ID code: '3NNC' 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' --------------------------------------------------------------------------------- 1389 C1' U B 1 beta 1384 1390 1387 1409 C1' U B 2 beta 1404 1410 1407 1429 C1' G B 3 beta 1424 1430 1427 1452 C1' U B 4 beta 1447 1453 1450 1472 C1' G B 5 beta 1467 1473 1470 1495 C1' U B 6 beta 1490 1496 1493 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 1387 C2' U B 1 OK 1389 1385 1388 1407 C2' U B 2 OK 1409 1405 1408 1427 C2' G B 3 OK 1429 1425 1428 1450 C2' U B 4 OK 1452 1448 1451 1470 C2' G B 5 OK 1472 1468 1471 1493 C2' U B 6 OK 1495 1491 1494 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 1385 C3' U B 1 OK 1383 1386 1387 1405 C3' U B 2 OK 1403 1406 1407 1425 C3' G B 3 OK 1423 1426 1427 1448 C3' U B 4 OK 1446 1449 1450 1468 C3' G B 5 OK 1466 1469 1470 1491 C3' U B 6 OK 1489 1492 1493 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 1383 C4' U B 1 OK 1385 1382 1384 1403 C4' U B 2 OK 1405 1402 1404 1423 C4' G B 3 OK 1425 1422 1424 1446 C4' U B 4 OK 1448 1445 1447 1466 C4' G B 5 OK 1468 1465 1467 1489 C4' U B 6 OK 1491 1488 1490 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 1382 C5' U B 1 1381 1383 1402 C5' U B 2 1401 1403 1422 C5' G B 3 1421 1423 1445 C5' U B 4 1444 1446 1465 C5' G B 5 1464 1466 1488 C5' U B 6 1487 1489 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1378 P U B 1 distorted distorted 1379 1380 1381 1398 P U B 2 distorted distorted 1386 1399 1400 1401 1418 P G B 3 distorted distorted 1406 1419 1420 1421 1441 P U B 4 distorted distorted 1426 1442 1443 1444 1461 P G B 5 distorted distorted 1449 1462 1463 1464 1484 P U B 6 distorted distorted 1469 1485 1486 1487 1504 P G B 7 distorted distorted 1492 1505 1506 1507 ---------------------------------------------------------------------------------