**************************************************************************** File name: 6sqn.pdb no. of DNA/RNA chains: 3 [X=16,Y=17,Z=16] no. of nucleotides: 49 no. of atoms: 3423 no. of waters: 95 no. of metals: 0 **************************************************************************** List of 12 base pairs nt1 nt2 bp name Saenger LW DSSR 1 X.A2 X.U19 A-U WC 20-XX cWW cW-W 2 X.U3 X.A18 U-A WC 20-XX cWW cW-W 3 X.C4 X.G17 C-G WC 19-XIX cWW cW-W 4 X.C5 X.G16 C-G WC 19-XIX cWW cW-W 5 Y.A2 Y.U19 A-U WC 20-XX cWW cW-W 6 Y.U3 Y.A18 U-A WC 20-XX cWW cW-W 7 Y.C4 Y.G17 C-G WC 19-XIX cWW cW-W 8 Y.C5 Y.G16 C-G WC 19-XIX cWW cW-W 9 Y.U7 Y.G9 U-G -- -- c.W c.-W 10 Z.A2 Z.U19 A-U WC 20-XX cWW cW-W 11 Z.U3 Z.A18 U-A WC 20-XX cWW cW-W 12 Z.C4 Z.G17 C-G WC 19-XIX cWW cW-W **************************************************************************** List of 3 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=4 strand-1 5'-AUCC-3' bp-type |||| strand-2 3'-UAGG-5' helix-form AAA 1 X.A2 X.U19 A-U WC 20-XX cWW cW-W 2 X.U3 X.A18 U-A WC 20-XX cWW cW-W 3 X.C4 X.G17 C-G WC 19-XIX cWW cW-W 4 X.C5 X.G16 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#2[1] bps=4 strand-1 5'-AUCC-3' bp-type |||| strand-2 3'-UAGG-5' helix-form .AA 1 Y.A2 Y.U19 A-U WC 20-XX cWW cW-W 2 Y.U3 Y.A18 U-A WC 20-XX cWW cW-W 3 Y.C4 Y.G17 C-G WC 19-XIX cWW cW-W 4 Y.C5 Y.G16 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#3[1] bps=3 strand-1 5'-AUC-3' bp-type ||| strand-2 3'-UAG-5' helix-form .A 1 Z.A2 Z.U19 A-U WC 20-XX cWW cW-W 2 Z.U3 Z.A18 U-A WC 20-XX cWW cW-W 3 Z.C4 Z.G17 C-G 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'-AUCC-3' bp-type |||| strand-2 3'-UAGG-5' helix-form AAA 1 X.A2 X.U19 A-U WC 20-XX cWW cW-W 2 X.U3 X.A18 U-A WC 20-XX cWW cW-W 3 X.C4 X.G17 C-G WC 19-XIX cWW cW-W 4 X.C5 X.G16 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#2[#2] bps=4 strand-1 5'-AUCC-3' bp-type |||| strand-2 3'-UAGG-5' helix-form .AA 1 Y.A2 Y.U19 A-U WC 20-XX cWW cW-W 2 Y.U3 Y.A18 U-A WC 20-XX cWW cW-W 3 Y.C4 Y.G17 C-G WC 19-XIX cWW cW-W 4 Y.C5 Y.G16 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#3[#3] bps=3 strand-1 5'-AUC-3' bp-type ||| strand-2 3'-UAG-5' helix-form .A 1 Z.A2 Z.U19 A-U WC 20-XX cWW cW-W 2 Z.U3 Z.A18 U-A WC 20-XX cWW cW-W 3 Z.C4 Z.G17 C-G WC 19-XIX cWW cW-W **************************************************************************** List of 15 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 YC A.TYR13,X.C10 2 nts=2 YC B.TYR13,Y.C10 3 nts=2 YC C.TYR13,Z.C10 4 nts=2 AA X.A1,X.A2 5 nts=2 AA Y.A1,Y.A2 6 nts=2 AA Z.A1,Z.A2 7 nts=3 QGU A.GLN54,X.G9,X.U8 8 nts=3 QGU B.GLN54,Y.G9,Y.U8 9 nts=3 QGU C.GLN54,Z.G9,Z.U8 10 nts=3 CAU X.C5,X.A6,X.U7 11 nts=3 CAU Y.C5,Y.A6,Y.U7 12 nts=4 WACD A.TRP56,X.A11,X.C12,A.ASP92 13 nts=4 WACD B.TRP56,Y.A11,Y.C12,B.ASP92 14 nts=4 WACD C.TRP56,Z.A11,Z.C12,C.ASP92 15 nts=4 UACG Z.U7,Z.A6,Z.C5,Z.G17 **************************************************************************** List of 3 atom-base capping interactions dv: vertical distance of the atom above the nucleotide base ----------------------------------------------------------- type atom nt dv 1 sugar O4'@X.U8 X.G9 2.82 2 sugar O4'@Y.U8 Y.G9 2.80 3 sugar O4'@Z.U8 Z.G9 2.88 **************************************************************************** List of 6 non-loop single-stranded segments 1 nts=1 A X.A1 2 nts=7 AUUGCAC X.A6,X.U7,X.U8,X.G9,X.C10,X.A11,X.C12 3 nts=1 A Y.A1 4 nts=8 AUUGCACU Y.A6,Y.U7,Y.U8,Y.G9,Y.C10,Y.A11,Y.C12,Y.U13 5 nts=1 A Z.A1 6 nts=9 CAUUGCACU Z.C5,Z.A6,Z.U7,Z.U8,Z.G9,Z.C10,Z.A11,Z.C12,Z.U13 **************************************************************************** List of 3 splayed-apart dinucleotides 1 X.G9 X.C10 angle=96 distance=14.9 ratio=0.74 2 Y.G9 Y.C10 angle=98 distance=15.0 ratio=0.75 3 Z.G9 Z.C10 angle=98 distance=14.9 ratio=0.75 ---------------------------------------------------------------- Summary of 3 splayed-apart units 1 nts=2 GC X.G9,X.C10 2 nts=2 GC Y.G9,Y.C10 3 nts=2 GC Z.G9,Z.C10 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >6sqn nts=49 [whole] AAUCCAUUGCAC&GGAU&AAUCCAUUGCACU&GGAU&AAUCCAUUGCACU&GAU .((((.......&))))&.((((........&))))&.(((.........&))) >6sqn-X #1 nts=16 0.44(2.34) [chain] RNA* AAUCCAUUGCAC&GGAU .