ID code: '2HW8' 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' --------------------------------------------------------------------------------- 13 C1' G B 2 beta 8 14 11 36 C1' G B 3 beta 31 37 34 59 C1' G B 4 beta 54 60 57 82 C1' G B 5 beta 77 83 80 105 C1' U B 6 beta 100 106 103 125 C1' G B 7 beta 120 126 123 148 C1' A B 8 beta 143 149 146 170 C1' A B 9 beta 165 171 168 192 C1' G B 10 beta 187 193 190 215 C1' G B 11 beta 210 216 213 238 C1' A B 12 beta 233 239 236 260 C1' G B 13 beta 255 261 258 283 C1' G B 14 beta 278 284 281 306 C1' C B 15 beta 301 307 304 326 C1' U B 16 beta 321 327 324 346 C1' U B 17 beta 341 347 344 366 C1' C B 18 beta 361 367 364 386 C1' G B 19 beta 381 387 384 409 C1' G B 20 beta 404 410 407 432 C1' C B 21 beta 427 433 430 452 C1' C B 22 beta 447 453 450 472 C1' G B 23 beta 467 473 470 495 C1' C B 24 beta 490 496 493 515 C1' G B 25 beta 510 516 513 538 C1' A B 26 beta 533 539 536 560 C1' A B 27 beta 555 561 558 582 C1' A B 28 beta 577 583 580 604 C1' C B 29 beta 599 605 602 624 C1' U B 30 beta 619 625 622 644 C1' U B 31 beta 639 645 642 664 C1' C B 32 beta 659 665 662 684 C1' A B 33 beta 679 685 682 706 C1' C B 34 beta 701 707 704 726 C1' C B 35 beta 721 727 724 746 C1' C B 36 beta 741 747 744 766 C1' C B 37 beta 761 767 764 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 11 C2' G B 2 OK 13 9 12 34 C2' G B 3 OK 36 32 35 57 C2' G B 4 OK 59 55 58 80 C2' G B 5 OK 82 78 81 103 C2' U B 6 OK 105 101 104 123 C2' G B 7 OK 125 121 124 146 C2' A B 8 OK 148 144 147 168 C2' A B 9 OK 170 166 169 190 C2' G B 10 OK 192 188 191 213 C2' G B 11 OK 215 211 214 236 C2' A B 12 OK 238 234 237 258 C2' G B 13 OK 260 256 259 281 C2' G B 14 OK 283 279 282 304 C2' C B 15 OK 306 302 305 324 C2' U B 16 OK 326 322 325 344 C2' U B 17 OK 346 342 345 364 C2' C B 18 OK 366 362 365 384 C2' G B 19 OK 386 382 385 407 C2' G B 20 OK 409 405 408 430 C2' C B 21 OK 432 428 431 450 C2' C B 22 OK 452 448 451 470 C2' G B 23 OK 472 468 471 493 C2' C B 24 OK 495 491 494 513 C2' G B 25 OK 515 511 514 536 C2' A B 26 OK 538 534 537 558 C2' A B 27 OK 560 556 559 580 C2' A B 28 OK 582 578 581 602 C2' C B 29 OK 604 600 603 622 C2' U B 30 OK 624 620 623 642 C2' U B 31 OK 644 640 643 662 C2' C B 32 OK 664 660 663 682 C2' A B 33 OK 684 680 683 704 C2' C B 34 OK 706 702 705 724 C2' C B 35 OK 726 722 725 744 C2' C B 36 OK 746 742 745 764 C2' C B 37 OK 766 762 765 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 9 C3' G B 2 OK 7 10 11 32 C3' G B 3 OK 30 33 34 55 C3' G B 4 OK 53 56 57 78 C3' G B 5 OK 76 79 80 101 C3' U B 6 OK 99 102 103 121 C3' G B 7 OK 119 122 123 144 C3' A B 8 OK 142 145 146 166 C3' A B 9 OK 164 167 168 188 C3' G B 10 OK 186 189 190 211 C3' G B 11 OK 209 212 213 234 C3' A B 12 OK 232 235 236 256 C3' G B 13 OK 254 257 258 279 C3' G B 14 OK 277 280 281 302 C3' C B 15 OK 300 303 304 322 C3' U B 16 OK 320 323 324 342 C3' U B 17 OK 340 343 344 362 C3' C B 18 OK 360 363 364 382 C3' G B 19 OK 380 383 384 405 C3' G B 20 OK 403 406 407 428 C3' C B 21 OK 426 429 430 448 C3' C B 22 OK 446 449 450 468 C3' G B 23 OK 466 469 470 491 C3' C B 24 OK 489 492 493 511 C3' G B 25 OK 509 512 513 534 C3' A B 26 OK 532 535 536 556 C3' A B 27 OK 554 557 558 578 C3' A B 28 OK 576 579 580 600 C3' C B 29 OK 598 601 602 620 C3' U B 30 OK 618 621 622 640 C3' U B 31 OK 638 641 642 660 C3' C B 32 OK 658 661 662 680 C3' A B 33 OK 678 681 682 702 C3' C B 34 OK 700 703 704 722 C3' C B 35 OK 720 723 724 742 C3' C B 36 OK 740 743 744 762 C3' C B 37 OK 760 763 764 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 7 C4' G B 2 OK 9 6 8 30 C4' G B 3 OK 32 29 31 53 C4' G B 4 OK 55 52 54 76 C4' G B 5 OK 78 75 