**************************************************************************** File name: 5uop.pdb no. of DNA/RNA chains: 2 [C=19,D=17] no. of nucleotides: 36 no. of atoms: 5333 no. of waters: 180 no. of metals: 4 [Mg=3,Zn=1] **************************************************************************** List of 16 base pairs nt1 nt2 bp name Saenger LW DSSR 1 C.DG4 D.DC16 G-C WC 19-XIX cWW cW-W 2 C.DT5 D.DA15 T-A WC 20-XX cWW cW-W 3 C.DC6 D.DG14 C-G WC 19-XIX cWW cW-W 4 C.DA7 D.DT13 A-T WC 20-XX cWW cW-W 5 C.DT8 D.DA12 T-A WC 20-XX cWW cW-W 6 C.DG9 D.DC11 G-C WC 19-XIX cWW cW-W 7 C.DG10 D.DC10 G-C WC 19-XIX cWW cW-W 8 C.DA11 D.DT9 A-T WC 20-XX cWW cW-W 9 C.DA12 D.DT8 A-T WC 20-XX cWW cW-W 10 C.DT13 D.DA7 T-A WC 20-XX cWW cW-W 11 C.DT14 D.DA6 T-A WC 20-XX cWW cW-W 12 C.DT15 D.DA5 T-A WC 20-XX cWW cW-W 13 C.DC16 D.DG4 C-G WC 19-XIX cWW cW-W 14 C.DG17 D.DC3 G-C WC 19-XIX cWW cW-W 15 C.DC18 D.DG2 C-G WC 19-XIX cWW cW-W 16 C.DA19 D.DT1 A-T WC 20-XX cWW cW-W **************************************************************************** List of 1 helix 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=16 strand-1 5'-GTCATGGAATTTCGCA-3' bp-type |||||||||||||||| strand-2 3'-CAGTACCTTAAAGCGT-5' helix-form .B.B.BBBBBBBBBB 1 C.DG4 D.DC16 G-C WC 19-XIX cWW cW-W 2 C.DT5 D.DA15 T-A WC 20-XX cWW cW-W 3 C.DC6 D.DG14 C-G WC 19-XIX cWW cW-W 4 C.DA7 D.DT13 A-T WC 20-XX cWW cW-W 5 C.DT8 D.DA12 T-A WC 20-XX cWW cW-W 6 C.DG9 D.DC11 G-C WC 19-XIX cWW cW-W 7 C.DG10 D.DC10 G-C WC 19-XIX cWW cW-W 8 C.DA11 D.DT9 A-T WC 20-XX cWW cW-W 9 C.DA12 D.DT8 A-T WC 20-XX cWW cW-W 10 C.DT13 D.DA7 T-A WC 20-XX cWW cW-W 11 C.DT14 D.DA6 T-A WC 20-XX cWW cW-W 12 C.DT15 D.DA5 T-A WC 20-XX cWW cW-W 13 C.DC16 D.DG4 C-G WC 19-XIX cWW cW-W 14 C.DG17 D.DC3 G-C WC 19-XIX cWW cW-W 15 C.DC18 D.DG2 C-G WC 19-XIX cWW cW-W 16 C.DA19 D.DT1 A-T WC 20-XX cWW cW-W **************************************************************************** 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=16 strand-1 5'-GTCATGGAATTTCGCA-3' bp-type |||||||||||||||| strand-2 3'-CAGTACCTTAAAGCGT-5' helix-form .B.B.BBBBBBBBBB 1 C.DG4 D.DC16 G-C WC 19-XIX cWW cW-W 2 C.DT5 D.DA15 T-A WC 20-XX cWW cW-W 3 C.DC6 D.DG14 C-G WC 19-XIX cWW cW-W 4 C.DA7 D.DT13 A-T WC 20-XX cWW cW-W 5 C.DT8 D.DA12 T-A WC 20-XX cWW cW-W 6 C.DG9 D.DC11 G-C WC 19-XIX cWW cW-W 7 C.DG10 D.DC10 G-C WC 19-XIX cWW cW-W 8 C.DA11 D.DT9 A-T WC 20-XX cWW cW-W 9 C.DA12 D.DT8 A-T WC 20-XX cWW cW-W 10 C.DT13 D.DA7 T-A WC 20-XX cWW cW-W 11 C.DT14 D.DA6 T-A WC 20-XX cWW cW-W 12 C.DT15 D.DA5 T-A WC 20-XX cWW cW-W 13 C.DC16 D.DG4 C-G WC 19-XIX cWW cW-W 14 C.DG17 D.DC3 G-C WC 19-XIX cWW cW-W 15 C.DC18 D.DG2 C-G WC 19-XIX cWW cW-W 16 C.DA19 D.DT1 A-T WC 20-XX cWW cW-W **************************************************************************** List of 1 base stack 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 TT C.DT2,C.DT3 **************************************************************************** Nucleotides not involved in stacking interactions nts=2 AA C.DA1,D.DA17 **************************************************************************** List of 2 non-loop single-stranded segments 1 nts=3 ATT C.DA1,C.DT2,C.DT3 2 nts=1 A D.DA17 **************************************************************************** List of 1 splayed-apart dinucleotide 1 C.DT3 C.DG4 angle=120 distance=18.0 ratio=0.87 ---------------------------------------------------------------- Summary of 1 splayed-apart unit 1 nts=2 TG C.DT3,C.DG4 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >5uop nts=36 [whole] ATTGTCATGGAATTTCGCA&TGCGAAATTCCATGACA ...