ID code: '1T0E' 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 beta 4 10 7 32 C1' G A 2 beta 27 33 30 55 C1' U A 3 beta 50 56 53 75 C1' G A 4 beta 70 76 73 98 C1' G A 5 beta 93 99 96 121 C1' U A 6 beta 116 122 119 141 C1' G A 7 beta 136 142 139 298 C1' U A 11 beta 293 299 296 318 C1' C A 12 beta 313 319 316 338 C1' G A 13 beta 333 339 336 361 C1' C A 14 beta 356 362 359 381 C1' U A 15 beta 376 382 379 401 C1' C A 16 beta 396 402 399 421 C1' G A 17 beta 416 422 419 444 C1' G A 18 beta 439 445 442 465 C1' C C 9 beta 460 466 463 485 C1' G C 10 beta 480 486 483 508 C1' A C 11 beta 503 509 506 530 C1' G C 12 beta 525 531 528 553 C1' C C 13 beta 548 554 551 573 C1' G C 14 beta 568 574 571 596 C1' U C 15 beta 591 597 594 616 C1' C C 16 beta 611 617 614 636 C1' A C 17 beta 631 637 634 658 C1' C C 18 beta 653 659 656 678 C1' A C 19 beta 673 679 676 700 C1' C C 20 beta 695 701 698 720 C1' C C 21 beta 715 721 718 740 C1' A C 22 beta 735 741 738 762 C1' C C 23 beta 757 763 760 782 C1' C C 24 beta 777 783 780 802 C1' C C 25 beta 797 803 800 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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 9 5 8 30 C2' G A 2 OK 32 28 31 53 C2' U A 3 OK 55 51 54 73 C2' G A 4 OK 75 71 74 96 C2' G A 5 OK 98 94 97 119 C2' U A 6 OK 121 117 120 139 C2' G A 7 OK 141 137 140 296 C2' U A 11 OK 298 294 297 316 C2' C A 12 OK 318 314 317 336 C2' G A 13 OK 338 334 337 359 C2' C A 14 OK 361 357 360 379 C2' U A 15 OK 381 377 380 399 C2' C A 16 OK 401 397 400 419 C2' G A 17 OK 421 417 420 442 C2' G A 18 OK 444 440 443 463 C2' C C 9 OK 465 461 464 483 C2' G C 10 OK 485 481 484 506 C2' A C 11 OK 508 504 507 528 C2' G C 12 OK 530 526 529 551 C2' C C 13 OK 553 549 552 571 C2' G C 14 OK 573 569 572 594 C2' U C 15 OK 596 592 595 614 C2' C C 16 OK 616 612 615 634 C2' A C 17 OK 636 632 635 656 C2' C C 18 OK 658 654 657 676 C2' A C 19 OK 678 674 677 698 C2' C C 20 OK 700 696 699 718 C2' C C 21 OK 720 716 719 738 C2' A C 22 OK 740 736 739 760 C2' C C 23 OK 762 758 761 780 C2' C C 24 OK 782 778 781 800 C2' C C 25 OK 802 798 801 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK 3 6 7 28 C3' G A 2 OK 26 29 30 51 C3' U A 3 OK 49 52 53 71 C3' G A 4 OK 69 72 73 94 C3' G A 5 OK 92 95 96 117 C3' U A 6 OK 115 118 119 137 C3' G A 7 OK 135 138 139 294 C3' U A 11 OK 292 295 296 314 C3' C A 12 OK 312 315 316 334 C3' G A 13 OK 332 335 336 357 C3' C A 14 OK 355 358 359 377 C3' U A 15 OK 375 378 379 397 C3' C A 16 OK 395 398 399 417 C3' G A 17 OK 415 418 419 440 C3' G A 18 OK 438 441 442 461 C3' C C 9 OK 459 462 463 481 C3' G C 10 OK 479 482 483 504 C3' A C 11 OK 502 505 506 526 C3' G C 12 OK 524 527 528 549 C3' C C 13 OK 547 550 551 569 C3' G C 14 OK 567 570 571 592 C3' U C 15 OK 590 593 594 612 C3' C C 16 OK 610 613 614 632 C3' A C 17 OK 630 633 634 654 C3' C C 18 OK 652 655 656 674 C3' A C 19 OK 672 675 676 696 C3' C C 20 OK 694 697 698 716 C3' C C 21 OK 714 717 718 736 C3' A C 22 OK 734 737 738 758 C3' C C 23 OK 756 759 760 778 C3' C C 24 OK 776 779 780 798 C3' C C 25 OK 796 799 800 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK 5 2 4 26 C4' G A 2 OK 28 25 27 49 C4' U A 3 OK 51 48 50 69 C4' G A 4 OK 71 68 70 92 C4' G A 5 OK 94 91 93 115 C4' U