**************************************************************************** Note: By default, each nucleotide is identified by chainId.name#. So a common case would be B.A1689, meaning adenosine #1689 on chain B. One-letter base names for modified nucleotides are put in lower case (e.g., 'c' for 5MC). For further information about the output notation, please refer to the DSSR User Manual. Questions and suggestions are *always* welcome on the 3DNA Forum. Command: x3dna-dssr -i=4yit.pdb -o=4yit.out File name: 4yit.pdb no. of DNA/RNA chains: 4 [B=25,C=25,E=24,F=24] no. of nucleotides: 98 no. of atoms: 6162 no. of waters: 19 no. of metals: 5 [Ca=5] **************************************************************************** List of 47 base pairs nt1 nt2 bp name Saenger LW DSSR 1 B.DA2 C.DT24 A-T WC 20-XX cWW cW-W 2 B.DG3 C.DC23 G-C WC 19-XIX cWW cW-W 3 B.DG4 C.DC22 G-C WC 19-XIX cWW cW-W 4 B.DT5 C.DA21 T-A WC 20-XX cWW cW-W 5 B.DA6 C.DT20 A-T WC 20-XX cWW cW-W 6 B.DC7 C.DG19 C-G WC 19-XIX cWW cW-W 7 B.DC8 C.DG18 C-G WC 19-XIX cWW cW-W 8 B.DC9 C.DG17 C-G WC 19-XIX cWW cW-W 9 B.DT10 C.DA16 T-A WC 20-XX cWW cW-W 10 B.DT11 C.DA15 T-A WC 20-XX cWW cW-W 11 B.DT12 C.DA14 T-A WC 20-XX cWW cW-W 12 B.DA13 C.DT13 A-T WC 20-XX cWW cW-W 13 B.DA14 C.DT12 A-T WC 20-XX cWW cW-W 14 B.DA15 C.DT11 A-T WC 20-XX cWW cW-W 15 B.DC16 C.DG10 C-G WC 19-XIX cWW cW-W 16 B.DC17 C.DG9 C-G WC 19-XIX cWW cW-W 17 B.DT18 C.DA8 T-A WC 20-XX cWW cW-W 18 B.DA19 C.DT7 A-T WC 20-XX cWW cW-W 19 B.DC20 C.DG6 C-G WC 19-XIX cWW cW-W 20 B.DT21 C.DA5 T-A WC 20-XX cWW cW-W 21 B.DA22 C.DT4 A-T WC 20-XX cWW cW-W 22 B.DA23 C.DT3 A-T WC 20-XX cWW cW-W 23 B.DC24 C.DG2 C-G WC 19-XIX cWW cW-W 24 B.DC25 C.DG1 C-G WC 19-XIX cWW cW-W 25 E.DA2 F.DT24 A-T WC 20-XX cWW cW-W 26 E.DG3 F.DC23 G-C WC 19-XIX cWW cW-W 27 E.DG4 F.DC22 G-C WC 19-XIX cWW cW-W 28 E.DT5 F.DA21 T-A WC 20-XX cWW cW-W 29 E.DA6 F.DT20 A-T WC 20-XX cWW cW-W 30 E.DC7 F.DG19 C-G WC 19-XIX cWW cW-W 31 E.DC8 F.DG18 C-G WC 19-XIX cWW cW-W 32 E.DC9 F.DG17 C-G WC 19-XIX cWW cW-W 33 E.DT10 F.DA16 T-A WC 20-XX cWW cW-W 34 E.DT11 F.DA15 T-A WC 20-XX cWW cW-W 35 E.DT12 F.DA14 T-A WC 20-XX cWW cW-W 36 E.DA13 F.DT13 A-T WC 20-XX cWW cW-W 37 E.DA14 F.DT12 A-T WC 20-XX cWW cW-W 38 E.DA15 F.DT11 A-T WC 20-XX cWW cW-W 39 E.DC16 F.DG10 C-G WC 19-XIX cWW cW-W 40 E.DC17 F.DG9 C-G WC 19-XIX cWW cW-W 41 E.DT18 F.DA8 T-A WC 20-XX cWW cW-W 42 E.DA19 F.DT7 A-T WC 20-XX cWW cW-W 43 E.DC20 F.DG6 C-G WC 19-XIX cWW cW-W 44 E.DT21 F.DA5 T-A WC 20-XX cWW cW-W 45 E.DA22 F.DT4 A-T WC 20-XX cWW cW-W 46 E.DA23 F.DT3 A-T WC 20-XX cWW cW-W 47 E.DC24 F.DG2 C-G WC 19-XIX cWW cW-W **************************************************************************** List of 2 helices Note: a helix is defined by base-stacking interactions, regardless of bp 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=24 strand-1 5'-AGGTACCCTTTAAACCTACTAACC-3' bp-type |||||||||||||||||||||||| strand-2 3'-TCCATGGGAAATTTGGATGATTGG-5' helix-form B...B...BB.B....BBBBB.. 