ID code: '3V6Y' 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' --------------------------------------------------------------------------------- 3142 C1' C B 3 beta 3137 3143 3140 3162 C1' U B 4 beta 3157 3163 3160 3182 C1' G B 5 beta 3177 3183 3180 3205 C1' U B 6 beta 3200 3206 3203 3225 C1' G B 7 beta 3220 3226 3223 3248 C1' C B 8 beta 3243 3249 3246 3268 C1' C B 9 beta 3263 3269 3266 3288 C1' A B 10 beta 3283 3289 3286 3310 C1' U B 11 beta 3305 3311 3308 3330 C1' A B 12 beta 3325 3331 3328 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 3140 C2' C B 3 OK 3142 3138 3141 3160 C2' U B 4 OK 3162 3158 3161 3180 C2' G B 5 OK 3182 3178 3181 3203 C2' U B 6 OK 3205 3201 3204 3223 C2' G B 7 OK 3225 3221 3224 3246 C2' C B 8 OK 3248 3244 3247 3266 C2' C B 9 OK 3268 3264 3267 3286 C2' A B 10 OK 3288 3284 3287 3308 C2' U B 11 OK 3310 3306 3309 3328 C2' A B 12 OK 3330 3326 3329 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 3138 C3' C B 3 OK 3136 3139 3140 3158 C3' U B 4 OK 3156 3159 3160 3178 C3' G B 5 OK 3176 3179 3180 3201 C3' U B 6 OK 3199 3202 3203 3221 C3' G B 7 OK 3219 3222 3223 3244 C3' C B 8 OK 3242 3245 3246 3264 C3' C B 9 OK 3262 3265 3266 3284 C3' A B 10 OK 3282 3285 3286 3306 C3' U B 11 OK 3304 3307 3308 3326 C3' A B 12 OK 3324 3327 3328 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3136 C4' C B 3 OK 3138 3135 3137 3156 C4' U B 4 OK 3158 3155 3157 3176 C4' G B 5 OK 3178 3175 3177 3199 C4' U B 6 OK 3201 3198 3200 3219 C4' G B 7 OK 3221 3218 3220 3242 C4' C B 8 OK 3244 3241 3243 3262 C4' C B 9 OK 3264 3261 3263 3282 C4' A B 10 OK 3284 3281 3283 3304 C4' U B 11 OK 3306 3303 3305 3324 C4' A B 12 OK 3326 3323 3325 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 3135 C5' C B 3 3134 3136 3155 C5' U B 4 3154 3156 3175 C5' G B 5 3174 3176 3198 C5' U B 6 3197 3199 3218 C5' G B 7 3217 3219 3241 C5' C B 8 3240 3242 3261 C5' C B 9 3260 3262 3281 C5' A B 10 3280 3282 3303 C5' U B 11 3302 3304 3323 C5' A B 12 3322 3324 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 3131 P C B 3 OK OK 3132 3133 3134 3151 P U B 4 distorted distorted 3139 3152 3153 3154 3171 P G B 5 distorted distorted 3159 3172 3173 3174 3194 P U B 6 distorted distorted 3179 3195 3196 3197 3214 P G B 7 distorted distorted 3202 3215 3216 3217 3237 P C B 8 distorted distorted 3222 3238 3239 3240 3257 P C B 9 distorted distorted 3245 3258 3259 3260 3277 P A B 10 distorted distorted 3265 3278 3279 3280 3299 P U B 11 distorted distorted 3285 3300 3301 3302 3319 P A B 12 distorted distorted 3307 3320 3321 3322 3341 P C B 13 distorted distorted 3327 3342 3343 3344 ---------------------------------------------------------------------------------