ID code: '2BS0' 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' --------------------------------------------------------------------------------- 2898 C1' U R 6 beta 2893 2899 2896 2918 C1' G R 7 beta 2913 2919 2916 2941 C1' U R 8 beta 2936 2942 2939 2961 C1' C R 9 beta 2956 2962 2959 2981 C1' U R 10 beta 2976 2982 2979 3001 C1' A R 11 beta 2996 3002 2999 3023 C1' A R 12 beta 3018 3024 3021 3045 C1' G R 13 beta 3040 3046 3043 3068 C1' A R 14 beta 3063 3069 3066 3090 C1' C R 15 beta 3085 3091 3088 3110 C1' U R 16 beta 3105 3111 3108 3130 C1' G R 17 beta 3125 3131 3128 3151 C1' G S 7 beta 3146 3152 3149 3174 C1' U S 8 beta 3169 3175 3172 3194 C1' C S 9 beta 3189 3195 3192 3214 C1' U S 10 beta 3209 3215 3212 3234 C1' A S 11 beta 3229 3235 3232 3256 C1' A S 12 beta 3251 3257 3254 3278 C1' G S 13 beta 3273 3279 3276 3301 C1' A S 14 beta 3296 3302 3299 3323 C1' C S 15 beta 3318 3324 3321 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2896 C2' U R 6 OK 2898 2894 2897 2916 C2' G R 7 OK 2918 2914 2917 2939 C2' U R 8 OK 2941 2937 2940 2959 C2' C R 9 OK 2961 2957 2960 2979 C2' U R 10 OK 2981 2977 2980 2999 C2' A R 11 OK 3001 2997 3000 3021 C2' A R 12 OK 3023 3019 3022 3043 C2' G R 13 OK 3045 3041 3044 3066 C2' A R 14 OK 3068 3064 3067 3088 C2' C R 15 OK 3090 3086 3089 3108 C2' U R 16 OK 3110 3106 3109 3128 C2' G R 17 OK 3130 3126 3129 3149 C2' G S 7 OK 3151 3147 3150 3172 C2' U S 8 OK 3174 3170 3173 3192 C2' C S 9 OK 3194 3190 3193 3212 C2' U S 10 OK 3214 3210 3213 3232 C2' A S 11 OK 3234 3230 3233 3254 C2' A S 12 OK 3256 3252 3255 3276 C2' G S 13 OK 3278 3274 3277 3299 C2' A S 14 OK 3301 3297 3300 3321 C2' C S 15 OK 3323 3319 3322 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2894 C3' U R 6 OK 2892 2895 2896 2914 C3' G R 7 OK 2912 2915 2916 2937 C3' U R 8 OK 2935 2938 2939 2957 C3' C R 9 OK 2955 2958 2959 2977 C3' U R 10 OK 2975 2978 2979 2997 C3' A R 11 OK 2995 2998 2999 3019 C3' A R 12 OK 3017 3020 3021 3041 C3' G R 13 OK 3039 3042 3043 3064 C3' A R 14 OK 3062 3065 3066 3086 C3' C R 15 OK 3084 3087 3088 3106 C3' U R 16 OK 3104 3107 3108 3126 C3' G R 17 OK 3124 3127 3128 3147 C3' G S 7 OK 3145 3148 3149 3170 C3' U S 8 OK 3168 3171 3172 3190 C3' C S 9 OK 3188 3191 3192 3210 C3' U S 10 OK 3208 3211 3212 3230 C3' A S 11 OK 3228 3231 3232 3252 C3' A S 12 OK 3250 3253 3254 3274 C3' G S 13 OK 3272 3275 3276 3297 C3' A S 14 OK 3295 3298 3299 3319 C3' C S 15 OK 3317 3320 3321 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2892 C4' U R 6 OK 2894 2891 2893 2912 C4' G R 7 OK 2914 2911 2913 2935 C4' U R 8 OK 2937 2934 2936 2955 C4' C R 9 OK 2957 2954 2956 2975 C4' U R 10 OK 2977 2974 2976 2995 C4' A R 11 OK 2997 2994 2996 3017 C4' A R 12 OK 3019 3016 3018 3039 C4' G R 13 OK 3041 3038 3040 3062 C4' A R 14 OK 3064 3061 3063 3084 C4' C R 15 OK 3086 3083 3085 3104 C4' U R 16 OK 3106 3103 3105 3124 C4' G R 17 OK 3126 3123 3125 3145 C4' G S 7 OK 3147 3144 3146 3168 C4' U S 8 OK 3170 3167 3169 3188 C4' C S 9 OK 3190 3187 3189 3208 C4' U S 10 OK 3210 3207 3209 3228 C4' A S 11 OK 3230 3227 3229 3250 C4' A S 12 OK 3252 3249 3251 3272 C4' G S 13 OK 3274 3271 3273 3295 C4' A S 14 OK 3297 3294 3296 3317 C4' C S 15 OK 3319 3316 3318 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2891 C5' U R 6 2890 2892 2911 C5' G R 7 2910 2912 2934 C5' U R 8 2933 2935 2954 C5' C R 9 2953 2955 2974 C5' U R 10 2973 2975 2994 C5' A R 11 2993 2995 3016 C5' A R 12 3015 3017 3038 C5' G R 13 3037 3039 3061 C5' A R 14 3060 3062 3083 C5' C R 15 3082 3084 3103 C5' U R 16 3102 3104 3123 C5' G R 17 3122 3124 3144 C5' G S 7 3143 3145 3167 C5' U S 8 3166 3168 3187 C5' C S 9 3186 3188 3207 C5' U S 10 3206 3208 3227 C5' A S 11 3226 3228 3249 C5' A S 12 3248 3250 3271 C5' G S 13 3270 3272 3294 C5' A S 14 3293 3295 3316 C5' C S 15 3315 3317 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2907 P G R 7 distorted distorted 2895 2908 2909 2910 2930 P U R 8 distorted distorted 2915 2931 2932 2933 2950 P C R 9 distorted distorted 2938 2951 2952 2953 2970 P U R 10 distorted distorted 2958 2971 2972 2973 2990 P A R 11 distorted distorted 2978 2991 2992 2993 3012 P A R 12 distorted distorted 2998 3013 3014 3015 3034 P G R 13 distorted distorted 3020 3035 3036 3037 3057 P A R 14 distorted distorted 3042 3058 3059 3060 3079 P C R 15 distorted distorted 3065 3080 3081 3082 3099 P U R 16 distorted distorted 3087 3100 3101 3102 3119 P G R 17 distorted distorted 3107 3120 3121 3122 3163 P U S 8 distorted distorted 3148 3164 3165 3166 3183 P C S 9 distorted distorted 3171 3184 3185 3186 3203 P U S 10 distorted distorted 3191 3204 3205 3206 3223 P A S 11 distorted distorted 3211 3224 3225 3226 3245 P A S 12 distorted distorted 3231 3246 3247 3248 3267 P G S 13 distorted distorted 3253 3268 3269 3270 3290 P A S 14 distorted distorted 3275 3291 3292 3293 3312 P C S 15 distorted distorted 3298 3313 3314 3315 ---------------------------------------------------------------------------------