ID code: '4TUX' 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' --------------------------------------------------------------------------------- 1146 C1' G D 1 beta 1141 1147 1144 1169 C1' G D 2 beta 1164 1170 1167 1192 C1' C D 3 beta 1187 1193 1190 1212 C1' C D 4 beta 1207 1213 1210 1232 C1' A D 5 beta 1227 1233 1230 1254 C1' A D 6 beta 1249 1255 1252 1276 C1' A D 7 beta 1271 1277 1274 1298 C1' G D 8 beta 1293 1299 1296 1321 C1' G D 9 beta 1316 1322 1319 1344 C1' C D 10 beta 1339 1345 1342 1364 C1' C D 11 beta 1359 1365 1362 1384 C1' C D 12 beta 1379 1385 1382 1404 C1' U D 13 beta 1399 1405 1402 1424 C1' U D 14 beta 1419 1425 1422 1444 C1' U D 15 beta 1439 1445 1442 1464 C1' U D 16 beta 1459 1465 1462 1484 C1' C D 17 beta 1479 1485 1482 1504 C1' A D 18 beta 1499 1505 1502 1526 C1' G D 19 beta 1521 1527 1524 1549 C1' G D 20 beta 1544 1550 1547 1572 C1' G D 21 beta 1567 1573 1570 1595 C1' C D 22 beta 1590 1596 1593 1615 C1' C D 23 beta 1610 1616 1613 1635 C1' A D 24 beta 1630 1636 1633 1657 C1' C D 25 beta 1652 1658 1655 1677 C1' C D 26 beta 1672 1678 1675 1695 C1' G C 1 beta 1690 1696 1693 1718 C1' G C 2 beta 1713 1719 1716 1741 C1' C C 3 beta 1736 1742 1739 1761 C1' C C 4 beta 1756 1762 1759 1781 C1' A C 5 beta 1776 1782 1779 1803 C1' A C 6 beta 1798 1804 1801 1825 C1' A C 7 beta 1820 1826 1823 1847 C1' G C 8 beta 1842 1848 1845 1870 C1' G C 9 beta 1865 1871 1868 1893 C1' C C 10 beta 1888 1894 1891 1913 C1' C C 11 beta 1908 1914 1911 1933 C1' C C 12 beta 1928 1934 1931 1953 C1' U C 13 beta 1948 1954 1951 1973 C1' U C 14 beta 1968 1974 1971 1993 C1' U C 15 beta 1988 1994 1991 2013 C1' U C 16 beta 2008 2014 2011 2033 C1' C C 17 beta 2028 2034 2031 2053 C1' A C 18 beta 2048 2054 2051 2075 C1' G C 19 beta 2070 2076 2073 2098 C1' G C 20 beta 2093 2099 2096 2121 C1' G C 21 beta 2116 2122 2119 2144 C1' C C 22 beta 2139 2145 2142 2164 C1' C C 23 beta 2159 2165 2162 2184 C1' A C 24 beta 2179 2185 2182 2206 C1' C C 25 beta 2201 2207 2204 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 1144 C2' G D 1 OK 1146 1142 1145 1167 C2' G D 2 OK 1169 1165 1168 1190 C2' C D 3 OK 1192 1188 1191 1210 C2' C D 4 OK 1212 1208 1211 1230 C2' A D 5 OK 1232 1228 1231 1252 C2' A D 6 OK 1254 1250 1253 1274 C2' A D 7 OK 1276 1272 1275 1296 C2' G D 8 OK 1298 1294 1297 1319 C2' G D 9 OK 1321 1317 1320 1342 C2' C D 10 OK 1344 1340 1343 1362 C2' C D 11 OK 1364 1360 1363 1382 C2' C D 12 OK 1384 1380 1383 1402 C2' U D 13 OK 1404 1400 1403 1422 C2' U D 14 OK 1424 1420 1423 1442 C2' U D 15 OK 1444 1440 1443 1462 C2' U D 16 OK 1464 1460 1463 1482 C2' C D 17 OK 1484 1480 1483 1502 C2' A D 18 OK 1504 1500 1503 1524 C2' G D 19 OK 1526 1522 1525 1547 C2' G D 20 OK 1549 1545 1548 1570 C2' G D 21 OK 1572 1568 1571 1593 C2' C D 22 OK 1595 1591 1594 1613 C2' C D 23 OK 1615 1611 1614 1633 C2' A D 24 OK 1635 1631 1634 1655 C2' C D 