ID code: '1OLN' 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' --------------------------------------------------------------------------------- 1124 C1' G C1051 beta 1119 1125 1122 1147 C1' C C1052 beta 1142 1148 1145 1167 C1' U C1053 beta 1162 1168 1165 1187 C1' G C1054 beta 1182 1188 1185 1210 C1' G C1055 beta 1205 1211 1208 1233 C1' G C1056 beta 1228 1234 1231 1256 C1' A C1057 beta 1251 1257 1254 1278 C1' U C1058 beta 1273 1279 1276 1298 C1' G C1059 beta 1293 1299 1296 1321 C1' U C1060 beta 1316 1322 1319 1341 C1' U C1061 beta 1336 1342 1339 1361 C1' G C1062 beta 1356 1362 1359 1384 C1' G C1063 beta 1379 1385 1382 1407 C1' C C1064 beta 1402 1408 1405 1427 C1' U C1065 beta 1422 1428 1425 1447 C1' U C1066 beta 1442 1448 1445 1467 C1' A C1067 beta 1462 1468 1465 1489 C1' G C1068 beta 1484 1490 1487 1512 C1' A C1069 beta 1507 1513 1510 1534 C1' A C1070 beta 1529 1535 1532 1556 C1' G C1071 beta 1551 1557 1554 1579 C1' C C1072 beta 1574 1580 1577 1599 C1' A C1073 beta 1594 1600 1597 1621 C1' G C1074 beta 1616 1622 1619 1644 C1' C C1075 beta 1639 1645 1642 1664 C1' C C1076 beta 1659 1665 1662 1684 C1' A C1077 beta 1679 1685 1682 1706 C1' U C1078 beta 1701 1707 1704 1726 C1' C C1079 beta 1721 1727 1724 1746 C1' A C1080 beta 1741 1747 1744 1768 C1' U C1081 beta 1763 1769 1766 1788 C1' U C1082 beta 1783 1789 1786 1808 C1' U C1083 beta 1803 1809 1806 1828 C1' A C1084 beta 1823 1829 1826 1850 C1' A C1085 beta 1845 1851 1848 1872 C1' A C1086 beta 1867 1873 1870 1894 C1' G C1087 beta 1889 1895 1892 1917 C1' A C1088 beta 1912 1918 1915 1939 C1' G C1089 beta 1934 1940 1937 1962 C1' U C1090 beta 1957 1963 1960 1982 C1' G C1091 beta 1977 1983 1980 2005 C1' C C1092 beta 2000 2006 2003 2025 C1' G C1093 beta 2020 2026 2023 2048 C1' U C1094 beta 2043 2049 2046 2068 C1' A C1095 beta 2063 2069 2066 2090 C1' A C1096 beta 2085 2091 2088 2112 C1' C C1097 beta 2107 2113 2110 2132 C1' A C1098 beta 2127 2133 2130 2154 C1' G C1099 beta 2149 2155 2152 2177 C1' C C1100 beta 2172 2178 2175 2197 C1' U C1101 beta 2192 2198 2195 2217 C1' C C1102 beta 2212 2218 2215 2237 C1' A C1103 beta 2232 2238 2235 2259 C1' C C1104 beta 2254 2260 2257 2279 C1' C C1105 beta 2274 2280 2277 2299 C1' A C1106 beta 2294 2300 2297 2321 C1' G C1107 beta 2316 2322 2319 2344 C1' C C1108 beta 2339 2345 2342 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 1122 C2' G C1051 OK 1124 1120 1123 1145 C2' C C1052 OK 1147 1143 1146 1165 C2' U C1053 OK 1167 1163 1166 1185 C2' G C1054 OK 1187 1183 1186 1208 C2' G C1055 OK 1210 1206 1209 1231 C2' G C1056 OK 1233 1229 1232 1254 C2' A C1057 OK 1256 1252 1255 1276 C2' U C1058 OK 1278 1274 1277 1296 C2' G C1059 OK 1298 1294 1297 1319 C2' U C1060 