ID code: '1BPX' 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' --------------------------------------------------------------------------------- 2785 C1' G T 7 beta 2781 2786 2784 2807 C1' C T 8 beta 2803 2808 2806 2826 C1' G T 9 beta 2822 2827 2825 2848 C1' C T 10 beta 2844 2849 2847 2867 C1' A T 11 beta 2863 2868 2866 2888 C1' T T 12 beta 2884 2889 2887 2908 C1' C T 13 beta 2904 2909 2907 2927 C1' A T 14 beta 2923 2928 2926 2948 C1' G T 15 beta 2944 2949 2947 2970 C1' C T 16 beta 2966 2971 2969 2987 C1' G P 1 beta 2983 2988 2986 3009 C1' C P 2 beta 3005 3010 3008 3028 C1' T P 3 beta 3024 3029 3027 3048 C1' G P 4 beta 3044 3049 3047 3070 C1' A P 5 beta 3066 3071 3069 3091 C1' T P 6 beta 3087 3092 3090 3111 C1' G P 7 beta 3107 3112 3110 3133 C1' C P 8 beta 3129 3134 3132 3152 C1' G P 9 beta 3148 3153 3151 3174 C1' C P 10 beta 3170 3175 3173 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2784 C2' G T 7 2785 2782 2806 C2' C T 8 2807 2804 2825 C2' G T 9 2826 2823 2847 C2' C T 10 2848 2845 2866 C2' A T 11 2867 2864 2887 C2' T T 12 2888 2885 2907 C2' C T 13 2908 2905 2926 C2' A T 14 2927 2924 2947 C2' G T 15 2948 2945 2969 C2' C T 16 2970 2967 2986 C2' G P 1 2987 2984 3008 C2' C P 2 3009 3006 3027 C2' T P 3 3028 3025 3047 C2' G P 4 3048 3045 3069 C2' A P 5 3070 3067 3090 C2' T P 6 3091 3088 3110 C2' G P 7 3111 3108 3132 C2' C P 8 3133 3130 3151 C2' G P 9 3152 3149 3173 C2' C P 10 3174 3171 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2782 C3' G T 7 OK 2780 2783 2784 2804 C3' C T 8 OK 2802 2805 2806 2823 C3' G T 9 OK 2821 2824 2825 2845 C3' C T 10 OK 2843 2846 2847 2864 C3' A T 11 OK 2862 2865 2866 2885 C3' T T 12 OK 2883 2886 2887 2905 C3' C T 13 OK 2903 2906 2907 2924 C3' A T 14 OK 2922 2925 2926 2945 C3' G T 15 OK 2943 2946 2947 2967 C3' C T 16 OK 2965 2968 2969 2984 C3' G P 1 OK 2982 2985 2986 3006 C3' C P 2 OK 3004 3007 3008 3025 C3' T P 3 OK 3023 3026 3027 3045 C3' G P 4 OK 3043 3046 3047 3067 C3' A P 5 OK 3065 3068 3069 3088 C3' T P 6 OK 3086 3089 3090 3108 C3' G P 7 OK 3106 3109 3110 3130 C3' C P 8 OK 3128 3131 3132 3149 C3' G P 9 OK 3147 3150 3151 3171 C3' C P 10 OK 3169 3172 3173 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2780 C4' G T 7 OK 2782 2779 2781 2802 C4' C T 8 OK 2804 2801 2803 2821 C4' G T 9 OK 2823 2820 2822 2843 C4' C T 10 OK 2845 2842 2844 2862 C4' A T 11 OK 2864 2861 2863 2883 C4' T T 12 OK 2885 2882 2884 2903 C4' C T 13 OK 2905 2902 2904 2922 C4' A T 14 OK 2924 2921 2923 2943 C4' G T 15 OK 2945 2942 2944 2965 C4' C T 16 OK 2967 2964 2966 2982 C4' G P 1 OK 2984 2981 2983 3004 C4' C P 2 OK 3006 3003 3005 3023 C4' T P 3 OK 3025 3022 3024 3043 C4' G P 4 OK 3045 3042 3044 3065 C4' A P 5 OK 3067 3064 3066 3086 C4' T P 6 OK 3088 3085 3087 3106 C4' G P 7 OK 3108 3105 3107 3128 C4' C P 8 OK 3130 3127 3129 3147 C4' G P 9 OK 3149 3146 3148 3169 C4' C P 10 OK 3171 3168 3170 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2779 C5' G T 7 2778 2780 2801 C5' C T 8 2800 2802 2820 C5' G T 9 2819 2821 2842 C5' C T 10 2841 2843 2861 C5' A T 11 2860 2862 2882 C5' T T 12 2881 2883 2902 C5' C T 13 2901 2903 2921 C5' A T 14 2920 2922 2942 C5' G T 15 2941 2943 2964 C5' C T 16 2963 2965 2981 C5' G P 1 2980 2982 3003 C5' C P 2 3002 3004 3022 C5' T P 3 3021 3023 3042 C5' G P 4 3041 3043 3064 C5' A P 5 3063 3065 3085 C5' T P 6 3084 3086 3105 C5' G P 7 3104 3106 3127 C5' C P 8 3126 3128 3146 C5' G P 9 3145 3147 3168 C5' C P 10 3167 3169 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2797 P C T 8 OK OK 2783 2798 2799 2800 2816 P G T 9 OK OK 2805 2817 2818 2819 2838 P C T 10 OK OK 2824 2839 2840 2841 2857 P A T 11 OK OK 2846 2858 2859 2860 2878 P T T 12 distorted distorted 2865 2879 2880 2881 2898 P C T 13 distorted distorted 2886 2899 2900 2901 2917 P A T 14 distorted distorted 2906 2918 2919 2920 2938 P G T 15 distorted distorted 2925 2939 2940 2941 2960 P C T 16 distorted distorted 2946 2961 2962 2963 2999 P C P 2 distorted distorted 2985 3000 3001 3002 3018 P T P 3 distorted distorted 3007 3019 3020 3021 3038 P G P 4 distorted distorted 3026 3039 3040 3041 3060 P A P 5 distorted distorted 3046 3061 3062 3063 3081 P T P 6 OK OK 3068 3082 3083 3084 3101 P G P 7 OK OK 3089 3102 3103 3104 3123 P C P 8 distorted distorted 3109 3124 3125 3126 3142 P G P 9 distorted distorted 3131 3143 3144 3145 3164 P C P 10 OK OK 3150 3165 3166 3167 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