**************************************************************************** File name: 6xlm.pdb no. of DNA/RNA chains: 3 [N=14,R=9,T=17] no. of nucleotides: 40 no. of atoms: 28244 no. of waters: 0 no. of metals: 3 [Mg=1,Zn=2] **************************************************************************** List of 16 base pairs nt1 nt2 bp name Saenger LW DSSR 1 N.DG83 T.DC6 G-C WC 19-XIX cWW cW-W 2 N.DC84 T.DG5 C-G WC 19-XIX cWW cW-W 3 N.DG85 T.DC4 G-C WC 19-XIX cWW cW-W 4 N.DG86 T.DC3 G-C WC 19-XIX cWW cW-W 5 N.DC87 T.DG2 C-G WC 19-XIX cWW cW-W 6 N.DG88 T.DC1 G-C WC 19-XIX cWW cW-W 7 T.DT8 R.A9 T-A WC 20-XX cWW cW-W 8 T.DC9 R.G8 C-G WC 19-XIX cWW cW-W 9 T.DA10 R.U7 A-U WC 20-XX cWW cW-W 10 T.DG11 R.C6 G-C WC 19-XIX cWW cW-W 11 T.DA12 R.U5 A-U WC 20-XX cWW cW-W 12 T.DC13 R.G4 C-G WC 19-XIX cWW cW-W 13 T.DT14 R.A3 T-A WC 20-XX cWW cW-W 14 T.DG15 R.C2 G-C WC 19-XIX cWW cW-W 15 T.DC16 R.G1 C-G WC 19-XIX cWW cW-W 16 T.DA17 R.G1 A-G -- -- cWW cW-W **************************************************************************** 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=6 strand-1 5'-GCGGCG-3' bp-type |||||| strand-2 3'-CGCCGC-5' helix-form ..B.B 1 N.DG83 T.DC6 G-C WC 19-XIX cWW cW-W 2 N.DC84 T.DG5 C-G WC 19-XIX cWW cW-W 3 N.DG85 T.DC4 G-C WC 19-XIX cWW cW-W 4 N.DG86 T.DC3 G-C WC 19-XIX cWW cW-W 5 N.DC87 T.DG2 C-G WC 19-XIX cWW cW-W 6 N.DG88 T.DC1 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#2[1] bps=9 strand-1 5'-TCAGACTGC-3' bp-type ||||||||| strand-2 3'-AGUCUGACG-5' helix-form AAAAAA.. 1 T.DT8 R.A9 T-A WC 20-XX cWW cW-W 2 T.DC9 R.G8 C-G WC 19-XIX cWW cW-W 3 T.DA10 R.U7 A-U WC 20-XX cWW cW-W 4 T.DG11 R.C6 G-C WC 19-XIX cWW cW-W 5 T.DA12 R.U5 A-U WC 20-XX cWW cW-W 6 T.DC13 R.G4 C-G WC 19-XIX cWW cW-W 7 T.DT14 R.A3 T-A WC 20-XX cWW cW-W 8 T.DG15 R.C2 G-C WC 19-XIX cWW cW-W 9 T.DC16 R.G1 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=6 strand-1 5'-GCGGCG-3' bp-type |||||| strand-2 3'-CGCCGC-5' helix-form ..B.B 1 N.DG83 T.DC6 G-C WC 19-XIX cWW cW-W 2 N.DC84 T.DG5 C-G WC 19-XIX cWW cW-W 3 N.DG85 T.DC4 G-C WC 19-XIX cWW cW-W 4 N.DG86 T.DC3 G-C WC 19-XIX cWW cW-W 5 N.DC87 T.DG2 C-G WC 19-XIX cWW cW-W 6 N.DG88 T.DC1 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#2[#2] bps=9 strand-1 5'-TCAGACTGC-3' bp-type ||||||||| strand-2 3'-AGUCUGACG-5' helix-form AAAAAA.. 1 T.DT8 R.A9 T-A WC 20-XX cWW cW-W 2 T.DC9 R.G8 C-G WC 19-XIX cWW cW-W 3 T.DA10 R.U7 A-U WC 20-XX cWW cW-W 4 T.DG11 R.C6 G-C WC 19-XIX cWW cW-W 5 T.DA12 R.U5 A-U WC 20-XX cWW cW-W 6 T.DC13 R.G4 C-G WC 19-XIX cWW cW-W 7 T.DT14 R.A3 T-A WC 20-XX cWW cW-W 8 T.DG15 R.C2 G-C WC 19-XIX cWW cW-W 9 T.DC16 R.G1 C-G WC 19-XIX cWW cW-W **************************************************************************** List of 4 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 RC C.ARG180,N.DC78 2 nts=2 GT T.DG7,T.DT8 3 nts=2 CA T.DC16,T.DA17 4 nts=7 WAGTTGA C.TRP183,N.DA81,N.DG80,N.DT79,N.DT77,N.DG76,N.DA75 **************************************************************************** Nucleotides not involved in stacking interactions nts=1 C N.DC82 **************************************************************************** List of 3 non-loop single-stranded segments 1 nts=8 AGTCTGAC N.DA75,N.DG76,N.DT77,N.DC78,N.DT79,N.DG80,N.DA81,N.DC82 2 nts=1 G T.DG7 3 nts=1 A T.DA17 **************************************************************************** List of 3 splayed-apart dinucleotides 1 N.DT77 N.DC78 angle=128 distance=19.2 ratio=0.90 2 N.DC78 N.DT79 angle=146 distance=19.1 ratio=0.96 3 T.DC6 T.DG7 angle=129 distance=17.5 ratio=0.90 ---------------------------------------------------------------- Summary of 2 splayed-apart units 1 nts=3 TCT N.DT77,N.DC78,N.DT79 2 nts=2 CG T.DC6,T.DG7 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >6xlm nts=40 [whole] AGTCTGACGCGGCG&CGCCGCGTCAGACTGCA&GCAGUCUGA ........