**************************************************************************** File name: 4xrm.pdb no. of DNA/RNA chains: 2 [L=17,M=17] no. of nucleotides: 34 no. of atoms: 3089 no. of waters: 309 no. of metals: 0 **************************************************************************** List of 16 base pairs nt1 nt2 bp name Saenger LW DSSR 1 M.DG2 L.DC37 G-C WC 19-XIX cWW cW-W 2 M.DC3 L.DG36 C-G WC 19-XIX cWW cW-W 3 M.DT4 L.DA35 T-A WC 20-XX cWW cW-W 4 M.DG5 L.DC34 G-C WC 19-XIX cWW cW-W 5 M.DA6 L.DT33 A-T WC 20-XX cWW cW-W 6 M.DC7 L.DG32 C-G WC 19-XIX cWW cW-W 7 M.DA8 L.DT31 A-T WC 20-XX cWW cW-W 8 M.DG9 L.DC30 G-C WC 19-XIX cWW cW-W 9 M.DC10 L.DG29 C-G WC 19-XIX cWW cW-W 10 M.DT11 L.DA28 T-A WC 20-XX cWW cW-W 11 M.DG12 L.DC27 G-C WC 19-XIX cWW cW-W 12 M.DT13 L.DA26 T-A WC 20-XX cWW cW-W 13 M.DC14 L.DG25 C-G WC 19-XIX cWW cW-W 14 M.DA15 L.DT24 A-T WC 20-XX cWW cW-W 15 M.DA16 L.DT23 A-T WC 20-XX cWW cW-W 16 M.DG17 L.DC22 G-C 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[1] bps=16 strand-1 5'-GCTGACAGCTGTCAAG-3' bp-type |||||||||||||||| strand-2 3'-CGACTGTCGACAGTTC-5' helix-form BBBBBBBBBBBBBBB 1 M.DG2 L.DC37 G-C WC 19-XIX cWW cW-W 2 M.DC3 L.DG36 C-G WC 19-XIX cWW cW-W 3 M.DT4 L.DA35 T-A WC 20-XX cWW cW-W 4 M.DG5 L.DC34 G-C WC 19-XIX cWW cW-W 5 M.DA6 L.DT33 A-T WC 20-XX cWW cW-W 6 M.DC7 L.DG32 C-G WC 19-XIX cWW cW-W 7 M.DA8 L.DT31 A-T WC 20-XX cWW cW-W 8 M.DG9 L.DC30 G-C WC 19-XIX cWW cW-W 9 M.DC10 L.DG29 C-G WC 19-XIX cWW cW-W 10 M.DT11 L.DA28 T-A WC 20-XX cWW cW-W 11 M.DG12 L.DC27 G-C WC 19-XIX cWW cW-W 12 M.DT13 L.DA26 T-A WC 20-XX cWW cW-W 13 M.DC14 L.DG25 C-G WC 19-XIX cWW cW-W 14 M.DA15 L.DT24 A-T WC 20-XX cWW cW-W 15 M.DA16 L.DT23 A-T WC 20-XX cWW cW-W 16 M.DG17 L.DC22 G-C WC 19-XIX 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'-GCTGACAGCTGTCAAG-3' bp-type |||||||||||||||| strand-2 3'-CGACTGTCGACAGTTC-5' helix-form BBBBBBBBBBBBBBB 1 M.DG2 L.DC37 G-C WC 19-XIX cWW cW-W 2 M.DC3 L.DG36 C-G WC 19-XIX cWW cW-W 3 M.DT4 L.DA35 T-A WC 20-XX cWW cW-W 4 M.DG5 L.DC34 G-C WC 19-XIX cWW cW-W 5 M.DA6 L.DT33 A-T WC 20-XX cWW cW-W 6 M.DC7 L.DG32 C-G WC 19-XIX cWW cW-W 7 M.DA8 L.DT31 A-T WC 20-XX cWW cW-W 8 M.DG9 L.DC30 G-C WC 19-XIX cWW cW-W 9 M.DC10 L.DG29 C-G WC 19-XIX cWW cW-W 10 M.DT11 L.DA28 T-A WC 20-XX cWW cW-W 11 M.DG12 L.DC27 G-C WC 19-XIX cWW cW-W 12 M.DT13 L.DA26 T-A WC 20-XX cWW cW-W 13 M.DC14 L.DG25 C-G WC 19-XIX cWW cW-W 14 M.DA15 L.DT24 A-T WC 20-XX cWW cW-W 15 M.DA16 L.DT23 A-T WC 20-XX cWW cW-W 16 M.DG17 L.DC22 G-C WC 19-XIX 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 GT M.DG17,L.DT21 **************************************************************************** Nucleotides not involved in stacking interactions nts=1 A M.DA1 **************************************************************************** List of 2 non-loop single-stranded segments 1 nts=1 A M.DA1 2 nts=1 T L.DT21 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >4xrm nts=34 [whole] AGCTGACAGCTGTCAAG&TCTTGACAGCTGTCAGC .((((((((((((((((&.)))))))))))))))) >4xrm-M #1 nts=17 3.33(0.38) [chain] DNA AGCTGACAGCTGTCAAG .(((((((((((((((( >4xrm-L #2 nts=17 3.27(0.32) [chain] DNA TCTTGACAGCTGTCAGC .)))))))))))))))) **************************************************************************** Summary of structural features of 34 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 . M.DA1 0.003 ~C2'-endo,non-stack,ss-non-loop 2 G ( M.DG2 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 3 C ( M.DC3 0.002 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 4 T ( M.DT4 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 5 G ( M.DG5 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 6 A ( M.DA6 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 7 C ( M.DC7 0.004 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem 8 A ( M.DA8 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 9 G ( M.DG9 0.007 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 10 C ( M.DC10 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 11 T ( M.DT11 0.008 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 12 G ( M.DG12 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 13 T ( M.DT13 0.003 anti,BI,canonical,non-pair-contact,helix,stem 14 C ( M.DC14 0.003 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem 15 A ( M.DA15 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 16 A ( M.DA16 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 17 G ( M.DG17 0.003 anti,canonical,non-pair-contact,helix-end,stem-end 18 T . L.DT21 0.002 ~C2'-endo,BII,non-pair-contact,ss-non-loop 19 C ) L.DC22 0.002 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 20 T ) L.DT23 0.002 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 21 T ) L.DT24 0.004 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem 22 G ) L.DG25 0.008 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 23 A ) L.DA26 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 24 C ) L.DC27 0.004 anti,~C2'-endo,BII,canonical,non-pair-contact,helix,stem 25 A ) L.DA28 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 26 G ) L.DG29 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 27 C ) L.DC30 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 28 T ) L.DT31 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 29 G ) L.DG32 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 30 T ) L.DT33 0.004 anti,BI,canonical,non-pair-contact,helix,stem 31 C ) L.DC34 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 32 A ) L.DA35 0.003 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 33 G ) L.DG36 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 34 C ) L.DC37 0.002 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end **************************************************************************** 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