : G unknown unknown -M18 : A unknown unknown -M19 : C unknown unknown -M20 : C unknown unknown -M21 : G unknown unknown -M22 : G unknown unknown -M23 : A unknown unknown -M24 : G unknown unknown -M25 : U unknown unknown -M26 : G unknown unknown -O1 : C unknown unknown -O2 : G unknown unknown -O3 : C unknown unknown -O4 : G unknown unknown -O5 : G unknown unknown -O6 : G unknown unknown -O7 : G unknown unknown -O8 : 4SU -O9 : G unknown unknown -O10 : G unknown unknown -O11 : A unknown unknown -O12 : G unknown unknown -O13 : C unknown unknown -O14 : A unknown unknown -O15 : G unknown unknown -O16 : C unknown unknown -O17 : C unknown unknown -O18 : G unknown unknown -O19 : G unknown unknown -O20 : H2U -O21 : A unknown unknown -O22 : G unknown unknown -O23 : C unknown unknown -O24 : U unknown unknown -O25 : C unknown unknown -O26 : G unknown unknown -O27 : U unknown unknown -O28 : C unknown unknown -O29 : G unknown unknown -O30 : G unknown unknown -O31 : G unknown unknown -O32 : OMC -O33 : U unknown unknown -O34 : C unknown unknown -O35 : A unknown unknown -O36 : U unknown unknown -O37 : A unknown unknown -O38 : A unknown unknown -O39 : C unknown unknown -O40 : C unknown unknown -O41 : C unknown unknown -O42 : G unknown unknown -O43 : A unknown unknown -O44 : A unknown unknown -O45 : G unknown unknown -O46 : A unknown unknown -O47 : U unknown unknown -O48 : C unknown unknown -O49 : G unknown unknown -O50 : U unknown unknown -O51 : C unknown unknown -O52 : G unknown unknown -O53 : G unknown unknown -O54 : 5MU -O55 : PSU -O56 : C unknown unknown -O57 : A unknown unknown -O58 : A unknown unknown -O59 : A unknown unknown -O60 : U unknown unknown -O61 : C unknown unknown -O62 : C unknown unknown -O63 : G unknown unknown -O64 : G unknown unknown -O65 : C unknown unknown -O66 : C unknown unknown -O67 : C unknown unknown -O68 : C unknown unknown -O69 : C unknown unknown -O70 : G unknown unknown -O71 : C unknown unknown -O72 : A unknown unknown -O73 : A unknown unknown -O74 : C unknown unknown -O75 : C unknown unknown -O76 : A unknown unknown -A1 : MET -A2 : LYS -A3 : LEU -A4 : SER -A5 : GLU -A6 : TYR -A7 : GLY -A8 : LEU -A9 : GLN -A10 : LEU -A11 : GLN -A12 : GLU -A13 : LYS -A14 : GLN -A15 : LYS -A16 : LEU -A17 : ARG -A18 : HIS -A19 : MET -A20 : TYR -A21 : GLY -A22 : VAL -A23 : ASN -A24 : GLU -A25 : ARG -A26 : GLN -A27 : PHE -A28 : ARG -A29 : LYS -A30 : THR -A31 : PHE -A32 : GLU -A33 : GLU -A34 : ALA -A35 : GLY -A36 : LYS -A37 : MET -A38 : PRO -A39 : GLY -A40 : LYS -A41 : HIS -A42 : GLY -A43 : GLU -A44 : ASN -A45 : PHE -A46 : MET -A47 : ILE -A48 : LEU -A49 : LEU -A50 : GLU -A51 : SER -A52 : ARG -A53 : LEU -A54 : ASP -A55 : ASN -A56 : LEU -A57 : VAL -A58 : TYR -A59 : ARG -A60 : LEU -A61 : GLY -A62 : LEU -A63 : ALA -A64 : ARG -A65 : THR -A66 : ARG -A67 : ARG -A68 : GLN -A69 : ALA -A70 : ARG -A71 : GLN -A72 : LEU -A73 : VAL -A74 : THR -A75 : HIS -A76 : GLY -A77 : HIS -A78 : ILE -A79 : LEU -A80 : VAL -A81 : ASP -A82 : GLY -A83 : SER -A84 : ARG -A85 : VAL -A86 : ASN -A87 : ILE -A88 : PRO -A89 : SER -A90 : TYR -A91 : ARG -A92 : VAL -A93 : LYS -A94 : PRO -A95 : GLY -A96 : GLN -A97 : THR -A98 : ILE -A99 : ALA -A100 : VAL -A101 : ARG -A102 : GLU -A103 : LYS -A104 : SER -A105 : ARG -A106 : ASN -A107 : LEU -A108 : GLN -A109 : VAL -A110 : ILE -A111 : LYS -A112 : GLU -A113 : ALA -A114 : LEU -A115 : GLU -A116 : ALA -A117 : ASN -A118 : ASN -A119 : TYR -A120 : ILE -A121 : PRO -A122 : ASP -A123 : TYR -A124 : LEU -A125 : SER -A126 : PHE -A127 : ASP -A128 : PRO -A129 : GLU -A130 : LYS -A131 : MET -A132 : GLU -A133 : GLY -A134 : THR -A135 : TYR -A136 : THR -A137 : ARG -A138 : LEU -A139 : PRO -A140 : GLU -A141 : ARG -A142 : SER -A143 : GLU -A144 : LEU -A145 : PRO -A146 : ALA -A147 : GLU -A148 : ILE -A149 : ASN -A150 : GLU -A151 : ALA -A152 : LEU -A153 : ILE -A154 : VAL -A155 : GLU -A156 : PHE -A157 : TYR -A158 : SER -A159 : ARG -B1 : ILE -B2 : ASN -B3 : PRO -B4 : ASN -B5 : LYS -B6 : LEU -B7 : GLU -B8 : LEU -B9 : GLU -B10 : GLU -B11 : ARG -B12 : VAL -B13 : VAL -B14 : ALA -B15 : VAL -B16 : ASN -B17 : ARG -B18 : VAL -B19 : ALA -B20 : LYS -B21 : VAL -B22 : VAL -B23 : LYS -B24 : GLY -B25 : GLY -B26 : ARG -B27 : ARG -B28 : LEU -B29 : ARG -B30 : PHE -B31 : SER -B32 : ALA -B33 : LEU -B34 : VAL -B35 : VAL -B36 : VAL -B37 : GLY -B38 : ASP -B39 : LYS -B40 : ASN -B41 : GLY -B42 : HIS -B43 : VAL -B44 : GLY -B45 : PHE -B46 : GLY -B47 : THR -B48 : GLY -B49 : LYS -B50 : ALA -B51 : GLN -B52 : GLU -B53 : VAL -B54 : PRO -B55 : GLU -B56 : ALA -B57 : ILE -B58 : ARG -B59 : LYS -B60 : ALA -B61 : ILE -B62 : GLU -B63 : ASP -B64 : ALA -B65 : LYS -B66 : LYS -B67 : ASN -B68 : LEU -B69 : ILE -B70 : GLU -B71 : VAL -B72 : PRO -B73 : ILE -B74 : VAL -B75 : GLY -B76 : THR -B77 : THR -B78 : ILE -B79 : PRO -B80 : HIS -B81 : GLU -B82 : VAL -B83 : ILE -B84 : GLY -B85 : HIS -B86 : PHE -B87 : GLY -B88 : ALA -B89 : GLY -B90 : GLU -B91 : ILE -B92 : ILE -B93 : LEU -B94 : LYS -B95 : PRO -B96 : ALA -B97 : SER -B98 : GLU -B99 : GLY -B100 : THR -B101 : GLY -B102 : VAL -B103 : ILE -B104 : ALA -B105 : GLY -B106 : GLY -B107 : PRO -B108 : ALA -B109 : ARG -B110 : ALA -B111 : VAL -B112 : LEU -B113 : GLU -B114 : LEU -B115 : ALA -B116 : GLY -B117 : ILE -B118 : SER -B119 : ASP -B120 : ILE -B121 : LEU -B122 : SER -B123 : LYS -B124 : SER -B125 : ILE -B126 : GLY -B127 : SER -B128 : ASN -B129 : THR -B130 : PRO -B131 : ILE -B132 : ASN -B133 : MET -B134 : VAL -B135 : ARG -B136 : ALA -B137 : THR -B138 : PHE -B139 : ASP -B140 : GLY -B141 : LEU -B142 : LYS -B143 : GLN -B144 : LEU -B145 : LYS -C1 : MET -C2 : ARG -C3 : ARG -C4 : TYR -C5 : GLU -C6 : VAL -C7 : ASN -C8 : ILE -C9 : VAL -C10 : LEU -C11 : ASN -C12 : PRO -C13 : ASN -C14 : LEU -C15 : ASP -C16 : GLN -C17 : SER -C18 : GLN -C19 : LEU -C20 : ALA -C21 : LEU -C22 : GLU -C23 : LYS -C24 : GLU -C25 : ILE -C26 : ILE -C27 : GLN -C28 : ARG -C29 : ALA -C30 : LEU -C31 : GLU -C32 : ASN -C33 : TYR -C34 : GLY -C35 : ALA -C36 : ARG -C37 : VAL -C38 : GLU -C39 : LYS -C40 : VAL -C41 : GLU -C42 : GLU -C43 : LEU -C44 : GLY -C45 : LEU -C46 : ARG -C47 : ARG -C48 : LEU -C49 : ALA -C50 : TYR -C51 : PRO -C52 : ILE -C53 : ALA -C54 : LYS -C55 : ASP -C56 : PRO -C57 : GLN -C58 : GLY -C59 : TYR -C60 : PHE -C61 : LEU -C62 : TRP -C63 : TYR -C64 : GLN -C65 : VAL -C66 : GLU -C67 : MET -C68 : PRO -C69 : GLU -C70 : ASP -C71 : ARG -C72 : VAL -C73 : ASN -C74 : ASP -C75 : LEU -C76 : ALA -C77 : ARG -C78 : GLU -C79 : LEU -C80 : ARG -C81 : ILE -C82 : ARG -C83 : ASP -C84 : ASN -C85 : VAL -C86 : ARG -C87 : ARG -C88 : VAL -C89 : MET -C90 : VAL -C91 : VAL -C92 : LYS -C93 : SER -C94 : GLN -C95 : GLU -C96 : PRO -C97 : PHE -D1 : LEU -D2 : GLN -D3 : PRO -D4 : ASP -D5 : LEU -D6 : VAL -D7 : TYR -D8 : GLY -D9 : ASP -D10 : VAL -D11 : LEU -D12 : VAL -D13 : THR -D14 : ALA -D15 : PHE -D16 : ILE -D17 : ASN -D18 : LYS -D19 : ILE -D20 : MET -D21 : ARG -D22 : ASP -D23 : GLY -D24 : LYS -D25 : LYS -D26 : ASN -D27 : LEU -D28 : ALA -D29 : ALA -D30 : ARG -D31 : ILE -D32 : PHE -D33 : TYR -D34 : ASP -D35 : ALA -D36 : CYS -D37 : LYS -D38 : ILE -D39 : ILE -D40 : GLN -D41 : GLU -D42 : LYS -D43 : THR -D44 : GLY -D45 : GLN -D46 : GLU -D47 : PRO -D48 : LEU -D49 : LYS -D50 : VAL -D51 : PHE -D52 : LYS -D53 : GLN -D54 : ALA -D55 : VAL -D56 : GLU -D57 : ASN -D58 : VAL -D59 : LYS -D60 : PRO -D61 : ARG -D62 : MET -D63 : GLU -D64 : VAL -D65 : ARG -D66 : SER -D67 : ARG -D68 : ARG -D69 : VAL -D70 : GLY -D71 : GLY -D72 : ALA -D73 : ASN -D74 : TYR -D75 : GLN -D76 : VAL -D77 : PRO -D78 : MET -D79 : GLU -D80 : VAL -D81 : SER -D82 : PRO -D83 : ARG -D84 : ARG -D85 : GLN -D86 : GLN -D87 : SER -D88 : LEU -D89 : ALA -D90 : LEU -D91 : ARG -D92 : TRP -D93 : LEU -D94 : VAL -D95 : GLN -D96 : ALA -D97 : ALA -D98 : ASN -D99 : GLN -D100 : ARG -D101 : PRO -D102 : GLU -D103 : ARG -D104 : ARG -D105 : ALA -D106 : ALA -D107 : VAL -D108 : ARG -D109 : ILE -D110 : ALA -D111 : HIS -D112 : GLU -D113 : LEU -D114 : MET -D115 : ASP -D116 : ALA -D117 : ALA -D118 : GLU -D119 : GLY -D120 : LYS -D121 : GLY -D122 : GLY -D123 : ALA -D124 : VAL -D125 : LYS -D126 : LYS -D127 : LYS -D128 : GLU -D129 : ASP -D130 : VAL -D131 : GLU -D132 : ARG -D133 : MET -D134 : ALA -D135 : GLU -E1 : THR -E2 : ASP -E3 : PRO -E4 : ILE -E5 : ALA -E6 : ASP -E7 : MET -E8 : LEU -E9 : THR -E10 : ARG -E11 : ILE -E12 : ARG -E13 : ASN -E14 : ALA -E15 : THR -E16 : ARG -E17 : VAL -E18 : TYR -E19 : LYS -E20 : GLU -E21 : SER -E22 : THR -E23 : ASP -E24 : VAL -E25 : PRO -E26 : ALA -E27 : SER -E28 : ARG -E29 : PHE -E30 : LYS -E31 : GLU -E32 : GLU -E33 : ILE -E34 : LEU -E35 : ARG -E36 : ILE -E37 : LEU -E38 : ALA -E39 : ARG -E40 : GLU -E41 : GLY -E42 : PHE -E43 : ILE -E44 : LYS -E45 : GLY -E46 : TYR -E47 : GLU -E48 : ARG -E49 : VAL -E50 : ASP -E51 : VAL -E52 : ASP -E53 : GLY -E54 : LYS -E55 : PRO -E56 : TYR -E57 : LEU -E58 : ARG -E59 : VAL -E60 : TYR -E61 : LEU -E62 : LYS -E63 : TYR -E64 : GLY -E65 : PRO -E66 : ARG -E67 : ARG -E68 : GLN -E69 : GLY -E70 : PRO -E71 : ASP -E72 : PRO -E73 : ARG -E74 : PRO -E75 : GLU -E76 : GLN -E77 : VAL -E78 : ILE -E79 : HIS -E80 : HIS -E81 : ILE -E82 : ARG -E83 : ARG -E84 : ILE -E85 : SER -E86 : LYS -E87 : PRO -E88 : GLY -E89 : ARG -E90 : ARG -E91 : VAL -E92 : TYR -E93 : VAL -E94 : GLY -E95 : VAL -E96 : LYS -E97 : GLU -E98 : ILE -E99 : PRO -E100 : ARG -E101 : VAL -E102 : ARG -E103 : ARG -E104 : GLY -E105 : LEU -E106 : GLY -E107 : ILE -E108 : ALA -E109 : ILE -E110 : LEU -E111 : SER -E112 : THR -E113 : SER -E114 : LYS -E115 : GLY -E116 : VAL -E117 : LEU -E118 : THR -E119 : ASP -E120 : ARG -E121 : GLU -E122 : ALA -E123 : ARG -E124 : LYS -E125 : LEU -E126 : GLY -E127 : VAL -E128 : GLY -E129 : GLY -E130 : GLU -E131 : LEU -E132 : ILE -E133 : CYS -E134 : GLU -E135 : VAL -E136 : TRP -F1 : PRO -F2 : ILE -F3 : THR -F4 : LYS -F5 : GLU -F6 : GLU -F7 : LYS -F8 : GLN -F9 : LYS -F10 : VAL -F11 : ILE -F12 : GLN -F13 : GLU -F14 : PHE -F15 : ALA -F16 : ARG -F17 : PHE -F18 : PRO -F19 : GLY -F20 : ASP -F21 : THR -F22 : GLY -F23 : SER -F24 : THR -F25 : GLU -F26 : VAL -F27 : GLN -F28 : VAL -F29 : ALA -F30 : LEU -F31 : LEU -F32 : THR -F33 : LEU -F34 : ARG -F35 : ILE -F36 : ASN -F37 : ARG -F38 : LEU -F39 : SER -F40 : GLU -F41 : HIS -F42 : LEU -F43 : LYS -F44 : VAL -F45 : HIS -F46 : LYS -F47 : LYS -F48 : ASP -F49 : HIS -F50 : HIS -F51 : SER -F52 : HIS -F53 : ARG -F54 : GLY -F55 : LEU -F56 : LEU -F57 : MET -F58 : MET -F59 : VAL -F60 : GLY -F61 : GLN -F62 : ARG -F63 : ARG -F64 : ARG -F65 : LEU -F66 : LEU -F67 : ARG -F68 : TYR -F69 : LEU -F70 : GLN -F71 : ARG -F72 : GLU -F73 : ASP -F74 : PRO -F75 : GLU -F76 : ARG -F77 : TYR -F78 : ARG -F79 : ALA -F80 : LEU -F81 : ILE -F82 : GLU -F83 : LYS -F84 : LEU -F85 : GLY -F86 : ILE -F87 : ARG -F88 : GLY -G1 : GLN -G2 : ARG -G3 : LYS -G4 : VAL -G5 : TYR -G6 : VAL -G7 : GLY -G8 : ARG -G9 : VAL -G10 : VAL -G11 : SER -G12 : ASP -G13 : LYS -G14 : MET -G15 : ASP -G16 : LYS -G17 : THR -G18 : ILE -G19 : THR -G20 : VAL -G21 : LEU -G22 : VAL -G23 : GLU -G24 : THR -G25 : TYR -G26 : LYS -G27 : LYS -G28 : HIS -G29 : PRO -G30 : LEU -G31 : TYR -G32 : GLY -G33 : LYS -G34 : ARG -G35 : VAL -G36 : LYS -G37 : TYR -G38 : SER -G39 : LYS -G40 : LYS -G41 : TYR -G42 : LYS -G43 : ALA -G44 : HIS -G45 : ASP -G46 : GLU -G47 : HIS -G48 : ASN -G49 : GLU -G50 : ALA -G51 : LYS -G52 : VAL -G53 : GLY -G54 : ASP -G55 : ILE -G56 : VAL -G57 : LYS -G58 : ILE -G59 : MET -G60 : GLU -G61 : THR -G62 : ARG -G63 : PRO -G64 : LEU -G65 : SER -G66 : ALA -G67 : THR -G68 : LYS -G69 : ARG -G70 : PHE -G71 : ARG -G72 : LEU -G73 : VAL -G74 : GLU -G75 : ILE -G76 : VAL -G77 : GLU -G78 : LYS -G79 : ALA -G80 : VAL -G81 : ARG -G82 : ALA -G83 : GLY -G84 : ALA -G85 : GLY -G86 : ALA -G87 : GLY -G88 : ALA -G89 : ALA -H1 : UNK -H2 : UNK -H3 : UNK -H4 : UNK -H5 : UNK -H6 : UNK -H7 : UNK -H8 : UNK -H9 : UNK -H10 : UNK -H11 : UNK -H12 : UNK -H13 : UNK -H14 : UNK -H15 : UNK -H16 : UNK -H17 : UNK -H18 : UNK -H19 : UNK -H20 : UNK -H21 : UNK -H22 : UNK -H23 : UNK -H24 : UNK -H25 : UNK -H26 : UNK -H27 : UNK -H28 : UNK -H29 : UNK -H30 : UNK -H31 : UNK -H32 : UNK -H33 : UNK -H34 : UNK -H35 : UNK -H36 : UNK -H37 : UNK -H38 : UNK -H39 : UNK -H40 : UNK -H41 : UNK -H42 : UNK -H43 : UNK -H44 : UNK -H45 : UNK -H46 : UNK -H47 : UNK -H48 : UNK -H49 : UNK -H50 : UNK -H51 : UNK -H52 : UNK -H53 : UNK -H54 : UNK -H55 : UNK -H56 : UNK -H57 : UNK -H58 : UNK -H59 : UNK -H60 : UNK -H61 : UNK -H62 : UNK -H63 : UNK -H64 : UNK -H65 : UNK -H66 : UNK -H67 : UNK -H68 : UNK -H69 : UNK -H70 : UNK -H71 : UNK -H72 : UNK -H73 : UNK -H74 : UNK -H75 : UNK -H76 : UNK -H77 : UNK -H78 : UNK -H79 : UNK -H80 : UNK -H81 : UNK -H82 : UNK -H83 : UNK -H84 : UNK -H85 : UNK -H86 : UNK -H87 : UNK -H88 : UNK -H89 : UNK -H90 : UNK -H91 : UNK -H92 : UNK -H93 : UNK -H94 : UNK -H95 : UNK -H96 : UNK -H97 : UNK -H98 : UNK -H99 : UNK -H100 : UNK -N1 : ALA -N2 : LEU -N3 : LEU -N4 : GLU -N5 : LYS -N6 : VAL -N7 : ASP -N8 : PRO -N9 : ASN -N10 : LYS -N11 : ILE -N12 : TYR -N13 : THR -N14 : ILE -N15 : ASP -N16 : GLU -N17 : ALA -N18 : ALA -N19 : HIS -N20 : LEU -N21 : VAL -N22 : LYS -N23 : GLU -N24 : LEU -N25 : ALA -N26 : THR -N27 : ALA -N28 : LYS -N29 : PHE -N30 : ASP -N31 : GLU -N32 : THR -N33 : VAL -N34 : GLU -N35 : VAL -N36 : HIS -N37 : ALA -N38 : LYS -N39 : LEU -N40 : GLY -N41 : ILE -N42 : ASP -N43 : PRO -N44 : ARG -N45 : ARG -N46 : SER -N47 : ASP -N48 : GLN -N49 : ASN -N50 : VAL -N51 : ARG -N52 : GLY -N53 : THR -N54 : VAL -N55 : SER -N56 : LEU -N57 : PRO -N58 : HIS -N59 : GLY -N60 : LEU -N61 : GLY -N62 : LYS -N63 : GLN -N64 : VAL -N65 : ARG -N66 : VAL -N67 : LEU -N68 : ALA -N69 : ILE -N70 : ALA -N71 : LYS -N72 : GLY -N73 : GLU -N74 : LYS -N75 : ILE -N76 : LYS -N77 : GLU -N78 : ALA -N79 : GLU -N80 : GLU -N81 : ALA -N82 : GLY -N83 : ALA -N84 : ASP -N85 : TYR -N86 : VAL -N87 : GLY -N88 : GLY -N89 : GLU -N90 : GLU -N91 : ILE -N92 : ILE -N93 : GLN -N94 : LYS -N95 : ILE -N96 : LEU -N97 : ASP -N98 : GLY -N99 : TRP -N100 : MET -N101 : ASP -N102 : PHE -N103 : ASP -N104 : ALA -N105 : VAL -N106 : VAL -N107 : ALA -N108 : THR -N109 : PRO -N110 : ASP -N111 : VAL -N112 : MET -N113 : GLY -N114 : ALA -N115 : VAL -N116 : GLY -N117 : SER -N118 : LYS -N119 : LEU -N120 : GLY -N121 : ARG -N122 : ILE -N123 : LEU -N124 : GLY -N125 : PRO -N126 : ARG -N127 : GLY -N128 : LEU -N129 : LEU -N130 : PRO -N131 : ASN -N132 : PRO -N133 : LYS -N134 : ALA -N135 : GLY -N136 : THR -N137 : VAL -N138 : GLY -N139 : PHE -N140 : ASN -N141 : ILE -N142 : GLY -N143 : GLU -N144 : ILE -N145 : ILE -N146 : ARG -N147 : GLU -N148 : ILE -N149 : LYS -N150 : ALA -N151 : GLY -N152 : ARG -N153 : ILE -N154 : GLU -N155 : PHE -N156 : ARG -N157 : ASN -N158 : ASP -N159 : LYS -N160 : THR -N161 : GLY -N162 : ALA -N163 : ILE -N164 : HIS -N165 : ALA -N166 : PRO -N167 : VAL -N168 : GLY -N169 : LYS -N170 : ALA -N171 : SER -N172 : PHE -N173 : PRO -N174 : PRO -N175 : GLU -N176 : LYS -N177 : LEU -N178 : ALA -N179 : ASP -N180 : ASN -N181 : ILE -N182 : ARG -N183 : ALA -N184 : PHE -N185 : ILE -N186 : ARG -N187 : ALA -N188 : LEU -N189 : GLU -N190 : ALA -N191 : HIS -N192 : LYS -N193 : PRO -N194 : GLU -N195 : GLY -N196 : ALA -N197 : LYS -N198 : GLY -N199 : THR -N200 : PHE -N201 : LEU -N202 : ARG -N203 : SER -N204 : VAL -N205 : TYR -N206 : VAL -N207 : THR -N208 : THR -N209 : THR -N210 : MET -N211 : GLY -N212 : PRO -N213 : SER -N214 : VAL -N215 : ARG -N216 : ILE -N217 : ASN -N218 : PRO -N219 : HIS -N220 : SER -J1 : PRO -J2 : ILE -J3 : GLU -J4 : ILE -J5 : PRO -J6 : ALA -J7 : GLY -J8 : VAL -J9 : THR -J10 : VAL -J11 : THR -J12 : VAL -J13 : ASN -J14 : GLY -J15 : ASN -J16 : THR -J17 : VAL -J18 : THR -J19 : VAL -J20 : LYS -J21 : GLY -J22 : PRO -J23 : LYS -J24 : GLY -J25 : GLU -J26 : LEU -J27 : THR -J28 : ARG -J29 : THR -J30 : PHE -J31 : HIS -J32 : PRO -J33 : ASP -J34 : MET -J35 : THR -J36 : ILE -J37 : THR -J38 : VAL -J39 : GLU -J40 : GLY -J41 : ASN -J42 : VAL -J43 : ILE -J44 : THR -J45 : VAL -J46 : THR -J47 : ARG -J48 : PRO -J49 : SER -J50 : ASP -J51 : GLU -J52 : LYS -J53 : HIS -J54 : HIS -J55 : ARG -J56 : ALA -J57 : LEU -J58 : HIS -J59 : GLY -J60 : THR -J61 : THR -J62 : ARG -J63 : SER -J64 : LEU -J65 : LEU -J66 : ALA -J67 : ASN -J68 : MET -J69 : VAL -J70 : GLU -J71 : GLY -J72 : VAL -J73 : SER -J74 : LYS -J75 : GLY -J76 : TYR -J77 : GLU -J78 : LYS -J79 : ALA -J80 : LEU -J81 : GLU -J82 : LEU -J83 : VAL -J84 : GLY -J85 : VAL -J86 : GLY -J87 : TYR -J88 : ARG -J89 : ALA -J90 : SER -J91 : LYS -J92 : GLN -J93 : GLY -J94 : LYS -J95 : LYS -J96 : LEU -J97 : VAL -J98 : LEU -J99 : SER -J100 : VAL -J101 : GLY -J102 : TYR -J103 : SER -J104 : HIS -J105 : PRO -J106 : VAL -J107 : GLU -J108 : ILE -J109 : GLU -J110 : PRO -J111 : GLU -J112 : GLU -J113 : GLY -J114 : LEU -J115 : GLU -J116 : ILE -J117 : GLU -J118 : VAL -J119 : PRO -J120 : SER -J121 : GLN -J122 : THR -J123 : LYS -J124 : ILE -J125 : ILE -J126 : VAL -J127 : LYS -J128 : GLY -J129 : ALA -J130 : ASP -J131 : LYS -J132 : GLN -J133 : ARG -J134 : VAL -J135 : GLY -J136 : GLU -J137 : LEU -J138 : ALA -J139 : ALA -J140 : ASN -J141 : ILE -J142 : ARG -J143 : ALA -J144 : VAL -J145 : ARG -J146 : PRO -J147 : PRO -J148 : GLU -J149 : PRO -J150 : TYR -J151 : LYS -J152 : GLY -J153 : LYS -J154 : GLY -J155 : ILE -J156 : ARG -J157 : TYR -J158 : GLU -J159 : GLY -J160 : GLU -J161 : LEU -J162 : VAL -J163 : ARG -J164 : LEU -K1 : GLN -K2 : ILE -K3 : LYS -K4 : LEU -K5 : GLN -K6 : LEU -K7 : PRO -K8 : ALA -K9 : GLY -K10 : LYS -K11 : ALA -K12 : THR -K13 : PRO -K14 : ALA -K15 : PRO -K16 : PRO -K17 : VAL -K18 : GLY -K19 : PRO -K20 : ALA -K21 : LEU -K22 : GLY -K23 : GLN -K24 : HIS -K25 : GLY -K26 : VAL -K27 : ASN -K28 : ILE -K29 : MET -K30 : GLU -K31 : PHE -K32 : CYS -K33 : LYS -K34 : ARG -K35 : PHE -K36 : ASN -K37 : ALA -K38 : GLU -K39 : THR -K40 : ALA -K41 : ASP -K42 : LYS -K43 : ALA -K44 : GLY -K45 : MET -K46 : ILE -K47 : LEU -K48 : PRO -K49 : VAL -K50 : VAL -K51 : ILE -K52 : THR -K53 : VAL -K54 : TYR -K55 : GLU -K56 : ASP -K57 : LYS -K58 : SER -K59 : PHE -K60 : THR -K61 : PHE -K62 : ILE -K63 : ILE -K64 : LYS -K65 : THR -K66 : PRO -K67 : PRO -K68 : ALA -K69 : SER -K70 : PHE -K71 : LEU -K72 : LEU -K73 : LYS -K74 : LYS -K75 : ALA -K76 : ALA -K77 : GLY -K78 : ILE -K79 : GLU -K80 : LYS -K81 : GLY -K82 : SER -K83 : SER -K84 : GLU -K85 : PRO -K86 : LYS -K87 : ARG -K88 : LYS -K89 : ILE -K90 : VAL -K91 : GLY -K92 : LYS -K93 : VAL -K94 : THR -K95 : ARG -K96 : LYS -K97 : GLN -K98 : ILE -K99 : GLU -K100 : GLU -K101 : ILE -K102 : ALA -K103 : LYS -K104 : THR -K105 : LYS -K106 : MET -K107 : PRO -K108 : ASP -K109 : LEU -K110 : ASN -K111 : ALA -K112 : ASN -K113 : SER -K114 : LEU -K115 : GLU -K116 : ALA -K117 : ALA -K118 : MET -K119 : LYS -K120 : ILE -K121 : ILE -K122 : GLU -K123 : GLY -K124 : THR -K125 : ALA -K126 : LYS -K127 : SER -K128 : MET -K129 : GLY -K130 : ILE -K131 : GLU -K132 : VAL -K133 : VAL -Adjacent stackings ---------------------------------------------- -Non-Adjacent stackings ------------------------------------------ -Number of stackings = 0 -Number of adjacent stackings = 0 -Number of non adjacent stackings = 0 -Base-pairs ------------------------------------------------------ diff --git a/MCdata/1egk_MC b/MCdata/1egk_MC deleted file mode 100644 index 3fc630768f823df00500cc3e6891dbbc792c597b..0000000000000000000000000000000000000000 --- a/MCdata/1egk_MC +++ /dev/null @@ -1,352 +0,0 @@ -Residue conformations ------------------------------------------- -A1 : A O4p_exo anti -A2 : G C3p_endo anti -A3 : G C3p_endo anti -A4 : A C3p_endo anti -A5 : G C3p_endo anti -A6 : A C3p_endo anti -A7 : G C3p_endo anti -A8 : A C3p_endo anti -A9 : G C3p_endo anti -A10 : A C3p_endo anti -A11 : U C3p_endo anti -A12 : G C3p_endo anti -A13 : G C3p_endo anti -A14 : G C3p_endo anti -A15 : U C3p_endo anti -A16 : G C3p_endo anti -A17 : C C3p_endo anti -A18 : G C3p_endo anti -A19 : A C3p_endo anti -A20 : G C3p_endo anti -B21 : C C3p_endo anti -B22 : T C3p_endo anti -B23 : C C3p_endo anti -B24 : G C3p_endo anti -B25 : C C3p_endo anti -B26 : A C3p_endo anti -B27 : C C3p_endo anti -B28 : C C3p_endo anti -B29 : C C3p_endo anti -B30 : A C3p_endo anti -B31 : G C1p_exo anti -B32 : G C3p_endo anti -B33 : C O4p_endo anti -B34 : T C2p_endo anti -B35 : A C3p_exo anti -B36 : G C1p_exo anti -B37 : C C3p_endo anti -B38 : T C3p_endo anti -B39 : A C2p_endo anti -B40 : C C2p_endo anti -B41 : A O4p_endo anti -B42 : A C2p_endo anti -B43 : C C1p_exo anti -B44 : G C2p_endo anti -B45 : A C2p_exo anti -B46 : C C3p_endo anti -B47 : T C3p_endo anti -B48 : C C4p_exo anti -B49 : T C3p_endo anti -B50 : C C3p_endo anti -B51 : T C3p_endo anti -B52 : C C3p_endo anti -B53 : C C3p_endo anti -B54 : T C2p_endo anti -C101 : A O4p_endo syn -C102 : G C3p_endo anti -C103 : G C3p_endo anti -C104 : A C3p_endo anti -C105 : G C3p_endo anti -C106 : A C3p_endo anti -C107 : G C3p_endo anti -C108 : A C3p_endo anti -C109 : G C3p_endo anti -C110 : A C3p_endo anti -C111 : U C3p_endo anti -C112 : G C3p_endo anti -C113 : G C3p_endo anti -C114 : G C3p_endo anti -C115 : U C3p_endo anti -C116 : G C3p_endo anti -C117 : C C3p_endo anti -C118 : G C3p_endo anti -C119 : A C3p_endo anti -C120 : G C3p_endo anti -D121 : C C2p_exo anti -D122 : T C3p_endo anti -D123 : C C3p_endo anti -D124 : G C3p_endo anti -D125 : C C3p_endo anti -D126 : A C3p_endo anti -D127 : C C3p_endo anti -D128 : C C3p_endo anti -D129 : C C3p_endo anti -D130 : A C3p_endo anti -D131 : G C2p_endo anti -D132 : G C3p_endo anti -D133 : C C1p_exo anti -D134 : T C2p_endo anti -D135 : A C2p_endo anti -D136 : G C1p_exo anti -D137 : C C2p_endo anti -D138 : T C3p_endo anti -D139 : A C3p_exo anti -D140 : C C2p_endo anti -D141 : A C1p_exo anti -D142 : A C1p_exo anti -D143 : C C1p_exo anti -D144 : G C1p_exo syn -D145 : A C2p_endo syn -D146 : C C3p_endo anti -D147 : T C3p_endo anti -D148 : C C3p_endo anti -D149 : T C3p_endo anti -D150 : C C3p_endo anti -D151 : T C3p_endo anti -D152 : C C3p_endo anti -D153 : C C3p_endo anti -D154 : T C3p_endo anti -A21 : MG -A22 : MG -A23 : MG -A24 : MG -A25 : MG -A26 : MG -A27 : MG -C3 : MG -C4 : MG -C6 : MG -C7 : MG -C9 : MG -C13 : MG -C14 : MG -A28 : HOH -A29 : HOH -A30 : HOH -A31 : HOH -A32 : HOH -A33 : HOH -A34 : HOH -A35 : HOH -A36 : HOH -A37 : HOH -A38 : HOH -A39 : HOH -A40 : HOH -A41 : HOH -A42 : HOH -A43 : HOH -A44 : HOH -A45 : HOH -A46 : HOH -A47 : HOH -A48 : HOH -A49 : HOH -A50 : HOH -A51 : HOH -A52 : HOH -A53 : HOH -A54 : HOH -A55 : HOH -A56 : HOH -A57 : HOH -A58 : HOH -A59 : HOH -A60 : HOH -B55 : HOH -B56 : HOH -B57 : HOH -B58 : HOH -B59 : HOH -B60 : HOH -B61 : HOH -B62 : HOH -B63 : HOH -B64 : HOH -B65 : HOH -B66 : HOH -C28 : HOH -C29 : HOH -C30 : HOH -C31 : HOH -C32 : HOH -C34 : HOH -C35 : HOH -C36 : HOH -C37 : HOH -C45 : HOH -C46 : HOH -C47 : HOH -C48 : HOH -C49 : HOH -C50 : HOH -C51 : HOH -C53 : HOH -C56 : HOH -C64 : HOH -C65 : HOH -C67 : HOH -C68 : HOH -C87 : HOH -C88 : HOH -C90 : HOH -C91 : HOH -C92 : HOH -C93 : HOH -C94 : HOH -C95 : HOH -C96 : HOH -C97 : HOH -C98 : HOH -D52 : HOH -D54 : HOH -D55 : HOH -D63 : HOH -D70 : HOH -D89 : HOH -Adjacent stackings ---------------------------------------------- -A2-A3 : adjacent_5p upward -A3-A4 : adjacent_5p upward -A4-A5 : adjacent_5p upward -A5-A6 : adjacent_5p upward -A6-A7 : adjacent_5p upward -A7-A8 : adjacent_5p upward -A8-A9 : adjacent_5p upward -A9-A10 : adjacent_5p upward -A10-A11 : adjacent_5p upward -A11-A12 : adjacent_5p upward -A12-A13 : adjacent_5p upward -A13-A14 : adjacent_5p upward -A14-A15 : adjacent_5p upward -A15-A16 : adjacent_5p upward -A16-A17 : adjacent_5p upward -A17-A18 : adjacent_5p upward -A18-A19 : adjacent_5p upward -A19-A20 : adjacent_5p upward -B21-B22 : adjacent_5p upward -B24-B25 : adjacent_5p upward -B26-B27 : adjacent_5p upward -B27-B28 : adjacent_5p upward -B28-B29 : adjacent_5p upward -B29-B30 : adjacent_5p upward -B30-B31 : adjacent_5p upward -B32-B33 : adjacent_5p upward -B33-B34 : adjacent_5p upward -B34-B35 : adjacent_5p upward -B35-B36 : adjacent_5p upward -B36-B37 : adjacent_5p upward -B39-B40 : adjacent_5p upward -B40-B41 : adjacent_5p upward -B41-B42 : adjacent_5p upward -B43-B44 : adjacent_5p upward -B47-B48 : adjacent_5p upward -B49-B50 : adjacent_5p upward -B51-B52 : adjacent_5p upward -B53-B54 : adjacent_5p upward -C102-C103 : adjacent_5p upward -C103-C104 : adjacent_5p upward -C104-C105 : adjacent_5p upward -C105-C106 : adjacent_5p upward -C106-C107 : adjacent_5p upward -C107-C108 : adjacent_5p upward -C108-C109 : adjacent_5p upward -C109-C110 : adjacent_5p upward -C110-C111 : adjacent_5p upward -C111-C112 : adjacent_5p upward -C112-C113 : adjacent_5p upward -C113-C114 : adjacent_5p upward -C114-C115 : adjacent_5p upward -C115-C116 : adjacent_5p upward -C116-C117 : adjacent_5p upward -C117-C118 : adjacent_5p upward -C118-C119 : adjacent_5p upward -C119-C120 : adjacent_5p upward -D123-D124 : adjacent_5p upward -D124-D125 : adjacent_5p upward -D126-D127 : adjacent_5p upward -D127-D128 : adjacent_5p upward -D128-D129 : adjacent_5p upward -D130-D131 : adjacent_5p upward -D132-D133 : adjacent_5p upward -D133-D134 : adjacent_5p upward -D134-D135 : adjacent_5p upward -D135-D136 : adjacent_5p upward -D136-D137 : adjacent_5p upward -D139-D140 : adjacent_5p outward -D140-D141 : adjacent_5p upward -D141-D142 : adjacent_5p upward -D143-D144 : adjacent_5p upward -D149-D150 : adjacent_5p upward -D151-D152 : adjacent_5p upward -D153-D154 : adjacent_5p upward -Non-Adjacent stackings ------------------------------------------ -A1-D144 : downward -A1-D145 : upward -A3-D153 : outward -A12-B30 : outward -A16-B26 : outward -A18-B24 : outward -B32-D145 : downward -B44-C101 : inward -B45-D132 : upward -B53-C103 : outward -C112-D130 : outward -C116-D126 : outward -C118-D124 : outward -Number of stackings = 87 -Number of adjacent stackings = 74 -Number of non adjacent stackings = 13 -Base-pairs ------------------------------------------------------ -A1-D139 : A-A Wh/Hh pairing parallel trans one_hbond 35 -A2-D153 : G-C Ww/Ww pairing antiparallel cis XIX -A3-D152 : G-C Ww/Ww pairing antiparallel cis XIX -A4-D151 : A-T Ww/Ww pairing antiparallel cis -A5-D150 : G-C Ww/Ww pairing antiparallel cis XIX -A6-D149 : A-T Ww/Ww pairing antiparallel cis -A7-D148 : G-C Ww/Ww pairing antiparallel cis XIX -A8-D147 : A-T Ww/Ww pairing antiparallel cis -A9-D146 : G-C Ww/Ww pairing antiparallel cis XIX -A10-B31 : A-G Ww/Ww pairing antiparallel cis VIII -A11-B30 : U-A Ww/Ww pairing antiparallel cis XX -A12-B29 : G-C Ww/Ww pairing antiparallel cis XIX -A13-B28 : G-C Ww/Ww pairing antiparallel cis XIX -A14-B27 : G-C Ww/Ww pairing antiparallel cis XIX -A15-B26 : U-A Ww/Ww pairing antiparallel cis XX -A16-B25 : G-C Ww/Ww pairing antiparallel cis XIX -A17-B24 : C-G Ww/Ww pairing antiparallel cis XIX -A18-B23 : G-C Ww/Ww pairing antiparallel cis XIX -A19-B22 : A-T Ww/Ww pairing antiparallel cis -A20-B21 : G-C Ww/Ww pairing antiparallel cis XIX -B32-D137 : G-C Ww/Ww pairing antiparallel cis XIX -B33-D136 : C-G Ww/Ww pairing antiparallel cis XIX -B34-D135 : T-A Ww/Ww pairing antiparallel cis -B35-D134 : A-T Ww/Ww pairing antiparallel cis -B36-D133 : G-C Ww/Ww pairing antiparallel cis XIX -B37-D132 : C-G Ww/Ww pairing antiparallel cis XIX -B38-B45 : T-A Ww/Ww pairing antiparallel cis -B39-C101 : A-A Hh/Hh pairing parallel trans II -B40-B44 : C-G Ww/Ww pairing antiparallel cis XIX -B41-B43 : A-C Ss/Hw pairing antiparallel trans one_hbond 72 -B46-C109 : C-G Ww/Ww pairing antiparallel cis XIX -B47-C108 : T-A Ww/Ww pairing antiparallel cis -B48-C107 : C-G Ww/Ww pairing antiparallel cis XIX -B49-C106 : T-A Ww/Ww pairing antiparallel cis -B50-C105 : C-G Ww/Ww pairing antiparallel cis XIX -B51-C104 : T-A Ww/Ww pairing antiparallel cis -B52-C103 : C-G Ww/Ww pairing antiparallel cis XIX -B53-C102 : C-G Ww/Ww pairing antiparallel cis XIX -C110-D131 : A-G Ww/Ww pairing antiparallel cis VIII -C111-D130 : U-A Ww/Ww pairing antiparallel cis XX -C112-D129 : G-C Ww/Ww pairing antiparallel cis XIX -C113-D128 : G-C Ww/Ww pairing antiparallel cis XIX -C114-D127 : G-C Ww/Ww pairing antiparallel cis XIX -C115-D126 : U-A Ww/Ww pairing antiparallel cis XX -C116-D125 : G-C Ww/Ww pairing antiparallel cis XIX -C117-D124 : C-G Ww/Ww pairing antiparallel cis XIX -C118-D123 : G-C Ww/Ww pairing antiparallel cis XIX -C119-D122 : A-T Ww/Ww pairing antiparallel cis -C120-D121 : G-C Ww/Ww pairing antiparallel cis XIX -D138-D145 : T-A Ww/Ww pairing antiparallel cis -D140-D144 : C-G Ww/Ww pairing antiparallel cis XIX -D141-D143 : A-C Ss/Hw pairing antiparallel trans one_hbond 72