**************************************************************************** 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=143d.pdb -o=143d.out File name: 143d.pdb no. of DNA/RNA chains: 1 [A=22] no. of nucleotides: 22 no. of atoms: 715 no. of waters: 0 no. of metals: 0 **************************************************************************** List of 17 base pairs nt1 nt2 bp name Saenger LW DSSR 1 A.DA1 A.DA13 A-A -- -- cHH cM-M 2 A.DG2 A.DG10 G+G -- 06-VI cWH cW+M 3 A.DG2 A.DG14 G+G -- 06-VI cHW cM+W 4 A.DG3 A.DG9 G+G -- 06-VI cHW cM+W 5 A.DG3 A.DG15 G+G -- 06-VI cWH cW+M 6 A.DG4 A.DG8 G+G -- 06-VI cWH cW+M 7 A.DG4 A.DG15 G-G -- -- cHH cM-M 8 A.DG4 A.DG16 G+G -- 06-VI cHW cM+W 9 A.DT6 A.DG16 T+G -- -- tWW tW+W 10 A.DT6 A.DA19 T-A -- -- cWW cW-W 11 A.DA7 A.DT18 A-T rHoogsteen 24-XXIV tHW tM-W 12 A.DG8 A.DG20 G+G -- 06-VI cWH cW+M 13 A.DG9 A.DG21 G+G -- 06-VI cHW cM+W 14 A.DG10 A.DG22 G+G -- 06-VI cWH cW+M 15 A.DG14 A.DG22 G+G -- 06-VI cHW cM+W 16 A.DG15 A.DG21 G+G -- 06-VI cWH cW+M 17 A.DG16 A.DG20 G+G -- 06-VI cHW cM+W **************************************************************************** List of 3 multiplets 1 nts=4 GGGG A.DG2,A.DG10,A.DG14,A.DG22 2 nts=4 GGGG A.DG3,A.DG9,A.DG15,A.DG21 3 nts=4 GGGG A.DG4,A.DG8,A.DG16,A.DG20 **************************************************************************** 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=6 strand-1 5'-AGGGTA-3' bp-type ....|. strand-2 5'-AGGGAT-3' helix-form ...x. 1 A.DA1 A.DA13 A-A -- -- cHH cM-M 2 A.DG2 A.DG14 G+G -- 06-VI cHW cM+W 3 A.DG3 A.DG15 G+G -- 06-VI cWH cW+M 4 A.DG4 A.DG16 G+G -- 06-VI cHW cM+W 5 A.DT6 A.DA19 T-A WC 20-XX cWW cW-W 6 A.DA7 A.DT18 A-T rHoogsteen 24-XXIV tHW tM-W -------------------------------------------------------------------------- helix#2[0] bps=3 parallel strand-1 5'-GGG-3' bp-type ... strand-2 5'-GGG-3' helix-form .. 1 A.DG8 A.DG20 G+G -- 06-VI cWH cW+M 2 A.DG9 A.DG21 G+G -- 06-VI cHW cM+W 3 A.DG10 A.DG22 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=3 GGG A.DG8,A.DG9,A.DG10 2 nts=4 AGGG A.DA13,A.DG22,A.DG21,A.DG20 3 nts=5 GGGAT A.DG14,A.DG15,A.DG16,A.DA19,A.DT18 4 nts=6 TGGGAT A.DT6,A.DG4,A.DG3,A.DG2,A.DA1,A.DT12 **************************************************************************** Nucleotides not involved in stacking interactions nts=4 TATT A.DT5,A.DA7,A.DT11,A.DT17 **************************************************************************** List of 1 non-loop single-stranded segment 1 nts=22 AGGGTTAGGGTTAGGGTTAGGG A.DA1,A.DG2,A.DG3,A.DG4,A.DT5,A.DT6,A.DA7,A.DG8,A.DG9,A.DG10,A.DT11,A.DT12,A.DA13,A.DG14,A.DG15,A.DG16,A.DT17,A.DT18,A.DA19,A.DG20,A.DG21,A.DG22 **************************************************************************** List of 3 G-tetrads 1 glyco-bond=-ss- sugar=---- groove=w-n- planarity=0.412 type=other nts=4 GGGG A.DG2,A.DG10,A.DG22,A.DG14 2 glyco-bond=s--s sugar=3--- groove=w-n- planarity=0.275 type=bowl nts=4 GGGG A.DG3,A.DG9,A.DG21,A.DG15 3 glyco-bond=-ss- sugar=---- groove=w-n- planarity=0.341 type=other nts=4 GGGG