ID code: '1A6Y' 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' --------------------------------------------------------------------------------- 1298 C1' C C 600 beta 1294 1299 1297 1317 C1' A C 601 beta 1313 1318 1316 1338 C1' A C 602 beta 1334 1339 1337 1359 C1' C C 603 beta 1355 1360 1358 1378 C1' T C 604 beta 1374 1379 1377 1398 C1' A C 605 beta 1394 1399 1397 1419 C1' G C 606 beta 1415 1420 1418 1441 C1' G C 607 beta 1437 1442 1440 1463 C1' T C 608 beta 1459 1464 1462 1483 C1' C C 609 beta 1479 1484 1482 1502 C1' A C 610 beta 1498 1503 1501 1523 C1' C C 611 beta 1519 1524 1522 1542 C1' 5IT C 612 beta 1538 1543 1541 1562 C1' A C 613 beta 1558 1563 1561 1583 C1' G C 614 beta 1579 1584 1582 1605 C1' G C 615 beta 1601 1606 1604 1627 C1' T C 616 beta 1623 1628 1626 1647 C1' C C 617 beta 1643 1648 1646 1666 C1' A C 618 beta 1662 1667 1665 1687 C1' G C 619 beta 1683 1688 1686 1707 C1' C D 621 beta 1703 1708 1706 1726 C1' T D 622 beta 1722 1727 1725 1746 C1' G D 623 beta 1742 1747 1745 1768 C1' A D 624 beta 1764 1769 1767 1789 C1' C D 625 beta 1785 1790 1788 1808 C1' C D 626 beta 1804 1809 1807 1827 C1' T D 627 beta 1823 1828 1826 1847 C1' A D 628 beta 1843 1848 1846 1868 C1' G D 629 beta 1864 1869 1867 1890 C1' T D 630 beta 1886 1891 1889 1910 C1' G D 631 beta 1906 1911 1909 1932 C1' A D 632 beta 1928 1933 1931 1953 C1' C D 633 beta 1949 1954 1952 1972 C1' C D 634 beta 1968 1973 1971 1991 C1' T D 635 beta 1987 1992 1990 2011 C1' A D 636 beta 2007 2012 2010 2032 C1' G D 637 beta 2028 2033 2031 2054 C1' T D 638 beta 2050 2055 2053 2074 C1' T D 639 beta 2070 2075 2073 2094 C1' G D 640 beta 2090 2095 2093 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 1297 C2' C C 600 1298 1295 1316 C2' A C 601 1317 1314 1337 C2' A C 602 1338 1335 1358 C2' C C 603 1359 1356 1377 C2' T C 604 1378 1375 1397 C2' A C 605 1398 1395 1418 C2' G C 606 1419 1416 1440 C2' G C 607 1441 1438 1462 C2' T C 608 1463 1460 1482 C2' C C 609 1483 1480 1501 C2' A C 610 1502 1499 1522 C2' C C 611 1523 1520 1541 C2' 5IT C 612 1542 1539 1561 C2' A C 613 1562 1559 1582 C2' G C 614 1583 1580 1604 C2' G C 615 1605 1602 1626 C2' T C 616 1627 1624 1646 C2' C C 617 1647 1644 1665 C2' A C 618 1666 1663 1686 C2' G C 619 1687 1684 1706 C2' C D 621 1707 1704 1725 C2' T D 622 1726 1723 1745 C2' G D 623 1746 1743 1767 C2' A D 624 1768 1765 1788 C2' C D 625 1789 1786 1807 C2' C D 626 1808 1805 1826 C2' T D 627 1827 1824 1846 C2' A D 628 1847 1844 1867 C2' G D 629 1868 1865 1889 C2' T D 630 1890 1887 1909 C2' G D 631 1910 1907 1931 C2' A D 632 1932 1929 1952 C2' C D 633 1953 1950 1971 C2' C D 634 1972 1969 1990 C2' T D 635 1991 1988 2010 C2' A D 636 2011 2008 2031 C2' G D 637 2032 2029 2053 C2' T D 638 2054 2051 2073 C2' T D 639 2074 2071 2093 C2' G D 640 2094 2091 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 1295 C3' C C 600 OK 1293 1296 1297 1314 C3' A C 601 OK 1312 1315 1316 1335 C3' A C 602 OK 1333 1336 1337 1356 C3' C C 603 OK 1354 1357 1358 1375 C3' T C 604 OK 1373 1376 1377 1395 C3' A C 