1 B.DA2 C.DT24 A-T WC 20-XX cWW cW-W 2 B.DG3 C.DC23 G-C WC 19-XIX cWW cW-W 3 B.DG4 C.DC22 G-C WC 19-XIX cWW cW-W 4 B.DT5 C.DA21 T-A WC 20-XX cWW cW-W 5 B.DA6 C.DT20 A-T WC 20-XX cWW cW-W 6 B.DC7 C.DG19 C-G WC 19-XIX cWW cW-W 7 B.DC8 C.DG18 C-G WC 19-XIX cWW cW-W 8 B.DC9 C.DG17 C-G WC 19-XIX cWW cW-W 9 B.DT10 C.DA16 T-A WC 20-XX cWW cW-W 10 B.DT11 C.DA15 T-A WC 20-XX cWW cW-W 11 B.DT12 C.DA14 T-A WC 20-XX cWW cW-W 12 B.DA13 C.DT13 A-T WC 20-XX cWW cW-W 13 B.DA14 C.DT12 A-T WC 20-XX cWW cW-W 14 B.DA15 C.DT11 A-T WC 20-XX cWW cW-W 15 B.DC16 C.DG10 C-G WC 19-XIX cWW cW-W 16 B.DC17 C.DG9 C-G WC 19-XIX cWW cW-W 17 B.DT18 C.DA8 T-A WC 20-XX cWW cW-W 18 B.DA19 C.DT7 A-T WC 20-XX cWW cW-W 19 B.DC20 C.DG6 C-G WC 19-XIX cWW cW-W 20 B.DT21 C.DA5 T-A WC 20-XX cWW cW-W 21 B.DA22 C.DT4 A-T WC 20-XX cWW cW-W 22 B.DA23 C.DT3 A-T WC 20-XX cWW cW-W 23 B.DC24 C.DG2 C-G WC 19-XIX cWW cW-W 24 B.DC25 C.DG1 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#2[1] bps=23 strand-1 5'-AGGTACCCTTTAAACCTACTAAC-3' bp-type ||||||||||||||||||||||| strand-2 3'-TCCATGGGAAATTTGGATGATTG-5' helix-form ..B.....BB......B..B.. 1 E.DA2 F.DT24 A-T WC 20-XX cWW cW-W 2 E.DG3 F.DC23 G-C WC 19-XIX cWW cW-W 3 E.DG4 F.DC22 G-C WC 19-XIX cWW cW-W 4 E.DT5 F.DA21 T-A WC 20-XX cWW cW-W 5 E.DA6 F.DT20 A-T WC 20-XX cWW cW-W 6 E.DC7 F.DG19 C-G WC 19-XIX cWW cW-W 7 E.DC8 F.DG18 C-G WC 19-XIX cWW cW-W 8 E.DC9 F.DG17 C-G WC 19-XIX cWW cW-W 9 E.DT10 F.DA16 T-A WC 20-XX cWW cW-W 10 E.DT11 F.DA15 T-A WC 20-XX cWW cW-W 11 E.DT12 F.DA14 T-A WC 20-XX cWW cW-W 12 E.DA13 F.DT13 A-T WC 20-XX cWW cW-W 13 E.DA14 F.DT12 A-T WC 20-XX cWW cW-W 14 E.DA15 F.DT11 A-T WC 20-XX cWW cW-W 15 E.DC16 F.DG10 C-G WC 19-XIX cWW cW-W 16 E.DC17 F.DG9 C-G WC 19-XIX cWW cW-W 17 E.DT18 F.DA8 T-A WC 20-XX cWW cW-W 18 E.DA19 F.DT7 A-T WC 20-XX cWW cW-W 19 E.DC20 F.DG6 C-G WC 19-XIX cWW cW-W 20 E.DT21 F.DA5 T-A WC 20-XX cWW cW-W 21 E.DA22 F.DT4 A-T WC 20-XX cWW cW-W 22 E.DA23 F.DT3 A-T WC 20-XX cWW cW-W 23 E.DC24 F.DG2 C-G WC 19-XIX cWW cW-W **************************************************************************** List of 2 stems Note: a stem is defined as a helix consisting of only 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=24 strand-1 5'-AGGTACCCTTTAAACCTACTAACC-3' bp-type |||||||||||||||||||||||| strand-2 3'-TCCATGGGAAATTTGGATGATTGG-5' helix-form B...B...BB.B....BBBBB.. 1 B.DA2 C.DT24 A-T WC 20-XX cWW cW-W 2 B.DG3 C.DC23 G-C WC 19-XIX cWW cW-W 3 B.DG4 C.DC22 G-C WC 19-XIX cWW cW-W 4 B.DT5 C.DA21 T-A WC 20-XX cWW cW-W 5 B.DA6 C.DT20 A-T WC 20-XX cWW cW-W 6 B.DC7 C.DG19 C-G WC 19-XIX cWW cW-W 7 B.DC8 C.DG18 C-G WC 19-XIX cWW cW-W 8 B.DC9 C.DG17 C-G WC 19-XIX cWW cW-W 9 B.DT10 C.DA16 T-A WC 20-XX cWW cW-W 10 B.DT11 C.DA15 T-A WC 20-XX cWW cW-W 11 B.DT12 C.DA14 T-A WC 20-XX cWW cW-W 12 B.DA13 C.DT13 A-T WC 20-XX cWW cW-W 13 B.DA14 C.DT12 A-T WC 20-XX cWW cW-W 14 B.DA15 C.DT11 A-T WC 20-XX cWW cW-W 15 B.DC16 C.DG10 C-G WC 19-XIX cWW cW-W 16 B.DC17 C.DG9 C-G WC 19-XIX cWW cW-W 17 B.DT18 C.DA8 T-A WC 20-XX cWW cW-W 18 B.DA19 C.DT7 A-T WC 20-XX cWW cW-W 19 B.DC20 C.DG6 C-G WC 19-XIX cWW cW-W 20 B.DT21 C.DA5 T-A WC 20-XX cWW cW-W 21 B.DA22 C.DT4 A-T WC 20-XX cWW cW-W 22 B.DA23 C.DT3 A-T WC 20-XX cWW cW-W 23 B.DC24 