((((((((((((((((&)))))))))))))))). >5uop-C #1 nts=19 3.36(0.75) [chain] DNA ATTGTCATGGAATTTCGCA ...(((((((((((((((( >5uop-D #2 nts=17 3.48(1.13) [chain] DNA TGCGAAATTCCATGACA )))))))))))))))). **************************************************************************** Summary of structural features of 36 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 . C.DA1 0.026 syn,~C2'-endo,non-stack,ss-non-loop 2 T . C.DT2 0.012 anti,~C2'-endo,BI,non-pair-contact,ss-non-loop 3 T . C.DT3 0.010 anti,~C2'-endo,non-pair-contact,ss-non-loop,phosphate,splayed-apart 4 G ( C.DG4 0.025 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,phosphate,splayed-apart 5 T ( C.DT5 0.020 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 6 C ( C.DC6 0.008 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem 7 A ( C.DA7 0.015 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 8 T ( C.DT8 0.007 anti,BI,canonical,non-pair-contact,helix,stem,phosphate 9 G ( C.DG9 0.014 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem 10 G ( C.DG10 0.016 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 11 A ( C.DA11 0.012 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 12 A ( C.DA12 0.019 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 13 T ( C.DT13 0.010 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 14 T ( C.DT14 0.011 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 15 T ( C.DT15 0.015 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 16 C ( C.DC16 0.016 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 17 G ( C.DG17 0.013 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 18 C ( C.DC18 0.011 anti,BI,canonical,non-pair-contact,helix,stem 19 A ( C.DA19 0.015 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end 20 T ) D.DT1 0.014 ~C2'-endo,canonical,non-pair-contact,helix-end,stem-end 21 G ) D.DG2 0.010 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 22 C ) D.DC3 0.013 anti,BI,canonical,non-pair-contact,helix,stem 23 G ) D.DG4 0.016 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 24 A ) D.DA5 0.013 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 25 A ) D.DA6 0.016 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 26 A ) D.DA7 0.015 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 27 T ) D.DT8 0.014 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 28 T ) D.DT9 0.015 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 29 C ) D.DC10 0.014 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 30 C ) D.DC11 0.010 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem 31 A ) D.DA12 0.023 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 32 T ) D.DT13 0.017 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 33 G ) D.DG14 0.024 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 34 A ) D.DA15 0.014 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 35 C ) D.DC16 0.011 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end 36 A . D.DA17 0.035 syn,~C2'-endo,non-stack,ss-non-loop,phosphate **************************************************************************** List of 13 additional files 1 dssr-pairs.pdb -- an ensemble of base pairs 2 dssr-stems.pdb -- an ensemble of stems 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-rotmat.txt -- position vector and rotation matrix 11 dssr-viewV.pdb -- vertical view of the principal moment of inertia 12 dssr-viewH.pdb -- horizontal view of the principal moment of inertia 13 dssr-viewT.pdb -- top view of the principal moment of inertia