605 OK 1393 1396 1397 1416 C3' G C 606 OK 1414 1417 1418 1438 C3' G C 607 OK 1436 1439 1440 1460 C3' T C 608 OK 1458 1461 1462 1480 C3' C C 609 OK 1478 1481 1482 1499 C3' A C 610 OK 1497 1500 1501 1520 C3' C C 611 OK 1518 1521 1522 1539 C3' 5IT C 612 OK 1537 1540 1541 1559 C3' A C 613 OK 1557 1560 1561 1580 C3' G C 614 OK 1578 1581 1582 1602 C3' G C 615 OK 1600 1603 1604 1624 C3' T C 616 OK 1622 1625 1626 1644 C3' C C 617 OK 1642 1645 1646 1663 C3' A C 618 OK 1661 1664 1665 1684 C3' G C 619 OK 1682 1685 1686 1704 C3' C D 621 OK 1702 1705 1706 1723 C3' T D 622 OK 1721 1724 1725 1743 C3' G D 623 OK 1741 1744 1745 1765 C3' A D 624 OK 1763 1766 1767 1786 C3' C D 625 OK 1784 1787 1788 1805 C3' C D 626 OK 1803 1806 1807 1824 C3' T D 627 OK 1822 1825 1826 1844 C3' A D 628 OK 1842 1845 1846 1865 C3' G D 629 OK 1863 1866 1867 1887 C3' T D 630 OK 1885 1888 1889 1907 C3' G D 631 OK 1905 1908 1909 1929 C3' A D 632 OK 1927 1930 1931 1950 C3' C D 633 OK 1948 1951 1952 1969 C3' C D 634 OK 1967 1970 1971 1988 C3' T D 635 OK 1986 1989 1990 2008 C3' A D 636 OK 2006 2009 2010 2029 C3' G D 637 OK 2027 2030 2031 2051 C3' T D 638 OK 2049 2052 2053 2071 C3' T D 639 OK 2069 2072 2073 2091 C3' G D 640 OK 2089 2092 2093 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 1293 C4' C C 600 OK 1295 1292 1294 1312 C4' A C 601 OK 1314 1311 1313 1333 C4' A C 602 OK 1335 1332 1334 1354 C4' C C 603 OK 1356 1353 1355 1373 C4' T C 604 OK 1375 1372 1374 1393 C4' A C 605 OK 1395 1392 1394 1414 C4' G C 606 OK 1416 1413 1415 1436 C4' G C 607 OK 1438 1435 1437 1458 C4' T C 608 OK 1460 1457 1459 1478 C4' C C 609 OK 1480 1477 1479 1497 C4' A C 610 OK 1499 1496 1498 1518 C4' C C 611 OK 1520 1517 1519 1537 C4' 5IT C 612 OK 1539 1536 1538 1557 C4' A C 613 OK 1559 1556 1558 1578 C4' G C 614 OK 1580 1577 1579 1600 C4' G C 615 OK 1602 1599 1601 1622 C4' T C 616 OK 1624 1621 1623 1642 C4' C C 617 OK 1644 1641 1643 1661 C4' A C 618 OK 1663 1660 1662 1682 C4' G C 619 OK 1684 1681 1683 1702 C4' C D 621 OK 1704 1701 1703 1721 C4' T D 622 OK 1723 1720 1722 1741 C4' G D 623 OK 1743 1740 1742 1763 C4' A D 624 OK 1765 1762 1764 1784 C4' C D 625 OK 1786 1783 1785 1803 C4' C D 626 OK 1805 1802 1804 1822 C4' T D 627 OK 1824 1821 1823 1842 C4' A D 628 OK 1844 1841 1843 1863 C4' G D 629 OK 1865 1862 1864 1885 C4' T D 630 OK 1887 1884 1886 1905 C4' G D 631 OK 1907 1904 1906 1927 C4' A D 632 OK 1929 1926 1928 1948 C4' C D 633 OK 1950 1947 1949 1967 C4' C D 634 OK 1969 1966 1968 1986 C4' T D 635 OK 1988 1985 1987 2006 C4' A D 636 OK 2008 2005 2007 2027 C4' G D 637 OK 2029 2026 2028 2049 C4' T D 638 OK 2051 2048 2050 2069 C4' T D 639 OK 2071 2068 2070 2089 C4' G D 640 OK 2091 2088 2090 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 1292 C5' C C 600 1291 1293 1311 C5' A C 601 1310 1312 1332 C5' A C 602 1331 1333 1353 C5' C C 603 1352 1354 1372 C5' T C 604 1371 1373 1392 C5' A C 605 1391 1393 1413 C5' G C 606 1412 1414 1435 C5' G C 607 1434 1436 1457 C5' T C 608 1456 1458 1477 C5' C C 609 1476 1478 1496 C5' A C 610 1495 