C.DG2 C-G WC 19-XIX cWW cW-W 24 B.DC25 C.DG1 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#2[#2] bps=23 strand-1 5'-AGGTACCCTTTAAACCTACTAAC-3' bp-type ||||||||||||||||||||||| strand-2 3'-TCCATGGGAAATTTGGATGATTG-5' helix-form ..B.....BB......B..B.. 1 E.DA2 F.DT24 A-T WC 20-XX cWW cW-W 2 E.DG3 F.DC23 G-C WC 19-XIX cWW cW-W 3 E.DG4 F.DC22 G-C WC 19-XIX cWW cW-W 4 E.DT5 F.DA21 T-A WC 20-XX cWW cW-W 5 E.DA6 F.DT20 A-T WC 20-XX cWW cW-W 6 E.DC7 F.DG19 C-G WC 19-XIX cWW cW-W 7 E.DC8 F.DG18 C-G WC 19-XIX cWW cW-W 8 E.DC9 F.DG17 C-G WC 19-XIX cWW cW-W 9 E.DT10 F.DA16 T-A WC 20-XX cWW cW-W 10 E.DT11 F.DA15 T-A WC 20-XX cWW cW-W 11 E.DT12 F.DA14 T-A WC 20-XX cWW cW-W 12 E.DA13 F.DT13 A-T WC 20-XX cWW cW-W 13 E.DA14 F.DT12 A-T WC 20-XX cWW cW-W 14 E.DA15 F.DT11 A-T WC 20-XX cWW cW-W 15 E.DC16 F.DG10 C-G WC 19-XIX cWW cW-W 16 E.DC17 F.DG9 C-G WC 19-XIX cWW cW-W 17 E.DT18 F.DA8 T-A WC 20-XX cWW cW-W 18 E.DA19 F.DT7 A-T WC 20-XX cWW cW-W 19 E.DC20 F.DG6 C-G WC 19-XIX cWW cW-W 20 E.DT21 F.DA5 T-A WC 20-XX cWW cW-W 21 E.DA22 F.DT4 A-T WC 20-XX cWW cW-W 22 E.DA23 F.DT3 A-T WC 20-XX cWW cW-W 23 E.DC24 F.DG2 C-G WC 19-XIX 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 CC B.DC25,B.DC26 2 nts=2 TG C.DT24,C.DG25 3 nts=2 CC E.DC24,E.DC25 4 nts=2 TG F.DT24,F.DG25 **************************************************************************** List of 4 non-loop single-stranded segments 1 nts=1 C B.DC26 2 nts=1 G C.DG25 3 nts=1 C E.DC25 4 nts=1 G F.DG25 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >4yit nts=98 [whole] AGGTACCCTTTAAACCTACTAACCC&GGTTAGTAGGTTTAAAGGGTACCTG&AGGTACCCTTTAAACCTACTAACC>TAGTAGGTTTAAAGGGTACCTG ((((((((((((((((((((((((.&)))))))))))))))))))))))).&(((((((((((((((((((((((.&))))))))))))))))))))))). >4yit-B #1 nts=25 3.15(0.81) [chain] DNA AGGTACCCTTTAAACCTACTAACCC ((((((((((((((((((((((((. >4yit-C #2 nts=25 3.31(0.78) [chain] DNA GGTTAGTAGGTTTAAAGGGTACCTG )))))))))))))))))))))))). >4yit-E #3 nts=24 3.13(0.80) [chain] DNA AGGTACCCTTTAAACCTACTAACC (((((((((((((((((((((((. >4yit-F #4 nts=24 3.32(0.81) [chain] DNA GTTAGTAGGTTTAAAGGGTACCTG ))))))))))))))))))))))). **************************************************************************** Summary of structural features of 98 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 ( B.DA2 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 2 G ( B.DG3 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 3 G ( B.DG4 0.007 anti,BI,canonical,non-pair-contact,helix,stem,phosphate 4 T ( B.DT5 0.007 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 5 A ( B.DA6 0.004 anti,canonical,non-pair-contact,helix,stem 6 C ( B.DC7 0.009 anti,~C3'-endo,canonical,non-pair-contact,helix,stem 7 C ( B.DC8 0.004 anti,~C3'-endo,canonical,non-pair-contact,helix,stem 8 C ( B.DC9 0.004 anti,BI,canonical,non-pair-contact,helix,stem 9 T ( B.DT10 0.002 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 10 T ( B.DT11 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 11 T ( B.DT12 0.007 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 12 A ( B.DA13 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 