**************************************************************************** File name: 8q72.pdb no. of DNA/RNA chains: 4 [P=40,Q=40,R=40,S=40] no. of nucleotides: 164 no. of atoms: 84390 no. of waters: 0 no. of metals: 0 **************************************************************************** List of 1 type of 4 modified nucleotides nt count list 1 ADP-a 4 A.ADP1101,B.ADP1101,F.ADP1101,G.ADP1101 **************************************************************************** List of 80 base pairs nt1 nt2 bp name Saenger LW DSSR 1 P.DA1 Q.DT40 A-T WC 20-XX cWW cW-W 2 P.DT2 Q.DA39 T-A WC 20-XX cWW cW-W 3 P.DA3 Q.DT38 A-T WC 20-XX cWW cW-W 4 P.DT4 Q.DA37 T-A WC 20-XX cWW cW-W 5 P.DA5 Q.DT36 A-T WC 20-XX cWW cW-W 6 P.DT6 Q.DA35 T-A WC 20-XX cWW cW-W 7 P.DA7 Q.DT34 A-T WC 20-XX cWW cW-W 8 P.DT8 Q.DA33 T-A WC 20-XX cWW cW-W 9 P.DA9 Q.DT32 A-T WC 20-XX cWW cW-W 10 P.DT10 Q.DA31 T-A WC 20-XX cWW cW-W 11 P.DA11 Q.DT30 A-T WC 20-XX cWW cW-W 12 P.DT12 Q.DA29 T-A WC 20-XX cWW cW-W 13 P.DA13 Q.DT28 A-T WC 20-XX cWW cW-W 14 P.DT14 Q.DA27 T-A WC 20-XX cWW cW-W 15 P.DA15 Q.DT26 A-T WC 20-XX cWW cW-W 16 P.DT16 Q.DA25 T-A WC 20-XX cWW cW-W 17 P.DA17 Q.DT24 A-T WC 20-XX cWW cW-W 18 P.DT18 Q.DA23 T-A WC 20-XX cWW cW-W 19 P.DA19 Q.DT22 A-T WC 20-XX cWW cW-W 20 P.DT20 Q.DA21 T-A WC 20-XX cWW cW-W 21 P.DA21 Q.DT20 A-T WC 20-XX cWW cW-W 22 P.DT22 Q.DA19 T-A WC 20-XX cWW cW-W 23 P.DA23 Q.DT18 A-T WC 20-XX cWW cW-W 24 P.DT24 Q.DA17 T-A WC 20-XX cWW cW-W 25 P.DA25 Q.DT16 A-T WC 20-XX cWW cW-W 26 P.DT26 Q.DA15 T-A WC 20-XX cWW cW-W 27 P.DA27 Q.DT14 A-T WC 20-XX cWW cW-W 28 P.DT28 Q.DA13 T-A WC 20-XX cWW cW-W 29 P.DA29 Q.DT12 A-T WC 20-XX cWW cW-W 30 P.DT30 Q.DA11 T-A WC 20-XX cWW cW-W 31 P.DA31 Q.DT10 A-T WC 20-XX cWW cW-W 32 P.DT32 Q.DA9 T-A WC 20-XX cWW cW-W 33 P.DA33 Q.DT8 A-T WC 20-XX cWW cW-W 34 P.DT34 Q.DA7 T-A WC 20-XX cWW cW-W 35 P.DA35 Q.DT6 A-T WC 20-XX cWW cW-W 36 P.DT36 Q.DA5 T-A WC 20-XX cWW cW-W 37 P.DA37 Q.DT4 A-T WC 20-XX cWW cW-W 38 P.DT38 Q.DA3 T-A WC 20-XX cWW cW-W 39 P.DA39 Q.DT2 A-T WC 20-XX cWW cW-W 40 P.DT40 Q.DA1 T-A WC 20-XX cWW cW-W 41 R.DA1 S.DT40 A-T WC 20-XX cWW cW-W 42 R.DT2 S.DA39 T-A WC 20-XX cWW cW-W 43 R.DA3 S.DT38 A-T WC 20-XX cWW cW-W 44 R.DT4 S.DA37 T-A WC 20-XX cWW cW-W 45 R.DA5 S.DT36 A-T WC 20-XX cWW cW-W 46 R.DT6 S.DA35 T-A WC 20-XX cWW cW-W 47 R.DA7 S.DT34 A-T WC 20-XX cWW cW-W 48 R.DT8 S.DA33 T-A WC 20-XX cWW cW-W 49 R.DA9 S.DT32 A-T WC 20-XX cWW cW-W 50 R.DT10 S.DA31 T-A WC 20-XX cWW cW-W 51 R.DA11 S.DT30 A-T WC 20-XX cWW cW-W 52 R.DT12 S.DA29 T-A WC 20-XX cWW cW-W 53 R.DA13 S.DT28 A-T WC 20-XX cWW cW-W 54 R.DT14 S.DA27 T-A WC 20-XX cWW cW-W 55 R.DA15 S.DT26 A-T WC 20-XX cWW cW-W 56 R.DT16 S.DA25 T-A WC 20-XX cWW cW-W 57 R.DA17 S.DT24 A-T WC 20-XX cWW cW-W 58 R.DT18 S.DA23 T-A WC 20-XX cWW cW-W 59 R.DA19 S.DT22 A-T WC 20-XX cWW cW-W 60 R.DT20 S.DA21 T-A WC 20-XX cWW cW-W 61 R.DA21 S.DT20 A-T WC 20-XX cWW cW-W 62 R.DT22 S.DA19 T-A WC 20-XX cWW cW-W 63 R.DA23 S.DT18 A-T WC 20-XX cWW cW-W 64 R.DT24 S.DA17 T-A WC 20-XX cWW cW-W 65 R.DA25 S.DT16 A-T WC 20-XX cWW cW-W 66 R.DT26 S.DA15 T-A WC 20-XX cWW cW-W 67 R.DA27 S.DT14 A-T WC 20-XX cWW cW-W 68 R.DT28 S.DA13 T-A WC 20-XX cWW cW-W 69 R.DA29 S.DT12 A-T WC 20-XX cWW cW-W 70 R.DT30 S.DA11 T-A WC 20-XX cWW cW-W 71 R.DA31 S.DT10 A-T