ID code: '2XLJ' 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' --------------------------------------------------------------------------------- 1427 C1' C B 6 beta 1422 1428 1425 1447 C1' U B 7 beta 1442 1448 1445 1467 C1' G B 8 beta 1462 1468 1465 1490 C1' C B 9 beta 1485 1491 1488 1510 C1' C B 10 beta 1505 1511 1508 1530 C1' G B 11 beta 1525 1531 1528 1553 C1' U B 12 beta 1548 1554 1551 1573 C1' A B 13 beta 1568 1574 1571 1595 C1' U B 14 beta 1590 1596 1593 1615 C1' A B 15 beta 1610 1616 1613 1637 C1' G B 16 beta 1632 1638 1635 1660 C1' G B 17 beta 1655 1661 1658 1683 C1' C B 18 beta 1678 1684 1681 1703 C1' A B 19 beta 1698 1704 1701 1724 C1' DG B 20 beta 1720 1725 1723 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 1425 C2' C B 6 OK 1427 1423 1426 1445 C2' U B 7 OK 1447 1443 1446 1465 C2' G B 8 OK 1467 1463 1466 1488 C2' C B 9 OK 1490 1486 1489 1508 C2' C B 10 OK 1510 1506 1509 1528 C2' G B 11 OK 1530 1526 1529 1551 C2' U B 12 OK 1553 1549 1552 1571 C2' A B 13 OK 1573 1569 1572 1593 C2' U B 14 OK 1595 1591 1594 1613 C2' A B 15 OK 1615 1611 1614 1635 C2' G B 16 OK 1637 1633 1636 1658 C2' G B 17 OK 1660 1656 1659 1681 C2' C B 18 OK 1683 1679 1682 1701 C2' A B 19 OK 1703 1699 1702 1723 C2' DG B 20 1724 1721 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 1423 C3' C B 6 OK 1421 1424 1425 1443 C3' U B 7 OK 1441 1444 1445 1463 C3' G B 8 OK 1461 1464 1465 1486 C3' C B 9 OK 1484 1487 1488 1506 C3' C B 10 OK 1504 1507 1508 1526 C3' G B 11 OK 1524 1527 1528 1549 C3' U B 12 OK 1547 1550 1551 1569 C3' A B 13 OK 1567 1570 1571 1591 C3' U B 14 OK 1589 1592 1593 1611 C3' A B 15 OK 1609 1612 1613 1633 C3' G B 16 OK 1631 1634 1635 1656 C3' G B 17 OK 1654 1657 1658 1679 C3' C B 18 OK 1677 1680 1681 1699 C3' A B 19 OK 1697 1700 1701 1721 C3' DG B 20 OK 1719 1722 1723 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 1421 C4' C B 6 OK 1423 1420 1422 1441 C4' U B 7 OK 1443 1440 1442 1461 C4' G B 8 OK 1463 1460 1462 1484 C4' C B 9 OK 1486 1483 1485 1504 C4' C B 10 OK 1506 1503 1505 1524 C4' G B 11 OK 1526 1523 1525 1547 C4' U B 12 OK 1549 1546 1548 1567 C4' A B 13 OK 1569 1566 1568 1589 C4' U B 14 OK 1591 1588 1590 1609 C4' A B 15 OK 1611 1608 1610 1631 C4' G B 16 OK 1633 1630 1632 1654 C4' G B 17 OK 1656 1653 1655 1677 C4' C B 18 OK 1679 1676 1678 1697 C4' A B 19 OK 1699 1696 1698 1719 C4' DG B 20 OK 1721 1718 1720 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 1420 C5' C B 6 1419 1421 1440 C5' U B 7 1439 1441 1460 C5' G B 8 1459 1461 1483 C5' C B 9 1482 1484 1503 C5' C B 10 1502 1504 1523 C5' G B 11 1522 1524 1546 C5' U B 12 1545 1547 1566 C5' A B 13 1565 1567 1588 C5' U B 14 1587 1589 1608 C5' A B 15 1607 1609 1630 C5' G B 16 1629 1631 1653 C5' G B 17 1652 1654 1676 C5' C B 18 1675 1677 1696 C5' A B 19 1695 1697 1718 C5' DG B 20 1717 1719 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1436 P U B 7 distorted distorted 1424 1437 1438 1439 1456 P G B 8 distorted distorted 1444 1457 1458 1459 1479 P C B 9 distorted distorted 1464 1480 1481 1482 1499 P C B 10 distorted distorted 1487 1500 1501 1502 1519 P G B 11 distorted distorted 1507 1520 1521 1522 1542 P U B 12 OK OK 1527 1543 1544 1545 1562 P A B 13 distorted distorted 1550 1563 1564 1565 1584 P U B 14 distorted distorted 1570 1585 1586 1587 1604 P A B 15 OK OK 1592 1605 1606 1607 1626 P G B 16 distorted distorted 1612 1627 1628 1629 1649 P G B 17 OK OK 1634 1650 1651 1652 1672 P C B 18 distorted distorted 1657 1673 1674 1675 1692 P A B 19 distorted distorted 1680 1693 1694 1695 1714 P DG B 20 distorted distorted 1700 1715 1716 1717 1736 P C B 21 distorted distorted 1722 1737 1738 1739 ---------------------------------------------------------------------------------