ID code: '5KL1' 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' --------------------------------------------------------------------------------- 3203 C1' A C 1 beta 3198 3204 3201 3225 C1' A C 2 beta 3220 3226 3223 3247 C1' A C 3 beta 3242 3248 3245 3269 C1' U C 4 beta 3264 3270 3267 3289 C1' U C 5 beta 3284 3290 3287 3309 C1' G C 6 beta 3304 3310 3307 3332 C1' U C 7 beta 3327 3333 3330 3352 C1' A C 8 beta 3347 3353 3350 3374 C1' C C 9 beta 3369 3375 3372 3394 C1' A C 10 beta 3389 3395 3392 3416 C1' U C 11 beta 3411 3417 3414 3436 C1' A C 12 beta 3431 3437 3434 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 3201 C2' A C 1 OK 3203 3199 3202 3223 C2' A C 2 OK 3225 3221 3224 3245 C2' A C 3 OK 3247 3243 3246 3267 C2' U C 4 OK 3269 3265 3268 3287 C2' U C 5 OK 3289 3285 3288 3307 C2' G C 6 OK 3309 3305 3308 3330 C2' U C 7 OK 3332 3328 3331 3350 C2' A C 8 OK 3352 3348 3351 3372 C2' C C 9 OK 3374 3370 3373 3392 C2' A C 10 OK 3394 3390 3393 3414 C2' U C 11 OK 3416 3412 3415 3434 C2' A C 12 OK 3436 3432 3435 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 3199 C3' A C 1 OK 3197 3200 3201 3221 C3' A C 2 OK 3219 3222 3223 3243 C3' A C 3 OK 3241 3244 3245 3265 C3' U C 4 OK 3263 3266 3267 3285 C3' U C 5 OK 3283 3286 3287 3305 C3' G C 6 OK 3303 3306 3307 3328 C3' U C 7 OK 3326 3329 3330 3348 C3' A C 8 OK 3346 3349 3350 3370 C3' C C 9 OK 3368 3371 3372 3390 C3' A C 10 OK 3388 3391 3392 3412 C3' U C 11 OK 3410 3413 3414 3432 C3' A C 12 OK 3430 3433 3434 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3197 C4' A C 1 OK 3199 3196 3198 3219 C4' A C 2 OK 3221 3218 3220 3241 C4' A C 3 OK 3243 3240 3242 3263 C4' U C 4 OK 3265 3262 3264 3283 C4' U C 5 OK 3285 3282 3284 3303 C4' G C 6 OK 3305 3302 3304 3326 C4' U C 7 OK 3328 3325 3327 3346 C4' A C 8 OK 3348 3345 3347 3368 C4' C C 9 OK 3370 3367 3369 3388 C4' A C 10 OK 3390 3387 3389 3410 C4' U C 11 OK 3412 3409 3411 3430 C4' A C 12 OK 3432 3429 3431 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 3196 C5' A C 1 3195 3197 3218 C5' A C 2 3217 3219 3240 C5' A C 3 3239 3241 3262 C5' U C 4 3261 3263 3282 C5' U C 5 3281 3283 3302 C5' G C 6 3301 3303 3325 C5' U C 7 3324 3326 3345 C5' A C 8 3344 3346 3367 C5' C C 9 3366 3368 3387 C5' A C 10 3386 3388 3409 C5' U C 11 3408 3410 3429 C5' A C 12 3428 3430 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 3214 P A C 2 distorted distorted 3200 3215 3216 3217 3236 P A C 3 distorted distorted 3222 3237 3238 3239 3258 P U C 4 distorted distorted 3244 3259 3260 3261 3278 P U C 5 distorted distorted 3266 3279 3280 3281 3298 P G C 6 distorted distorted 3286 3299 3300 3301 3321 P U C 7 distorted distorted 3306 3322 3323 3324 3341 P A C 8 distorted distorted 3329 3342 3343 3344 3363 P C C 9 distorted distorted 3349 3364 3365 3366 3383 P A C 10 distorted distorted 3371 3384 3385 3386 3405 P U C 11 distorted distorted 3391 3406 3407 3408 3425 P A C 12 distorted distorted 3413 3426 3427 3428 ---------------------------------------------------------------------------------