ID code: '1LU6' 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' --------------------------------------------------------------------------------- 1187 C1' A B 1 beta 1183 1188 1186 1208 C1' G B 2 beta 1204 1209 1207 1230 C1' C B 3 beta 1226 1231 1229 1249 C1' G B 4 beta 1245 1250 1248 1271 C1' T B 5 beta 1267 1272 1270 1291 C1' G B 6 beta 1287 1292 1290 1313 C1' G B 7 beta 1309 1314 1312 1335 C1' G B 8 beta 1331 1336 1334 1357 C1' C B 9 beta 1353 1358 1356 1376 C1' G B 10 beta 1372 1377 1375 1398 C1' T B 11 beta 1394 1399 1397 1416 C1' T C 51 beta 1412 1417 1415 1436 C1' A C 52 beta 1432 1437 1435 1457 C1' C C 53 beta 1453 1458 1456 1476 C1' G C 54 beta 1472 1477 1475 1498 C1' C C 55 beta 1494 1499 1497 1517 C1' C C 56 beta 1513 1518 1516 1536 C1' C C 57 beta 1532 1537 1535 1555 C1' A C 58 beta 1551 1556 1554 1576 C1' C C 59 beta 1572 1577 1575 1595 C1' G C 60 beta 1591 1596 1594 1617 C1' C C 61 beta 1613 1618 1616 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 1186 C2' A B 1 1187 1184 1207 C2' G B 2 1208 1205 1229 C2' C B 3 1230 1227 1248 C2' G B 4 1249 1246 1270 C2' T B 5 1271 1268 1290 C2' G B 6 1291 1288 1312 C2' G B 7 1313 1310 1334 C2' G B 8 1335 1332 1356 C2' C B 9 1357 1354 1375 C2' G B 10 1376 1373 1397 C2' T B 11 1398 1395 1415 C2' T C 51 1416 1413 1435 C2' A C 52 1436 1433 1456 C2' C C 53 1457 1454 1475 C2' G C 54 1476 1473 1497 C2' C C 55 1498 1495 1516 C2' C C 56 1517 1514 1535 C2' C C 57 1536 1533 1554 C2' A C 58 1555 1552 1575 C2' C C 59 1576 1573 1594 C2' G C 60 1595 1592 1616 C2' C C 61 1617 1614 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 1184 C3' A B 1 OK 1182 1185 1186 1205 C3' G B 2 OK 1203 1206 1207 1227 C3' C B 3 OK 1225 1228 1229 1246 C3' G B 4 OK 1244 1247 1248 1268 C3' T B 5 OK 1266 1269 1270 1288 C3' G B 6 OK 1286 1289 1290 1310 C3' G B 7 OK 1308 1311 1312 1332 C3' G B 8 OK 1330 1333 1334 1354 C3' C B 9 OK 1352 1355 1356 1373 C3' G B 10 OK 1371 1374 1375 1395 C3' T B 11 OK 1393 1396 1397 1413 C3' T C 51 OK 1411 1414 1415 1433 C3' A C 52 OK 1431 1434 1435 1454 C3' C C 53 OK 1452 1455 1456 1473 C3' G C 54 OK 1471 1474 1475 1495 C3' C C 55 OK 1493 1496 1497 1514 C3' C C 56 OK 1512 1515 1516 1533 C3' C C 57 OK 1531 1534 1535 1552 C3' A C 58 OK 1550 1553 1554 1573 C3' C C 59 OK 1571 1574 1575 1592 C3' G C 60 OK 1590 1593 1594 1614 C3' C C 61 OK 1612 1615 1616 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 1182 C4' A B 1 OK 1184 1181 1183 1203 C4' G B 2 OK 1205 1202 1204 1225 C4' C B 3 OK 1227 1224 1226 1244 C4' G B 4 OK 1246 1243 1245 1266 C4' T B 5 OK 1268 1265 1267 1286 C4' G B 6 OK 1288 1285 1287 1308 C4' G B 7 OK 1310 1307 1309 1330 C4' G B 8 OK 1332 1329 1331 1352 C4' C B 9 OK 1354 1351 1353 1371 C4' G B 10 OK 1373 1370 1372 1393 C4' T B 11 OK 1395 1392 1394 1411 C4' T C 51 OK 1413 1410 1412 1431 C4' A C 52 OK 1433 1430 1432 1452 C4' C C 53 OK 1454 1451 1453 1471 C4' G C 54 OK 1473 1470 1472 1493 C4' C C 55 OK 1495 1492 1494 1512 C4' C C 56 OK 1514 1511 1513 1531 C4' C C 57 OK 1533 1530 1532 1550 C4' A C 58 OK 1552 1549 1551 1571 C4' C C 59 OK 1573 1570 1572 1590 C4' G C 60 OK 1592 1589 1591 1612 C4' C C 61 OK 1614 1611 1613 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 1181 C5' A B 1 1180 1182 1202 C5' G B 2 1201 1203 1224 C5' C B 3 1223 1225 1243 C5' G B 4 1242 1244 1265 C5' T B 5 1264 1266 1285 C5' G B 6 1284 1286 1307 C5' G B 7 1306 1308 1329 C5' G B 8 1328 1330 1351 C5' C B 9 1350 1352 1370 C5' G B 10 1369 1371 1392 C5' T B 11 1391 1393 1410 C5' T C 51 1409 1411 1430 C5' A C 52 1429 1431 1451 C5' C C 53 1450 1452 1470 C5' G C 54 1469 1471 1492 C5' C C 55 1491 1493 1511 C5' C C 56 1510 1512 1530 C5' C C 57 1529 1531 1549 C5' A C 58 1548 1550 1570 C5' C C 59 1569 1571 1589 C5' G C 60 1588 1590 1611 C5' C C 61 1610 1612 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1198 P G B 2 distorted distorted 1185 1199 1200 1201 1220 P C B 3 distorted distorted 1206 1221 1222 1223 1239 P G B 4 distorted distorted 1228 1240 1241 1242 1261 P T B 5 distorted distorted 1247 1262 1263 1264 1281 P G B 6 distorted distorted 1269 1282 1283 1284 1303 P G B 7 distorted distorted 1289 1304 1305 1306 1325 P G B 8 distorted distorted 1311 1326 1327 1328 1347 P C B 9 distorted distorted 1333 1348 1349 1350 1366 P G B 10 distorted distorted 1355 1367 1368 1369 1388 P T B 11 distorted distorted 1374 1389 1390 1391 1426 P A C 52 distorted distorted 1414 1427 1428 1429 1447 P C C 53 distorted distorted 1434 1448 1449 1450 1466 P G C 54 distorted distorted 1455 1467 1468 1469 1488 P C C 55 distorted distorted 1474 1489 1490 1491 1507 P C C 56 distorted distorted 1496 1508 1509 1510 1526 P C C 57 distorted distorted 1515 1527 1528 1529 1545 P A C 58 distorted distorted 1534 1546 1547 1548 1566 P C C 59 distorted distorted 1553 1567 1568 1569 1585 P G C 60 distorted distorted 1574 1586 1587 1588 1607 P C C 61 distorted distorted 1593 1608 1609 1610 ---------------------------------------------------------------------------------