ID code: '1YRN' 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' --------------------------------------------------------------------------------- 1047 C1' C C 3 beta 1043 1048 1046 1066 C1' A C 4 beta 1062 1067 1065 1087 C1' T C 5 beta 1083 1088 1086 1107 C1' G C 6 beta 1103 1108 1106 1129 C1' T C 7 beta 1125 1130 1128 1149 C1' A C 8 beta 1145 1150 1148 1170 C1' A C 9 beta 1166 1171 1169 1191 C1' T C 10 beta 1187 1192 1190 1211 C1' T C 11 beta 1207 1212 1210 1231 C1' T C 12 beta 1227 1232 1230 1251 C1' A C 13 beta 1247 1252 1250 1272 C1' T C 14 beta 1268 1273 1271 1292 C1' T C 15 beta 1288 1293 1291 1312 C1' A C 16 beta 1308 1313 1311 1333 C1' C C 17 beta 1329 1334 1332 1352 C1' A C 18 beta 1348 1353 1351 1373 C1' T C 19 beta 1369 1374 1372 1393 C1' C C 20 beta 1389 1394 1392 1412 C1' A C 21 beta 1408 1413 1411 1471 C1' T C 24 beta 1467 1472 1470 1491 C1' G C 25 beta 1487 1492 1490 1513 C1' A C 26 beta 1509 1514 1512 1534 C1' T C 27 beta 1530 1535 1533 1554 C1' G C 28 beta 1550 1555 1553 1576 C1' T C 29 beta 1572 1577 1575 1596 C1' A C 30 beta 1592 1597 1595 1617 C1' A C 31 beta 1613 1618 1616 1638 C1' T C 32 beta 1634 1639 1637 1658 C1' A C 33 beta 1654 1659 1657 1679 C1' A C 34 beta 1675 1680 1678 1700 C1' A C 35 beta 1696 1701 1699 1721 C1' T C 36 beta 1717 1722 1720 1741 C1' T C 37 beta 1737 1742 1740 1761 C1' A C 38 beta 1757 1762 1760 1782 C1' C C 39 beta 1778 1783 1781 1801 C1' A C 40 beta 1797 1802 1800 1822 C1' T C 41 beta 1818 1823 1821 1842 C1' G C 42 beta 1838 1843 1841 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 1046 C2' C C 3 1047 1044 1065 C2' A C 4 1066 1063 1086 C2' T C 5 1087 1084 1106 C2' G C 6 1107 1104 1128 C2' T C 7 1129 1126 1148 C2' A C 8 1149 1146 1169 C2' A C 9 1170 1167 1190 C2' T C 10 1191 1188 1210 C2' T C 11 1211 1208 1230 C2' T C 12 1231 1228 1250 C2' A C 13 1251 1248 1271 C2' T C 14 1272 1269 1291 C2' T C 15 1292 1289 1311 C2' A C 16 1312 1309 1332 C2' C C 17 1333 1330 1351 C2' A C 18 1352 1349 1372 C2' T C 19 1373 1370 1392 C2' C C 20 1393 1390 1411 C2' A C 21 1412 1409 1470 C2' T C 24 1471 1468 1490 C2' G C 25 1491 1488 1512 C2' A C 26 1513 1510 1533 C2' T C 27 1534 1531 1553 C2' G C 28 1554 1551 1575 C2' T C 29 1576 1573 1595 C2' A C 30 1596 1593 1616 C2' A C 31 1617 1614 1637 C2' T C 32 1638 1635 1657 C2' A C 33 1658 1655 1678 C2' A C 34 1679 1676 1699 C2' A C 35 1700 1697 1720 C2' T C 36 1721 1718 1740 C2' T C 37 1741 1738 1760 C2' A C 38 1761 1758 1781 C2' C C 39 1782 1779 1800 C2' A C 40 1801 1798 1821 C2' T C 41 1822 1819 1841 C2' G C 42 1842 1839 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 1044 