ID code: '5HK0' 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' --------------------------------------------------------------------------------- 3264 C1' U E 1 beta 3259 3265 3262 3284 C1' C E 2 beta 3279 3285 3282 3303 C1' DU E 3 beta 3299 3304 3302 3323 C1' C E 4 beta 3318 3324 3321 3343 C1' C E 5 beta 3338 3344 3341 3363 C1' DU F 3 beta 3359 3364 3362 3383 C1' C F 4 beta 3378 3384 3381 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 3262 C2' U E 1 OK 3264 3260 3263 3282 C2' C E 2 OK 3284 3280 3283 3302 C2' DU E 3 3303 3300 3321 C2' C E 4 OK 3323 3319 3322 3341 C2' C E 5 OK 3343 3339 3342 3362 C2' DU F 3 3363 3360 3381 C2' C F 4 OK 3383 3379 3382 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 3260 C3' U E 1 OK 3258 3261 3262 3280 C3' C E 2 OK 3278 3281 3282 3300 C3' DU E 3 OK 3298 3301 3302 3319 C3' C E 4 OK 3317 3320 3321 3339 C3' C E 5 OK 3337 3340 3341 3360 C3' DU F 3 OK 3358 3361 3362 3379 C3' C F 4 OK 3377 3380 3381 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3258 C4' U E 1 OK 3260 3257 3259 3278 C4' C E 2 OK 3280 3277 3279 3298 C4' DU E 3 OK 3300 3297 3299 3317 C4' C E 4 OK 3319 3316 3318 3337 C4' C E 5 OK 3339 3336 3338 3358 C4' DU F 3 OK 3360 3357 3359 3377 C4' C F 4 OK 3379 3376 3378 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 3257 C5' U E 1 3256 3258 3277 C5' C E 2 3276 3278 3297 C5' DU E 3 3296 3298 3316 C5' C E 4 3315 3317 3336 C5' C E 5 3335 3337 3357 C5' DU F 3 3356 3358 3376 C5' C F 4 3375 3377 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 3253 P U E 1 distorted distorted 3254 3255 3256 3273 P C E 2 distorted distorted 3261 3274 3275 3276 3293 P DU E 3 distorted distorted 3281 3294 3295 3296 3312 P C E 4 distorted distorted 3301 3313 3314 3315 3332 P C E 5 distorted distorted 3320 3333 3334 3335 3353 P DU F 3 distorted distorted 3354 3355 3356 3372 P C F 4 distorted distorted 3361 3373 3374 3375 ---------------------------------------------------------------------------------