**************************************************************************** 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=4da3.pdb -o=4da3.out File name: 4da3.pdb no. of DNA/RNA chains: 1 [A=21] no. of nucleotides: 21 no. of atoms: 532 no. of waters: 25 no. of metals: 3 [K=3] **************************************************************************** List of 12 base pairs nt1 nt2 bp name Saenger LW DSSR 1 A.DG1 A.DG7 G+G -- 06-VI cWH cW+M 2 A.DG1 A.DG19 G+G -- 06-VI cHW cM+W 3 A.DG2 A.DG8 G+G -- 06-VI cWH cW+M 4 A.DG2 A.DG20 G+G -- 06-VI cHW cM+W 5 A.DG3 A.DG9 G+G -- 06-VI cWH cW+M 6 A.DG3 A.DG21 G+G -- 06-VI cHW cM+W 7 A.DG7 A.DG13 G+G -- 06-VI cWH cW+M 8 A.DG8 A.DG14 G+G -- 06-VI cWH cW+M 9 A.DG9 A.DG15 G+G -- 06-VI cWH cW+M 10 A.DG13 A.DG19 G+G -- 06-VI cWH cW+M 11 A.DG14 A.DG20 G+G -- 06-VI cWH cW+M 12 A.DG15 A.DG21 G+G -- 06-VI cWH cW+M **************************************************************************** List of 3 multiplets 1 nts=4 GGGG A.DG1,A.DG7,A.DG13,A.DG19 2 nts=4 GGGG A.DG2,A.DG8,A.DG14,A.DG20 3 nts=4 GGGG A.DG3,A.DG9,A.DG15,A.DG21 **************************************************************************** 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=3 parallel strand-1 5'-GGG-3' bp-type ... strand-2 5'-GGG-3' helix-form .. 1 A.DG1 A.DG7 G+G -- 06-VI cWH cW+M 2 A.DG2 A.DG8 G+G -- 06-VI cWH cW+M 3 A.DG3 A.DG9 G+G -- 06-VI cWH cW+M -------------------------------------------------------------------------- helix#2[0] bps=3 parallel strand-1 5'-GGG-3' bp-type ... strand-2 5'-GGG-3' helix-form .. 1 A.DG13 A.DG19 G+G -- 06-VI cWH cW+M 2 A.DG14 A.DG20 G+G -- 06-VI cWH cW+M 3 A.DG15 A.DG21 G+G -- 06-VI cWH cW+M **************************************************************************** List of 7 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 TA A.DT4,A.DA6 2 nts=2 TA A.DT11,A.DA12 3 nts=2 TA A.DT17,A.DA18 4 nts=3 GGG A.DG1,A.DG2,A.DG3 5 nts=3 GGG A.DG7,A.DG8,A.DG9 6 nts=3 GGG A.DG13,A.DG14,A.DG15 7 nts=3 GGG A.DG19,A.DG20,A.DG21 **************************************************************************** Nucleotides not involved in stacking interactions nts=2 TT A.DT10,A.DT16 **************************************************************************** List of 2 atom-base capping interactions dv: vertical distance of the atom above the nucleotide base ----------------------------------------------------------- type atom nt dv 1 other NBM@A.0DX104 A.DG3 3.28 2 other NBN@A.0DX104 A.DG9 3.25 **************************************************************************** List of 1 non-loop single-stranded segment 1 nts=21 GGGTTAGGGTTAGGGTTAGGG A.DG1,A.DG2,A.DG3,A.DT4,A.DT5,A.DA6,A.DG7,A.DG8,A.DG9,A.DT10,A.DT11,A.DA12,A.DG13,A.DG14,A.DG15,A.DT16,A.DT17,A.DA18,A.DG19,A.DG20,A.DG21 **************************************************************************** List of 3 G-tetrads 1 glyco-bond=---- sugar=3--- groove=---- planarity=0.201 type=other nts=4 GGGG A.DG1,A.DG7,A.DG13,A.DG19 2 glyco-bond=---- sugar=3-3- groove=---- planarity=0.095 type=planar nts=4 GGGG A.DG2,A.DG8,A.DG14,A.DG20 3 glyco-bond=---- sugar=---- groove=---- planarity=0.337 type=bowl nts=4 GGGG