**************************************************************************** File name: 1bf5.pdb no. of DNA/RNA chains: 2 [B=18,C=18] no. of nucleotides: 36 no. of atoms: 5117 no. of waters: 0 no. of metals: 0 **************************************************************************** List of 16 base pairs nt1 nt2 bp name Saenger LW DSSR 1 B.DC1002 C.DG2018 C-G -- -- cWW cW-W 2 B.DG1004 C.DC2016 G-C WC 19-XIX cWW cW-W 3 B.DT1005 C.DA2015 T-A WC 20-XX cWW cW-W 4 B.DT1006 C.DA2014 T-A WC 20-XX cWW cW-W 5 B.DT1007 C.DA2013 T-A WC 20-XX cWW cW-W 6 B.DC1008 C.DG2012 C-G WC 19-XIX cWW cW-W 7 B.DC1009 C.DG2011 C-G WC 19-XIX cWW cW-W 8 B.DC1010 C.DG2010 C-G WC 19-XIX cWW cW-W 9 B.DG1011 C.DC2009 G-C WC 19-XIX cWW cW-W 10 B.DT1012 C.DA2008 T-A WC 20-XX cWW cW-W 11 B.DA1013 C.DT2007 A-T WC 20-XX cWW cW-W 12 B.DA1014 C.DT2006 A-T WC 20-XX cWW cW-W 13 B.DA1015 C.DT2005 A-T WC 20-XX cWW cW-W 14 B.DT1016 C.DA2004 T-A WC 20-XX cWW cW-W 15 B.DG1017 C.DC2003 G-C WC 19-XIX cWW cW-W 16 B.DC1018 C.DG2002 C-G WC 19-XIX 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=15 strand-1 5'-GTTTCCCGTAAATGC-3' bp-type ||||||||||||||| strand-2 3'-CAAAGGGCATTTACG-5' helix-form .B..B.x.B..... 1 B.DG1004 C.DC2016 G-C WC 19-XIX cWW cW-W 2 B.DT1005 C.DA2015 T-A WC 20-XX cWW cW-W 3 B.DT1006 C.DA2014 T-A WC 20-XX cWW cW-W 4 B.DT1007 C.DA2013 T-A WC 20-XX cWW cW-W 5 B.DC1008 C.DG2012 C-G WC 19-XIX cWW cW-W 6 B.DC1009 C.DG2011 C-G WC 19-XIX cWW cW-W 7 B.DC1010 C.DG2010 C-G WC 19-XIX cWW cW-W 8 B.DG1011 C.DC2009 G-C WC 19-XIX cWW cW-W 9 B.DT1012 C.DA2008 T-A WC 20-XX cWW cW-W 10 B.DA1013 C.DT2007 A-T WC 20-XX cWW cW-W 11 B.DA1014 C.DT2006 A-T WC 20-XX cWW cW-W 12 B.DA1015 C.DT2005 A-T WC 20-XX cWW cW-W 13 B.DT1016 C.DA2004 T-A WC 20-XX cWW cW-W 14 B.DG1017 C.DC2003 G-C WC 19-XIX cWW cW-W 15 B.DC1018 C.DG2002 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=7 strand-1 5'-GTTTCCC-3' bp-type ||||||| strand-2 3'-CAAAGGG-5' helix-form .B..B. 1 B.DG1004 C.DC2016 G-C WC 19-XIX cWW cW-W 2 B.DT1005 C.DA2015 T-A WC 20-XX cWW cW-W 3 B.DT1006 C.DA2014 T-A WC 20-XX cWW cW-W 4 B.DT1007 C.DA2013 T-A WC 20-XX cWW cW-W 5 B.DC1008 C.DG2012 C-G WC 19-XIX cWW cW-W 6 B.DC1009 C.DG2011 C-G WC 19-XIX cWW cW-W 7 B.DC1010 C.DG2010 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#2[#1] bps=8 strand-1 5'-GTAAATGC-3' bp-type |||||||| strand-2 3'-CATTTACG-5' helix-form .B..... 1 B.DG1011 C.DC2009 G-C WC 19-XIX cWW cW-W 2 B.DT1012 C.DA2008 T-A WC 20-XX cWW cW-W 3 B.DA1013 C.DT2007 A-T WC 20-XX cWW cW-W 4 B.DA1014 C.DT2006 A-T WC 20-XX cWW cW-W 5 B.DA1015 C.DT2005 A-T WC 20-XX cWW cW-W 6 B.DT1016 C.DA2004 T-A WC 20-XX cWW cW-W 7 B.DG1017 C.DC2003 G-C WC 19-XIX cWW cW-W 8 B.DC1018 C.DG2002 C-G WC 19-XIX cWW cW-W **************************************************************************** List of 1 coaxial stack 1 Helix#1 contains 2 stems: [#1,#2] **************************************************************************** List of 3 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 CG B.DC1010,B.DG1011 2 nts=3 CTG C.DC2016,C.DT2017,C.DG2018 3 nts=4 ACAG B.DA1001,B.DC1002,B.DA1003,B.DG1004 **************************************************************************** Nucleotides not involved in stacking interactions nts=1 T C.DT2001 **************************************************************************** List of 3 non-loop single-stranded segments 1 nts=3 ACA B.DA1001,B.DC1002,B.DA1003 2 nts=1 T C.DT2001 3 nts=2 TG C.DT2017,C.DG2018 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >1bf5 nts=36 [whole] ACAGTTTCCC>AAATGC&TGCATTTACGGGAAACTG ...