**************************************************************************** File name: 3wtv.pdb no. of DNA/RNA chains: 4 [D=15,E=15,I=15,J=15] no. of nucleotides: 60 no. of atoms: 7002 no. of waters: 9 no. of metals: 0 **************************************************************************** List of 30 base pairs nt1 nt2 bp name Saenger LW DSSR 1 D.DG1 E.DC15 G-C WC 19-XIX cWW cW-W 2 D.DA2 E.DT14 A-T WC 20-XX cWW cW-W 3 D.DA3 E.DT13 A-T WC 20-XX cWW cW-W 4 D.DG4 E.DC12 G-C WC 19-XIX cWW cW-W 5 D.DC5 E.DG11 C-G WC 19-XIX cWW cW-W 6 D.DC6 E.DG10 C-G WC 19-XIX cWW cW-W 7 D.DA7 E.DT9 A-T WC 20-XX cWW cW-W 8 D.DC8 E.DG8 C-G WC 19-XIX cWW cW-W 9 D.DA9 E.DT7 A-T WC 20-XX cWW cW-W 10 D.DT10 E.DA6 T-A WC 20-XX cWW cW-W 11 D.DC11 E.DG5 C-G WC 19-XIX cWW cW-W 12 D.DC12 E.DG4 C-G WC 19-XIX cWW cW-W 13 D.DT13 E.DA3 T-A WC 20-XX cWW cW-W 14 D.DC14 E.DG2 C-G WC 19-XIX cWW cW-W 15 D.DT15 E.DA1 T-A WC 20-XX cWW cW-W 16 I.DG1 J.DC15 G-C WC 19-XIX cWW cW-W 17 I.DA2 J.DT14 A-T WC 20-XX cWW cW-W 18 I.DA3 J.DT13 A-T WC 20-XX cWW cW-W 19 I.DG4 J.DC12 G-C WC 19-XIX cWW cW-W 20 I.DC5 J.DG11 C-G WC 19-XIX cWW cW-W 21 I.DC6 J.DG10 C-G WC 19-XIX cWW cW-W 22 I.DA7 J.DT9 A-T WC 20-XX cWW cW-W 23 I.DC8 J.DG8 C-G WC 19-XIX cWW cW-W 24 I.DA9 J.DT7 A-T WC 20-XX cWW cW-W 25 I.DT10 J.DA6 T-A WC 20-XX cWW cW-W 26 I.DC11 J.DG5 C-G WC 19-XIX cWW cW-W 27 I.DC12 J.DG4 C-G WC 19-XIX cWW cW-W 28 I.DT13 J.DA3 T-A WC 20-XX cWW cW-W 29 I.DC14 J.DG2 C-G WC 19-XIX cWW cW-W 30 I.DT15 J.DA1 T-A 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[2] bps=30 strand-1 5'-AGAGGATGTGGCTTCAGAGGATGTGGCTTC-3' bp-type |||||||||||||||||||||||||||||| strand-2 3'-TCTCCTACACCGAAGTCTCCTACACCGAAG-5' helix-form .BB.BBBBB..BBBxBB.BBBBBB..BBB 1 E.DA1 D.DT15 A-T WC 20-XX cWW cW-W 2 E.DG2 D.DC14 G-C WC 19-XIX cWW cW-W 3 E.DA3 D.DT13 A-T WC 20-XX cWW cW-W 4 E.DG4 D.DC12 G-C WC 19-XIX cWW cW-W 5 E.DG5 D.DC11 G-C WC 19-XIX cWW cW-W 6 E.DA6 D.DT10 A-T WC 20-XX cWW cW-W 7 E.DT7 D.DA9 T-A WC 20-XX cWW cW-W 8 E.DG8 D.DC8 G-C WC 19-XIX cWW cW-W 9 E.DT9 D.DA7 T-A WC 20-XX cWW cW-W 10 E.DG10 D.DC6 G-C WC 19-XIX cWW cW-W 11 E.DG11 D.DC5 G-C WC 19-XIX cWW cW-W 12 E.DC12 D.DG4 C-G WC 19-XIX cWW cW-W 13 E.DT13 D.DA3 T-A WC 20-XX cWW cW-W 14 E.DT14 D.DA2 T-A WC 20-XX cWW cW-W 15 E.DC15 D.DG1 C-G WC 19-XIX cWW cW-W 16 J.DA1 I.DT15 A-T WC 20-XX cWW cW-W 17 J.DG2 I.DC14 G-C WC 19-XIX cWW cW-W 18 J.DA3 I.DT13 A-T WC 20-XX cWW cW-W 19 J.DG4 I.DC12 G-C WC 19-XIX cWW cW-W 20 J.DG5 I.DC11 G-C WC 19-XIX cWW cW-W 21 J.DA6 I.DT10 A-T WC 20-XX cWW cW-W 22 J.DT7 I.DA9 T-A WC 20-XX cWW cW-W 23 J.DG8 I.DC8 G-C WC 19-XIX cWW cW-W 24 J.DT9 I.DA7 T-A WC 20-XX cWW cW-W 25 J.DG10 I.DC6 G-C WC 19-XIX cWW cW-W 26 J.DG11 I.DC5 G-C WC 19-XIX cWW cW-W 27 J.DC12 I.DG4 C-G WC 19-XIX cWW cW-W 28 J.DT13 I.DA3 T-A WC 20-XX cWW cW-W 29 J.DT14 I.DA2 T-A WC 20-XX cWW cW-W 30 J.DC15 I.DG1 C-G WC 19-XIX cWW cW-W **************************************************************************** List of 2 stems 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=15 strand-1 5'-GAAGCCACATCCTCT-3' bp-type ||||||||||||||| strand-2 3'-CTTCGGTGTAGGAGA-5' helix-form BBB..BBBBB.BB. 1 D.DG1 E.DC15 G-C WC 19-XIX cWW cW-W 2 D.DA2 E.DT14 A-T WC 20-XX cWW cW-W 3 D.DA3 E.DT13 A-T WC 20-XX cWW cW-W 4 D.DG4 E.DC12 G-C WC 19-XIX cWW cW-W 5 D.DC5 E.DG11 C-G WC 19-XIX cWW cW-W 6 D.DC6 E.DG10 C-G WC 19-XIX cWW cW-W 7 D.DA7 E.DT9 A-T WC 20-XX cWW cW-W 8 