ID code: '3K5L' 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' --------------------------------------------------------------------------------- 6340 C1' DT T 801 beta 6336 6341 6339 6360 C1' DA T 802 beta 6356 6361 6359 6381 C1' DT T 803 beta 6377 6382 6380 6399 C1' 3DR T 804 6398 6395 6412 C1' DG T 805 beta 6408 6413 6411 6434 C1' DT T 806 beta 6430 6435 6433 6454 C1' DA T 807 beta 6450 6455 6453 6475 C1' DC T 808 beta 6471 6476 6474 6494 C1' DG T 809 beta 6490 6495 6493 6516 C1' DC T 810 beta 6512 6517 6515 6535 C1' DT T 811 beta 6531 6536 6534 6555 C1' DA T 812 beta 6551 6556 6554 6576 C1' DG T 813 beta 6572 6577 6575 6598 C1' DG T 814 beta 6594 6599 6597 6620 C1' DC T 815 beta 6616 6621 6619 6639 C1' DA T 816 beta 6635 6640 6638 6660 C1' DC T 817 beta 6656 6661 6659 6679 C1' DA T 818 beta 6675 6680 6678 6698 C1' DG P 901 beta 6694 6699 6697 6720 C1' DT P 902 beta 6716 6721 6719 6740 C1' DG P 903 beta 6736 6741 6739 6762 C1' DC P 904 beta 6758 6763 6761 6781 C1' DC P 905 beta 6777 6782 6780 6800 C1' DT P 906 beta 6796 6801 6799 6820 C1' DA P 907 beta 6816 6821 6819 6841 C1' DG P 908 beta 6837 6842 6840 6863 C1' DC P 909 beta 6859 6864 6862 6882 C1' DG P 910 beta 6878 6883 6881 6904 C1' DT P 911 beta 6900 6905 6903 6924 C1' DA P 912 beta 6920 6925 6923 6943 C1' DOC P 913 beta 6947 6935 6944 6973 C1' DTP A 914 beta 6969 6974 6972 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 6339 C2' DT T 801 6340 6337 6359 C2' DA T 802 6360 6357 6380 C2' DT T 803 6381 6378 6395 C2' 3DR T 804 6399 6400 6411 C2' DG T 805 6412 6409 6433 C2' DT T 806 6434 6431 6453 C2' DA T 807 6454 6451 6474 C2' DC T 808 6475 6472 6493 C2' DG T 809 6494 6491 6515 C2' DC T 810 6516 6513 6534 C2' DT T 811 6535 6532 6554 C2' DA T 812 6555 6552 6575 C2' DG T 813 6576 6573 6597 C2' DG T 814 6598 6595 6619 C2' DC T 815 6620 6617 6638 C2' DA T 816 6639 6636 6659 C2' DC T 817 6660 6657 6678 C2' DA T 818 6679 6676 6697 C2' DG P 901 6698 6695 6719 C2' DT P 902 6720 6717 6739 C2' DG P 903 6740 6737 6761 C2' DC P 904 6762 6759 6780 C2' DC P 905 6781 6778 6799 C2' DT P 906 6800 6797 6819 C2' DA P 907 6820 6817 6840 C2' DG P 908 6841 6838 6862 C2' DC P 909 6863 6860 6881 C2' DG P 910 6882 6879 6903 C2' DT P 911 6904 6901 6923 C2' DA P 912 6924 6921 6944 C2' DOC P 913 6943 6945 6972 C2' DTP A 914 6973 6970 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 6337 C3' DT T 801 OK 6335 6338 6339 6357 C3' DA T 802 OK 6355 6358 6359 6378 C3' DT T 803 OK 6376 6379 6380 6400 C3' 3DR T 804 OK 6397 6401 6395 6409 C3' DG T 805 OK 6407 6410 6411 6431 C3' DT T 806 OK 6429 6432 6433 6451 C3' DA T 807 OK 6449 6452 6453 6472 C3' DC T 808 OK 6470 6473 6474 6491 C3' DG T 809 OK 6489 6492 6493 6513 C3' DC T 810 OK 6511 6514 6515 6532 C3' DT T 811 OK 6530 6533 6534 6552 C3' DA T 812 OK 6550 6553 6554 6573 C3' DG T 813 OK 6571 6574 6575 6595 C3' DG T 814 OK 6593 6596 6597 6617 C3' DC T 815 OK 6615 6618 6619 6636 C3' DA T 816 OK 6634 6637 6638 6657 C3' DC T 817 OK 6655 6658 6659 6676 C3' DA T 818 OK 6674 6677 6678 6695 C3' DG P 901 OK 6693 6696 6697 6717 C3' DT P 902 OK 6715 6718 6719 6737 C3' DG P 903 OK 6735 6738 6739 6759 C3' DC P 904 OK 6757 6760 6761 6778 C3' DC P 905 OK 6776 6779 6780 6797 C3' DT P 906 OK 6795 6798 6799 6817 C3' DA P 907 OK 6815 6818 6819 6838 C3' DG P 908 OK 6836 6839 6840 6860 C3' DC P 909 OK 6858 6861 6862 6879 C3' DG P 910 OK 6877 6880 6881 6901 C3' DT P 911 OK 6899 6902 6903 6921 C3' DA P 912 OK 6919 6922 6923 6945 C3' DOC P 913 6946 6944 6970 C3' DTP A 914 OK 6968 6971 6972 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6335 C4' DT T 801 OK 6337 6334 6336 6355 C4' DA T 802 OK 6357 6354 6356 6376 C4' DT T 803 OK 6378 6375 6377 6397 C4' 3DR T 804 OK 6400 6396 6398 