**************************************************************************** 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=1rcs.pdb -o=1rcs.out File name: 1rcs.pdb no. of DNA/RNA chains: 2 [E=20,F=20] no. of nucleotides: 40 no. of atoms: 4704 no. of waters: 0 no. of metals: 0 **************************************************************************** List of 20 base pairs nt1 nt2 bp name Saenger LW DSSR 1 E.DC1 F.DG20 C-G WC 19-XIX cWW cW-W 2 E.DG2 F.DC19 G-C WC 19-XIX cWW cW-W 3 E.DT3 F.DA18 T-A WC 20-XX cWW cW-W 4 E.DA4 F.DT17 A-T WC 20-XX cWW cW-W 5 E.DC5 F.DG16 C-G WC 19-XIX cWW cW-W 6 E.DT6 F.DA15 T-A WC 20-XX cWW cW-W 7 E.DA7 F.DT14 A-T WC 20-XX cWW cW-W 8 E.DG8 F.DC13 G-C WC 19-XIX cWW cW-W 9 E.DT9 F.DA12 T-A WC 20-XX cWW cW-W 10 E.DT10 F.DA11 T-A WC 20-XX cWW cW-W 11 E.DA11 F.DT10 A-T WC 20-XX cWW cW-W 12 E.DA12 F.DT9 A-T WC 20-XX cWW cW-W 13 E.DC13 F.DG8 C-G WC 19-XIX cWW cW-W 14 E.DT14 F.DA7 T-A WC 20-XX cWW cW-W 15 E.DA15 F.DT6 A-T WC 20-XX cWW cW-W 16 E.DG16 F.DC5 G-C WC 19-XIX cWW cW-W 17 E.DT17 F.DA4 T-A WC 20-XX cWW cW-W 18 E.DA18 F.DT3 A-T WC 20-XX cWW cW-W 19 E.DC19 F.DG2 C-G WC 19-XIX cWW cW-W 20 E.DG20 F.DC1 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=20 strand-1 5'-CGTACTAGTTAACTAGTACG-3' bp-type |||||||||||||||||||| strand-2 3'-GCATGATCAATTGATCATGC-5' helix-form .BB.B.....B...B.... 1 E.DC1 F.DG20 C-G WC 19-XIX cWW cW-W 2 E.DG2 F.DC19 G-C WC 19-XIX cWW cW-W 3 E.DT3 F.DA18 T-A WC 20-XX cWW cW-W 4 E.DA4 F.DT17 A-T WC 20-XX cWW cW-W 5 E.DC5 F.DG16 C-G WC 19-XIX cWW cW-W 6 E.DT6 F.DA15 T-A WC 20-XX cWW cW-W 7 E.DA7 F.DT14 A-T WC 20-XX cWW cW-W 8 E.DG8 F.DC13 G-C WC 19-XIX cWW cW-W 9 E.DT9 F.DA12 T-A WC 20-XX cWW cW-W 10 E.DT10 F.DA11 T-A WC 20-XX cWW cW-W 11 E.DA11 F.DT10 A-T WC 20-XX cWW cW-W 12 E.DA12 F.DT9 A-T WC 20-XX cWW cW-W 13 E.DC13 F.DG8 C-G WC 19-XIX cWW cW-W 14 E.DT14 F.DA7 T-A WC 20-XX cWW cW-W 15 E.DA15 F.DT6 A-T WC 20-XX cWW cW-W 16 E.DG16 F.DC5 G-C WC 19-XIX cWW cW-W 17 E.DT17 F.DA4 T-A WC 20-XX cWW cW-W 18 E.DA18 F.DT3 A-T WC 20-XX cWW cW-W 19 E.DC19 F.DG2 C-G WC 19-XIX cWW cW-W 20 E.DG20 F.DC1 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=20 strand-1 5'-CGTACTAGTTAACTAGTACG-3' bp-type |||||||||||||||||||| strand-2 3'-GCATGATCAATTGATCATGC-5' helix-form .BB.B.....B...B.... 1 E.DC1 F.DG20 C-G WC 19-XIX cWW cW-W 2 E.DG2 F.DC19 G-C WC 19-XIX cWW cW-W 3 E.DT3 F.DA18 T-A WC 20-XX cWW cW-W 4 E.DA4 F.DT17 A-T WC 20-XX cWW cW-W 5 E.DC5 F.DG16 C-G WC 19-XIX cWW cW-W 6 E.DT6 F.DA15 T-A WC 20-XX cWW cW-W 7 E.DA7 F.DT14 A-T WC 20-XX cWW cW-W 8 E.DG8 F.DC13 G-C WC 19-XIX cWW cW-W 9 E.DT9 F.DA12 T-A WC 20-XX cWW cW-W 10 E.DT10 F.DA11 T-A WC 20-XX cWW cW-W 11 E.DA11 F.DT10 A-T WC 20-XX cWW cW-W 12 E.DA12 F.DT9 A-T WC 20-XX cWW cW-W 13 E.DC13 F.DG8 C-G WC 19-XIX cWW cW-W 14 E.DT14 F.DA7 T-A WC 20-XX cWW cW-W 15 E.DA15 F.DT6 A-T WC 20-XX cWW cW-W 16 E.DG16 F.DC5 G-C WC 19-XIX cWW cW-W 17 E.DT17 F.DA4 T-A WC 20-XX cWW cW-W 18 E.DA18 F.DT3 A-T WC 20-XX cWW cW-W 19 E.DC19 F.DG2 C-G WC 19-XIX cWW cW-W 20 E.DG20 F.DC1 G-C WC 19-XIX cWW cW-W **************************************************************************** Nucleotides not involved in stacking