WC 20-XX cWW cW-W 72 R.DT32 S.DA9 T-A WC 20-XX cWW cW-W 73 R.DA33 S.DT8 A-T WC 20-XX cWW cW-W 74 R.DT34 S.DA7 T-A WC 20-XX cWW cW-W 75 R.DA35 S.DT6 A-T WC 20-XX cWW cW-W 76 R.DT36 S.DA5 T-A WC 20-XX cWW cW-W 77 R.DA37 S.DT4 A-T WC 20-XX cWW cW-W 78 R.DT38 S.DA3 T-A WC 20-XX cWW cW-W 79 R.DA39 S.DT2 A-T WC 20-XX cWW cW-W 80 R.DT40 S.DA1 T-A WC 20-XX cWW cW-W **************************************************************************** List of 2 helices Note: A helix is defined by base-stacking interactions, regardless of pair type and backbone connectivity, and may contain more than one stem. helix#number[stems-contained] bps=number-of-base-pairs in the helix bp-type: '|' for a canonical WC/wobble pair, '.' otherwise helix-form: classification of a dinucleotide step comprising the bp above the given designation and the bp that follows it. Types include 'A', 'B' or 'Z' for the common A-, B- and Z-form helices, '.' for an unclassified step, and 'x' for a step without a continuous backbone. -------------------------------------------------------------------- helix#1[1] bps=40 strand-1 5'-ATATATATATATATATATATATATATATATATATATATAT-3' bp-type |||||||||||||||||||||||||||||||||||||||| strand-2 3'-TATATATATATATATATATATATATATATATATATATATA-5' helix-form BBBBBBBBBBBBBBBBBBBBBBBBBBBBB.BBBBBBBBB 1 P.DA1 Q.DT40 A-T WC 20-XX cWW cW-W 2 P.DT2 Q.DA39 T-A WC 20-XX cWW cW-W 3 P.DA3 Q.DT38 A-T WC 20-XX cWW cW-W 4 P.DT4 Q.DA37 T-A WC 20-XX cWW cW-W 5 P.DA5 Q.DT36 A-T WC 20-XX cWW cW-W 6 P.DT6 Q.DA35 T-A WC 20-XX cWW cW-W 7 P.DA7 Q.DT34 A-T WC 20-XX cWW cW-W 8 P.DT8 Q.DA33 T-A WC 20-XX cWW cW-W 9 P.DA9 Q.DT32 A-T WC 20-XX cWW cW-W 10 P.DT10 Q.DA31 T-A WC 20-XX cWW cW-W 11 P.DA11 Q.DT30 A-T WC 20-XX cWW cW-W 12 P.DT12 Q.DA29 T-A WC 20-XX cWW cW-W 13 P.DA13 Q.DT28 A-T WC 20-XX cWW cW-W 14 P.DT14 Q.DA27 T-A WC 20-XX cWW cW-W 15 P.DA15 Q.DT26 A-T WC 20-XX cWW cW-W 16 P.DT16 Q.DA25 T-A WC 20-XX cWW cW-W 17 P.DA17 Q.DT24 A-T WC 20-XX cWW cW-W 18 P.DT18 Q.DA23 T-A WC 20-XX cWW cW-W 19 P.DA19 Q.DT22 A-T WC 20-XX cWW cW-W 20 P.DT20 Q.DA21 T-A WC 20-XX cWW cW-W 21 P.DA21 Q.DT20 A-T WC 20-XX cWW cW-W 22 P.DT22 Q.DA19 T-A WC 20-XX cWW cW-W 23 P.DA23 Q.DT18 A-T WC 20-XX cWW cW-W 24 P.DT24 Q.DA17 T-A WC 20-XX cWW cW-W 25 P.DA25 Q.DT16 A-T WC 20-XX cWW cW-W 26 P.DT26 Q.DA15 T-A WC 20-XX cWW cW-W 27 P.DA27 Q.DT14 A-T WC 20-XX cWW cW-W 28 P.DT28 Q.DA13 T-A WC 20-XX cWW cW-W 29 P.DA29 Q.DT12 A-T WC 20-XX cWW cW-W 30 P.DT30 Q.DA11 T-A WC 20-XX cWW cW-W 31 P.DA31 Q.DT10 A-T WC 20-XX cWW cW-W 32 P.DT32 Q.DA9 T-A WC 20-XX cWW cW-W 33 P.DA33 Q.DT8 A-T WC 20-XX cWW cW-W 34 P.DT34 Q.DA7 T-A WC 20-XX cWW cW-W 35 P.DA35 Q.DT6 A-T WC 20-XX cWW cW-W 36 P.DT36 Q.DA5 T-A WC 20-XX cWW cW-W 37 P.DA37 Q.DT4 A-T WC 20-XX cWW cW-W 38 P.DT38 Q.DA3 T-A WC 20-XX cWW cW-W 39 P.DA39 Q.DT2 A-T WC 20-XX cWW cW-W 40 P.DT40 Q.DA1 T-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- helix#2[1] bps=40 strand-1 5'-ATATATATATATATATATATATATATATATATATATATAT-3' bp-type |||||||||||||||||||||||||||||||||||||||| strand-2 3'-TATATATATATATATATATATATATATATATATATATATA-5' helix-form BBBBBBBBBBBBBBBBBBBBBBBBBBBBB.BBBBBBBBB 1 R.DA1 S.DT40 A-T WC 20-XX cWW cW-W 2 R.DT2 S.DA39 T-A WC 20-XX cWW cW-W 3 R.DA3 S.DT38 A-T WC 20-XX cWW cW-W 4 R.DT4 S.DA37 T-A WC 20-XX cWW cW-W 5 