ID code: '2G8W' CHIRALITY (03 Nov 1998) Checks the chirality and the naming of substituents of chiral and prochiral centers in nucleic acid structures. The molecular structure is read from a PDB file. Only the first model is evaluated. ---------------------------------------------------------- Center Reference for correct naming ---------------------------------------------------------- C1' alpha/beta nomenclature of anomeric sugars, base in beta position in natural nucleosids. C2' IUPAC. 1983. Eur J Biochem, 131: 9-15. C3' IUPAC. 1983. Eur J Biochem, 131: 9-15. C4' IUPAC. 1983. Eur J Biochem, 131: 9-15. C5' IUPAC. 1983. Eur J Biochem, 131: 9-15. P Brookhaven PDB entry '1BNA', O1P -> major groove, O2P -> minor groove. ---------------------------------------------------------- Author: Peter Slickers (slickers@imb-jena.de) Biocomputing, IMB Jena, Germany --------------------------------------------------------------------------------- Seq No Atom Residue H1' base O4' H1' base C2' --------------------------------------------------------------------------------- 13 C1' U B 1 beta 8 14 11 33 C1' C B 2 beta 28 34 31 53 C1' G B 3 beta 48 54 51 76 C1' A B 4 beta 71 77 74 98 C1' C B 5 beta 93 99 96 118 C1' A B 6 beta 113 119 116 137 C1' DA C 1 beta 133 138 136 158 C1' DT C 2 beta 154 159 157 178 C1' DG C 3 beta 174 179 177 200 C1' DT C 4 beta 196 201 199 220 C1' DC C 5 beta 216 221 219 239 C1' DG C 6 beta 235 240 238 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 11 C2' U B 1 OK 13 9 12 31 C2' C B 2 OK 33 29 32 51 C2' G B 3 OK 53 49 52 74 C2' A B 4 OK 76 72 75 96 C2' C B 5 OK 98 94 97 116 C2' A B 6 OK 118 114 117 136 C2' DA C 1 137 134 157 C2' DT C 2 158 155 177 C2' DG C 3 178 175 199 C2' DT C 4 200 197 219 C2' DC C 5 220 217 238 C2' DG C 6 239 236 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 9 C3' U B 1 OK 7 10 11 29 C3' C B 2 OK 27 30 31 49 C3' G B 3 OK 47 50 51 72 C3' A B 4 OK 70 73 74 94 C3' C B 5 OK 92 95 96 114 C3' A B 6 OK 112 115 116 134 C3' DA C 1 OK 132 135 136 155 C3' DT C 2 OK 153 156 157 175 C3' DG C 3 OK 173 176 177 197 C3' DT C 4 OK 195 198 199 217 C3' DC C 5 OK 215 218 219 236 C3' DG C 6 OK 234 237 238 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 7 C4' U B 1 OK 9 6 8 27 C4' C B 2 OK 29 26 28 47 C4' G B 3 OK 49 46 48 70 C4' A B 4 OK 72 69 71 92 C4' C B 5 OK 94 91 93 112 C4' A B 6 OK 114 111 113 132 C4' DA C 1 OK 134 131 133 153 C4' DT C 2 OK 155 152 154 173 C4' DG C 3 OK 175 172 174 195 C4' DT C 4 OK 197 194 196 215 C4' DC C 5 OK 217 214 216 234 C4' DG C 6 OK 236 233 235 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 6 C5' U B 1 5 7 26 C5' C B 2 25 27 46 C5' G B 3 45 47 69 C5' A B 4 68 70 91 C5' C B 5 90 92 111 C5' A B 6 110 112 131 C5' DA C 1 130 132 152 C5' DT C 2 151 153 172 C5' DG C 3 171 173 194 C5' DT C 4 193 195 214 C5' DC C 5 213 215 233 C5' DG C 6 232 234 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2 P U B 1 distorted distorted 3 4 5 22 P C B 2 distorted distorted 10 23 24 25 42 P G B 3 distorted distorted 30 43 44 45 65 P A B 4 distorted distorted 50 66 67 68 87 P C B 5 distorted distorted 73 88 89 90 107 P A B 6 distorted distorted 95 108 109 110 148 P DT C 2 distorted distorted 135 149 150 151 168 P DG C 3 distorted distorted 156 169 170 171 190 P DT C 4 distorted distorted 176 191 192 193 210 P DC C 5 distorted distorted 198 211 212 213 229 P DG C 6 distorted distorted 218 230 231 232 ---------------------------------------------------------------------------------