**************************************************************************** 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=4xjn.pdb -o=4xjn.out File name: 4xjn.pdb no. of DNA/RNA chains: 1 [N=78] no. of nucleotides: 78 no. of atoms: 42329 no. of waters: 0 no. of metals: 14 [Pb=14] **************************************************************************** List of 26 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 UU N.U29,N.U30 2 nts=2 UU N.U41,N.U42 3 nts=2 UU N.U71,N.U72 4 nts=3 UUU N.U4,N.U5,N.U6 5 nts=3 UUU N.U7,N.U8,N.U9 6 nts=3 UUU N.U10,N.U11,N.U12 7 nts=3 UUU N.U13,N.U14,N.U15 8 nts=3 UUU N.U16,N.U17,N.U18 9 nts=3 UUU N.U19,N.U20,N.U21 10 nts=3 UUU N.U22,N.U23,N.U24 11 nts=3 UUU N.U25,N.U26,N.U27 12 nts=3 UUU N.U34,N.U35,N.U36 13 nts=3 UUU N.U37,N.U38,N.U39 14 nts=3 UUU N.U46,N.U47,N.U48 15 nts=3 UUU N.U52,N.U53,N.U54 16 nts=3 UUU N.U58,N.U59,N.U60 17 nts=3 UUU N.U64,N.U65,N.U66 18 nts=3 UUU N.U76,N.U77,N.U78 19 nts=4 YUUU C.TYR350,N.U31,N.U32,N.U33 20 nts=4 YUUU D.TYR350,N.U73,N.U74,N.U75 21 nts=4 YUUU G.TYR350,N.U55,N.U56,N.U57 22 nts=4 YUUU H.TYR350,N.U49,N.U50,N.U51 23 nts=4 YUUU I.TYR350,N.U1,N.U2,N.U3 24 nts=4 YUUU J.TYR260,N.U69,N.U68,N.U67 25 nts=4 YUUU K.TYR260,N.U63,N.U62,N.U61 26 nts=5 YUUUY B.TYR260,N.U45,N.U44,N.U43,B.TYR350 **************************************************************************** Nucleotides not involved in stacking interactions nts=3 UUU N.U28,N.U40,N.U70 **************************************************************************** List of 1 non-loop single-stranded segment 1 nts=78 UUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUU N.U1,N.U2,N.U3,N.U4,N.U5,N.U6,N.U7,N.U8,N.U9,N.U10,N.U11,N.U12,N.U13,N.U14,N.U15,N.U16,N.U17,N.U18,N.U19,N.U20,N.U21,N.U22,N.U23,N.U24,N.U25,N.U26,N.U27,N.U28,N.U29,N.U30,N.U31,N.U32,N.U33,N.U34,N.U35,N.U36,N.U37,N.U38,N.U39,N.U40,N.U41,N.U42,N.U43,N.U44,N.U45,N.U46,N.U47,N.U48,N.U49,N.U50,N.U51,N.U52,N.U53,N.U54,N.U55,N.U56,N.U57,N.U58,N.U59,N.U60,N.U61,N.U62,N.U63,N.U64,N.U65,N.U66,N.U67,N.U68,N.U69,N.U70,N.U71,N.U72,N.U73,N.U74,N.U75,N.U76,N.U77,N.U78 **************************************************************************** List of 25 splayed-apart dinucleotides 1 N.U3 N.U4 angle=148 distance=18.4 ratio=0.96 2 N.U6 N.U7 angle=116 distance=17.0 ratio=0.85 3 N.U9 N.U10 angle=146 distance=18.2 ratio=0.96 4 N.U12 N.U13 angle=121 distance=17.5 ratio=0.87 5 N.U15 N.U16 angle=147 distance=18.1 ratio=0.96 6 N.U18 N.U19 angle=121 distance=16.8 ratio=0.87 7 N.U21 N.U22 angle=149 distance=18.2 ratio=0.96 8 N.U24 N.U25 angle=122 distance=17.4 ratio=0.88 9 N.U27 N.U28 angle=142 distance=18.0 ratio=0.95 10 N.U30 N.U31 angle=120 distance=16.8 ratio=0.87 11 N.U33 N.U34 angle=147 distance=18.3 ratio=0.96 12 N.U36 N.U37 angle=115 distance=17.0 ratio=0.84 13 N.U39 N.U40 angle=146 distance=17.6 ratio=0.96 14 N.U42 N.U43 angle=119 distance=17.4 ratio=0.86 15 N.U45 N.U46 angle=144 distance=18.2 ratio=0.95 16 N.U48 N.U49 angle=118 distance=16.9 ratio=0.86 17 N.U51 N.U52 angle=144 distance=18.4 ratio=0.95 18 N.U54 N.U55 angle=124 distance=17.7 ratio=0.88 19 N.U57 N.U58 angle=147 distance=18.7 ratio=0.96 20 N.U60 N.U61 angle=121 distance=17.9 ratio=0.87 21 N.U63 N.U64 angle=144 distance=18.5 ratio=0.95 22 N.U66 N.U67 angle=122 distance=16.9 ratio=0.87 23 N.U69 N.U70 angle=143 distance=18.3 ratio=0.95 24 N.U72 N.U73 angle=119 distance=17.3 ratio=0.86 25 N.U75 N.U76 angle=142 distance=18.0 ratio=0.95 ---------------------------------------------------------------- Summary of 25 splayed-apart units 1 nts=2 UU N.U3,N.U4 2 nts=2 UU N.U6,N.U7 3 nts=2 UU N.U9,N.U10 4 nts=2 UU N.U12,N.U13 5 nts=2 UU N.U15,N.U16 6 nts=2 UU N.U18,N.U19 7 nts=2 UU N.U21,N.U22 8 nts=2 UU N.U24,N.U25 9 nts=2 UU N.U27,N.U28 10 nts=2 UU N.U30,N.U31 11 nts=2 UU N.U33,N.U34 12 nts=2 UU N.U36,N.U37 13 nts=2 UU N.U39,N.U40 14 nts=2 UU N.U42,N.U43 15 nts=2 UU N.U45,N.U46 16 nts=2 UU