ID code: '3K57' 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' --------------------------------------------------------------------------------- 6352 C1' DT T 802 beta 6348 6353 6351 6372 C1' DA T 803 beta 6368 6373 6371 6393 C1' DT T 804 beta 6389 6394 6392 6413 C1' DG T 805 beta 6409 6414 6412 6435 C1' DT T 806 beta 6431 6436 6434 6455 C1' DA T 807 beta 6451 6456 6454 6476 C1' DC T 808 beta 6472 6477 6475 6495 C1' DG T 809 beta 6491 6496 6494 6517 C1' DC T 810 beta 6513 6518 6516 6536 C1' DT T 811 beta 6532 6537 6535 6556 C1' DA T 812 beta 6552 6557 6555 6577 C1' DG T 813 beta 6573 6578 6576 6599 C1' DG T 814 beta 6595 6600 6598 6621 C1' DC T 815 beta 6617 6622 6620 6640 C1' DA T 816 beta 6636 6641 6639 6661 C1' DC T 817 beta 6657 6662 6660 6680 C1' DG T 818 beta 6676 6681 6679 6700 C1' DG P 901 beta 6696 6701 6699 6722 C1' DT P 902 beta 6718 6723 6721 6742 C1' DG P 903 beta 6738 6743 6741 6764 C1' DC P 904 beta 6760 6765 6763 6783 C1' DC P 905 beta 6779 6784 6782 6802 C1' DT P 906 beta 6798 6803 6801 6822 C1' DA P 907 beta 6818 6823 6821 6843 C1' DG P 908 beta 6839 6844 6842 6865 C1' DC P 909 beta 6861 6866 6864 6884 C1' DG P 910 beta 6880 6885 6883 6906 C1' DT P 911 beta 6902 6907 6905 6926 C1' DA P 912 beta 6922 6927 6925 6945 C1' DOC P 913 beta 6949 6937 6946 6975 C1' DTP A 914 beta 6971 6976 6974 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 6351 C2' DT T 802 6352 6349 6371 C2' DA T 803 6372 6369 6392 C2' DT T 804 6393 6390 6412 C2' DG T 805 6413 6410 6434 C2' DT T 806 6435 6432 6454 C2' DA T 807 6455 6452 6475 C2' DC T 808 6476 6473 6494 C2' DG T 809 6495 6492 6516 C2' DC T 810 6517 6514 6535 C2' DT T 811 6536 6533 6555 C2' DA T 812 6556 6553 6576 C2' DG T 813 6577 6574 6598 C2' DG T 814 6599 6596 6620 C2' DC T 815 6621 6618 6639 C2' DA T 816 6640 6637 6660 C2' DC T 817 6661 6658 6679 C2' DG T 818 6680 6677 6699 C2' DG P 901 6700 6697 6721 C2' DT P 902 6722 6719 6741 C2' DG P 903 6742 6739 6763 C2' DC P 904 6764 6761 6782 C2' DC P 905 6783 6780 6801 C2' DT P 906 6802 6799 6821 C2' DA P 907 6822 6819 6842 C2' DG P 908 6843 6840 6864 C2' DC P 909 6865 6862 6883 C2' DG P 910 6884 6881 6905 C2' DT P 911 6906 6903 6925 C2' DA P 912 6926 6923 6946 C2' DOC P 913 6945 6947 6974 C2' DTP A 914 6975 6972 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 6349 C3' DT T 802 OK 6347 6350 6351 6369 C3' DA T 803 OK 6367 6370 6371 6390 C3' DT T 804 OK 6388 6391 6392 6410 C3' DG T 805 OK 6408 6411 6412 6432 C3' DT T 806 OK 6430 6433 6434 6452 C3' DA T 807 OK 6450 6453 6454 6473 C3' DC T 808 OK 6471 6474 6475 6492 C3' DG T 809 OK 6490 6493 6494 6514 C3' DC T 810 OK 6512 6515 6516 6533 C3' DT T 811 OK 6531 6534 6535 6553 C3' DA T 812 OK 6551 6554 6555 6574 C3' DG T 813 OK 6572 6575 6576 6596 C3' DG T 814 OK 6594 6597 6598 6618 C3' DC T 815 OK 6616 6619 6620 6637 C3' DA T 816 OK 6635 6638 6639 6658 C3' DC T 817 OK 6656 6659 6660 6677 C3' DG T 818 OK 6675 6678 6679 6697 C3' DG P 901 OK 6695 6698 6699 6719 C3' DT P 902 OK 6717 6720 6721 6739 C3' DG P 903 OK 6737 6740 6741 6761 C3' DC P 904 OK 6759 6762 6763 6780 C3' DC P 905 OK 6778 6781 6782 6799 C3' DT P 906 OK 6797 6800 6801 6819 C3' DA P 907 OK 6817 6820 6821 6840 C3' DG P 908 OK 6838 6841 6842 6862 C3' DC P 909 OK 6860 6863 6864 6881 C3' DG P 910 OK 6879 6882 6883 6903 C3' DT P 911 OK 6901 6904 6905 6923 C3' DA P 912 OK 6921 6924 6925 6947 C3' DOC P 913 6948 6946 6972 C3' DTP A 914 OK 6970 6973 6974 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6347 C4' DT T 802 OK 6349 6346 6348 6367 C4' DA T 803 OK 6369 6366 6368 6388 C4' DT T 804 OK 6390 6387 6389 6408 C4' DG T 