ID code: '3T3O' 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' --------------------------------------------------------------------------------- 4340 C1' OMC B 901 beta 4346 4332 4341 4362 C1' OMU B 902 beta 4369 4354 4363 4387 C1' OMG B 903 beta 4381 4388 4384 4411 C1' OMG B 904 beta 4405 4412 4408 4434 C1' U B 905 beta 4429 4435 4432 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 4341 C2' OMC B 901 OK 4340 4344 4342 4363 C2' OMU B 902 OK 4362 4366 4364 4384 C2' OMG B 903 OK 4387 4382 4385 4408 C2' OMG B 904 OK 4411 4406 4409 4432 C2' U B 905 OK 4434 4430 4433 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 4344 C3' OMC B 901 OK 4345 4347 4341 4366 C3' OMU B 902 OK 4367 4368 4363 4382 C3' OMG B 903 OK 4380 4383 4384 4406 C3' OMG B 904 OK 4404 4407 4408 4430 C3' U B 905 OK 4428 4431 4432 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 4345 C4' OMC B 901 OK 4344 4348 4346 4367 C4' OMU B 902 OK 4366 4370 4369 4380 C4' OMG B 903 OK 4382 4379 4381 4404 C4' OMG B 904 OK 4406 4403 4405 4428 C4' U B 905 OK 4430 4427 4429 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 4348 C5' OMC B 901 4349 4345 4370 C5' OMU B 902 4371 4367 4379 C5' OMG B 903 4378 4380 4403 C5' OMG B 904 4402 4404 4427 C5' U B 905 4426 4428 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 4350 P OMC B 901 distorted distorted 4351 4352 4349 4372 P OMU B 902 distorted distorted 4347 4373 4374 4371 4375 P OMG B 903 distorted distorted 4368 4376 4377 4378 4399 P OMG B 904 distorted distorted 4383 4400 4401 4402 4423 P U B 905 distorted distorted 4407 4424 4425 4426 ---------------------------------------------------------------------------------