ID code: '3NCI' 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' --------------------------------------------------------------------------------- 7564 C1' DT T 1 beta 7560 7565 7563 7584 C1' DC T 2 beta 7580 7585 7583 7603 C1' DA T 3 beta 7599 7604 7602 7624 C1' DG T 4 beta 7620 7625 7623 7646 C1' DG T 5 beta 7642 7647 7645 7668 C1' DT T 6 beta 7664 7669 7667 7688 C1' DA T 7 beta 7684 7689 7687 7709 C1' DA T 8 beta 7705 7710 7708 7730 C1' DG T 9 beta 7726 7731 7729 7752 C1' DC T 10 beta 7748 7753 7751 7771 C1' DA T 11 beta 7767 7772 7770 7792 C1' DG T 12 beta 7788 7793 7791 7814 C1' DT T 13 beta 7810 7815 7813 7834 C1' DC T 14 beta 7830 7835 7833 7853 C1' DC T 15 beta 7849 7854 7852 7872 C1' DG T 16 beta 7868 7873 7871 7894 C1' DC T 17 beta 7890 7895 7893 7913 C1' DG T 18 beta 7909 7914 7912 7933 C1' DG P 103 beta 7929 7934 7932 7955 C1' DC P 104 beta 7951 7956 7954 7974 C1' DG P 105 beta 7970 7975 7973 7996 C1' DG P 106 beta 7992 7997 7995 8018 C1' DA P 107 beta 8014 8019 8017 8039 C1' DC P 108 beta 8035 8040 8038 8058 C1' DT P 109 beta 8054 8059 8057 8078 C1' DG P 110 beta 8074 8079 8077 8100 C1' DC P 111 beta 8096 8101 8099 8119 C1' DT P 112 beta 8115 8120 8118 8139 C1' DT P 113 beta 8135 8140 8138 8159 C1' DA P 114 beta 8155 8160 8158 8178 C1' DOC P 115 beta 8182 8170 8179 8197 C1' DCP A 904 beta 8201 8189 8198 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7563 C2' DT T 1 7564 7561 7583 C2' DC T 2 7584 7581 7602 C2' DA T 3 7603 7600 7623 C2' DG T 4 7624 7621 7645 C2' DG T 5 7646 7643 7667 C2' DT T 6 7668 7665 7687 C2' DA T 7 7688 7685 7708 C2' DA T 8 7709 7706 7729 C2' DG T 9 7730 7727 7751 C2' DC T 10 7752 7749 7770 C2' DA T 11 7771 7768 7791 C2' DG T 12 7792 7789 7813 C2' DT T 13 7814 7811 7833 C2' DC T 14 7834 7831 7852 C2' DC T 15 7853 7850 7871 C2' DG T 16 7872 7869 7893 C2' DC T 17 7894 7891 7912 C2' DG T 18 7913 7910 7932 C2' DG P 103 7933 7930 7954 C2' DC P 104 7955 7952 7973 C2' DG P 105 7974 7971 7995 C2' DG P 106 7996 7993 8017 C2' DA P 107 8018 8015 8038 C2' DC P 108 8039 8036 8057 C2' DT P 109 8058 8055 8077 C2' DG P 110 8078 8075 8099 C2' DC P 111 8100 8097 8118 C2' DT P 112 8119 8116 8138 C2' DT P 113 8139 8136 8158 C2' DA P 114 8159 8156 8179 C2' DOC P 115 8178 8180 8198 C2' DCP A 904 8197 8199 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 7561 C3' DT T 1 OK 7559 7562 7563 7581 C3' DC T 2 OK 7579 7582 7583 7600 C3' DA T 3 OK 7598 7601 7602 7621 C3' DG T 4 OK 7619 7622 7623 7643 C3' DG T 5 OK 7641 7644 7645 7665 C3' DT T 6 OK 7663 7666 7667 7685 C3' DA T 7 OK 7683 7686 7687 7706 C3' DA T 8 OK 7704 7707 7708 7727 C3' DG T 9 OK 7725 7728 7729 7749 C3' DC T 10 OK 7747 7750 7751 7768 C3' DA T 11 OK 7766 7769 7770 7789 C3' DG T 12 OK 7787 7790 7791 7811 C3' DT T 13 OK 7809 7812 7813 7831 C3' DC T 14 OK 7829 7832 7833 7850 C3' DC T 15 OK 7848 7851 7852 7869 C3' DG T 16 OK 7867 7870 7871 7891 C3' DC T 17 OK 7889 7892 7893 7910 C3' DG T 18 OK 7908 7911 7912 7930 C3' DG P 103 OK 7928 7931 7932 7952 C3' DC P 104 OK 7950 7953 7954 7971 C3' DG P 105 OK 7969 7972 7973 7993 C3' DG P 106 OK 7991 7994 7995 8015 C3' DA P 107 OK 8013 8016 8017 8036 C3' DC P 108 OK 8034 8037 8038 8055 C3' DT P 109 OK 8053 8056 8057 8075 C3' DG P 110 OK 8073 8076 8077 8097 C3' DC P 111 OK 8095 8098 8099 8116 C3' DT P 112 OK 8114 8117 8118 8136 C3' DT P 113 OK 8134 8137 8138 8156 C3' DA P 114 OK 8154 8157 8158 8180 C3' DOC P 115 8181 8179 8199 C3' DCP A 904 OK 8200 8202 8198 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 7559 C4' DT T 1 OK 7561 7558 7560 7579 C4' DC T 2 OK 7581 7578 7580 7598 C4' DA T 3 OK 7600 7597 7599 7619 C4' DG T 4 OK 7621 7618 