ID code: '3HDD' 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' --------------------------------------------------------------------------------- 986 C1' T C 202 beta 982 987 985 1006 C1' T C 203 beta 1002 1007 1005 1026 C1' T C 204 beta 1022 1027 1025 1046 C1' G C 205 beta 1042 1047 1045 1068 C1' C C 206 beta 1064 1069 1067 1087 C1' C C 207 beta 1083 1088 1086 1106 C1' A C 208 beta 1102 1107 1105 1127 C1' T C 209 beta 1123 1128 1126 1147 C1' G C 210 beta 1143 1148 1146 1169 C1' T C 211 beta 1165 1170 1168 1189 C1' A C 212 beta 1185 1190 1188 1210 C1' A C 213 beta 1206 1211 1209 1231 C1' T C 214 beta 1227 1232 1230 1251 C1' T C 215 beta 1247 1252 1250 1271 C1' A C 216 beta 1267 1272 1270 1292 C1' C C 217 beta 1288 1293 1291 1311 C1' C C 218 beta 1307 1312 1310 1330 C1' T C 219 beta 1326 1331 1329 1350 C1' A C 220 beta 1346 1351 1349 1371 C1' A C 221 beta 1367 1372 1370 1411 C1' T D 323 beta 1407 1412 1410 1431 C1' T D 324 beta 1427 1432 1430 1451 C1' A D 325 beta 1447 1452 1450 1472 C1' G D 326 beta 1468 1473 1471 1494 C1' G D 327 beta 1490 1495 1493 1516 C1' T D 328 beta 1512 1517 1515 1536 C1' A D 329 beta 1532 1537 1535 1557 C1' A D 330 beta 1553 1558 1556 1578 C1' T D 331 beta 1574 1579 1577 1598 C1' T D 332 beta 1594 1599 1597 1618 C1' A D 333 beta 1614 1619 1617 1639 C1' C D 334 beta 1635 1640 1638 1658 C1' A D 335 beta 1654 1659 1657 1679 C1' T D 336 beta 1675 1680 1678 1699 C1' G D 337 beta 1695 1700 1698 1721 C1' G D 338 beta 1717 1722 1720 1743 C1' C D 339 beta 1739 1744 1742 1762 C1' A D 340 beta 1758 1763 1761 1783 C1' A D 341 beta 1779 1784 1782 1804 C1' A D 342 beta 1800 1805 1803 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 985 C2' T C 202 986 983 1005 C2' T C 203 1006 1003 1025 C2' T C 204 1026 1023 1045 C2' G C 205 1046 1043 1067 C2' C C 206 1068 1065 1086 C2' C C 207 1087 1084 1105 C2' A C 208 1106 1103 1126 C2' T C 209 1127 1124 1146 C2' G C 210 1147 1144 1168 C2' T C 211 1169 1166 1188 C2' A C 212 1189 1186 1209 C2' A C 213 1210 1207 1230 C2' T C 214 1231 1228 1250 C2' T C 215 1251 1248 1270 C2' A C 216 1271 1268 1291 C2' C C 217 1292 1289 1310 C2' C C 218 1311 1308 1329 C2' T C 219 1330 1327 1349 C2' A C 220 1350 1347 1370 C2' A C 221 1371 1368 1410 C2' T D 323 1411 1408 1430 C2' T D 324 1431 1428 1450 C2' A D 325 1451 1448 1471 C2' G D 326 1472 1469 1493 C2' G D 327 1494 1491 1515 C2' T D 328 1516 1513 1535 C2' A D 329 1536 1533 1556 C2' A D 330 1557 1554 1577 C2' T D 331 1578 1575 1597 C2' T D 332 1598 1595 1617 C2' A D 333 1618 1615 1638 C2' C D 334 1639 1636 1657 C2' A D 335 1658 1655 1678 C2' T D 336 1679 1676 1698 C2' G D 337 1699 1696 1720 C2' G D 338 1721 1718 1742 C2' C D 339 1743 1740 1761 C2' A D 340 1762 1759 1782 C2' A D 341 1783 1780 1803 C2' A D 342 1804 1801 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 983 C3' T C 202 OK 981 984 985 1003 C3' T C 203 OK 1001 1004 1005 1023 C3' T C 204 OK 1021 1024 1025 1043 C3' G C 205 OK 1041 1044 1045 1065 C3' C C 206 OK 1063 