ID code: '3K5Q' 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' --------------------------------------------------------------------------------- 3195 C1' U B 1 beta 3190 3196 3193 3215 C1' G B 2 beta 3210 3216 3213 3238 C1' U B 3 beta 3233 3239 3236 3258 C1' A B 4 beta 3253 3259 3256 3280 C1' C B 5 beta 3275 3281 3278 3300 C1' U B 6 beta 3295 3301 3298 3320 C1' A B 7 beta 3315 3321 3318 3342 C1' U B 8 beta 3337 3343 3340 3362 C1' A B 9 beta 3357 3363 3360 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 3193 C2' U B 1 OK 3195 3191 3194 3213 C2' G B 2 OK 3215 3211 3214 3236 C2' U B 3 OK 3238 3234 3237 3256 C2' A B 4 OK 3258 3254 3257 3278 C2' C B 5 OK 3280 3276 3279 3298 C2' U B 6 OK 3300 3296 3299 3318 C2' A B 7 OK 3320 3316 3319 3340 C2' U B 8 OK 3342 3338 3341 3360 C2' A B 9 OK 3362 3358 3361 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 3191 C3' U B 1 OK 3189 3192 3193 3211 C3' G B 2 OK 3209 3212 3213 3234 C3' U B 3 OK 3232 3235 3236 3254 C3' A B 4 OK 3252 3255 3256 3276 C3' C B 5 OK 3274 3277 3278 3296 C3' U B 6 OK 3294 3297 3298 3316 C3' A B 7 OK 3314 3317 3318 3338 C3' U B 8 OK 3336 3339 3340 3358 C3' A B 9 OK 3356 3359 3360 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3189 C4' U B 1 OK 3191 3188 3190 3209 C4' G B 2 OK 3211 3208 3210 3232 C4' U B 3 OK 3234 3231 3233 3252 C4' A B 4 OK 3254 3251 3253 3274 C4' C B 5 OK 3276 3273 3275 3294 C4' U B 6 OK 3296 3293 3295 3314 C4' A B 7 OK 3316 3313 3315 3336 C4' U B 8 OK 3338 3335 3337 3356 C4' A B 9 OK 3358 3355 3357 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 3188 C5' U B 1 3187 3189 3208 C5' G B 2 3207 3209 3231 C5' U B 3 3230 3232 3251 C5' A B 4 3250 3252 3273 C5' C B 5 3272 3274 3293 C5' U B 6 3292 3294 3313 C5' A B 7 3312 3314 3335 C5' U B 8 3334 3336 3355 C5' A B 9 3354 3356 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 3184 P U B 1 distorted distorted 3185 3186 3187 3204 P G B 2 distorted distorted 3192 3205 3206 3207 3227 P U B 3 distorted distorted 3212 3228 3229 3230 3247 P A B 4 distorted distorted 3235 3248 3249 3250 3269 P C B 5 distorted distorted 3255 3270 3271 3272 3289 P U B 6 distorted distorted 3277 3290 3291 3292 3309 P A B 7 distorted distorted 3297 3310 3311 3312 3331 P U B 8 distorted distorted 3317 3332 3333 3334 3351 P A B 9 distorted distorted 3339 3352 3353 3354 ---------------------------------------------------------------------------------