**************************************************************************** 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=4h29.pdb -o=4h29.out File name: 4h29.pdb no. of DNA/RNA chains: 2 [A=20,B=20] no. of nucleotides: 40 no. of atoms: 898 no. of waters: 32 no. of metals: 6 [K=6] **************************************************************************** List of 33 base pairs nt1 nt2 bp name Saenger LW DSSR 1 A.DG1 A.DG6 G+G -- 06-VI cHW cM+W 2 A.DG1 B.DG6 G+G -- 06-VI cWH cW+M 3 A.DG2 A.DG5 G+G -- 06-VI cWH cW+M 4 A.DG2 B.DG5 G+G -- 06-VI cHW cM+W 5 A.DG3 A.DC4 G+C Platform -- cSH cm+M 6 A.DG3 B.DC4 G+C -- -- tSS tm+m 7 A.DC4 B.DG3 C+G -- -- tWW tW+W 8 A.DG5 B.DG2 G+G -- 06-VI cWH cW+M 9 A.DG6 B.DG1 G+G -- 06-VI cHW cM+W 10 A.DG7 A.DA9 G+A -- -- tSW tm+W 11 A.DG7 A.DG10 G+G -- 06-VI cWH cW+M 12 A.DG7 B.DG10 G+G -- 06-VI cHW cM+W 13 A.DG8 A.DG11 G+G -- 06-VI cWH cW+M 14 A.DG8 B.DG11 G+G -- 06-VI cHW cM+W 15 A.DG10 B.DG7 G+G -- 06-VI cWH cW+M 16 A.DG11 B.DG8 G+G -- 06-VI cWH cW+M 17 A.DG12 A.DG17 G+G -- 06-VI cWH cW+M 18 A.DG12 B.DG17 G+G -- 06-VI cHW cM+W 19 A.DG13 A.DG18 G+G -- 06-VI cWH cW+M 20 A.DG13 B.DG18 G+G -- 06-VI cHW cM+W 21 A.DG14 A.DG19 G+G -- 06-VI cWH cW+M 22 A.DG14 B.DG19 G+G -- 06-VI cHW cM+W 23 A.DG17 B.DG12 G+G -- 06-VI cWH cW+M 24 A.DG18 B.DG13 G+G -- 06-VI cWH cW+M 25 A.DG19 B.DG14 G+G -- 06-VI cWH cW+M 26 B.DG1 B.DG6 G+G -- 06-VI cHW cM+W 27 B.DG2 B.DG5 G+G -- 06-VI cWH cW+M 28 B.DG7 B.DA9 G+A -- -- tSW tm+W 29 B.DG7 B.DG10 G+G -- 06-VI cWH cW+M 30 B.DG8 B.DG11 G+G -- 06-VI cWH cW+M 31 B.DG12 B.DG17 G+G -- 06-VI cWH cW+M 32 B.DG13 B.DG18 G+G -- 06-VI cWH cW+M 33 B.DG14 B.DG19 G+G Metal 06-VI cWH cW+M **************************************************************************** List of 8 multiplets 1 nts=3 GCG A.DG3,A.DC4,B.DG3 2 nts=4 GGGG A.DG1,A.DG6,B.DG1,B.DG6 3 nts=4 GGGG A.DG2,A.DG5,B.DG2,B.DG5 4 nts=4 GGGG A.DG8,A.DG11,B.DG8,B.DG11 5 nts=4 GGGG A.DG12,A.DG17,B.DG12,B.DG17 6 nts=4 GGGG A.DG13,A.DG18,B.DG13,B.DG18 7 nts=4 GGGG A.DG14,A.DG19,B.DG14,B.DG19 8 nts=6 GAGGAG A.DG7,A.DA9,A.DG10,B.DG7,B.DA9,B.DG10 **************************************************************************** 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[0] bps=7 strand-1 5'-GGGGGGG-3' bp-type ....... strand-2 5'-GGGGGGG-3' helix-form xx.x.. 1 A.DG2 B.DG5 G+G -- 06-VI cHW cM+W 2 A.DG1 B.DG6 G+G -- 06-VI cWH cW+M 3 A.DG10 B.DG7 G+G -- 06-VI cWH cW+M 4 A.DG11 B.DG8 G+G -- 06-VI cWH cW+M 5 A.DG12 B.DG17 G+G -- 06-VI cHW cM+W 6 A.DG13 B.DG18 G+G -- 06-VI cHW cM+W 7 A.DG14 B.DG19 G+G -- 06-VI cHW cM+W -------------------------------------------------------------------------- helix#2[0] bps=9 strand-1 5'-GCGGGGGGG-3' bp-type ......... strand-2 5'-CGGGGGGGG-3' helix-form ..xx.x.. 1 A.DG3 B.DC4 G+C -- -- tSS tm+m 2 A.DC4 B.DG3 C+G -- -- tWW tW+W 3 A.DG5 B.DG2 G+G -- 06-VI cWH cW+M 4 A.DG6 B.DG1 G+G -- 06-VI cHW cM+W 5 A.DG7 B.DG10 G+G -- 06-VI cHW cM+W 6 A.DG8 B.DG11 G+G -- 06-VI cHW cM+W 7 A.DG17 B.DG12 G+G -- 06-VI cWH cW+M 8 A.DG18 B.DG13 G+G -- 06-VI cWH cW+M 9 A.DG19 B.DG14 G+G -- 06-VI cWH cW+M **************************************************************************** List of 4 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=7 GGGGGGG A.DG19,A.DG18,A.DG17,B.DG8,B.DG7,B.DG6,B.DG5 2 nts=8 GGGGGGGG A.DG3,A.DG2,A.DG1,A.DG10,A.DG11,A.DG12,A.DG13,A.DG14 3 nts=8 CGGGGGGG A.DC4,A.DG5,A.DG6,A.DG7,A.DG8,B.DG17,B.DG18,B.DG19 4 nts=9 CGGGGGGGG B.DC4,B.DG3,B.DG2,B.DG1,B.DG10,B.DG11,B.DG12,B.DG13,B.DG14 **************************************************************************** Nucleotides