C3' C C 3 OK 1042 1045 1046 1063 C3' A C 4 OK 1061 1064 1065 1084 C3' T C 5 OK 1082 1085 1086 1104 C3' G C 6 OK 1102 1105 1106 1126 C3' T C 7 OK 1124 1127 1128 1146 C3' A C 8 OK 1144 1147 1148 1167 C3' A C 9 OK 1165 1168 1169 1188 C3' T C 10 OK 1186 1189 1190 1208 C3' T C 11 OK 1206 1209 1210 1228 C3' T C 12 OK 1226 1229 1230 1248 C3' A C 13 OK 1246 1249 1250 1269 C3' T C 14 OK 1267 1270 1271 1289 C3' T C 15 OK 1287 1290 1291 1309 C3' A C 16 OK 1307 1310 1311 1330 C3' C C 17 OK 1328 1331 1332 1349 C3' A C 18 OK 1347 1350 1351 1370 C3' T C 19 OK 1368 1371 1372 1390 C3' C C 20 OK 1388 1391 1392 1409 C3' A C 21 OK 1407 1410 1411 1468 C3' T C 24 OK 1466 1469 1470 1488 C3' G C 25 OK 1486 1489 1490 1510 C3' A C 26 OK 1508 1511 1512 1531 C3' T C 27 OK 1529 1532 1533 1551 C3' G C 28 OK 1549 1552 1553 1573 C3' T C 29 OK 1571 1574 1575 1593 C3' A C 30 OK 1591 1594 1595 1614 C3' A C 31 OK 1612 1615 1616 1635 C3' T C 32 OK 1633 1636 1637 1655 C3' A C 33 OK 1653 1656 1657 1676 C3' A C 34 OK 1674 1677 1678 1697 C3' A C 35 OK 1695 1698 1699 1718 C3' T C 36 OK 1716 1719 1720 1738 C3' T C 37 OK 1736 1739 1740 1758 C3' A C 38 OK 1756 1759 1760 1779 C3' C C 39 OK 1777 1780 1781 1798 C3' A C 40 OK 1796 1799 1800 1819 C3' T C 41 OK 1817 1820 1821 1839 C3' G C 42 OK 1837 1840 1841 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 1042 C4' C C 3 OK 1044 1041 1043 1061 C4' A C 4 OK 1063 1060 1062 1082 C4' T C 5 OK 1084 1081 1083 1102 C4' G C 6 OK 1104 1101 1103 1124 C4' T C 7 OK 1126 1123 1125 1144 C4' A C 8 OK 1146 1143 1145 1165 C4' A C 9 OK 1167 1164 1166 1186 C4' T C 10 OK 1188 1185 1187 1206 C4' T C 11 OK 1208 1205 1207 1226 C4' T C 12 OK 1228 1225 1227 1246 C4' A C 13 OK 1248 1245 1247 1267 C4' T C 14 OK 1269 1266 1268 1287 C4' T C 15 OK 1289 1286 1288 1307 C4' A C 16 OK 1309 1306 1308 1328 C4' C C 17 OK 1330 1327 1329 1347 C4' A C 18 OK 1349 1346 1348 1368 C4' T C 19 OK 1370 1367 1369 1388 C4' C C 20 OK 1390 1387 1389 1407 C4' A C 21 OK 1409 1406 1408 1466 C4' T C 24 OK 1468 1465 1467 1486 C4' G C 25 OK 1488 1485 1487 1508 C4' A C 26 OK 1510 1507 1509 1529 C4' T C 27 OK 1531 1528 1530 1549 C4' G C 28 OK 1551 1548 1550 1571 C4' T C 29 OK 1573 1570 1572 1591 C4' A C 30 OK 1593 1590 1592 1612 C4' A C 31 OK 1614 1611 1613 1633 C4' T C 32 OK 1635 1632 1634 1653 C4' A C 33 OK 1655 1652 1654 1674 C4' A C 34 OK 1676 1673 1675 1695 C4' A C 35 OK 1697 1694 1696 1716 C4' T C 36 OK 1718 1715 1717 1736 C4' T C 37 OK 1738 1735 1737 1756 C4' A C 38 OK 1758 1755 1757 1777 C4' C C 39 OK 1779 1776 1778 1796 C4' A C 40 OK 1798 1795 1797 1817 C4' T C 41 OK 1819 1816 1818 1837 C4' G C 42 OK 1839 1836 