ID code: '1AKH' 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' --------------------------------------------------------------------------------- 1052 C1' C C 3 beta 1048 1053 1051 1071 C1' A C 4 beta 1067 1072 1070 1092 C1' T C 5 beta 1088 1093 1091 1112 C1' G C 6 beta 1108 1113 1111 1134 C1' T C 7 beta 1130 1135 1133 1154 C1' A C 8 beta 1150 1155 1153 1175 C1' A C 9 beta 1171 1176 1174 1196 C1' A C 10 beta 1192 1197 1195 1217 C1' A C 11 beta 1213 1218 1216 1238 C1' A C 12 beta 1234 1239 1237 1259 C1' T C 13 beta 1255 1260 1258 1279 C1' T C 14 beta 1275 1280 1278 1299 C1' T C 15 beta 1295 1300 1298 1319 C1' A C 16 beta 1315 1320 1318 1340 C1' C C 17 beta 1336 1341 1339 1359 C1' A C 18 beta 1355 1360 1358 1380 C1' T C 19 beta 1376 1381 1379 1400 C1' C C 20 beta 1396 1401 1399 1419 C1' A C 21 beta 1415 1420 1418 1479 C1' T D 24 beta 1475 1480 1478 1499 C1' G D 25 beta 1495 1500 1498 1521 C1' A D 26 beta 1517 1522 1520 1542 C1' T D 27 beta 1538 1543 1541 1562 C1' G D 28 beta 1558 1563 1561 1584 C1' T D 29 beta 1580 1585 1583 1604 C1' A D 30 beta 1600 1605 1603 1625 C1' A D 31 beta 1621 1626 1624 1646 C1' A D 32 beta 1642 1647 1645 1667 C1' T D 33 beta 1663 1668 1666 1687 C1' T D 34 beta 1683 1688 1686 1707 C1' T D 35 beta 1703 1708 1706 1727 C1' T D 36 beta 1723 1728 1726 1747 C1' T D 37 beta 1743 1748 1746 1767 C1' A D 38 beta 1763 1768 1766 1788 C1' C D 39 beta 1784 1789 1787 1807 C1' A D 40 beta 1803 1808 1806 1828 C1' T D 41 beta 1824 1829 1827 1848 C1' G D 42 beta 1844 1849 1847 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 1051 C2' C C 3 1052 1049 1070 C2' A C 4 1071 1068 1091 C2' T C 5 1092 1089 1111 C2' G C 6 1112 1109 1133 C2' T C 7 1134 1131 1153 C2' A C 8 1154 1151 1174 C2' A C 9 1175 1172 1195 C2' A C 10 1196 1193 1216 C2' A C 11 1217 1214 1237 C2' A C 12 1238 1235 1258 C2' T C 13 1259 1256 1278 C2' T C 14 1279 1276 1298 C2' T C 15 1299 1296 1318 C2' A C 16 1319 1316 1339 C2' C C 17 1340 1337 1358 C2' A C 18 1359 1356 1379 C2' T C 19 1380 1377 1399 C2' C C 20 1400 1397 1418 C2' A C 21 1419 1416 1478 C2' T D 24 1479 1476 1498 C2' G D 25 1499 1496 1520 C2' A D 26 1521 1518 1541 C2' T D 27 1542 1539 1561 C2' G D 28 1562 1559 1583 C2' T D 29 1584 1581 1603 C2' A D 30 1604 1601 1624 C2' A D 31 1625 1622 1645 C2' A D 32 1646 1643 1666 C2' T D 33 1667 1664 1686 C2' T D 34 1687 1684 1706 C2' T D 35 1707 1704 1726 C2' T D 36 1727 1724 1746 C2' T D 37 1747 1744 1766 C2' A D 38 1767 1764 1787 C2' C D 39 1788 1785 1806 C2' A D 40 1807 1804 1827 C2' T D 41 1828 1825 1847 C2' G D 42 1848 1845 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 1049 C3' C C 3 OK 1047 1050 1051 1068 C3' A C 4 OK 1066 1069 1070 1089 C3' T C 5 OK 1087 1090 1091 1109 C3' G C 6 OK 1107 1110 1111 1131 C3' T C 7 OK 1129 1132 1133 1151 C3' A