ID code: '1HOQ' 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' --------------------------------------------------------------------------------- 9 C1' G A 1 alpha beta 4 27 10 7 44 C1' G A 2 alpha beta 39 62 45 42 78 C1' A A 3 alpha beta 73 95 79 76 111 C1' C A 4 alpha beta 106 126 112 109 141 C1' DT A 5 alpha beta 137 157 142 140 173 C1' DT A 6 alpha beta 169 189 174 172 205 C1' DC A 7 alpha beta 201 220 206 204 235 C1' DG A 8 alpha beta 231 253 236 234 268 C1' DG A 9 alpha beta 264 286 269 267 301 C1' DT A 10 alpha beta 297 317 302 300 333 C1' DC A 11 alpha beta 329 348 334 332 363 C1' DC A 12 alpha beta 359 379 364 362 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G A 1 OK OK 9 5 25 8 42 C2' G A 2 OK OK 44 40 60 43 76 C2' A A 3 OK OK 78 74 93 77 109 C2' C A 4 OK OK 111 107 124 110 140 C2' DT A 5 OK OK 141 138 155 156 172 C2' DT A 6 OK OK 173 170 187 188 204 C2' DC A 7 OK OK 205 202 218 219 234 C2' DG A 8 OK OK 235 232 251 252 267 C2' DG A 9 OK OK 268 265 284 285 300 C2' DT A 10 OK OK 301 298 315 316 332 C2' DC A 11 OK OK 333 330 346 347 362 C2' DC A 12 OK OK 363 360 377 378 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK OK 3 24 6 7 40 C3' G A 2 OK OK 38 59 41 42 74 C3' A A 3 OK OK 72 92 75 76 107 C3' C A 4 OK OK 105 123 108 109 138 C3' DT A 5 OK OK 136 154 139 140 170 C3' DT A 6 OK OK 168 186 171 172 202 C3' DC A 7 OK OK 200 217 203 204 232 C3' DG A 8 OK OK 230 250 233 234 265 C3' DG A 9 OK OK 263 283 266 267 298 C3' DT A 10 OK OK 296 314 299 300 330 C3' DC A 11 OK OK 328 345 331 332 360 C3' DC A 12 OK OK 358 375 361 362 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK OK 5 23 2 4 38 C4' G A 2 OK OK 40 58 37 39 72 C4' A A 3 OK OK 74 91 71 73 105 C4' C A 4 OK OK 107 122 104 106 136 C4' DT A 5 OK OK 138 153 135 137 168 C4' DT A 6 OK OK 170 185 167 169 200 C4' DC A 7 OK OK 202 216 199 201 230 C4' DG A 8 OK OK 232 249 229 231 263 C4' DG A 9 OK OK 265 282 262 264 296 C4' DT A 10 OK OK 298 313 295 297 328 C4' DC A 11 OK OK 330 344 327 329 358 C4' DC A 12 OK OK 360 374 357 359 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 1 OK OK 1 21 22 3 37 C5' G A 2 OK OK 36 56 57 38 71 C5' A A 3 OK OK 70 89 90 72 104 C5' C A 4 OK OK 103 120 121 105 135 C5' DT A 5 OK OK 134 151 152 136 167 C5' DT A 6 OK OK 166 183 184 168 199 C5' DC A 7 OK OK 198 214 215 200 229 C5' DG A 8 OK OK 228 247 248 230 262 C5' DG A 9 OK OK 261 280 281 263 295 C5' DT A 10 OK OK 294 311 312 296 327 C5' DC A 11 OK OK 326 342 343 328 357 C5' DC A 12 OK OK 356 372 373 358 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 2 distorted distorted 6 34 35 36 67 P A A 3 distorted distorted 41 68 69 70 100 P C A 4 distorted distorted 75 101 102 103 131 P DT A 5 distorted distorted 108 132 133 134 163 P DT A 6 distorted distorted 139 164 165 166 195 P DC A 7 distorted distorted 171 196 197 198 225 P DG A 8 distorted distorted 203 226 227 228 258 P DG A 9 distorted distorted 233 259 260 261 291 P DT A 10 distorted distorted 266 292 293 294 323 P DC A 11 distorted distorted 299 324 325 326 353 P DC A 12 distorted distorted 331 354 355 356 ---------------------------------------------------------------------------------