((((((&)))))).(((((((((.&))))))))) >6xlm-N #1 nts=14 1.28(1.24) [chain] DNA AGTCTGACGCGGCG ........(((((( >6xlm-T #2 nts=17 2.21(1.30) [chain] DNA CGCCGCGTCAGACTGCA )))))).(((((((((. >6xlm-R #3 nts=9 3.22(0.32) [chain] RNA GCAGUCUGA ))))))))) **************************************************************************** Summary of structural features of 40 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 . N.DA75 0.003 anti,~C2'-endo,BII,non-pair-contact,ss-non-loop 2 G . N.DG76 0.006 anti,~C2'-endo,BI,non-pair-contact,ss-non-loop 3 T . N.DT77 0.005 anti,~C2'-endo,non-pair-contact,ss-non-loop,phosphate,splayed-apart 4 C . N.DC78 0.002 turn,anti,~C3'-endo,ss-non-loop,phosphate,splayed-apart 5 T . N.DT79 0.003 anti,~C2'-endo,BI,non-pair-contact,ss-non-loop,splayed-apart 6 G . N.DG80 0.008 ~C2'-endo,non-pair-contact,ss-non-loop 7 A . N.DA81 0.005 ~C2'-endo,BI,non-pair-contact,ss-non-loop 8 C . N.DC82 0.005 syn,~C3'-endo,non-stack,ss-non-loop 9 G ( N.DG83 0.008 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 10 C ( N.DC84 0.007 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 11 G ( N.DG85 0.010 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 12 G ( N.DG86 0.009 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem 13 C ( N.DC87 0.009 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 14 G ( N.DG88 0.011 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end 15 C ) T.DC1 0.008 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end 16 G ) T.DG2 0.011 anti,~C2'-endo,canonical,non-pair-contact,helix,stem 17 C ) T.DC3 0.007 anti,~C2'-endo,canonical,non-pair-contact,helix,stem,phosphate 18 C ) T.DC4 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 19 G ) T.DG5 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 20 C ) T.DC6 0.008 anti,~C3'-endo,BII,canonical,non-pair-contact,helix-end,stem-end,phosphate,splayed-apart 21 G . T.DG7 0.011 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,phosphate,splayed-apart 22 T ( T.DT8 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,phosphate 23 C ( T.DC9 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 24 A ( T.DA10 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 25 G ( T.DG11 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 26 A ( T.DA12 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 27 C ( T.DC13 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 28 T ( T.DT14 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 29 G ( T.DG15 0.007 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 30 C ( T.DC16 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end 31 A . T.DA17 0.005 anti,~C3'-endo,non-canonical,non-pair-contact,ss-non-loop 32 G ) R.G1 0.005 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix-end,stem-end 33 C ) R.C2 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 34 A ) R.A3 0.012 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 35 G ) R.G4 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 36 U ) R.U5 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 37 C ) R.C6 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 38 U ) R.U7 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 39 G ) R.G8 0.016 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,phosphate 40 A ) R.A9 0.001 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end,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