**************************************************************************** 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=5o63.pdb -o=5o63.out File name: 5o63.pdb no. of DNA/RNA chains: 4 [C=9,D=9,E=9,F=9] no. of nucleotides: 36 no. of atoms: 3661 no. of waters: 419 no. of metals: 0 **************************************************************************** List of 18 base pairs nt1 nt2 bp name Saenger LW DSSR 1 C.DG-4 D.DC4 G-C WC 19-XIX cWW cW-W 2 C.DC-3 D.DG3 C-G WC 19-XIX cWW cW-W 3 C.DC-2 D.DG2 C-G WC 19-XIX cWW cW-W 4 C.DC-1 D.DG1 C-G WC 19-XIX cWW cW-W 5 C.DT0 D.DA0 T-A WC 20-XX cWW cW-W 6 C.DG1 D.DC-1 G-C WC 19-XIX cWW cW-W 7 C.DG2 D.DC-2 G-C WC 19-XIX cWW cW-W 8 C.DC3 D.DG-3 C-G WC 19-XIX cWW cW-W 9 C.DG4 D.DC-4 G-C WC 19-XIX cWW cW-W 10 E.DG-4 F.DC4 G-C WC 19-XIX cWW cW-W 11 E.DC-3 F.DG3 C-G WC 19-XIX cWW cW-W 12 E.DC-2 F.DG2 C-G WC 19-XIX cWW cW-W 13 E.DC-1 F.DG1 C-G WC 19-XIX cWW cW-W 14 E.DT0 F.DA0 T-A WC 20-XX cWW cW-W 15 E.DG1 F.DC-1 G-C WC 19-XIX cWW cW-W 16 E.DG2 F.DC-2 G-C WC 19-XIX cWW cW-W 17 E.DC3 F.DG-3 C-G WC 19-XIX cWW cW-W 18 E.DG4 F.DC-4 G-C 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=9 strand-1 5'-GCCCTGGCG-3' bp-type ||||||||| strand-2 3'-CGGGACCGC-5' helix-form B......B 1 C.DG-4 D.DC4 G-C WC 19-XIX cWW cW-W 2 C.DC-3 D.DG3 C-G WC 19-XIX cWW cW-W 3 C.DC-2 D.DG2 C-G WC 19-XIX cWW cW-W 4 C.DC-1 D.DG1 C-G WC 19-XIX cWW cW-W 5 C.DT0 D.DA0 T-A WC 20-XX cWW cW-W 6 C.DG1 D.DC-1 G-C WC 19-XIX cWW cW-W 7 C.DG2 D.DC-2 G-C WC 19-XIX cWW cW-W 8 C.DC3 D.DG-3 C-G WC 19-XIX cWW cW-W 9 C.DG4 D.DC-4 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#2[1] bps=9 strand-1 5'-GCCCTGGCG-3' bp-type ||||||||| strand-2 3'-CGGGACCGC-5' helix-form .......B 1 E.DG-4 F.DC4 G-C WC 19-XIX cWW cW-W 2 E.DC-3 F.DG3 C-G WC 19-XIX cWW cW-W 3 E.DC-2 F.DG2 C-G WC 19-XIX cWW cW-W 4 E.DC-1 F.DG1 C-G WC 19-XIX cWW cW-W 5 E.DT0 F.DA0 T-A WC 20-XX cWW cW-W 6 E.DG1 F.DC-1 G-C WC 19-XIX cWW cW-W 7 E.DG2 F.DC-2 G-C WC 19-XIX cWW cW-W 8 E.DC3 F.DG-3 C-G WC 19-XIX cWW cW-W 9 E.DG4 F.DC-4 G-C 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=9 strand-1 5'-GCCCTGGCG-3' bp-type ||||||||| strand-2 3'-CGGGACCGC-5' helix-form B......B 1 C.DG-4 D.DC4 G-C WC 19-XIX cWW cW-W 2 C.DC-3 D.DG3 C-G WC 19-XIX cWW cW-W 3 C.DC-2 D.DG2 C-G WC 19-XIX cWW cW-W 4 C.DC-1 D.DG1 C-G WC 19-XIX cWW cW-W 5 C.DT0 D.DA0 T-A WC 20-XX cWW cW-W 6 C.DG1 D.DC-1 G-C WC 19-XIX cWW cW-W 7 C.DG2 D.DC-2 G-C WC 19-XIX cWW cW-W 8 C.DC3 D.DG-3 C-G WC 19-XIX cWW cW-W 9 C.DG4 D.DC-4 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#2[#2] bps=9 strand-1 5'-GCCCTGGCG-3' bp-type ||||||||| strand-2 3'-CGGGACCGC-5' helix-form .......B 1 E.DG-4 F.DC4 G-C WC 19-XIX cWW cW-W 2 E.DC-3 F.DG3 C-G WC 19-XIX cWW cW-W 3 E.DC-2 F.DG2 C-G WC 19-XIX cWW cW-W 4 E.DC-1 F.DG1 C-G WC 19-XIX cWW cW-W 5 E.DT0 F.DA0 T-A WC 20-XX cWW cW-W 6 E.DG1 F.DC-1 G-C WC 19-XIX cWW cW-W 7 E.DG2 F.DC-2 G-C WC 19-XIX cWW cW-W 8 E.DC3 F.DG-3 C-G WC 19-XIX cWW cW-W 9 E.DG4 F.DC-4 G-C WC 19-XIX cWW cW-W **************************************************************************** List of 1 base stack 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 HC B.HIS76,D.DC4 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >5o63 nts=36 [whole] GCCCTGGCG&CGCCAGGGC&GCCCTGGCG&CGCCAGGGC (((((((((&)))))))))&(((((((((&))))))))) >5o63-C #1 nts=9 3.72(0.61) [chain] DNA GCCCTGGCG ((((((((( >5o63-D #2 nts=9 3.41(0.37) [chain] DNA CGCCAGGGC ))))))))) >5o63-E #3 nts=9 3.75(0.57) [chain] DNA GCCCTGGCG ((((((((( >5o63-F #4 nts=9 3.77(0.46) [chain] DNA CGCCAGGGC ))))))))) **************************************************************************** Summary of structural features of 36 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 ( C.DG-4 0.023 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 2 C ( C.DC-3 0.032 anti,BI,canonical,non-pair-contact,helix,stem,phosphate 3 C ( C.DC-2 0.029 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 4 C ( C.DC-1 0.019 anti,BI,canonical,non-pair-contact,helix,stem,phosphate 5 T ( C.DT0 0.017 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,phosphate 6 G ( C.DG1 0.018 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 7 G ( C.DG2 0.024 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 8 C ( C.DC3 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 9 G ( C.DG4 0.015 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end 10 C ) D.DC-4 0.019 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 11 G ) D.DG-3 0.022 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 12 C ) D.DC-2 0.021 anti,BI,canonical,non-pair-contact,helix,stem 13 C ) D.DC-1 0.024 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 14 A ) D.DA0 0.024 anti,BI,canonical,non-pair-contact,helix,stem 15 G ) D.DG1 0.024 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem 16 G ) D.DG2 0.020 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 17 G ) D.DG3 0.018 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 18 C ) D.DC4 0.013 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end 19 G ( E.DG-4 0.016 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 20 C ( E.DC-3 0.014 anti,BI,canonical,non-pair-contact,helix,stem 21 C ( E.DC-2 0.022 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 22 C ( E.DC-1 0.017 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 23 T ( E.DT0 0.021 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,phosphate 24 G ( E.DG1 0.017 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 25 G ( E.DG2 0.027 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 26 C ( E.DC3 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 27 G ( E.DG4 0.011 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end 28 C ) F.DC-4 0.024 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 29 G ) F.DG-3 0.016 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 30 C ) F.DC-2 0.016 anti,BI,canonical,non-pair-contact,helix,stem 31 C ) F.DC-1 0.025 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 32 A ) F.DA0 0.019 anti,BI,canonical,non-pair-contact,helix,stem 33 G ) F.DG1 0.017 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem 34 G ) F.DG2 0.019 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 35 G ) F.DG3 0.016 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 36 C ) F.DC4 0.017 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end **************************************************************************** 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