**************************************************************************** Note: By default, each nucleotide is identified by chainId.name#. So a common case would be B.A1689, meaning adenosine #1689 on chain B. One-letter base names for modified nucleotides are put in lower case (e.g., 'c' for 5MC). For further information about the output notation, please refer to the DSSR User Manual. Questions and suggestions are *always* welcome on the 3DNA Forum. Command: x3dna-dssr -i=4x4q.pdb -o=4x4q.out File name: 4x4q.pdb no. of DNA/RNA chains: 2 [B=36,D=30] no. of nucleotides: 68 no. of atoms: 16912 no. of waters: 12 no. of metals: 3 [Mg=3] **************************************************************************** List of 1 type of 2 modified nucleotides nt count list 1 CTP-c 2 A.CTP503,C.CTP501 **************************************************************************** List of 23 base pairs nt1 nt2 bp name Saenger LW DSSR 1 B.G1 B.C34 G-C WC 19-XIX cWW cW-W 2 B.G2 B.C33 G-C WC 19-XIX cWW cW-W 3 B.C3 B.G32 C-G WC 19-XIX cWW cW-W 4 B.C4 B.G28 C-G WC 19-XIX cWW cW-W 5 B.G5 B.C27 G-C WC 19-XIX cWW cW-W 6 B.C6 B.G26 C-G WC 19-XIX cWW cW-W 7 B.G7 B.C25 G-C WC 19-XIX cWW cW-W 8 B.G8 B.C24 G-C WC 19-XIX cWW cW-W 9 B.C9 B.G23 C-G WC 19-XIX cWW cW-W 10 B.A10 B.U22 A-U WC 20-XX cWW cW-W 11 B.G11 B.C21 G-C WC 19-XIX cWW cW-W 12 B.G12 B.C20 G-C WC 19-XIX cWW cW-W 13 B.U13 B.A17 U-A rHoogsteen 24-XXIV tWH tW-M 14 D.G1 D.C34 G-C WC 19-XIX cWW cW-W 15 D.G2 D.C33 G-C WC 19-XIX cWW cW-W 16 D.C3 D.G32 C-G WC 19-XIX cWW cW-W 17 D.C6 D.G26 C-G WC 19-XIX cWW cW-W 18 D.G7 D.C25 G-C WC 19-XIX cWW cW-W 19 D.G8 D.C24 G-C WC 19-XIX cWW cW-W 20 D.C9 D.G23 C-G WC 19-XIX cWW cW-W 21 D.A10 D.U22 A-U WC 20-XX cWW cW-W 22 D.G11 D.C21 G-C WC 19-XIX cWW cW-W 23 D.G12 D.C20 G-C WC 19-XIX cWW cW-W **************************************************************************** List of 2 helices Note: a helix is defined by base-stacking interactions, regardless of bp 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[2] bps=13 strand-1 5'-GGCCGCGGCAGGU-3' bp-type ||||||||||||. strand-2 3'-CCGGCGCCGUCCA-5' helix-form AAx...AAAAAx 1 B.G1 B.C34 G-C WC 19-XIX cWW cW-W 2 B.G2 B.C33 G-C WC 19-XIX cWW cW-W 3 B.C3 B.G32 C-G WC 19-XIX cWW cW-W 4 B.C4 B.G28 C-G WC 19-XIX cWW cW-W 5 B.G5 B.C27 G-C WC 19-XIX cWW cW-W 6 B.C6 B.G26 C-G WC 19-XIX cWW cW-W 7 B.G7 B.C25 G-C WC 19-XIX cWW cW-W 8 B.G8 B.C24 G-C WC 19-XIX cWW cW-W 9 B.C9 B.G23 C-G WC 19-XIX cWW cW-W 10 B.A10 B.U22 A-U WC 20-XX cWW cW-W 11 B.G11 B.C21 G-C WC 19-XIX cWW cW-W 12 B.G12 B.C20 G-C WC 19-XIX cWW cW-W 13 B.U13 B.A17 U-A rHoogsteen 24-XXIV tWH tW-M -------------------------------------------------------------------------- helix#2[2] bps=10 strand-1 5'-GGCCGGCAGG-3' bp-type |||||||||| strand-2 3'-CCGGCCGUCC-5' helix-form AAx.AAA.. 1 D.G1 D.C34 G-C WC 19-XIX cWW cW-W 2 D.G2 D.C33 G-C WC 19-XIX cWW cW-W 3 D.C3 D.G32 C-G WC 19-XIX cWW cW-W 4 D.C6 D.G26 C-G WC 19-XIX cWW cW-W 5 D.G7 D.C25 G-C WC 19-XIX cWW cW-W 6 D.G8 D.C24 G-C WC 19-XIX cWW cW-W 7 D.C9 D.G23 C-G WC 19-XIX cWW cW-W 8 D.A10 D.U22 A-U WC 20-XX cWW cW-W 9 D.G11 D.C21 G-C WC 19-XIX cWW cW-W 10 D.G12 D.C20 G-C WC 19-XIX cWW cW-W **************************************************************************** List of 4 stems Note: a stem is defined as a helix consisting of only 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=3 strand-1 5'-GGC-3' bp-type ||| strand-2 3'-CCG-5' helix-form AA 1 B.G1 B.C34 G-C WC 19-XIX cWW cW-W 2 B.G2 B.C33 G-C WC 19-XIX cWW cW-W 3 B.C3 B.G32 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#2[#1] bps=9 