**************************************************************************** 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=2hy9.pdb -o=2hy9.out File name: 2hy9.pdb no. of DNA/RNA chains: 1 [1=26] no. of nucleotides: 26 no. of atoms: 843 no. of waters: 0 no. of metals: 0 **************************************************************************** List of 18 base pairs nt1 nt2 bp name Saenger LW DSSR 1 1.DA2 1.DT20 A+T -- -- cHW cM+W 2 1.DA3 1.DA21 A+A -- -- cHW cM+W 3 1.DG4 1.DT7 G+T -- -- cHW cM+W 4 1.DG4 1.DG10 G+G -- 06-VI cHW cM+W 5 1.DG4 1.DG22 G+G -- 06-VI cWH cW+M 6 1.DG5 1.DG11 G+G -- 06-VI cWH cW+M 7 1.DG5 1.DG23 G+G -- 06-VI cHW cM+W 8 1.DG6 1.DG12 G+G -- 06-VI cWH cW+M 9 1.DG6 1.DG24 G+G -- 06-VI cHW cM+W 10 1.DT7 1.DG10 T+G -- -- cHS cM+m 11 1.DG10 1.DG18 G+G -- 06-VI cHW cM+W 12 1.DG11 1.DG17 G+G -- 06-VI cWH cW+M 13 1.DG12 1.DG16 G+G -- 06-VI cWH cW+M 14 1.DT14 1.DA25 T+A rWC 21-XXI tWW tW+W 15 1.DA15 1.DA25 A+A -- -- tSW tm+W 16 1.DG16 1.DG24 G+G -- 06-VI cWH cW+M 17 1.DG17 1.DG23 G+G -- 06-VI cWH cW+M 18 1.DG18 1.DG22 G+G -- 06-VI cHW cM+W **************************************************************************** List of 3 multiplets 1 nts=4 GGGG 1.DG5,1.DG11,1.DG17,1.DG23 2 nts=4 GGGG 1.DG6,1.DG12,1.DG16,1.DG24 3 nts=5 GTGGG 1.DG4,1.DT7,1.DG10,1.DG18,1.DG22 **************************************************************************** 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'-AAGGGT-3' bp-type ...... strand-2 5'-TAGGGA-3' helix-form ....x 1 1.DA2 1.DT20 A+T -- -- cHW cM+W 2 1.DA3 1.DA21 A+A -- -- cHW cM+W 3 1.DG4 1.DG22 G+G -- 06-VI cWH cW+M 4 1.DG5 1.DG23 G+G -- 06-VI cHW cM+W 5 1.DG6 1.DG24 G+G -- 06-VI cHW cM+W 6 1.DT14 1.DA25 T+A rWC 21-XXI tWW tW+W -------------------------------------------------------------------------- helix#2[0] bps=3 strand-1 5'-GGG-3' bp-type ... strand-2 3'-GGG-5' helix-form .. 1 1.DG10 1.DG18 G+G -- 06-VI cHW cM+W 2 1.DG11 1.DG17 G+G -- 06-VI cWH cW+M 3 1.DG12 1.DG16 G+G -- 06-VI cWH cW+M **************************************************************************** List of 5 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 1.DT7,1.DA9 2 nts=5 AAGGG 1.DA2,1.DA3,1.DG4,1.DG5,1.DG6 3 nts=5 GGGTA 1.DG10,1.DG11,1.DG12,1.DT14,1.DA15 4 nts=5 GGGAA 1.DG22,1.DG23,1.DG24,1.DA25,1.DA26 5 nts=6 ATAGGG 1.DA1,1.DT20,1.DA21,1.DG18,1.DG17,1.DG16 **************************************************************************** Nucleotides not involved in stacking interactions nts=2 TT 1.DT8,1.DT19 **************************************************************************** List of 1 atom-base capping interaction dv: vertical distance of the atom above the nucleotide base ----------------------------------------------------------- type atom nt dv 1 sugar O4'@1.DT14 1.DG12 3.12 **************************************************************************** List of 1 non-loop single-stranded segment 1 nts=26 AAAGGGTTAGGGTTAGGGTTAGGGAA 1.DA1,1.DA2,1.DA3,1.DG4,1.DG5,1.DG6,1.DT7,1.DT8,1.DA9,1.DG10,1.DG11,1.DG12,1.DT13,1.DT14,1.DA15,1.DG16,1.DG17,1.DG18,1.DT19,1.DT20,1.DA21,1.DG22,1.DG23,1.DG24,1.DA25,1.DA26 **************************************************************************** List of 3 G-tetrads 1 glyco-bond=ss-s sugar=-... groove=-wn- planarity=0.077 