**************************************************************************** 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=1llm.pdb -o=1llm.out File name: 1llm.pdb no. of DNA/RNA chains: 2 [A=13,B=13] no. of nucleotides: 26 no. of atoms: 2279 no. of waters: 312 no. of metals: 4 [Zn=4] **************************************************************************** List of 12 base pairs nt1 nt2 bp name Saenger LW DSSR 1 A.DC2 B.DG33 C-G WC 19-XIX cWW cW-W 2 A.DC3 B.DG32 C-G WC 19-XIX cWW cW-W 3 A.DC4 B.DG31 C-G WC 19-XIX cWW cW-W 4 A.DA5 B.DT30 A-T WC 20-XX cWW cW-W 5 A.DC6 B.DG29 C-G WC 19-XIX cWW cW-W 6 A.DG7 B.DC28 G-C WC 19-XIX cWW cW-W 7 A.DC8 B.DG27 C-G WC 19-XIX cWW cW-W 8 A.DG9 B.DC26 G-C WC 19-XIX cWW cW-W 9 A.DT10 B.DA25 T-A WC 20-XX cWW cW-W 10 A.DG11 B.DC24 G-C WC 19-XIX cWW cW-W 11 A.DG12 B.DC23 G-C WC 19-XIX cWW cW-W 12 A.DG13 B.DC22 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'-CCCACGCGTGGG-3' bp-type |||||||||||| strand-2 3'-GGGTGCGCACCC-5' helix-form BBBBBBBBB.. 1 A.DC2 B.DG33 C-G WC 19-XIX cWW cW-W 2 A.DC3 B.DG32 C-G WC 19-XIX cWW cW-W 3 A.DC4 B.DG31 C-G WC 19-XIX cWW cW-W 4 A.DA5 B.DT30 A-T WC 20-XX cWW cW-W 5 A.DC6 B.DG29 C-G WC 19-XIX cWW cW-W 6 A.DG7 B.DC28 G-C WC 19-XIX cWW cW-W 7 A.DC8 B.DG27 C-G WC 19-XIX cWW cW-W 8 A.DG9 B.DC26 G-C WC 19-XIX cWW cW-W 9 A.DT10 B.DA25 T-A WC 20-XX cWW cW-W 10 A.DG11 B.DC24 G-C WC 19-XIX cWW cW-W 11 A.DG12 B.DC23 G-C WC 19-XIX cWW cW-W 12 A.DG13 B.DC22 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'-CCCACGCGTGGG-3' bp-type |||||||||||| strand-2 3'-GGGTGCGCACCC-5' helix-form BBBBBBBBB.. 1 A.DC2 B.DG33 C-G WC 19-XIX cWW cW-W 2 A.DC3 B.DG32 C-G WC 19-XIX cWW cW-W 3 A.DC4 B.DG31 C-G WC 19-XIX cWW cW-W 4 A.DA5 B.DT30 A-T WC 20-XX cWW cW-W 5 A.DC6 B.DG29 C-G WC 19-XIX cWW cW-W 6 A.DG7 B.DC28 G-C WC 19-XIX cWW cW-W 7 A.DC8 B.DG27 C-G WC 19-XIX cWW cW-W 8 A.DG9 B.DC26 G-C WC 19-XIX cWW cW-W 9 A.DT10 B.DA25 T-A WC 20-XX cWW cW-W 10 A.DG11 B.DC24 G-C WC 19-XIX cWW cW-W 11 A.DG12 B.DC23 G-C WC 19-XIX cWW cW-W 12 A.DG13 B.DC22 G-C WC 19-XIX cWW cW-W **************************************************************************** List of 2 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 TC A.DT1,A.DC2 2 nts=2 TD B.DT21,D.ASP217 **************************************************************************** List of 2 non-loop single-stranded segments 1 nts=1 T A.DT1 2 nts=1 T B.DT21 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >1llm nts=26 [whole] TCCCACGCGTGGG&TCCCACGCGTGGG .((((((((((((&.)))))))))))) >1llm-A #1 nts=13 3.31(0.42) [chain] DNA TCCCACGCGTGGG .(((((((((((( >1llm-B #2 nts=13 3.09(0.79) [chain] DNA TCCCACGCGTGGG .)))))))))))) **************************************************************************** Summary of structural features of 26 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 T . A.DT1 0.014 anti,~C2'-endo,BI,non-pair-contact,ss-non-loop 2 C ( A.DC2 0.023 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end 3 C ( A.DC3 0.014 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 4 C ( A.DC4 0.012 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 5 A ( A.DA5 0.015 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 6 C ( A.DC6 0.013 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 7 G ( A.DG7 0.009 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 8 C ( A.DC8 0.022 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 9 G ( A.DG9 0.011 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 10 T ( A.DT10 0.014 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 11 G ( A.DG11 0.011 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 12 G ( A.DG12 0.016 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 13 G ( A.DG13 0.017 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end 14 T . B.DT21 0.017 anti,ss-non-loop 15 C ) B.DC22 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 16 C ) B.DC23 0.020 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 17 C ) B.DC24 0.013 anti,BI,canonical,non-pair-contact,helix,stem 18 A ) B.DA25 0.017 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 19 C ) B.DC26 0.013 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 20 G ) B.DG27 0.019 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 21 C ) B.DC28 0.022 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 22 G ) B.DG29 0.013 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 23 T ) B.DT30 0.018 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 24 G ) B.DG31 0.012 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 25 G ) B.DG32 0.010 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 26 G ) B.DG33 0.010 anti,~C2'-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