N.U48,N.U49 17 nts=2 UU N.U51,N.U52 18 nts=2 UU N.U54,N.U55 19 nts=2 UU N.U57,N.U58 20 nts=2 UU N.U60,N.U61 21 nts=2 UU N.U63,N.U64 22 nts=2 UU N.U66,N.U67 23 nts=2 UU N.U69,N.U70 24 nts=2 UU N.U72,N.U73 25 nts=2 UU N.U75,N.U76 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >4xjn nts=78 [whole] UUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUU .............................................................................. >4xjn-N #1 nts=78 0.04(3.00) [chain] RNA UUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUU .............................................................................. **************************************************************************** Summary of structural features of 78 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 . N.U1 0.007 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 2 U . N.U2 0.012 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,phosphate 3 U . N.U3 0.014 anti,~C3'-endo,BII,non-pair-contact,ss-non-loop,phosphate,splayed-apart 4 U . N.U4 0.005 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,phosphate,splayed-apart 5 U . N.U5 0.007 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 6 U . N.U6 0.006 anti,~C2'-endo,non-pair-contact,ss-non-loop,phosphate,splayed-apart 7 U . N.U7 0.006 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,splayed-apart 8 U . N.U8 0.006 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 9 U . N.U9 0.010 anti,~C3'-endo,BII,non-pair-contact,ss-non-loop,phosphate,splayed-apart 10 U . N.U10 0.007 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,phosphate,splayed-apart 11 U . N.U11 0.010 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 12 U . N.U12 0.006 anti,~C2'-endo,non-pair-contact,ss-non-loop,phosphate,splayed-apart 13 U . N.U13 0.007 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,splayed-apart 14 U . N.U14 0.008 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 15 U . N.U15 0.007 anti,~C3'-endo,non-pair-contact,ss-non-loop,phosphate,splayed-apart 16 U . N.U16 0.006 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,phosphate,splayed-apart 17 U . N.U17 0.010 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 18 U . N.U18 0.007 anti,~C2'-endo,non-pair-contact,ss-non-loop,phosphate,splayed-apart 19 U . N.U19 0.005 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,splayed-apart 20 U . N.U20 0.003 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 21 U . N.U21 0.007 anti,~C3'-endo,non-pair-contact,ss-non-loop,phosphate,splayed-apart 22 U . N.U22 0.002 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,phosphate,splayed-apart 23 U . N.U23 0.005 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 24 U . N.U24 0.003 anti,~C2'-endo,non-pair-contact,ss-non-loop,phosphate,splayed-apart 25 U . N.U25 0.009 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,splayed-apart 26 U . N.U26 0.004 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 27 U . N.U27 0.005 anti,~C3'-endo,non-pair-contact,ss-non-loop,phosphate,splayed-apart 28 U . N.U28 0.010 anti,~C3'-endo,BI,non-stack,ss-non-loop,phosphate,splayed-apart 29 U . N.U29 0.013 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 30 U . N.U30 0.007 anti,~C2'-endo,non-pair-contact,ss-non-loop,phosphate,splayed-apart 31 U . N.U31 0.008 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,splayed-apart 32 U . N.U32 0.010 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,phosphate 33 U . N.U33 0.010 anti,~C3'-endo,BII,non-pair-contact,ss-non-loop,phosphate,splayed-apart 34 U . N.U34 0.005 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,phosphate,splayed-apart 35 U . N.U35 0.006 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 36 U . N.U36 0.006 anti,~C2'-endo,non-pair-contact,ss-non-loop,phosphate,splayed-apart 37 U . N.U37 0.007 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,splayed-apart 38 U . N.U38 0.007 