ID code: '3T3N' 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' --------------------------------------------------------------------------------- 4321 C1' OMU B 901 beta 4328 4313 4322 4343 C1' OMU B 902 beta 4350 4335 4344 4364 C1' OMC B 903 beta 4370 4356 4365 4385 C1' OMC B 904 beta 4391 4377 4386 4410 C1' OMG B 905 beta 4404 4411 4407 4430 C1' OMU B 906 beta 4437 4422 4431 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 4322 C2' OMU B 901 OK 4321 4325 4323 4344 C2' OMU B 902 OK 4343 4347 4345 4365 C2' OMC B 903 OK 4364 4368 4366 4386 C2' OMC B 904 OK 4385 4389 4387 4407 C2' OMG B 905 OK 4410 4405 4408 4431 C2' OMU B 906 OK 4430 4434 4432 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 4325 C3' OMU B 901 OK 4326 4327 4322 4347 C3' OMU B 902 OK 4348 4349 4344 4368 C3' OMC B 903 OK 4369 4371 4365 4389 C3' OMC B 904 OK 4390 4392 4386 4405 C3' OMG B 905 OK 4403 4406 4407 4434 C3' OMU B 906 OK 4435 4436 4431 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 4326 C4' OMU B 901 OK 4325 4329 4328 4348 C4' OMU B 902 OK 4347 4351 4350 4369 C4' OMC B 903 OK 4368 4372 4370 4390 C4' OMC B 904 OK 4389 4393 4391 4403 C4' OMG B 905 OK 4405 4402 4404 4435 C4' OMU B 906 OK 4434 4438 4437 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 4329 C5' OMU B 901 4330 4326 4351 C5' OMU B 902 4352 4348 4372 C5' OMC B 903 4373 4369 4393 C5' OMC B 904 4394 4390 4402 C5' OMG B 905 4401 4403 4438 C5' OMU B 906 4439 4435 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 4331 P OMU B 901 distorted distorted 4332 4333 4330 4353 P OMU B 902 distorted distorted 4327 4354 4355 4352 4374 P OMC B 903 distorted distorted 4349 4375 4376 4373 4395 P OMC B 904 distorted distorted 4371 4396 4397 4394 4398 P OMG B 905 distorted distorted 4392 4399 4400 4401 4440 P OMU B 906 distorted distorted 4406 4441 4442 4439 ---------------------------------------------------------------------------------