ID code: '4H5P' 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' --------------------------------------------------------------------------------- 7655 C1' U E 1 beta 7650 7656 7653 7675 C1' U E 2 beta 7670 7676 7673 7695 C1' U E 3 beta 7690 7696 7693 7715 C1' U E 4 beta 7710 7716 7713 7735 C1' U E 5 beta 7730 7736 7733 7755 C1' U E 6 beta 7750 7756 7753 7775 C1' U E 7 beta 7770 7776 7773 7795 C1' U E 8 beta 7790 7796 7793 7815 C1' U E 9 beta 7810 7816 7813 7835 C1' U E 10 beta 7830 7836 7833 7855 C1' U E 11 beta 7850 7856 7853 7875 C1' U E 12 beta 7870 7876 7873 7895 C1' U E 13 beta 7890 7896 7893 7915 C1' U E 14 beta 7910 7916 7913 7936 C1' U F 1 beta 7931 7937 7934 7956 C1' U F 2 beta 7951 7957 7954 7976 C1' U F 3 beta 7971 7977 7974 7996 C1' U F 4 beta 7991 7997 7994 8016 C1' U F 5 beta 8011 8017 8014 8036 C1' U F 6 beta 8031 8037 8034 8056 C1' U F 7 beta 8051 8057 8054 8076 C1' U F 8 beta 8071 8077 8074 8096 C1' U F 9 beta 8091 8097 8094 8116 C1' U F 10 beta 8111 8117 8114 8136 C1' U F 11 beta 8131 8137 8134 8156 C1' U F 12 beta 8151 8157 8154 8176 C1' U F 13 beta 8171 8177 8174 8196 C1' U F 14 beta 8191 8197 8194 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7653 C2' U E 1 OK 7655 7651 7654 7673 C2' U E 2 OK 7675 7671 7674 7693 C2' U E 3 OK 7695 7691 7694 7713 C2' U E 4 OK 7715 7711 7714 7733 C2' U E 5 OK 7735 7731 7734 7753 C2' U E 6 OK 7755 7751 7754 7773 C2' U E 7 OK 7775 7771 7774 7793 C2' U E 8 OK 7795 7791 7794 7813 C2' U E 9 OK 7815 7811 7814 7833 C2' U E 10 OK 7835 7831 7834 7853 C2' U E 11 OK 7855 7851 7854 7873 C2' U E 12 OK 7875 7871 7874 7893 C2' U E 13 OK 7895 7891 7894 7913 C2' U E 14 OK 7915 7911 7914 7934 C2' U F 1 OK 7936 7932 7935 7954 C2' U F 2 OK 7956 7952 7955 7974 C2' U F 3 OK 7976 7972 7975 7994 C2' U F 4 OK 7996 7992 7995 8014 C2' U F 5 OK 8016 8012 8015 8034 C2' U F 6 OK 8036 8032 8035 8054 C2' U F 7 OK 8056 8052 8055 8074 C2' U F 8 OK 8076 8072 8075 8094 C2' U F 9 OK 8096 8092 8095 8114 C2' U F 10 OK 8116 8112 8115 8134 C2' U F 11 OK 8136 8132 8135 8154 C2' U F 12 OK 8156 8152 8155 8174 C2' U F 13 OK 8176 8172 8175 8194 C2' U F 14 OK 8196 8192 8195 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 7651 C3' U E 1 OK 7649 7652 7653 7671 C3' U E 2 OK 7669 7672 7673 7691 C3' U E 3 OK 7689 7692 7693 7711 C3' U E 4 OK 7709 7712 7713 7731 C3' U E 5 OK 7729 7732 7733 7751 C3' U E 6 OK 7749 7752 7753 7771 C3' U E 7 OK 7769 7772 7773 7791 C3' U E 8 OK 7789 7792 7793 7811 C3' U E 9 OK 7809 7812 7813 7831 C3' U E 10 OK 7829 7832 7833 7851 C3' U E 11 OK 7849 7852 7853 7871 C3' U E 12 OK 7869 7872 7873 7891 C3' U E 13 OK 7889 7892 7893 7911 C3' U E 14 OK 7909 7912 7913 7932 C3' U F 1 OK 7930 7933 7934 7952 C3' U F 2 OK 7950 7953 7954 7972 C3' U F 3 OK 7970 7973 7974 7992 C3' U F 4 OK 7990 7993 7994 8012 C3' U F 5 OK 8010 8013 8014 8032 C3' U F 6 OK 8030 8033 8034 8052 C3' U F 7 OK 8050 8053 8054 8072 C3' U F 8 OK 8070 8073 8074 8092 C3' U F 9 OK 8090 8093 8094 8112 C3' U F 10 OK 8110 8113 8114 8132 C3' U F 11 OK 8130 8133 8134 8152 C3' U F 12 OK 8150 8153 8154 8172 C3' U F 13 OK 8170 8173 8174 8192 C3' U F 14 OK 8190 8193 8194 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 7649 C4' U E 1 OK 7651 7648 7650 7669 