6407 C4' DG T 805 OK 6409 6406 6408 6429 C4' DT T 806 OK 6431 6428 6430 6449 C4' DA T 807 OK 6451 6448 6450 6470 C4' DC T 808 OK 6472 6469 6471 6489 C4' DG T 809 OK 6491 6488 6490 6511 C4' DC T 810 OK 6513 6510 6512 6530 C4' DT T 811 OK 6532 6529 6531 6550 C4' DA T 812 OK 6552 6549 6551 6571 C4' DG T 813 OK 6573 6570 6572 6593 C4' DG T 814 OK 6595 6592 6594 6615 C4' DC T 815 OK 6617 6614 6616 6634 C4' DA T 816 OK 6636 6633 6635 6655 C4' DC T 817 OK 6657 6654 6656 6674 C4' DA T 818 OK 6676 6673 6675 6693 C4' DG P 901 OK 6695 6692 6694 6715 C4' DT P 902 OK 6717 6714 6716 6735 C4' DG P 903 OK 6737 6734 6736 6757 C4' DC P 904 OK 6759 6756 6758 6776 C4' DC P 905 OK 6778 6775 6777 6795 C4' DT P 906 OK 6797 6794 6796 6815 C4' DA P 907 OK 6817 6814 6816 6836 C4' DG P 908 OK 6838 6835 6837 6858 C4' DC P 909 OK 6860 6857 6859 6877 C4' DG P 910 OK 6879 6876 6878 6899 C4' DT P 911 OK 6901 6898 6900 6919 C4' DA P 912 OK 6921 6918 6920 6946 C4' DOC P 913 OK 6945 6948 6947 6968 C4' DTP A 914 OK 6970 6967 6969 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 6334 C5' DT T 801 6333 6335 6354 C5' DA T 802 6353 6355 6375 C5' DT T 803 6374 6376 6396 C5' 3DR T 804 6391 6397 6406 C5' DG T 805 6405 6407 6428 C5' DT T 806 6427 6429 6448 C5' DA T 807 6447 6449 6469 C5' DC T 808 6468 6470 6488 C5' DG T 809 6487 6489 6510 C5' DC T 810 6509 6511 6529 C5' DT T 811 6528 6530 6549 C5' DA T 812 6548 6550 6570 C5' DG T 813 6569 6571 6592 C5' DG T 814 6591 6593 6614 C5' DC T 815 6613 6615 6633 C5' DA T 816 6632 6634 6654 C5' DC T 817 6653 6655 6673 C5' DA T 818 6672 6674 6692 C5' DG P 901 6691 6693 6714 C5' DT P 902 6713 6715 6734 C5' DG P 903 6733 6735 6756 C5' DC P 904 6755 6757 6775 C5' DC P 905 6774 6776 6794 C5' DT P 906 6793 6795 6814 C5' DA P 907 6813 6815 6835 C5' DG P 908 6834 6836 6857 C5' DC P 909 6856 6858 6876 C5' DG P 910 6875 6877 6898 C5' DT P 911 6897 6899 6918 C5' DA P 912 6917 6919 6948 C5' DOC P 913 6949 6946 6967 C5' DTP A 914 6966 6968 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 6350 P DA T 802 distorted distorted 6338 6351 6352 6353 6371 P DT T 803 distorted distorted 6358 6372 6373 6374 6392 P 3DR T 804 OK OK 6379 6393 6394 6391 6402 P DG T 805 distorted distorted 6401 6403 6404 6405 6424 P DT T 806 distorted distorted 6410 6425 6426 6427 6444 P DA T 807 distorted distorted 6432 6445 6446 6447 6465 P DC T 808 distorted distorted 6452 6466 6467 6468 6484 P DG T 809 distorted distorted 6473 6485 6486 6487 6506 P DC T 810 distorted distorted 6492 6507 6508 6509 6525 P DT T 811 distorted distorted 6514 6526 6527 6528 6545 P DA T 812 distorted distorted 6533 6546 6547 6548 6566 P DG T 813 distorted distorted 6553 6567 6568 6569 6588 P DG T 814 distorted distorted 6574 6589 6590 6591 6610 P DC T 815 distorted distorted 6596 6611 6612 6613 6629 P DA T 816 distorted distorted 6618 6630 6631 6632 6650 P DC T 817 distorted distorted 6637 6651 6652 6653 6669 P DA T 818 distorted distorted 6658 6670 6671 6672 6710 P DT P 902 distorted distorted 6696 6711 6712 6713 6730 P DG P 903 distorted distorted 6718 6731 6732 6733 6752 P DC P 904 distorted distorted 6738 6753 6754 6755 6771 P DC P 905 distorted distorted 6760 6772 6773 6774 6790 P DT P 906 distorted distorted 6779 6791 6792 6793 6810 P DA P 907 distorted distorted 6798 6811 6812 6813 6831 P DG P 908 distorted distorted 6818 6832 6833 6834 6853 P DC P 909 distorted distorted 6839 6854 6855 6856 6872 P DG P 910 distorted distorted 6861 6873 6874 6875 6894 P DT P 911 distorted distorted 6880 6895 6896 6897 6914 P DA P 912 distorted distorted 6902 6915 6916 6917 6950 P DOC P 913 distorted distorted 6922 6951 6952 6949 ---------------------------------------------------------------------------------