13 A ( B.DA14 0.007 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,phosphate 14 A ( B.DA15 0.008 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 15 C ( B.DC16 0.004 anti,BI,canonical,non-pair-contact,helix,stem,phosphate 16 C ( B.DC17 0.012 anti,BI,canonical,non-pair-contact,helix,stem,phosphate 17 T ( B.DT18 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 18 A ( B.DA19 0.006 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 19 C ( B.DC20 0.002 anti,BI,canonical,non-pair-contact,helix,stem 20 T ( B.DT21 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 21 A ( B.DA22 0.008 anti,canonical,non-pair-contact,helix,stem 22 A ( B.DA23 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 23 C ( B.DC24 0.006 anti,~C3'-endo,canonical,non-pair-contact,helix,stem 24 C ( B.DC25 0.003 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end 25 C . B.DC26 0.003 anti,~C2'-endo,non-pair-contact,ss-non-loop 26 G ) C.DG1 0.007 anti,canonical,non-pair-contact,helix-end,stem-end 27 G ) C.DG2 0.007 anti,BI,canonical,non-pair-contact,helix,stem 28 T ) C.DT3 0.006 anti,BI,canonical,non-pair-contact,helix,stem,phosphate 29 T ) C.DT4 0.007 anti,canonical,non-pair-contact,helix,stem,phosphate 30 A ) C.DA5 0.005 anti,BI,canonical,non-pair-contact,helix,stem,phosphate 31 G ) C.DG6 0.010 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 32 T ) C.DT7 0.002 anti,BI,canonical,non-pair-contact,helix,stem 33 A ) C.DA8 0.003 anti,BI,canonical,non-pair-contact,helix,stem 34 G ) C.DG9 0.005 anti,BI,canonical,non-pair-contact,helix,stem 35 G ) C.DG10 0.005 anti,BI,canonical,non-pair-contact,helix,stem 36 T ) C.DT11 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 37 T ) C.DT12 0.006 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 38 T ) C.DT13 0.005 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem 39 A ) C.DA14 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 40 A ) C.DA15 0.008 anti,canonical,non-pair-contact,helix,stem,phosphate 41 A ) C.DA16 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 42 G ) C.DG17 0.009 anti,canonical,non-pair-contact,helix,stem 43 G ) C.DG18 0.006 anti,BI,canonical,non-pair-contact,helix,stem,phosphate 44 G ) C.DG19 0.007 anti,BI,canonical,non-pair-contact,helix,stem,phosphate 45 T ) C.DT20 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 46 A ) C.DA21 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 47 C ) C.DC22 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 48 C ) C.DC23 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 49 T ) C.DT24 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 50 G . C.DG25 0.005 anti,non-pair-contact,ss-non-loop 51 A ( E.DA2 0.014 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 52 G ( E.DG3 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 53 G ( E.DG4 0.007 anti,BI,canonical,non-pair-contact,helix,stem 54 T ( E.DT5 0.006 anti,BI,canonical,non-pair-contact,helix,stem,phosphate 55 A ( E.DA6 0.006 anti,canonical,non-pair-contact,helix,stem 56 C ( E.DC7 0.002 anti,~C3'-endo,canonical,non-pair-contact,helix,stem 