ID code: '3EGZ' 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' --------------------------------------------------------------------------------- 741 C1' G B 1 beta 736 742 739 764 C1' A B 2 beta 759 765 762 786 C1' G B 3 beta 781 787 784 809 C1' G B 4 beta 804 810 807 832 C1' G B 5 beta 827 833 830 855 C1' A B 6 beta 850 856 853 877 C1' G B 7 beta 872 878 875 900 C1' A B 8 beta 895 901 898 922 C1' G B 9 beta 917 923 920 945 C1' G B 10 beta 940 946 943 968 C1' U B 11 beta 963 969 966 988 C1' G B 12 beta 983 989 986 1011 C1' A B 13 beta 1006 1012 1009 1033 C1' A B 14 beta 1028 1034 1031 1055 C1' G B 15 beta 1050 1056 1053 1078 C1' A B 16 beta 1073 1079 1076 1100 C1' A B 17 beta 1095 1101 1098 1122 C1' U B 18 beta 1117 1123 1120 1142 C1' A B 19 beta 1137 1143 1140 1164 C1' C B 20 beta 1159 1165 1162 1184 C1' G B 21 beta 1179 1185 1182 1207 C1' A B 22 beta 1202 1208 1205 1229 C1' C B 23 beta 1224 1230 1227 1249 C1' C B 24 beta 1244 1250 1247 1269 C1' A B 25 beta 1264 1270 1267 1291 C1' C B 26 beta 1286 1292 1289 1311 C1' C B 27 beta 1306 1312 1309 1331 C1' U B 28 beta 1326 1332 1329 1351 C1' A B 29 beta 1346 1352 1349 1373 C1' G B 30 beta 1368 1374 1371 1396 C1' G B 31 beta 1391 1397 1394 1419 C1' U B 32 beta 1414 1420 1417 1439 C1' A B 33 beta 1434 1440 1437 1461 C1' C B 34 beta 1456 1462 1459 1481 C1' C B 35 beta 1476 1482 1479 1501 C1' A B 36 beta 1496 1502 1499 1523 C1' U B 37 beta 1518 1524 1521 1543 C1' U B 38 beta 1538 1544 1541 1563 C1' G B 39 beta 1558 1564 1561 1586 C1' C B 40 beta 1581 1587 1584 1606 C1' A B 41 beta 1601 1607 1604 1628 C1' C B 42 beta 1623 1629 1626 1648 C1' U B 43 1643 1646 1660 C1' C B 44 beta 1655 1661 1658 1680 C1' C B 45 beta 1675 1681 1678 1700 C1' G B 46 beta 1695 1701 1698 1723 C1' G B 47 beta 1718 1724 1721 1746 C1' U B 48 beta 1741 1747 1744 1766 C1' A B 49 beta 1761 1767 1764 1788 C1' C B 50 beta 1783 1789 1786 1808 C1' C B 51 beta 1803 1809 1806 1828 C1' U B 52 beta 1823 1829 1826 1848 C1' A B 53 beta 1843 1849 1846 1870 C1' A B 54 beta 1865 1871 1868 1892 C1' A B 55 beta 1887 1893 1890 1914 C1' A B 56 beta 1909 1915 1912 1936 C1' C B 57 beta 1931 1937 1934 1956 C1' A B 58 beta 1951 1957 1954 1978 C1' U B 59 beta 1973 1979 1976 1998 C1' A B 60 beta 1993 1999 1996 2020 C1' C B 61 beta 2015 2021 2018 2040 C1' C B 62 beta 2035 2041 2038 2060 C1' C B 63 beta 2055 2061 2058 2080 C1' U B 64 beta 2075 2081 2078 2100 C1' C B 65 beta 2095 2101 2098 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 739 C2' G B 1 OK 741 737 740 762 C2' A B 2 OK 764 760 763 784 C2' G B 3 OK 786 782 785 807 C2' G B 4 OK 809 805 808 830 C2' G B 5 OK 832 828 831 853 C2' A B 6 OK 855 851 854 875 C2' G B 7 OK 877 873 876 898 C2' A B 8 OK 900 896 899 920 C2' G B 9 OK 922 918 921 943 C2' G B 10 OK 945 941 944 966 C2' U B 11 OK 968 964 967 986 C2' G B 12 OK 988 984 987 1009 C2' A B 13 OK 1011 1007 1010 