ID code: '2H49' 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' C A 3 alpha beta 73 93 79 76 109 C1' U A 4 alpha beta 104 124 110 107 139 C1' A A 5 alpha beta 134 156 140 137 172 C1' A A 6 alpha beta 167 189 173 170 205 C1' G A 7 alpha beta 200 223 206 203 239 C1' A A 8 alpha beta 234 256 240 237 272 C1' C A 9 alpha beta 267 288 273 270 302 C1' G B 10 alpha beta 297 320 303 300 337 C1' U B 11 alpha beta 332 352 338 335 367 C1' C B 12 alpha beta 362 382 368 365 398 C1' G B 13 alpha beta 393 416 399 396 432 C1' A B 14 alpha beta 427 449 433 430 465 C1' A B 15 alpha beta 460 482 466 463 498 C1' G B 16 alpha beta 493 516 499 496 532 C1' C B 17 alpha beta 527 547 533 530 563 C1' C B 18 alpha beta 558 579 564 561 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' C A 3 OK OK 78 74 91 77 107 C2' U A 4 OK OK 109 105 122 108 137 C2' A A 5 OK OK 139 135 154 138 170 C2' A A 6 OK OK 172 168 187 171 203 C2' G A 7 OK OK 205 201 221 204 237 C2' A A 8 OK OK 239 235 254 238 270 C2' C A 9 OK OK 272 268 286 271 300 C2' G B 10 OK OK 302 298 318 301 335 C2' U B 11 OK OK 337 333 350 336 365 C2' C B 12 OK OK 367 363 380 366 396 C2' G B 13 OK OK 398 394 414 397 430 C2' A B 14 OK OK 432 428 447 431 463 C2' A B 15 OK OK 465 461 480 464 496 C2' G B 16 OK OK 498 494 514 497 530 C2' C B 17 OK OK 532 528 545 531 561 C2' C B 18 OK OK 563 559 577 562 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' C A 3 OK OK 72 90 75 76 105 C3' U A 4 OK OK 103 121 106 107 135 C3' A A 5 OK OK 133 153 136 137 168 C3' A A 6 OK OK 166 186 169 170 201 C3' G A 7 OK OK 199 220 202 203 235 C3' A A 8 OK OK 233 253 236 237 268 C3' C A 9 OK OK 266 284 269 270 298 C3' G B 10 OK OK 296 317 299 300 333 C3' U B 11 OK OK 331 349 334 335 363 C3' C B 12 OK OK 361 379 364 365 394 C3' G B 13 OK OK 392 413 395 396 428 C3' A B 14 OK OK 426 446 429 430 461 C3' A B 15 OK OK 459 479 462 463 494 C3' G B 16 OK OK 492 513 495 496 528 C3' C B 17 OK OK 526 544 529 530 559 C3' C B 18 OK OK 557 575 560 561 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' C A 3 OK OK 74 89 71 73 103 C4' U A 4 OK OK 105 120 102 104 133 C4' A A 5 OK OK 135 152 132 134 166 C4' A A 6 OK OK 168 185 165 167 199 C4' G A 7 OK OK 201 219 198 200 233 C4' A A 8 OK OK 235 252 232 234 266 C4' C A 9 OK OK 268 283 265 267 296 C4' G B 10 OK OK 298 316 295 297 331 C4' U B 11 OK OK 333 348 330 332 361 C4' C B 12 OK OK 363 378 360 362 392 C4' G B 13 OK OK 394 412 391 393 426 C4' A B 14 OK OK 428 445 425 427 459 C4' A B 15 OK OK 461 478 458 460 492 C4' G B 16 OK OK 494 512 491 493 526 C4' C B 17 OK OK 528 543 525 527 557 C4' C B 18 OK OK 559 574 556 558 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' C A 3 OK OK 70 87 88 72 102 C5' U A 4 OK OK 101 118 119 103 132 C5' A A 5 OK OK 131 150 151 133 165 C5' A A 6 OK OK 164 183 184 166 198 C5' G A 7 OK OK 197 217 218 199 232 C5' A A 8 OK OK 231 250 251 233 265 C5' C A 9 OK OK 264 281 282 266 295 C5' G B 10 OK OK 294 314 315 296 330 C5' U B 11 OK OK 329 346 347 331 360 C5' C B 12 OK OK 359 376 377 361 391 C5' G B 13 OK OK 390 410 411 392 425 C5' A B 14 OK OK 424 443 444 426 458 C5' A B 15 OK OK 457 476 477 459 491 C5' G B 16 OK OK 490 510 511 492 525 C5' C B 17 OK OK 524 541 542 526 556 C5' C B 18 OK OK 555 572 573 557 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 2 distorted distorted 6 34 35 36 67 P C A 3 distorted distorted 41 68 69 70 98 P U A 4 distorted distorted 75 99 100 101 128 P A A 5 distorted distorted 106 129 130 131 161 P A A 6 distorted distorted 136 162 163 164 194 P G A 7 distorted distorted 169 195 196 197 228 P A A 8 distorted distorted 202 229 230 231 261 P C A 9 distorted distorted 236 262 263 264 326 P U B 11 distorted distorted 299 327 328 329 356 P C B 12 distorted distorted 334 357 358 359 387 P G B 13 distorted distorted 364 388 389 390 421 P A B 14 distorted distorted 395 422 423 424 454 P A B 15 distorted distorted 429 455 456 457 487 P G B 16 distorted distorted 462 488 489 490 521 P C B 17 distorted distorted 495 522 523 524 552 P C B 18 distorted distorted 529 553 554 555 ---------------------------------------------------------------------------------