ID code: '4TV0' 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' --------------------------------------------------------------------------------- 390 C1' G B 1 beta 385 391 388 413 C1' G B 2 beta 408 414 411 436 C1' C B 3 beta 431 437 434 456 C1' C B 4 beta 451 457 454 476 C1' A B 5 beta 471 477 474 498 C1' A B 6 beta 493 499 496 520 C1' A B 7 beta 515 521 518 542 C1' G B 8 beta 537 543 540 565 C1' G B 9 beta 560 566 563 588 C1' C B 10 beta 583 589 586 608 C1' C B 11 beta 603 609 606 628 C1' C B 12 beta 623 629 626 648 C1' U B 13 beta 643 649 646 668 C1' U B 14 beta 663 669 666 688 C1' U B 15 beta 683 689 686 708 C1' U B 16 beta 703 709 706 728 C1' C B 17 beta 723 729 726 748 C1' A B 18 beta 743 749 746 770 C1' G B 19 beta 765 771 768 793 C1' G B 20 beta 788 794 791 816 C1' G B 21 beta 811 817 814 839 C1' C B 22 beta 834 840 837 859 C1' C B 23 beta 854 860 857 879 C1' A B 24 beta 874 880 877 901 C1' C B 25 beta 896 902 899 921 C1' C B 26 916 919 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 388 C2' G B 1 OK 390 386 389 411 C2' G B 2 OK 413 409 412 434 C2' C B 3 OK 436 432 435 454 C2' C B 4 OK 456 452 455 474 C2' A B 5 OK 476 472 475 496 C2' A B 6 OK 498 494 497 518 C2' A B 7 OK 520 516 519 540 C2' G B 8 OK 542 538 541 563 C2' G B 9 OK 565 561 564 586 C2' C B 10 OK 588 584 587 606 C2' C B 11 OK 608 604 607 626 C2' C B 12 OK 628 624 627 646 C2' U B 13 OK 648 644 647 666 C2' U B 14 OK 668 664 667 686 C2' U B 15 OK 688 684 687 706 C2' U B 16 OK 708 704 707 726 C2' C B 17 OK 728 724 727 746 C2' A B 18 OK 748 744 747 768 C2' G B 19 OK 770 766 769 791 C2' G B 20 OK 793 789 792 814 C2' G B 21 OK 816 812 815 837 C2' C B 22 OK 839 835 838 857 C2' C B 23 OK 859 855 858 877 C2' A B 24 OK 879 875 878 899 C2' C B 25 OK 901 897 900 919 C2' C B 26 OK 921 917 920 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 386 C3' G B 1 OK 384 387 388 409 C3' G B 2 OK 407 410 411 432 C3' C B 3 OK 430 433 434 452 C3' C B 4 OK 450 453 454 472 C3' A B 5 OK 470 473 474 494 C3' A B 6 OK 492 495 496 516 C3' A B 7 OK 514 517 518 538 C3' G B 8 OK 536 539 540 561 C3' G B 9 OK 559 562 563 584 C3' C B 10 OK 582 585 586 604 C3' C B 11 OK 602 605 606 624 C3' C B 12 OK 622 625 626 644 C3' U B 13 OK 642 645 646 664 C3' U B 14 OK 662 665 666 684 C3' U B 15 OK 682 685 686 704 C3' U B 16 OK 702 705 706 724 C3' C B 17 OK 722 725 726 744 C3' A B 18 OK 742 745 746 766 C3' G B 19 OK 764 767 768 789 C3' G B 20 OK 787 790 791 812 C3' G B 21 OK 810 813 814 835 C3' C B 22 OK 833 836 837 855 C3' C B 23 OK 853 856 857 875 C3' A B 24 OK 873 876 877 897 C3' C B 25 OK 895 898 899 917 C3' C B 26 OK 915 918 919 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 384 C4' G B 1 OK 386 383 385 407 C4' G B 2 OK 409 406 408 430 C4' C B 3 OK 432 429 431 450 C4' C B 4 OK 452 449 451 470 C4' A B 5 OK 472 469 471 492 C4' A B 6 OK 494 491 493 514 C4' A B 7 OK 516 513 515 536 C4' G B 8 OK 538 535 537 559 C4' G B 9 OK 561 558 560 582 C4' C B 10 OK 584 581 583 602 C4' C B 11 OK 604 601 603 622 C4' C B 12 OK 624 621 623 642 C4' U B 13 OK 644 641 643 662 C4' U B 14 OK 664 661 663 682 C4' U B 15 OK 684 681 683 702 C4' U B 16 OK 704 701 703 722 C4' C B 17 OK 724 721 723 742 C4' A B 18 OK 744 741 743 764 C4' G B 19 OK 766 763 765 787 C4' G B 20 OK 789 786 788 810 C4' G B 21 OK 812 809 811 833 C4' C B 22 OK 835 832 834 853 C4' C B 23 OK 855 852 854 873 C4' A B 24 OK 875 872 874 895 C4' C B 25 OK 897 894 896 915 C4' C B 26 OK 917 914 916 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 383 C5' G B 1 382 384 406 C5' G B 2 405 407 429 C5' C B 3 428 430 449 C5' C B 4 448 450 469 C5' A B 5 468 470 491 C5' A B 6 490 492 513 C5' A B 7 512 514 535 C5' G B 8 534 536 558 C5' G B 9 557 559 581 C5' C B 10 580 582 601 C5' C B 11 600 602 621 C5' C B 12 620 622 641 C5' U B 13 640 642 661 C5' U B 14 660 662 681 C5' U B 15 680 682 701 C5' U B 16 700 702 721 C5' C B 17 720 722 741 C5' A B 18 740 742 763 C5' G B 19 762 764 786 C5' G B 20 785 787 809 C5' G B 21 808 810 832 C5' C B 22 831 833 852 C5' C B 23 851 853 872 C5' A B 24 871 873 894 C5' C B 25 893 895 914 C5' C B 26 913 915 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 402 P G B 2 distorted distorted 387 403 404 405 425 P C B 3 distorted distorted 410 426 427 428 445 P C B 4 distorted distorted 433 446 447 448 465 P A B 5 distorted distorted 453 466 467 468 487 P A B 6 distorted distorted 473 488 489 490 509 P A B 7 distorted distorted 495 510 511 512 531 P G B 8 distorted distorted 517 532 533 534 554 P G B 9 distorted distorted 539 555 556 557 577 P C B 10 distorted distorted 562 578 579 580 597 P C B 11 distorted distorted 585 598 599 600 617 P C B 12 distorted distorted 605 618 619 620 637 P U B 13 distorted distorted 625 638 639 640 657 P U B 14 distorted distorted 645 658 659 660 677 P U B 15 distorted distorted 665 678 679 680 697 P U B 16 distorted distorted 685 698 699 700 717 P C B 17 distorted distorted 705 718 719 720 737 P A B 18 distorted distorted 725 738 739 740 759 P G B 19 distorted distorted 745 760 761 762 782 P G B 20 distorted distorted 767 783 784 785 805 P G B 21 distorted distorted 790 806 807 808 828 P C B 22 distorted distorted 813 829 830 831 848 P C B 23 distorted distorted 836 849 850 851 868 P A B 24 distorted distorted 856 869 870 871 890 P C B 25 distorted distorted 876 891 892 893 910 P C B 26 distorted distorted 898 911 912 913 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