(((((((&((((((((&.))))))))))))))).. >1bf5-B #1 nts=18 3.27(0.61) [chain] DNA* ACAGTTTCCC>AAATGC ...(((((((&(((((((( >1bf5-C #2 nts=18 3.31(0.57) [chain] DNA TGCATTTACGGGAAACTG .))))))))))))))).. **************************************************************************** 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 . B.DA1001 0.014 ~C2'-endo,non-pair-contact,ss-non-loop 2 C . B.DC1002 0.015 anti,~C2'-endo,non-canonical,non-pair-contact,ss-non-loop 3 A . B.DA1003 0.009 ~C2'-endo,non-pair-contact,ss-non-loop 4 G ( B.DG1004 0.015 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 5 T ( B.DT1005 0.007 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 6 T ( B.DT1006 0.020 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 7 T ( B.DT1007 0.025 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 8 C ( B.DC1008 0.010 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 9 C ( B.DC1009 0.020 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 10 C ( B.DC1010 0.007 break,anti,~C2'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,phosphate 11 G ( B.DG1011 0.010 anti,~C2'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,phosphate 12 T ( B.DT1012 0.012 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 13 A ( B.DA1013 0.010 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 14 A ( B.DA1014 0.021 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 15 A ( B.DA1015 0.010 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 16 T ( B.DT1016 0.009 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 17 G ( B.DG1017 0.013 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 18 C ( B.DC1018 0.010 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,phosphate 19 T . C.DT2001 0.009 anti,~C2'-endo,BI,non-stack,non-pair-contact,ss-non-loop 20 G ) C.DG2002 0.013 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 21 C ) C.DC2003 0.006 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem,coaxial-stack 22 A ) C.DA2004 0.007 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 23 T ) C.DT2005 0.009 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 24 T ) C.DT2006 0.007 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 25 T ) C.DT2007 0.022 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 26 A ) C.DA2008 0.012 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 27 C ) C.DC2009 0.010 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem-end,coaxial-stack 28 G ) C.DG2010 0.020 anti,~C2'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack 29 G ) C.DG2011 0.010 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 30 G ) C.DG2012 0.019 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 31 A ) C.DA2013 0.009 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 32 A ) C.DA2014 0.011 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 33 A ) C.DA2015 0.011 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 34 C ) C.DC2016 0.018 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 35 T . C.DT2017 0.010 ~C2'-endo,non-pair-contact,ss-non-loop 36 G . C.DG2018 0.010 anti,~C2'-endo,non-canonical,non-pair-contact,ss-non-loop **************************************************************************** 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