C4' U E 2 OK 7671 7668 7670 7689 C4' U E 3 OK 7691 7688 7690 7709 C4' U E 4 OK 7711 7708 7710 7729 C4' U E 5 OK 7731 7728 7730 7749 C4' U E 6 OK 7751 7748 7750 7769 C4' U E 7 OK 7771 7768 7770 7789 C4' U E 8 OK 7791 7788 7790 7809 C4' U E 9 OK 7811 7808 7810 7829 C4' U E 10 OK 7831 7828 7830 7849 C4' U E 11 OK 7851 7848 7850 7869 C4' U E 12 OK 7871 7868 7870 7889 C4' U E 13 OK 7891 7888 7890 7909 C4' U E 14 OK 7911 7908 7910 7930 C4' U F 1 OK 7932 7929 7931 7950 C4' U F 2 OK 7952 7949 7951 7970 C4' U F 3 OK 7972 7969 7971 7990 C4' U F 4 OK 7992 7989 7991 8010 C4' U F 5 OK 8012 8009 8011 8030 C4' U F 6 OK 8032 8029 8031 8050 C4' U F 7 OK 8052 8049 8051 8070 C4' U F 8 OK 8072 8069 8071 8090 C4' U F 9 OK 8092 8089 8091 8110 C4' U F 10 OK 8112 8109 8111 8130 C4' U F 11 OK 8132 8129 8131 8150 C4' U F 12 OK 8152 8149 8151 8170 C4' U F 13 OK 8172 8169 8171 8190 C4' U F 14 OK 8192 8189 8191 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 7648 C5' U E 1 7647 7649 7668 C5' U E 2 7667 7669 7688 C5' U E 3 7687 7689 7708 C5' U E 4 7707 7709 7728 C5' U E 5 7727 7729 7748 C5' U E 6 7747 7749 7768 C5' U E 7 7767 7769 7788 C5' U E 8 7787 7789 7808 C5' U E 9 7807 7809 7828 C5' U E 10 7827 7829 7848 C5' U E 11 7847 7849 7868 C5' U E 12 7867 7869 7888 C5' U E 13 7887 7889 7908 C5' U E 14 7907 7909 7929 C5' U F 1 7928 7930 7949 C5' U F 2 7948 7950 7969 C5' U F 3 7968 7970 7989 C5' U F 4 7988 7990 8009 C5' U F 5 8008 8010 8029 C5' U F 6 8028 8030 8049 C5' U F 7 8048 8050 8069 C5' U F 8 8068 8070 8089 C5' U F 9 8088 8090 8109 C5' U F 10 8108 8110 8129 C5' U F 11 8128 8130 8149 C5' U F 12 8148 8150 8169 C5' U F 13 8168 8170 8189 C5' U F 14 8188 8190 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 7645 P U E 1 7646 7647 7664 P U E 2 distorted distorted 7652 7665 7666 7667 7684 P U E 3 distorted distorted 7672 7685 7686 7687 7704 P U E 4 distorted distorted 7692 7705 7706 7707 7724 P U E 5 distorted distorted 7712 7725 7726 7727 7744 P U E 6 distorted distorted 7732 7745 7746 7747 7764 P U E 7 distorted distorted 7752 7765 7766 7767 7784 P U E 8 distorted distorted 7772 7785 7786 7787 7804 P U E 9 distorted distorted 7792 7805 7806 7807 7824 P U E 10 distorted distorted 7812 7825 7826 7827 7844 P U E 11 distorted distorted 7832 7845 7846 7847 7864 P U E 12 distorted distorted 7852 7865 7866 7867 7884 P U E 13 distorted distorted 7872 7885 7886 7887 7904 P U E 14 distorted distorted 7892 7905 7906 7907 7925 P U F 1 OK OK 7926 7927 7928 7945 P U F 2 distorted distorted 7933 7946 7947 7948 7965 P U F 3 distorted distorted 7953 7966 7967 7968 7985 P U F 4 distorted distorted 7973 7986 7987 7988 8005 P U F 5 distorted distorted 7993 8006 8007 8008 8025 P U F 6 distorted distorted 8013 8026 8027 8028 8045 P U F 7 distorted distorted 8033 8046 8047 8048 8065 P U F 8 distorted distorted 8053 8066 8067 8068 8085 P U F 9 distorted distorted 8073 8086 8087 8088 8105 P U F 10 distorted distorted 8093 8106 8107 8108 8125 P U F 11 distorted distorted 8113 8126 8127 8128 8145 P U F 12 distorted distorted 8133 8146 8147 8148 8165 P U F 13 distorted distorted 8153 8166 8167 8168 8185 P U F 14 distorted distorted 8173 8186 8187 8188 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