ID code: '4R3I' 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' --------------------------------------------------------------------------------- 1290 C1' G B 1 beta 1285 1291 1288 1313 C1' G B 2 beta 1308 1314 1311 1342 C1' 6MZ B 3 beta 1341 1330 1343 1359 C1' C B 4 beta 1354 1360 1357 1379 C1' U B 5 beta 1374 1380 1377 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 1288 C2' G B 1 OK 1290 1286 1289 1311 C2' G B 2 OK 1313 1309 1312 1343 C2' 6MZ B 3 OK 1342 1345 1344 1357 C2' C B 4 OK 1359 1355 1358 1377 C2' U B 5 OK 1379 1375 1378 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 1286 C3' G B 1 OK 1284 1287 1288 1309 C3' G B 2 OK 1307 1310 1311 1345 C3' 6MZ B 3 OK 1340 1346 1343 1355 C3' C B 4 OK 1353 1356 1357 1375 C3' U B 5 OK 1373 1376 1377 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 1284 C4' G B 1 OK 1286 1283 1285 1307 C4' G B 2 OK 1309 1306 1308 1340 C4' 6MZ B 3 OK 1345 1339 1341 1353 C4' C B 4 OK 1355 1352 1354 1373 C4' U B 5 OK 1375 1372 1374 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 1283 C5' G B 1 1282 1284 1306 C5' G B 2 1305 1307 1339 C5' 6MZ B 3 1338 1340 1352 C5' C B 4 1351 1353 1372 C5' U B 5 1371 1373 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1302 P G B 2 distorted distorted 1287 1303 1304 1305 1347 P 6MZ B 3 distorted distorted 1310 1328 1329 1338 1348 P C B 4 distorted distorted 1346 1349 1350 1351 1368 P U B 5 distorted distorted 1356 1369 1370 1371 ---------------------------------------------------------------------------------