ID code: '2KH9' 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' --------------------------------------------------------------------------------- 1426 C1' A B 49 alpha beta 1421 1443 1427 1424 1460 C1' G B 50 alpha beta 1455 1478 1461 1458 1494 C1' A B 51 alpha beta 1489 1511 1495 1492 1527 C1' G B 52 alpha beta 1522 1545 1528 1525 1561 C1' A B 53 alpha beta 1556 1578 1562 1559 1594 C1' U B 54 alpha beta 1589 1610 1595 1592 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 1424 C2' A B 49 OK OK 1426 1422 1441 1425 1458 C2' G B 50 OK OK 1460 1456 1476 1459 1492 C2' A B 51 OK OK 1494 1490 1509 1493 1525 C2' G B 52 OK OK 1527 1523 1543 1526 1559 C2' A B 53 OK OK 1561 1557 1576 1560 1592 C2' U B 54 OK OK 1594 1590 1608 1593 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 1422 C3' A B 49 OK OK 1420 1440 1423 1424 1456 C3' G B 50 OK OK 1454 1475 1457 1458 1490 C3' A B 51 OK OK 1488 1508 1491 1492 1523 C3' G B 52 OK OK 1521 1542 1524 1525 1557 C3' A B 53 OK OK 1555 1575 1558 1559 1590 C3' U B 54 OK OK 1588 1606 1591 1592 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 1420 C4' A B 49 OK OK 1422 1439 1419 1421 1454 C4' G B 50 OK OK 1456 1474 1453 1455 1488 C4' A B 51 OK OK 1490 1507 1487 1489 1521 C4' G B 52 OK OK 1523 1541 1520 1522 1555 C4' A B 53 OK OK 1557 1574 1554 1556 1588 C4' U B 54 OK OK 1590 1605 1587 1589 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 1419 C5' A B 49 OK OK 1418 1437 1438 1420 1453 C5' G B 50 OK OK 1452 1472 1473 1454 1487 C5' A B 51 OK OK 1486 1505 1506 1488 1520 C5' G B 52 OK OK 1519 1539 1540 1521 1554 C5' A B 53 OK OK 1553 1572 1573 1555 1587 C5' U B 54 OK OK 1586 1603 1604 1588 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1449 P G B 50 distorted distorted 1423 1450 1451 1452 1483 P A B 51 distorted distorted 1457 1484 1485 1486 1516 P G B 52 distorted distorted 1491 1517 1518 1519 1550 P A B 53 distorted distorted 1524 1551 1552 1553 1583 P U B 54 distorted distorted 1558 1584 1585 1586 ---------------------------------------------------------------------------------