**************************************************************************** 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=5w43.pdb -o=5w43.out File name: 5w43.pdb no. of DNA/RNA chains: 2 [E=22,F=22] no. of nucleotides: 44 no. of atoms: 3970 no. of waters: 0 no. of metals: 0 **************************************************************************** List of 22 base pairs nt1 nt2 bp name Saenger LW DSSR 1 E.DG1 F.DC44 G-C WC 19-XIX cWW cW-W 2 E.DA2 F.DT43 A-T WC 20-XX cWW cW-W 3 E.DT3 F.DA42 T-A WC 20-XX cWW cW-W 4 E.DT4 F.DA41 T-A WC 20-XX cWW cW-W 5 E.DT5 F.DA40 T-A WC 20-XX cWW cW-W 6 E.DA6 F.DT39 A-T WC 20-XX cWW cW-W 7 E.DG7 F.DC38 G-C WC 19-XIX cWW cW-W 8 E.DG8 F.DC37 G-C WC 19-XIX cWW cW-W 9 E.DA9 F.DT36 A-T WC 20-XX cWW cW-W 10 E.DA10 F.DT35 A-T WC 20-XX cWW cW-W 11 E.DA11 F.DT34 A-T WC 20-XX cWW cW-W 12 E.DA12 F.DT33 A-T WC 20-XX cWW cW-W 13 E.DA13 F.DT32 A-T WC 20-XX cWW cW-W 14 E.DT14 F.DA31 T-A WC 20-XX cWW cW-W 15 E.DC15 F.DG30 C-G WC 19-XIX cWW cW-W 16 E.DT16 F.DA29 T-A WC 20-XX cWW cW-W 17 E.DT17 F.DA28 T-A WC 20-XX cWW cW-W 18 E.DA18 F.DT27 A-T WC 20-XX cWW cW-W 19 E.DG19 F.DC26 G-C WC 19-XIX cWW cW-W 20 E.DA20 F.DT25 A-T WC 20-XX cWW cW-W 21 E.DT21 F.DA24 T-A WC 20-XX cWW cW-W 22 E.DA22 F.DT23 A-T WC 20-XX cWW cW-W **************************************************************************** List of 1 helix 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=22 strand-1 5'-GATTTAGGAAAAATCTTAGATA-3' bp-type |||||||||||||||||||||| strand-2 3'-CTAAATCCTTTTTAGAATCTAT-5' helix-form BB....BBBBBB.B..BBBBB 1 E.DG1 F.DC44 G-C WC 19-XIX cWW cW-W 2 E.DA2 F.DT43 A-T WC 20-XX cWW cW-W 3 E.DT3 F.DA42 T-A WC 20-XX cWW cW-W 4 E.DT4 F.DA41 T-A WC 20-XX cWW cW-W 5 E.DT5 F.DA40 T-A WC 20-XX cWW cW-W 6 E.DA6 F.DT39 A-T WC 20-XX cWW cW-W 7 E.DG7 F.DC38 G-C WC 19-XIX cWW cW-W 8 E.DG8 F.DC37 G-C WC 19-XIX cWW cW-W 9 E.DA9 F.DT36 A-T WC 20-XX cWW cW-W 10 E.DA10 F.DT35 A-T WC 20-XX cWW cW-W 11 E.DA11 F.DT34 A-T WC 20-XX cWW cW-W 12 E.DA12 F.DT33 A-T WC 20-XX cWW cW-W 13 E.DA13 F.DT32 A-T WC 20-XX cWW cW-W 14 E.DT14 F.DA31 T-A WC 20-XX cWW cW-W 15 E.DC15 F.DG30 C-G WC 19-XIX cWW cW-W 16 E.DT16 F.DA29 T-A WC 20-XX cWW cW-W 17 E.DT17 F.DA28 T-A WC 20-XX cWW cW-W 18 E.DA18 F.DT27 A-T WC 20-XX cWW cW-W 19 E.DG19 F.DC26 G-C WC 19-XIX cWW cW-W 20 E.DA20 F.DT25 A-T WC 20-XX cWW cW-W 21 E.DT21 F.DA24 T-A WC 20-XX cWW cW-W 22 E.DA22 F.DT23 A-T WC 20-XX cWW cW-W **************************************************************************** List of 1 stem 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=22 strand-1 5'-GATTTAGGAAAAATCTTAGATA-3' bp-type |||||||||||||||||||||| strand-2 3'-CTAAATCCTTTTTAGAATCTAT-5' helix-form BB....BBBBBB.B..BBBBB 1 E.DG1 F.DC44 G-C WC 19-XIX cWW cW-W 2 E.DA2 F.DT43 A-T WC 20-XX cWW cW-W 3 E.DT3 F.DA42 T-A WC 20-XX cWW cW-W 4 E.DT4 F.DA41 T-A WC 20-XX cWW cW-W 5 E.DT5 F.DA40 T-A WC 20-XX cWW cW-W 6 E.DA6 F.DT39 A-T WC 20-XX cWW cW-W 7 E.DG7 F.DC38 G-C WC 19-XIX cWW cW-W 8 E.DG8 F.DC37 G-C WC 19-XIX cWW cW-W 9 E.DA9 F.DT36 A-T WC 20-XX cWW cW-W 10 E.DA10 F.DT35 A-T WC 20-XX cWW cW-W 11 E.DA11 F.DT34 A-T WC 20-XX cWW cW-W 12 E.DA12 F.DT33 A-T WC 20-XX cWW cW-W 13 E.DA13 F.DT32 A-T WC 20-XX cWW cW-W 14 E.DT14 F.DA31 T-A WC 20-XX cWW cW-W 15 E.DC15 F.DG30 C-G WC 19-XIX cWW cW-W 16 E.DT16 F.DA29 T-A WC 20-XX cWW cW-W 17 E.DT17 F.DA28 T-A WC 20-XX cWW cW-W 18 E.DA18 F.DT27 A-T WC 20-XX cWW cW-W 19 E.DG19 F.DC26 G-C WC 19-XIX cWW cW-W 20 E.DA20 F.DT25 A-T WC 20-XX cWW cW-W 21 E.DT21 F.DA24 T-A WC 20-XX cWW cW-W 22 E.DA22 F.DT23 A-T WC 20-XX cWW cW-W **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >5w43 nts=44 [whole] GATTTAGGAAAAATCTTAGATA&TATCTAAGATTTTTCCTAAATC ((((((((((((((((((((((&)))))))))))))))))))))) >5w43-E #1 nts=22 3.09(0.66) [chain] DNA GATTTAGGAAAAATCTTAGATA (((((((((((((((((((((( >5w43-F #2 nts=22 3.04(0.67) [chain] DNA TATCTAAGATTTTTCCTAAATC )))))))))))))))))))))) **************************************************************************** Summary of structural features of 44 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 G ( E.DG1 0.007 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end 2 A ( E.DA2 0.007 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 3 T ( E.DT3 0.010 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 4 T ( E.DT4 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 5 T ( E.DT5 0.006 anti,BI,canonical,non-pair-contact,helix,stem,phosphate 6 A ( E.DA6 0.012 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,phosphate 7 G ( E.DG7 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 8 G ( E.DG8 0.009 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 9 A ( E.DA9 0.009 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 10 A ( E.DA10 0.015 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 11 A ( E.DA11 0.021 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 12 A ( E.DA12 0.016 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 13 A ( E.DA13 0.010 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 14 T ( E.DT14 0.009 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 15 C ( E.DC15 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 16 T ( E.DT16 0.004 anti,BI,canonical,non-pair-contact,helix,stem 17 T ( E.DT17 0.003 anti,canonical,non-pair-contact,helix,stem 18 A ( E.DA18 0.008 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 19 G ( E.DG19 0.007 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 20 A ( E.DA20 0.010 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 21 T ( E.DT21 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 22 A ( E.DA22 0.010 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end 23 T ) F.DT23 0.008 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 24 A ) F.DA24 0.012 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 25 T ) F.DT25 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 26 C ) F.DC26 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 27 T ) F.DT27 0.012 anti,BI,canonical,non-pair-contact,helix,stem,phosphate 28 A ) F.DA28 0.018 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,phosphate 29 A ) F.DA29 0.013 anti,BI,canonical,non-pair-contact,helix,stem 30 G ) F.DG30 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 31 A ) F.DA31 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 32 T ) F.DT32 0.008 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 33 T ) F.DT33 0.007 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 34 T ) F.DT34 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 35 T ) F.DT35 0.005 anti,BI,canonical,non-pair-contact,helix,stem,phosphate 36 T ) F.DT36 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 37 C ) F.DC37 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 38 C ) F.DC38 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 39 T ) F.DT39 0.003 anti,BI,canonical,non-pair-contact,helix,stem 40 A ) F.DA40 0.005 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 41 A ) F.DA41 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 42 A ) F.DA42 0.007 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 43 T ) F.DT43 0.002 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 44 C ) F.DC44 0.007 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end **************************************************************************** List of 7 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