ID code: '4KHY' 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' --------------------------------------------------------------------------------- 7348 C1' DA T 1 beta 7344 7349 7347 7369 C1' DC T 2 beta 7365 7370 7368 7388 C1' DA T 3 beta 7384 7389 7387 7409 C1' DG T 4 beta 7405 7410 7408 7431 C1' DG T 5 beta 7427 7432 7430 7454 C1' U T 6 beta 7449 7455 7452 7473 C1' DA T 7 beta 7469 7474 7472 7494 C1' DA T 8 beta 7490 7495 7493 7515 C1' DG T 9 beta 7511 7516 7514 7537 C1' DC T 10 beta 7533 7538 7536 7556 C1' DA T 11 beta 7552 7557 7555 7577 C1' DG T 12 beta 7573 7578 7576 7599 C1' DT T 13 beta 7595 7600 7598 7619 C1' DC T 14 beta 7615 7620 7618 7638 C1' DC T 15 beta 7634 7639 7637 7657 C1' DG T 16 beta 7653 7658 7656 7679 C1' DC T 17 beta 7675 7680 7678 7698 C1' DG T 18 beta 7694 7699 7697 7717 C1' DG P 102 beta 7713 7718 7716 7739 C1' DC P 103 beta 7735 7740 7738 7758 C1' DG P 104 beta 7754 7759 7757 7780 C1' DG P 105 beta 7776 7781 7779 7802 C1' DA P 106 beta 7798 7803 7801 7823 C1' DC P 107 beta 7819 7824 7822 7842 C1' DT P 108 beta 7838 7843 7841 7862 C1' DG P 109 beta 7858 7863 7861 7884 C1' DC P 110 beta 7880 7885 7883 7903 C1' DT P 111 beta 7899 7904 7902 7923 C1' DT P 112 beta 7919 7924 7922 7943 C1' DA P 113 beta 7939 7944 7942 7964 C1' DC P 114 beta 7960 7965 7963 7982 C1' DC P 115 beta 7979 7983 7981 8011 C1' TTP A1001 beta 8007 8012 8010 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7347 C2' DA T 1 7348 7345 7368 C2' DC T 2 7369 7366 7387 C2' DA T 3 7388 7385 7408 C2' DG T 4 7409 7406 7430 C2' DG T 5 7431 7428 7452 C2' U T 6 OK 7454 7450 7453 7472 C2' DA T 7 7473 7470 7493 C2' DA T 8 7494 7491 7514 C2' DG T 9 7515 7512 7536 C2' DC T 10 7537 7534 7555 C2' DA T 11 7556 7553 7576 C2' DG T 12 7577 7574 7598 C2' DT T 13 7599 7596 7618 C2' DC T 14 7619 7616 7637 C2' DC T 15 7638 7635 7656 C2' DG T 16 7657 7654 7678 C2' DC T 17 7679 7676 7697 C2' DG T 18 7698 7695 7716 C2' DG P 102 7717 7714 7738 C2' DC P 103 7739 7736 7757 C2' DG P 104 7758 7755 7779 C2' DG P 105 7780 7777 7801 C2' DA P 106 7802 7799 7822 C2' DC P 107 7823 7820 7841 C2' DT P 108 7842 7839 7861 C2' DG P 109 7862 7859 7883 C2' DC P 110 7884 7881 7902 C2' DT P 111 7903 7900 7922 C2' DT P 112 7923 7920 7942 C2' DA P 113 7943 7940 7963 C2' DC P 114 7964 7961 7981 C2' DC P 115 7982 7980 8010 C2' TTP A1001 8011 8008 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 7345 C3' DA T 1 OK 7343 7346 7347 7366 C3' DC T 2 OK 7364 7367 7368 7385 C3' DA T 3 OK 7383 7386 7387 7406 C3' DG T 4 OK 7404 7407 7408 7428 C3' DG T 5 OK 7426 7429 7430 7450 C3' U T 6 OK 7448 7451 7452 7470 C3' DA T 7 OK 7468 7471 7472 7491 C3' DA T 8 OK 7489 7492 7493 7512 C3' DG T 9 OK 7510 7513 7514 7534 C3' DC T 10 OK 7532 7535 7536 7553 C3' DA T 11 OK 7551 7554 7555 7574 C3' DG T 12 OK 7572 7575 7576 7596 C3' DT T 13 OK 7594 7597 7598 7616 C3' DC T 14 OK 7614 7617 7618 7635 C3' DC T 15 OK 7633 7636 7637 7654 C3' DG T 16 OK 7652 7655 7656 7676 C3' DC T 17 OK 7674 7677 7678 7695 C3' DG T 18 OK 7693 7696 7697 7714 C3' DG P 102 OK 7712 7715 7716 7736 C3' DC P 103 OK 7734 7737 7738 7755 C3' DG P 104 OK 7753 7756 7757 7777 C3' DG P 105 OK 7775 7778 7779 7799 C3' DA P 106 OK 7797 7800 7801 7820 C3' DC P 107 OK 7818 7821 7822 7839 C3' DT P 108 OK 7837 7840 7841 7859 C3' DG P 109 OK 7857 7860 7861 7881 C3' DC P 110 OK 7879 7882 7883 7900 C3' DT P 111 OK 7898 7901 7902 7920 C3' DT P 112 OK 7918 7921 7922 7940 C3' DA P 113 OK 7938 7941 7942 7961 C3' DC P 114 OK 7959 7962 7963 7980 C3' DC P 115 7978 7981 8008 C3' TTP A1001 OK 8006 8009 8010 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 7343 C4' DA T 1 OK 7345 7342 7344 7364 C4' DC T 2 OK 7366 7363 7365 7383 C4' DA T 3 OK 7385 7382 7384 7404 C4' DG T 4 OK 7406 7403 7405 7426 C4' DG