805 OK 6410 6407 6409 6430 C4' DT T 806 OK 6432 6429 6431 6450 C4' DA T 807 OK 6452 6449 6451 6471 C4' DC T 808 OK 6473 6470 6472 6490 C4' DG T 809 OK 6492 6489 6491 6512 C4' DC T 810 OK 6514 6511 6513 6531 C4' DT T 811 OK 6533 6530 6532 6551 C4' DA T 812 OK 6553 6550 6552 6572 C4' DG T 813 OK 6574 6571 6573 6594 C4' DG T 814 OK 6596 6593 6595 6616 C4' DC T 815 OK 6618 6615 6617 6635 C4' DA T 816 OK 6637 6634 6636 6656 C4' DC T 817 OK 6658 6655 6657 6675 C4' DG T 818 OK 6677 6674 6676 6695 C4' DG P 901 OK 6697 6694 6696 6717 C4' DT P 902 OK 6719 6716 6718 6737 C4' DG P 903 OK 6739 6736 6738 6759 C4' DC P 904 OK 6761 6758 6760 6778 C4' DC P 905 OK 6780 6777 6779 6797 C4' DT P 906 OK 6799 6796 6798 6817 C4' DA P 907 OK 6819 6816 6818 6838 C4' DG P 908 OK 6840 6837 6839 6860 C4' DC P 909 OK 6862 6859 6861 6879 C4' DG P 910 OK 6881 6878 6880 6901 C4' DT P 911 OK 6903 6900 6902 6921 C4' DA P 912 OK 6923 6920 6922 6948 C4' DOC P 913 OK 6947 6950 6949 6970 C4' DTP A 914 OK 6972 6969 6971 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 6346 C5' DT T 802 6345 6347 6366 C5' DA T 803 6365 6367 6387 C5' DT T 804 6386 6388 6407 C5' DG T 805 6406 6408 6429 C5' DT T 806 6428 6430 6449 C5' DA T 807 6448 6450 6470 C5' DC T 808 6469 6471 6489 C5' DG T 809 6488 6490 6511 C5' DC T 810 6510 6512 6530 C5' DT T 811 6529 6531 6550 C5' DA T 812 6549 6551 6571 C5' DG T 813 6570 6572 6593 C5' DG T 814 6592 6594 6615 C5' DC T 815 6614 6616 6634 C5' DA T 816 6633 6635 6655 C5' DC T 817 6654 6656 6674 C5' DG T 818 6673 6675 6694 C5' DG P 901 6693 6695 6716 C5' DT P 902 6715 6717 6736 C5' DG P 903 6735 6737 6758 C5' DC P 904 6757 6759 6777 C5' DC P 905 6776 6778 6796 C5' DT P 906 6795 6797 6816 C5' DA P 907 6815 6817 6837 C5' DG P 908 6836 6838 6859 C5' DC P 909 6858 6860 6878 C5' DG P 910 6877 6879 6900 C5' DT P 911 6899 6901 6920 C5' DA P 912 6919 6921 6950 C5' DOC P 913 6951 6948 6969 C5' DTP A 914 6968 6970 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 6362 P DA T 803 distorted distorted 6350 6363 6364 6365 6383 P DT T 804 distorted distorted 6370 6384 6385 6386 6403 P DG T 805 distorted distorted 6391 6404 6405 6406 6425 P DT T 806 distorted distorted 6411 6426 6427 6428 6445 P DA T 807 distorted distorted 6433 6446 6447 6448 6466 P DC T 808 distorted distorted 6453 6467 6468 6469 6485 P DG T 809 distorted distorted 6474 6486 6487 6488 6507 P DC T 810 distorted distorted 6493 6508 6509 6510 6526 P DT T 811 distorted distorted 6515 6527 6528 6529 6546 P DA T 812 distorted distorted 6534 6547 6548 6549 6567 P DG T 813 distorted distorted 6554 6568 6569 6570 6589 P DG T 814 distorted distorted 6575 6590 6591 6592 6611 P DC T 815 distorted distorted 6597 6612 6613 6614 6630 P DA T 816 distorted distorted 6619 6631 6632 6633 6651 P DC T 817 distorted distorted 6638 6652 6653 6654 6670 P DG T 818 distorted distorted 6659 6671 6672 6673 6712 P DT P 902 distorted distorted 6698 6713 6714 6715 6732 P DG P 903 distorted distorted 6720 6733 6734 6735 6754 P DC P 904 distorted distorted 6740 6755 6756 6757 6773 P DC P 905 distorted distorted 6762 6774 6775 6776 6792 P DT P 906 distorted distorted 6781 6793 6794 6795 6812 P DA P 907 distorted distorted 6800 6813 6814 6815 6833 P DG P 908 distorted distorted 6820 6834 6835 6836 6855 P DC P 909 distorted distorted 6841 6856 6857 6858 6874 P DG P 910 distorted distorted 6863 6875 6876 6877 6896 P DT P 911 distorted distorted 6882 6897 6898 6899 6916 P DA P 912 distorted distorted 6904 6917 6918 6919 6952 P DOC P 913 distorted distorted 6924 6953 6954 6951 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