ID code: '2QH2' 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' A A 3 alpha beta 73 95 79 76 111 C1' G A 4 alpha beta 106 129 112 109 145 C1' U A 5 alpha beta 140 160 146 143 175 C1' G A 6 alpha beta 170 193 176 173 209 C1' C A 7 alpha beta 204 224 210 207 240 C1' C A 8 alpha beta 235 255 241 238 271 C1' U A 9 alpha beta 266 286 272 269 301 C1' G A 10 alpha beta 296 319 302 299 335 C1' A A 11 alpha beta 330 352 336 333 368 C1' G A 12 alpha beta 363 386 369 366 402 C1' C A 13 alpha beta 397 417 403 400 433 C1' U A 14 alpha beta 428 448 434 431 463 C1' G A 15 alpha beta 458 481 464 461 497 C1' U A 16 alpha beta 492 512 498 495 527 C1' G A 17 alpha beta 522 545 528 525 561 C1' G A 18 alpha beta 556 579 562 559 595 C1' C A 19 alpha beta 590 610 596 593 626 C1' A A 20 alpha beta 621 643 627 624 659 C1' C A 21 alpha beta 654 674 660 657 690 C1' U A 22 alpha beta 685 705 691 688 720 C1' C A 23 alpha beta 715 735 721 718 751 C1' C A 24 alpha beta 746 767 752 749 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' A A 3 OK OK 78 74 93 77 109 C2' G A 4 OK OK 111 107 127 110 143 C2' U A 5 OK OK 145 141 158 144 173 C2' G A 6 OK OK 175 171 191 174 207 C2' C A 7 OK OK 209 205 222 208 238 C2' C A 8 OK OK 240 236 253 239 269 C2' U A 9 OK OK 271 267 284 270 299 C2' G A 10 OK OK 301 297 317 300 333 C2' A A 11 OK OK 335 331 350 334 366 C2' G A 12 OK OK 368 364 384 367 400 C2' C A 13 OK OK 402 398 415 401 431 C2' U A 14 OK OK 433 429 446 432 461 C2' G A 15 OK OK 463 459 479 462 495 C2' U A 16 OK OK 497 493 510 496 525 C2' G A 17 OK OK 527 523 543 526 559 C2' G A 18 OK OK 561 557 577 560 593 C2' C A 19 OK OK 595 591 608 594 624 C2' A A 20 OK OK 626 622 641 625 657 C2' C A 21 OK OK 659 655 672 658 688 C2' U A 22 OK OK 690 686 703 689 718 C2' C A 23 OK OK 720 716 733 719 749 C2' C A 24 OK OK 751 747 765 750 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' A A 3 OK OK 72 92 75 76 107 C3' G A 4 OK OK 105 126 108 109 141 C3' U A 5 OK OK 139 157 142 143 171 C3' G A 6 OK OK 169 190 172 173 205 C3' C A 7 OK OK 203 221 206 207 236 C3' C A 8 OK OK 234 252 237 238 267 C3' U A 9 OK OK 265 283 268 269 297 C3' G A 10 OK OK 295 316 298 299 331 C3' A A 11 OK OK 329 349 332 333 364 C3' G A 12 OK OK 362 383 365 366 398 C3' C A 13 OK OK 396 414 399 400 429 C3' U A 14 OK OK 427 445 430 431 459 C3' G A 15 OK OK 457 478 460 461 493 C3' U A 16 OK OK 491 509 494 495 523 C3' G A 17 OK OK 521 542 524 525 557 C3' G A 18 OK OK 555 576 558 559 591 C3' C A 19 OK OK 589 607 592 593 622 C3' A A 20 OK OK 620 640 623 624 655 C3' C A 21 OK OK 653 671 656 657 686 C3' U A 22 OK OK 684 702 687 688 716 C3' C A 23 OK OK 714 732 717 718 747 C3' C A 24 OK OK 745 763 748 749 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' A A 3 OK OK 74 91 71 73 105 C4' G A 4 OK OK 107 125 104 106 139 C4' U A 5 