25 OK 1657 1653 1656 1675 C2' C D 26 OK 1677 1673 1676 1693 C2' G C 1 OK 1695 1691 1694 1716 C2' G C 2 OK 1718 1714 1717 1739 C2' C C 3 OK 1741 1737 1740 1759 C2' C C 4 OK 1761 1757 1760 1779 C2' A C 5 OK 1781 1777 1780 1801 C2' A C 6 OK 1803 1799 1802 1823 C2' A C 7 OK 1825 1821 1824 1845 C2' G C 8 OK 1847 1843 1846 1868 C2' G C 9 OK 1870 1866 1869 1891 C2' C C 10 OK 1893 1889 1892 1911 C2' C C 11 OK 1913 1909 1912 1931 C2' C C 12 OK 1933 1929 1932 1951 C2' U C 13 OK 1953 1949 1952 1971 C2' U C 14 OK 1973 1969 1972 1991 C2' U C 15 OK 1993 1989 1992 2011 C2' U C 16 OK 2013 2009 2012 2031 C2' C C 17 OK 2033 2029 2032 2051 C2' A C 18 OK 2053 2049 2052 2073 C2' G C 19 OK 2075 2071 2074 2096 C2' G C 20 OK 2098 2094 2097 2119 C2' G C 21 OK 2121 2117 2120 2142 C2' C C 22 OK 2144 2140 2143 2162 C2' C C 23 OK 2164 2160 2163 2182 C2' A C 24 OK 2184 2180 2183 2204 C2' C C 25 OK 2206 2202 2205 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 1142 C3' G D 1 OK 1140 1143 1144 1165 C3' G D 2 OK 1163 1166 1167 1188 C3' C D 3 OK 1186 1189 1190 1208 C3' C D 4 OK 1206 1209 1210 1228 C3' A D 5 OK 1226 1229 1230 1250 C3' A D 6 OK 1248 1251 1252 1272 C3' A D 7 OK 1270 1273 1274 1294 C3' G D 8 OK 1292 1295 1296 1317 C3' G D 9 OK 1315 1318 1319 1340 C3' C D 10 OK 1338 1341 1342 1360 C3' C D 11 OK 1358 1361 1362 1380 C3' C D 12 OK 1378 1381 1382 1400 C3' U D 13 OK 1398 1401 1402 1420 C3' U D 14 OK 1418 1421 1422 1440 C3' U D 15 OK 1438 1441 1442 1460 C3' U D 16 OK 1458 1461 1462 1480 C3' C D 17 OK 1478 1481 1482 1500 C3' A D 18 OK 1498 1501 1502 1522 C3' G D 19 OK 1520 1523 1524 1545 C3' G D 20 OK 1543 1546 1547 1568 C3' G D 21 OK 1566 1569 1570 1591 C3' C D 22 OK 1589 1592 1593 1611 C3' C D 23 OK 1609 1612 1613 1631 C3' A D 24 OK 1629 1632 1633 1653 C3' C D 25 OK 1651 1654 1655 1673 C3' C D 26 OK 1671 1674 1675 1691 C3' G C 1 OK 1689 1692 1693 1714 C3' G C 2 OK 1712 1715 1716 1737 C3' C C 3 OK 1735 1738 1739 1757 C3' C C 4 OK 1755 1758 1759 1777 C3' A C 5 OK 1775 1778 1779 1799 C3' A C 6 OK 1797 1800 1801 1821 C3' A C 7 OK 1819 1822 1823 1843 C3' G C 8 OK 1841 1844 1845 1866 C3' G C 9 OK 1864 1867 1868 1889 C3' C C 10 OK 1887 1890 1891 1909 C3' C C 11 OK 1907 1910 1911 1929 C3' C C 12 OK 1927 1930 1931 1949 C3' U C 13 OK 1947 1950 1951 1969 C3' U C 14 OK 1967 1970 1971 1989 C3' U C 15 OK 1987 1990 1991 2009 C3' U C 16 OK 2007 2010 2011 2029 C3' C C 17 OK 2027 2030 2031 2049 C3' A C 18 OK 2047 2050 2051 2071 C3' G C 19 OK 2069 2072 2073 2094 C3' G C 20 OK 2092 2095 2096 2117 C3' G C 21 OK 2115 2118 2119 2140 C3' C C 22 OK 2138 2141 2142 2160 C3' C C 23 OK 2158 2161 2162 2180 C3' A C 24 OK 2178 2181 2182 2202 C3' C C 25 OK 2200 2203 2204 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 1140 C4' G D 1 OK 1142 1139 1141 1163 C4' G D 2 OK 1165 1162 1164 1186 C4' C D 3 OK 1188 1185 1187 1206 C4' C D 4 OK 1208 