R.DA5 S.DT36 A-T WC 20-XX cWW cW-W 6 R.DT6 S.DA35 T-A WC 20-XX cWW cW-W 7 R.DA7 S.DT34 A-T WC 20-XX cWW cW-W 8 R.DT8 S.DA33 T-A WC 20-XX cWW cW-W 9 R.DA9 S.DT32 A-T WC 20-XX cWW cW-W 10 R.DT10 S.DA31 T-A WC 20-XX cWW cW-W 11 R.DA11 S.DT30 A-T WC 20-XX cWW cW-W 12 R.DT12 S.DA29 T-A WC 20-XX cWW cW-W 13 R.DA13 S.DT28 A-T WC 20-XX cWW cW-W 14 R.DT14 S.DA27 T-A WC 20-XX cWW cW-W 15 R.DA15 S.DT26 A-T WC 20-XX cWW cW-W 16 R.DT16 S.DA25 T-A WC 20-XX cWW cW-W 17 R.DA17 S.DT24 A-T WC 20-XX cWW cW-W 18 R.DT18 S.DA23 T-A WC 20-XX cWW cW-W 19 R.DA19 S.DT22 A-T WC 20-XX cWW cW-W 20 R.DT20 S.DA21 T-A WC 20-XX cWW cW-W 21 R.DA21 S.DT20 A-T WC 20-XX cWW cW-W 22 R.DT22 S.DA19 T-A WC 20-XX cWW cW-W 23 R.DA23 S.DT18 A-T WC 20-XX cWW cW-W 24 R.DT24 S.DA17 T-A WC 20-XX cWW cW-W 25 R.DA25 S.DT16 A-T WC 20-XX cWW cW-W 26 R.DT26 S.DA15 T-A WC 20-XX cWW cW-W 27 R.DA27 S.DT14 A-T WC 20-XX cWW cW-W 28 R.DT28 S.DA13 T-A WC 20-XX cWW cW-W 29 R.DA29 S.DT12 A-T WC 20-XX cWW cW-W 30 R.DT30 S.DA11 T-A WC 20-XX cWW cW-W 31 R.DA31 S.DT10 A-T WC 20-XX cWW cW-W 32 R.DT32 S.DA9 T-A WC 20-XX cWW cW-W 33 R.DA33 S.DT8 A-T WC 20-XX cWW cW-W 34 R.DT34 S.DA7 T-A WC 20-XX cWW cW-W 35 R.DA35 S.DT6 A-T WC 20-XX cWW cW-W 36 R.DT36 S.DA5 T-A WC 20-XX cWW cW-W 37 R.DA37 S.DT4 A-T WC 20-XX cWW cW-W 38 R.DT38 S.DA3 T-A WC 20-XX cWW cW-W 39 R.DA39 S.DT2 A-T WC 20-XX cWW cW-W 40 R.DT40 S.DA1 T-A WC 20-XX cWW cW-W **************************************************************************** List of 2 stems Note: A stem is defined as a helix consisting strictly of canonical WC/wobble pairs with a continuous backbone. stem#number[#helix-number containing this stem] Other terms are defined as in the above Helix section. -------------------------------------------------------------------- stem#1[#1] bps=40 strand-1 5'-ATATATATATATATATATATATATATATATATATATATAT-3' bp-type |||||||||||||||||||||||||||||||||||||||| strand-2 3'-TATATATATATATATATATATATATATATATATATATATA-5' helix-form BBBBBBBBBBBBBBBBBBBBBBBBBBBBB.BBBBBBBBB 1 P.DA1 Q.DT40 A-T WC 20-XX cWW cW-W 2 P.DT2 Q.DA39 T-A WC 20-XX cWW cW-W 3 P.DA3 Q.DT38 A-T WC 20-XX cWW cW-W 4 P.DT4 Q.DA37 T-A WC 20-XX cWW cW-W 5 P.DA5 Q.DT36 A-T WC 20-XX cWW cW-W 6 P.DT6 Q.DA35 T-A WC 20-XX cWW cW-W 7 P.DA7 Q.DT34 A-T WC 20-XX cWW cW-W 8 P.DT8 Q.DA33 T-A WC 20-XX cWW cW-W 9 P.DA9 Q.DT32 A-T WC 20-XX cWW cW-W 10 P.DT10 Q.DA31 T-A WC 20-XX cWW cW-W 11 P.DA11 Q.DT30 A-T WC 20-XX cWW cW-W 12 P.DT12 Q.DA29 T-A WC 20-XX cWW cW-W 13 P.DA13 Q.DT28 A-T WC 20-XX cWW cW-W 14 P.DT14 Q.DA27 T-A WC 20-XX cWW cW-W 15 P.DA15 Q.DT26 A-T WC 20-XX cWW cW-W 16 P.DT16 Q.DA25 T-A WC 20-XX cWW cW-W 17 P.DA17 Q.DT24 A-T WC 20-XX cWW cW-W 18 P.DT18 Q.DA23 T-A WC 20-XX cWW cW-W 19 P.DA19 Q.DT22 A-T WC 20-XX cWW cW-W 20 P.DT20 Q.DA21 T-A WC 20-XX cWW cW-W 21 P.DA21 Q.DT20 A-T WC 20-XX cWW cW-W 22 P.DT22 Q.DA19 T-A WC 20-XX cWW cW-W 23 P.DA23 Q.DT18 A-T WC 20-XX cWW cW-W 24 P.DT24 Q.DA17 T-A WC 20-XX cWW cW-W 25 P.DA25 Q.DT16 A-T WC 20-XX cWW cW-W 26 P.DT26 Q.DA15 T-A WC 20-XX cWW cW-W 27 P.DA27 Q.DT14 A-T WC 20-XX cWW cW-W 28 P.DT28 Q.DA13 T-A WC 20-XX cWW cW-W 29 P.DA29 Q.DT12 A-T WC 20-XX cWW cW-W 30 P.DT30 Q.DA11 T-A WC 20-XX cWW cW-W 31 P.DA31 Q.DT10 A-T WC 20-XX cWW cW-W 32 P.DT32 Q.DA9 T-A WC 20-XX cWW cW-W 33 P.DA33 Q.DT8 A-T WC 20-XX cWW