D.DC8 E.DG8 C-G WC 19-XIX cWW cW-W 9 D.DA9 E.DT7 A-T WC 20-XX cWW cW-W 10 D.DT10 E.DA6 T-A WC 20-XX cWW cW-W 11 D.DC11 E.DG5 C-G WC 19-XIX cWW cW-W 12 D.DC12 E.DG4 C-G WC 19-XIX cWW cW-W 13 D.DT13 E.DA3 T-A WC 20-XX cWW cW-W 14 D.DC14 E.DG2 C-G WC 19-XIX cWW cW-W 15 D.DT15 E.DA1 T-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#2[#1] bps=15 strand-1 5'-GAAGCCACATCCTCT-3' bp-type ||||||||||||||| strand-2 3'-CTTCGGTGTAGGAGA-5' helix-form BBB..BBBBBB.BB 1 I.DG1 J.DC15 G-C WC 19-XIX cWW cW-W 2 I.DA2 J.DT14 A-T WC 20-XX cWW cW-W 3 I.DA3 J.DT13 A-T WC 20-XX cWW cW-W 4 I.DG4 J.DC12 G-C WC 19-XIX cWW cW-W 5 I.DC5 J.DG11 C-G WC 19-XIX cWW cW-W 6 I.DC6 J.DG10 C-G WC 19-XIX cWW cW-W 7 I.DA7 J.DT9 A-T WC 20-XX cWW cW-W 8 I.DC8 J.DG8 C-G WC 19-XIX cWW cW-W 9 I.DA9 J.DT7 A-T WC 20-XX cWW cW-W 10 I.DT10 J.DA6 T-A WC 20-XX cWW cW-W 11 I.DC11 J.DG5 C-G WC 19-XIX cWW cW-W 12 I.DC12 J.DG4 C-G WC 19-XIX cWW cW-W 13 I.DT13 J.DA3 T-A WC 20-XX cWW cW-W 14 I.DC14 J.DG2 C-G WC 19-XIX cWW cW-W 15 I.DT15 J.DA1 T-A WC 20-XX cWW cW-W **************************************************************************** List of 1 coaxial stack 1 Helix#1 contains 2 stems: [#1,#2] **************************************************************************** List of 2 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 GT D.DG1,I.DT15 2 nts=2 CA E.DC15,J.DA1 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >3wtv nts=60 [whole] GAAGCCACATCCTCT&AGAGGATGTGGCTTC&GAAGCCACATCCTCT&AGAGGATGTGGCTTC (((((((((((((((&)))))))))))))))&(((((((((((((((&))))))))))))))) >3wtv-D #1 nts=15 3.28(0.43) [chain] DNA GAAGCCACATCCTCT ((((((((((((((( >3wtv-E #2 nts=15 3.21(0.34) [chain] DNA AGAGGATGTGGCTTC ))))))))))))))) >3wtv-I #3 nts=15 3.24(0.44) [chain] DNA GAAGCCACATCCTCT ((((((((((((((( >3wtv-J #4 nts=15 3.24(0.46) [chain] DNA AGAGGATGTGGCTTC ))))))))))))))) **************************************************************************** Summary of structural features of 60 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 ( D.DG1 0.007 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack 2 A ( D.DA2 0.011 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 3 A ( D.DA3 0.006 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 4 G ( D.DG4 0.034 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 5 C ( D.DC5 0.021 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 6 C ( D.DC6 0.012 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 7 A ( D.DA7 0.007 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 8 C ( D.DC8 0.013 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 9 A ( D.DA9 0.018 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 10 T ( D.DT10 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 11 C ( D.DC11 0.009 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 12 C ( D.DC12 0.011 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 13 T ( D.DT13 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 14 C ( D.DC14 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 15 T ( D.DT15 0.013 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 16 A ) E.DA1 0.011 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 17 G ) E.DG2 0.006 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 18 A ) E.DA3 0.008 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 19 G ) E.DG4 0.014 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 20 G ) E.DG5 