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