ID code: '1HHX' 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' DC A 1 alpha beta 4 23 9 7 36 C1' TLN A 2 alpha beta 35 53 37 47 73 C1' DG A 3 alpha beta 69 91 74 72 106 C1' DA A 4 alpha beta 102 123 107 105 135 C1' TLN A 5 alpha beta 134 152 136 146 172 C1' DA A 6 alpha beta 168 189 173 171 201 C1' TLN A 7 alpha beta 200 218 202 212 238 C1' DG A 8 alpha beta 234 256 239 237 271 C1' DC A 9 alpha beta 267 286 272 270 301 C1' G B 10 alpha beta 296 319 302 299 336 C1' C B 11 alpha beta 331 351 337 334 367 C1' A B 12 alpha beta 362 384 368 365 400 C1' U B 13 alpha beta 395 415 401 398 430 C1' A B 14 alpha beta 425 447 431 428 463 C1' U B 15 alpha beta 458 478 464 461 493 C1' C B 16 alpha beta 488 508 494 491 524 C1' A B 17 alpha beta 519 541 525 522 557 C1' G B 18 alpha beta 552 575 558 555 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' DC A 1 OK OK 8 5 21 22 47 C2' TLN A 2 OK OK 36 46 60 48 72 C2' DG A 3 OK OK 73 70 89 90 105 C2' DA A 4 OK OK 106 103 121 122 146 C2' TLN A 5 OK OK 135 145 159 147 171 C2' DA A 6 OK OK 172 169 187 188 212 C2' TLN A 7 OK OK 201 211 225 213 237 C2' DG A 8 OK OK 238 235 254 255 270 C2' DC A 9 OK OK 271 268 284 285 299 C2' G B 10 OK OK 301 297 317 300 334 C2' C B 11 OK OK 336 332 349 335 365 C2' A B 12 OK OK 367 363 382 366 398 C2' U B 13 OK OK 400 396 413 399 428 C2' A B 14 OK OK 430 426 445 429 461 C2' U B 15 OK OK 463 459 476 462 491 C2' C B 16 OK OK 493 489 506 492 522 C2' A B 17 OK OK 524 520 539 523 555 C2' G B 18 OK OK 557 553 573 556 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' DC A 1 OK OK 3 20 6 7 46 C3' TLN A 2 OK OK 34 59 49 47 70 C3' DG A 3 OK OK 68 88 71 72 103 C3' DA A 4 OK OK 101 120 104 105 145 C3' TLN A 5 OK OK 133 158 148 146 169 C3' DA A 6 OK OK 167 186 170 171 211 C3' TLN A 7 OK OK 199 224 214 212 235 C3' DG A 8 OK OK 233 253 236 237 268 C3' DC A 9 OK OK 266 283 269 270 297 C3' G B 10 OK OK 295 316 298 299 332 C3' C B 11 OK OK 330 348 333 334 363 C3' A B 12 OK OK 361 381 364 365 396 C3' U B 13 OK OK 394 412 397 398 426 C3' A B 14 OK OK 424 444 427 428 459 C3' U B 15 OK OK 457 475 460 461 489 C3' C B 16 OK OK 487 505 490 491 520 C3' A B 17 OK OK 518 538 521 522 553 C3' G B 18 OK OK 551 572 554 555 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' DC A 1 OK OK 5 19 2 4 34 C4' TLN A 2 OK 46 33 35 68 C4' DG A 3 OK OK 70 87 67 69 101 C4' DA A 4 OK OK 103 119 100 102 133 C4' TLN A 5 OK 145 132 134 167 C4' DA A 6 OK OK 169 185 166 168 199 C4' TLN A 7 OK 211 198 200 233 C4' DG A 8 OK OK 235 252 232 234 266 C4' DC A 9 OK OK 268 282 265 267 295 C4' G B 10 OK OK 297 315 294 296 330 C4' C B 11 OK OK 332 347 329 331 361 C4' A B 12 OK OK 363 380 360 362 394 C4' U B 13 OK OK 396 411 393 395 424 C4' A B 14 OK OK 426 443 423 425 457 C4' U B 15 OK OK 459 474 456 458 487 C4' C B 16 OK OK 489 504 486 488 518 C4' A B 17 OK OK 520 537 517 519 551 C4' G B 18 OK OK 553 571 550 552 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' DC A 1 OK OK 1 17 18 3 33 C5' TLN A 2 OK OK 32 51 52 34 67 C5' DG A 3 distorted distorted 66 85 86 68 100 C5' DA A 4 OK OK 99 117 118 101 132 C5' TLN A 5 OK OK 131 150 151 133 166 C5' DA A 6 distorted distorted 165 183 184 167 198 C5' TLN A 7 OK OK 197 216 217 199 232 C5' DG A 8 distorted distorted 231 250 251 233 265 C5' DC A 9 OK OK 264 280 281 266 294 C5' G B 10 distorted distorted 293 313 314 295 329 C5' C B 11 OK OK 328 345 346 330 360 C5' A B 12 OK OK 359 378 379 361 393 C5' U B 13 OK OK 392 409 410 394 423 C5' A B 14 OK OK 422 441 442 424 456 C5' U B 15 OK OK 455 472 473 457 486 C5' C B 16 OK OK 485 502 503 487 517 C5' A B 17 distorted distorted 516 535 536 518 550 C5' G B 18 OK OK 549 569 570 551 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 29 P TLN A 2 distorted distorted 6 30 31 32 63 P DG A 3 distorted distorted 49 64 65 66 96 P DA A 4 distorted distorted 71 97 98 99 128 P TLN A 5 distorted distorted 104 129 130 131 162 P DA A 6 distorted distorted 148 163 164 165 194 P TLN A 7 distorted distorted 170 195 196 197 228 P DG A 8 distorted distorted 214 229 230 231 261 P DC A 9 distorted distorted 236 262 263 264 325 P C B 11 distorted distorted 298 326 327 328 356 P A B 12 distorted distorted 333 357 358 359 389 P U B 13 distorted distorted 364 390 391 392 419 P A B 14 distorted distorted 397 420 421 422 452 P U B 15 distorted distorted 427 453 454 455 482 P C B 16 distorted distorted 460 483 484 485 513 P A B 17 distorted distorted 490 514 515 516 546 P G B 18 distorted distorted 521 547 548 549 ---------------------------------------------------------------------------------