ID code: '3QGB' 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' --------------------------------------------------------------------------------- 3193 C1' U B 1 beta 3188 3194 3191 3213 C1' G B 2 beta 3208 3214 3211 3236 C1' U B 3 beta 3231 3237 3234 3256 C1' G B 4 beta 3251 3257 3254 3279 C1' C B 5 beta 3274 3280 3277 3299 C1' C B 6 beta 3294 3300 3297 3319 C1' A B 7 beta 3314 3320 3317 3341 C1' U B 8 beta 3336 3342 3339 3361 C1' A B 9 beta 3356 3362 3359 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 3191 C2' U B 1 OK 3193 3189 3192 3211 C2' G B 2 OK 3213 3209 3212 3234 C2' U B 3 OK 3236 3232 3235 3254 C2' G B 4 OK 3256 3252 3255 3277 C2' C B 5 OK 3279 3275 3278 3297 C2' C B 6 OK 3299 3295 3298 3317 C2' A B 7 OK 3319 3315 3318 3339 C2' U B 8 OK 3341 3337 3340 3359 C2' A B 9 OK 3361 3357 3360 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 3189 C3' U B 1 OK 3187 3190 3191 3209 C3' G B 2 OK 3207 3210 3211 3232 C3' U B 3 OK 3230 3233 3234 3252 C3' G B 4 OK 3250 3253 3254 3275 C3' C B 5 OK 3273 3276 3277 3295 C3' C B 6 OK 3293 3296 3297 3315 C3' A B 7 OK 3313 3316 3317 3337 C3' U B 8 OK 3335 3338 3339 3357 C3' A B 9 OK 3355 3358 3359 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3187 C4' U B 1 OK 3189 3186 3188 3207 C4' G B 2 OK 3209 3206 3208 3230 C4' U B 3 OK 3232 3229 3231 3250 C4' G B 4 OK 3252 3249 3251 3273 C4' C B 5 OK 3275 3272 3274 3293 C4' C B 6 OK 3295 3292 3294 3313 C4' A B 7 OK 3315 3312 3314 3335 C4' U B 8 OK 3337 3334 3336 3355 C4' A B 9 OK 3357 3354 3356 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 3186 C5' U B 1 3185 3187 3206 C5' G B 2 3205 3207 3229 C5' U B 3 3228 3230 3249 C5' G B 4 3248 3250 3272 C5' C B 5 3271 3273 3292 C5' C B 6 3291 3293 3312 C5' A B 7 3311 3313 3334 C5' U B 8 3333 3335 3354 C5' A B 9 3353 3355 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 3202 P G B 2 distorted distorted 3190 3203 3204 3205 3225 P U B 3 distorted distorted 3210 3226 3227 3228 3245 P G B 4 distorted distorted 3233 3246 3247 3248 3268 P C B 5 distorted distorted 3253 3269 3270 3271 3288 P C B 6 distorted distorted 3276 3289 3290 3291 3308 P A B 7 distorted distorted 3296 3309 3310 3311 3330 P U B 8 distorted distorted 3316 3331 3332 3333 3350 P A B 9 distorted distorted 3338 3351 3352 3353 ---------------------------------------------------------------------------------