ID code: '3K61' 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' --------------------------------------------------------------------------------- 3141 C1' U B 1 beta 3136 3142 3139 3161 C1' G B 2 beta 3156 3162 3159 3184 C1' U B 3 beta 3179 3185 3182 3204 C1' A B 4 beta 3199 3205 3202 3226 C1' A B 5 beta 3221 3227 3224 3248 C1' A B 6 beta 3243 3249 3246 3270 C1' A B 7 beta 3265 3271 3268 3292 C1' U B 8 beta 3287 3293 3290 3312 C1' C B 9 beta 3307 3313 3310 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 3139 C2' U B 1 OK 3141 3137 3140 3159 C2' G B 2 OK 3161 3157 3160 3182 C2' U B 3 OK 3184 3180 3183 3202 C2' A B 4 OK 3204 3200 3203 3224 C2' A B 5 OK 3226 3222 3225 3246 C2' A B 6 OK 3248 3244 3247 3268 C2' A B 7 OK 3270 3266 3269 3290 C2' U B 8 OK 3292 3288 3291 3310 C2' C B 9 OK 3312 3308 3311 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 3137 C3' U B 1 OK 3135 3138 3139 3157 C3' G B 2 OK 3155 3158 3159 3180 C3' U B 3 OK 3178 3181 3182 3200 C3' A B 4 OK 3198 3201 3202 3222 C3' A B 5 OK 3220 3223 3224 3244 C3' A B 6 OK 3242 3245 3246 3266 C3' A B 7 OK 3264 3267 3268 3288 C3' U B 8 OK 3286 3289 3290 3308 C3' C B 9 OK 3306 3309 3310 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3135 C4' U B 1 OK 3137 3134 3136 3155 C4' G B 2 OK 3157 3154 3156 3178 C4' U B 3 OK 3180 3177 3179 3198 C4' A B 4 OK 3200 3197 3199 3220 C4' A B 5 OK 3222 3219 3221 3242 C4' A B 6 OK 3244 3241 3243 3264 C4' A B 7 OK 3266 3263 3265 3286 C4' U B 8 OK 3288 3285 3287 3306 C4' C B 9 OK 3308 3305 3307 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 3134 C5' U B 1 3133 3135 3154 C5' G B 2 3153 3155 3177 C5' U B 3 3176 3178 3197 C5' A B 4 3196 3198 3219 C5' A B 5 3218 3220 3241 C5' A B 6 3240 3242 3263 C5' A B 7 3262 3264 3285 C5' U B 8 3284 3286 3305 C5' C B 9 3304 3306 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 3150 P G B 2 distorted distorted 3138 3151 3152 3153 3173 P U B 3 distorted distorted 3158 3174 3175 3176 3193 P A B 4 distorted distorted 3181 3194 3195 3196 3215 P A B 5 distorted distorted 3201 3216 3217 3218 3237 P A B 6 distorted distorted 3223 3238 3239 3240 3259 P A B 7 distorted distorted 3245 3260 3261 3262 3281 P U B 8 distorted distorted 3267 3282 3283 3284 3301 P C B 9 distorted distorted 3289 3302 3303 3304 ---------------------------------------------------------------------------------