**************************************************************************** File name: 1po6.pdb no. of DNA/RNA chains: 1 [B=11] no. of nucleotides: 11 no. of atoms: 1855 no. of waters: 155 no. of metals: 0 **************************************************************************** List of 1 type of 1 modified nucleotide nt count list 1 6MI-? 1 B.6MI206 **************************************************************************** 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=3 GGG B.DG210,B.DG211,B.DG212 2 nts=3 FAH A.PHE17,B.DA203,A.HIS101 3 nts=4 TRGF B.DT207,A.ARG92,B.DG204,A.PHE59 **************************************************************************** Nucleotides not involved in stacking interactions nts=3 GTA B.DG205,B.DT208,B.DA209 **************************************************************************** List of 1 non-loop single-stranded segment 1 nts=11 TAGG?TTAGGG B.DT202,B.DA203,B.DG204,B.DG205,B.6MI206,B.DT207,B.DT208,B.DA209,B.DG210,B.DG211,B.DG212 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >1po6 nts=11 [whole] TAGG?TTAGGG ........... >1po6-B #1 nts=11 3.05(1.71) [chain] DNA TAGG?TTAGGG ........... **************************************************************************** Summary of structural features of 11 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 . B.DT202 0.011 anti,~C2'-endo,ss-non-loop 2 A . B.DA203 0.009 anti,~C2'-endo,ss-non-loop 3 G . B.DG204 0.011 syn,~C2'-endo,ss-non-loop,phosphate 4 G . B.DG205 0.009 anti,~C2'-endo,non-stack,ss-non-loop 5 ? . B.6MI206 --- modified,turn,~C2'-endo,BII,non-stack,ss-non-loop 6 T . B.DT207 0.013 anti,~C2'-endo,BII,ss-non-loop 7 T . B.DT208 0.013 anti,~C2'-endo,non-stack,ss-non-loop 8 A . B.DA209 0.011 anti,~C2'-endo,non-stack,ss-non-loop 9 G . B.DG210 0.018 syn,~C2'-endo,BI,non-pair-contact,ss-non-loop 10 G . B.DG211 0.007 anti,~C2'-endo,non-pair-contact,ss-non-loop 11 G . B.DG212 0.007 anti,~C2'-endo,non-pair-contact,ss-non-loop **************************************************************************** List of 9 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-stacks.pdb -- an ensemble of base stacks 6 dssr-rotmat.txt -- position vector and rotation matrix 7 dssr-viewV.pdb -- vertical view of the principal moment of inertia 8 dssr-viewH.pdb -- horizontal view of the principal moment of inertia 9 dssr-viewT.pdb -- top view of the principal moment of inertia