1031 C2' A B 14 OK 1033 1029 1032 1053 C2' G B 15 OK 1055 1051 1054 1076 C2' A B 16 OK 1078 1074 1077 1098 C2' A B 17 OK 1100 1096 1099 1120 C2' U B 18 OK 1122 1118 1121 1140 C2' A B 19 OK 1142 1138 1141 1162 C2' C B 20 OK 1164 1160 1163 1182 C2' G B 21 OK 1184 1180 1183 1205 C2' A B 22 OK 1207 1203 1206 1227 C2' C B 23 OK 1229 1225 1228 1247 C2' C B 24 OK 1249 1245 1248 1267 C2' A B 25 OK 1269 1265 1268 1289 C2' C B 26 OK 1291 1287 1290 1309 C2' C B 27 OK 1311 1307 1310 1329 C2' U B 28 OK 1331 1327 1330 1349 C2' A B 29 OK 1351 1347 1350 1371 C2' G B 30 OK 1373 1369 1372 1394 C2' G B 31 OK 1396 1392 1395 1417 C2' U B 32 OK 1419 1415 1418 1437 C2' A B 33 OK 1439 1435 1438 1459 C2' C B 34 OK 1461 1457 1460 1479 C2' C B 35 OK 1481 1477 1480 1499 C2' A B 36 OK 1501 1497 1500 1521 C2' U B 37 OK 1523 1519 1522 1541 C2' U B 38 OK 1543 1539 1542 1561 C2' G B 39 OK 1563 1559 1562 1584 C2' C B 40 OK 1586 1582 1585 1604 C2' A B 41 OK 1606 1602 1605 1626 C2' C B 42 OK 1628 1624 1627 1646 C2' U B 43 OK 1648 1644 1647 1658 C2' C B 44 OK 1660 1656 1659 1678 C2' C B 45 OK 1680 1676 1679 1698 C2' G B 46 OK 1700 1696 1699 1721 C2' G B 47 OK 1723 1719 1722 1744 C2' U B 48 OK 1746 1742 1745 1764 C2' A B 49 OK 1766 1762 1765 1786 C2' C B 50 OK 1788 1784 1787 1806 C2' C B 51 OK 1808 1804 1807 1826 C2' U B 52 OK 1828 1824 1827 1846 C2' A B 53 OK 1848 1844 1847 1868 C2' A B 54 OK 1870 1866 1869 1890 C2' A B 55 OK 1892 1888 1891 1912 C2' A B 56 OK 1914 1910 1913 1934 C2' C B 57 OK 1936 1932 1935 1954 C2' A B 58 OK 1956 1952 1955 1976 C2' U B 59 OK 1978 1974 1977 1996 C2' A B 60 OK 1998 1994 1997 2018 C2' C B 61 OK 2020 2016 2019 2038 C2' C B 62 OK 2040 2036 2039 2058 C2' C B 63 OK 2060 2056 2059 2078 C2' U B 64 OK 2080 2076 2079 2098 C2' C B 65 OK 2100 2096 2099 2114 C2' CTC B 601 2115 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 737 C3' G B 1 OK 735 738 739 760 C3' A B 2 OK 758 761 762 782 C3' G B 3 OK 780 783 784 805 C3' G B 4 OK 803 806 807 828 C3' G B 5 OK 826 829 830 851 C3' A B 6 OK 849 852 853 873 C3' G B 7 OK 871 874 875 896 C3' A B 8 OK 894 897 898 918 C3' G B 9 OK 916 919 920 941 C3' G B 10 OK 939 942 943 964 C3' U B 11 OK 962 965 966 984 C3' G B 12 OK 982 985 986 1007 C3' A B 13 OK 1005 1008 1009 1029 C3' A B 14 OK 1027 1030 1031 1051 C3' G B 15 OK 1049 1052 1053 1074 C3' A B 16 OK 1072 1075 1076 1096 C3' A B 17 OK 1094 1097 1098 1118 C3' U B 18 OK 1116 1119 1120 1138 C3' A B 19 OK 1136 1139 1140 1160 C3' C B 20 OK 1158 1161 1162 1180 C3' G B 21 OK 1178 1181 1182 1203 C3' A B 22 OK 1201 1204 1205 1225 C3' C B 23 OK 1223 1226 1227 1245 C3' C B 24 OK 1243 1246 1247 1265 C3' A B 25 OK 1263 1266 1267 1287 C3' C B 26 OK 1285 1288 1289 1307 C3' C B 27 OK 1305 1308 1309 1327 C3' U B 28 OK 1325 1328 1329 1347 C3' A B 29 OK 1345 1348 1349 1369 C3' G B 30 OK 1367 1370 1371 1392 C3' G B 31 OK 1390 1393 1394 1415 C3' U B 32 OK 1413 