ID code: '5GXH' 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' --------------------------------------------------------------------------------- 5230 C1' A B 2 beta 5225 5231 5228 5252 C1' U B 3 beta 5247 5253 5250 5272 C1' U B 4 beta 5267 5273 5270 5292 C1' U B 5 beta 5287 5293 5290 5337 C1' G B 8 beta 5332 5338 5335 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 5228 C2' A B 2 OK 5230 5226 5229 5250 C2' U B 3 OK 5252 5248 5251 5270 C2' U B 4 OK 5272 5268 5271 5290 C2' U B 5 OK 5292 5288 5291 5335 C2' G B 8 OK 5337 5333 5336 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5226 C3' A B 2 OK 5224 5227 5228 5248 C3' U B 3 OK 5246 5249 5250 5268 C3' U B 4 OK 5266 5269 5270 5288 C3' U B 5 OK 5286 5289 5290 5333 C3' G B 8 OK 5331 5334 5335 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 5224 C4' A B 2 OK 5226 5223 5225 5246 C4' U B 3 OK 5248 5245 5247 5266 C4' U B 4 OK 5268 5265 5267 5286 C4' U B 5 OK 5288 5285 5287 5331 C4' G B 8 OK 5333 5330 5332 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5223 C5' A B 2 5222 5224 5245 C5' U B 3 5244 5246 5265 C5' U B 4 5264 5266 5285 C5' U B 5 5284 5286 5330 C5' G B 8 5329 5331 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 5241 P U B 3 distorted distorted 5227 5242 5243 5244 5261 P U B 4 distorted distorted 5249 5262 5263 5264 5281 P U B 5 distorted distorted 5269 5282 5283 5284 5301 P U B 6 5289 5306 P U B 7 5326 P G B 8 distorted distorted 5327 5328 5329 ---------------------------------------------------------------------------------