strand-1 5'-CGCGGCAGG-3' bp-type ||||||||| strand-2 3'-GCGCCGUCC-5' helix-form ...AAAAA 1 B.C4 B.G28 C-G WC 19-XIX cWW cW-W 2 B.G5 B.C27 G-C WC 19-XIX cWW cW-W 3 B.C6 B.G26 C-G WC 19-XIX cWW cW-W 4 B.G7 B.C25 G-C WC 19-XIX cWW cW-W 5 B.G8 B.C24 G-C WC 19-XIX cWW cW-W 6 B.C9 B.G23 C-G WC 19-XIX cWW cW-W 7 B.A10 B.U22 A-U WC 20-XX cWW cW-W 8 B.G11 B.C21 G-C WC 19-XIX cWW cW-W 9 B.G12 B.C20 G-C WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#3[#2] bps=3 strand-1 5'-GGC-3' bp-type ||| strand-2 3'-CCG-5' helix-form AA 1 D.G1 D.C34 G-C WC 19-XIX cWW cW-W 2 D.G2 D.C33 G-C WC 19-XIX cWW cW-W 3 D.C3 D.G32 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- stem#4[#2] bps=7 strand-1 5'-CGGCAGG-3' bp-type ||||||| strand-2 3'-GCCGUCC-5' helix-form .AAA.. 1 D.C6 D.G26 C-G WC 19-XIX cWW cW-W 2 D.G7 D.C25 G-C WC 19-XIX cWW cW-W 3 D.G8 D.C24 G-C WC 19-XIX cWW cW-W 4 D.C9 D.G23 C-G WC 19-XIX cWW cW-W 5 D.A10 D.U22 A-U WC 20-XX cWW cW-W 6 D.G11 D.C21 G-C WC 19-XIX cWW cW-W 7 D.G12 D.C20 G-C WC 19-XIX cWW cW-W **************************************************************************** List of 2 coaxial stacks 1 Helix#1 contains 2 stems: [#1,#2] 2 Helix#2 contains 2 stems: [#3,#4] **************************************************************************** List of 13 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 CG B.C15,B.G16 2 nts=2 AC B.A17,B.C20 3 nts=2 GU B.G18,B.U19 4 nts=2 GG B.G28,B.G32 5 nts=2 Cc B.C36,A.CTP503 6 nts=2 GA D.G1,D.A35 7 nts=2 CC D.C3,D.C4 8 nts=2 GC D.G5,D.C6 9 nts=2 Cc D.C36,C.CTP501 10 nts=3 EAG A.GLU96,B.A35,B.G1 11 nts=3 GUU B.G12,B.U13,B.U14 12 nts=3 GUU D.G12,D.U13,D.U14 13 nts=5 CGAUC D.C15,D.G16,D.A17,D.U19,D.C20 **************************************************************************** Nucleotides not involved in stacking interactions nts=4 AUCC B.A29,B.U30,B.C31,D.C25 **************************************************************************** List of 4 atom-base capping interactions dv: vertical distance of the atom above the nucleotide base ----------------------------------------------------------- type atom nt dv 1 sugar O4'@B.G7 B.C6 3.49 2 phosphate OP2@B.G16 B.U14 3.22 3 sugar O2'@B.C31 B.A29 3.41 4 phosphate OP2@D.G16 D.U14 2.95 **************************************************************************** Note: for the various types of loops listed below, numbers within the first set of brackets are the number of loop nts, and numbers in the second set of brackets are the identities of the stems (positive number) or isolated WC/wobble pairs (negative numbers) to which they are linked. **************************************************************************** List of 1 hairpin loop 1 hairpin loop: nts=9; [7]; linked by [#2] summary: [1] 7 [B.12 B.20] 9 nts=9 GUUCGAGUC B.G12,B.U13,B.U14,B.C15,B.G16,B.A17,B.G18,B.U19,B.C20 nts=7 UUCGAGU B.U13,B.U14,B.C15,B.G16,B.A17,B.G18,B.U19 **************************************************************************** List of 1 bulge 1 bulge: nts=7; [0,3]; linked by [#1,#2] summary: [2] 0 3 [B.3 B.32 B.4 B.28] 3 9 nts=7 CCGAUCG B.C3,B.C4,B.G28,B.A29,B.U30,B.C31,B.G32 nts=0 nts=3 AUC B.A29,B.U30,B.C31 **************************************************************************** List of 6 non-loop single-stranded segments 1 nts=2 AC B.A35,B.C36 2 nts=2 CG D.C4,D.G5 3 nts=6* UUCGAU D.U13,D.U14,D.C15,D.G16,D.A17,D.U19 4 nts=2 AC D.A35,D.C36 5 nts=1 c A.CTP503 6 nts=1 c C.CTP501 **************************************************************************** List of 6 splayed-apart dinucleotides 