ID code: '8DRH' 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' --------------------------------------------------------------------------------- 8 C1' DG A 1 beta 4 9 7 30 C1' DC A 2 beta 26 31 29 49 C1' DG A 3 beta 45 50 48 71 C1' DT A 4 beta 67 72 70 91 C1' DC A 5 beta 87 92 90 110 C1' DA A 6 beta 106 111 109 131 C1' DG A 7 beta 127 132 130 153 C1' DG A 8 beta 149 154 152 174 C1' C B 9 beta 169 175 172 194 C1' C B 10 beta 189 195 192 214 C1' U B 11 beta 209 215 212 234 C1' G B 12 beta 229 235 232 257 C1' A B 13 beta 252 258 255 279 C1' C B 14 beta 274 280 277 299 C1' G B 15 beta 294 300 297 322 C1' C B 16 beta 317 323 320 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' DG A 1 8 5 29 C2' DC A 2 30 27 48 C2' DG A 3 49 46 70 C2' DT A 4 71 68 90 C2' DC A 5 91 88 109 C2' DA A 6 110 107 130 C2' DG A 7 131 128 152 C2' DG A 8 153 150 172 C2' C B 9 OK 174 170 173 192 C2' C B 10 OK 194 190 193 212 C2' U B 11 OK 214 210 213 232 C2' G B 12 OK 234 230 233 255 C2' A B 13 OK 257 253 256 277 C2' C B 14 OK 279 275 278 297 C2' G B 15 OK 299 295 298 320 C2' C B 16 OK 322 318 321 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' DG A 1 OK 3 6 7 27 C3' DC A 2 OK 25 28 29 46 C3' DG A 3 OK 44 47 48 68 C3' DT A 4 OK 66 69 70 88 C3' DC A 5 OK 86 89 90 107 C3' DA A 6 OK 105 108 109 128 C3' DG A 7 OK 126 129 130 150 C3' DG A 8 OK 148 151 152 170 C3' C B 9 OK 168 171 172 190 C3' C B 10 OK 188 191 192 210 C3' U B 11 OK 208 211 212 230 C3' G B 12 OK 228 231 232 253 C3' A B 13 OK 251 254 255 275 C3' C B 14 OK 273 276 277 295 C3' G B 15 OK 293 296 297 318 C3' C B 16 OK 316 319 320 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' DG A 1 OK 5 2 4 25 C4' DC A 2 OK 27 24 26 44 C4' DG A 3 OK 46 43 45 66 C4' DT A 4 OK 68 65 67 86 C4' DC A 5 OK 88 85 87 105 C4' DA A 6 OK 107 104 106 126 C4' DG A 7 OK 128 125 127 148 C4' DG A 8 OK 150 147 149 168 C4' C B 9 OK 170 167 169 188 C4' C B 10 OK 190 187 189 208 C4' U B 11 OK 210 207 209 228 C4' G B 12 OK 230 227 229 251 C4' A B 13 OK 253 250 252 273 C4' C B 14 OK 275 272 274 293 C4' G B 15 OK 295 292 294 316 C4' C B 16 OK 318 315 317 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' DG A 1 1 3 24 C5' DC A 2 23 25 43 C5' DG A 3 42 44 65 C5' DT A 4 64 66 85 C5' DC A 5 84 86 104 C5' DA A 6 103 105 125 C5' DG A 7 124 126 147 C5' DG A 8 146 148 167 C5' C B 9 166 168 187 C5' C B 10 186 188 207 C5' U B 11 206 208 227 C5' G B 12 226 228 250 C5' A B 13 249 251 272 C5' C B 14 271 273 292 C5' G B 15 291 293 315 C5' C B 16 314 316 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 20 P DC A 2 distorted distorted 6 21 22 23 39 P DG A 3 distorted distorted 28 40 41 42 61 P DT A 4 distorted distorted 47 62 63 64 81 P DC A 5 distorted distorted 69 82 83 84 100 P DA A 6 distorted distorted 89 101 102 103 121 P DG A 7 distorted distorted 108 122 123 124 143 P DG A 8 distorted distorted 129 144 145 146 183 P C B 10 distorted distorted 171 184 185 186 203 P U B 11 distorted distorted 191 204 205 206 223 P G B 12 distorted distorted 211 224 225 226 246 P A B 13 distorted distorted 231 247 248 249 268 P C B 14 distorted distorted 254 269 270 271 288 P G B 15 distorted distorted 276 289 290 291 311 P C B 16 distorted distorted 296 312 313 314 ---------------------------------------------------------------------------------