ID code: '4BS2' 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' --------------------------------------------------------------------------------- 2784 C1' G B 1 alpha beta 2779 2802 2785 2782 2815 C1' U B 2 alpha beta 2810 2830 2816 2813 2845 C1' G B 3 alpha beta 2840 2863 2846 2843 2876 C1' U B 4 alpha beta 2871 2891 2877 2874 2906 C1' G B 5 alpha beta 2901 2924 2907 2904 2937 C1' A B 6 alpha beta 2932 2954 2938 2935 2969 C1' A B 7 alpha beta 2964 2986 2970 2967 3001 C1' U B 8 alpha beta 2996 3016 3002 2999 3031 C1' G B 9 alpha beta 3026 3049 3032 3029 3062 C1' A B 10 alpha beta 3057 3079 3063 3060 3094 C1' A B 11 alpha beta 3089 3111 3095 3092 3126 C1' U B 12 alpha beta 3121 3141 3127 3124 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2782 C2' G B 1 OK OK 2784 2780 2800 2783 2813 C2' U B 2 OK OK 2815 2811 2828 2814 2843 C2' G B 3 OK OK 2845 2841 2861 2844 2874 C2' U B 4 OK OK 2876 2872 2889 2875 2904 C2' G B 5 OK OK 2906 2902 2922 2905 2935 C2' A B 6 OK OK 2937 2933 2952 2936 2967 C2' A B 7 OK OK 2969 2965 2984 2968 2999 C2' U B 8 OK OK 3001 2997 3014 3000 3029 C2' G B 9 OK OK 3031 3027 3047 3030 3060 C2' A B 10 OK OK 3062 3058 3077 3061 3092 C2' A B 11 OK OK 3094 3090 3109 3093 3124 C2' U B 12 OK OK 3126 3122 3139 3125 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2780 C3' G B 1 OK OK 2778 2799 2781 2782 2811 C3' U B 2 OK OK 2809 2827 2812 2813 2841 C3' G B 3 OK OK 2839 2860 2842 2843 2872 C3' U B 4 OK OK 2870 2888 2873 2874 2902 C3' G B 5 OK OK 2900 2921 2903 2904 2933 C3' A B 6 OK OK 2931 2951 2934 2935 2965 C3' A B 7 OK OK 2963 2983 2966 2967 2997 C3' U B 8 OK OK 2995 3013 2998 2999 3027 C3' G B 9 OK OK 3025 3046 3028 3029 3058 C3' A B 10 OK OK 3056 3076 3059 3060 3090 C3' A B 11 OK OK 3088 3108 3091 3092 3122 C3' U B 12 OK OK 3120 3138 3123 3124 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2778 C4' G B 1 OK OK 2780 2798 2777 2779 2809 C4' U B 2 OK OK 2811 2826 2808 2810 2839 C4' G B 3 OK OK 2841 2859 2838 2840 2870 C4' U B 4 OK OK 2872 2887 2869 2871 2900 C4' G B 5 OK OK 2902 2920 2899 2901 2931 C4' A B 6 OK OK 2933 2950 2930 2932 2963 C4' A B 7 OK OK 2965 2982 2962 2964 2995 C4' U B 8 OK OK 2997 3012 2994 2996 3025 C4' G B 9 OK OK 3027 3045 3024 3026 3056 C4' A B 10 OK OK 3058 3075 3055 3057 3088 C4' A B 11 OK OK 3090 3107 3087 3089 3120 C4' U B 12 OK OK 3122 3137 3119 3121 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2777 C5' G B 1 OK OK 2776 2796 2797 2778 2808 C5' U B 2 OK OK 2807 2824 2825 2809 2838 C5' G B 3 OK OK 2837 2857 2858 2839 2869 C5' U B 4 OK OK 2868 2885 2886 2870 2899 C5' G B 5 OK OK 2898 2918 2919 2900 2930 C5' A B 6 OK OK 2929 2948 2949 2931 2962 C5' A B 7 OK OK 2961 2980 2981 2963 2994 C5' U B 8 OK OK 2993 3010 3011 2995 3024 C5' G B 9 OK OK 3023 3043 3044 3025 3055 C5' A B 10 OK OK 3054 3073 3074 3056 3087 C5' A B 11 OK OK 3086 3105 3106 3088 3119 C5' U B 12 OK OK 3118 3135 3136 3120 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2804 P U B 2 distorted distorted 2781 2805 2806 2807 2834 P G B 3 distorted distorted 2812 2835 2836 2837 2865 P U B 4 distorted distorted 2842 2866 2867 2868 2895 P G B 5 distorted distorted 2873 2896 2897 2898 2926 P A B 6 distorted distorted 2903 2927 2928 2929 2958 P A B 7 distorted distorted 2934 2959 2960 2961 2990 P U B 8 distorted distorted 2966 2991 2992 2993 3020 P G B 9 distorted distorted 2998 3021 3022 3023 3051 P A B 10 distorted distorted 3028 3052 3053 3054 3083 P A B 11 distorted distorted 3059 3084 3085 3086 3115 P U B 12 distorted distorted 3091 3116 3117 3118 ---------------------------------------------------------------------------------