**************************************************************************** File name: 7xi4.pdb no. of DNA/RNA chains: 2 [C=15,D=16] no. of nucleotides: 31 no. of atoms: 5300 no. of waters: 0 no. of metals: 0 **************************************************************************** List of 14 base pairs nt1 nt2 bp name Saenger LW DSSR 1 C.DA3 D.DT16 A-T WC 20-XX cWW cW-W 2 C.DG4 D.DC15 G-C WC 19-XIX cWW cW-W 3 C.DG5 D.DC14 G-C WC 19-XIX cWW cW-W 4 C.DT6 D.DA13 T-A WC 20-XX cWW cW-W 5 C.DC7 D.DG12 C-G -- -- cWW cW-W 6 C.DG8 D.DC11 G-C WC 19-XIX cWW cW-W 7 C.DT9 D.DA10 T-A WC 20-XX cWW cW-W 8 C.DG10 D.DC9 G-C WC 19-XIX cWW cW-W 9 C.DA11 D.DT8 A-T WC 20-XX cWW cW-W 10 C.DT13 D.DA6 T-A WC 20-XX cWW cW-W 11 C.DG14 D.DC5 G-C WC 19-XIX cWW cW-W 12 C.DA15 D.DA3 A-A -- -- cWW cW-W 13 C.DT16 D.DC2 T-C -- -- cWW cW-W 14 C.DT16 D.DA3 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[3] bps=11 strand-1 5'-AGGTCGTGATG-3' bp-type ||||.|||||| strand-2 3'-TCCAGCACTAC-5' helix-form ......B.x. 1 C.DA3 D.DT16 A-T WC 20-XX cWW cW-W 2 C.DG4 D.DC15 G-C WC 19-XIX cWW cW-W 3 C.DG5 D.DC14 G-C WC 19-XIX cWW cW-W 4 C.DT6 D.DA13 T-A WC 20-XX cWW cW-W 5 C.DC7 D.DG12 C-G -- -- cWW cW-W 6 C.DG8 D.DC11 G-C WC 19-XIX cWW cW-W 7 C.DT9 D.DA10 T-A WC 20-XX cWW cW-W 8 C.DG10 D.DC9 G-C WC 19-XIX cWW cW-W 9 C.DA11 D.DT8 A-T WC 20-XX cWW cW-W 10 C.DT13 D.DA6 T-A WC 20-XX cWW cW-W 11 C.DG14 D.DC5 G-C WC 19-XIX cWW cW-W **************************************************************************** List of 3 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=4 strand-1 5'-AGGT-3' bp-type |||| strand-2 3'-TCCA-5' helix-form ... 1 C.DA3 D.DT16 A-T WC 20-XX cWW cW-W 2 C.DG4 D.DC15 G-C WC 19-XIX cWW cW-W 3 C.DG5 D.DC14 G-C WC 19-XIX cWW cW-W 4 C.DT6 D.DA13 T-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#2[#1] bps=4 strand-1 5'-GTGA-3' bp-type |||| strand-2 3'-CACT-5' helix-form .B. 1 C.DG8 D.DC11 G-C WC 19-XIX cWW cW-W 2 C.DT9 D.DA10 T-A WC 20-XX cWW cW-W 3 C.DG10 D.DC9 G-C WC 19-XIX cWW cW-W 4 C.DA11 D.DT8 A-T WC 20-XX cWW cW-W -------------------------------------------------------------------------- stem#3[#1] bps=2 strand-1 5'-TG-3' bp-type || strand-2 3'-AC-5' helix-form . 1 C.DT13 D.DA6 T-A WC 20-XX cWW cW-W 2 C.DG14 D.DC5 G-C WC 19-XIX cWW cW-W **************************************************************************** List of 1 isolated WC/wobble pair Note: Isolated WC/wobble pairs are assigned negative indices to differentiate them from the stem numbers, which are positive. -------------------------------------------------------------------- -- -1 C.DT16 D.DA3 T-A WC 20-XX cWW cW-W **************************************************************************** List of 1 coaxial stack 1 Helix#1 contains 3 stems: [#1,#2,#3] **************************************************************************** List of 6 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 AT C.DA15,C.DT16 2 nts=2 GA D.DG12,D.DA13 3 nts=3 TCG C.DT6,C.DC7,C.DG8 4 nts=3 AGT C.DA11,C.DG12,C.DT13 5 nts=3 ACT D.DA6,D.DC7,D.DT8 6 nts=5 CCATC D.DC1,D.DC2,D.DA3,D.DT4,D.DC5 **************************************************************************** Nucleotides not involved in stacking interactions nts=1 G C.DG2 **************************************************************************** Note: For the various types of loops listed below, numbers within the first set of brackets are the number of loop nts. Numbers in the second set of brackets are the identities of the stems (positive) or isolated WC/wobble pairs (negative) to which they are linked. **************************************************************************** List of 3 internal loops 1 symmetric internal loop: nts=6; [1,1]; linked by [#1,#2] summary: [2] 1 1 [C.6 D.13 C.8 D.11] 4 4 nts=6 TCGCGA C.DT6,C.DC7,C.DG8,D.DC11,D.DG12,D.DA13 nts=1 C