type=planar nts=4 GGGG 1.DG4,1.DG10,1.DG18,1.DG22 2 glyco-bond=--s- sugar=.... groove=-wn- planarity=0.066 type=planar nts=4 GGGG 1.DG5,1.DG11,1.DG17,1.DG23 3 glyco-bond=--s- sugar=---- groove=-wn- planarity=0.076 type=planar nts=4 GGGG 1.DG6,1.DG12,1.DG16,1.DG24 **************************************************************************** List of 1 splayed-apart dinucleotide 1 1.DT19 1.DT20 angle=98 distance=13.1 ratio=0.76 ---------------------------------------------------------------- Summary of 1 splayed-apart unit 1 nts=2 TT 1.DT19,1.DT20 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >2hy9 nts=26 [whole] AAAGGGTTAGGGTTAGGGTTAGGGAA .......................... >2hy9-1 #1 nts=26 0.09(2.68) [chain] DNA AAAGGGTTAGGGTTAGGGTTAGGGAA .......................... **************************************************************************** Summary of structural features of 26 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 . 1.DA1 0.019 syn,~C3'-endo,non-pair-contact,ss-non-loop 2 A . 1.DA2 0.019 anti,non-canonical,non-pair-contact,helix-end,ss-non-loop 3 A . 1.DA3 0.020 anti,non-canonical,non-pair-contact,helix,ss-non-loop 4 G . 1.DG4 0.018 syn,~C2'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,ss-non-loop,G-tetrad,phosphate 5 G . 1.DG5 0.022 anti,BI,non-canonical,non-pair-contact,helix,multiplet,ss-non-loop,G-tetrad 6 G . 1.DG6 0.021 anti,~C2'-endo,non-canonical,non-pair-contact,helix,multiplet,ss-non-loop,G-tetrad 7 T . 1.DT7 0.030 anti,non-canonical,non-pair-contact,multiplet,ss-non-loop 8 T . 1.DT8 0.025 turn,anti,non-stack,ss-non-loop 9 A . 1.DA9 0.030 anti,BI,non-pair-contact,ss-non-loop 10 G . 1.DG10 0.020 syn,non-canonical,non-pair-contact,helix-end,multiplet,ss-non-loop,G-tetrad 11 G . 1.DG11 0.019 anti,non-canonical,non-pair-contact,helix,multiplet,ss-non-loop,G-tetrad 12 G . 1.DG12 0.022 anti,~C2'-endo,non-canonical,non-pair-contact,helix-end,multiplet,ss-non-loop,G-tetrad,cap-acceptor 13 T . 1.DT13 0.024 turn,non-pair-contact,ss-non-loop 14 T . 1.DT14 0.021 anti,BI,non-canonical,non-pair-contact,helix-end,ss-non-loop,cap-donor 15 A . 1.DA15 0.020 anti,non-canonical,non-pair-contact,ss-non-loop 16 G . 1.DG16 0.022 syn,~C2'-endo,non-canonical,non-pair-contact,helix-end,multiplet,ss-non-loop,G-tetrad 17 G . 1.DG17 0.022 syn,non-canonical,non-pair-contact,helix,multiplet,ss-non-loop,G-tetrad 18 G . 1.DG18 0.018 anti,non-canonical,non-pair-contact,helix-end,multiplet,ss-non-loop,G-tetrad 19 T . 1.DT19 0.021 anti,~C2'-endo,non-stack,ss-non-loop,splayed-apart 20 T . 1.DT20 0.020 anti,non-canonical,non-pair-contact,helix-end,ss-non-loop,splayed-apart 21 A . 1.DA21 0.018 anti,~C3'-endo,non-canonical,non-pair-contact,helix,ss-non-loop 22 G . 1.DG22 0.019 syn,non-canonical,non-pair-contact,helix,multiplet,ss-non-loop,G-tetrad 23 G . 1.DG23 0.021 anti,non-canonical,non-pair-contact,helix,multiplet,ss-non-loop,G-tetrad 24 G . 1.DG24 0.020 anti,~C2'-endo,non-canonical,non-pair-contact,helix,multiplet,ss-non-loop,G-tetrad 25 A . 1.DA25 0.024 anti,non-canonical,non-pair-contact,helix-end,ss-non-loop 26 A . 1.DA26 0.018 anti,non-pair-contact,ss-non-loop **************************************************************************** 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