not involved in stacking interactions nts=6 AAAAAA A.DA15,A.DA16,A.DA20,B.DA15,B.DA16,B.DA20 **************************************************************************** List of 1 atom-base capping interaction dv: vertical distance of the atom above the nucleotide base ----------------------------------------------------------- type atom nt dv 1 sugar O4'@A.DA15 A.DA16 3.16 **************************************************************************** List of 2 non-loop single-stranded segments 1 nts=20 GGGCGGGGAGGGGGAAGGGA A.DG1,A.DG2,A.DG3,A.DC4,A.DG5,A.DG6,A.DG7,A.DG8,A.DA9,A.DG10,A.DG11,A.DG12,A.DG13,A.DG14,A.DA15,A.DA16,A.DG17,A.DG18,A.DG19,A.DA20 2 nts=20 GGGCGGGGAGGGGGAAGGGA B.DG1,B.DG2,B.DG3,B.DC4,B.DG5,B.DG6,B.DG7,B.DG8,B.DA9,B.DG10,B.DG11,B.DG12,B.DG13,B.DG14,B.DA15,B.DA16,B.DG17,B.DG18,B.DG19,B.DA20 **************************************************************************** List of 7 G-tetrads 1 glyco-bond=s-s- sugar=---- groove=wnwn planarity=0.391 type=saddle nts=4 GGGG A.DG1,A.DG6,B.DG1,B.DG6 2 glyco-bond=-s-s sugar=---- groove=wnwn planarity=0.468 type=bowl-2 nts=4 GGGG A.DG2,A.DG5,B.DG2,B.DG5 3 glyco-bond=---- sugar=-.-- groove=---- planarity=0.159 type=planar nts=4 GGGG A.DG7,A.DG10,B.DG7,B.DG10 4 glyco-bond=---- sugar=---- groove=---- planarity=0.177 type=bowl-2 nts=4 GGGG A.DG8,A.DG11,B.DG8,B.DG11 5 glyco-bond=---- sugar=---- groove=---- planarity=0.187 type=bowl-2 nts=4 GGGG A.DG12,A.DG17,B.DG12,B.DG17 6 glyco-bond=---- sugar=---- groove=---- planarity=0.161 type=other nts=4 GGGG A.DG13,A.DG18,B.DG13,B.DG18 7 glyco-bond=---- sugar=---- groove=---- planarity=0.311 type=bowl nts=4 GGGG A.DG14,A.DG19,B.DG14,B.DG19 **************************************************************************** List of 5 splayed-apart dinucleotides 1 A.DG14 A.DA15 angle=165 distance=19.0 ratio=0.99 2 A.DA16 A.DG17 angle=138 distance=18.2 ratio=0.93 3 B.DG14 B.DA15 angle=174 distance=19.5 ratio=1.00 4 B.DA16 B.DG17 angle=120 distance=16.8 ratio=0.87 5 B.DG19 B.DA20 angle=105 distance=14.5 ratio=0.80 ---------------------------------------------------------------- Summary of 5 splayed-apart units 1 nts=2 GA A.DG14,A.DA15 2 nts=2 AG A.DA16,A.DG17 3 nts=2 GA B.DG14,B.DA15 4 nts=2 AG B.DA16,B.DG17 5 nts=2 GA B.DG19,B.DA20 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >4h29 nts=40 [whole] GGGCGGGGAGGGGGAAGGGA&GGGCGGGGAGGGGGAAGGGA ....................&.................... >4h29-A #1 nts=20 0.50(2.57) [chain] DNA GGGCGGGGAGGGGGAAGGGA .................... >4h29-B #2 nts=20 0.47(2.52) [chain] DNA GGGCGGGGAGGGGGAAGGGA .................... **************************************************************************** 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 G . A.DG1 0.007 syn,~C2'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,ss-non-loop,G-tetrad 2 G . A.DG2 0.007 anti,~C2'-endo,BI,non-canonical,non-pair-contact,helix-end,multiplet,ss-non-loop,G-tetrad 3 G . A.DG3 0.009 anti,~C2'-endo,non-canonical,non-pair-contact,helix-end,multiplet,ss-non-loop 4 C . A.DC4 0.007 anti,~C2'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,ss-non-loop 5 G . A.DG5 0.015 syn,~C2'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,ss-non-loop,G-tetrad 6 G . A.DG6 0.015 anti,~C2'-endo,non-canonical,non-pair-contact,helix,multiplet,ss-non-loop,G-tetrad 7 G . A.DG7 0.014 anti,~C2'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,ss-non-loop,G-tetrad 8 G . A.DG8 0.016 anti,~C2'-endo,non-canonical,non-pair-contact,helix,multiplet,ss-non-loop,G-tetrad 