A.DG3,A.DG9,A.DG15,A.DG21 **************************************************************************** List of 6 splayed-apart dinucleotides 1 A.DA6 A.DG7 angle=90 distance=15.4 ratio=0.71 2 A.DG9 A.DT10 angle=123 distance=14.6 ratio=0.88 3 A.DT10 A.DT11 angle=158 distance=19.1 ratio=0.98 4 A.DA12 A.DG13 angle=112 distance=18.0 ratio=0.83 5 A.DG15 A.DT16 angle=151 distance=18.6 ratio=0.97 6 A.DA18 A.DG19 angle=153 distance=18.9 ratio=0.97 ---------------------------------------------------------------- Summary of 5 splayed-apart units 1 nts=2 AG A.DA6,A.DG7 2 nts=3 GTT A.DG9,A.DT10,A.DT11 3 nts=2 AG A.DA12,A.DG13 4 nts=2 GT A.DG15,A.DT16 5 nts=2 AG A.DA18,A.DG19 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >4da3 nts=21 [whole] GGGTTAGGGTTAGGGTTAGGG ..................... >4da3-A #1 nts=21 0.22(3.61) [chain] DNA GGGTTAGGGTTAGGGTTAGGG ..................... **************************************************************************** Summary of structural features of 21 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 0.005 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,multiplet,ss-non-loop,G-tetrad 2 G . A.DG2 0.005 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,ss-non-loop,G-tetrad 3 G . A.DG3 0.007 anti,~C2'-endo,non-canonical,non-pair-contact,helix-end,multiplet,ss-non-loop,G-tetrad,cap-acceptor,phosphate 4 T . A.DT4 0.002 anti,~C2'-endo,non-pair-contact,ss-non-loop 5 T . A.DT5 0.003 turn,anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 6 A . A.DA6 0.004 anti,~C2'-endo,non-pair-contact,ss-non-loop,splayed-apart 7 G . A.DG7 0.007 anti,~C2'-endo,BI,non-canonical,non-pair-contact,helix-end,multiplet,ss-non-loop,G-tetrad,splayed-apart 8 G . A.DG8 0.005 anti,~C2'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,ss-non-loop,G-tetrad 9 G . A.DG9 0.005 anti,~C2'-endo,non-canonical,non-pair-contact,helix-end,multiplet,ss-non-loop,G-tetrad,cap-acceptor,splayed-apart 10 T . A.DT10 0.002 syn,~C2'-endo,non-stack,ss-non-loop,splayed-apart 11 T . A.DT11 0.008 anti,~C2'-endo,non-pair-contact,ss-non-loop,splayed-apart 12 A . A.DA12 0.006 anti,non-pair-contact,ss-non-loop,splayed-apart 13 G . A.DG13 0.007 anti,~C2'-endo,non-canonical,non-pair-contact,helix-end,multiplet,ss-non-loop,G-tetrad,splayed-apart 14 G . A.DG14 0.005 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,ss-non-loop,G-tetrad 15 G . A.DG15 0.005 anti,~C2'-endo,non-canonical,non-pair-contact,helix-end,multiplet,ss-non-loop,G-tetrad,splayed-apart 16 T . A.DT16 0.002 turn,anti,~C2'-endo,non-stack,ss-non-loop,splayed-apart 17 T . A.DT17 0.002 anti,~C2'-endo,non-pair-contact,ss-non-loop 18 A . A.DA18 0.003 ~C2'-endo,BII,non-pair-contact,ss-non-loop,splayed-apart 19 G . A.DG19 0.004 anti,~C2'-endo,BI,non-canonical,non-pair-contact,helix-end,multiplet,ss-non-loop,G-tetrad,splayed-apart 20 G . A.DG20 0.010 anti,~C2'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,ss-non-loop,G-tetrad 21 G . A.DG21 0.008 anti,~C2'-endo,non-canonical,non-pair-contact,helix-end,multiplet,ss-non-loop,G-tetrad **************************************************************************** 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