ID code: '4AL5' 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' --------------------------------------------------------------------------------- 2839 C1' A B 5 alpha beta 2834 2856 2840 2837 2872 C1' C B 6 alpha beta 2867 2887 2873 2870 2903 C1' U B 7 alpha beta 2898 2918 2904 2901 2933 C1' G B 8 alpha beta 2928 2951 2934 2931 2967 C1' C B 9 alpha beta 2962 2982 2968 2965 2998 C1' C B 10 alpha beta 2993 3013 2999 2996 3029 C1' G B 11 alpha beta 3024 3047 3030 3027 3063 C1' U B 12 alpha beta 3058 3078 3064 3061 3093 C1' A B 13 alpha beta 3088 3110 3094 3091 3126 C1' U B 14 alpha beta 3121 3141 3127 3124 3156 C1' A B 15 alpha beta 3151 3173 3157 3154 3189 C1' G B 16 alpha beta 3184 3207 3190 3187 3223 C1' G B 17 alpha beta 3218 3241 3224 3221 3257 C1' C B 18 alpha beta 3252 3272 3258 3255 3288 C1' A B 19 alpha beta 3283 3305 3289 3286 3321 C1' G B 20 alpha beta 3316 3339 3322 3319 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2837 C2' A B 5 OK OK 2839 2835 2854 2838 2870 C2' C B 6 OK OK 2872 2868 2885 2871 2901 C2' U B 7 OK OK 2903 2899 2916 2902 2931 C2' G B 8 OK OK 2933 2929 2949 2932 2965 C2' C B 9 OK OK 2967 2963 2980 2966 2996 C2' C B 10 OK OK 2998 2994 3011 2997 3027 C2' G B 11 OK OK 3029 3025 3045 3028 3061 C2' U B 12 OK OK 3063 3059 3076 3062 3091 C2' A B 13 OK OK 3093 3089 3108 3092 3124 C2' U B 14 OK OK 3126 3122 3139 3125 3154 C2' A B 15 OK OK 3156 3152 3171 3155 3187 C2' G B 16 OK OK 3189 3185 3205 3188 3221 C2' G B 17 OK OK 3223 3219 3239 3222 3255 C2' C B 18 OK OK 3257 3253 3270 3256 3286 C2' A B 19 OK OK 3288 3284 3303 3287 3319 C2' G B 20 OK OK 3321 3317 3337 3320 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2835 C3' A B 5 OK OK 2833 2853 2836 2837 2868 C3' C B 6 OK OK 2866 2884 2869 2870 2899 C3' U B 7 OK OK 2897 2915 2900 2901 2929 C3' G B 8 OK OK 2927 2948 2930 2931 2963 C3' C B 9 OK OK 2961 2979 2964 2965 2994 C3' C B 10 OK OK 2992 3010 2995 2996 3025 C3' G B 11 OK OK 3023 3044 3026 3027 3059 C3' U B 12 OK OK 3057 3075 3060 3061 3089 C3' A B 13 OK OK 3087 3107 3090 3091 3122 C3' U B 14 OK OK 3120 3138 3123 3124 3152 C3' A B 15 OK OK 3150 3170 3153 3154 3185 C3' G B 16 OK OK 3183 3204 3186 3187 3219 C3' G B 17 OK OK 3217 3238 3220 3221 3253 C3' C B 18 OK OK 3251 3269 3254 3255 3284 C3' A B 19 OK OK 3282 3302 3285 3286 3317 C3' G B 20 OK OK 3315 3336 3318 3319 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2833 C4' A B 5 OK OK 2835 2852 2832 2834 2866 C4' C B 6 OK OK 2868 2883 2865 2867 2897 C4' U B 7 OK OK 2899 2914 2896 2898 2927 C4' G B 8 OK OK 2929 2947 2926 2928 2961 C4' C B 9 OK OK 2963 2978 2960 2962 2992 C4' C B 10 OK OK 2994 3009 2991 2993 3023 C4' G B 11 OK OK 3025 3043 3022 3024 3057 C4' U B 12 OK OK 3059 3074 3056 3058 3087 C4' A B 13 OK OK 3089 3106 3086 3088 3120 C4' U B 14 OK OK 3122 3137 3119 3121 3150 C4' A B 15 OK OK 3152 3169 3149 3151 3183 C4' G B 16 OK OK 3185 3203 3182 3184 3217 C4' G B 17 OK OK 3219 3237 3216 3218 3251 C4' C B 18 OK OK 3253 3268 3250 3252 3282 C4' A B 19 OK OK 3284 3301 3281 3283 3315 C4' G B 20 OK OK 3317 3335 3314 3316 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2832 C5' A B 5 OK OK 2831 2850 2851 2833 2865 C5' C B 6 OK OK 2864 2881 2882 2866 2896 C5' U B 7 distorted distorted 2895 2912 2913 2897 2926 C5' G B 8 OK OK 2925 2945 2946 2927 2960 C5' C B 9 OK OK 2959 2976 2977 2961 2991 C5' C B 10 OK OK 2990 3007 3008 2992 3022 C5' G B 11 OK OK 3021 3041 3042 3023 3056 C5' U B 12 OK OK 3055 3072 3073 3057 3086 C5' A B 13 distorted distorted 3085 3104 3105 3087 3119 C5' U B 14 OK OK 3118 3135 3136 3120 3149 C5' A B 15 OK OK 3148 3167 3168 3150 3182 C5' G B 16 OK OK 3181 3201 3202 3183 3216 C5' G B 17 OK OK 3215 3235 3236 3217 3250 C5' C B 18 OK OK 3249 3266 3267 3251 3281 C5' A B 19 OK OK 3280 3299 3300 3282 3314 C5' G B 20 distorted distorted 3313 3333 3334 3315 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2828 P A B 5 distorted distorted 2827 2829 2830 2831 2861 P C B 6 distorted distorted 2836 2862 2863 2864 2892 P U B 7 distorted distorted 2869 2893 2894 2895 2922 P G B 8 distorted distorted 2900 2923 2924 2925 2956 P C B 9 distorted distorted 2930 2957 2958 2959 2987 P C B 10 distorted distorted 2964 2988 2989 2990 3018 P G B 11 distorted distorted 2995 3019 3020 3021 3052 P U B 12 OK OK 3026 3053 3054 3055 3082 P A B 13 distorted distorted 3060 3083 3084 3085 3115 P U B 14 distorted distorted 3090 3116 3117 3118 3145 P A B 15 distorted distorted 3123 3146 3147 3148 3178 P G B 16 distorted distorted 3153 3179 3180 3181 3212 P G B 17 OK OK 3186 3213 3214 3215 3246 P C B 18 distorted distorted 3220 3247 3248 3249 3277 P A B 19 distorted distorted 3254 3278 3279 3280 3310 P G B 20 distorted distorted 3285 3311 3312 3313 3344 P C B 21 distorted distorted 3318 3345 3346 3347 ---------------------------------------------------------------------------------