C 8 OK 1149 1152 1153 1172 C3' A C 9 OK 1170 1173 1174 1193 C3' A C 10 OK 1191 1194 1195 1214 C3' A C 11 OK 1212 1215 1216 1235 C3' A C 12 OK 1233 1236 1237 1256 C3' T C 13 OK 1254 1257 1258 1276 C3' T C 14 OK 1274 1277 1278 1296 C3' T C 15 OK 1294 1297 1298 1316 C3' A C 16 OK 1314 1317 1318 1337 C3' C C 17 OK 1335 1338 1339 1356 C3' A C 18 OK 1354 1357 1358 1377 C3' T C 19 OK 1375 1378 1379 1397 C3' C C 20 OK 1395 1398 1399 1416 C3' A C 21 OK 1414 1417 1418 1476 C3' T D 24 OK 1474 1477 1478 1496 C3' G D 25 OK 1494 1497 1498 1518 C3' A D 26 OK 1516 1519 1520 1539 C3' T D 27 OK 1537 1540 1541 1559 C3' G D 28 OK 1557 1560 1561 1581 C3' T D 29 OK 1579 1582 1583 1601 C3' A D 30 OK 1599 1602 1603 1622 C3' A D 31 OK 1620 1623 1624 1643 C3' A D 32 OK 1641 1644 1645 1664 C3' T D 33 OK 1662 1665 1666 1684 C3' T D 34 OK 1682 1685 1686 1704 C3' T D 35 OK 1702 1705 1706 1724 C3' T D 36 OK 1722 1725 1726 1744 C3' T D 37 OK 1742 1745 1746 1764 C3' A D 38 OK 1762 1765 1766 1785 C3' C D 39 OK 1783 1786 1787 1804 C3' A D 40 OK 1802 1805 1806 1825 C3' T D 41 OK 1823 1826 1827 1845 C3' G D 42 OK 1843 1846 1847 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 1047 C4' C C 3 OK 1049 1046 1048 1066 C4' A C 4 OK 1068 1065 1067 1087 C4' T C 5 OK 1089 1086 1088 1107 C4' G C 6 OK 1109 1106 1108 1129 C4' T C 7 OK 1131 1128 1130 1149 C4' A C 8 OK 1151 1148 1150 1170 C4' A C 9 OK 1172 1169 1171 1191 C4' A C 10 OK 1193 1190 1192 1212 C4' A C 11 OK 1214 1211 1213 1233 C4' A C 12 OK 1235 1232 1234 1254 C4' T C 13 OK 1256 1253 1255 1274 C4' T C 14 OK 1276 1273 1275 1294 C4' T C 15 OK 1296 1293 1295 1314 C4' A C 16 OK 1316 1313 1315 1335 C4' C C 17 OK 1337 1334 1336 1354 C4' A C 18 OK 1356 1353 1355 1375 C4' T C 19 OK 1377 1374 1376 1395 C4' C C 20 OK 1397 1394 1396 1414 C4' A C 21 OK 1416 1413 1415 1474 C4' T D 24 OK 1476 1473 1475 1494 C4' G D 25 OK 1496 1493 1495 1516 C4' A D 26 OK 1518 1515 1517 1537 C4' T D 27 OK 1539 1536 1538 1557 C4' G D 28 OK 1559 1556 1558 1579 C4' T D 29 OK 1581 1578 1580 1599 C4' A D 30 OK 1601 1598 1600 1620 C4' A D 31 OK 1622 1619 1621 1641 C4' A D 32 OK 1643 1640 1642 1662 C4' T D 33 OK 1664 1661 1663 1682 C4' T D 34 OK 1684 1681 1683 1702 C4' T D 35 OK 1704 1701 1703 1722 C4' T D 36 OK 1724 1721 1723 1742 C4' T D 37 OK 1744 1741 1743 1762 C4' A D 38 OK 1764 1761 1763 1783 C4' C D 39 OK 1785 1782 1784 1802 C4' A D 40 OK 1804 1801 1803 1823 C4' T D 41 OK 1825 1822 1824 1843 C4' G D 42 OK 1845 1842 1844 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 1046 C5' C C 3 1045 1047 1065 C5' A C 4 1064 1066 1086 C5' T C 5 1085 1087 1106 C5' G C 6 1105 1107 1128 C5' T C 7 1127 1129 1148 C5' A C 8 1147 1149 1169 C5' A C 9 1168 1170 1190 C5' A C 10 1189 1191 1211 C5' A C 11 1210 1212 1232 C5' A C 12 1231 1233 1253 C5' T C 13 1252 