OK 1321 1317 1320 1339 C2' U C1061 OK 1341 1337 1340 1359 C2' G C1062 OK 1361 1357 1360 1382 C2' G C1063 OK 1384 1380 1383 1405 C2' C C1064 OK 1407 1403 1406 1425 C2' U C1065 OK 1427 1423 1426 1445 C2' U C1066 OK 1447 1443 1446 1465 C2' A C1067 OK 1467 1463 1466 1487 C2' G C1068 OK 1489 1485 1488 1510 C2' A C1069 OK 1512 1508 1511 1532 C2' A C1070 OK 1534 1530 1533 1554 C2' G C1071 OK 1556 1552 1555 1577 C2' C C1072 OK 1579 1575 1578 1597 C2' A C1073 OK 1599 1595 1598 1619 C2' G C1074 OK 1621 1617 1620 1642 C2' C C1075 OK 1644 1640 1643 1662 C2' C C1076 OK 1664 1660 1663 1682 C2' A C1077 OK 1684 1680 1683 1704 C2' U C1078 OK 1706 1702 1705 1724 C2' C C1079 OK 1726 1722 1725 1744 C2' A C1080 OK 1746 1742 1745 1766 C2' U C1081 OK 1768 1764 1767 1786 C2' U C1082 OK 1788 1784 1787 1806 C2' U C1083 OK 1808 1804 1807 1826 C2' A C1084 OK 1828 1824 1827 1848 C2' A C1085 OK 1850 1846 1849 1870 C2' A C1086 OK 1872 1868 1871 1892 C2' G C1087 OK 1894 1890 1893 1915 C2' A C1088 OK 1917 1913 1916 1937 C2' G C1089 OK 1939 1935 1938 1960 C2' U C1090 OK 1962 1958 1961 1980 C2' G C1091 OK 1982 1978 1981 2003 C2' C C1092 OK 2005 2001 2004 2023 C2' G C1093 OK 2025 2021 2024 2046 C2' U C1094 OK 2048 2044 2047 2066 C2' A C1095 OK 2068 2064 2067 2088 C2' A C1096 OK 2090 2086 2089 2110 C2' C C1097 OK 2112 2108 2111 2130 C2' A C1098 OK 2132 2128 2131 2152 C2' G C1099 OK 2154 2150 2153 2175 C2' C C1100 OK 2177 2173 2176 2195 C2' U C1101 OK 2197 2193 2196 2215 C2' C C1102 OK 2217 2213 2216 2235 C2' A C1103 OK 2237 2233 2236 2257 C2' C C1104 OK 2259 2255 2258 2277 C2' C C1105 OK 2279 2275 2278 2297 C2' A C1106 OK 2299 2295 2298 2319 C2' G C1107 OK 2321 2317 2320 2342 C2' C C1108 OK 2344 2340 2343 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 1120 C3' G C1051 OK 1118 1121 1122 1143 C3' C C1052 OK 1141 1144 1145 1163 C3' U C1053 OK 1161 1164 1165 1183 C3' G C1054 OK 1181 1184 1185 1206 C3' G C1055 OK 1204 1207 1208 1229 C3' G C1056 OK 1227 1230 1231 1252 C3' A C1057 OK 1250 1253 1254 1274 C3' U C1058 OK 1272 1275 1276 1294 C3' G C1059 OK 1292 1295 1296 1317 C3' U C1060 OK 1315 1318 1319 1337 C3' U C1061 OK 1335 1338 1339 1357 C3' G C1062 OK 1355 1358 1359 1380 C3' G C1063 OK 1378 1381 1382 1403 C3' C C1064 OK 1401 1404 1405 1423 C3' U C1065 OK 1421 1424 1425 1443 C3' U C1066 OK 1441 1444 1445 1463 C3' A C1067 OK 1461 1464 1465 1485 C3' G C1068 OK 1483 1486 1487 1508 C3' A C1069 OK 1506 1509 1510 1530 C3' A C1070 OK 1528 1531 1532 1552 C3' G C1071 OK 1550 1553 1554 1575 C3' C C1072 OK 1573 1576 1577 1595 C3' A C1073 OK 1593 1596 1597 1617 C3' G C1074 OK 1615 1618 1619 1640 C3' C C1075 OK 1638 1641 1642 1660 C3' C C1076 OK 1658 1661 1662 1680 C3' A C1077 