1416 1417 1435 C3' A B 33 OK 1433 1436 1437 1457 C3' C B 34 OK 1455 1458 1459 1477 C3' C B 35 OK 1475 1478 1479 1497 C3' A B 36 OK 1495 1498 1499 1519 C3' U B 37 OK 1517 1520 1521 1539 C3' U B 38 OK 1537 1540 1541 1559 C3' G B 39 OK 1557 1560 1561 1582 C3' C B 40 OK 1580 1583 1584 1602 C3' A B 41 OK 1600 1603 1604 1624 C3' C B 42 OK 1622 1625 1626 1644 C3' U B 43 OK 1642 1645 1646 1656 C3' C B 44 OK 1654 1657 1658 1676 C3' C B 45 OK 1674 1677 1678 1696 C3' G B 46 OK 1694 1697 1698 1719 C3' G B 47 OK 1717 1720 1721 1742 C3' U B 48 OK 1740 1743 1744 1762 C3' A B 49 OK 1760 1763 1764 1784 C3' C B 50 OK 1782 1785 1786 1804 C3' C B 51 OK 1802 1805 1806 1824 C3' U B 52 OK 1822 1825 1826 1844 C3' A B 53 OK 1842 1845 1846 1866 C3' A B 54 OK 1864 1867 1868 1888 C3' A B 55 OK 1886 1889 1890 1910 C3' A B 56 OK 1908 1911 1912 1932 C3' C B 57 OK 1930 1933 1934 1952 C3' A B 58 OK 1950 1953 1954 1974 C3' U B 59 OK 1972 1975 1976 1994 C3' A B 60 OK 1992 1995 1996 2016 C3' C B 61 OK 2014 2017 2018 2036 C3' C B 62 OK 2034 2037 2038 2056 C3' C B 63 OK 2054 2057 2058 2076 C3' U B 64 OK 2074 2077 2078 2096 C3' C B 65 OK 2094 2097 2098 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 735 C4' G B 1 OK 737 734 736 758 C4' A B 2 OK 760 757 759 780 C4' G B 3 OK 782 779 781 803 C4' G B 4 OK 805 802 804 826 C4' G B 5 OK 828 825 827 849 C4' A B 6 OK 851 848 850 871 C4' G B 7 OK 873 870 872 894 C4' A B 8 OK 896 893 895 916 C4' G B 9 OK 918 915 917 939 C4' G B 10 OK 941 938 940 962 C4' U B 11 OK 964 961 963 982 C4' G B 12 OK 984 981 983 1005 C4' A B 13 OK 1007 1004 1006 1027 C4' A B 14 OK 1029 1026 1028 1049 C4' G B 15 OK 1051 1048 1050 1072 C4' A B 16 OK 1074 1071 1073 1094 C4' A B 17 OK 1096 1093 1095 1116 C4' U B 18 OK 1118 1115 1117 1136 C4' A B 19 OK 1138 1135 1137 1158 C4' C B 20 OK 1160 1157 1159 1178 C4' G B 21 OK 1180 1177 1179 1201 C4' A B 22 OK 1203 1200 1202 1223 C4' C B 23 OK 1225 1222 1224 1243 C4' C B 24 OK 1245 1242 1244 1263 C4' A B 25 OK 1265 1262 1264 1285 C4' C B 26 OK 1287 1284 1286 1305 C4' C B 27 OK 1307 1304 1306 1325 C4' U B 28 OK 1327 1324 1326 1345 C4' A B 29 OK 1347 1344 1346 1367 C4' G B 30 OK 1369 1366 1368 1390 C4' G B 31 OK 1392 1389 1391 1413 C4' U B 32 OK 1415 1412 1414 1433 C4' A B 33 OK 1435 1432 1434 1455 C4' C B 34 OK 1457 1454 1456 1475 C4' C B 35 OK 1477 1474 1476 1495 C4' A B 36 OK 1497 1494 1496 1517 C4' U B 37 OK 1519 1516 1518 1537 C4' U B 38 OK 1539 1536 1538 1557 C4' G B 39 OK 1559 1556 1558 1580 C4' C B 40 OK 1582 1579 1581 1600 C4' A B 41 OK 1602 1599 1601 1622 C4' C B 42 OK 1624 1621 1623 1642 C4' U B 43 OK 1644 1641 1643 1654 C4' C B 44 OK 1656 1653 1655 1674 C4' C B 45 OK 1676 1673 1675 1694 C4' G B 46 OK 1696 1693 1695 1717 C4' G B 47 OK 1719 1716 1718 1740 C4' U B 48 OK 1742 1739 1741 1760 C4' A B 49 OK 1762 1759 1761 1782 C4' C B 50 OK 1784 1781 1783 1802 C4' C B 51 OK 1804 1801 1803 1822 