cW-W 34 P.DT34 Q.DA7 T-A WC 20-XX cWW cW-W 35 P.DA35 Q.DT6 A-T WC 20-XX cWW cW-W 36 P.DT36 Q.DA5 T-A WC 20-XX cWW cW-W 37 P.DA37 Q.DT4 A-T WC 20-XX cWW cW-W 38 P.DT38 Q.DA3 T-A WC 20-XX cWW cW-W 39 P.DA39 Q.DT2 A-T WC 20-XX cWW cW-W 40 P.DT40 Q.DA1 T-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#2[#2] bps=40 strand-1 5'-ATATATATATATATATATATATATATATATATATATATAT-3' bp-type |||||||||||||||||||||||||||||||||||||||| strand-2 3'-TATATATATATATATATATATATATATATATATATATATA-5' helix-form BBBBBBBBBBBBBBBBBBBBBBBBBBBBB.BBBBBBBBB 1 R.DA1 S.DT40 A-T WC 20-XX cWW cW-W 2 R.DT2 S.DA39 T-A WC 20-XX cWW cW-W 3 R.DA3 S.DT38 A-T WC 20-XX cWW cW-W 4 R.DT4 S.DA37 T-A WC 20-XX cWW cW-W 5 R.DA5 S.DT36 A-T WC 20-XX cWW cW-W 6 R.DT6 S.DA35 T-A WC 20-XX cWW cW-W 7 R.DA7 S.DT34 A-T WC 20-XX cWW cW-W 8 R.DT8 S.DA33 T-A WC 20-XX cWW cW-W 9 R.DA9 S.DT32 A-T WC 20-XX cWW cW-W 10 R.DT10 S.DA31 T-A WC 20-XX cWW cW-W 11 R.DA11 S.DT30 A-T WC 20-XX cWW cW-W 12 R.DT12 S.DA29 T-A WC 20-XX cWW cW-W 13 R.DA13 S.DT28 A-T WC 20-XX cWW cW-W 14 R.DT14 S.DA27 T-A WC 20-XX cWW cW-W 15 R.DA15 S.DT26 A-T WC 20-XX cWW cW-W 16 R.DT16 S.DA25 T-A WC 20-XX cWW cW-W 17 R.DA17 S.DT24 A-T WC 20-XX cWW cW-W 18 R.DT18 S.DA23 T-A WC 20-XX cWW cW-W 19 R.DA19 S.DT22 A-T WC 20-XX cWW cW-W 20 R.DT20 S.DA21 T-A WC 20-XX cWW cW-W 21 R.DA21 S.DT20 A-T WC 20-XX cWW cW-W 22 R.DT22 S.DA19 T-A WC 20-XX cWW cW-W 23 R.DA23 S.DT18 A-T WC 20-XX cWW cW-W 24 R.DT24 S.DA17 T-A WC 20-XX cWW cW-W 25 R.DA25 S.DT16 A-T WC 20-XX cWW cW-W 26 R.DT26 S.DA15 T-A WC 20-XX cWW cW-W 27 R.DA27 S.DT14 A-T WC 20-XX cWW cW-W 28 R.DT28 S.DA13 T-A WC 20-XX cWW cW-W 29 R.DA29 S.DT12 A-T WC 20-XX cWW cW-W 30 R.DT30 S.DA11 T-A WC 20-XX cWW cW-W 31 R.DA31 S.DT10 A-T WC 20-XX cWW cW-W 32 R.DT32 S.DA9 T-A WC 20-XX cWW cW-W 33 R.DA33 S.DT8 A-T WC 20-XX cWW cW-W 34 R.DT34 S.DA7 T-A WC 20-XX cWW cW-W 35 R.DA35 S.DT6 A-T WC 20-XX cWW cW-W 36 R.DT36 S.DA5 T-A WC 20-XX cWW cW-W 37 R.DA37 S.DT4 A-T WC 20-XX cWW cW-W 38 R.DT38 S.DA3 T-A WC 20-XX cWW cW-W 39 R.DA39 S.DT2 A-T WC 20-XX cWW cW-W 40 R.DT40 S.DA1 T-A WC 20-XX cWW cW-W **************************************************************************** List of 4 base stacks Note: A stack is an ordered list of nucleotides assembled together via base-stacking interactions, regardless of backbone connectivity. Stacking interactions within a stem are *not* included. 1 nts=2 Ra A.ARG78,A.ADP1101 2 nts=2 Ra B.ARG78,B.ADP1101 3 nts=2 Ra F.ARG78,F.ADP1101 4 nts=2 Ra G.ARG78,G.ADP1101 **************************************************************************** List of 4 non-loop single-stranded segments 1 nts=1 a A.ADP1101 2 nts=1 a B.ADP1101 3 nts=1 a F.ADP1101 4 nts=1 a G.ADP1101 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >8q72 nts=164 [whole] ATATATATATATATATATATATATATATATATATATATAT&ATATATATATATATATATATATATATATATATATATATAT&ATATATATATATATATATATATATATATATATATATATAT&ATATATATATATATATATATATATATATATATATATATAT&a&a&a&a ((((((((((((((((((((((((((((((((((((((((&))))))))))))))))))))))))))))))))))))))))&((((((((((((((((((((((((((((((((((((((((&))))))))))))))))))))))))))))))))))))))))&.&.&.