**************************************************************************** File name: 9vs5.pdb no. of DNA/RNA chains: 2 [P=10,T=13] no. of nucleotides: 23 no. of atoms: 16710 no. of waters: 0 no. of metals: 0 **************************************************************************** List of 13 base pairs nt1 nt2 bp name Saenger LW DSSR 1 P.U4 T.A20 U-A WC 20-XX cWW cW-W 2 P.A5 T.U19 A+U -- -- cHW cM+W 3 P.A6 T.U18 A-U WC 20-XX cWW cW-W 4 P.A6 T.U19 A-U -- -- cWW cW-W 5 P.A7 T.U17 A-U WC 20-XX cWW cW-W 6 P.A7 T.U18 A-U -- -- cWW cW-W 7 P.A8 T.U16 A-U WC 20-XX cWW cW-W 8 P.A8 T.U17 A-U -- -- cWW cW-W 9 P.A9 T.U15 A-U WC 20-XX cWW cW-W 10 P.U10 T.A14 U-A WC 20-XX cWW cW-W 11 P.A11 T.U13 A-U WC 20-XX cWW cW-W 12 P.A12 T.U12 A-U WC 20-XX cWW cW-W 13 P.U13 T.A11 U-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[1] bps=10 strand-1 5'-UAAAAAUAAU-3' bp-type |.|||||||| strand-2 3'-AUUUUUAUUA-5' helix-form ....A..AA 1 P.U4 T.A20 U-A WC 20-XX cWW cW-W 2 P.A5 T.U19 A+U -- -- cHW cM+W 3 P.A6 T.U18 A-U WC 20-XX cWW cW-W 4 P.A7 T.U17 A-U WC 20-XX cWW cW-W 5 P.A8 T.U16 A-U WC 20-XX cWW cW-W 6 P.A9 T.U15 A-U WC 20-XX cWW cW-W 7 P.U10 T.A14 U-A WC 20-XX cWW cW-W 8 P.A11 T.U13 A-U WC 20-XX cWW cW-W 9 P.A12 T.U12 A-U WC 20-XX cWW cW-W 10 P.U13 T.A11 U-A WC 20-XX 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=8 strand-1 5'-AAAAUAAU-3' bp-type |||||||| strand-2 3'-UUUUAUUA-5' helix-form ..A..AA 1 P.A6 T.U18 A-U WC 20-XX cWW cW-W 2 P.A7 T.U17 A-U WC 20-XX cWW cW-W 3 P.A8 T.U16 A-U WC 20-XX cWW cW-W 4 P.A9 T.U15 A-U WC 20-XX cWW cW-W 5 P.U10 T.A14 U-A WC 20-XX cWW cW-W 6 P.A11 T.U13 A-U WC 20-XX cWW cW-W 7 P.A12 T.U12 A-U WC 20-XX cWW cW-W 8 P.U13 T.A11 U-A WC 20-XX 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] -1 P.U4 T.A20 U-A WC 20-XX cWW cW-W **************************************************************************** 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 RU A.ARG959,P.U13 2 nts=2 AA P.A5,P.A6 3 nts=2 UA T.U19,T.A20 **************************************************************************** Nucleotides not involved in stacking interactions nts=4 UUCC P.U4,T.U8,T.C9,T.C10 **************************************************************************** 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 1 internal loop 1 symmetric internal loop: nts=6; [1,1]; linked by [#-1,#1] summary: [2] 1 1 [P.4 T.20 P.6 T.18] 1 8 nts=6 UAAUUA P.U4,P.A5,P.A6,T.U18,T.U19,T.A20 nts=1 A P.A5 nts=1 U T.U19 **************************************************************************** List of 1 non-loop single-stranded segment 1 nts=3 UCC T.U8,T.C9,T.C10 **************************************************************************** List of 1 splayed-apart dinucleotide 1 T.C10 T.A11 angle=130 distance=16.7 ratio=0.91 ---------------------------------------------------------------- Summary of 1 splayed-apart unit 1 nts=2 CA T.C10,T.A11 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >9vs5 nts=23 [whole] UAAAAAUAAU&UCCAUUAUUUUUA (.((((((((&...)))))))).) >9vs5-P #1 nts=10 3.00(0.38) [chain] RNA UAAAAAUAAU (.(((((((( >9vs5-T #2 nts=13 2.33(1.01) [chain] RNA UCCAUUAUUUUUA ...)))))))).) **************************************************************************** Summary of structural features of 23 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 U ( P.U4 0.002 anti,~C3'-endo,BI,non-stack,isolated-canonical,non-pair-contact,helix-end,internal-loop,phosphate 2 A . P.A5 0.008 syn,~C3'-endo,BI,non-canonical,non-pair-contact,helix,internal-loop,phosphate 3 A ( P.A6 0.012 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem-end,internal-loop,phosphate 4 A ( P.A7 0.008 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem,phosphate 5 A ( P.A8 0.010 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem 6 A ( P.A9 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 7 U ( P.U10 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 8 A ( P.A11 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 9 A ( P.A12 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 10 U ( P.U13 0.005 anti,~C2'-endo,canonical,non-pair-contact,helix-end,stem-end,phosphate 11 U . T.U8 0.003 anti,~C3'-endo,BI,non-stack,non-pair-contact,ss-non-loop 12 C . T.C9 0.004 anti,~C3'-endo,BI,non-stack,non-pair-contact,ss-non-loop,phosphate 13 C . T.C10 0.003 anti,~C3'-endo,BII,non-stack,non-pair-contact,ss-non-loop,phosphate,splayed-apart 14 A ) T.A11 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,phosphate,splayed-apart 15 U ) T.U12 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 16 U ) T.U13 0.003 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,phosphate 17 A ) T.A14 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,phosphate 18 U ) T.U15 0.010 anti,~C3'-endo,canonical,non-pair-contact,helix,stem 19 U ) T.U16 0.010 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,phosphate 20 U ) T.U17 0.007 anti,~C3'-endo,BI,canonical,non-canonical,non-pair-contact,helix,stem 21 U ) T.U18 0.008 anti,~C3'-endo,canonical,non-canonical,non-pair-contact,helix,stem-end,internal-loop 22 U . T.U19 0.004 anti,~C3'-endo,non-canonical,non-pair-contact,helix,internal-loop 23 A ) T.A20 0.003 anti,~C3'-endo,isolated-canonical,non-pair-contact,helix-end,internal-loop **************************************************************************** List of 14 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-splays.pdb -- an ensemble of splayed-apart units 10 dssr-stacks.pdb -- an ensemble of base stacks 11 dssr-rotmat.txt -- position vector and rotation matrix 12 dssr-viewV.pdb -- vertical view of the principal moment of inertia 13 dssr-viewH.pdb -- horizontal view of the principal moment of inertia 14 dssr-viewT.pdb -- top view of the principal moment of inertia