ID code: '4TZ0' 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' --------------------------------------------------------------------------------- 7733 C1' A B 1 alpha beta 7728 7750 7734 7731 7767 C1' A B 2 alpha beta 7762 7784 7768 7765 7800 C1' A B 3 alpha beta 7795 7817 7801 7798 7833 C1' A B 4 alpha beta 7828 7850 7834 7831 7866 C1' A B 5 alpha beta 7861 7883 7867 7864 7899 C1' A B 6 alpha beta 7894 7916 7900 7897 7932 C1' A B 7 alpha beta 7927 7950 7933 7930 7972 C1' GDP A 601 alpha beta 7967 7989 7973 7970 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7731 C2' A B 1 OK OK 7733 7729 7748 7732 7765 C2' A B 2 OK OK 7767 7763 7782 7766 7798 C2' A B 3 OK OK 7800 7796 7815 7799 7831 C2' A B 4 OK OK 7833 7829 7848 7832 7864 C2' A B 5 OK OK 7866 7862 7881 7865 7897 C2' A B 6 OK OK 7899 7895 7914 7898 7930 C2' A B 7 OK OK 7932 7928 7948 7931 7970 C2' GDP A 601 OK OK 7972 7968 7987 7971 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 7729 C3' A B 1 OK OK 7727 7747 7730 7731 7763 C3' A B 2 OK OK 7761 7781 7764 7765 7796 C3' A B 3 OK OK 7794 7814 7797 7798 7829 C3' A B 4 OK OK 7827 7847 7830 7831 7862 C3' A B 5 OK OK 7860 7880 7863 7864 7895 C3' A B 6 OK OK 7893 7913 7896 7897 7928 C3' A B 7 OK OK 7926 7946 7929 7930 7968 C3' GDP A 601 OK OK 7966 7985 7969 7970 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 7727 C4' A B 1 OK OK 7729 7746 7726 7728 7761 C4' A B 2 OK OK 7763 7780 7760 7762 7794 C4' A B 3 OK OK 7796 7813 7793 7795 7827 C4' A B 4 OK OK 7829 7846 7826 7828 7860 C4' A B 5 OK OK 7862 7879 7859 7861 7893 C4' A B 6 OK OK 7895 7912 7892 7894 7926 C4' A B 7 OK OK 7928 7945 7925 7927 7966 C4' GDP A 601 OK OK 7968 7984 7965 7967 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 7726 C5' A B 1 OK OK 7725 7744 7745 7727 7760 C5' A B 2 OK OK 7759 7778 7779 7761 7793 C5' A B 3 OK OK 7792 7811 7812 7794 7826 C5' A B 4 OK OK 7825 7844 7845 7827 7859 C5' A B 5 OK OK 7858 7877 7878 7860 7892 C5' A B 6 OK OK 7891 7910 7911 7893 7925 C5' A B 7 OK OK 7924 7943 7944 7926 7965 C5' GDP A 601 7964 7966 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 7756 P A B 2 distorted distorted 7730 7757 7758 7759 7789 P A B 3 distorted distorted 7764 7790 7791 7792 7822 P A B 4 distorted distorted 7797 7823 7824 7825 7855 P A B 5 distorted distorted 7830 7856 7857 7858 7888 P A B 6 distorted distorted 7863 7889 7890 7891 7921 P A B 7 distorted distorted 7896 7922 7923 7924 ---------------------------------------------------------------------------------