ID code: '4B8T' 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' --------------------------------------------------------------------------------- 1548 C1' A B 1 alpha beta 1543 1565 1549 1546 1581 C1' G B 2 alpha beta 1576 1599 1582 1579 1615 C1' G B 3 alpha beta 1610 1633 1616 1613 1649 C1' G B 4 alpha beta 1644 1667 1650 1647 1683 C1' U B 5 alpha beta 1678 1699 1684 1681 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 1546 C2' A B 1 OK OK 1548 1544 1563 1547 1579 C2' G B 2 OK OK 1581 1577 1597 1580 1613 C2' G B 3 OK OK 1615 1611 1631 1614 1647 C2' G B 4 OK OK 1649 1645 1665 1648 1681 C2' U B 5 OK OK 1683 1679 1697 1682 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 1544 C3' A B 1 OK OK 1542 1562 1545 1546 1577 C3' G B 2 OK OK 1575 1596 1578 1579 1611 C3' G B 3 OK OK 1609 1630 1612 1613 1645 C3' G B 4 OK OK 1643 1664 1646 1647 1679 C3' U B 5 OK OK 1677 1695 1680 1681 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 1542 C4' A B 1 OK OK 1544 1561 1541 1543 1575 C4' G B 2 OK OK 1577 1595 1574 1576 1609 C4' G B 3 OK OK 1611 1629 1608 1610 1643 C4' G B 4 OK OK 1645 1663 1642 1644 1677 C4' U B 5 OK OK 1679 1694 1676 1678 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 1541 C5' A B 1 OK OK 1540 1559 1560 1542 1574 C5' G B 2 OK OK 1573 1593 1594 1575 1608 C5' G B 3 OK OK 1607 1627 1628 1609 1642 C5' G B 4 OK OK 1641 1661 1662 1643 1676 C5' U B 5 OK OK 1675 1692 1693 1677 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1537 P A B 1 OK OK 1538 1539 1540 1570 P G B 2 OK OK 1545 1571 1572 1573 1604 P G B 3 OK OK 1578 1605 1606 1607 1638 P G B 4 OK OK 1612 1639 1640 1641 1672 P U B 5 OK OK 1646 1673 1674 1675 ---------------------------------------------------------------------------------