ID code: '3VAM' 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' --------------------------------------------------------------------------------- 2693 C1' DC P 2 beta 2689 2694 2692 2712 C1' DU P 3 beta 2708 2713 2711 2731 C1' DU P 4 beta 2727 2732 2730 2749 C1' BRU P 5 beta 2754 2740 2750 2770 C1' DU P 6 beta 2766 2771 2769 2789 C1' DU P 7 beta 2785 2790 2788 2847 C1' DU E 3 beta 2843 2848 2846 2866 C1' DU E 4 beta 2862 2867 2865 2884 C1' BRU E 5 beta 2889 2875 2885 2905 C1' DU E 6 beta 2901 2906 2904 2924 C1' DU E 7 beta 2920 2925 2923 2936 C1' DIO A 401 2939 2942 C1' DIO A 402 2945 2991 C1' DIO B 402 2994 2997 C1' DIO B 403 3000 3003 C1' DIO B 404 3006 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2692 C2' DC P 2 2693 2690 2711 C2' DU P 3 2712 2709 2730 C2' DU P 4 2731 2728 2750 C2' BRU P 5 2749 2751 2769 C2' DU P 6 2770 2767 2788 C2' DU P 7 2789 2786 2846 C2' DU E 3 2847 2844 2865 C2' DU E 4 2866 2863 2885 C2' BRU E 5 2884 2886 2904 C2' DU E 6 2905 2902 2923 C2' DU E 7 2924 2921 2937 C2' DIO A 401 2943 C2' DIO A 402 2992 C2' DIO B 402 2998 C2' DIO B 403 3004 C2' DIO B 404 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2690 C3' DC P 2 OK 2688 2691 2692 2709 C3' DU P 3 OK 2707 2710 2711 2728 C3' DU P 4 OK 2726 2729 2730 2751 C3' BRU P 5 OK 2752 2753 2750 2767 C3' DU P 6 OK 2765 2768 2769 2786 C3' DU P 7 OK 2784 2787 2788 2844 C3' DU E 3 OK 2842 2845 2846 2863 C3' DU E 4 OK 2861 2864 2865 2886 C3' BRU E 5 OK 2887 2888 2885 2902 C3' DU E 6 OK 2900 2903 2904 2921 C3' DU E 7 OK 2919 2922 2923 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2688 C4' DC P 2 OK 2690 2687 2689 2707 C4' DU P 3 OK 2709 2706 2708 2726 C4' DU P 4 OK 2728 2725 2727 2752 C4' BRU P 5 OK 2751 2755 2754 2765 C4' DU P 6 OK 2767 2764 2766 2784 C4' DU P 7 OK 2786 2783 2785 2842 C4' DU E 3 OK 2844 2841 2843 2861 C4' DU E 4 OK 2863 2860 2862 2887 C4' BRU E 5 OK 2886 2890 2889 2900 C4' DU E 6 OK 2902 2899 2901 2919 C4' DU E 7 OK 2921 2918 2920 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2687 C5' DC P 2 2686 2688 2706 C5' DU P 3 2705 2707 2725 C5' DU P 4 2724 2726 2755 C5' BRU P 5 2756 2752 2764 C5' DU P 6 2763 2765 2783 C5' DU P 7 2782 2784 2841 C5' DU E 3 2840 2842 2860 C5' DU E 4 2859 2861 2890 C5' BRU E 5 2891 2887 2899 C5' DU E 6 2898 2900 2918 C5' DU E 7 2917 2919 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2683 P DC P 2 distorted distorted 2684 2685 2686 2702 P DU P 3 distorted distorted 2691 2703 2704 2705 2721 P DU P 4 distorted distorted 2710 2722 2723 2724 2757 P BRU P 5 distorted distorted 2729 2758 2759 2756 2760 P DU P 6 distorted distorted 2753 2761 2762 2763 2779 P DU P 7 distorted distorted 2768 2780 2781 2782 2799 P DC E 2 2800 P DC E 2 2837 P DU E 3 distorted distorted 2838 2839 2840 2856 P DU E 4 distorted distorted 2845 2857 2858 2859 2892 P BRU E 5 distorted distorted 2864 2893 2894 2891 2895 P DU E 6 distorted distorted 2888 2896 2897 2898 2914 P DU E 7 distorted distorted 2903 2915 2916 2917 ---------------------------------------------------------------------------------