ID code: '3K5Z' 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' --------------------------------------------------------------------------------- 3149 C1' U B 1 beta 3144 3150 3147 3169 C1' G B 2 beta 3164 3170 3167 3192 C1' U B 3 beta 3187 3193 3190 3212 C1' A B 4 beta 3207 3213 3210 3234 C1' C B 5 beta 3229 3235 3232 3254 C1' C B 6 beta 3249 3255 3252 3274 C1' A B 7 beta 3269 3275 3272 3296 C1' U B 8 beta 3291 3297 3294 3316 C1' A B 9 beta 3311 3317 3314 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 3147 C2' U B 1 OK 3149 3145 3148 3167 C2' G B 2 OK 3169 3165 3168 3190 C2' U B 3 OK 3192 3188 3191 3210 C2' A B 4 OK 3212 3208 3211 3232 C2' C B 5 OK 3234 3230 3233 3252 C2' C B 6 OK 3254 3250 3253 3272 C2' A B 7 OK 3274 3270 3273 3294 C2' U B 8 OK 3296 3292 3295 3314 C2' A B 9 OK 3316 3312 3315 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 3145 C3' U B 1 OK 3143 3146 3147 3165 C3' G B 2 OK 3163 3166 3167 3188 C3' U B 3 OK 3186 3189 3190 3208 C3' A B 4 OK 3206 3209 3210 3230 C3' C B 5 OK 3228 3231 3232 3250 C3' C B 6 OK 3248 3251 3252 3270 C3' A B 7 OK 3268 3271 3272 3292 C3' U B 8 OK 3290 3293 3294 3312 C3' A B 9 OK 3310 3313 3314 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3143 C4' U B 1 OK 3145 3142 3144 3163 C4' G B 2 OK 3165 3162 3164 3186 C4' U B 3 OK 3188 3185 3187 3206 C4' A B 4 OK 3208 3205 3207 3228 C4' C B 5 OK 3230 3227 3229 3248 C4' C B 6 OK 3250 3247 3249 3268 C4' A B 7 OK 3270 3267 3269 3290 C4' U B 8 OK 3292 3289 3291 3310 C4' A B 9 OK 3312 3309 3311 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 3142 C5' U B 1 3141 3143 3162 C5' G B 2 3161 3163 3185 C5' U B 3 3184 3186 3205 C5' A B 4 3204 3206 3227 C5' C B 5 3226 3228 3247 C5' C B 6 3246 3248 3267 C5' A B 7 3266 3268 3289 C5' U B 8 3288 3290 3309 C5' A B 9 3308 3310 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 3158 P G B 2 distorted distorted 3146 3159 3160 3161 3181 P U B 3 distorted distorted 3166 3182 3183 3184 3201 P A B 4 distorted distorted 3189 3202 3203 3204 3223 P C B 5 distorted distorted 3209 3224 3225 3226 3243 P C B 6 distorted distorted 3231 3244 3245 3246 3263 P A B 7 distorted distorted 3251 3264 3265 3266 3285 P U B 8 distorted distorted 3271 3286 3287 3288 3305 P A B 9 distorted distorted 3293 3306 3307 3308 ---------------------------------------------------------------------------------