T 5 OK 7428 7425 7427 7448 C4' U T 6 OK 7450 7447 7449 7468 C4' DA T 7 OK 7470 7467 7469 7489 C4' DA T 8 OK 7491 7488 7490 7510 C4' DG T 9 OK 7512 7509 7511 7532 C4' DC T 10 OK 7534 7531 7533 7551 C4' DA T 11 OK 7553 7550 7552 7572 C4' DG T 12 OK 7574 7571 7573 7594 C4' DT T 13 OK 7596 7593 7595 7614 C4' DC T 14 OK 7616 7613 7615 7633 C4' DC T 15 OK 7635 7632 7634 7652 C4' DG T 16 OK 7654 7651 7653 7674 C4' DC T 17 OK 7676 7673 7675 7693 C4' DG T 18 OK 7695 7692 7694 7712 C4' DG P 102 OK 7714 7711 7713 7734 C4' DC P 103 OK 7736 7733 7735 7753 C4' DG P 104 OK 7755 7752 7754 7775 C4' DG P 105 OK 7777 7774 7776 7797 C4' DA P 106 OK 7799 7796 7798 7818 C4' DC P 107 OK 7820 7817 7819 7837 C4' DT P 108 OK 7839 7836 7838 7857 C4' DG P 109 OK 7859 7856 7858 7879 C4' DC P 110 OK 7881 7878 7880 7898 C4' DT P 111 OK 7900 7897 7899 7918 C4' DT P 112 OK 7920 7917 7919 7938 C4' DA P 113 OK 7940 7937 7939 7959 C4' DC P 114 OK 7961 7958 7960 7978 C4' DC P 115 OK 7980 7977 7979 8006 C4' TTP A1001 OK 8008 8005 8007 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 7342 C5' DA T 1 7341 7343 7363 C5' DC T 2 7362 7364 7382 C5' DA T 3 7381 7383 7403 C5' DG T 4 7402 7404 7425 C5' DG T 5 7424 7426 7447 C5' U T 6 7446 7448 7467 C5' DA T 7 7466 7468 7488 C5' DA T 8 7487 7489 7509 C5' DG T 9 7508 7510 7531 C5' DC T 10 7530 7532 7550 C5' DA T 11 7549 7551 7571 C5' DG T 12 7570 7572 7593 C5' DT T 13 7592 7594 7613 C5' DC T 14 7612 7614 7632 C5' DC T 15 7631 7633 7651 C5' DG T 16 7650 7652 7673 C5' DC T 17 7672 7674 7692 C5' DG T 18 7691 7693 7711 C5' DG P 102 7712 7733 C5' DC P 103 7732 7734 7752 C5' DG P 104 7751 7753 7774 C5' DG P 105 7773 7775 7796 C5' DA P 106 7795 7797 7817 C5' DC P 107 7816 7818 7836 C5' DT P 108 7835 7837 7856 C5' DG P 109 7855 7857 7878 C5' DC P 110 7877 7879 7897 C5' DT P 111 7896 7898 7917 C5' DT P 112 7916 7918 7937 C5' DA P 113 7936 7938 7958 C5' DC P 114 7957 7959 7977 C5' DC P 115 7976 7978 8005 C5' TTP A1001 8004 8006 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 7359 P DC T 2 distorted distorted 7346 7360 7361 7362 7378 P DA T 3 distorted distorted 7367 7379 7380 7381 7399 P DG T 4 distorted distorted 7386 7400 7401 7402 7421 P DG T 5 distorted distorted 7407 7422 7423 7424 7443 P U T 6 distorted distorted 7429 7444 7445 7446 7463 P DA T 7 distorted distorted 7451 7464 7465 7466 7484 P DA T 8 distorted distorted 7471 7485 7486 7487 7505 P DG T 9 distorted distorted 7492 7506 7507 7508 7527 P DC T 10 distorted distorted 7513 7528 7529 7530 7546 P DA T 11 distorted distorted 7535 7547 7548 7549 7567 P DG T 12 distorted distorted 7554 7568 7569 7570 7589 P DT T 13 distorted distorted 7575 7590 7591 7592 7609 P DC T 14 distorted distorted 7597 7610 7611 7612 7628 P DC T 15 distorted distorted 7617 7629 7630 7631 7647 P DG T 16 distorted distorted 7636 7648 7649 7650 7669 P DC T 17 distorted distorted 7655 7670 7671 7672 7688 P DG T 18 distorted distorted 7677 7689 7690 7691 7729 P DC P 103 distorted distorted 7715 7730 7731 7732 7748 P DG P 104 distorted distorted 7737 7749 7750 7751 7770 P DG P 105 distorted distorted 7756 7771 7772 7773 7792 P DA P 106 distorted distorted 7778 7793 7794 7795 7813 P DC P 107 distorted distorted 7800 7814 7815 7816 7832 P DT P 108 distorted distorted 7821 7833 7834 7835 7852 P DG P 109 distorted distorted 7840 7853 7854 7855 7874 P DC P 110 distorted distorted 7860 7875 7876 7877 7893 P DT P 111 distorted distorted 7882 7894 7895 7896 7913 P DT P 112 distorted distorted 7901 7914 7915 7916 7933 P DA P 113 distorted distorted 7921 7934 7935 7936 7954 P DC P 114 distorted distorted 7941 7955 7956 7957 7973 P DC P 115 distorted distorted 7962 7974 7975 7976 ---------------------------------------------------------------------------------