OK OK 141 156 138 140 169 C4' G A 6 OK OK 171 189 168 170 203 C4' C A 7 OK OK 205 220 202 204 234 C4' C A 8 OK OK 236 251 233 235 265 C4' U A 9 OK OK 267 282 264 266 295 C4' G A 10 OK OK 297 315 294 296 329 C4' A A 11 OK OK 331 348 328 330 362 C4' G A 12 OK OK 364 382 361 363 396 C4' C A 13 OK OK 398 413 395 397 427 C4' U A 14 OK OK 429 444 426 428 457 C4' G A 15 OK OK 459 477 456 458 491 C4' U A 16 OK OK 493 508 490 492 521 C4' G A 17 OK OK 523 541 520 522 555 C4' G A 18 OK OK 557 575 554 556 589 C4' C A 19 OK OK 591 606 588 590 620 C4' A A 20 OK OK 622 639 619 621 653 C4' C A 21 OK OK 655 670 652 654 684 C4' U A 22 OK OK 686 701 683 685 714 C4' C A 23 OK OK 716 731 713 715 745 C4' C A 24 OK OK 747 762 744 746 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' A A 3 OK OK 70 89 90 72 104 C5' G A 4 OK OK 103 123 124 105 138 C5' U A 5 OK OK 137 154 155 139 168 C5' G A 6 OK OK 167 187 188 169 202 C5' C A 7 OK OK 201 218 219 203 233 C5' C A 8 OK OK 232 249 250 234 264 C5' U A 9 OK OK 263 280 281 265 294 C5' G A 10 OK OK 293 313 314 295 328 C5' A A 11 OK OK 327 346 347 329 361 C5' G A 12 OK OK 360 380 381 362 395 C5' C A 13 OK OK 394 411 412 396 426 C5' U A 14 OK OK 425 442 443 427 456 C5' G A 15 OK OK 455 475 476 457 490 C5' U A 16 OK OK 489 506 507 491 520 C5' G A 17 OK OK 519 539 540 521 554 C5' G A 18 OK OK 553 573 574 555 588 C5' C A 19 OK OK 587 604 605 589 619 C5' A A 20 OK OK 618 637 638 620 652 C5' C A 21 OK OK 651 668 669 653 683 C5' U A 22 OK OK 682 699 700 684 713 C5' C A 23 OK OK 712 729 730 714 744 C5' C A 24 OK OK 743 760 761 745 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 2 distorted distorted 6 34 35 36 67 P A A 3 distorted distorted 41 68 69 70 100 P G A 4 distorted distorted 75 101 102 103 134 P U A 5 distorted distorted 108 135 136 137 164 P G A 6 distorted distorted 142 165 166 167 198 P C A 7 distorted distorted 172 199 200 201 229 P C A 8 distorted distorted 206 230 231 232 260 P U A 9 distorted distorted 237 261 262 263 290 P G A 10 distorted distorted 268 291 292 293 324 P A A 11 distorted distorted 298 325 326 327 357 P G A 12 distorted distorted 332 358 359 360 391 P C A 13 distorted distorted 365 392 393 394 422 P U A 14 distorted distorted 399 423 424 425 452 P G A 15 distorted distorted 430 453 454 455 486 P U A 16 distorted distorted 460 487 488 489 516 P G A 17 distorted distorted 494 517 518 519 550 P G A 18 distorted distorted 524 551 552 553 584 P C A 19 distorted distorted 558 585 586 587 615 P A A 20 distorted distorted 592 616 617 618 648 P C A 21 distorted distorted 623 649 650 651 679 P U A 22 distorted distorted 656 680 681 682 709 P C A 23 distorted distorted 687 710 711 712 740 P C A 24 distorted distorted 717 741 742 743 ---------------------------------------------------------------------------------