OK 1678 1681 1682 1702 C3' U C1078 OK 1700 1703 1704 1722 C3' C C1079 OK 1720 1723 1724 1742 C3' A C1080 OK 1740 1743 1744 1764 C3' U C1081 OK 1762 1765 1766 1784 C3' U C1082 OK 1782 1785 1786 1804 C3' U C1083 OK 1802 1805 1806 1824 C3' A C1084 OK 1822 1825 1826 1846 C3' A C1085 OK 1844 1847 1848 1868 C3' A C1086 OK 1866 1869 1870 1890 C3' G C1087 OK 1888 1891 1892 1913 C3' A C1088 OK 1911 1914 1915 1935 C3' G C1089 OK 1933 1936 1937 1958 C3' U C1090 OK 1956 1959 1960 1978 C3' G C1091 OK 1976 1979 1980 2001 C3' C C1092 OK 1999 2002 2003 2021 C3' G C1093 OK 2019 2022 2023 2044 C3' U C1094 OK 2042 2045 2046 2064 C3' A C1095 OK 2062 2065 2066 2086 C3' A C1096 OK 2084 2087 2088 2108 C3' C C1097 OK 2106 2109 2110 2128 C3' A C1098 OK 2126 2129 2130 2150 C3' G C1099 OK 2148 2151 2152 2173 C3' C C1100 OK 2171 2174 2175 2193 C3' U C1101 OK 2191 2194 2195 2213 C3' C C1102 OK 2211 2214 2215 2233 C3' A C1103 OK 2231 2234 2235 2255 C3' C C1104 OK 2253 2256 2257 2275 C3' C C1105 OK 2273 2276 2277 2295 C3' A C1106 OK 2293 2296 2297 2317 C3' G C1107 OK 2315 2318 2319 2340 C3' C C1108 OK 2338 2341 2342 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 1118 C4' G C1051 OK 1120 1117 1119 1141 C4' C C1052 OK 1143 1140 1142 1161 C4' U C1053 OK 1163 1160 1162 1181 C4' G C1054 OK 1183 1180 1182 1204 C4' G C1055 OK 1206 1203 1205 1227 C4' G C1056 OK 1229 1226 1228 1250 C4' A C1057 OK 1252 1249 1251 1272 C4' U C1058 OK 1274 1271 1273 1292 C4' G C1059 OK 1294 1291 1293 1315 C4' U C1060 OK 1317 1314 1316 1335 C4' U C1061 OK 1337 1334 1336 1355 C4' G C1062 OK 1357 1354 1356 1378 C4' G C1063 OK 1380 1377 1379 1401 C4' C C1064 OK 1403 1400 1402 1421 C4' U C1065 OK 1423 1420 1422 1441 C4' U C1066 OK 1443 1440 1442 1461 C4' A C1067 OK 1463 1460 1462 1483 C4' G C1068 OK 1485 1482 1484 1506 C4' A C1069 OK 1508 1505 1507 1528 C4' A C1070 OK 1530 1527 1529 1550 C4' G C1071 OK 1552 1549 1551 1573 C4' C C1072 OK 1575 1572 1574 1593 C4' A C1073 OK 1595 1592 1594 1615 C4' G C1074 OK 1617 1614 1616 1638 C4' C C1075 OK 1640 1637 1639 1658 C4' C C1076 OK 1660 1657 1659 1678 C4' A C1077 OK 1680 1677 1679 1700 C4' U C1078 OK 1702 1699 1701 1720 C4' C C1079 OK 1722 1719 1721 1740 C4' A C1080 OK 1742 1739 1741 1762 C4' U C1081 OK 1764 1761 1763 1782 C4' U C1082 OK 1784 1781 1783 1802 C4' U C1083 OK 1804 1801 1803 1822 C4' A C1084 OK 1824 1821 1823 1844 C4' A C1085 OK 1846 1843 1845 1866 C4' A C1086 OK 1868 1865 1867 1888 C4' G C1087 OK 1890 1887 1889 1911 C4' A C1088 OK 1913 1910 1912 1933 C4' G C1089 OK 1935 1932 1934 1956 C4' U C1090 OK 1958 1955 1957 1976 C4' G C1091 OK 1978 1975 1977 1999 C4' C C1092 OK 2001 1998 2000 2019 C4' G C1093 OK 2021 2018 2020 2042 C4' U C1094 OK 