1 B.G28 B.A29 angle=94 distance=14.8 ratio=0.73 2 B.A29 B.U30 angle=116 distance=15.6 ratio=0.85 3 B.U30 B.C31 angle=132 distance=17.9 ratio=0.91 4 B.C31 B.G32 angle=121 distance=16.4 ratio=0.87 5 B.A35 B.C36 angle=92 distance=13.9 ratio=0.72 6 D.A35 D.C36 angle=90 distance=13.7 ratio=0.71 ---------------------------------------------------------------- Summary of 3 splayed-apart units 1 nts=5 GAUCG B.G28,B.A29,B.U30,B.C31,B.G32 2 nts=2 AC B.A35,B.C36 3 nts=2 AC D.A35,D.C36 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >4x4q nts=68 [whole] GGCCGCGGCAGGUUCGAGUCCUGCCGCGAUCGCCAC&GGCCGCGGCAGGUUCGA&UCCUGCCG&GCCAC&c&c ((((((((((((.......)))))))))...)))..&(((..(((((((.....&.)))))))&)))..&.&. >4x4q-B #1 nts=36 0.35(3.09) [chain] RNA GGCCGCGGCAGGUUCGAGUCCUGCCGCGAUCGCCAC ((((((((((((.......)))))))))...))).. >4x4q-D #2 nts=30 0.04(3.10) [chain] RNA* GGCCGCGGCAGGUUCGA&UCCUGCCG&GCCAC (((..(((((((.....&.)))))))&))).. **************************************************************************** Summary of structural features of 68 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 ( B.G1 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 2 G ( B.G2 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 3 C ( B.C3 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,phosphate 4 C ( B.C4 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge 5 G ( B.G5 0.009 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 6 C ( B.C6 0.002 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack,cap-acceptor 7 G ( B.G7 0.003 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack,cap-donor 8 G ( B.G8 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 9 C ( B.C9 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 10 A ( B.A10 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 11 G ( B.G11 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 12 G ( B.G12 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop 13 U . B.U13 0.002 anti,~C3'-endo,BI,non-canonical,non-pair-contact,helix-end,hairpin-loop 14 U . B.U14 0.003 u-turn,anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,cap-acceptor,phosphate 15 C . B.C15 0.003 turn,u-turn,anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,phosphate 16 G . B.G16 0.004 u-turn,anti,~C3'-endo,BI,non-pair-contact,hairpin-loop,cap-donor,phosphate 17 A . B.A17 0.005 u-turn,anti,~C2'-endo,BII,non-canonical,non-pair-contact,helix-end,hairpin-loop,phosphate 18 G . B.G18 0.001 turn,anti,~C3'-endo,BI,non-pair-contact,hairpin-loop 19 U . B.U19 0.005 anti,~C2'-endo,non-pair-contact,hairpin-loop,phosphate 20 C ) B.C20 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,hairpin-loop 21 C ) B.C21 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 22 U ) B.U22 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 23 G ) B.G23 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 24 C ) B.C24 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 25 C ) B.C25 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 26 G ) B.G26 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 27 C ) B.C27 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 28 G ) B.G28 0.012 anti,~C2'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,splayed-apart 29 A . B.A29 0.002 anti,~C2'-endo,BII,non-stack,non-pair-contact,bulge,cap-acceptor,phosphate,splayed-apart 30 U . B.U30 0.009 turn,anti,~C3'-endo,non-stack,non-pair-contact,bulge,phosphate,splayed-apart 31 C . B.C31 0.004 turn,anti,~C3'-endo,non-stack,non-pair-contact,bulge,cap-donor,phosphate,splayed-apart 32 G ) B.G32 