ID code: '3NNA' 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' --------------------------------------------------------------------------------- 1388 C1' U B 1 beta 1383 1389 1386 1408 C1' U B 2 beta 1403 1409 1406 1428 C1' G B 3 beta 1423 1429 1426 1451 C1' U B 4 beta 1446 1452 1449 1471 C1' U B 5 beta 1466 1472 1469 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 1386 C2' U B 1 OK 1388 1384 1387 1406 C2' U B 2 OK 1408 1404 1407 1426 C2' G B 3 OK 1428 1424 1427 1449 C2' U B 4 OK 1451 1447 1450 1469 C2' U B 5 OK 1471 1467 1470 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 1384 C3' U B 1 OK 1382 1385 1386 1404 C3' U B 2 OK 1402 1405 1406 1424 C3' G B 3 OK 1422 1425 1426 1447 C3' U B 4 OK 1445 1448 1449 1467 C3' U B 5 OK 1465 1468 1469 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 1382 C4' U B 1 OK 1384 1381 1383 1402 C4' U B 2 OK 1404 1401 1403 1422 C4' G B 3 OK 1424 1421 1423 1445 C4' U B 4 OK 1447 1444 1446 1465 C4' U B 5 OK 1467 1464 1466 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 1381 C5' U B 1 1380 1382 1401 C5' U B 2 1400 1402 1421 C5' G B 3 1420 1422 1444 C5' U B 4 1443 1445 1464 C5' U B 5 1463 1465 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1377 P U B 1 distorted distorted 1378 1379 1380 1397 P U B 2 distorted distorted 1385 1398 1399 1400 1417 P G B 3 distorted distorted 1405 1418 1419 1420 1440 P U B 4 distorted distorted 1425 1441 1442 1443 1460 P U B 5 distorted distorted 1448 1461 1462 1463 ---------------------------------------------------------------------------------