ID code: '4Z92' 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' --------------------------------------------------------------------------------- 5297 C1' A D 1 beta 5292 5298 5295 5319 C1' U D 2 beta 5314 5320 5317 5339 C1' U D 3 beta 5334 5340 5337 5359 C1' U D 4 beta 5354 5360 5357 5379 C1' U D 5 beta 5374 5380 5377 5399 C1' U D 6 beta 5394 5400 5397 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 5295 C2' A D 1 OK 5297 5293 5296 5317 C2' U D 2 OK 5319 5315 5318 5337 C2' U D 3 OK 5339 5335 5338 5357 C2' U D 4 OK 5359 5355 5358 5377 C2' U D 5 OK 5379 5375 5378 5397 C2' U D 6 OK 5399 5395 5398 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5293 C3' A D 1 OK 5291 5294 5295 5315 C3' U D 2 OK 5313 5316 5317 5335 C3' U D 3 OK 5333 5336 5337 5355 C3' U D 4 OK 5353 5356 5357 5375 C3' U D 5 OK 5373 5376 5377 5395 C3' U D 6 OK 5393 5396 5397 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 5291 C4' A D 1 OK 5293 5290 5292 5313 C4' U D 2 OK 5315 5312 5314 5333 C4' U D 3 OK 5335 5332 5334 5353 C4' U D 4 OK 5355 5352 5354 5373 C4' U D 5 OK 5375 5372 5374 5393 C4' U D 6 OK 5395 5392 5394 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5290 C5' A D 1 5289 5291 5312 C5' U D 2 5311 5313 5332 C5' U D 3 5331 5333 5352 C5' U D 4 5351 5353 5372 C5' U D 5 5371 5373 5392 C5' U D 6 5391 5393 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 5308 P U D 2 distorted distorted 5294 5309 5310 5311 5328 P U D 3 distorted distorted 5316 5329 5330 5331 5348 P U D 4 distorted distorted 5336 5349 5350 5351 5368 P U D 5 distorted distorted 5356 5369 5370 5371 5388 P U D 6 distorted distorted 5376 5389 5390 5391 ---------------------------------------------------------------------------------