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,bulge,splayed-apart 33 C ) B.C33 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 34 C ) B.C34 0.007 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 35 A . B.A35 0.004 anti,~C2'-endo,non-pair-contact,ss-non-loop,phosphate,splayed-apart 36 C . B.C36 0.005 anti,~C3'-endo,non-pair-contact,ss-non-loop,phosphate,splayed-apart 37 G ( D.G1 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 38 G ( D.G2 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 39 C ( D.C3 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,phosphate 40 C . D.C4 0.004 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 41 G . D.G5 0.003 anti,~C3'-endo,non-pair-contact,ss-non-loop 42 C ( D.C6 0.005 anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack 43 G ( D.G7 0.002 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 44 G ( D.G8 0.005 anti,~C3'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack 45 C ( D.C9 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 46 A ( D.A10 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 47 G ( D.G11 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 48 G ( D.G12 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 49 U . D.U13 0.005 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 50 U . D.U14 0.005 u-turn,anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,cap-acceptor 51 C . D.C15 0.005 turn,u-turn,anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,phosphate 52 G . D.G16 0.004 u-turn,anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,cap-donor,phosphate 53 A . D.A17 0.004 break,u-turn,anti,~C3'-endo,non-pair-contact,ss-non-loop,phosphate 54 U . D.U19 0.005 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 55 C ) D.C20 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack 56 C ) D.C21 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 57 U ) D.U22 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 58 G ) D.G23 0.003 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack,phosphate 59 C ) D.C24 0.002 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 60 C ) D.C25 0.002 anti,~C3'-endo,BI,non-stack,canonical,non-pair-contact,helix,stem,coaxial-stack 61 G ) D.G26 0.006 break,anti,~C3'-endo,canonical,non-pair-contact,helix,stem-end,coaxial-stack 62 G ) D.G32 0.004 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack 63 C ) D.C33 0.005 anti,~C3'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack 64 C ) D.C34 0.006 anti,~C3'-endo,BI,canonical,non-pair-contact,helix-end,stem-end,coaxial-stack,phosphate 65 A . D.A35 0.003 anti,~C2'-endo,non-pair-contact,ss-non-loop,phosphate,splayed-apart 66 C . D.C36 0.006 anti,~C3'-endo,non-pair-contact,ss-non-loop,phosphate,splayed-apart 67 c . A.CTP503 0.048 modified,anti,~C3'-endo,non-pair-contact,ss-non-loop 68 c . C.CTP501 0.052 modified,anti,non-pair-contact,ss-non-loop **************************************************************************** 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-hairpins.pdb -- an ensemble of hairpin loops 5 dssr-bulges.pdb -- an ensemble of bulges 6 dssr-2ndstrs.bpseq -- secondary structure in bpseq format 7 dssr-2ndstrs.ct -- secondary structure in connectivity table format 8 dssr-2ndstrs.dbn -- secondary structure in dot-bracket notation 9 dssr-torsions.txt -- backbone torsion angles and suite names 10 dssr-splays.pdb -- an ensemble of splayed-apart units 11 dssr-stacks.pdb -- an ensemble of base stacks 12 dssr-atom2bases.pdb -- an ensemble of atom-base stacking interactions