**************************************************************************** File name: 6r9k.pdb no. of DNA/RNA chains: 1 [A=25] no. of nucleotides: 25 no. of atoms: 806 no. of waters: 0 no. of metals: 0 **************************************************************************** List of 1 type of 2 modified nucleotides nt count list 1 BGM-g 2 A.BGM6,A.BGM7 **************************************************************************** List of 16 base pairs nt1 nt2 bp name Saenger LW DSSR 1 A.DG1 A.DC25 G-C WC 19-XIX cWW cW-W 2 A.DC2 A.DG24 C-G WC 19-XIX cWW cW-W 3 A.DG3 A.DC23 G-C WC 19-XIX cWW cW-W 4 A.DT4 A.DA22 T-A WC 20-XX cWW cW-W 5 A.DG5 A.DG13 G+G -- 06-VI cWH cW+M 6 A.DG5 A.DG21 G+G -- 06-VI cHW cM+W 7 A.BGM6 A.DG12 g+G -- 06-VI cWH cW+M 8 A.BGM6 A.DG20 g+G -- 06-VI cHW cM+W 9 A.BGM7 A.DG11 g+G -- 06-VI cWH cW+M 10 A.BGM7 A.DG19 g+G -- 06-VI cHW cM+W 11 A.DG11 A.DG15 G+G -- 06-VI cWH cW+M 12 A.DG12 A.DG16 G+G -- 06-VI cWH cW+M 13 A.DG13 A.DG17 G+G -- 06-VI cWH cW+M 14 A.DG15 A.DG19 G+G -- 06-VI cWH cW+M 15 A.DG16 A.DG20 G+G -- 06-VI cWH cW+M 16 A.DG17 A.DG21 G+G -- 06-VI cWH cW+M **************************************************************************** List of 3 multiplets 1 nts=4 GGGG A.DG5,A.DG13,A.DG17,A.DG21 2 nts=4 gGGG A.BGM6,A.DG12,A.DG16,A.DG20 3 nts=4 gGGG A.BGM7,A.DG11,A.DG15,A.DG19 **************************************************************************** List of 2 helices Note: A helix is defined by base-stacking interactions, regardless of pair 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=7 strand-1 5'-GCGTGgg-3' bp-type ||||... strand-2 3'-CGCAGGG-5' helix-form .BB... 1 A.DG1 A.DC25 G-C WC 19-XIX cWW cW-W 2 A.DC2 A.DG24 C-G WC 19-XIX cWW cW-W 3 A.DG3 A.DC23 G-C WC 19-XIX cWW cW-W 4 A.DT4 A.DA22 T-A WC 20-XX cWW cW-W 5 A.DG5 A.DG21 G+G -- 06-VI cHW cM+W 6 A.BGM6 A.DG20 g+G -- 06-VI cHW cM+W 7 A.BGM7 A.DG19 g+G -- 06-VI cHW cM+W -------------------------------------------------------------------------- helix#2[0] bps=3 parallel strand-1 5'-GGG-3' bp-type ... strand-2 5'-GGG-3' helix-form .. 1 A.DG11 A.DG15 G+G -- 06-VI cWH cW+M 2 A.DG12 A.DG16 G+G -- 06-VI cWH cW+M 3 A.DG13 A.DG17 G+G -- 06-VI cWH cW+M **************************************************************************** List of 1 stem Note: A stem is defined as a helix consisting strictly of 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=4 strand-1 5'-GCGT-3' bp-type |||| strand-2 3'-CGCA-5' helix-form .BB 1 A.DG1 A.DC25 G-C WC 19-XIX cWW cW-W 2 A.DC2 A.DG24 C-G WC 19-XIX cWW cW-W 3 A.DG3 A.DC23 G-C WC 19-XIX cWW cW-W 4 A.DT4 A.DA22 T-A WC 20-XX cWW cW-W **************************************************************************** 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 TC A.DT8,A.DC9 2 nts=3 GGG A.DG11,A.DG12,A.DG13 3 nts=3 GGG A.DG15,A.DG16,A.DG17 4 nts=4 GGGA A.DG19,A.DG20,A.DG21,A.DA22 5 nts=5 TGggA A.DT4,A.DG5,A.BGM6,A.BGM7,A.DA10 **************************************************************************** Nucleotides not involved in stacking interactions nts=2 TT A.DT14,A.DT18 **************************************************************************** Note: For the various types of loops listed below, numbers within the first set of brackets are the number of loop nts. Numbers in the second set of brackets are the identities of the stems (positive) or isolated WC/wobble pairs (negative) to which they are linked. **************************************************************************** List of 1 hairpin loop 1 hairpin loop: nts=19; [17]; linked