**************************************************************************** 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=2p66.pdb -o=2p66.out File name: 2p66.pdb no. of DNA/RNA chains: 3 [B=16,C=11,D=6] no. of nucleotides: 33 no. of atoms: 3363 no. of waters: 136 no. of metals: 3 [Na=3] **************************************************************************** List of 1 type of 1 modified nucleotide nt count list 1 3DR-? 1 D.3DR0 **************************************************************************** List of 15 base pairs nt1 nt2 bp name Saenger LW DSSR 1 B.DC1 D.DG5 C-G WC 19-XIX cWW cW-W 2 B.DC2 D.DG4 C-G WC 19-XIX cWW cW-W 3 B.DG3 D.DC3 G-C WC 19-XIX cWW cW-W 4 B.DA4 D.DT2 A-T WC 20-XX cWW cW-W 5 B.DC5 D.DG1 C-G WC 19-XIX cWW cW-W 6 B.DG7 C.DC10 G-C WC 19-XIX cWW cW-W 7 B.DC8 C.DG9 C-G WC 19-XIX cWW cW-W 8 B.DG9 C.DC8 G-C WC 19-XIX cWW cW-W 9 B.DC10 C.DG7 C-G WC 19-XIX cWW cW-W 10 B.DA11 C.DT6 A-T WC 20-XX cWW cW-W 11 B.DT12 C.DA5 T-A WC 20-XX cWW cW-W 12 B.DC13 C.DG4 C-G WC 19-XIX cWW cW-W 13 B.DA14 C.DT3 A-T WC 20-XX cWW cW-W 14 B.DG15 C.DC2 G-C WC 19-XIX cWW cW-W 15 B.DC16 C.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 BB.B 1 B.DC1 D.DG5 C-G WC 19-XIX cWW cW-W 2 B.DC2 D.DG4 C-G WC 19-XIX cWW cW-W 3 B.DG3 D.DC3 G-C WC 19-XIX cWW cW-W 4 B.DA4 D.DT2 A-T WC 20-XX cWW cW-W 5 B.DC5 D.DG1 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#2[1] bps=10 strand-1 5'-GCGCATCAGC-3' bp-type |||||||||| strand-2 3'-CGCGTAGTCG-5' helix-form BBBBBBBB. 1 B.DG7 C.DC10 G-C WC 19-XIX cWW cW-W 2 B.DC8 C.DG9 C-G WC 19-XIX cWW cW-W 3 B.DG9 C.DC8 G-C WC 19-XIX cWW cW-W 4 B.DC10 C.DG7 C-G WC 19-XIX cWW cW-W 5 B.DA11 C.DT6 A-T WC 20-XX cWW cW-W 6 B.DT12 C.DA5 T-A WC 20-XX cWW cW-W 7 B.DC13 C.DG4 C-G WC 19-XIX cWW cW-W 8 B.DA14 C.DT3 A-T WC 20-XX cWW cW-W 9 B.DG15 C.DC2 G-C WC 19-XIX cWW cW-W 10 B.DC16 C.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 BB.B 1 B.DC1 D.DG5 C-G WC 19-XIX cWW cW-W 2 B.DC2 D.DG4 C-G WC 19-XIX cWW cW-W 3 B.DG3 D.DC3 G-C WC 19-XIX cWW cW-W 4 B.DA4 D.DT2 A-T WC 20-XX cWW cW-W 5 B.DC5 D.DG1 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#2[#2] bps=10 strand-1 5'-GCGCATCAGC-3' bp-type |||||||||| strand-2 3'-CGCGTAGTCG-5' helix-form BBBBBBBB. 1 B.DG7 C.DC10 G-C WC 19-XIX cWW cW-W 2 B.DC8 C.DG9 C-G WC 19-XIX cWW cW-W 3 B.DG9 C.DC8 G-C WC 19-XIX cWW cW-W 4 B.DC10 C.DG7 C-G WC 19-XIX cWW cW-W 5 B.DA11 C.DT6 A-T WC 20-XX cWW cW-W 6 B.DT12 C.DA5 T-A WC 20-XX cWW cW-W 7 B.DC13 C.DG4 C-G WC 19-XIX cWW cW-W 8 B.DA14 C.DT3 A-T WC 20-XX cWW cW-W 9 B.DG15 C.DC2 G-C WC 19-XIX cWW cW-W 10 B.DC16 C.DG1 C-G WC 19-XIX cWW cW-W **************************************************************************** List of 3 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 CH B.DC5,A.HIS34 2 nts=2 AG B.DA6,B.DG7 3 nts=2 CY C.DC11,A.TYR271 **************************************************************************** List of 3 non-loop single-stranded segments 1 nts=1 A B.DA6 2 nts=1 C C.DC11 3 nts=1 ? D.3DR0 **************************************************************************** List of 1 splayed-apart dinucleotide 1 B.DC5 B.DA6 angle=148 distance=17.4 ratio=0.96 ---------------------------------------------------------------- Summary of 1 splayed-apart unit 1 nts=2 CA B.DC5,B.DA6 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >2p66 nts=33 [whole] CCGACAGCGCATCAGC&GCTGATGCGCC&?GTCGG (((((.((((((((((&)))))))))).&.))))) >2p66-B #1 nts=16 2.57(1.24) [chain] DNA CCGACAGCGCATCAGC (((((.(((((((((( >2p66-C #2 nts=11 3.62(0.51) [chain] DNA GCTGATGCGCC )))))))))). >2p66-D #3 nts=6 2.22(0.55) [chain] DNA ?GTCGG .))))) **************************************************************************** Summary of structural features of 33 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 ( B.DC1 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 2 C ( B.DC2 0.008 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 3 G ( B.DG3 0.010 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 4 A ( B.DA4 0.016 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 5 C ( B.DC5 0.005 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end,splayed-apart 6 A . B.DA6 0.007 anti,~C2'-endo,BI,non-pair-contact,ss-non-loop,splayed-apart 7 G ( B.DG7 0.005 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end 8 C ( B.DC8 0.007 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 9 G ( B.DG9 0.015 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 10 C ( B.DC10 0.010 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 11 A ( B.DA11 0.010 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 12 T ( B.DT12 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 13 C ( B.DC13 0.008 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 14 A ( B.DA14 0.014 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 15 G ( B.DG15 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 16 C ( B.DC16 0.006 anti,canonical,non-pair-contact,helix-end,stem-end 17 G ) C.DG1 0.016 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 18 C ) C.DC2 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 19 T ) C.DT3 0.010 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 20 G ) C.DG4 0.018 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 21 A ) C.DA5 0.012 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 22 T ) C.DT6 0.010 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 23 G ) C.DG7 0.013 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 24 C ) C.DC8 0.011 anti,BI,canonical,non-pair-contact,helix,stem,phosphate 25 G ) C.DG9 0.017 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 26 C ) C.DC10 0.012 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end,phosphate 27 C . C.DC11 0.005 anti,~C2'-endo,ss-non-loop,phosphate 28 ? . D.3DR0 --- modified,~C2'-endo,BI,non-stack,ss-non-loop 29 G ) D.DG1 0.012 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,phosphate 30 T ) D.DT2 0.017 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 31 C ) D.DC3 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 32 G ) D.DG4 0.005 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 33 G ) D.DG5 0.020 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