ID code: '3SQ1' 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' --------------------------------------------------------------------------------- 7451 C1' DT T 1 beta 7447 7452 7450 7471 C1' DC T 2 beta 7467 7472 7470 7490 C1' DG T 3 beta 7486 7491 7489 7512 C1' DA T 4 beta 7508 7513 7511 7533 C1' DG T 5 beta 7529 7534 7532 7555 C1' DT T 6 beta 7551 7556 7554 7575 C1' DA T 7 beta 7571 7576 7574 7596 C1' DA T 8 beta 7592 7597 7595 7617 C1' DG T 9 beta 7613 7618 7616 7639 C1' DC T 10 beta 7635 7640 7638 7658 C1' DA T 11 beta 7654 7659 7657 7679 C1' DG T 12 beta 7675 7680 7678 7701 C1' DT T 13 beta 7697 7702 7700 7721 C1' DC T 14 beta 7717 7722 7720 7740 C1' DC T 15 beta 7736 7741 7739 7759 C1' DG T 16 beta 7755 7760 7758 7781 C1' DC T 17 beta 7777 7782 7780 7800 C1' DG T 18 beta 7796 7801 7799 7820 C1' DG P 103 beta 7816 7821 7819 7842 C1' DC P 104 beta 7838 7843 7841 7861 C1' DG P 105 beta 7857 7862 7860 7883 C1' DG P 106 beta 7879 7884 7882 7905 C1' DA P 107 beta 7901 7906 7904 7926 C1' DC P 108 beta 7922 7927 7925 7945 C1' DT P 109 beta 7941 7946 7944 7965 C1' DG P 110 beta 7961 7966 7964 7987 C1' DC P 111 beta 7983 7988 7986 8006 C1' DT P 112 beta 8002 8007 8005 8026 C1' DT P 113 beta 8022 8027 8025 8046 C1' DA P 114 beta 8042 8047 8045 8065 C1' DOC P 115 beta 8069 8057 8066 8084 C1' DUP A 902 beta 8088 8083 8085 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7450 C2' DT T 1 7451 7448 7470 C2' DC T 2 7471 7468 7489 C2' DG T 3 7490 7487 7511 C2' DA T 4 7512 7509 7532 C2' DG T 5 7533 7530 7554 C2' DT T 6 7555 7552 7574 C2' DA T 7 7575 7572 7595 C2' DA T 8 7596 7593 7616 C2' DG T 9 7617 7614 7638 C2' DC T 10 7639 7636 7657 C2' DA T 11 7658 7655 7678 C2' DG T 12 7679 7676 7700 C2' DT T 13 7701 7698 7720 C2' DC T 14 7721 7718 7739 C2' DC T 15 7740 7737 7758 C2' DG T 16 7759 7756 7780 C2' DC T 17 7781 7778 7799 C2' DG T 18 7800 7797 7819 C2' DG P 103 7820 7817 7841 C2' DC P 104 7842 7839 7860 C2' DG P 105 7861 7858 7882 C2' DG P 106 7883 7880 7904 C2' DA P 107 7905 7902 7925 C2' DC P 108 7926 7923 7944 C2' DT P 109 7945 7942 7964 C2' DG P 110 7965 7962 7986 C2' DC P 111 7987 7984 8005 C2' DT P 112 8006 8003 8025 C2' DT P 113 8026 8023 8045 C2' DA P 114 8046 8043 8066 C2' DOC P 115 8065 8067 8085 C2' DUP A 902 8084 8086 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 7448 C3' DT T 1 OK 7446 7449 7450 7468 C3' DC T 2 OK 7466 7469 7470 7487 C3' DG T 3 OK 7485 7488 7489 7509 C3' DA T 4 OK 7507 7510 7511 7530 C3' DG T 5 OK 7528 7531 7532 7552 C3' DT T 6 OK 7550 7553 7554 7572 C3' DA T 7 OK 7570 7573 7574 7593 C3' DA T 8 OK 7591 7594 7595 7614 C3' DG T 9 OK 7612 7615 7616 7636 C3' DC T 10 OK 7634 7637 7638 7655 C3' DA T 11 OK 7653 7656 7657 7676 C3' DG T 12 OK 7674 7677 7678 7698 C3' DT T 13 OK 7696 7699 7700 7718 C3' DC T 14 OK 7716 7719 7720 7737 C3' DC T 15 OK 7735 7738 7739 7756 C3' DG T 16 OK 7754 7757 7758 7778 C3' DC T 17 OK 7776 7779 7780 7797 C3' DG T 18 OK 7795 7798 7799 7817 C3' DG P 103 OK 7815 7818 7819 7839 C3' DC P 104 OK 7837 7840 7841 7858 C3' DG P 105 OK 7856 7859 7860 7880 C3' DG P 106 OK 7878 7881 7882 7902 C3' DA P 107 OK 7900 7903 7904 7923 C3' DC P 108 OK 7921 7924 7925 7942 C3' DT P 109 OK 7940 7943 7944 7962 C3' DG P 110 OK 7960 7963 7964 7984 C3' DC P 111 OK 7982 7985 7986 8003 C3' DT P 112 OK 8001 8004 8005 8023 C3' DT P 113 OK 8021 8024 8025 8043 C3' DA P 114 OK 8041 8044 8045 8067 C3' DOC P 115 8068 8066 8086 C3' DUP A 902 OK 8089 8087 8085 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 7446 C4' DT T 1 OK 7448 7445 7447 7466 C4' DC T 2 OK 7468 7465 7467 7485 C4' DG T 3 OK 7487 7484 7486 7507 C4' DA T 4 OK 7509 7506 