by [#1] summary: [1] 17 [A.4 A.22] 4 nts=19 TGggTCAGGGTGGGTGGGA A.DT4,A.DG5,A.BGM6,A.BGM7,A.DT8,A.DC9,A.DA10,A.DG11,A.DG12,A.DG13,A.DT14,A.DG15,A.DG16,A.DG17,A.DT18,A.DG19,A.DG20,A.DG21,A.DA22 nts=17 GggTCAGGGTGGGTGGG A.DG5,A.BGM6,A.BGM7,A.DT8,A.DC9,A.DA10,A.DG11,A.DG12,A.DG13,A.DT14,A.DG15,A.DG16,A.DG17,A.DT18,A.DG19,A.DG20,A.DG21 **************************************************************************** List of 3 G-tetrads 1 glyco-bond=s--- sugar=---- groove=w--n planarity=0.108 type=planar nts=4 GGGG A.DG5,A.DG21,A.DG17,A.DG13 2 glyco-bond=s--- sugar=---3 groove=w--n planarity=0.139 type=planar nts=4 gGGG A.BGM6,A.DG20,A.DG16,A.DG12 3 glyco-bond=s--- sugar=---- groove=w--n planarity=0.284 type=other nts=4 gGGG A.BGM7,A.DG19,A.DG15,A.DG11 **************************************************************************** List of 1 G4-helix Note: a G4-helix is defined by stacking interactions of G4-tetrads, regardless of backbone connectivity, and may contain more than one G4-stem. helix#1[1] stems=[#1] layers=3 INTRA-molecular 1 glyco-bond=s--- sugar=---- groove=w--n Major-->WC nts=4 GGGG A.DG5,A.DG21,A.DG17,A.DG13 2 glyco-bond=s--- sugar=---3 groove=w--n Major-->WC nts=4 gGGG A.BGM6,A.DG20,A.DG16,A.DG12 3 glyco-bond=s--- sugar=---- groove=w--n Major-->WC nts=4 gGGG A.BGM7,A.DG19,A.DG15,A.DG11 step#1 mp(<<,backward) area=13.79 rise=3.40 twist=27.9 step#2 mp(<<,backward) area=18.55 rise=3.43 twist=23.5 strand#1 DNA glyco-bond=sss sugar=--- nts=3 Ggg A.DG5,A.BGM6,A.BGM7 strand#2 DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG21,A.DG20,A.DG19 strand#3 DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG17,A.DG16,A.DG15 strand#4 DNA glyco-bond=--- sugar=-3- nts=3 GGG A.DG13,A.DG12,A.DG11 **************************************************************************** List of 1 G4-stem Note: a G4-stem is defined as a G4-helix with backbone connectivity. Bulges are also allowed along each of the four strands. stem#1[#1] layers=3 INTRA-molecular loops=3 descriptor=3(+Ln+P+P) note=1+3 UDDD hybrid4 1 glyco-bond=s--- sugar=---- groove=w--n Major-->WC nts=4 GGGG A.DG5,A.DG21,A.DG17,A.DG13 2 glyco-bond=s--- sugar=---3 groove=w--n Major-->WC nts=4 gGGG A.BGM6,A.DG20,A.DG16,A.DG12 3 glyco-bond=s--- sugar=---- groove=w--n Major-->WC nts=4 gGGG A.BGM7,A.DG19,A.DG15,A.DG11 step#1 mp(<<,backward) area=13.79 rise=3.40 twist=27.9 step#2 mp(<<,backward) area=18.55 rise=3.43 twist=23.5 strand#1 U DNA glyco-bond=sss sugar=--- nts=3 Ggg A.DG5,A.BGM6,A.BGM7 strand#2 D DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG21,A.DG20,A.DG19 strand#3 D DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG17,A.DG16,A.DG15 strand#4 D DNA glyco-bond=--- sugar=-3- nts=3 GGG A.DG13,A.DG12,A.DG11 loop#1 type=lateral strands=[#1,#4] nts=3 TCA A.DT8,A.DC9,A.DA10 loop#2 type=propeller strands=[#4,#3] nts=1 T A.DT14 loop#3 type=propeller strands=[#3,#2] nts=1 T A.DT18 **************************************************************************** List of 3 splayed-apart dinucleotides 1 A.BGM7 A.DT8 angle=104 distance=15.0 ratio=0.79 2 A.DG13 A.DT14 angle=116 distance=17.6 ratio=0.85 3 A.DT14 A.DG15 angle=138 distance=17.2 ratio=0.93 ---------------------------------------------------------------- Summary of 2 splayed-apart units 1 nts=2 gT A.BGM7,A.DT8 2 nts=3 GTG A.DG13,A.DT14,A.DG15 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >6r9k nts=25 [whole] GCGTGggTCAGGGTGGGTGGGACGC ((((.................)))) >6r9k-A #1 nts=25 0.36(2.37) [chain] DNA GCGTGggTCAGGGTGGGTGGGACGC ((((.................)))) **************************************************************************** Summary of structural features of 25 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 0.025 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 2 C ( A.DC2 0.021 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 3 G ( A.DG3 0.036 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 4 T ( A.DT4 0.030 anti,canonical,non-pair-contact,helix,stem-end,hairpin-loop 5 G . A.DG5 0.031 syn,~C2'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,hairpin-loop,G-tetrad 6 g . A.BGM6 0.028 modified,syn,~C2'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,hairpin-loop,G-tetrad 7 g . A.BGM7 0.034 modified,syn,~C2'-endo,non-canonical,non-pair-contact,helix-end,multiplet,hairpin-loop,G-tetrad,splayed-apart 8 T . A.DT8 0.030 anti,~C2'-endo,BI,non-pair-contact,hairpin-loop,splayed-apart 9 C . A.DC9 0.017 anti,~C2'-endo,non-pair-contact,hairpin-loop 10 A . A.DA10 0.045 anti,~C3'-endo,non-pair-contact,hairpin-loop 11 G . A.DG11 0.022 anti,~C2'-endo,non-canonical,non-pair-contact,helix-end,multiplet,hairpin-loop,G-tetrad 12 G . A.DG12 0.023 u-turn,anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix,multiplet,hairpin-loop,G-tetrad 13 G . A.DG13 0.029 turn,u-turn,anti,~C2'-endo,non-canonical,non-pair-contact,helix-end,multiplet,hairpin-loop,G-tetrad,splayed-apart 14 T . A.DT14 0.030 turn,u-turn,anti,~C2'-endo,BII,non-stack,hairpin-loop,splayed-apart 15 G . A.DG15 0.022 u-turn,anti,~C2'-endo,BI,non-canonical,non-pair-contact,helix-end,multiplet,hairpin-loop,G-tetrad,phosphate,splayed-apart 16 G . A.DG16 0.023 anti,~C2'-endo,non-canonical,non-pair-contact,helix,multiplet,hairpin-loop,G-tetrad 17 G . A.DG17 0.020 anti,~C2'-endo,non-canonical,non-pair-contact,helix-end,multiplet,hairpin-loop,G-tetrad 18 T . A.DT18 0.028 anti,~C2'-endo,BII,non-stack,non-pair-contact,hairpin-loop 19 G . A.DG19 0.027 turn,anti,~C2'-endo,BI,non-canonical,non-pair-contact,helix-end,multiplet,hairpin-loop,G-tetrad 20 G . A.DG20 0.023 anti,~C2'-endo,BII,non-canonical,non-pair-contact,helix,multiplet,hairpin-loop,G-tetrad 21 G . A.DG21 0.027 anti,~C2'-endo,BII,non-canonical,non-pair-contact,helix,multiplet,hairpin-loop,G-tetrad 22 A ) A.DA22 0.031 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem-end,hairpin-loop 23 C ) A.DC23 0.018 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 24 G ) A.DG24 0.024 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 25 C ) A.DC25 0.015 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end **************************************************************************** List of 15 additional files 1 dssr-pairs.pdb -- an ensemble of base pairs 2 dssr-multiplets.pdb -- an ensemble of multiplets 3 dssr-stems.pdb -- an ensemble of stems 4 dssr-helices.pdb -- an ensemble of helices (coaxial stacking) 5 dssr-hairpins.pdb -- an ensemble of hairpin loops 6 dssr-2ndstrs.bpseq -- secondary structure in bpseq format 7 dssr-2ndstrs.ct -- secondary structure in connectivity table format 8 dssr-2ndstrs.dbn -- secondary structure in dot-bracket notation 9 dssr-torsions.txt -- backbone torsion angles and suite names 10 dssr-splays.pdb -- an ensemble of splayed-apart units 11 dssr-stacks.pdb -- an ensemble of base stacks 12 dssr-rotmat.txt -- position vector and rotation matrix 13 dssr-viewV.pdb -- vertical view of the principal moment of inertia 14 dssr-viewH.pdb -- horizontal view of the principal moment of inertia 15 dssr-viewT.pdb -- top view of the principal moment of inertia