ID code: '3G6X' 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' --------------------------------------------------------------------------------- 2885 C1' DA P 867 beta 2881 2886 2884 2906 C1' DG P 868 beta 2902 2907 2905 2928 C1' DG P 869 beta 2924 2929 2927 2950 C1' DA P 870 beta 2946 2951 2949 2971 C1' DC P 871 beta 2967 2972 2970 2990 C1' DC P 872 beta 2986 2991 2989 3007 C1' DOC P 873 beta 3011 2999 3008 3026 C1' 3DR T 840 3025 3022 3039 C1' DG T 841 beta 3035 3040 3038 3061 C1' DG T 842 beta 3057 3062 3060 3083 C1' DG T 843 beta 3079 3084 3082 3105 C1' DT T 844 beta 3101 3106 3104 3125 C1' DC T 845 beta 3121 3126 3124 3144 C1' DC T 846 beta 3140 3145 3143 3163 C1' DT T 847 beta 3159 3164 3162 3193 C1' DGT A 875 beta 3189 3194 3192 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2884 C2' DA P 867 2885 2882 2905 C2' DG P 868 2906 2903 2927 C2' DG P 869 2928 2925 2949 C2' DA P 870 2950 2947 2970 C2' DC P 871 2971 2968 2989 C2' DC P 872 2990 2987 3008 C2' DOC P 873 3007 3009 3022 C2' 3DR T 840 3026 3027 3038 C2' DG T 841 3039 3036 3060 C2' DG T 842 3061 3058 3082 C2' DG T 843 3083 3080 3104 C2' DT T 844 3105 3102 3124 C2' DC T 845 3125 3122 3143 C2' DC T 846 3144 3141 3162 C2' DT T 847 3163 3160 3192 C2' DGT A 875 3193 3190 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2882 C3' DA P 867 OK 2880 2883 2884 2903 C3' DG P 868 OK 2901 2904 2905 2925 C3' DG P 869 OK 2923 2926 2927 2947 C3' DA P 870 OK 2945 2948 2949 2968 C3' DC P 871 OK 2966 2969 2970 2987 C3' DC P 872 OK 2985 2988 2989 3009 C3' DOC P 873 3010 3008 3027 C3' 3DR T 840 OK 3024 3028 3022 3036 C3' DG T 841 OK 3034 3037 3038 3058 C3' DG T 842 OK 3056 3059 3060 3080 C3' DG T 843 OK 3078 3081 3082 3102 C3' DT T 844 OK 3100 3103 3104 3122 C3' DC T 845 OK 3120 3123 3124 3141 C3' DC T 846 OK 3139 3142 3143 3160 C3' DT T 847 OK 3158 3161 3162 3190 C3' DGT A 875 OK 3188 3191 3192 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2880 C4' DA P 867 OK 2882 2879 2881 2901 C4' DG P 868 OK 2903 2900 2902 2923 C4' DG P 869 OK 2925 2922 2924 2945 C4' DA P 870 OK 2947 2944 2946 2966 C4' DC P 871 OK 2968 2965 2967 2985 C4' DC P 872 OK 2987 2984 2986 3010 C4' DOC P 873 OK 3009 3012 3011 3024 C4' 3DR T 840 OK 3027 3023 3025 3034 C4' DG T 841 OK 3036 3033 3035 3056 C4' DG T 842 OK 3058 3055 3057 3078 C4' DG T 843 OK 3080 3077 3079 3100 C4' DT T 844 OK 3102 3099 3101 3120 C4' DC T 845 OK 3122 3119 3121 3139 C4' DC T 846 OK 3141 3138 3140 3158 C4' DT T 847 OK 3160 3157 3159 3188 C4' DGT A 875 OK 3190 3187 3189 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2879 C5' DA P 867 2878 2880 2900 C5' DG P 868 2899 2901 2922 C5' DG P 869 2921 2923 2944 C5' DA P 870 2943 2945 2965 C5' DC P 871 2964 2966 2984 C5' DC P 872 2983 2985 3012 C5' DOC P 873 3013 3010 3023 C5' 3DR T 840 3018 3024 3033 C5' DG T 841 3032 3034 3055 C5' DG T 842 3054 3056 3077 C5' DG T 843 3076 3078 3099 C5' DT T 844 3098 3100 3119 C5' DC T 845 3118 3120 3138 C5' DC T 846 3137 3139 3157 C5' DT T 847 3156 3158 3187 C5' DGT A 875 3186 3188 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2896 P DG P 868 distorted distorted 2883 2897 2898 2899 2918 P DG P 869 distorted distorted 2904 2919 2920 2921 2940 P DA P 870 distorted distorted 2926 2941 2942 2943 2961 P DC P 871 distorted distorted 2948 2962 2963 2964 2980 P DC P 872 distorted distorted 2969 2981 2982 2983 3014 P DOC P 873 distorted distorted 2988 3015 3016 3013 3019 P 3DR T 840 OK OK 3020 3021 3018 3029 P DG T 841 distorted distorted 3028 3030 3031 3032 3051 P DG T 842 distorted distorted 3037 3052 3053 3054 3073 P DG T 843 distorted distorted 3059 3074 3075 3076 3095 P DT T 844 distorted distorted 3081 3096 3097 3098 3115 P DC T 845 distorted distorted 3103 3116 3117 3118 3134 P DC T 846 distorted distorted 3123 3135 3136 3137 3153 P DT T 847 distorted distorted 3142 3154 3155 3156 ---------------------------------------------------------------------------------