ID code: '2G7X' 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' --------------------------------------------------------------------------------- 1186 C1' A B 1 beta 1182 1187 1185 1207 C1' G B 2 beta 1203 1208 1206 1229 C1' C B 3 beta 1225 1230 1228 1248 C1' G B 4 beta 1244 1249 1247 1270 C1' T B 5 beta 1266 1271 1269 1290 C1' G B 6 beta 1286 1291 1289 1312 C1' G B 7 beta 1308 1313 1311 1334 C1' G B 8 beta 1330 1335 1333 1356 C1' C B 9 beta 1352 1357 1355 1375 C1' G B 10 beta 1371 1376 1374 1397 C1' T B 11 beta 1393 1398 1396 1415 C1' T C 51 beta 1411 1416 1414 1435 C1' A C 52 beta 1431 1436 1434 1456 C1' C C 53 beta 1452 1457 1455 1475 C1' G C 54 beta 1471 1476 1474 1497 C1' C C 55 beta 1493 1498 1496 1516 C1' C C 56 beta 1512 1517 1515 1535 C1' C C 57 beta 1531 1536 1534 1554 C1' A C 58 beta 1550 1555 1553 1575 C1' C C 59 beta 1571 1576 1574 1594 C1' G C 60 beta 1590 1595 1593 1616 C1' C C 61 beta 1612 1617 1615 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 1185 C2' A B 1 1186 1183 1206 C2' G B 2 1207 1204 1228 C2' C B 3 1229 1226 1247 C2' G B 4 1248 1245 1269 C2' T B 5 1270 1267 1289 C2' G B 6 1290 1287 1311 C2' G B 7 1312 1309 1333 C2' G B 8 1334 1331 1355 C2' C B 9 1356 1353 1374 C2' G B 10 1375 1372 1396 C2' T B 11 1397 1394 1414 C2' T C 51 1415 1412 1434 C2' A C 52 1435 1432 1455 C2' C C 53 1456 1453 1474 C2' G C 54 1475 1472 1496 C2' C C 55 1497 1494 1515 C2' C C 56 1516 1513 1534 C2' C C 57 1535 1532 1553 C2' A C 58 1554 1551 1574 C2' C C 59 1575 1572 1593 C2' G C 60 1594 1591 1615 C2' C C 61 1616 1613 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 1183 C3' A B 1 OK 1181 1184 1185 1204 C3' G B 2 OK 1202 1205 1206 1226 C3' C B 3 OK 1224 1227 1228 1245 C3' G B 4 OK 1243 1246 1247 1267 C3' T B 5 OK 1265 1268 1269 1287 C3' G B 6 OK 1285 1288 1289 1309 C3' G B 7 OK 1307 1310 1311 1331 C3' G B 8 OK 1329 1332 1333 1353 C3' C B 9 OK 1351 1354 1355 1372 C3' G B 10 OK 1370 1373 1374 1394 C3' T B 11 OK 1392 1395 1396 1412 C3' T C 51 OK 1410 1413 1414 1432 C3' A C 52 OK 1430 1433 1434 1453 C3' C C 53 OK 1451 1454 1455 1472 C3' G C 54 OK 1470 1473 1474 1494 C3' C C 55 OK 1492 1495 1496 1513 C3' C C 56 OK 1511 1514 1515 1532 C3' C C 57 OK 1530 1533 1534 1551 C3' A C 58 OK 1549 1552 1553 1572 C3' C C 59 OK 1570 1573 1574 1591 C3' G C 60 OK 1589 1592 1593 1613 C3' C C 61 OK 1611 1614 1615 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 1181 C4' A B 1 OK 1183 1180 1182 1202 C4' G B 2 OK 1204 1201 1203 1224 C4' C B 3 OK 1226 1223 1225 1243 C4' G B 4 OK 1245 1242 1244 1265 C4' T B 5 OK 1267 1264 1266 1285 C4' G B 6 OK 1287 1284 1286 1307 C4' G B 7 OK 1309 1306 1308 1329 C4' G B 8 OK 1331 1328 1330 1351 C4' C B 9 OK 1353 1350 1352 1370 C4' G B 10 OK 1372 1369 1371 1392 C4' T B 11 OK 1394 1391 1393 1410 C4' T C 51 OK 1412 1409 1411 1430 C4' A C 52 OK 1432 1429 1431 1451 C4' C C 53 OK 1453 1450 1452 1470 C4' G C 54 OK 1472 1469 1471 1492 C4' C C 55 OK 1494 1491 1493 1511 C4' C C 56 OK 1513 1510 1512 1530 C4' C C 57 OK 1532 1529 1531 1549 C4' A C 58 OK 1551 1548 1550 1570 C4' C C 59 OK 1572 1569 1571 1589 C4' G C 60 OK 1591 1588 1590 1611 C4' C C 61 OK 1613 1610 1612 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 1180 C5' A B 1 1179 1181 1201 C5' G B 2 1200 1202 1223 C5' C B 3 1222 1224 1242 C5' G B 4 1241 1243 1264 C5' T B 5 1263 1265 1284 C5' G B 6 1283 1285 1306 C5' G B 7 1305 1307 1328 C5' G B 8 1327 1329 1350 C5' C B 9 1349 1351 1369 C5' G B 10 1368 1370 1391 C5' T B 11 1390 1392 1409 C5' T C 51 1408 1410 1429 C5' A C 52 1428 1430 1450 C5' C C 53 1449 1451 1469 C5' G C 54 1468 1470 1491 C5' C C 55 1490 1492 1510 C5' C C 56 1509 1511 1529 C5' C C 57 1528 1530 1548 C5' A C 58 1547 1549 1569 C5' C C 59 1568 1570 1588 C5' G C 60 1587 1589 1610 C5' C C 61 1609 1611 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1197 P G B 2 distorted distorted 1184 1198 1199 1200 1219 P C B 3 distorted distorted 1205 1220 1221 1222 1238 P G B 4 distorted distorted 1227 1239 1240 1241 1260 P T B 5 distorted distorted 1246 1261 1262 1263 1280 P G B 6 distorted distorted 1268 1281 1282 1283 1302 P G B 7 distorted distorted 1288 1303 1304 1305 1324 P G B 8 distorted distorted 1310 1325 1326 1327 1346 P C B 9 distorted distorted 1332 1347 1348 1349 1365 P G B 10 distorted distorted 1354 1366 1367 1368 1387 P T B 11 distorted distorted 1373 1388 1389 1390 1425 P A C 52 distorted distorted 1413 1426 1427 1428 1446 P C C 53 distorted distorted 1433 1447 1448 1449 1465 P G C 54 distorted distorted 1454 1466 1467 1468 1487 P C C 55 distorted distorted 1473 1488 1489 1490 1506 P C C 56 distorted distorted 1495 1507 1508 1509 1525 P C C 57 distorted distorted 1514 1526 1527 1528 1544 P A C 58 distorted distorted 1533 1545 1546 1547 1565 P C C 59 distorted distorted 1552 1566 1567 1568 1584 P G C 60 distorted distorted 1573 1585 1586 1587 1606 P C C 61 distorted distorted 1592 1607 1608 1609 ---------------------------------------------------------------------------------