2044 2041 2043 2062 C4' A C1095 OK 2064 2061 2063 2084 C4' A C1096 OK 2086 2083 2085 2106 C4' C C1097 OK 2108 2105 2107 2126 C4' A C1098 OK 2128 2125 2127 2148 C4' G C1099 OK 2150 2147 2149 2171 C4' C C1100 OK 2173 2170 2172 2191 C4' U C1101 OK 2193 2190 2192 2211 C4' C C1102 OK 2213 2210 2212 2231 C4' A C1103 OK 2233 2230 2232 2253 C4' C C1104 OK 2255 2252 2254 2273 C4' C C1105 OK 2275 2272 2274 2293 C4' A C1106 OK 2295 2292 2294 2315 C4' G C1107 OK 2317 2314 2316 2338 C4' C C1108 OK 2340 2337 2339 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 1117 C5' G C1051 1116 1118 1140 C5' C C1052 1139 1141 1160 C5' U C1053 1159 1161 1180 C5' G C1054 1179 1181 1203 C5' G C1055 1202 1204 1226 C5' G C1056 1225 1227 1249 C5' A C1057 1248 1250 1271 C5' U C1058 1270 1272 1291 C5' G C1059 1290 1292 1314 C5' U C1060 1313 1315 1334 C5' U C1061 1333 1335 1354 C5' G C1062 1353 1355 1377 C5' G C1063 1376 1378 1400 C5' C C1064 1399 1401 1420 C5' U C1065 1419 1421 1440 C5' U C1066 1439 1441 1460 C5' A C1067 1459 1461 1482 C5' G C1068 1481 1483 1505 C5' A C1069 1504 1506 1527 C5' A C1070 1526 1528 1549 C5' G C1071 1548 1550 1572 C5' C C1072 1571 1573 1592 C5' A C1073 1591 1593 1614 C5' G C1074 1613 1615 1637 C5' C C1075 1636 1638 1657 C5' C C1076 1656 1658 1677 C5' A C1077 1676 1678 1699 C5' U C1078 1698 1700 1719 C5' C C1079 1718 1720 1739 C5' A C1080 1738 1740 1761 C5' U C1081 1760 1762 1781 C5' U C1082 1780 1782 1801 C5' U C1083 1800 1802 1821 C5' A C1084 1820 1822 1843 C5' A C1085 1842 1844 1865 C5' A C1086 1864 1866 1887 C5' G C1087 1886 1888 1910 C5' A C1088 1909 1911 1932 C5' G C1089 1931 1933 1955 C5' U C1090 1954 1956 1975 C5' G C1091 1974 1976 1998 C5' C C1092 1997 1999 2018 C5' G C1093 2017 2019 2041 C5' U C1094 2040 2042 2061 C5' A C1095 2060 2062 2083 C5' A C1096 2082 2084 2105 C5' C C1097 2104 2106 2125 C5' A C1098 2124 2126 2147 C5' G C1099 2146 2148 2170 C5' C C1100 2169 2171 2190 C5' U C1101 2189 2191 2210 C5' C C1102 2209 2211 2230 C5' A C1103 2229 2231 2252 C5' C C1104 2251 2253 2272 C5' C C1105 2271 2273 2292 C5' A C1106 2291 2293 2314 C5' G C1107 2313 2315 2337 C5' C C1108 2336 2338 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1136 P C C1052 distorted distorted 1121 1137 1138 1139 1156 P U C1053 distorted distorted 1144 1157 1158 1159 1176 P G C1054 distorted distorted 1164 1177 1178 1179 1199 P G C1055 distorted distorted 1184 1200 1201 1202 1222 P G C1056 distorted distorted 1207 1223 1224 1225 1245 P A C1057 distorted distorted 1230 1246 1247 1248 1267 P U C1058 distorted distorted 1253 1268 1269 1270 1287 P G C1059 distorted distorted 1275 1288 1289 1290 1310 P U C1060 distorted distorted 1295 1311 1312 1313 1330 P U