ID code: '3QEI' 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' --------------------------------------------------------------------------------- 7407 C1' DT T 1 beta 7403 7408 7406 7427 C1' DC T 2 beta 7423 7428 7426 7446 C1' DG T 3 beta 7442 7447 7445 7468 C1' DFT T 4 7464 7467 7488 C1' DG T 5 beta 7484 7489 7487 7510 C1' DT T 6 beta 7506 7511 7509 7530 C1' DA T 7 beta 7526 7531 7529 7551 C1' DA T 8 beta 7547 7552 7550 7572 C1' DG T 9 beta 7568 7573 7571 7594 C1' DC T 10 beta 7590 7595 7593 7613 C1' DA T 11 beta 7609 7614 7612 7634 C1' DG T 12 beta 7630 7635 7633 7656 C1' DT T 13 beta 7652 7657 7655 7676 C1' DC T 14 beta 7672 7677 7675 7695 C1' DC T 15 beta 7691 7696 7694 7714 C1' DG T 16 beta 7710 7715 7713 7736 C1' DC T 17 beta 7732 7737 7735 7755 C1' DG T 18 beta 7751 7756 7754 7775 C1' DG P 103 beta 7771 7776 7774 7797 C1' DC P 104 beta 7793 7798 7796 7816 C1' DG P 105 beta 7812 7817 7815 7838 C1' DG P 106 beta 7834 7839 7837 7860 C1' DA P 107 beta 7856 7861 7859 7881 C1' DC P 108 beta 7877 7882 7880 7900 C1' DT P 109 beta 7896 7901 7899 7920 C1' DG P 110 beta 7916 7921 7919 7942 C1' DC P 111 beta 7938 7943 7941 7961 C1' DT P 112 beta 7957 7962 7960 7981 C1' DT P 113 beta 7977 7982 7980 8001 C1' DA P 114 beta 7997 8002 8000 8020 C1' DOC P 115 beta 8024 8012 8021 8039 C1' DCP A 904 beta 8043 8031 8040 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7406 C2' DT T 1 7407 7404 7426 C2' DC T 2 7427 7424 7445 C2' DG T 3 7446 7443 7467 C2' DFT T 4 7468 7465 7487 C2' DG T 5 7488 7485 7509 C2' DT T 6 7510 7507 7529 C2' DA T 7 7530 7527 7550 C2' DA T 8 7551 7548 7571 C2' DG T 9 7572 7569 7593 C2' DC T 10 7594 7591 7612 C2' DA T 11 7613 7610 7633 C2' DG T 12 7634 7631 7655 C2' DT T 13 7656 7653 7675 C2' DC T 14 7676 7673 7694 C2' DC T 15 7695 7692 7713 C2' DG T 16 7714 7711 7735 C2' DC T 17 7736 7733 7754 C2' DG T 18 7755 7752 7774 C2' DG P 103 7775 7772 7796 C2' DC P 104 7797 7794 7815 C2' DG P 105 7816 7813 7837 C2' DG P 106 7838 7835 7859 C2' DA P 107 7860 7857 7880 C2' DC P 108 7881 7878 7899 C2' DT P 109 7900 7897 7919 C2' DG P 110 7920 7917 7941 C2' DC P 111 7942 7939 7960 C2' DT P 112 7961 7958 7980 C2' DT P 113 7981 7978 8000 C2' DA P 114 8001 7998 8021 C2' DOC P 115 8020 8022 8040 C2' DCP A 904 8039 8041 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 7404 C3' DT T 1 OK 7402 7405 7406 7424 C3' DC T 2 OK 7422 7425 7426 7443 C3' DG T 3 OK 7441 7444 7445 7465 C3' DFT T 4 OK 7463 7466 7467 7485 C3' DG T 5 OK 7483 7486 7487 7507 C3' DT T 6 OK 7505 7508 7509 7527 C3' DA T 7 OK 7525 7528 7529 7548 C3' DA T 8 OK 7546 7549 7550 7569 C3' DG T 9 OK 7567 7570 7571 7591 C3' DC T 10 OK 7589 7592 7593 7610 C3' DA T 11 OK 7608 7611 7612 7631 C3' DG T 12 OK 7629 7632 7633 7653 C3' DT T 13 OK 7651 7654 7655 7673 C3' DC T 14 OK 7671 7674 7675 7692 C3' DC T 15 OK 7690 7693 7694 7711 C3' DG T 16 OK 7709 7712 7713 7733 C3' DC T 17 OK 7731 7734 7735 7752 C3' DG T 18 OK 7750 7753 7754 7772 C3' DG P 103 OK 7770 7773 7774 7794 C3' DC P 104 OK 7792 7795 7796 7813 C3' DG P 105 OK 7811 7814 7815 7835 C3' DG P 106 OK 7833 7836 7837 7857 C3' DA P 107 OK 7855 7858 7859 7878 C3' DC P 108 OK 7876 7879 7880 7897 C3' DT P 109 OK 7895 7898 7899 7917 C3' DG P 110 OK 7915 7918 7919 7939 C3' DC P 111 OK 7937 7940 7941 7958 C3' DT P 112 OK 7956 7959 7960 7978 C3' DT P 113 OK 7976 7979 7980 7998 C3' DA P 114 OK 7996 7999 8000 8022 C3' DOC P 115 8023 8021 8041 C3' DCP A 904 OK 8042 8044 8040 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 7402 C4' DT T 1 OK 7404 7401 7403 7422 C4' DC T 2 OK 7424 7421 7423 7441 C4' DG T 3 OK 7443 7440 7442 7463 C4' DFT T 4 OK 7465 7462 7464 7483 C4' DG T 5 OK 7485 7482 7484 7505 