9 A . A.DA9 0.009 turn,non-canonical,non-pair-contact,multiplet,ss-non-loop 10 G . A.DG10 0.011 anti,BI,non-canonical,non-pair-contact,helix,multiplet,ss-non-loop,G-tetrad 11 G . A.DG11 0.011 anti,~C2'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,ss-non-loop,G-tetrad 12 G . A.DG12 0.021 anti,~C2'-endo,non-canonical,non-pair-contact,helix,multiplet,ss-non-loop,G-tetrad 13 G . A.DG13 0.019 anti,~C2'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,ss-non-loop,G-tetrad 14 G . A.DG14 0.014 anti,~C2'-endo,non-canonical,non-pair-contact,helix-end,multiplet,ss-non-loop,G-tetrad,splayed-apart 15 A . A.DA15 0.011 turn,anti,~C2'-endo,non-stack,ss-non-loop,cap-donor,splayed-apart 16 A . A.DA16 0.012 syn,~C2'-endo,non-stack,non-pair-contact,ss-non-loop,cap-acceptor,splayed-apart 17 G . A.DG17 0.013 anti,~C2'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,ss-non-loop,G-tetrad,splayed-apart 18 G . A.DG18 0.020 anti,~C2'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,ss-non-loop,G-tetrad 19 G . A.DG19 0.013 anti,~C2'-endo,non-canonical,non-pair-contact,helix-end,multiplet,ss-non-loop,G-tetrad 20 A . A.DA20 0.009 anti,~C2'-endo,non-stack,ss-non-loop 21 G . B.DG1 0.011 syn,~C2'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,ss-non-loop,G-tetrad 22 G . B.DG2 0.010 anti,~C2'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,ss-non-loop,G-tetrad 23 G . B.DG3 0.009 anti,~C2'-endo,BII,non-canonical,non-pair-contact,helix,multiplet,ss-non-loop 24 C . B.DC4 0.009 anti,~C2'-endo,non-canonical,non-pair-contact,helix-end,ss-non-loop 25 G . B.DG5 0.017 syn,~C2'-endo,BI,non-canonical,non-pair-contact,helix-end,multiplet,ss-non-loop,G-tetrad,phosphate 26 G . B.DG6 0.014 anti,~C2'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,ss-non-loop,G-tetrad 27 G . B.DG7 0.016 anti,~C2'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,ss-non-loop,G-tetrad 28 G . B.DG8 0.018 anti,~C2'-endo,non-canonical,non-pair-contact,helix,multiplet,ss-non-loop,G-tetrad 29 A . B.DA9 0.015 turn,syn,non-canonical,non-pair-contact,multiplet,ss-non-loop 30 G . B.DG10 0.011 anti,~C2'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,ss-non-loop,G-tetrad 31 G . B.DG11 0.020 anti,~C2'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,ss-non-loop,G-tetrad 32 G . B.DG12 0.015 anti,~C2'-endo,non-canonical,non-pair-contact,helix,multiplet,ss-non-loop,G-tetrad 33 G . B.DG13 0.021 anti,~C2'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,ss-non-loop,G-tetrad 34 G . B.DG14 0.013 anti,~C2'-endo,non-canonical,non-pair-contact,helix-end,multiplet,ss-non-loop,G-tetrad,splayed-apart 35 A . B.DA15 0.010 turn,anti,~C2'-endo,non-stack,ss-non-loop,splayed-apart 36 A . B.DA16 0.006 ~C2'-endo,BII,non-stack,ss-non-loop,splayed-apart 37 G . B.DG17 0.011 anti,~C2'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,ss-non-loop,G-tetrad,splayed-apart 38 G . B.DG18 0.011 anti,~C2'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,ss-non-loop,G-tetrad 39 G . B.DG19 0.011 anti,~C2'-endo,non-canonical,non-pair-contact,helix-end,multiplet,ss-non-loop,G-tetrad,splayed-apart 40 A . B.DA20 0.006 anti,~C3'-endo,non-stack,ss-non-loop,splayed-apart **************************************************************************** List of 10 additional files 1 dssr-pairs.pdb -- an ensemble of base pairs 2 dssr-multiplets.pdb -- an ensemble of multiplets 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 10 dssr-atom2bases.pdb -- an ensemble of atom-base stacking interactions