7508 7528 C4' DG T 5 OK 7530 7527 7529 7550 C4' DT T 6 OK 7552 7549 7551 7570 C4' DA T 7 OK 7572 7569 7571 7591 C4' DA T 8 OK 7593 7590 7592 7612 C4' DG T 9 OK 7614 7611 7613 7634 C4' DC T 10 OK 7636 7633 7635 7653 C4' DA T 11 OK 7655 7652 7654 7674 C4' DG T 12 OK 7676 7673 7675 7696 C4' DT T 13 OK 7698 7695 7697 7716 C4' DC T 14 OK 7718 7715 7717 7735 C4' DC T 15 OK 7737 7734 7736 7754 C4' DG T 16 OK 7756 7753 7755 7776 C4' DC T 17 OK 7778 7775 7777 7795 C4' DG T 18 OK 7797 7794 7796 7815 C4' DG P 103 OK 7817 7814 7816 7837 C4' DC P 104 OK 7839 7836 7838 7856 C4' DG P 105 OK 7858 7855 7857 7878 C4' DG P 106 OK 7880 7877 7879 7900 C4' DA P 107 OK 7902 7899 7901 7921 C4' DC P 108 OK 7923 7920 7922 7940 C4' DT P 109 OK 7942 7939 7941 7960 C4' DG P 110 OK 7962 7959 7961 7982 C4' DC P 111 OK 7984 7981 7983 8001 C4' DT P 112 OK 8003 8000 8002 8021 C4' DT P 113 OK 8023 8020 8022 8041 C4' DA P 114 OK 8043 8040 8042 8068 C4' DOC P 115 OK 8067 8070 8069 8089 C4' DUP A 902 OK 8086 8090 8088 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 7445 C5' DT T 1 7444 7446 7465 C5' DC T 2 7464 7466 7484 C5' DG T 3 7483 7485 7506 C5' DA T 4 7505 7507 7527 C5' DG T 5 7526 7528 7549 C5' DT T 6 7548 7550 7569 C5' DA T 7 7568 7570 7590 C5' DA T 8 7589 7591 7611 C5' DG T 9 7610 7612 7633 C5' DC T 10 7632 7634 7652 C5' DA T 11 7651 7653 7673 C5' DG T 12 7672 7674 7695 C5' DT T 13 7694 7696 7715 C5' DC T 14 7714 7716 7734 C5' DC T 15 7733 7735 7753 C5' DG T 16 7752 7754 7775 C5' DC T 17 7774 7776 7794 C5' DG T 18 7793 7795 7814 C5' DG P 103 7813 7815 7836 C5' DC P 104 7835 7837 7855 C5' DG P 105 7854 7856 7877 C5' DG P 106 7876 7878 7899 C5' DA P 107 7898 7900 7920 C5' DC P 108 7919 7921 7939 C5' DT P 109 7938 7940 7959 C5' DG P 110 7958 7960 7981 C5' DC P 111 7980 7982 8000 C5' DT P 112 7999 8001 8020 C5' DT P 113 8019 8021 8040 C5' DA P 114 8039 8041 8070 C5' DOC P 115 8071 8068 8090 C5' DUP A 902 8091 8089 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 7461 P DC T 2 distorted distorted 7449 7462 7463 7464 7480 P DG T 3 distorted distorted 7469 7481 7482 7483 7502 P DA T 4 distorted distorted 7488 7503 7504 7505 7523 P DG T 5 distorted distorted 7510 7524 7525 7526 7545 P DT T 6 distorted distorted 7531 7546 7547 7548 7565 P DA T 7 distorted distorted 7553 7566 7567 7568 7586 P DA T 8 distorted distorted 7573 7587 7588 7589 7607 P DG T 9 distorted distorted 7594 7608 7609 7610 7629 P DC T 10 distorted distorted 7615 7630 7631 7632 7648 P DA T 11 distorted distorted 7637 7649 7650 7651 7669 P DG T 12 distorted distorted 7656 7670 7671 7672 7691 P DT T 13 distorted distorted 7677 7692 7693 7694 7711 P DC T 14 distorted distorted 7699 7712 7713 7714 7730 P DC T 15 distorted distorted 7719 7731 7732 7733 7749 P DG T 16 distorted distorted 7738 7750 7751 7752 7771 P DC T 17 distorted distorted 7757 7772 7773 7774 7790 P DG T 18 distorted distorted 7779 7791 7792 7793 7832 P DC P 104 distorted distorted 7818 7833 7834 7835 7851 P DG P 105 distorted distorted 7840 7852 7853 7854 7873 P DG P 106 distorted distorted 7859 7874 7875 7876 7895 P DA P 107 distorted distorted 7881 7896 7897 7898 7916 P DC P 108 distorted distorted 7903 7917 7918 7919 7935 P DT P 109 distorted distorted 7924 7936 7937 7938 7955 P DG P 110 distorted distorted 7943 7956 7957 7958 7977 P DC P 111 distorted distorted 7963 7978 7979 7980 7996 P DT P 112 distorted distorted 7985 7997 7998 7999 8016 P DT P 113 distorted distorted 8004 8017 8018 8019 8036 P DA P 114 distorted distorted 8024 8037 8038 8039 8072 P DOC P 115 distorted distorted 8044 8073 8074 8071 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