C1061 distorted distorted 1318 1331 1332 1333 1350 P G C1062 distorted distorted 1338 1351 1352 1353 1373 P G C1063 distorted distorted 1358 1374 1375 1376 1396 P C C1064 distorted distorted 1381 1397 1398 1399 1416 P U C1065 distorted distorted 1404 1417 1418 1419 1436 P U C1066 distorted distorted 1424 1437 1438 1439 1456 P A C1067 distorted distorted 1444 1457 1458 1459 1478 P G C1068 distorted distorted 1464 1479 1480 1481 1501 P A C1069 distorted distorted 1486 1502 1503 1504 1523 P A C1070 distorted distorted 1509 1524 1525 1526 1545 P G C1071 distorted distorted 1531 1546 1547 1548 1568 P C C1072 distorted distorted 1553 1569 1570 1571 1588 P A C1073 distorted distorted 1576 1589 1590 1591 1610 P G C1074 distorted distorted 1596 1611 1612 1613 1633 P C C1075 distorted distorted 1618 1634 1635 1636 1653 P C C1076 distorted distorted 1641 1654 1655 1656 1673 P A C1077 distorted distorted 1661 1674 1675 1676 1695 P U C1078 distorted distorted 1681 1696 1697 1698 1715 P C C1079 distorted distorted 1703 1716 1717 1718 1735 P A C1080 distorted distorted 1723 1736 1737 1738 1757 P U C1081 distorted distorted 1743 1758 1759 1760 1777 P U C1082 distorted distorted 1765 1778 1779 1780 1797 P U C1083 distorted distorted 1785 1798 1799 1800 1817 P A C1084 distorted distorted 1805 1818 1819 1820 1839 P A C1085 distorted distorted 1825 1840 1841 1842 1861 P A C1086 distorted distorted 1847 1862 1863 1864 1883 P G C1087 distorted distorted 1869 1884 1885 1886 1906 P A C1088 distorted distorted 1891 1907 1908 1909 1928 P G C1089 distorted distorted 1914 1929 1930 1931 1951 P U C1090 distorted distorted 1936 1952 1953 1954 1971 P G C1091 distorted distorted 1959 1972 1973 1974 1994 P C C1092 distorted distorted 1979 1995 1996 1997 2014 P G C1093 distorted distorted 2002 2015 2016 2017 2037 P U C1094 distorted distorted 2022 2038 2039 2040 2057 P A C1095 distorted distorted 2045 2058 2059 2060 2079 P A C1096 distorted distorted 2065 2080 2081 2082 2101 P C C1097 distorted distorted 2087 2102 2103 2104 2121 P A C1098 distorted distorted 2109 2122 2123 2124 2143 P G C1099 distorted distorted 2129 2144 2145 2146 2166 P C C1100 distorted distorted 2151 2167 2168 2169 2186 P U C1101 distorted distorted 2174 2187 2188 2189 2206 P C C1102 distorted distorted 2194 2207 2208 2209 2226 P A C1103 distorted distorted 2214 2227 2228 2229 2248 P C C1104 distorted distorted 2234 2249 2250 2251 2268 P C C1105 distorted distorted 2256 2269 2270 2271 2288 P A C1106 distorted distorted 2276 2289 2290 2291 2310 P G C1107 distorted distorted 2296 2311 2312 2313 2333 P C C1108 distorted distorted 2318 2334 2335 2336 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