57 C ( E.DC8 0.006 anti,~C3'-endo,canonical,non-pair-contact,helix,stem 58 C ( E.DC9 0.003 anti,BI,canonical,non-pair-contact,helix,stem 59 T ( E.DT10 0.002 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 60 T ( E.DT11 0.002 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 61 T ( E.DT12 0.009 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem 62 A ( E.DA13 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 63 A ( E.DA14 0.008 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,phosphate 64 A ( E.DA15 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 65 C ( E.DC16 0.003 anti,BI,canonical,non-pair-contact,helix,stem 66 C ( E.DC17 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 67 T ( E.DT18 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 68 A ( E.DA19 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 69 C ( E.DC20 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 70 T ( E.DT21 0.002 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 71 A ( E.DA22 0.007 anti,canonical,non-pair-contact,helix,stem 72 A ( E.DA23 0.007 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 73 C ( E.DC24 0.005 anti,canonical,non-pair-contact,helix-end,stem-end 74 C . E.DC25 0.003 anti,non-pair-contact,ss-non-loop 75 G ) F.DG2 0.004 anti,BI,canonical,non-pair-contact,helix-end,stem-end 76 T ) F.DT3 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 77 T ) F.DT4 0.004 anti,canonical,non-pair-contact,helix,stem,phosphate 78 A ) F.DA5 0.005 anti,BI,canonical,non-pair-contact,helix,stem,phosphate 79 G ) F.DG6 0.003 anti,BI,canonical,non-pair-contact,helix,stem 80 T ) F.DT7 0.003 anti,BI,canonical,non-pair-contact,helix,stem 81 A ) F.DA8 0.004 anti,BI,canonical,non-pair-contact,helix,stem 82 G ) F.DG9 0.004 anti,BI,canonical,non-pair-contact,helix,stem 83 G ) F.DG10 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 84 T ) F.DT11 0.002 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 85 T ) F.DT12 0.002 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 86 T ) F.DT13 0.002 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem 87 A ) F.DA14 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 88 A ) F.DA15 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 89 A ) F.DA16 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 90 G ) F.DG17 0.006 anti,BI,canonical,non-pair-contact,helix,stem 91 G ) F.DG18 0.008 anti,BI,canonical,non-pair-contact,helix,stem,phosphate 92 G ) F.DG19 0.009 anti,canonical,non-pair-contact,helix,stem,phosphate 93 T ) F.DT20 0.011 anti,BI,canonical,non-pair-contact,helix,stem 94 A ) F.DA21 0.007 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 95 C ) F.DC22 0.006 anti,BI,canonical,non-pair-contact,helix,stem 96 C ) F.DC23 0.003 anti,~C3'-endo,canonical,non-pair-contact,helix,stem 97 T ) F.DT24 0.004 anti,BI,canonical,non-pair-contact,helix-end,stem-end 98 G . F.DG25 0.003 anti,~C3'-endo,non-pair-contact,ss-non-loop **************************************************************************** List of 8 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