ID code: '3Q0Q' 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' --------------------------------------------------------------------------------- 2793 C1' U B 1 beta 2788 2794 2791 2813 C1' G B 2 beta 2808 2814 2811 2836 C1' U B 3 beta 2831 2837 2834 2856 C1' A B 4 beta 2851 2857 2854 2878 C1' A B 5 beta 2873 2879 2876 2900 C1' A B 6 beta 2895 2901 2898 2922 C1' U B 7 beta 2917 2923 2920 2942 C1' A B 8 beta 2937 2943 2940 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2791 C2' U B 1 OK 2793 2789 2792 2811 C2' G B 2 OK 2813 2809 2812 2834 C2' U B 3 OK 2836 2832 2835 2854 C2' A B 4 OK 2856 2852 2855 2876 C2' A B 5 OK 2878 2874 2877 2898 C2' A B 6 OK 2900 2896 2899 2920 C2' U B 7 OK 2922 2918 2921 2940 C2' A B 8 OK 2942 2938 2941 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2789 C3' U B 1 OK 2787 2790 2791 2809 C3' G B 2 OK 2807 2810 2811 2832 C3' U B 3 OK 2830 2833 2834 2852 C3' A B 4 OK 2850 2853 2854 2874 C3' A B 5 OK 2872 2875 2876 2896 C3' A B 6 OK 2894 2897 2898 2918 C3' U B 7 OK 2916 2919 2920 2938 C3' A B 8 OK 2936 2939 2940 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2787 C4' U B 1 OK 2789 2786 2788 2807 C4' G B 2 OK 2809 2806 2808 2830 C4' U B 3 OK 2832 2829 2831 2850 C4' A B 4 OK 2852 2849 2851 2872 C4' A B 5 OK 2874 2871 2873 2894 C4' A B 6 OK 2896 2893 2895 2916 C4' U B 7 OK 2918 2915 2917 2936 C4' A B 8 OK 2938 2935 2937 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2786 C5' U B 1 2785 2787 2806 C5' G B 2 2805 2807 2829 C5' U B 3 2828 2830 2849 C5' A B 4 2848 2850 2871 C5' A B 5 2870 2872 2893 C5' A B 6 2892 2894 2915 C5' U B 7 2914 2916 2935 C5' A B 8 2934 2936 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2802 P G B 2 distorted distorted 2790 2803 2804 2805 2825 P U B 3 distorted distorted 2810 2826 2827 2828 2845 P A B 4 distorted distorted 2833 2846 2847 2848 2867 P A B 5 distorted distorted 2853 2868 2869 2870 2889 P A B 6 distorted distorted 2875 2890 2891 2892 2911 P U B 7 distorted distorted 2897 2912 2913 2914 2931 P A B 8 distorted distorted 2919 2932 2933 2934 ---------------------------------------------------------------------------------