ID code: '3K62' 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' --------------------------------------------------------------------------------- 3192 C1' U B 1 beta 3187 3193 3190 3212 C1' G B 2 beta 3207 3213 3210 3235 C1' U B 3 beta 3230 3236 3233 3255 C1' G B 4 beta 3250 3256 3253 3278 C1' U B 5 beta 3273 3279 3276 3298 C1' U B 6 beta 3293 3299 3296 3318 C1' A B 7 beta 3313 3319 3316 3340 C1' U B 8 beta 3335 3341 3338 3360 C1' C B 9 beta 3355 3361 3358 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 3190 C2' U B 1 OK 3192 3188 3191 3210 C2' G B 2 OK 3212 3208 3211 3233 C2' U B 3 OK 3235 3231 3234 3253 C2' G B 4 OK 3255 3251 3254 3276 C2' U B 5 OK 3278 3274 3277 3296 C2' U B 6 OK 3298 3294 3297 3316 C2' A B 7 OK 3318 3314 3317 3338 C2' U B 8 OK 3340 3336 3339 3358 C2' C B 9 OK 3360 3356 3359 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 3188 C3' U B 1 OK 3186 3189 3190 3208 C3' G B 2 OK 3206 3209 3210 3231 C3' U B 3 OK 3229 3232 3233 3251 C3' G B 4 OK 3249 3252 3253 3274 C3' U B 5 OK 3272 3275 3276 3294 C3' U B 6 OK 3292 3295 3296 3314 C3' A B 7 OK 3312 3315 3316 3336 C3' U B 8 OK 3334 3337 3338 3356 C3' C B 9 OK 3354 3357 3358 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3186 C4' U B 1 OK 3188 3185 3187 3206 C4' G B 2 OK 3208 3205 3207 3229 C4' U B 3 OK 3231 3228 3230 3249 C4' G B 4 OK 3251 3248 3250 3272 C4' U B 5 OK 3274 3271 3273 3292 C4' U B 6 OK 3294 3291 3293 3312 C4' A B 7 OK 3314 3311 3313 3334 C4' U B 8 OK 3336 3333 3335 3354 C4' C B 9 OK 3356 3353 3355 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 3185 C5' U B 1 3184 3186 3205 C5' G B 2 3204 3206 3228 C5' U B 3 3227 3229 3248 C5' G B 4 3247 3249 3271 C5' U B 5 3270 3272 3291 C5' U B 6 3290 3292 3311 C5' A B 7 3310 3312 3333 C5' U B 8 3332 3334 3353 C5' C B 9 3352 3354 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 3201 P G B 2 distorted distorted 3189 3202 3203 3204 3224 P U B 3 distorted distorted 3209 3225 3226 3227 3244 P G B 4 distorted distorted 3232 3245 3246 3247 3267 P U B 5 distorted distorted 3252 3268 3269 3270 3287 P U B 6 distorted distorted 3275 3288 3289 3290 3307 P A B 7 distorted distorted 3295 3308 3309 3310 3329 P U B 8 distorted distorted 3315 3330 3331 3332 3349 P C B 9 distorted distorted 3337 3350 3351 3352 ---------------------------------------------------------------------------------