C4' U B 52 OK 1824 1821 1823 1842 C4' A B 53 OK 1844 1841 1843 1864 C4' A B 54 OK 1866 1863 1865 1886 C4' A B 55 OK 1888 1885 1887 1908 C4' A B 56 OK 1910 1907 1909 1930 C4' C B 57 OK 1932 1929 1931 1950 C4' A B 58 OK 1952 1949 1951 1972 C4' U B 59 OK 1974 1971 1973 1992 C4' A B 60 OK 1994 1991 1993 2014 C4' C B 61 OK 2016 2013 2015 2034 C4' C B 62 OK 2036 2033 2035 2054 C4' C B 63 OK 2056 2053 2055 2074 C4' U B 64 OK 2076 2073 2075 2094 C4' C B 65 OK 2096 2093 2095 2121 C4' CTC B 601 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 734 C5' G B 1 733 735 757 C5' A B 2 756 758 779 C5' G B 3 778 780 802 C5' G B 4 801 803 825 C5' G B 5 824 826 848 C5' A B 6 847 849 870 C5' G B 7 869 871 893 C5' A B 8 892 894 915 C5' G B 9 914 916 938 C5' G B 10 937 939 961 C5' U B 11 960 962 981 C5' G B 12 980 982 1004 C5' A B 13 1003 1005 1026 C5' A B 14 1025 1027 1048 C5' G B 15 1047 1049 1071 C5' A B 16 1070 1072 1093 C5' A B 17 1092 1094 1115 C5' U B 18 1114 1116 1135 C5' A B 19 1134 1136 1157 C5' C B 20 1156 1158 1177 C5' G B 21 1176 1178 1200 C5' A B 22 1199 1201 1222 C5' C B 23 1221 1223 1242 C5' C B 24 1241 1243 1262 C5' A B 25 1261 1263 1284 C5' C B 26 1283 1285 1304 C5' C B 27 1303 1305 1324 C5' U B 28 1323 1325 1344 C5' A B 29 1343 1345 1366 C5' G B 30 1365 1367 1389 C5' G B 31 1388 1390 1412 C5' U B 32 1411 1413 1432 C5' A B 33 1431 1433 1454 C5' C B 34 1453 1455 1474 C5' C B 35 1473 1475 1494 C5' A B 36 1493 1495 1516 C5' U B 37 1515 1517 1536 C5' U B 38 1535 1537 1556 C5' G B 39 1555 1557 1579 C5' C B 40 1578 1580 1599 C5' A B 41 1598 1600 1621 C5' C B 42 1620 1622 1641 C5' U B 43 1640 1642 1653 C5' C B 44 1652 1654 1673 C5' C B 45 1672 1674 1693 C5' G B 46 1692 1694 1716 C5' G B 47 1715 1717 1739 C5' U B 48 1738 1740 1759 C5' A B 49 1758 1760 1781 C5' C B 50 1780 1782 1801 C5' C B 51 1800 1802 1821 C5' U B 52 1820 1822 1841 C5' A B 53 1840 1842 1863 C5' A B 54 1862 1864 1885 C5' A B 55 1884 1886 1907 C5' A B 56 1906 1908 1929 C5' C B 57 1928 1930 1949 C5' A B 58 1948 1950 1971 C5' U B 59 1970 1972 1991 C5' A B 60 1990 1992 2013 C5' C B 61 2012 2014 2033 C5' C B 62 2032 2034 2053 C5' C B 63 2052 2054 2073 C5' U B 64 2072 2074 2093 C5' C B 65 2092 2094 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 730 P G B 1 distorted distorted 731 732 733 753 P A B 2 distorted distorted 738 754 755 756 775 P G B 3 distorted distorted 761 776 777 778 798 P G B 4 distorted distorted 783 799 800 801 821 P G B 5 distorted distorted 806 822 823 824 844 P A B 6 distorted distorted 829 845 846 847 866 P G B 7 distorted distorted 852 867 868 869 889 P A B 8 distorted distorted 874 890 891 892 911 P G B 9 distorted distorted 897 912 913 914 934 P G B 10 distorted distorted 919 935 936 937 957 P U B 11 distorted distorted 942 958 959 960 977 P G B 12 distorted distorted 965 978 979 980 1000 P A B 13 distorted distorted 985 1001 1002 