0.007 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 21 A ) E.DA6 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 22 T ) E.DT7 0.007 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 23 G ) E.DG8 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 24 T ) E.DT9 0.008 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 25 G ) E.DG10 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 26 G ) E.DG11 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 27 C ) E.DC12 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 28 T ) E.DT13 0.015 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 29 T ) E.DT14 0.009 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 30 C ) E.DC15 0.006 anti,~C2'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack 31 G ( I.DG1 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 32 A ( I.DA2 0.013 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 33 A ( I.DA3 0.010 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 34 G ( I.DG4 0.033 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 35 C ( I.DC5 0.016 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 36 C ( I.DC6 0.014 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 37 A ( I.DA7 0.007 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 38 C ( I.DC8 0.007 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 39 A ( I.DA9 0.013 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 40 T ( I.DT10 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 41 C ( I.DC11 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 42 C ( I.DC12 0.013 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 43 T ( I.DT13 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 44 C ( I.DC14 0.008 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 45 T ( I.DT15 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack 46 A ) J.DA1 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack 47 G ) J.DG2 0.008 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 48 A ) J.DA3 0.007 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 49 G ) J.DG4 0.011 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack 50 G ) J.DG5 0.008 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 51 A ) J.DA6 0.008 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 52 T ) J.DT7 0.007 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 53 G ) J.DG8 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 54 T ) J.DT9 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 55 G ) J.DG10 0.005 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 56 G ) J.DG11 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 57 C ) J.DC12 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 58 T ) J.DT13 0.010 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 59 T ) J.DT14 0.009 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 60 C ) J.DC15 0.005 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack **************************************************************************** List of 12 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-stacks.pdb -- an ensemble of base stacks 9 dssr-rotmat.txt -- position vector and rotation matrix 10 dssr-viewV.pdb -- vertical view of the principal moment of inertia 11 dssr-viewH.pdb -- horizontal view of the principal moment of inertia 12 dssr-viewT.pdb -- top view of the principal moment of inertia