ID code: '9ANT' 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' --------------------------------------------------------------------------------- 1071 C1' G C 101 beta 1067 1072 1070 1093 C1' A C 102 beta 1089 1094 1092 1114 C1' A C 103 beta 1110 1115 1113 1135 C1' A C 104 beta 1131 1136 1134 1156 C1' G C 105 beta 1152 1157 1155 1178 C1' C C 106 beta 1174 1179 1177 1197 C1' C C 107 beta 1193 1198 1196 1216 C1' A C 108 beta 1212 1217 1215 1237 C1' T C 109 beta 1233 1238 1236 1257 C1' T C 110 beta 1253 1258 1256 1277 C1' A C 111 beta 1273 1278 1276 1298 C1' G C 112 beta 1294 1299 1297 1320 C1' A C 113 beta 1316 1321 1319 1341 C1' G C 114 beta 1337 1342 1340 1381 C1' C D 215 beta 1377 1382 1380 1400 C1' T D 216 beta 1396 1401 1399 1420 C1' C D 217 beta 1416 1421 1419 1439 C1' T D 218 beta 1435 1440 1438 1459 C1' A D 219 beta 1455 1460 1458 1480 C1' A D 220 beta 1476 1481 1479 1501 C1' T D 221 beta 1497 1502 1500 1521 C1' G D 222 beta 1517 1522 1520 1543 C1' G D 223 beta 1539 1544 1542 1565 C1' C D 224 beta 1561 1566 1564 1584 C1' T D 225 beta 1580 1585 1583 1604 C1' T D 226 beta 1600 1605 1603 1624 C1' T D 227 beta 1620 1625 1623 1644 C1' C D 228 beta 1640 1645 1643 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 1070 C2' G C 101 1071 1068 1092 C2' A C 102 1093 1090 1113 C2' A C 103 1114 1111 1134 C2' A C 104 1135 1132 1155 C2' G C 105 1156 1153 1177 C2' C C 106 1178 1175 1196 C2' C C 107 1197 1194 1215 C2' A C 108 1216 1213 1236 C2' T C 109 1237 1234 1256 C2' T C 110 1257 1254 1276 C2' A C 111 1277 1274 1297 C2' G C 112 1298 1295 1319 C2' A C 113 1320 1317 1340 C2' G C 114 1341 1338 1380 C2' C D 215 1381 1378 1399 C2' T D 216 1400 1397 1419 C2' C D 217 1420 1417 1438 C2' T D 218 1439 1436 1458 C2' A D 219 1459 1456 1479 C2' A D 220 1480 1477 1500 C2' T D 221 1501 1498 1520 C2' G D 222 1521 1518 1542 C2' G D 223 1543 1540 1564 C2' C D 224 1565 1562 1583 C2' T D 225 1584 1581 1603 C2' T D 226 1604 1601 1623 C2' T D 227 1624 1621 1643 C2' C D 228 1644 1641 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 1068 C3' G C 101 OK 1066 1069 1070 1090 C3' A C 102 OK 1088 1091 1092 1111 C3' A C 103 OK 1109 1112 1113 1132 C3' A C 104 OK 1130 1133 1134 1153 C3' G C 105 OK 1151 1154 1155 1175 C3' C C 106 OK 1173 1176 1177 1194 C3' C C 107 OK 1192 1195 1196 1213 C3' A C 108 OK 1211 1214 1215 1234 C3' T C 109 OK 1232 1235 1236 1254 C3' T C 110 OK 1252 1255 1256 1274 C3' A C 111 OK 1272 1275 1276 1295 C3' G C 112 OK 1293 1296 1297 1317 C3' A C 113 OK 1315 1318 1319 1338 C3' G C 114 OK 1336 1339 1340 1378 C3' C D 215 OK 1376 1379 1380 1397 C3' T D 216 OK 1395 1398 1399 1417 C3' C D 217 OK 1415 1418 1419 1436 C3' T D 218 OK 1434 1437 1438 1456 C3' A D 219 OK 1454 1457 1458 1477 C3' A D 220 OK 1475 1478 1479 1498 C3' T D 221 OK 1496 1499 1500 1518 C3' G D 222 OK 1516 1519 1520 1540 C3' G D 223 OK 1538 1541 1542 1562 C3' C D 224 OK 1560 1563 1564 1581 C3' T D 225 OK 1579 1582 1583 1601 C3' T D 226 OK 1599 1602 1603 1621 C3' T D 227 OK 1619 1622 1623 1641 C3' C D 228 OK 1639 1642 1643 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 1066 C4' G C 101 OK 1068 1065 1067 1088 C4' A C 102 OK 1090 1087 1089 1109 C4' A C 103 OK 1111 1108 1110 1130 C4' A C 