1066 1067 1084 C3' C C 207 OK 1082 1085 1086 1103 C3' A C 208 OK 1101 1104 1105 1124 C3' T C 209 OK 1122 1125 1126 1144 C3' G C 210 OK 1142 1145 1146 1166 C3' T C 211 OK 1164 1167 1168 1186 C3' A C 212 OK 1184 1187 1188 1207 C3' A C 213 OK 1205 1208 1209 1228 C3' T C 214 OK 1226 1229 1230 1248 C3' T C 215 OK 1246 1249 1250 1268 C3' A C 216 OK 1266 1269 1270 1289 C3' C C 217 OK 1287 1290 1291 1308 C3' C C 218 OK 1306 1309 1310 1327 C3' T C 219 OK 1325 1328 1329 1347 C3' A C 220 OK 1345 1348 1349 1368 C3' A C 221 OK 1366 1369 1370 1408 C3' T D 323 OK 1406 1409 1410 1428 C3' T D 324 OK 1426 1429 1430 1448 C3' A D 325 OK 1446 1449 1450 1469 C3' G D 326 OK 1467 1470 1471 1491 C3' G D 327 OK 1489 1492 1493 1513 C3' T D 328 OK 1511 1514 1515 1533 C3' A D 329 OK 1531 1534 1535 1554 C3' A D 330 OK 1552 1555 1556 1575 C3' T D 331 OK 1573 1576 1577 1595 C3' T D 332 OK 1593 1596 1597 1615 C3' A D 333 OK 1613 1616 1617 1636 C3' C D 334 OK 1634 1637 1638 1655 C3' A D 335 OK 1653 1656 1657 1676 C3' T D 336 OK 1674 1677 1678 1696 C3' G D 337 OK 1694 1697 1698 1718 C3' G D 338 OK 1716 1719 1720 1740 C3' C D 339 OK 1738 1741 1742 1759 C3' A D 340 OK 1757 1760 1761 1780 C3' A D 341 OK 1778 1781 1782 1801 C3' A D 342 OK 1799 1802 1803 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 981 C4' T C 202 OK 983 980 982 1001 C4' T C 203 OK 1003 1000 1002 1021 C4' T C 204 OK 1023 1020 1022 1041 C4' G C 205 OK 1043 1040 1042 1063 C4' C C 206 OK 1065 1062 1064 1082 C4' C C 207 OK 1084 1081 1083 1101 C4' A C 208 OK 1103 1100 1102 1122 C4' T C 209 OK 1124 1121 1123 1142 C4' G C 210 OK 1144 1141 1143 1164 C4' T C 211 OK 1166 1163 1165 1184 C4' A C 212 OK 1186 1183 1185 1205 C4' A C 213 OK 1207 1204 1206 1226 C4' T C 214 OK 1228 1225 1227 1246 C4' T C 215 OK 1248 1245 1247 1266 C4' A C 216 OK 1268 1265 1267 1287 C4' C C 217 OK 1289 1286 1288 1306 C4' C C 218 OK 1308 1305 1307 1325 C4' T C 219 OK 1327 1324 1326 1345 C4' A C 220 OK 1347 1344 1346 1366 C4' A C 221 OK 1368 1365 1367 1406 C4' T D 323 OK 1408 1405 1407 1426 C4' T D 324 OK 1428 1425 1427 1446 C4' A D 325 OK 1448 1445 1447 1467 C4' G D 326 OK 1469 1466 1468 1489 C4' G D 327 OK 1491 1488 1490 1511 C4' T D 328 OK 1513 1510 1512 1531 C4' A D 329 OK 1533 1530 1532 1552 C4' A D 330 OK 1554 1551 1553 1573 C4' T D 331 OK 1575 1572 1574 1593 C4' T D 332 OK 1595 1592 1594 1613 C4' A D 333 OK 1615 1612 1614 1634 C4' C D 334 OK 1636 1633 1635 1653 C4' A D 335 OK 1655 1652 1654 1674 C4' T D 336 OK 1676 1673 1675 1694 C4' G D 337 OK 1696 1693 1695 1716 C4' G D 338 OK 1718 1715 1717 1738 C4' C D 339 OK 1740 1737 1739 1757 C4' A D 340 OK 1759 1756 1758 1778 C4' A D 341 OK 1780 1777 1779 1799 C4' A D 342 OK 1801 1798 1800 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 980 C5' T C 202 979 981 1000 C5' T C 203 999 1001 1020 C5' T C 204 1019 1021 1040 C5' G C 205 1039 1041 1062 C5' C C 206 1061 1063 1081 C5' C C 207 1080 1082 1100 C5' A C 208 1099 1101 1121 C5' T C 209 1120 1122 1141 C5' G C 210 1140 1142 