**************************************************************************** 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=5ju4.pdb -o=5ju4.out File name: 5ju4.pdb no. of DNA/RNA chains: 2 [A=12,B=12] no. of nucleotides: 24 no. of atoms: 544 no. of waters: 56 no. of metals: 1 [Mg=1] **************************************************************************** List of 12 base pairs nt1 nt2 bp name Saenger LW DSSR 1 A.DC1 B.DG24 C-G WC 19-XIX cWW cW-W 2 A.DG2 B.DC23 G-C WC 19-XIX cWW cW-W 3 A.DT3 B.DA22 T-A WC 20-XX cWW cW-W 4 A.DG4 B.DC21 G-C WC 19-XIX cWW cW-W 5 A.DA5 B.DT20 A-T WC 20-XX cWW cW-W 6 A.DA6 B.DT19 A-T WC 20-XX cWW cW-W 7 A.DT7 B.DA18 T-A WC 20-XX cWW cW-W 8 A.DT8 B.DA17 T-A WC 20-XX cWW cW-W 9 A.DC9 B.DG16 C-G WC 19-XIX cWW cW-W 10 A.DA10 B.DT15 A-T WC 20-XX cWW cW-W 11 A.DC11 B.DG14 C-G WC 19-XIX cWW cW-W 12 A.DG12 B.DC13 G-C WC 19-XIX 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=12 strand-1 5'-CGTGAATTCACG-3' bp-type |||||||||||| strand-2 3'-GCACTTAAGTGC-5' helix-form BBBBBBBBBBB 1 A.DC1 B.DG24 C-G WC 19-XIX cWW cW-W 2 A.DG2 B.DC23 G-C WC 19-XIX cWW cW-W 3 A.DT3 B.DA22 T-A WC 20-XX cWW cW-W 4 A.DG4 B.DC21 G-C WC 19-XIX cWW cW-W 5 A.DA5 B.DT20 A-T WC 20-XX cWW cW-W 6 A.DA6 B.DT19 A-T WC 20-XX cWW cW-W 7 A.DT7 B.DA18 T-A WC 20-XX cWW cW-W 8 A.DT8 B.DA17 T-A WC 20-XX cWW cW-W 9 A.DC9 B.DG16 C-G WC 19-XIX cWW cW-W 10 A.DA10 B.DT15 A-T WC 20-XX cWW cW-W 11 A.DC11 B.DG14 C-G WC 19-XIX cWW cW-W 12 A.DG12 B.DC13 G-C WC 19-XIX 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=12 strand-1 5'-CGTGAATTCACG-3' bp-type |||||||||||| strand-2 3'-GCACTTAAGTGC-5' helix-form BBBBBBBBBBB 1 A.DC1 B.DG24 C-G WC 19-XIX cWW cW-W 2 A.DG2 B.DC23 G-C WC 19-XIX cWW cW-W 3 A.DT3 B.DA22 T-A WC 20-XX cWW cW-W 4 A.DG4 B.DC21 G-C WC 19-XIX cWW cW-W 5 A.DA5 B.DT20 A-T WC 20-XX cWW cW-W 6 A.DA6 B.DT19 A-T WC 20-XX cWW cW-W 7 A.DT7 B.DA18 T-A WC 20-XX cWW cW-W 8 A.DT8 B.DA17 T-A WC 20-XX cWW cW-W 9 A.DC9 B.DG16 C-G WC 19-XIX cWW cW-W 10 A.DA10 B.DT15 A-T WC 20-XX cWW cW-W 11 A.DC11 B.DG14 C-G WC 19-XIX cWW cW-W 12 A.DG12 B.DC13 G-C WC 19-XIX cWW cW-W **************************************************************************** Nucleotides not involved in stacking interactions nts=1 C B.DC13 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >5ju4 nts=24 [whole] CGTGAATTCACG&CGTGAATTCACG ((((((((((((&)))))))))))) >5ju4-A #1 nts=12 3.14(0.39) [chain] DNA CGTGAATTCACG (((((((((((( >5ju4-B #2 nts=12 3.34(0.32) [chain] DNA CGTGAATTCACG )))))))))))) **************************************************************************** Summary of structural features of 24 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 C ( A.DC1 0.013 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end 2 G ( A.DG2 0.011 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 3 T ( A.DT3 0.016 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 4 G ( A.DG4 0.017 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 5 A ( A.DA5 0.026 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 6 A ( A.DA6 0.017 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 7 T ( A.DT7 0.013 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 8 T ( A.DT8 0.008 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 9 C ( A.DC9 0.014 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 10 A ( A.DA10 0.015 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem 11 C ( A.DC11 0.014 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 12 G ( A.DG12 0.011 anti,canonical,non-pair-contact,helix-end,stem-end 13 C ) B.DC13 0.010 anti,~C2'-endo,BII,non-stack,canonical,helix-end,stem-end 14 G ) B.DG14 0.013 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 15 T ) B.DT15 0.012 anti,BI,canonical,non-pair-contact,helix,stem 16 G ) B.DG16 0.018 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 17 A ) B.DA17 0.014 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 18 A ) B.DA18 0.020 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 19 T ) B.DT19 0.015 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 20 T ) B.DT20 0.013 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 21 C ) B.DC21 0.014 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 22 A ) B.DA22 0.010 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 23 C ) B.DC23 0.010 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 24 G ) B.DG24 0.012 anti,~C3'-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