A.DG4,A.DG8,A.DG20,A.DG16 **************************************************************************** List of 2 splayed-apart dinucleotides 1 A.DG10 A.DT11 angle=109 distance=14.2 ratio=0.82 2 A.DT12 A.DA13 angle=99 distance=12.4 ratio=0.77 ---------------------------------------------------------------- Summary of 2 splayed-apart units 1 nts=2 GT A.DG10,A.DT11 2 nts=2 TA A.DT12,A.DA13 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >143d nts=22 [whole] AGGGTTAGGGTTAGGGTTAGGG ...................... >143d-A #1 nts=22 0.47(2.73) [chain] DNA AGGGTTAGGGTTAGGGTTAGGG ...................... **************************************************************************** Summary of structural features of 22 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 A . A.DA1 0.011 anti,~C2'-endo,BI,non-canonical,non-pair-contact,helix-end,ss-non-loop 2 G . A.DG2 0.014 anti,~C2'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,ss-non-loop,G-tetrad 3 G . A.DG3 0.015 syn,~C3'-endo,non-canonical,non-pair-contact,helix,multiplet,ss-non-loop,G-tetrad 4 G . A.DG4 0.013 anti,~C2'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,ss-non-loop,G-tetrad 5 T . A.DT5 0.025 turn,anti,~C2'-endo,non-stack,non-pair-contact,ss-non-loop 6 T . A.DT6 0.013 anti,~C2'-endo,BI,non-canonical,non-pair-contact,helix,ss-non-loop 7 A . A.DA7 0.014 turn,anti,~C2'-endo,non-stack,non-canonical,non-pair-contact,helix-end,ss-non-loop 8 G . A.DG8 0.017 syn,~C2'-endo,non-canonical,non-pair-contact,helix-end,multiplet,ss-non-loop,G-tetrad 9 G . A.DG9 0.017 anti,~C2'-endo,non-canonical,non-pair-contact,helix,multiplet,ss-non-loop,G-tetrad 10 G . A.DG10 0.013 syn,~C2'-endo,BI,non-canonical,non-pair-contact,helix-end,multiplet,ss-non-loop,G-tetrad,splayed-apart 11 T . A.DT11 0.021 anti,~C2'-endo,BII,non-stack,ss-non-loop,splayed-apart 12 T . A.DT12 0.020 anti,~C2'-endo,BI,non-pair-contact,ss-non-loop,splayed-apart 13 A . A.DA13 0.013 anti,~C2'-endo,non-canonical,non-pair-contact,helix-end,ss-non-loop,splayed-apart 14 G . A.DG14 0.010 anti,~C2'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,ss-non-loop,G-tetrad 15 G . A.DG15 0.011 syn,~C2'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,ss-non-loop,G-tetrad 16 G . A.DG16 0.011 anti,~C2'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,ss-non-loop,G-tetrad 17 T . A.DT17 0.020 turn,anti,~C2'-endo,non-stack,ss-non-loop 18 T . A.DT18 0.026 anti,~C2'-endo,BI,non-canonical,non-pair-contact,helix-end,ss-non-loop 19 A . A.DA19 0.016 anti,~C2'-endo,non-canonical,non-pair-contact,helix,ss-non-loop 20 G . A.DG20 0.009 syn,~C2'-endo,BI,non-canonical,non-pair-contact,helix-end,multiplet,ss-non-loop,G-tetrad,phosphate 21 G . A.DG21 0.009 anti,~C2'-endo,BII,non-canonical,non-pair-contact,helix,multiplet,ss-non-loop,G-tetrad 22 G . A.DG22 0.010 syn,~C2'-endo,non-canonical,non-pair-contact,helix-end,multiplet,ss-non-loop,G-tetrad **************************************************************************** List of 9 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