C4' DT T 6 OK 7507 7504 7506 7525 C4' DA T 7 OK 7527 7524 7526 7546 C4' DA T 8 OK 7548 7545 7547 7567 C4' DG T 9 OK 7569 7566 7568 7589 C4' DC T 10 OK 7591 7588 7590 7608 C4' DA T 11 OK 7610 7607 7609 7629 C4' DG T 12 OK 7631 7628 7630 7651 C4' DT T 13 OK 7653 7650 7652 7671 C4' DC T 14 OK 7673 7670 7672 7690 C4' DC T 15 OK 7692 7689 7691 7709 C4' DG T 16 OK 7711 7708 7710 7731 C4' DC T 17 OK 7733 7730 7732 7750 C4' DG T 18 OK 7752 7749 7751 7770 C4' DG P 103 OK 7772 7769 7771 7792 C4' DC P 104 OK 7794 7791 7793 7811 C4' DG P 105 OK 7813 7810 7812 7833 C4' DG P 106 OK 7835 7832 7834 7855 C4' DA P 107 OK 7857 7854 7856 7876 C4' DC P 108 OK 7878 7875 7877 7895 C4' DT P 109 OK 7897 7894 7896 7915 C4' DG P 110 OK 7917 7914 7916 7937 C4' DC P 111 OK 7939 7936 7938 7956 C4' DT P 112 OK 7958 7955 7957 7976 C4' DT P 113 OK 7978 7975 7977 7996 C4' DA P 114 OK 7998 7995 7997 8023 C4' DOC P 115 OK 8022 8025 8024 8042 C4' DCP A 904 OK 8041 8045 8043 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 7401 C5' DT T 1 7400 7402 7421 C5' DC T 2 7420 7422 7440 C5' DG T 3 7439 7441 7462 C5' DFT T 4 7461 7463 7482 C5' DG T 5 7481 7483 7504 C5' DT T 6 7503 7505 7524 C5' DA T 7 7523 7525 7545 C5' DA T 8 7544 7546 7566 C5' DG T 9 7565 7567 7588 C5' DC T 10 7587 7589 7607 C5' DA T 11 7606 7608 7628 C5' DG T 12 7627 7629 7650 C5' DT T 13 7649 7651 7670 C5' DC T 14 7669 7671 7689 C5' DC T 15 7688 7690 7708 C5' DG T 16 7707 7709 7730 C5' DC T 17 7729 7731 7749 C5' DG T 18 7748 7750 7769 C5' DG P 103 7768 7770 7791 C5' DC P 104 7790 7792 7810 C5' DG P 105 7809 7811 7832 C5' DG P 106 7831 7833 7854 C5' DA P 107 7853 7855 7875 C5' DC P 108 7874 7876 7894 C5' DT P 109 7893 7895 7914 C5' DG P 110 7913 7915 7936 C5' DC P 111 7935 7937 7955 C5' DT P 112 7954 7956 7975 C5' DT P 113 7974 7976 7995 C5' DA P 114 7994 7996 8025 C5' DOC P 115 8026 8023 8045 C5' DCP A 904 8046 8042 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 7397 P DT T 1 distorted distorted 7398 7399 7400 7417 P DC T 2 distorted distorted 7405 7418 7419 7420 7436 P DG T 3 distorted distorted 7425 7437 7438 7439 7458 P DFT T 4 distorted distorted 7444 7459 7460 7461 7478 P DG T 5 distorted distorted 7466 7479 7480 7481 7500 P DT T 6 distorted distorted 7486 7501 7502 7503 7520 P DA T 7 distorted distorted 7508 7521 7522 7523 7541 P DA T 8 distorted distorted 7528 7542 7543 7544 7562 P DG T 9 distorted distorted 7549 7563 7564 7565 7584 P DC T 10 distorted distorted 7570 7585 7586 7587 7603 P DA T 11 distorted distorted 7592 7604 7605 7606 7624 P DG T 12 distorted distorted 7611 7625 7626 7627 7646 P DT T 13 distorted distorted 7632 7647 7648 7649 7666 P DC T 14 distorted distorted 7654 7667 7668 7669 7685 P DC T 15 distorted distorted 7674 7686 7687 7688 7704 P DG T 16 distorted distorted 7693 7705 7706 7707 7726 P DC T 17 distorted distorted 7712 7727 7728 7729 7745 P DG T 18 distorted distorted 7734 7746 7747 7748 7787 P DC P 104 distorted distorted 7773 7788 7789 7790 7806 P DG P 105 distorted distorted 7795 7807 7808 7809 7828 P DG P 106 distorted distorted 7814 7829 7830 7831 7850 P DA P 107 distorted distorted 7836 7851 7852 7853 7871 P DC P 108 distorted distorted 7858 7872 7873 7874 7890 P DT P 109 distorted distorted 7879 7891 7892 7893 7910 P DG P 110 distorted distorted 7898 7911 7912 7913 7932 P DC P 111 distorted distorted 7918 7933 7934 7935 7951 P DT P 112 distorted distorted 7940 7952 7953 7954 7971 P DT P 113 distorted distorted 7959 7972 7973 7974 7991 P DA P 114 distorted distorted 7979 7992 7993 7994 8027 P DOC P 115 distorted distorted 7999 8028 8029 8026 ---------------------------------------------------------------------------------