7620 7641 C4' DG T 5 OK 7643 7640 7642 7663 C4' DT T 6 OK 7665 7662 7664 7683 C4' DA T 7 OK 7685 7682 7684 7704 C4' DA T 8 OK 7706 7703 7705 7725 C4' DG T 9 OK 7727 7724 7726 7747 C4' DC T 10 OK 7749 7746 7748 7766 C4' DA T 11 OK 7768 7765 7767 7787 C4' DG T 12 OK 7789 7786 7788 7809 C4' DT T 13 OK 7811 7808 7810 7829 C4' DC T 14 OK 7831 7828 7830 7848 C4' DC T 15 OK 7850 7847 7849 7867 C4' DG T 16 OK 7869 7866 7868 7889 C4' DC T 17 OK 7891 7888 7890 7908 C4' DG T 18 OK 7910 7907 7909 7928 C4' DG P 103 OK 7930 7927 7929 7950 C4' DC P 104 OK 7952 7949 7951 7969 C4' DG P 105 OK 7971 7968 7970 7991 C4' DG P 106 OK 7993 7990 7992 8013 C4' DA P 107 OK 8015 8012 8014 8034 C4' DC P 108 OK 8036 8033 8035 8053 C4' DT P 109 OK 8055 8052 8054 8073 C4' DG P 110 OK 8075 8072 8074 8095 C4' DC P 111 OK 8097 8094 8096 8114 C4' DT P 112 OK 8116 8113 8115 8134 C4' DT P 113 OK 8136 8133 8135 8154 C4' DA P 114 OK 8156 8153 8155 8181 C4' DOC P 115 OK 8180 8183 8182 8200 C4' DCP A 904 OK 8199 8203 8201 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 7558 C5' DT T 1 7557 7559 7578 C5' DC T 2 7577 7579 7597 C5' DA T 3 7596 7598 7618 C5' DG T 4 7617 7619 7640 C5' DG T 5 7639 7641 7662 C5' DT T 6 7661 7663 7682 C5' DA T 7 7681 7683 7703 C5' DA T 8 7702 7704 7724 C5' DG T 9 7723 7725 7746 C5' DC T 10 7745 7747 7765 C5' DA T 11 7764 7766 7786 C5' DG T 12 7785 7787 7808 C5' DT T 13 7807 7809 7828 C5' DC T 14 7827 7829 7847 C5' DC T 15 7846 7848 7866 C5' DG T 16 7865 7867 7888 C5' DC T 17 7887 7889 7907 C5' DG T 18 7906 7908 7927 C5' DG P 103 7926 7928 7949 C5' DC P 104 7948 7950 7968 C5' DG P 105 7967 7969 7990 C5' DG P 106 7989 7991 8012 C5' DA P 107 8011 8013 8033 C5' DC P 108 8032 8034 8052 C5' DT P 109 8051 8053 8072 C5' DG P 110 8071 8073 8094 C5' DC P 111 8093 8095 8113 C5' DT P 112 8112 8114 8133 C5' DT P 113 8132 8134 8153 C5' DA P 114 8152 8154 8183 C5' DOC P 115 8184 8181 8203 C5' DCP A 904 8204 8200 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 7574 P DC T 2 distorted distorted 7562 7575 7576 7577 7593 P DA T 3 distorted distorted 7582 7594 7595 7596 7614 P DG T 4 distorted distorted 7601 7615 7616 7617 7636 P DG T 5 distorted distorted 7622 7637 7638 7639 7658 P DT T 6 distorted distorted 7644 7659 7660 7661 7678 P DA T 7 distorted distorted 7666 7679 7680 7681 7699 P DA T 8 distorted distorted 7686 7700 7701 7702 7720 P DG T 9 distorted distorted 7707 7721 7722 7723 7742 P DC T 10 distorted distorted 7728 7743 7744 7745 7761 P DA T 11 distorted distorted 7750 7762 7763 7764 7782 P DG T 12 distorted distorted 7769 7783 7784 7785 7804 P DT T 13 distorted distorted 7790 7805 7806 7807 7824 P DC T 14 distorted distorted 7812 7825 7826 7827 7843 P DC T 15 distorted distorted 7832 7844 7845 7846 7862 P DG T 16 distorted distorted 7851 7863 7864 7865 7884 P DC T 17 distorted distorted 7870 7885 7886 7887 7903 P DG T 18 distorted distorted 7892 7904 7905 7906 7945 P DC P 104 distorted distorted 7931 7946 7947 7948 7964 P DG P 105 distorted distorted 7953 7965 7966 7967 7986 P DG P 106 distorted distorted 7972 7987 7988 7989 8008 P DA P 107 distorted distorted 7994 8009 8010 8011 8029 P DC P 108 distorted distorted 8016 8030 8031 8032 8048 P DT P 109 distorted distorted 8037 8049 8050 8051 8068 P DG P 110 distorted distorted 8056 8069 8070 8071 8090 P DC P 111 distorted distorted 8076 8091 8092 8093 8109 P DT P 112 distorted distorted 8098 8110 8111 8112 8129 P DT P 113 distorted distorted 8117 8130 8131 8132 8149 P DA P 114 distorted distorted 8137 8150 8151 8152 8185 P DOC P 115 distorted distorted 8157 8186 8187 8184 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