ID code: '4ALP' 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' --------------------------------------------------------------------------------- 2796 C1' U E 1 beta 2791 2797 2794 2816 C1' U E 2 beta 2811 2817 2814 2836 C1' U E 3 beta 2831 2837 2834 2854 C1' U E 4 beta 2849 2855 2852 2874 C1' U E 5 beta 2869 2875 2872 2894 C1' U E 6 beta 2889 2895 2892 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2794 C2' U E 1 OK 2796 2792 2795 2814 C2' U E 2 OK 2816 2812 2815 2834 C2' U E 3 OK 2836 2832 2835 2852 C2' U E 4 OK 2854 2850 2853 2872 C2' U E 5 OK 2874 2870 2873 2892 C2' U E 6 OK 2894 2890 2893 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2792 C3' U E 1 OK 2790 2793 2794 2812 C3' U E 2 OK 2810 2813 2814 2832 C3' U E 3 OK 2830 2833 2834 2850 C3' U E 4 OK 2848 2851 2852 2870 C3' U E 5 OK 2868 2871 2872 2890 C3' U E 6 OK 2888 2891 2892 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2790 C4' U E 1 OK 2792 2789 2791 2810 C4' U E 2 OK 2812 2809 2811 2830 C4' U E 3 OK 2832 2829 2831 2848 C4' U E 4 OK 2850 2847 2849 2868 C4' U E 5 OK 2870 2867 2869 2888 C4' U E 6 OK 2890 2887 2889 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2789 C5' U E 1 2788 2790 2809 C5' U E 2 2808 2810 2829 C5' U E 3 2828 2830 2847 C5' U E 4 2846 2848 2867 C5' U E 5 2866 2868 2887 C5' U E 6 2886 2888 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2805 P U E 2 distorted distorted 2793 2806 2807 2808 2825 P U E 3 distorted distorted 2813 2826 2827 2828 2843 P U E 4 distorted distorted 2833 2844 2845 2846 2863 P U E 5 distorted distorted 2851 2864 2865 2866 2883 P U E 6 distorted distorted 2871 2884 2885 2886 ---------------------------------------------------------------------------------