ID code: '1EKA' 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' A A 2 alpha beta 39 61 45 42 77 C1' G A 3 alpha beta 72 95 78 75 111 C1' U A 4 alpha beta 106 126 112 109 141 C1' G A 5 alpha beta 136 159 142 139 175 C1' C A 6 alpha beta 170 190 176 173 206 C1' U A 7 alpha beta 201 221 207 204 236 C1' C A 8 alpha beta 231 252 237 234 266 C1' G B 1 alpha beta 261 284 267 264 301 C1' A B 2 alpha beta 296 318 302 299 334 C1' G B 3 alpha beta 329 352 335 332 368 C1' U B 4 alpha beta 363 383 369 366 398 C1' G B 5 alpha beta 393 416 399 396 432 C1' C B 6 alpha beta 427 447 433 430 463 C1' U B 7 alpha beta 458 478 464 461 493 C1' C B 8 alpha beta 488 509 494 491 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' A A 2 OK OK 44 40 59 43 75 C2' G A 3 OK OK 77 73 93 76 109 C2' U A 4 OK OK 111 107 124 110 139 C2' G A 5 OK OK 141 137 157 140 173 C2' C A 6 OK OK 175 171 188 174 204 C2' U A 7 OK OK 206 202 219 205 234 C2' C A 8 OK OK 236 232 250 235 264 C2' G B 1 OK OK 266 262 282 265 299 C2' A B 2 OK OK 301 297 316 300 332 C2' G B 3 OK OK 334 330 350 333 366 C2' U B 4 OK OK 368 364 381 367 396 C2' G B 5 OK OK 398 394 414 397 430 C2' C B 6 OK OK 432 428 445 431 461 C2' U B 7 OK OK 463 459 476 462 491 C2' C B 8 OK OK 493 489 507 492 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK OK 3 24 6 7 40 C3' A A 2 OK OK 38 58 41 42 73 C3' G A 3 OK OK 71 92 74 75 107 C3' U A 4 OK OK 105 123 108 109 137 C3' G A 5 OK OK 135 156 138 139 171 C3' C A 6 OK OK 169 187 172 173 202 C3' U A 7 OK OK 200 218 203 204 232 C3' C A 8 OK OK 230 248 233 234 262 C3' G B 1 OK OK 260 281 263 264 297 C3' A B 2 OK OK 295 315 298 299 330 C3' G B 3 OK OK 328 349 331 332 364 C3' U B 4 OK OK 362 380 365 366 394 C3' G B 5 OK OK 392 413 395 396 428 C3' C B 6 OK OK 426 444 429 430 459 C3' U B 7 OK OK 457 475 460 461 489 C3' C B 8 OK OK 487 505 490 491 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK OK 5 23 2 4 38 C4' A A 2 OK OK 40 57 37 39 71 C4' G A 3 OK OK 73 91 70 72 105 C4' U A 4 OK OK 107 122 104 106 135 C4' G A 5 OK OK 137 155 134 136 169 C4' C A 6 OK OK 171 186 168 170 200 C4' U A 7 OK OK 202 217 199 201 230 C4' C A 8 OK OK 232 247 229 231 260 C4' G B 1 OK OK 262 280 259 261 295 C4' A B 2 OK OK 297 314 294 296 328 C4' G B 3 OK OK 330 348 327 329 362 C4' U B 4 OK OK 364 379 361 363 392 C4' G B 5 OK OK 394 412 391 393 426 C4' C B 6 OK OK 428 443 425 427 457 C4' U B 7 OK OK 459 474 456 458 487 C4' C B 8 OK OK 489 504 486 488 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' A A 2 OK OK 36 55 56 38 70 C5' G A 3 OK OK 69 89 90 71 104 C5' U A 4 OK OK 103 120 121 105 134 C5' G A 5 OK OK 133 153 154 135 168 C5' C A 6 OK OK 167 184 185 169 199 C5' U A 7 OK OK 198 215 216 200 229 C5' C A 8 OK OK 228 245 246 230 259 C5' G B 1 OK OK 258 278 279 260 294 C5' A B 2 OK OK 293 312 313 295 327 C5' G B 3 OK OK 326 346 347 328 361 C5' U B 4 OK OK 360 377 378 362 391 C5' G B 5 OK OK 390 410 411 392 425 C5' C B 6 OK OK 424 441 442 426 456 C5' U B 7 OK OK 455 472 473 457 486 C5' C B 8 OK OK 485 502 503 487 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P A A 2 distorted distorted 6 34 35 36 66 P G A 3 distorted distorted 41 67 68 69 100 P U A 4 distorted distorted 74 101 102 103 130 P G A 5 distorted distorted 108 131 132 133 164 P C A 6 distorted distorted 138 165 166 167 195 P U A 7 distorted distorted 172 196 197 198 225 P C A 8 distorted distorted 203 226 227 228 290 P A B 2 distorted distorted 263 291 292 293 323 P G B 3 distorted distorted 298 324 325 326 357 P U B 4 distorted distorted 331 358 359 360 387 P G B 5 distorted distorted 365 388 389 390 421 P C B 6 distorted distorted 395 422 423 424 452 P U B 7 distorted distorted 429 453 454 455 482 P C B 8 distorted distorted 460 483 484 485 ---------------------------------------------------------------------------------