**************************************************************************** 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=6cly.pdb -o=6cly.out File name: 6cly.pdb no. of DNA/RNA chains: 3 [D=5,P=10,T=16] no. of nucleotides: 31 no. of atoms: 3354 no. of waters: 126 no. of metals: 2 [Na=2] **************************************************************************** List of 1 type of 1 modified nucleotide nt count list 1 F74-g 1 T.F74/6 **************************************************************************** List of 15 base pairs nt1 nt2 bp name Saenger LW DSSR 1 T.DC1 D.DG5 C-G WC 19-XIX cWW cW-W 2 T.DC2 D.DG4 C-G WC 19-XIX cWW cW-W 3 T.DG3 D.DC3 G-C WC 19-XIX cWW cW-W 4 T.DA4 D.DT2 A-T WC 20-XX cWW cW-W 5 T.DC5 D.DG1 C-G WC 19-XIX cWW cW-W 6 T.DT7 P.DA10 T-A WC 20-XX cWW cW-W 7 T.DC8 P.DG9 C-G WC 19-XIX cWW cW-W 8 T.DG9 P.DC8 G-C WC 19-XIX cWW cW-W 9 T.DC10 P.DG7 C-G WC 19-XIX cWW cW-W 10 T.DA11 P.DT6 A-T WC 20-XX cWW cW-W 11 T.DT12 P.DA5 T-A WC 20-XX cWW cW-W 12 T.DC13 P.DG4 C-G WC 19-XIX cWW cW-W 13 T.DA14 P.DT3 A-T WC 20-XX cWW cW-W 14 T.DG15 P.DC2 G-C WC 19-XIX cWW cW-W 15 T.DC16 P.DG1 C-G 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=5 strand-1 5'-CCGAC-3' bp-type ||||| strand-2 3'-GGCTG-5' helix-form BBBB 1 T.DC1 D.DG5 C-G WC 19-XIX cWW cW-W 2 T.DC2 D.DG4 C-G WC 19-XIX cWW cW-W 3 T.DG3 D.DC3 G-C WC 19-XIX cWW cW-W 4 T.DA4 D.DT2 A-T WC 20-XX cWW cW-W 5 T.DC5 D.DG1 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#2[1] bps=10 strand-1 5'-TCGCATCAGC-3' bp-type |||||||||| strand-2 3'-AGCGTAGTCG-5' helix-form BBBBBBBBB 1 T.DT7 P.DA10 T-A WC 20-XX cWW cW-W 2 T.DC8 P.DG9 C-G WC 19-XIX cWW cW-W 3 T.DG9 P.DC8 G-C WC 19-XIX cWW cW-W 4 T.DC10 P.DG7 C-G WC 19-XIX cWW cW-W 5 T.DA11 P.DT6 A-T WC 20-XX cWW cW-W 6 T.DT12 P.DA5 T-A WC 20-XX cWW cW-W 7 T.DC13 P.DG4 C-G WC 19-XIX cWW cW-W 8 T.DA14 P.DT3 A-T WC 20-XX cWW cW-W 9 T.DG15 P.DC2 G-C WC 19-XIX cWW cW-W 10 T.DC16 P.DG1 C-G 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=5 strand-1 5'-CCGAC-3' bp-type ||||| strand-2 3'-GGCTG-5' helix-form BBBB 1 T.DC1 D.DG5 C-G WC 19-XIX cWW cW-W 2 T.DC2 D.DG4 C-G WC 19-XIX cWW cW-W 3 T.DG3 D.DC3 G-C WC 19-XIX cWW cW-W 4 T.DA4 D.DT2 A-T WC 20-XX cWW cW-W 5 T.DC5 D.DG1 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#2[#2] bps=10 strand-1 5'-TCGCATCAGC-3' bp-type |||||||||| strand-2 3'-AGCGTAGTCG-5' helix-form BBBBBBBBB 1 T.DT7 P.DA10 T-A WC 20-XX cWW cW-W 2 T.DC8 P.DG9 C-G WC 19-XIX cWW cW-W 3 T.DG9 P.DC8 G-C WC 19-XIX cWW cW-W 4 T.DC10 P.DG7 C-G WC 19-XIX cWW cW-W 5 T.DA11 P.DT6 A-T WC 20-XX cWW cW-W 6 T.DT12 P.DA5 T-A WC 20-XX cWW cW-W 7 T.DC13 P.DG4 C-G WC 19-XIX cWW cW-W 8 T.DA14 P.DT3 A-T WC 20-XX cWW cW-W 9 T.DG15 P.DC2 G-C WC 19-XIX cWW cW-W 10 T.DC16 P.DG1 C-G 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 HC A.HIS34,T.DC5 2 nts=2 gT T.F74/6,T.DT7 **************************************************************************** List of 1 non-loop single-stranded segment 1 nts=1 g T.F74/6 **************************************************************************** List of 1 splayed-apart dinucleotide 1 T.DC5 T.F74/6 angle=130 distance=15.2 ratio=0.91 ---------------------------------------------------------------- Summary of 1 splayed-apart unit 1 nts=2 Cg T.DC5,T.F74/6 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >6cly nts=31 [whole] CCGACgTCGCATCAGC&GCTGATGCGA>CGG (((((.((((((((((&))))))))))&))))) >6cly-T #1 nts=16 2.57(1.30) [chain] DNA CCGACgTCGCATCAGC (((((.(((((((((( >6cly-P #2 nts=10 3.44(0.29) [chain] DNA GCTGATGCGA )))))))))) >6cly-D #3 nts=5 4.28(0.27) [chain] DNA GTCGG ))))) **************************************************************************** Summary of structural features of 31 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 ( T.DC1 0.002 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 2 C ( T.DC2 0.002 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 3 G ( T.DG3 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 4 A ( T.DA4 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 5 C ( T.DC5 0.002 anti,canonical,non-pair-contact,helix-end,stem-end,splayed-apart 6 g . T.F74/6 0.073 modified,syn,~C2'-endo,BI,non-pair-contact,ss-non-loop,phosphate,splayed-apart 7 T ( T.DT7 0.002 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 8 C ( T.DC8 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 9 G ( T.DG9 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 10 C ( T.DC10 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 11 A ( T.DA11 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 12 T ( T.DT12 0.002 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 13 C ( T.DC13 0.002 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 14 A ( T.DA14 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 15 G ( T.DG15 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 16 C ( T.DC16 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end 17 G ) P.DG1 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 18 C ) P.DC2 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 19 T ) P.DT3 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 20 G ) P.DG4 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 21 A ) P.DA5 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 22 T ) P.DT6 0.002 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 23 G ) P.DG7 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 24 C ) P.DC8 0.003 anti,BI,canonical,non-pair-contact,helix,stem,phosphate 25 G ) P.DG9 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 26 A ) P.DA10 0.003 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end,phosphate 27 G ) D.DG1 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,phosphate 28 T ) D.DT2 0.002 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 29 C ) D.DC3 0.002 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 30 G ) D.DG4 0.002 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem 31 G ) D.DG5 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end **************************************************************************** List of 9 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-splays.pdb -- an ensemble of splayed-apart units 9 dssr-stacks.pdb -- an ensemble of base stacks