**************************************************************************** File name: 8u0w.pdb no. of DNA/RNA chains: 1 [C=12] no. of nucleotides: 12 no. of atoms: 9086 no. of waters: 0 no. of metals: 0 **************************************************************************** List of 2 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=4 FATT A.PHE639,C.DA12,C.DT11,C.DT10 2 nts=9 YTTTTTTTT A.TYR194,C.DT20,C.DT19,C.DT18,C.DT17,C.DT16,C.DT15,C.DT14,C.DT13 **************************************************************************** Nucleotides not involved in stacking interactions nts=1 T C.DT21 **************************************************************************** List of 1 non-loop single-stranded segment 1 nts=12 TTATTTTTTTTT C.DT10,C.DT11,C.DA12,C.DT13,C.DT14,C.DT15,C.DT16,C.DT17,C.DT18,C.DT19,C.DT20,C.DT21 **************************************************************************** List of 1 splayed-apart dinucleotide 1 C.DA12 C.DT13 angle=126 distance=17.1 ratio=0.89 ---------------------------------------------------------------- Summary of 1 splayed-apart unit 1 nts=2 AT C.DA12,C.DT13 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >8u0w nts=12 [whole] TTATTTTTTTTT ............ >8u0w-C #1 nts=12 2.76(0.87) [chain] DNA TTATTTTTTTTT ............ **************************************************************************** Summary of structural features of 12 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 T . C.DT10 0.003 anti,~C2'-endo,BI,non-pair-contact,ss-non-loop 2 T . C.DT11 0.006 anti,~C2'-endo,BI,non-pair-contact,ss-non-loop 3 A . C.DA12 0.006 syn,~C2'-endo,non-pair-contact,ss-non-loop,splayed-apart 4 T . C.DT13 0.006 ~C2'-endo,non-pair-contact,ss-non-loop,phosphate,splayed-apart 5 T . C.DT14 0.007 anti,~C2'-endo,BI,non-pair-contact,ss-non-loop,phosphate 6 T . C.DT15 0.006 anti,~C3'-endo,non-pair-contact,ss-non-loop,phosphate 7 T . C.DT16 0.006 anti,~C3'-endo,non-pair-contact,ss-non-loop,phosphate 8 T . C.DT17 0.004 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop,phosphate 9 T . C.DT18 0.003 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 10 T . C.DT19 0.005 anti,~C2'-endo,BI,non-pair-contact,ss-non-loop,phosphate 11 T . C.DT20 0.002 anti,~C2'-endo,BI,non-pair-contact,ss-non-loop 12 T . C.DT21 0.002 syn,~C2'-endo,non-stack,ss-non-loop **************************************************************************** List of 10 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 7 dssr-rotmat.txt -- position vector and rotation matrix 8 dssr-viewV.pdb -- vertical view of the principal moment of inertia 9 dssr-viewH.pdb -- horizontal view of the principal moment of inertia 10 dssr-viewT.pdb -- top view of the principal moment of inertia