1003 1022 P A B 14 distorted distorted 1008 1023 1024 1025 1044 P G B 15 distorted distorted 1030 1045 1046 1047 1067 P A B 16 distorted distorted 1052 1068 1069 1070 1089 P A B 17 distorted distorted 1075 1090 1091 1092 1111 P U B 18 distorted distorted 1097 1112 1113 1114 1131 P A B 19 distorted distorted 1119 1132 1133 1134 1153 P C B 20 distorted distorted 1139 1154 1155 1156 1173 P G B 21 distorted distorted 1161 1174 1175 1176 1196 P A B 22 distorted distorted 1181 1197 1198 1199 1218 P C B 23 distorted distorted 1204 1219 1220 1221 1238 P C B 24 distorted distorted 1226 1239 1240 1241 1258 P A B 25 distorted distorted 1246 1259 1260 1261 1280 P C B 26 distorted distorted 1266 1281 1282 1283 1300 P C B 27 distorted distorted 1288 1301 1302 1303 1320 P U B 28 distorted distorted 1308 1321 1322 1323 1340 P A B 29 distorted distorted 1328 1341 1342 1343 1362 P G B 30 distorted distorted 1348 1363 1364 1365 1385 P G B 31 distorted distorted 1370 1386 1387 1388 1408 P U B 32 distorted distorted 1393 1409 1410 1411 1428 P A B 33 distorted distorted 1416 1429 1430 1431 1450 P C B 34 distorted distorted 1436 1451 1452 1453 1470 P C B 35 distorted distorted 1458 1471 1472 1473 1490 P A B 36 distorted distorted 1478 1491 1492 1493 1512 P U B 37 distorted distorted 1498 1513 1514 1515 1532 P U B 38 distorted distorted 1520 1533 1534 1535 1552 P G B 39 distorted distorted 1540 1553 1554 1555 1575 P C B 40 distorted distorted 1560 1576 1577 1578 1595 P A B 41 distorted distorted 1583 1596 1597 1598 1617 P C B 42 distorted distorted 1603 1618 1619 1620 1637 P U B 43 distorted distorted 1625 1638 1639 1640 1649 P C B 44 distorted distorted 1645 1650 1651 1652 1669 P C B 45 distorted distorted 1657 1670 1671 1672 1689 P G B 46 distorted distorted 1677 1690 1691 1692 1712 P G B 47 distorted distorted 1697 1713 1714 1715 1735 P U B 48 distorted distorted 1720 1736 1737 1738 1755 P A B 49 distorted distorted 1743 1756 1757 1758 1777 P C B 50 distorted distorted 1763 1778 1779 1780 1797 P C B 51 distorted distorted 1785 1798 1799 1800 1817 P U B 52 distorted distorted 1805 1818 1819 1820 1837 P A B 53 distorted distorted 1825 1838 1839 1840 1859 P A B 54 distorted distorted 1845 1860 1861 1862 1881 P A B 55 distorted distorted 1867 1882 1883 1884 1903 P A B 56 distorted distorted 1889 1904 1905 1906 1925 P C B 57 distorted distorted 1911 1926 1927 1928 1945 P A B 58 distorted distorted 1933 1946 1947 1948 1967 P U B 59 distorted distorted 1953 1968 1969 1970 1987 P A B 60 distorted distorted 1975 1988 1989 1990 2009 P C B 61 distorted distorted 1995 2010 2011 2012 2029 P C B 62 distorted distorted 2017 2030 2031 2032 2049 P C B 63 distorted distorted 2037 2050 2051 2052 2069 P U B 64 distorted distorted 2057 2070 2071 2072 2089 P C B 65 distorted distorted 2077 2090 2091 2092 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