ID code: '1A0A' 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' --------------------------------------------------------------------------------- 1006 C1' C C 1 beta 1002 1007 1005 1025 C1' T C 2 beta 1021 1026 1024 1045 C1' C C 3 beta 1041 1046 1044 1064 C1' A C 4 beta 1060 1065 1063 1085 C1' C C 5 beta 1081 1086 1084 1104 C1' A C 6 beta 1100 1105 1103 1125 C1' C C 7 beta 1121 1126 1124 1144 C1' G C 8 beta 1140 1145 1143 1166 C1' T C 9 beta 1162 1167 1165 1186 C1' G C 10 beta 1182 1187 1185 1208 C1' G C 11 beta 1204 1209 1207 1230 C1' G C 12 beta 1226 1231 1229 1252 C1' A C 13 beta 1248 1253 1251 1273 C1' C C 14 beta 1269 1274 1272 1292 C1' T C 15 beta 1288 1293 1291 1312 C1' A C 16 beta 1308 1313 1311 1333 C1' G C 17 beta 1329 1334 1332 1353 C1' C D 1 beta 1349 1354 1352 1372 C1' T D 2 beta 1368 1373 1371 1392 C1' A D 3 beta 1388 1393 1391 1413 C1' G D 4 beta 1409 1414 1412 1435 C1' T D 5 beta 1431 1436 1434 1455 C1' C D 6 beta 1451 1456 1454 1474 C1' C D 7 beta 1470 1475 1473 1493 C1' C D 8 beta 1489 1494 1492 1512 C1' A D 9 beta 1508 1513 1511 1533 C1' C D 10 beta 1529 1534 1532 1552 C1' G D 11 beta 1548 1553 1551 1574 C1' T D 12 beta 1570 1575 1573 1594 C1' G D 13 beta 1590 1595 1593 1616 C1' T D 14 beta 1612 1617 1615 1636 C1' G D 15 beta 1632 1637 1635 1658 C1' A D 16 beta 1654 1659 1657 1679 C1' G D 17 beta 1675 1680 1678 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 1005 C2' C C 1 1006 1003 1024 C2' T C 2 1025 1022 1044 C2' C C 3 1045 1042 1063 C2' A C 4 1064 1061 1084 C2' C C 5 1085 1082 1103 C2' A C 6 1104 1101 1124 C2' C C 7 1125 1122 1143 C2' G C 8 1144 1141 1165 C2' T C 9 1166 1163 1185 C2' G C 10 1186 1183 1207 C2' G C 11 1208 1205 1229 C2' G C 12 1230 1227 1251 C2' A C 13 1252 1249 1272 C2' C C 14 1273 1270 1291 C2' T C 15 1292 1289 1311 C2' A C 16 1312 1309 1332 C2' G C 17 1333 1330 1352 C2' C D 1 1353 1350 1371 C2' T D 2 1372 1369 1391 C2' A D 3 1392 1389 1412 C2' G D 4 1413 1410 1434 C2' T D 5 1435 1432 1454 C2' C D 6 1455 1452 1473 C2' C D 7 1474 1471 1492 C2' C D 8 1493 1490 1511 C2' A D 9 1512 1509 1532 C2' C D 10 1533 1530 1551 C2' G D 11 1552 1549 1573 C2' T D 12 1574 1571 1593 C2' G D 13 1594 1591 1615 C2' T D 14 1616 1613 1635 C2' G D 15 1636 1633 1657 C2' A D 16 1658 1655 1678 C2' G D 17 1679 1676 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 1003 C3' C C 1 OK 1001 1004 1005 1022 C3' T C 2 OK 1020 1023 1024 1042 C3' C C 3 OK 1040 1043 1044 1061 C3' A C 4 OK 1059 1062 1063 1082 C3' C C 5 OK 1080 1083 1084 1101 C3' A C 6 OK 1099 1102 1103 1122 C3' C C 7 OK 1120 1123 1124 1141 C3' G C 8 OK 1139 1142 1143 1163 C3' T C 9 OK 1161 1164 1165 1183 C3' G C 10 OK 1181 1184 1185 1205 C3' G C 11 OK 1203 1206 1207 1227 C3' G C 12 OK 1225 1228 1229 1249 C3' A C 13 OK 1247 1250 1251 1270 C3' C C 14 OK 1268 1271 1272 1289 C3' T C 15 OK 1287 1290 1291 1309 C3' A C 16 OK 1307 1310 1311 1330 C3' G C 17 OK 1328 1331 1332 1350 C3' C D 1 OK 1348 1351 1352 1369 C3' T D 2 OK 1367 1370 1371 1389 C3' A D 3 OK 1387 1390 1391 1410 C3' G D 4 OK 1408 1411 1412 1432 C3' T D 5 OK 1430 1433 1434 1452 C3' C D 6 OK 1450 1453 1454 1471 C3' C D 7 OK 1469 1472 1473 1490 C3' C D 8 OK 1488 1491 1492 1509 C3' A D 9 OK 1507 1510 1511 1530 C3' C D 10 OK 1528 1531 1532 1549 C3' G D 11 OK 1547 1550 1551 1571 C3' T D 12 OK 1569 1572 1573 1591 C3' G D 13 OK 1589 1592 1593 1613 C3' T D 14 OK 1611 1614 1615 1633 C3' G D 15 OK 1631 1634 1635 1655 C3' A D 16 OK 1653 1656 1657 1676 C3' G D 17 OK 1674 1677 1678 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 1001 C4' C C 1 OK 1003 1000 1002 1020 C4' T C 2 OK 1022 1019 1021 1040 C4' C C 3 OK 1042 1039 1041 1059 C4' A C 4 OK 1061 1058 1060 1080 C4' C C 5 