&. >8q72-P #1 nts=40 3.30(0.48) [chain] DNA ATATATATATATATATATATATATATATATATATATATAT (((((((((((((((((((((((((((((((((((((((( >8q72-Q #2 nts=40 3.38(0.49) [chain] DNA ATATATATATATATATATATATATATATATATATATATAT )))))))))))))))))))))))))))))))))))))))) >8q72-R #3 nts=40 3.29(0.47) [chain] DNA ATATATATATATATATATATATATATATATATATATATAT (((((((((((((((((((((((((((((((((((((((( >8q72-S #4 nts=40 3.38(0.49) [chain] DNA ATATATATATATATATATATATATATATATATATATATAT )))))))))))))))))))))))))))))))))))))))) **************************************************************************** Summary of structural features of 164 nucleotides Note: the first five columns are: (1) serial number, (2) one-letter shorthand name, (3) dbn, (4) id string, (5) rmsd (~zero) of base ring atoms fitted against those in a standard base reference frame. The sixth (last) column contains a comma-separated list of features whose meanings are mostly self-explanatory, except for: turn: angle C1'(i-1)--C1'(i)--C1'(i+1) < 90 degrees break: no backbone linkage between O3'(i-1) and P(i) 1 A ( P.DA1 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 2 T ( P.DT2 0.005 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 3 A ( P.DA3 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 4 T ( P.DT4 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 5 A ( P.DA5 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 6 T ( P.DT6 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 7 A ( P.DA7 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 8 T ( P.DT8 0.004 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem 9 A ( P.DA9 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 10 T ( P.DT10 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 11 A ( P.DA11 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 12 T ( P.DT12 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 13 A ( P.DA13 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 14 T ( P.DT14 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 15 A ( P.DA15 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 16 T ( P.DT16 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 17 A ( P.DA17 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 18 T ( P.DT18 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 19 A ( P.DA19 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 20 T ( P.DT20 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 21 A ( P.DA21 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 22 T ( P.DT22 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 23 A ( P.DA23 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 24 T ( P.DT24 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 25 A ( P.DA25 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 26 T ( P.DT26 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 27 A ( P.DA27 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 28 T ( P.DT28 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 29 A ( P.DA29 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 30 T ( P.DT30 0.006 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 31 A ( P.DA31 0.008 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,phosphate 32 T ( P.DT32 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 33 A ( P.DA33 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 34 T ( P.DT34 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 35 A ( P.DA35 