ID code: '5DET' 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' --------------------------------------------------------------------------------- 1505 C1' U Q 1 beta 1500 1506 1503 1525 C1' C Q 2 beta 1520 1526 1523 1545 C1' A Q 3 beta 1540 1546 1543 1567 C1' C Q 4 beta 1562 1568 1565 1587 C1' U Q 5 beta 1582 1588 1585 1605 C1' U P 1 beta 1600 1606 1603 1625 C1' C P 2 beta 1620 1626 1623 1645 C1' A P 3 beta 1640 1646 1643 1667 C1' C P 4 beta 1662 1668 1665 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 1503 C2' U Q 1 OK 1505 1501 1504 1523 C2' C Q 2 OK 1525 1521 1524 1543 C2' A Q 3 OK 1545 1541 1544 1565 C2' C Q 4 OK 1567 1563 1566 1585 C2' U Q 5 OK 1587 1583 1586 1603 C2' U P 1 OK 1605 1601 1604 1623 C2' C P 2 OK 1625 1621 1624 1643 C2' A P 3 OK 1645 1641 1644 1665 C2' C P 4 OK 1667 1663 1666 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 1501 C3' U Q 1 OK 1499 1502 1503 1521 C3' C Q 2 OK 1519 1522 1523 1541 C3' A Q 3 OK 1539 1542 1543 1563 C3' C Q 4 OK 1561 1564 1565 1583 C3' U Q 5 OK 1581 1584 1585 1601 C3' U P 1 OK 1599 1602 1603 1621 C3' C P 2 OK 1619 1622 1623 1641 C3' A P 3 OK 1639 1642 1643 1663 C3' C P 4 OK 1661 1664 1665 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 1499 C4' U Q 1 OK 1501 1498 1500 1519 C4' C Q 2 OK 1521 1518 1520 1539 C4' A Q 3 OK 1541 1538 1540 1561 C4' C Q 4 OK 1563 1560 1562 1581 C4' U Q 5 OK 1583 1580 1582 1599 C4' U P 1 OK 1601 1598 1600 1619 C4' C P 2 OK 1621 1618 1620 1639 C4' A P 3 OK 1641 1638 1640 1661 C4' C P 4 OK 1663 1660 1662 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 1498 C5' U Q 1 1497 1499 1518 C5' C Q 2 1517 1519 1538 C5' A Q 3 1537 1539 1560 C5' C Q 4 1559 1561 1580 C5' U Q 5 1579 1581 1598 C5' U P 1 1597 1599 1618 C5' C P 2 1617 1619 1638 C5' A P 3 1637 1639 1660 C5' C P 4 1659 1661 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1494 P U Q 1 distorted distorted 1495 1496 1497 1514 P C Q 2 distorted distorted 1502 1515 1516 1517 1534 P A Q 3 distorted distorted 1522 1535 1536 1537 1556 P C Q 4 distorted distorted 1542 1557 1558 1559 1576 P U Q 5 distorted distorted 1564 1577 1578 1579 1614 P C P 2 distorted distorted 1602 1615 1616 1617 1634 P A P 3 distorted distorted 1622 1635 1636 1637 1656 P C P 4 distorted distorted 1642 1657 1658 1659 ---------------------------------------------------------------------------------