ID code: '1JP0' 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' G A 4 alpha beta 104 127 110 107 143 C1' G A 5 alpha beta 138 161 144 141 177 C1' U A 6 alpha beta 172 192 178 175 207 C1' G A 7 alpha beta 202 225 208 205 241 C1' C A 8 alpha beta 236 256 242 239 272 C1' U A 9 alpha beta 267 287 273 270 302 C1' G A 10 alpha beta 297 320 303 300 336 C1' A A 11 alpha beta 331 353 337 334 369 C1' G A 12 alpha beta 364 387 370 367 403 C1' A A 13 alpha beta 398 420 404 401 436 C1' U A 14 alpha beta 431 451 437 434 466 C1' G A 15 alpha beta 461 484 467 464 500 C1' C A 16 alpha beta 495 515 501 498 531 C1' C A 17 alpha beta 526 546 532 529 562 C1' C A 18 alpha beta 557 577 563 560 593 C1' G A 19 alpha beta 588 611 594 591 627 C1' U A 20 alpha beta 622 642 628 625 657 C1' C A 21 alpha beta 652 672 658 655 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' G A 4 OK OK 109 105 125 108 141 C2' G A 5 OK OK 143 139 159 142 175 C2' U A 6 OK OK 177 173 190 176 205 C2' G A 7 OK OK 207 203 223 206 239 C2' C A 8 OK OK 241 237 254 240 270 C2' U A 9 OK OK 272 268 285 271 300 C2' G A 10 OK OK 302 298 318 301 334 C2' A A 11 OK OK 336 332 351 335 367 C2' G A 12 OK OK 369 365 385 368 401 C2' A A 13 OK OK 403 399 418 402 434 C2' U A 14 OK OK 436 432 449 435 464 C2' G A 15 OK OK 466 462 482 465 498 C2' C A 16 OK OK 500 496 513 499 529 C2' C A 17 OK OK 531 527 544 530 560 C2' C A 18 OK OK 562 558 575 561 591 C2' G A 19 OK OK 593 589 609 592 625 C2' U A 20 OK OK 627 623 640 626 655 C2' C A 21 OK OK 657 653 670 656 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' G A 4 OK OK 103 124 106 107 139 C3' G A 5 OK OK 137 158 140 141 173 C3' U A 6 OK OK 171 189 174 175 203 C3' G A 7 OK OK 201 222 204 205 237 C3' C A 8 OK OK 235 253 238 239 268 C3' U A 9 OK OK 266 284 269 270 298 C3' G A 10 OK OK 296 317 299 300 332 C3' A A 11 OK OK 330 350 333 334 365 C3' G A 12 OK OK 363 384 366 367 399 C3' A A 13 OK OK 397 417 400 401 432 C3' U A 14 OK OK 430 448 433 434 462 C3' G A 15 OK OK 460 481 463 464 496 C3' C A 16 OK OK 494 512 497 498 527 C3' C A 17 OK OK 525 543 528 529 558 C3' C A 18 OK OK 556 574 559 560 589 C3' G A 19 OK OK 587 608 590 591 623 C3' U A 20 OK OK 621 639 624 625 653 C3' C A 21 OK OK 651 669 654 655 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' G A 4 OK OK 105 123 102 104 137 C4' G A 5 OK OK 139 157 136 138 171 C4' U A 6 OK OK 173 188 170 172 201 C4' G A 7 OK OK 203 221 200 202 235 C4' C A 8 OK OK 237 252 234 236 266 C4' U A 9 OK OK 268 283 265 267 296 C4' G A 10 OK OK 298 316 295 297 330 C4' A A 11 OK OK 332 349 329 331 363 C4' G A 12 OK OK 365 383 362 364 397 C4' A A 13 OK OK 399 416 396 398 430 C4' U A 14 OK OK 432 447 429 431 460 C4' G A 15 OK OK 462 480 459 461 494 C4' C A 16 OK OK 496 511 493 495 525 C4' C A 17 OK OK 527 542 524 526 556 C4' C A 18 OK OK 558 573 555 557 587 C4' G A 19 OK OK 589 607 586 588 621 C4' U A 20 OK OK 623 638 620 622 651 C4' C A 21 OK OK 653 668 650 652 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' G A 4 OK OK 101 121 122 103 136 C5' G A 5 OK OK 135 155 156 137 170 C5' U A 6 OK OK 169 186 187 171 200 C5' G A 7 OK OK 199 219 220 201 234 C5' C A 8 OK OK 233 250 251 235 265 C5' U A 9 OK OK 264 281 282 266 295 C5' G A 10 OK OK 294 314 315 296 329 C5' A A 11 OK OK 328 347 348 330 362 C5' G A 12 OK OK 361 381 382 363 396 C5' A A 13 OK OK 395 414 415 397 429 C5' U A 14 OK OK 428 445 446 430 459 C5' G A 15 OK OK 458 478 479 460 493 C5' C A 16 OK OK 492 509 510 494 524 C5' C A 17 OK OK 523 540 541 525 555 C5' C A 18 OK OK 554 571 572 556 586 C5' G A 19 OK OK 585 605 606 587 620 C5' U A 20 OK OK 619 636 637 621 650 C5' C A 21 OK OK 649 666 667 651 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 G A 4 distorted distorted 75 99 100 101 132 P G A 5 distorted distorted 106 133 134 135 166 P U A 6 distorted distorted 140 167 168 169 196 P G A 7 distorted distorted 174 197 198 199 230 P C A 8 distorted distorted 204 231 232 233 261 P U A 9 distorted distorted 238 262 263 264 291 P G A 10 distorted distorted 269 292 293 294 325 P A A 11 distorted distorted 299 326 327 328 358 P G A 12 distorted distorted 333 359 360 361 392 P A A 13 distorted distorted 366 393 394 395 425 P U A 14 distorted distorted 400 426 427 428 455 P G A 15 distorted distorted 433 456 457 458 489 P C A 16 distorted distorted 463 490 491 492 520 P C A 17 distorted distorted 497 521 522 523 551 P C A 18 distorted distorted 528 552 553 554 582 P G A 19 distorted distorted 559 583 584 585 616 P U A 20 distorted distorted 590 617 618 619 646 P C A 21 distorted distorted 624 647 648 649 ---------------------------------------------------------------------------------