1163 C5' T C 211 1162 1164 1183 C5' A C 212 1182 1184 1204 C5' A C 213 1203 1205 1225 C5' T C 214 1224 1226 1245 C5' T C 215 1244 1246 1265 C5' A C 216 1264 1266 1286 C5' C C 217 1285 1287 1305 C5' C C 218 1304 1306 1324 C5' T C 219 1323 1325 1344 C5' A C 220 1343 1345 1365 C5' A C 221 1364 1366 1405 C5' T D 323 1404 1406 1425 C5' T D 324 1424 1426 1445 C5' A D 325 1444 1446 1466 C5' G D 326 1465 1467 1488 C5' G D 327 1487 1489 1510 C5' T D 328 1509 1511 1530 C5' A D 329 1529 1531 1551 C5' A D 330 1550 1552 1572 C5' T D 331 1571 1573 1592 C5' T D 332 1591 1593 1612 C5' A D 333 1611 1613 1633 C5' C D 334 1632 1634 1652 C5' A D 335 1651 1653 1673 C5' T D 336 1672 1674 1693 C5' G D 337 1692 1694 1715 C5' G D 338 1714 1716 1737 C5' C D 339 1736 1738 1756 C5' A D 340 1755 1757 1777 C5' A D 341 1776 1778 1798 C5' A D 342 1797 1799 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 996 P T C 203 distorted distorted 984 997 998 999 1016 P T C 204 distorted distorted 1004 1017 1018 1019 1036 P G C 205 distorted distorted 1024 1037 1038 1039 1058 P C C 206 distorted distorted 1044 1059 1060 1061 1077 P C C 207 OK OK 1066 1078 1079 1080 1096 P A C 208 distorted distorted 1085 1097 1098 1099 1117 P T C 209 distorted distorted 1104 1118 1119 1120 1137 P G C 210 distorted distorted 1125 1138 1139 1140 1159 P T C 211 distorted distorted 1145 1160 1161 1162 1179 P A C 212 distorted distorted 1167 1180 1181 1182 1200 P A C 213 distorted distorted 1187 1201 1202 1203 1221 P T C 214 distorted distorted 1208 1222 1223 1224 1241 P T C 215 distorted distorted 1229 1242 1243 1244 1261 P A C 216 distorted distorted 1249 1262 1263 1264 1282 P C C 217 distorted distorted 1269 1283 1284 1285 1301 P C C 218 distorted distorted 1290 1302 1303 1304 1320 P T C 219 distorted distorted 1309 1321 1322 1323 1340 P A C 220 distorted distorted 1328 1341 1342 1343 1361 P A C 221 distorted distorted 1348 1362 1363 1364 1421 P T D 324 OK OK 1409 1422 1423 1424 1441 P A D 325 distorted distorted 1429 1442 1443 1444 1462 P G D 326 distorted distorted 1449 1463 1464 1465 1484 P G D 327 distorted distorted 1470 1485 1486 1487 1506 P T D 328 distorted distorted 1492 1507 1508 1509 1526 P A D 329 distorted distorted 1514 1527 1528 1529 1547 P A D 330 distorted distorted 1534 1548 1549 1550 1568 P T D 331 distorted distorted 1555 1569 1570 1571 1588 P T D 332 distorted distorted 1576 1589 1590 1591 1608 P A D 333 distorted distorted 1596 1609 1610 1611 1629 P C D 334 OK OK 1616 1630 1631 1632 1648 P A D 335 OK OK 1637 1649 1650 1651 1669 P T D 336 distorted distorted 1656 1670 1671 1672 1689 P G D 337 distorted distorted 1677 1690 1691 1692 1711 P G D 338 distorted distorted 1697 1712 1713 1714 1733 P C D 339 distorted distorted 1719 1734 1735 1736 1752 P A D 340 OK OK 1741 1753 1754 1755 1773 P A D 341 OK OK 1760 1774 1775 1776 1794 P A D 342 distorted distorted 1781 1795 1796 1797 ---------------------------------------------------------------------------------