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 39 U . N.U39 0.005 anti,~C3'-endo,BII,non-pair-contact,ss-non-loop,phosphate,splayed-apart 40 U . N.U40 0.006 anti,~C3'-endo,BI,non-stack,ss-non-loop,phosphate,splayed-apart 41 U . N.U41 0.006 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 42 U . N.U42 0.005 anti,~C2'-endo,non-pair-contact,ss-non-loop,phosphate,splayed-apart 43 U . N.U43 0.008 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,splayed-apart 44 U . N.U44 0.004 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,phosphate 45 U . N.U45 0.014 anti,~C3'-endo,non-pair-contact,ss-non-loop,phosphate,splayed-apart 46 U . N.U46 0.008 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,phosphate,splayed-apart 47 U . N.U47 0.010 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 48 U . N.U48 0.012 anti,~C3'-endo,non-pair-contact,ss-non-loop,phosphate,splayed-apart 49 U . N.U49 0.006 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,splayed-apart 50 U . N.U50 0.007 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 51 U . N.U51 0.012 anti,~C3'-endo,BII,non-pair-contact,ss-non-loop,phosphate,splayed-apart 52 U . N.U52 0.008 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,phosphate,splayed-apart 53 U . N.U53 0.007 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 54 U . N.U54 0.004 anti,~C2'-endo,non-pair-contact,ss-non-loop,phosphate,splayed-apart 55 U . N.U55 0.007 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,splayed-apart 56 U . N.U56 0.005 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 57 U . N.U57 0.009 anti,~C3'-endo,non-pair-contact,ss-non-loop,phosphate,splayed-apart 58 U . N.U58 0.006 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,phosphate,splayed-apart 59 U . N.U59 0.005 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 60 U . N.U60 0.005 anti,~C2'-endo,non-pair-contact,ss-non-loop,phosphate,splayed-apart 61 U . N.U61 0.006 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,splayed-apart 62 U . N.U62 0.010 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,phosphate 63 U . N.U63 0.006 anti,~C3'-endo,BII,non-pair-contact,ss-non-loop,phosphate,splayed-apart 64 U . N.U64 0.008 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,phosphate,splayed-apart 65 U . N.U65 0.010 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 66 U . N.U66 0.011 anti,~C2'-endo,non-pair-contact,ss-non-loop,phosphate,splayed-apart 67 U . N.U67 0.010 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,phosphate,splayed-apart 68 U . N.U68 0.011 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 69 U . N.U69 0.009 anti,~C3'-endo,BII,non-pair-contact,ss-non-loop,phosphate,splayed-apart 70 U . N.U70 0.009 anti,~C3'-endo,BI,non-stack,ss-non-loop,phosphate,splayed-apart 71 U . N.U71 0.009 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 72 U . N.U72 0.005 anti,~C2'-endo,non-pair-contact,ss-non-loop,phosphate,splayed-apart 73 U . N.U73 0.006 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,splayed-apart 74 U . N.U74 0.005 anti,~C3'-endo,non-pair-contact,ss-non-loop,phosphate 75 U . N.U75 0.013 anti,~C3'-endo,BII,non-pair-contact,ss-non-loop,phosphate,splayed-apart 76 U . N.U76 0.006 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,phosphate,splayed-apart 77 U . N.U77 0.005 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 78 U . N.U78 0.004 anti,~C2'-endo,non-pair-contact,ss-non-loop,phosphate **************************************************************************** List of 6 additional files 1 dssr-2ndstrs.bpseq -- secondary structure in bpseq format 2 dssr-2ndstrs.ct -- secondary structure in connectivity table format 3 dssr-2ndstrs.dbn -- secondary structure in dot-bracket notation 4 dssr-torsions.txt -- backbone torsion angles and suite names 5 dssr-splays.pdb -- an ensemble of splayed-apart units 6 dssr-stacks.pdb -- an ensemble of base stacks