OK 1082 1079 1081 1099 C4' A C 6 OK 1101 1098 1100 1120 C4' C C 7 OK 1122 1119 1121 1139 C4' G C 8 OK 1141 1138 1140 1161 C4' T C 9 OK 1163 1160 1162 1181 C4' G C 10 OK 1183 1180 1182 1203 C4' G C 11 OK 1205 1202 1204 1225 C4' G C 12 OK 1227 1224 1226 1247 C4' A C 13 OK 1249 1246 1248 1268 C4' C C 14 OK 1270 1267 1269 1287 C4' T C 15 OK 1289 1286 1288 1307 C4' A C 16 OK 1309 1306 1308 1328 C4' G C 17 OK 1330 1327 1329 1348 C4' C D 1 OK 1350 1347 1349 1367 C4' T D 2 OK 1369 1366 1368 1387 C4' A D 3 OK 1389 1386 1388 1408 C4' G D 4 OK 1410 1407 1409 1430 C4' T D 5 OK 1432 1429 1431 1450 C4' C D 6 OK 1452 1449 1451 1469 C4' C D 7 OK 1471 1468 1470 1488 C4' C D 8 OK 1490 1487 1489 1507 C4' A D 9 OK 1509 1506 1508 1528 C4' C D 10 OK 1530 1527 1529 1547 C4' G D 11 OK 1549 1546 1548 1569 C4' T D 12 OK 1571 1568 1570 1589 C4' G D 13 OK 1591 1588 1590 1611 C4' T D 14 OK 1613 1610 1612 1631 C4' G D 15 OK 1633 1630 1632 1653 C4' A D 16 OK 1655 1652 1654 1674 C4' G D 17 OK 1676 1673 1675 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 1000 C5' C C 1 999 1001 1019 C5' T C 2 1018 1020 1039 C5' C C 3 1038 1040 1058 C5' A C 4 1057 1059 1079 C5' C C 5 1078 1080 1098 C5' A C 6 1097 1099 1119 C5' C C 7 1118 1120 1138 C5' G C 8 1137 1139 1160 C5' T C 9 1159 1161 1180 C5' G C 10 1179 1181 1202 C5' G C 11 1201 1203 1224 C5' G C 12 1223 1225 1246 C5' A C 13 1245 1247 1267 C5' C C 14 1266 1268 1286 C5' T C 15 1285 1287 1306 C5' A C 16 1305 1307 1327 C5' G C 17 1326 1328 1347 C5' C D 1 1346 1348 1366 C5' T D 2 1365 1367 1386 C5' A D 3 1385 1387 1407 C5' G D 4 1406 1408 1429 C5' T D 5 1428 1430 1449 C5' C D 6 1448 1450 1468 C5' C D 7 1467 1469 1487 C5' C D 8 1486 1488 1506 C5' A D 9 1505 1507 1527 C5' C D 10 1526 1528 1546 C5' G D 11 1545 1547 1568 C5' T D 12 1567 1569 1588 C5' G D 13 1587 1589 1610 C5' T D 14 1609 1611 1630 C5' G D 15 1629 1631 1652 C5' A D 16 1651 1653 1673 C5' G D 17 1672 1674 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1015 P T C 2 distorted distorted 1004 1016 1017 1018 1035 P C C 3 distorted distorted 1023 1036 1037 1038 1054 P A C 4 distorted distorted 1043 1055 1056 1057 1075 P C C 5 distorted distorted 1062 1076 1077 1078 1094 P A C 6 distorted distorted 1083 1095 1096 1097 1115 P C C 7 distorted distorted 1102 1116 1117 1118 1134 P G C 8 OK OK 1123 1135 1136 1137 1156 P T C 9 distorted distorted 1142 1157 1158 1159 1176 P G C 10 distorted distorted 1164 1177 1178 1179 1198 P G C 11 distorted distorted 1184 1199 1200 1201 1220 P G C 12 distorted distorted 1206 1221 1222 1223 1242 P A C 13 distorted distorted 1228 1243 1244 1245 1263 P C C 14 distorted distorted 1250 1264 1265 1266 1282 P T C 15 distorted distorted 1271 1283 1284 1285 1302 P A C 16 OK OK 1290 1303 1304 1305 1323 P G C 17 distorted distorted 1310 1324 1325 1326 1362 P T D 2 distorted distorted 1351 1363 1364 1365 1382 P A D 3 OK OK 1370 1383 1384 1385 1403 P G D 4 OK OK 1390 1404 1405 1406 1425 P T D 5 distorted distorted 1411 1426 1427 1428 1445 P C D 6 distorted distorted 1433 1446 1447 1448 1464 P C D 7 distorted distorted 1453 1465 1466 1467 1483 P C D 8 distorted distorted 1472 1484 1485 1486 1502 P A D 9 distorted distorted 1491 1503 1504 1505 1523 P C D 10 distorted distorted 1510 1524 1525 1526 1542 P G D 11 OK OK 1531 1543 1544 1545 1564 P T D 12 distorted distorted 1550 1565 1566 1567 1584 P G D 13 distorted distorted 1572 1585 1586 1587 1606 P T D 14 distorted distorted 1592 1607 1608 1609 1626 P G D 15 distorted distorted 1614 1627 1628 1629 1648 P A D 16 distorted distorted 1634 1649 1650 1651 1669 P G D 17 OK OK 1656 1670 1671 1672 ---------------------------------------------------------------------------------