ID code: '2VON' 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' --------------------------------------------------------------------------------- 3039 C1' A C -7 beta 3034 3040 3037 3061 C1' U C -6 beta 3056 3062 3059 3081 C1' A C -5 beta 3076 3082 3079 3103 C1' A C -4 beta 3098 3104 3101 3125 C1' U C -3 beta 3120 3126 3123 3145 C1' U C -2 beta 3140 3146 3143 3165 C1' U C -1 beta 3160 3166 3163 3183 C1' A D -7 beta 3178 3184 3181 3205 C1' U D -6 beta 3200 3206 3203 3225 C1' A D -5 beta 3220 3226 3223 3247 C1' A D -4 beta 3242 3248 3245 3269 C1' U D -3 beta 3264 3270 3267 3289 C1' U D -2 beta 3284 3290 3287 3309 C1' U D -1 beta 3304 3310 3307 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 3037 C2' A C -7 OK 3039 3035 3038 3059 C2' U C -6 OK 3061 3057 3060 3079 C2' A C -5 OK 3081 3077 3080 3101 C2' A C -4 OK 3103 3099 3102 3123 C2' U C -3 OK 3125 3121 3124 3143 C2' U C -2 OK 3145 3141 3144 3163 C2' U C -1 OK 3165 3161 3164 3181 C2' A D -7 OK 3183 3179 3182 3203 C2' U D -6 OK 3205 3201 3204 3223 C2' A D -5 OK 3225 3221 3224 3245 C2' A D -4 OK 3247 3243 3246 3267 C2' U D -3 OK 3269 3265 3268 3287 C2' U D -2 OK 3289 3285 3288 3307 C2' U D -1 OK 3309 3305 3308 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 3035 C3' A C -7 OK 3033 3036 3037 3057 C3' U C -6 OK 3055 3058 3059 3077 C3' A C -5 distorted 3075 3078 3079 3099 C3' A C -4 OK 3097 3100 3101 3121 C3' U C -3 OK 3119 3122 3123 3141 C3' U C -2 OK 3139 3142 3143 3161 C3' U C -1 OK 3159 3162 3163 3179 C3' A D -7 OK 3177 3180 3181 3201 C3' U D -6 OK 3199 3202 3203 3221 C3' A D -5 distorted 3219 3222 3223 3243 C3' A D -4 OK 3241 3244 3245 3265 C3' U D -3 OK 3263 3266 3267 3285 C3' U D -2 OK 3283 3286 3287 3305 C3' U D -1 OK 3303 3306 3307 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3033 C4' A C -7 OK 3035 3032 3034 3055 C4' U C -6 OK 3057 3054 3056 3075 C4' A C -5 OK 3077 3074 3076 3097 C4' A C -4 OK 3099 3096 3098 3119 C4' U C -3 OK 3121 3118 3120 3139 C4' U C -2 OK 3141 3138 3140 3159 C4' U C -1 OK 3161 3158 3160 3177 C4' A D -7 OK 3179 3176 3178 3199 C4' U D -6 OK 3201 3198 3200 3219 C4' A D -5 OK 3221 3218 3220 3241 C4' A D -4 OK 3243 3240 3242 3263 C4' U D -3 OK 3265 3262 3264 3283 C4' U D -2 OK 3285 3282 3284 3303 C4' U D -1 OK 3305 3302 3304 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 3032 C5' A C -7 3031 3033 3054 C5' U C -6 3053 3055 3074 C5' A C -5 3073 3075 3096 C5' A C -4 3095 3097 3118 C5' U C -3 3117 3119 3138 C5' U C -2 3137 3139 3158 C5' U C -1 3157 3159 3176 C5' A D -7 3175 3177 3198 C5' U D -6 3197 3199 3218 C5' A D -5 3217 3219 3240 C5' A D -4 3239 3241 3262 C5' U D -3 3261 3263 3282 C5' U D -2 3281 3283 3302 C5' U D -1 3301 3303 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 3050 P U C -6 distorted distorted 3036 3051 3052 3053 3070 P A C -5 distorted distorted 3058 3071 3072 3073 3092 P A C -4 distorted distorted 3078 3093 3094 3095 3114 P U C -3 distorted distorted 3100 3115 3116 3117 3134 P U C -2 distorted distorted 3122 3135 3136 3137 3154 P U C -1 distorted distorted 3142 3155 3156 3157 3194 P U D -6 distorted distorted 3180 3195 3196 3197 3214 P A D -5 distorted distorted 3202 3215 3216 3217 3236 P A D -4 distorted distorted 3222 3237 3238 3239 3258 P U D -3 distorted distorted 3244 3259 3260 3261 3278 P U D -2 distorted distorted 3266 3279 3280 3281 3298 P U D -1 distorted distorted 3286 3299 3300 3301 ---------------------------------------------------------------------------------