1254 1273 C5' T C 14 1272 1274 1293 C5' T C 15 1292 1294 1313 C5' A C 16 1312 1314 1334 C5' C C 17 1333 1335 1353 C5' A C 18 1352 1354 1374 C5' T C 19 1373 1375 1394 C5' C C 20 1393 1395 1413 C5' A C 21 1412 1414 1473 C5' T D 24 1472 1474 1493 C5' G D 25 1492 1494 1515 C5' A D 26 1514 1516 1536 C5' T D 27 1535 1537 1556 C5' G D 28 1555 1557 1578 C5' T D 29 1577 1579 1598 C5' A D 30 1597 1599 1619 C5' A D 31 1618 1620 1640 C5' A D 32 1639 1641 1661 C5' T D 33 1660 1662 1681 C5' T D 34 1680 1682 1701 C5' T D 35 1700 1702 1721 C5' T D 36 1720 1722 1741 C5' T D 37 1740 1742 1761 C5' A D 38 1760 1762 1782 C5' C D 39 1781 1783 1801 C5' A D 40 1800 1802 1822 C5' T D 41 1821 1823 1842 C5' G D 42 1841 1843 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1061 P A C 4 distorted distorted 1050 1062 1063 1064 1082 P T C 5 distorted distorted 1069 1083 1084 1085 1102 P G C 6 distorted distorted 1090 1103 1104 1105 1124 P T C 7 distorted distorted 1110 1125 1126 1127 1144 P A C 8 distorted distorted 1132 1145 1146 1147 1165 P A C 9 distorted distorted 1152 1166 1167 1168 1186 P A C 10 distorted distorted 1173 1187 1188 1189 1207 P A C 11 distorted distorted 1194 1208 1209 1210 1228 P A C 12 distorted distorted 1215 1229 1230 1231 1249 P T C 13 distorted distorted 1236 1250 1251 1252 1269 P T C 14 distorted distorted 1257 1270 1271 1272 1289 P T C 15 distorted distorted 1277 1290 1291 1292 1309 P A C 16 distorted distorted 1297 1310 1311 1312 1330 P C C 17 distorted distorted 1317 1331 1332 1333 1349 P A C 18 distorted distorted 1338 1350 1351 1352 1370 P T C 19 distorted distorted 1357 1371 1372 1373 1390 P C C 20 distorted distorted 1378 1391 1392 1393 1409 P A C 21 distorted distorted 1398 1410 1411 1412 1489 P G D 25 distorted distorted 1477 1490 1491 1492 1511 P A D 26 distorted distorted 1497 1512 1513 1514 1532 P T D 27 distorted distorted 1519 1533 1534 1535 1552 P G D 28 distorted distorted 1540 1553 1554 1555 1574 P T D 29 distorted distorted 1560 1575 1576 1577 1594 P A D 30 distorted distorted 1582 1595 1596 1597 1615 P A D 31 distorted distorted 1602 1616 1617 1618 1636 P A D 32 distorted distorted 1623 1637 1638 1639 1657 P T D 33 distorted distorted 1644 1658 1659 1660 1677 P T D 34 distorted distorted 1665 1678 1679 1680 1697 P T D 35 distorted distorted 1685 1698 1699 1700 1717 P T D 36 distorted distorted 1705 1718 1719 1720 1737 P T D 37 distorted distorted 1725 1738 1739 1740 1757 P A D 38 distorted distorted 1745 1758 1759 1760 1778 P C D 39 distorted distorted 1765 1779 1780 1781 1797 P A D 40 distorted distorted 1786 1798 1799 1800 1818 P T D 41 distorted distorted 1805 1819 1820 1821 1838 P G D 42 distorted distorted 1826 1839 1840 1841 ---------------------------------------------------------------------------------