A 6 OK 117 114 116 135 C4' G A 7 OK 137 134 136 292 C4' U A 11 OK 294 291 293 312 C4' C A 12 OK 314 311 313 332 C4' G A 13 OK 334 331 333 355 C4' C A 14 OK 357 354 356 375 C4' U A 15 OK 377 374 376 395 C4' C A 16 OK 397 394 396 415 C4' G A 17 OK 417 414 416 438 C4' G A 18 OK 440 437 439 459 C4' C C 9 OK 461 458 460 479 C4' G C 10 OK 481 478 480 502 C4' A C 11 OK 504 501 503 524 C4' G C 12 OK 526 523 525 547 C4' C C 13 OK 549 546 548 567 C4' G C 14 OK 569 566 568 590 C4' U C 15 OK 592 589 591 610 C4' C C 16 OK 612 609 611 630 C4' A C 17 OK 632 629 631 652 C4' C C 18 OK 654 651 653 672 C4' A C 19 OK 674 671 673 694 C4' C C 20 OK 696 693 695 714 C4' C C 21 OK 716 713 715 734 C4' A C 22 OK 736 733 735 756 C4' C C 23 OK 758 755 757 776 C4' C C 24 OK 778 775 777 796 C4' C C 25 OK 798 795 797 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 1 1 3 25 C5' G A 2 24 26 48 C5' U A 3 47 49 68 C5' G A 4 67 69 91 C5' G A 5 90 92 114 C5' U A 6 113 115 134 C5' G A 7 133 135 291 C5' U A 11 290 292 311 C5' C A 12 310 312 331 C5' G A 13 330 332 354 C5' C A 14 353 355 374 C5' U A 15 373 375 394 C5' C A 16 393 395 414 C5' G A 17 413 415 437 C5' G A 18 436 438 458 C5' C C 9 457 459 478 C5' G C 10 477 479 501 C5' A C 11 500 502 523 C5' G C 12 522 524 546 C5' C C 13 545 547 566 C5' G C 14 565 567 589 C5' U C 15 588 590 609 C5' C C 16 608 610 629 C5' A C 17 628 630 651 C5' C C 18 650 652 671 C5' A C 19 670 672 693 C5' C C 20 692 694 713 C5' C C 21 712 714 733 C5' A C 22 732 734 755 C5' C C 23 754 756 775 C5' C C 24 774 776 795 C5' C C 25 794 796 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 21 P G A 2 distorted distorted 6 22 23 24 44 P U A 3 distorted distorted 29 45 46 47 64 P G A 4 distorted distorted 52 65 66 67 87 P G A 5 distorted distorted 72 88 89 90 110 P U A 6 distorted distorted 95 111 112 113 130 P G A 7 distorted distorted 118 131 132 133 153 P A A 8 138 154 P A A 8 138 197 P A A 9 198 P A A 9 241 P G A 10 242 P G A 10 287 P U A 11 distorted distorted 288 289 290 307 P C A 12 distorted distorted 295 308 309 310 327 P G A 13 distorted distorted 315 328 329 330 350 P C A 14 distorted distorted 335 351 352 353 370 P U A 15 distorted distorted 358 371 372 373 390 P C A 16 distorted distorted 378 391 392 393 410 P G A 17 distorted distorted 398 411 412 413 433 P G A 18 distorted distorted 418 434 435 436 474 P G C 10 distorted distorted 462 475 476 477 497 P A C 11 distorted distorted 482 498 499 500 519 P G C 12 distorted distorted 505 520 521 522 542 P C C 13 distorted distorted 527 543 544 545 562 P G C 14 distorted distorted 550 563 564 565 585 P U C 15 distorted distorted 570 586 587 588 605 P C C 16 distorted distorted 593 606 607 608 625 P A C 17 distorted distorted 613 626 627 628 647 P C C 18 distorted distorted 633 648 649 650 667 P A C 19 distorted distorted 655 668 669 670 689 P C C 20 distorted distorted 675 690 691 692 709 P C C 21 distorted distorted 697 710 711 712 729 P A C 22 distorted distorted 717 730 731 732 751 P C C 23 distorted distorted 737 752 753 754 771 P C C 24 distorted distorted 759 772 773 774 791 P C C 25 distorted distorted 779 792 793 794 ---------------------------------------------------------------------------------