C.DC7 nts=1 G D.DG12 2 symmetric internal loop: nts=6; [1,1]; linked by [#2,#3] summary: [2] 1 1 [C.11 D.8 C.13 D.6] 4 2 nts=6 AGTACT C.DA11,C.DG12,C.DT13,D.DA6,D.DC7,D.DT8 nts=1 G C.DG12 nts=1 C D.DC7 3 symmetric internal loop: nts=6; [1,1]; linked by [#3,#-1] summary: [2] 1 1 [C.14 D.5 C.16 D.3] 2 1 nts=6 GATATC C.DG14,C.DA15,C.DT16,D.DA3,D.DT4,D.DC5 nts=1 A C.DA15 nts=1 T D.DT4 **************************************************************************** List of 2 non-loop single-stranded segments 1 nts=1 G C.DG2 2 nts=2 CC D.DC1,D.DC2 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >7xi4 nts=31 [whole] GAGGTCGTGAGTGAT&CCATCACTCACGACCT .((((.((((.((.(&..).)).)))).)))) >7xi4-C #1 nts=15 3.43(0.53) [chain] DNA GAGGTCGTGAGTGAT .((((.((((.((.( >7xi4-D #2 nts=16 3.28(0.52) [chain] DNA CCATCACTCACGACCT ..).)).)))).)))) **************************************************************************** Summary of structural features of 31 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 . C.DG2 0.003 anti,~C2'-endo,non-stack,ss-non-loop 2 A ( C.DA3 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 3 G ( C.DG4 0.007 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 4 G ( C.DG5 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 5 T ( C.DT6 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop,phosphate 6 C . C.DC7 0.003 anti,~C2'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop 7 G ( C.DG8 0.009 anti,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 8 T ( C.DT9 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 9 G ( C.DG10 0.016 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 10 A ( C.DA11 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 11 G . C.DG12 0.004 anti,~C2'-endo,BI,non-pair-contact,internal-loop 12 T ( C.DT13 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 13 G ( C.DG14 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,internal-loop 14 A . C.DA15 0.004 anti,~C2'-endo,BI,non-canonical,non-pair-contact,internal-loop 15 T ( C.DT16 0.002 anti,~C3'-endo,isolated-canonical,non-canonical,non-pair-contact,internal-loop 16 C . D.DC1 0.003 anti,~C2'-endo,non-pair-contact,ss-non-loop 17 C . D.DC2 0.003 anti,~C2'-endo,BI,non-canonical,non-pair-contact,ss-non-loop 18 A ) D.DA3 0.004 anti,~C2'-endo,isolated-canonical,non-canonical,non-pair-contact,internal-loop 19 T . D.DT4 0.002 anti,~C2'-endo,BI,non-pair-contact,internal-loop 20 C ) D.DC5 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,internal-loop 21 A ) D.DA6 0.004 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 22 C . D.DC7 0.003 anti,~C2'-endo,BI,non-pair-contact,internal-loop 23 T ) D.DT8 0.002 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 24 C ) D.DC9 0.008 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 25 A ) D.DA10 0.008 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 26 C ) D.DC11 0.005 anti,~C2'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 27 G . D.DG12 0.004 anti,~C2'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop,phosphate 28 A ) D.DA13 0.006 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop 29 C ) D.DC14 0.003 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 30 C ) D.DC15 0.005 anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 31 T ) D.DT16 0.004 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack **************************************************************************** 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-iloops.pdb -- an ensemble of internal loops 5 dssr-2ndstrs.bpseq -- secondary structure in bpseq format 6 dssr-2ndstrs.ct -- secondary structure in connectivity table format 7 dssr-2ndstrs.dbn -- secondary structure in dot-bracket notation 8 dssr-torsions.txt -- backbone torsion angles and suite names 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