1205 1207 1226 C4' A D 5 OK 1228 1225 1227 1248 C4' A D 6 OK 1250 1247 1249 1270 C4' A D 7 OK 1272 1269 1271 1292 C4' G D 8 OK 1294 1291 1293 1315 C4' G D 9 OK 1317 1314 1316 1338 C4' C D 10 OK 1340 1337 1339 1358 C4' C D 11 OK 1360 1357 1359 1378 C4' C D 12 OK 1380 1377 1379 1398 C4' U D 13 OK 1400 1397 1399 1418 C4' U D 14 OK 1420 1417 1419 1438 C4' U D 15 OK 1440 1437 1439 1458 C4' U D 16 OK 1460 1457 1459 1478 C4' C D 17 OK 1480 1477 1479 1498 C4' A D 18 OK 1500 1497 1499 1520 C4' G D 19 OK 1522 1519 1521 1543 C4' G D 20 OK 1545 1542 1544 1566 C4' G D 21 OK 1568 1565 1567 1589 C4' C D 22 OK 1591 1588 1590 1609 C4' C D 23 OK 1611 1608 1610 1629 C4' A D 24 OK 1631 1628 1630 1651 C4' C D 25 OK 1653 1650 1652 1671 C4' C D 26 OK 1673 1670 1672 1689 C4' G C 1 OK 1691 1688 1690 1712 C4' G C 2 OK 1714 1711 1713 1735 C4' C C 3 OK 1737 1734 1736 1755 C4' C C 4 OK 1757 1754 1756 1775 C4' A C 5 OK 1777 1774 1776 1797 C4' A C 6 OK 1799 1796 1798 1819 C4' A C 7 OK 1821 1818 1820 1841 C4' G C 8 OK 1843 1840 1842 1864 C4' G C 9 OK 1866 1863 1865 1887 C4' C C 10 OK 1889 1886 1888 1907 C4' C C 11 OK 1909 1906 1908 1927 C4' C C 12 OK 1929 1926 1928 1947 C4' U C 13 OK 1949 1946 1948 1967 C4' U C 14 OK 1969 1966 1968 1987 C4' U C 15 OK 1989 1986 1988 2007 C4' U C 16 OK 2009 2006 2008 2027 C4' C C 17 OK 2029 2026 2028 2047 C4' A C 18 OK 2049 2046 2048 2069 C4' G C 19 OK 2071 2068 2070 2092 C4' G C 20 OK 2094 2091 2093 2115 C4' G C 21 OK 2117 2114 2116 2138 C4' C C 22 OK 2140 2137 2139 2158 C4' C C 23 OK 2160 2157 2159 2178 C4' A C 24 OK 2180 2177 2179 2200 C4' C C 25 OK 2202 2199 2201 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 1139 C5' G D 1 1138 1140 1162 C5' G D 2 1161 1163 1185 C5' C D 3 1184 1186 1205 C5' C D 4 1204 1206 1225 C5' A D 5 1224 1226 1247 C5' A D 6 1246 1248 1269 C5' A D 7 1268 1270 1291 C5' G D 8 1290 1292 1314 C5' G D 9 1313 1315 1337 C5' C D 10 1336 1338 1357 C5' C D 11 1356 1358 1377 C5' C D 12 1376 1378 1397 C5' U D 13 1396 1398 1417 C5' U D 14 1416 1418 1437 C5' U D 15 1436 1438 1457 C5' U D 16 1456 1458 1477 C5' C D 17 1476 1478 1497 C5' A D 18 1496 1498 1519 C5' G D 19 1518 1520 1542 C5' G D 20 1541 1543 1565 C5' G D 21 1564 1566 1588 C5' C D 22 1587 1589 1608 C5' C D 23 1607 1609 1628 C5' A D 24 1627 1629 1650 C5' C D 25 1649 1651 1670 C5' C D 26 1669 1671 1688 C5' G C 1 1687 1689 1711 C5' G C 2 1710 1712 1734 C5' C C 3 1733 1735 1754 C5' C C 4 1753 1755 1774 C5' A C 5 1773 1775 1796 C5' A C 6 1795 1797 1818 C5' A C 7 1817 1819 1840 C5' G C 8 1839 1841 1863 C5' G C 9 1862 1864 1886 C5' C C 10 1885 1887 1906 C5' C C 11 1905 1907 1926 C5' C C 12 1925 1927 1946 C5' U C 13 1945 1947 1966 C5' U C 14 1965 1967 1986 C5' U C 15 1985 1987 2006 C5' U C 16 2005 2007 2026 C5' C C 17 2025 2027 2046 C5' A C 18 2045 2047 2068 C5' G C 19 2067 2069 2091 C5' G C 20 2090 2092 2114 C5' G C 21 2113 