ID code: '5JRC' 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' --------------------------------------------------------------------------------- 6218 C1' A E 1 beta 6213 6219 6216 6240 C1' A E 2 beta 6235 6241 6238 6262 C1' A E 3 beta 6257 6263 6260 6284 C1' A E 4 beta 6279 6285 6282 6306 C1' A E 5 beta 6301 6307 6304 6328 C1' A E 6 beta 6323 6329 6326 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 6216 C2' A E 1 OK 6218 6214 6217 6238 C2' A E 2 OK 6240 6236 6239 6260 C2' A E 3 OK 6262 6258 6261 6282 C2' A E 4 OK 6284 6280 6283 6304 C2' A E 5 OK 6306 6302 6305 6326 C2' A E 6 OK 6328 6324 6327 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 6214 C3' A E 1 OK 6212 6215 6216 6236 C3' A E 2 OK 6234 6237 6238 6258 C3' A E 3 OK 6256 6259 6260 6280 C3' A E 4 OK 6278 6281 6282 6302 C3' A E 5 OK 6300 6303 6304 6324 C3' A E 6 OK 6322 6325 6326 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6212 C4' A E 1 OK 6214 6211 6213 6234 C4' A E 2 OK 6236 6233 6235 6256 C4' A E 3 OK 6258 6255 6257 6278 C4' A E 4 OK 6280 6277 6279 6300 C4' A E 5 OK 6302 6299 6301 6322 C4' A E 6 OK 6324 6321 6323 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 6211 C5' A E 1 6210 6212 6233 C5' A E 2 6232 6234 6255 C5' A E 3 6254 6256 6277 C5' A E 4 6276 6278 6299 C5' A E 5 6298 6300 6321 C5' A E 6 6320 6322 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 6229 P A E 2 distorted distorted 6215 6230 6231 6232 6251 P A E 3 distorted distorted 6237 6252 6253 6254 6273 P A E 4 distorted distorted 6259 6274 6275 6276 6295 P A E 5 distorted distorted 6281 6296 6297 6298 6317 P A E 6 distorted distorted 6303 6318 6319 6320 6339 P A E 7 distorted distorted 6325 6340 6341 6342 ---------------------------------------------------------------------------------