77 99 C4' U B 6 OK 101 98 100 119 C4' G B 7 OK 121 118 120 142 C4' A B 8 OK 144 141 143 164 C4' A B 9 OK 166 163 165 186 C4' G B 10 OK 188 185 187 209 C4' G B 11 OK 211 208 210 232 C4' A B 12 OK 234 231 233 254 C4' G B 13 OK 256 253 255 277 C4' G B 14 OK 279 276 278 300 C4' C B 15 OK 302 299 301 320 C4' U B 16 OK 322 319 321 340 C4' U B 17 OK 342 339 341 360 C4' C B 18 OK 362 359 361 380 C4' G B 19 OK 382 379 381 403 C4' G B 20 OK 405 402 404 426 C4' C B 21 OK 428 425 427 446 C4' C B 22 OK 448 445 447 466 C4' G B 23 OK 468 465 467 489 C4' C B 24 OK 491 488 490 509 C4' G B 25 OK 511 508 510 532 C4' A B 26 OK 534 531 533 554 C4' A B 27 OK 556 553 555 576 C4' A B 28 OK 578 575 577 598 C4' C B 29 OK 600 597 599 618 C4' U B 30 OK 620 617 619 638 C4' U B 31 OK 640 637 639 658 C4' C B 32 OK 660 657 659 678 C4' A B 33 OK 680 677 679 700 C4' C B 34 OK 702 699 701 720 C4' C B 35 OK 722 719 721 740 C4' C B 36 OK 742 739 741 760 C4' C B 37 OK 762 759 761 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 6 C5' G B 2 5 7 29 C5' G B 3 28 30 52 C5' G B 4 51 53 75 C5' G B 5 74 76 98 C5' U B 6 97 99 118 C5' G B 7 117 119 141 C5' A B 8 140 142 163 C5' A B 9 162 164 185 C5' G B 10 184 186 208 C5' G B 11 207 209 231 C5' A B 12 230 232 253 C5' G B 13 252 254 276 C5' G B 14 275 277 299 C5' C B 15 298 300 319 C5' U B 16 318 320 339 C5' U B 17 338 340 359 C5' C B 18 358 360 379 C5' G B 19 378 380 402 C5' G B 20 401 403 425 C5' C B 21 424 426 445 C5' C B 22 444 446 465 C5' G B 23 464 466 488 C5' C B 24 487 489 508 C5' G B 25 507 509 531 C5' A B 26 530 532 553 C5' A B 27 552 554 575 C5' A B 28 574 576 597 C5' C B 29 596 598 617 C5' U B 30 616 618 637 C5' U B 31 636 638 657 C5' C B 32 656 658 677 C5' A B 33 676 678 699 C5' C B 34 698 700 719 C5' C B 35 718 720 739 C5' C B 36 738 740 759 C5' C B 37 758 760 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2 P G B 2 distorted distorted 3 4 5 25 P G B 3 distorted distorted 10 26 27 28 48 P G B 4 distorted distorted 33 49 50 51 71 P G B 5 distorted distorted 56 72 73 74 94 P U B 6 distorted distorted 79 95 96 97 114 P G B 7 distorted distorted 102 115 116 117 137 P A B 8 distorted distorted 122 138 139 140 159 P A B 9 distorted distorted 145 160 161 162 181 P G B 10 distorted distorted 167 182 183 184 204 P G B 11 distorted distorted 189 205 206 207 227 P A B 12 distorted distorted 212 228 229 230 249 P G B 13 distorted distorted 235 250 251 252 272 P G B 14 distorted distorted 257 273 274 275 295 P C B 15 distorted distorted 280 296 297 298 315 P U B 16 distorted distorted 303 316 317 318 335 P U B 17 distorted distorted 323 336 337 338 355 P C B 18 distorted distorted 343 356 357 358 375 P G B 19 distorted distorted 363 376 377 378 398 P G B 20 distorted distorted 383 399 400 401 421 P C B 21 distorted distorted 406 422 423 424 441 P C B 22 distorted distorted 429 442 443 444 461 P G B 23 distorted distorted 449 462 463 464 484 P C B 24 distorted distorted 469 485 486 487 504 P G B 25 distorted distorted 492 505 506 507 527 P A B 26 distorted distorted 512 528 529 530 549 P A B 27 distorted distorted 535 550 551 552 571 P A B 28 distorted distorted 557 572 573 574 593 P C B 29 distorted distorted 579 594 595 596 613 P U B 30 distorted distorted 601 614 615 616 633 P U B 31 distorted distorted 621 634 635 636 653 P C B 32 distorted distorted 641 654 655 656 673 P A B 33 distorted distorted 661 674 675 676 695 P C B 34 distorted distorted 681 696 697 698 715 P C B 35 distorted distorted 703 716 717 718 735 P C B 36 distorted distorted 723 736 737 738 755 P C B 37 distorted distorted 743 756 757 758 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