ID code: '4TU9' 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' --------------------------------------------------------------------------------- 2713 C1' DU P 1 beta 2709 2714 2712 2770 C1' DU P 3 beta 2766 2771 2769 2789 C1' DU P 4 beta 2785 2790 2788 2807 C1' BRU P 5 beta 2812 2798 2808 2828 C1' DG P 6 beta 2824 2829 2827 2848 C1' DU E 1 beta 2844 2849 2847 2867 C1' DU E 2 beta 2863 2868 2866 2886 C1' DU E 3 beta 2882 2887 2885 2905 C1' DU E 4 beta 2901 2906 2904 2923 C1' BRU E 5 beta 2928 2914 2924 2985 C1' DIO A 401 2988 2991 C1' DIO A 402 2994 2997 C1' DIO A 403 3000 3024 C1' DIO B 401 3027 3030 C1' DIO B 402 3033 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2712 C2' DU P 1 2713 2710 2769 C2' DU P 3 2770 2767 2788 C2' DU P 4 2789 2786 2808 C2' BRU P 5 2807 2809 2827 C2' DG P 6 2828 2825 2847 C2' DU E 1 2848 2845 2866 C2' DU E 2 2867 2864 2885 C2' DU E 3 2886 2883 2904 C2' DU E 4 2905 2902 2924 C2' BRU E 5 2923 2925 2986 C2' DIO A 401 2992 C2' DIO A 402 2998 C2' DIO A 403 3025 C2' DIO B 401 3031 C2' DIO B 402 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2710 C3' DU P 1 OK 2708 2711 2712 2767 C3' DU P 3 OK 2765 2768 2769 2786 C3' DU P 4 OK 2784 2787 2788 2809 C3' BRU P 5 OK 2810 2811 2808 2825 C3' DG P 6 OK 2823 2826 2827 2845 C3' DU E 1 OK 2843 2846 2847 2864 C3' DU E 2 OK 2862 2865 2866 2883 C3' DU E 3 OK 2881 2884 2885 2902 C3' DU E 4 OK 2900 2903 2904 2925 C3' BRU E 5 OK 2926 2927 2924 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2708 C4' DU P 1 OK 2710 2707 2709 2765 C4' DU P 3 OK 2767 2764 2766 2784 C4' DU P 4 OK 2786 2783 2785 2810 C4' BRU P 5 OK 2809 2813 2812 2823 C4' DG P 6 OK 2825 2822 2824 2843 C4' DU E 1 OK 2845 2842 2844 2862 C4' DU E 2 OK 2864 2861 2863 2881 C4' DU E 3 OK 2883 2880 2882 2900 C4' DU E 4 OK 2902 2899 2901 2926 C4' BRU E 5 OK 2925 2929 2928 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2707 C5' DU P 1 2706 2708 2764 C5' DU P 3 2763 2765 2783 C5' DU P 4 2782 2784 2813 C5' BRU P 5 2814 2810 2822 C5' DG P 6 2821 2823 2842 C5' DU E 1 2841 2843 2861 C5' DU E 2 2860 2862 2880 C5' DU E 3 2879 2881 2899 C5' DU E 4 2898 2900 2929 C5' BRU E 5 2930 2926 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2722 P DU P 2 2711 2723 P DU P 2 2711 2760 P DU P 3 distorted distorted 2761 2762 2763 2779 P DU P 4 distorted distorted 2768 2780 2781 2782 2815 P BRU P 5 distorted distorted 2787 2816 2817 2814 2818 P DG P 6 distorted distorted 2811 2819 2820 2821 2857 P DU E 2 distorted distorted 2846 2858 2859 2860 2876 P DU E 3 distorted distorted 2865 2877 2878 2879 2895 P DU E 4 distorted distorted 2884 2896 2897 2898 2931 P BRU E 5 distorted distorted 2903 2932 2933 2930 2934 P DG E 6 2927 2935 P DG E 6 2927 2978 P DU E 7 ---------------------------------------------------------------------------------