1838 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 1041 C5' C C 3 1040 1042 1060 C5' A C 4 1059 1061 1081 C5' T C 5 1080 1082 1101 C5' G C 6 1100 1102 1123 C5' T C 7 1122 1124 1143 C5' A C 8 1142 1144 1164 C5' A C 9 1163 1165 1185 C5' T C 10 1184 1186 1205 C5' T C 11 1204 1206 1225 C5' T C 12 1224 1226 1245 C5' A C 13 1244 1246 1266 C5' T C 14 1265 1267 1286 C5' T C 15 1285 1287 1306 C5' A C 16 1305 1307 1327 C5' C C 17 1326 1328 1346 C5' A C 18 1345 1347 1367 C5' T C 19 1366 1368 1387 C5' C C 20 1386 1388 1406 C5' A C 21 1405 1407 1465 C5' T C 24 1464 1466 1485 C5' G C 25 1484 1486 1507 C5' A C 26 1506 1508 1528 C5' T C 27 1527 1529 1548 C5' G C 28 1547 1549 1570 C5' T C 29 1569 1571 1590 C5' A C 30 1589 1591 1611 C5' A C 31 1610 1612 1632 C5' T C 32 1631 1633 1652 C5' A C 33 1651 1653 1673 C5' A C 34 1672 1674 1694 C5' A C 35 1693 1695 1715 C5' T C 36 1714 1716 1735 C5' T C 37 1734 1736 1755 C5' A C 38 1754 1756 1776 C5' C C 39 1775 1777 1795 C5' A C 40 1794 1796 1816 C5' T C 41 1815 1817 1836 C5' G C 42 1835 1837 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1056 P A C 4 OK OK 1045 1057 1058 1059 1077 P T C 5 OK OK 1064 1078 1079 1080 1097 P G C 6 OK OK 1085 1098 1099 1100 1119 P T C 7 OK OK 1105 1120 1121 1122 1139 P A C 8 OK OK 1127 1140 1141 1142 1160 P A C 9 OK OK 1147 1161 1162 1163 1181 P T C 10 OK OK 1168 1182 1183 1184 1201 P T C 11 OK OK 1189 1202 1203 1204 1221 P T C 12 OK OK 1209 1222 1223 1224 1241 P A C 13 OK OK 1229 1242 1243 1244 1262 P T C 14 OK OK 1249 1263 1264 1265 1282 P T C 15 OK OK 1270 1283 1284 1285 1302 P A C 16 OK OK 1290 1303 1304 1305 1323 P C C 17 OK OK 1310 1324 1325 1326 1342 P A C 18 OK OK 1331 1343 1344 1345 1363 P T C 19 OK OK 1350 1364 1365 1366 1383 P C C 20 OK OK 1371 1384 1385 1386 1402 P A C 21 OK OK 1391 1403 1404 1405 1481 P G C 25 OK OK 1469 1482 1483 1484 1503 P A C 26 OK OK 1489 1504 1505 1506 1524 P T C 27 OK OK 1511 1525 1526 1527 1544 P G C 28 OK OK 1532 1545 1546 1547 1566 P T C 29 OK OK 1552 1567 1568 1569 1586 P A C 30 OK OK 1574 1587 1588 1589 1607 P A C 31 OK OK 1594 1608 1609 1610 1628 P T C 32 OK OK 1615 1629 1630 1631 1648 P A C 33 OK OK 1636 1649 1650 1651 1669 P A C 34 OK OK 1656 1670 1671 1672 1690 P A C 35 OK OK 1677 1691 1692 1693 1711 P T C 36 OK OK 1698 1712 1713 1714 1731 P T C 37 OK OK 1719 1732 1733 1734 1751 P A C 38 OK OK 1739 1752 1753 1754 1772 P C C 39 OK OK 1759 1773 1774 1775 1791 P A C 40 OK OK 1780 1792 1793 1794 1812 P T C 41 OK OK 1799 1813 1814 1815 1832 P G C 42 OK OK 1820 1833 1834 1835 ---------------------------------------------------------------------------------