1497 1517 C5' C C 611 1516 1518 1536 C5' 5IT C 612 1535 1537 1556 C5' A C 613 1555 1557 1577 C5' G C 614 1576 1578 1599 C5' G C 615 1598 1600 1621 C5' T C 616 1620 1622 1641 C5' C C 617 1640 1642 1660 C5' A C 618 1659 1661 1681 C5' G C 619 1680 1682 1701 C5' C D 621 1700 1702 1720 C5' T D 622 1719 1721 1740 C5' G D 623 1739 1741 1762 C5' A D 624 1761 1763 1783 C5' C D 625 1782 1784 1802 C5' C D 626 1801 1803 1821 C5' T D 627 1820 1822 1841 C5' A D 628 1840 1842 1862 C5' G D 629 1861 1863 1884 C5' T D 630 1883 1885 1904 C5' G D 631 1903 1905 1926 C5' A D 632 1925 1927 1947 C5' C D 633 1946 1948 1966 C5' C D 634 1965 1967 1985 C5' T D 635 1984 1986 2005 C5' A D 636 2004 2006 2026 C5' G D 637 2025 2027 2048 C5' T D 638 2047 2049 2068 C5' T D 639 2067 2069 2088 C5' G D 640 2087 2089 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1307 P A C 601 distorted distorted 1296 1308 1309 1310 1328 P A C 602 distorted distorted 1315 1329 1330 1331 1349 P C C 603 distorted distorted 1336 1350 1351 1352 1368 P T C 604 distorted distorted 1357 1369 1370 1371 1388 P A C 605 distorted distorted 1376 1389 1390 1391 1409 P G C 606 distorted distorted 1396 1410 1411 1412 1431 P G C 607 distorted distorted 1417 1432 1433 1434 1453 P T C 608 distorted distorted 1439 1454 1455 1456 1473 P C C 609 distorted distorted 1461 1474 1475 1476 1492 P A C 610 distorted distorted 1481 1493 1494 1495 1513 P C C 611 distorted distorted 1500 1514 1515 1516 1532 P 5IT C 612 distorted distorted 1521 1533 1534 1535 1552 P A C 613 distorted distorted 1540 1553 1554 1555 1573 P G C 614 distorted distorted 1560 1574 1575 1576 1595 P G C 615 distorted distorted 1581 1596 1597 1598 1617 P T C 616 distorted distorted 1603 1618 1619 1620 1637 P C C 617 distorted distorted 1625 1638 1639 1640 1656 P A C 618 distorted distorted 1645 1657 1658 1659 1677 P G C 619 distorted distorted 1664 1678 1679 1680 1716 P T D 622 distorted distorted 1705 1717 1718 1719 1736 P G D 623 distorted distorted 1724 1737 1738 1739 1758 P A D 624 distorted distorted 1744 1759 1760 1761 1779 P C D 625 distorted distorted 1766 1780 1781 1782 1798 P C D 626 distorted distorted 1787 1799 1800 1801 1817 P T D 627 distorted distorted 1806 1818 1819 1820 1837 P A D 628 distorted distorted 1825 1838 1839 1840 1858 P G D 629 distorted distorted 1845 1859 1860 1861 1880 P T D 630 distorted distorted 1866 1881 1882 1883 1900 P G D 631 distorted distorted 1888 1901 1902 1903 1922 P A D 632 distorted distorted 1908 1923 1924 1925 1943 P C D 633 distorted distorted 1930 1944 1945 1946 1962 P C D 634 distorted distorted 1951 1963 1964 1965 1981 P T D 635 distorted distorted 1970 1982 1983 1984 2001 P A D 636 distorted distorted 1989 2002 2003 2004 2022 P G D 637 distorted distorted 2009 2023 2024 2025 2044 P T D 638 distorted distorted 2030 2045 2046 2047 2064 P T D 639 distorted distorted 2052 2065 2066 2067 2084 P G D 640 distorted distorted 2072 2085 2086 2087 ---------------------------------------------------------------------------------