ID code: '3H4B' 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' --------------------------------------------------------------------------------- 2886 C1' DA P 867 beta 2882 2887 2885 2907 C1' DG P 868 beta 2903 2908 2906 2929 C1' DG P 869 beta 2925 2930 2928 2951 C1' DA P 870 beta 2947 2952 2950 2972 C1' DC P 871 beta 2968 2973 2971 2991 C1' DC P 872 beta 2987 2992 2990 3008 C1' DOC P 873 beta 3012 3000 3009 3026 C1' DT T 839 beta 3022 3027 3025 3086 C1' DG T 841 beta 3082 3087 3085 3108 C1' DG T 842 beta 3104 3109 3107 3130 C1' DG T 843 beta 3126 3131 3129 3152 C1' DT T 844 beta 3148 3153 3151 3172 C1' DC T 845 beta 3168 3173 3171 3191 C1' DC T 846 beta 3187 3192 3190 3210 C1' DT T 847 beta 3206 3211 3209 3240 C1' DTP A 875 beta 3236 3241 3239 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2885 C2' DA P 867 2886 2883 2906 C2' DG P 868 2907 2904 2928 C2' DG P 869 2929 2926 2950 C2' DA P 870 2951 2948 2971 C2' DC P 871 2972 2969 2990 C2' DC P 872 2991 2988 3009 C2' DOC P 873 3008 3010 3025 C2' DT T 839 3026 3023 3085 C2' DG T 841 3086 3083 3107 C2' DG T 842 3108 3105 3129 C2' DG T 843 3130 3127 3151 C2' DT T 844 3152 3149 3171 C2' DC T 845 3172 3169 3190 C2' DC T 846 3191 3188 3209 C2' DT T 847 3210 3207 3239 C2' DTP A 875 3240 3237 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2883 C3' DA P 867 OK 2881 2884 2885 2904 C3' DG P 868 OK 2902 2905 2906 2926 C3' DG P 869 OK 2924 2927 2928 2948 C3' DA P 870 OK 2946 2949 2950 2969 C3' DC P 871 OK 2967 2970 2971 2988 C3' DC P 872 OK 2986 2989 2990 3010 C3' DOC P 873 3011 3009 3023 C3' DT T 839 OK 3021 3024 3025 3083 C3' DG T 841 OK 3081 3084 3085 3105 C3' DG T 842 OK 3103 3106 3107 3127 C3' DG T 843 OK 3125 3128 3129 3149 C3' DT T 844 OK 3147 3150 3151 3169 C3' DC T 845 OK 3167 3170 3171 3188 C3' DC T 846 OK 3186 3189 3190 3207 C3' DT T 847 OK 3205 3208 3209 3237 C3' DTP A 875 OK 3235 3238 3239 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2881 C4' DA P 867 OK 2883 2880 2882 2902 C4' DG P 868 OK 2904 2901 2903 2924 C4' DG P 869 OK 2926 2923 2925 2946 C4' DA P 870 OK 2948 2945 2947 2967 C4' DC P 871 OK 2969 2966 2968 2986 C4' DC P 872 OK 2988 2985 2987 3011 C4' DOC P 873 OK 3010 3013 3012 3021 C4' DT T 839 OK 3023 3020 3022 3081 C4' DG T 841 OK 3083 3080 3082 3103 C4' DG T 842 OK 3105 3102 3104 3125 C4' DG T 843 OK 3127 3124 3126 3147 C4' DT T 844 OK 3149 3146 3148 3167 C4' DC T 845 OK 3169 3166 3168 3186 C4' DC T 846 OK 3188 3185 3187 3205 C4' DT T 847 OK 3207 3204 3206 3235 C4' DTP A 875 OK 3237 3234 3236 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2880 C5' DA P 867 2879 2881 2901 C5' DG P 868 2900 2902 2923 C5' DG P 869 2922 2924 2945 C5' DA P 870 2944 2946 2966 C5' DC P 871 2965 2967 2985 C5' DC P 872 2984 2986 3013 C5' DOC P 873 3014 3011 3020 C5' DT T 839 3019 3021 3080 C5' DG T 841 3079 3081 3102 C5' DG T 842 3101 3103 3124 C5' DG T 843 3123 3125 3146 C5' DT T 844 3145 3147 3166 C5' DC T 845 3165 3167 3185 C5' DC T 846 3184 3186 3204 C5' DT T 847 3203 3205 3234 C5' DTP A 875 3233 3235 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2897 P DG P 868 distorted distorted 2884 2898 2899 2900 2919 P DG P 869 distorted distorted 2905 2920 2921 2922 2941 P DA P 870 distorted distorted 2927 2942 2943 2944 2962 P DC P 871 distorted distorted 2949 2963 2964 2965 2981 P DC P 872 distorted distorted 2970 2982 2983 2984 3015 P DOC P 873 distorted distorted 2989 3016 3017 3014 3070 P BRU T 840 3024 3071 P BRU T 840 3024 3076 P DG T 841 distorted distorted 3077 3078 3079 3098 P DG T 842 distorted distorted 3084 3099 3100 3101 3120 P DG T 843 distorted distorted 3106 3121 3122 3123 3142 P DT T 844 distorted distorted 3128 3143 3144 3145 3162 P DC T 845 distorted distorted 3150 3163 3164 3165 3181 P DC T 846 distorted distorted 3170 3182 3183 3184 3200 P DT T 847 distorted distorted 3189 3201 3202 3203 ---------------------------------------------------------------------------------