ID code: '2ERR' 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' --------------------------------------------------------------------------------- 1425 C1' U B 197 alpha beta 1420 1440 1426 1423 1456 C1' G B 198 alpha beta 1451 1474 1457 1454 1490 C1' C B 199 alpha beta 1485 1505 1491 1488 1521 C1' A B 200 alpha beta 1516 1538 1522 1519 1554 C1' U B 201 alpha beta 1549 1569 1555 1552 1584 C1' G B 202 alpha beta 1579 1602 1585 1582 1618 C1' U B 203 alpha beta 1613 1634 1619 1616 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 1423 C2' U B 197 OK OK 1425 1421 1438 1424 1454 C2' G B 198 OK OK 1456 1452 1472 1455 1488 C2' C B 199 OK OK 1490 1486 1503 1489 1519 C2' A B 200 OK OK 1521 1517 1536 1520 1552 C2' U B 201 OK OK 1554 1550 1567 1553 1582 C2' G B 202 OK OK 1584 1580 1600 1583 1616 C2' U B 203 OK OK 1618 1614 1632 1617 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 1421 C3' U B 197 OK OK 1419 1437 1422 1423 1452 C3' G B 198 OK OK 1450 1471 1453 1454 1486 C3' C B 199 OK OK 1484 1502 1487 1488 1517 C3' A B 200 OK OK 1515 1535 1518 1519 1550 C3' U B 201 OK OK 1548 1566 1551 1552 1580 C3' G B 202 OK OK 1578 1599 1581 1582 1614 C3' U B 203 OK OK 1612 1630 1615 1616 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 1419 C4' U B 197 OK OK 1421 1436 1418 1420 1450 C4' G B 198 OK OK 1452 1470 1449 1451 1484 C4' C B 199 OK OK 1486 1501 1483 1485 1515 C4' A B 200 OK OK 1517 1534 1514 1516 1548 C4' U B 201 OK OK 1550 1565 1547 1549 1578 C4' G B 202 OK OK 1580 1598 1577 1579 1612 C4' U B 203 OK OK 1614 1629 1611 1613 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 1418 C5' U B 197 OK OK 1417 1434 1435 1419 1449 C5' G B 198 OK OK 1448 1468 1469 1450 1483 C5' C B 199 OK OK 1482 1499 1500 1484 1514 C5' A B 200 OK OK 1513 1532 1533 1515 1547 C5' U B 201 OK OK 1546 1563 1564 1548 1577 C5' G B 202 OK OK 1576 1596 1597 1578 1611 C5' U B 203 OK OK 1610 1627 1628 1612 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1445 P G B 198 distorted distorted 1422 1446 1447 1448 1479 P C B 199 distorted distorted 1453 1480 1481 1482 1510 P A B 200 distorted distorted 1487 1511 1512 1513 1543 P U B 201 distorted distorted 1518 1544 1545 1546 1573 P G B 202 distorted distorted 1551 1574 1575 1576 1607 P U B 203 distorted distorted 1581 1608 1609 1610 ---------------------------------------------------------------------------------