ID code: '3ORC' 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' --------------------------------------------------------------------------------- 510 C1' T R 1 beta 506 511 509 530 C1' A R 2 beta 526 531 529 551 C1' T R 3 beta 547 552 550 571 C1' C R 4 beta 567 572 570 591 C1' G R 5 beta 587 592 590 613 C1' A R 6 beta 609 614 612 634 C1' T R 7 beta 630 635 633 654 C1' A R 8 beta 650 655 653 672 C1' T S 1 beta 668 673 671 692 C1' A S 2 beta 688 693 691 713 C1' T S 3 beta 709 714 712 733 C1' C S 4 beta 729 734 732 752 C1' G S 5 beta 748 753 751 774 C1' A S 6 beta 770 775 773 795 C1' T S 7 beta 791 796 794 815 C1' A S 8 beta 811 816 814 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 509 C2' T R 1 510 507 529 C2' A R 2 530 527 550 C2' T R 3 551 548 570 C2' C R 4 571 568 590 C2' G R 5 591 588 612 C2' A R 6 613 610 633 C2' T R 7 634 631 653 C2' A R 8 654 651 671 C2' T S 1 672 669 691 C2' A S 2 692 689 712 C2' T S 3 713 710 732 C2' C S 4 733 730 751 C2' G S 5 752 749 773 C2' A S 6 774 771 794 C2' T S 7 795 792 814 C2' A S 8 815 812 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 507 C3' T R 1 OK 505 508 509 527 C3' A R 2 OK 525 528 529 548 C3' T R 3 OK 546 549 550 568 C3' C R 4 OK 566 569 570 588 C3' G R 5 OK 586 589 590 610 C3' A R 6 OK 608 611 612 631 C3' T R 7 OK 629 632 633 651 C3' A R 8 OK 649 652 653 669 C3' T S 1 OK 667 670 671 689 C3' A S 2 OK 687 690 691 710 C3' T S 3 OK 708 711 712 730 C3' C S 4 OK 728 731 732 749 C3' G S 5 OK 747 750 751 771 C3' A S 6 OK 769 772 773 792 C3' T S 7 OK 790 793 794 812 C3' A S 8 OK 810 813 814 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 505 C4' T R 1 OK 507 504 506 525 C4' A R 2 OK 527 524 526 546 C4' T R 3 OK 548 545 547 566 C4' C R 4 OK 568 565 567 586 C4' G R 5 OK 588 585 587 608 C4' A R 6 OK 610 607 609 629 C4' T R 7 OK 631 628 630 649 C4' A R 8 OK 651 648 650 667 C4' T S 1 OK 669 666 668 687 C4' A S 2 OK 689 686 688 708 C4' T S 3 OK 710 707 709 728 C4' C S 4 OK 730 727 729 747 C4' G S 5 OK 749 746 748 769 C4' A S 6 OK 771 768 770 790 C4' T S 7 OK 792 789 791 810 C4' A S 8 OK 812 809 811 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 504 C5' T R 1 503 505 524 C5' A R 2 523 525 545 C5' T R 3 544 546 565 C5' C R 4 564 566 585 C5' G R 5 584 586 607 C5' A R 6 606 608 628 C5' T R 7 627 629 648 C5' A R 8 647 649 666 C5' T S 1 665 667 686 C5' A S 2 685 687 707 C5' T S 3 706 708 727 C5' C S 4 726 728 746 C5' G S 5 745 747 768 C5' A S 6 767 769 789 C5' T S 7 788 790 809 C5' A S 8 808 810 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 520 P A R 2 OK OK 508 521 522 523 541 P T R 3 OK OK 528 542 543 544 561 P C R 4 OK OK 549 562 563 564 581 P G R 5 OK OK 569 582 583 584 603 P A R 6 OK OK 589 604 605 606 624 P T R 7 OK OK 611 625 626 627 644 P A R 8 OK OK 632 645 646 647 682 P A S 2 OK OK 670 683 684 685 703 P T S 3 OK OK 690 704 705 706 723 P C S 4 OK OK 711 724 725 726 742 P G S 5 OK OK 731 743 744 745 764 P A S 6 OK OK 750 765 766 767 785 P T S 7 OK OK 772 786 787 788 805 P A S 8 OK OK 793 806 807 808 ---------------------------------------------------------------------------------