2115 2137 C5' C C 22 2136 2138 2157 C5' C C 23 2156 2158 2177 C5' A C 24 2176 2178 2199 C5' C C 25 2198 2200 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1158 P G D 2 distorted distorted 1143 1159 1160 1161 1181 P C D 3 distorted distorted 1166 1182 1183 1184 1201 P C D 4 distorted distorted 1189 1202 1203 1204 1221 P A D 5 distorted distorted 1209 1222 1223 1224 1243 P A D 6 distorted distorted 1229 1244 1245 1246 1265 P A D 7 distorted distorted 1251 1266 1267 1268 1287 P G D 8 distorted distorted 1273 1288 1289 1290 1310 P G D 9 distorted distorted 1295 1311 1312 1313 1333 P C D 10 distorted distorted 1318 1334 1335 1336 1353 P C D 11 distorted distorted 1341 1354 1355 1356 1373 P C D 12 distorted distorted 1361 1374 1375 1376 1393 P U D 13 distorted distorted 1381 1394 1395 1396 1413 P U D 14 distorted distorted 1401 1414 1415 1416 1433 P U D 15 distorted distorted 1421 1434 1435 1436 1453 P U D 16 distorted distorted 1441 1454 1455 1456 1473 P C D 17 distorted distorted 1461 1474 1475 1476 1493 P A D 18 distorted distorted 1481 1494 1495 1496 1515 P G D 19 distorted distorted 1501 1516 1517 1518 1538 P G D 20 distorted distorted 1523 1539 1540 1541 1561 P G D 21 distorted distorted 1546 1562 1563 1564 1584 P C D 22 distorted distorted 1569 1585 1586 1587 1604 P C D 23 distorted distorted 1592 1605 1606 1607 1624 P A D 24 distorted distorted 1612 1625 1626 1627 1646 P C D 25 distorted distorted 1632 1647 1648 1649 1666 P C D 26 distorted distorted 1654 1667 1668 1669 1707 P G C 2 distorted distorted 1692 1708 1709 1710 1730 P C C 3 distorted distorted 1715 1731 1732 1733 1750 P C C 4 distorted distorted 1738 1751 1752 1753 1770 P A C 5 distorted distorted 1758 1771 1772 1773 1792 P A C 6 distorted distorted 1778 1793 1794 1795 1814 P A C 7 distorted distorted 1800 1815 1816 1817 1836 P G C 8 distorted distorted 1822 1837 1838 1839 1859 P G C 9 distorted distorted 1844 1860 1861 1862 1882 P C C 10 distorted distorted 1867 1883 1884 1885 1902 P C C 11 distorted distorted 1890 1903 1904 1905 1922 P C C 12 distorted distorted 1910 1923 1924 1925 1942 P U C 13 distorted distorted 1930 1943 1944 1945 1962 P U C 14 distorted distorted 1950 1963 1964 1965 1982 P U C 15 distorted distorted 1970 1983 1984 1985 2002 P U C 16 distorted distorted 1990 2003 2004 2005 2022 P C C 17 distorted distorted 2010 2023 2024 2025 2042 P A C 18 distorted distorted 2030 2043 2044 2045 2064 P G C 19 distorted distorted 2050 2065 2066 2067 2087 P G C 20 distorted distorted 2072 2088 2089 2090 2110 P G C 21 distorted distorted 2095 2111 2112 2113 2133 P C C 22 distorted distorted 2118 2134 2135 2136 2153 P C C 23 distorted distorted 2141 2154 2155 2156 2173 P A C 24 distorted distorted 2161 2174 2175 2176 2195 P C C 25 distorted distorted 2181 2196 2197 2198 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