ID code: '219D' 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' DT A 3 beta 45 50 48 69 C1' DA A 4 beta 65 70 68 90 C1' DT A 5 beta 86 91 89 110 C1' DA A 6 beta 106 111 109 131 C1' DA A 7 beta 127 132 130 152 C1' PST A 8 beta 148 153 151 172 C1' DG A 9 beta 168 173 171 194 C1' DG A 10 beta 190 195 193 215 C1' C B 11 beta 210 216 213 235 C1' C B 12 beta 230 236 233 255 C1' A B 13 beta 250 256 253 277 C1' U B 14 beta 272 278 275 297 C1' U B 15 beta 292 298 295 317 C1' A B 16 beta 312 318 315 339 C1' U B 17 beta 334 340 337 359 C1' A B 18 beta 354 360 357 381 C1' G B 19 beta 376 382 379 404 C1' C B 20 beta 399 405 402 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' DT A 3 49 46 68 C2' DA A 4 69 66 89 C2' DT A 5 90 87 109 C2' DA A 6 110 107 130 C2' DA A 7 131 128 151 C2' PST A 8 152 149 171 C2' DG A 9 172 169 193 C2' DG A 10 194 191 213 C2' C B 11 OK 215 211 214 233 C2' C B 12 OK 235 231 234 253 C2' A B 13 OK 255 251 254 275 C2' U B 14 OK 277 273 276 295 C2' U B 15 OK 297 293 296 315 C2' A B 16 OK 317 313 316 337 C2' U B 17 OK 339 335 338 357 C2' A B 18 OK 359 355 358 379 C2' G B 19 OK 381 377 380 402 C2' C B 20 OK 404 400 403 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' DT A 3 OK 44 47 48 66 C3' DA A 4 OK 64 67 68 87 C3' DT A 5 OK 85 88 89 107 C3' DA A 6 OK 105 108 109 128 C3' DA A 7 OK 126 129 130 149 C3' PST A 8 OK 147 150 151 169 C3' DG A 9 OK 167 170 171 191 C3' DG A 10 OK 189 192 193 211 C3' C B 11 OK 209 212 213 231 C3' C B 12 OK 229 232 233 251 C3' A B 13 OK 249 252 253 273 C3' U B 14 OK 271 274 275 293 C3' U B 15 OK 291 294 295 313 C3' A B 16 OK 311 314 315 335 C3' U B 17 OK 333 336 337 355 C3' A B 18 OK 353 356 357 377 C3' G B 19 OK 375 378 379 400 C3' C B 20 OK 398 401 402 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' DT A 3 OK 46 43 45 64 C4' DA A 4 OK 66 63 65 85 C4' DT A 5 OK 87 84 86 105 C4' DA A 6 OK 107 104 106 126 C4' DA A 7 OK 128 125 127 147 C4' PST A 8 OK 149 146 148 167 C4' DG A 9 OK 169 166 168 189 C4' DG A 10 OK 191 188 190 209 C4' C B 11 OK 211 208 210 229 C4' C B 12 OK 231 228 230 249 C4' A B 13 OK 251 248 250 271 C4' U B 14 OK 273 270 272 291 C4' U B 15 OK 293 290 292 311 C4' A B 16 OK 313 310 312 333 C4' U B 17 OK 335 332 334 353 C4' A B 18 OK 355 352 354 375 C4' G B 19 OK 377 374 376 398 C4' C B 20 OK 400 397 399 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' DT A 3 42 44 63 C5' DA A 4 62 64 84 C5' DT A 5 83 85 104 C5' DA A 6 103 105 125 C5' DA A 7 124 126 146 C5' PST A 8 145 147 166 C5' DG A 9 165 167 188 C5' DG A 10 187 189 208 C5' C B 11 207 209 228 C5' C B 12 227 229 248 C5' A B 13 247 249 270 C5' U B 14 269 271 290 C5' U B 15 289 291 310 C5' A B 16 309 311 332 C5' U B 17 331 333 352 C5' A B 18 351 353 374 C5' G B 19 373 375 397 C5' C B 20 396 398 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 20 P DC A 2 distorted distorted 6 21 22 23 39 P DT A 3 distorted distorted 28 40 41 42 59 P DA A 4 distorted distorted 47 60 61 62 80 P DT A 5 distorted distorted 67 81 82 83 100 P DA A 6 distorted distorted 88 101 102 103 121 P DA A 7 distorted distorted 108 122 123 124 142 P PST A 8 129 143 145 162 P DG A 9 distorted distorted 150 163 164 165 184 P DG A 10 distorted distorted 170 185 186 187 224 P C B 12 distorted distorted 212 225 226 227 244 P A B 13 distorted distorted 232 245 246 247 266 P U B 14 distorted distorted 252 267 268 269 286 P U B 15 distorted distorted 274 287 288 289 306 P A B 16 distorted distorted 294 307 308 309 328 P U B 17 distorted distorted 314 329 330 331 348 P A B 18 distorted distorted 336 349 350 351 370 P G B 19 distorted distorted 356 371 372 373 393 P C B 20 distorted distorted 378 394 395 396 ---------------------------------------------------------------------------------