((((.......&)))) >6sqn-Y #2 nts=17 0.19(2.17) [chain] RNA[16]/1* AAUCCAUUGCACU&GGAU .((((........&)))) >6sqn-Z #3 nts=16 0.01(2.39) [chain] RNA[15]/1* AAUCCAUUGCACU&GAU .(((.........&))) **************************************************************************** Summary of structural features of 49 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 . X.A1 0.014 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 2 A ( X.A2 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,phosphate 3 U ( X.U3 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 4 C ( X.C4 0.013 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 5 C ( X.C5 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 6 A . X.A6 0.018 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 7 U . X.U7 0.015 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 8 U . X.U8 0.008 turn,anti,~C2'-endo,non-pair-contact,ss-non-loop,cap-donor 9 G . X.G9 0.012 ~C3'-endo,BI,non-pair-contact,ss-non-loop,cap-acceptor,splayed-apart 10 C . X.C10 0.005 anti,~C2'-endo,ss-non-loop,splayed-apart 11 A . X.A11 0.010 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 12 C . X.C12 0.004 break,anti,~C3'-endo,non-pair-contact,ss-non-loop 13 G ) X.G16 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 14 G ) X.G17 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 15 A ) X.A18 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 16 U ) X.U19 0.008 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end 17 A . Y.A1 0.013 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 18 A ( Y.A2 0.018 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,phosphate 19 U ( Y.U3 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 20 C ( Y.C4 0.010 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 21 C ( Y.C5 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 22 A . Y.A6 0.015 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 23 U . Y.U7 0.012 anti,~C3'-endo,BI,non-canonical,non-pair-contact,ss-non-loop 24 U . Y.U8 0.009 turn,anti,~C2'-endo,non-pair-contact,ss-non-loop,cap-donor 25 G . Y.G9 0.008 anti,~C3'-endo,BI,non-canonical,non-pair-contact,ss-non-loop,cap-acceptor,splayed-apart 26 C . Y.C10 0.010 anti,~C2'-endo,ss-non-loop,splayed-apart 27 A . Y.A11 0.015 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 28 C . Y.C12 0.004 anti,~C3'-endo,non-pair-contact,ss-non-loop 29 U . Y.U13 --- break,non-stack,ss-non-loop 30 G ) Y.G16 0.008 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,phosphate 31 G ) Y.G17 0.020 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 32 A ) Y.A18 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 33 U ) Y.U19 0.008 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end 34 A . Z.A1 0.004 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 35 A ( Z.A2 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,phosphate 36 U ( Z.U3 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 37 C ( Z.C4 0.009 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 38 C . Z.C5 0.004 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 39 A . Z.A6 0.015 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 40 U . Z.U7 0.005 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 41 U . Z.U8 0.007 turn,anti,~C2'-endo,non-pair-contact,ss-non-loop,cap-donor 42 G . Z.G9 0.013 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,cap-acceptor,splayed-apart 43 C . Z.C10 0.006 anti,~C2'-endo,ss-non-loop,splayed-apart 44 A . Z.A11 0.014 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 45 C . Z.C12 0.011 anti,~C3'-endo,BII,non-pair-contact,ss-non-loop 46 U . Z.U13 --- break,non-stack,ss-non-loop 47 G ) Z.G17 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end 48 A ) Z.A18 0.011 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem 49 U ) Z.U19 0.004 anti,~C3'-endo,canonical,non-pair-contact,helix-end,stem-end **************************************************************************** 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-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-atom2bases.pdb -- an ensemble of atom-base stacking interactions 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