104 OK 1132 1129 1131 1151 C4' G C 105 OK 1153 1150 1152 1173 C4' C C 106 OK 1175 1172 1174 1192 C4' C C 107 OK 1194 1191 1193 1211 C4' A C 108 OK 1213 1210 1212 1232 C4' T C 109 OK 1234 1231 1233 1252 C4' T C 110 OK 1254 1251 1253 1272 C4' A C 111 OK 1274 1271 1273 1293 C4' G C 112 OK 1295 1292 1294 1315 C4' A C 113 OK 1317 1314 1316 1336 C4' G C 114 OK 1338 1335 1337 1376 C4' C D 215 OK 1378 1375 1377 1395 C4' T D 216 OK 1397 1394 1396 1415 C4' C D 217 OK 1417 1414 1416 1434 C4' T D 218 OK 1436 1433 1435 1454 C4' A D 219 OK 1456 1453 1455 1475 C4' A D 220 OK 1477 1474 1476 1496 C4' T D 221 OK 1498 1495 1497 1516 C4' G D 222 OK 1518 1515 1517 1538 C4' G D 223 OK 1540 1537 1539 1560 C4' C D 224 OK 1562 1559 1561 1579 C4' T D 225 OK 1581 1578 1580 1599 C4' T D 226 OK 1601 1598 1600 1619 C4' T D 227 OK 1621 1618 1620 1639 C4' C D 228 OK 1641 1638 1640 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 1065 C5' G C 101 1064 1066 1087 C5' A C 102 1086 1088 1108 C5' A C 103 1107 1109 1129 C5' A C 104 1128 1130 1150 C5' G C 105 1149 1151 1172 C5' C C 106 1171 1173 1191 C5' C C 107 1190 1192 1210 C5' A C 108 1209 1211 1231 C5' T C 109 1230 1232 1251 C5' T C 110 1250 1252 1271 C5' A C 111 1270 1272 1292 C5' G C 112 1291 1293 1314 C5' A C 113 1313 1315 1335 C5' G C 114 1334 1336 1375 C5' C D 215 1374 1376 1394 C5' T D 216 1393 1395 1414 C5' C D 217 1413 1415 1433 C5' T D 218 1432 1434 1453 C5' A D 219 1452 1454 1474 C5' A D 220 1473 1475 1495 C5' T D 221 1494 1496 1515 C5' G D 222 1514 1516 1537 C5' G D 223 1536 1538 1559 C5' C D 224 1558 1560 1578 C5' T D 225 1577 1579 1598 C5' T D 226 1597 1599 1618 C5' T D 227 1617 1619 1638 C5' C D 228 1637 1639 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1083 P A C 102 distorted distorted 1069 1084 1085 1086 1104 P A C 103 distorted distorted 1091 1105 1106 1107 1125 P A C 104 distorted distorted 1112 1126 1127 1128 1146 P G C 105 distorted distorted 1133 1147 1148 1149 1168 P C C 106 OK OK 1154 1169 1170 1171 1187 P C C 107 distorted distorted 1176 1188 1189 1190 1206 P A C 108 distorted distorted 1195 1207 1208 1209 1227 P T C 109 distorted distorted 1214 1228 1229 1230 1247 P T C 110 distorted distorted 1235 1248 1249 1250 1267 P A C 111 distorted distorted 1255 1268 1269 1270 1288 P G C 112 distorted distorted 1275 1289 1290 1291 1310 P A C 113 distorted distorted 1296 1311 1312 1313 1331 P G C 114 distorted distorted 1318 1332 1333 1334 1390 P T D 216 distorted distorted 1379 1391 1392 1393 1410 P C D 217 distorted distorted 1398 1411 1412 1413 1429 P T D 218 distorted distorted 1418 1430 1431 1432 1449 P A D 219 distorted distorted 1437 1450 1451 1452 1470 P A D 220 distorted distorted 1457 1471 1472 1473 1491 P T D 221 distorted distorted 1478 1492 1493 1494 1511 P G D 222 distorted distorted 1499 1512 1513 1514 1533 P G D 223 distorted distorted 1519 1534 1535 1536 1555 P C D 224 distorted distorted 1541 1556 1557 1558 1574 P T D 225 OK OK 1563 1575 1576 1577 1594 P T D 226 distorted distorted 1582 1595 1596 1597 1614 P T D 227 distorted distorted 1602 1615 1616 1617 1634 P C D 228 distorted distorted 1622 1635 1636 1637 ---------------------------------------------------------------------------------