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 36 T ( P.DT36 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 37 A ( P.DA37 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 38 T ( P.DT38 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 39 A ( P.DA39 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 40 T ( P.DT40 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end 41 A ) Q.DA1 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 42 T ) Q.DT2 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 43 A ) Q.DA3 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 44 T ) Q.DT4 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 45 A ) Q.DA5 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 46 T ) Q.DT6 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 47 A ) Q.DA7 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 48 T ) Q.DT8 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 49 A ) Q.DA9 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 50 T ) Q.DT10 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 51 A ) Q.DA11 0.008 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem 52 T ) Q.DT12 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 53 A ) Q.DA13 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,phosphate 54 T ) Q.DT14 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 55 A ) Q.DA15 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 56 T ) Q.DT16 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 57 A ) Q.DA17 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 58 T ) Q.DT18 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 59 A ) Q.DA19 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 60 T ) Q.DT20 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 61 A ) Q.DA21 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 62 T ) Q.DT22 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 63 A ) Q.DA23 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 64 T ) Q.DT24 0.002 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 65 A ) Q.DA25 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 66 T ) Q.DT26 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 67 A ) Q.DA27 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 68 T ) Q.DT28 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 69 A ) Q.DA29 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 70 T ) Q.DT30 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 71 A ) Q.DA31 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 72 T ) Q.DT32 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 73 A ) Q.DA33 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 74 T ) Q.DT34 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 75 A ) Q.DA35 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 76 T ) Q.DT36 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 77 A ) Q.DA37 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,phosphate 78 T ) Q.DT38 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 79 A ) Q.DA39 0.005 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 80 T ) Q.DT40 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end 81 A ( R.DA1 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 82 T ( R.DT2 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 