ID code: '4TU8' 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' --------------------------------------------------------------------------------- 2715 C1' DU P 1 beta 2711 2716 2714 2772 C1' DU P 3 beta 2768 2773 2771 2791 C1' DU P 4 beta 2787 2792 2790 2809 C1' BRU P 5 beta 2814 2800 2810 2830 C1' DA P 6 beta 2826 2831 2829 2851 C1' DU P 7 beta 2847 2852 2850 2868 C1' DU E 1 beta 2864 2869 2867 2887 C1' DU E 2 beta 2883 2888 2886 2906 C1' DU E 3 beta 2902 2907 2905 2925 C1' DU E 4 beta 2921 2926 2924 2943 C1' BRU E 5 beta 2948 2934 2944 2964 C1' DA E 6 beta 2960 2965 2963 2978 C1' DIO A 401 2981 2984 C1' DIO A 402 2987 3026 C1' DIO B 401 3029 3032 C1' DIO B 402 3035 3038 C1' DIO B 403 3041 3044 C1' DIO B 404 3047 3050 C1' DIO B 405 3053 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2714 C2' DU P 1 2715 2712 2771 C2' DU P 3 2772 2769 2790 C2' DU P 4 2791 2788 2810 C2' BRU P 5 2809 2811 2829 C2' DA P 6 2830 2827 2850 C2' DU P 7 2851 2848 2867 C2' DU E 1 2868 2865 2886 C2' DU E 2 2887 2884 2905 C2' DU E 3 2906 2903 2924 C2' DU E 4 2925 2922 2944 C2' BRU E 5 2943 2945 2963 C2' DA E 6 2964 2961 2979 C2' DIO A 401 2985 C2' DIO A 402 3027 C2' DIO B 401 3033 C2' DIO B 402 3039 C2' DIO B 403 3045 C2' DIO B 404 3051 C2' DIO B 405 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2712 C3' DU P 1 OK 2710 2713 2714 2769 C3' DU P 3 OK 2767 2770 2771 2788 C3' DU P 4 OK 2786 2789 2790 2811 C3' BRU P 5 OK 2812 2813 2810 2827 C3' DA P 6 OK 2825 2828 2829 2848 C3' DU P 7 OK 2846 2849 2850 2865 C3' DU E 1 OK 2863 2866 2867 2884 C3' DU E 2 OK 2882 2885 2886 2903 C3' DU E 3 OK 2901 2904 2905 2922 C3' DU E 4 OK 2920 2923 2924 2945 C3' BRU E 5 OK 2946 2947 2944 2961 C3' DA E 6 OK 2959 2962 2963 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2710 C4' DU P 1 OK 2712 2709 2711 2767 C4' DU P 3 OK 2769 2766 2768 2786 C4' DU P 4 OK 2788 2785 2787 2812 C4' BRU P 5 OK 2811 2815 2814 2825 C4' DA P 6 OK 2827 2824 2826 2846 C4' DU P 7 OK 2848 2845 2847 2863 C4' DU E 1 OK 2865 2862 2864 2882 C4' DU E 2 OK 2884 2881 2883 2901 C4' DU E 3 OK 2903 2900 2902 2920 C4' DU E 4 OK 2922 2919 2921 2946 C4' BRU E 5 OK 2945 2949 2948 2959 C4' DA E 6 OK 2961 2958 2960 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2709 C5' DU P 1 2708 2710 2766 C5' DU P 3 2765 2767 2785 C5' DU P 4 2784 2786 2815 C5' BRU P 5 2816 2812 2824 C5' DA P 6 2823 2825 2845 C5' DU P 7 2844 2846 2862 C5' DU E 1 2861 2863 2881 C5' DU E 2 2880 2882 2900 C5' DU E 3 2899 2901 2919 C5' DU E 4 2918 2920 2949 C5' BRU E 5 2950 2946 2958 C5' DA E 6 2957 2959 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2724 P DU P 2 2713 2725 P DU P 2 2713 2762 P DU P 3 distorted distorted 2763 2764 2765 2781 P DU P 4 distorted distorted 2770 2782 2783 2784 2817 P BRU P 5 distorted distorted 2789 2818 2819 2816 2820 P DA P 6 distorted distorted 2813 2821 2822 2823 2841 P DU P 7 distorted distorted 2828 2842 2843 2844 2877 P DU E 2 distorted distorted 2866 2878 2879 2880 2896 P DU E 3 distorted distorted 2885 2897 2898 2899 2915 P DU E 4 distorted distorted 2904 2916 2917 2918 2951 P BRU E 5 distorted distorted 2923 2952 2953 2950 2954 P DA E 6 distorted distorted 2947 2955 2956 2957 ---------------------------------------------------------------------------------