interactions nts=1 C E.DC1 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >1rcs nts=40 [whole] CGTACTAGTTAACTAGTACG&CGTACTAGTTAACTAGTACG ((((((((((((((((((((&)))))))))))))))))))) >1rcs-E #1 nts=20 3.53(0.75) [chain] DNA CGTACTAGTTAACTAGTACG (((((((((((((((((((( >1rcs-F #2 nts=20 3.63(0.67) [chain] DNA CGTACTAGTTAACTAGTACG )))))))))))))))))))) **************************************************************************** Summary of structural features of 40 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 ( E.DC1 0.020 anti,non-stack,canonical,non-pair-contact,helix-end,stem-end 2 G ( E.DG2 0.028 anti,canonical,non-pair-contact,helix,stem 3 T ( E.DT3 0.030 anti,canonical,non-pair-contact,helix,stem 4 A ( E.DA4 0.029 anti,canonical,non-pair-contact,helix,stem 5 C ( E.DC5 0.020 anti,BII,canonical,non-pair-contact,helix,stem 6 T ( E.DT6 0.032 anti,canonical,non-pair-contact,helix,stem 7 A ( E.DA7 0.038 anti,canonical,non-pair-contact,helix,stem 8 G ( E.DG8 0.028 anti,canonical,non-pair-contact,helix,stem 9 T ( E.DT9 0.034 anti,canonical,non-pair-contact,helix,stem 10 T ( E.DT10 0.029 anti,canonical,non-pair-contact,helix,stem 11 A ( E.DA11 0.028 anti,BI,canonical,non-pair-contact,helix,stem 12 A ( E.DA12 0.028 anti,canonical,non-pair-contact,helix,stem 13 C ( E.DC13 0.027 anti,canonical,non-pair-contact,helix,stem,phosphate 14 T ( E.DT14 0.028 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 15 A ( E.DA15 0.034 anti,canonical,non-pair-contact,helix,stem 16 G ( E.DG16 0.030 anti,canonical,non-pair-contact,helix,stem 17 T ( E.DT17 0.034 anti,canonical,non-pair-contact,helix,stem 18 A ( E.DA18 0.029 anti,BI,canonical,non-pair-contact,helix,stem 19 C ( E.DC19 0.021 anti,canonical,non-pair-contact,helix,stem 20 G ( E.DG20 0.029 anti,canonical,non-pair-contact,helix-end,stem-end 21 C ) F.DC1 0.018 anti,BI,canonical,non-pair-contact,helix-end,stem-end 22 G ) F.DG2 0.029 anti,canonical,non-pair-contact,helix,stem 23 T ) F.DT3 0.034 anti,BI,canonical,non-pair-contact,helix,stem 24 A ) F.DA4 0.030 anti,BI,canonical,non-pair-contact,helix,stem 25 C ) F.DC5 0.024 anti,canonical,non-pair-contact,helix,stem 26 T ) F.DT6 0.031 anti,canonical,non-pair-contact,helix,stem 27 A ) F.DA7 0.035 anti,BI,canonical,non-pair-contact,helix,stem 28 G ) F.DG8 0.027 anti,BI,canonical,non-pair-contact,helix,stem 29 T ) F.DT9 0.036 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem 30 T ) F.DT10 0.031 anti,canonical,non-pair-contact,helix,stem 31 A ) F.DA11 0.030 anti,BI,canonical,non-pair-contact,helix,stem 32 A ) F.DA12 0.028 anti,BI,canonical,non-pair-contact,helix,stem 33 C ) F.DC13 0.018 anti,BI,canonical,non-pair-contact,helix,stem,phosphate 34 T ) F.DT14 0.031 anti,BI,canonical,non-pair-contact,helix,stem 35 A ) F.DA15 0.034 anti,BI,canonical,non-pair-contact,helix,stem 36 G ) F.DG16 0.031 anti,canonical,non-pair-contact,helix,stem 37 T ) F.DT17 0.033 anti,BI,canonical,non-pair-contact,helix,stem 38 A ) F.DA18 0.029 anti,canonical,non-pair-contact,helix,stem 39 C ) F.DC19 0.022 anti,canonical,non-pair-contact,helix,stem 40 G ) F.DG20 0.028 anti,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