83 A ( R.DA3 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 84 T ( R.DT4 0.003 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem 85 A ( R.DA5 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 86 T ( R.DT6 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 87 A ( R.DA7 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 88 T ( R.DT8 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 89 A ( R.DA9 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 90 T ( R.DT10 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 91 A ( R.DA11 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 92 T ( R.DT12 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 93 A ( R.DA13 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 94 T ( R.DT14 0.004 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem 95 A ( R.DA15 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 96 T ( R.DT16 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 97 A ( R.DA17 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 98 T ( R.DT18 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 99 A ( R.DA19 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 100 T ( R.DT20 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 101 A ( R.DA21 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 102 T ( R.DT22 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 103 A ( R.DA23 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 104 T ( R.DT24 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 105 A ( R.DA25 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 106 T ( R.DT26 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 107 A ( R.DA27 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 108 T ( R.DT28 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 109 A ( R.DA29 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 110 T ( R.DT30 0.006 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 111 A ( R.DA31 0.008 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem 112 T ( R.DT32 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 113 A ( R.DA33 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 114 T ( R.DT34 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 115 A ( R.DA35 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 116 T ( R.DT36 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 117 A ( R.DA37 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 118 T ( R.DT38 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 119 A ( R.DA39 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 120 T ( R.DT40 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end 121 A ) S.DA1 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 122 T ) S.DT2 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 123 A ) S.DA3 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 124 T ) S.DT4 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 125 A ) S.DA5 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 126 T ) S.DT6 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 127 A ) S.DA7 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 128 T ) S.DT8 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 129 A ) S.DA9 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 130 T ) S.DT10 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 131 A ) S.DA11 0.008 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem 132 T ) S.DT12 0.006 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 133 A ) S.DA13 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 134 T ) S.DT14 0.002 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 135 A ) S.DA15 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 136 T ) S.DT16 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 137 A ) S.DA17 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 138 T ) S.DT18 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 139 A ) S.DA19 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 140 T ) S.DT20 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 141 A ) S.DA21 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 142 T ) S.DT22 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 143 A ) S.DA23 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 144 T ) S.DT24 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 145 A ) S.DA25 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 146 T ) S.DT26 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 147 A ) S.DA27 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 148 T ) S.DT28 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 149 A ) S.DA29 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 150 T ) S.DT30 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 151 A ) S.DA31 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 152 T ) S.DT32 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 153 A ) S.DA33 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 154 T ) S.DT34 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 155 A ) S.DA35 0.005 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 156 T ) S.DT36 0.004 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem 157 A ) S.DA37 0.005 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,phosphate 158 T ) S.DT38 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 159 A ) S.DA39 0.005 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 160 T ) S.DT40 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end 161 a . A.ADP1101 0.040 modified,~C2'-endo,ss-non-loop 162 a . B.ADP1101 0.039 modified,ss-non-loop 163 a . F.ADP1101 0.041 modified,~C2'-endo,ss-non-loop 164 a . G.ADP1101 0.041 modified,~C2'-endo,ss-non-loop **************************************************************************** List of 12 additional files 1 dssr-pairs.pdb -- an ensemble of base pairs 2 dssr-stems.pdb -- an ensemble of stems 3 dssr-helices.pdb -- an ensemble of helices (coaxial stacking) 4 dssr-2ndstrs.bpseq -- secondary structure in bpseq format 5 dssr-2ndstrs.ct -- secondary structure in connectivity table format 6 dssr-2ndstrs.dbn -- secondary structure in dot-bracket notation 7 dssr-torsions.txt -- backbone torsion angles and suite names 8 dssr-stacks.pdb -- an ensemble of base stacks 9 dssr-rotmat.txt -- position vector and rotation matrix 10 dssr-viewV.pdb -- vertical view of the principal moment of inertia 11 dssr-viewH.pdb -- horizontal view of the principal moment of inertia 12 dssr-viewT.pdb -- top view of the principal moment of inertia