ID code: '2G7W' 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' --------------------------------------------------------------------------------- 1183 C1' A B 1 beta 1179 1184 1182 1204 C1' G B 2 beta 1200 1205 1203 1226 C1' C B 3 beta 1222 1227 1225 1245 C1' G B 4 beta 1241 1246 1244 1267 C1' T B 5 beta 1263 1268 1266 1287 C1' G B 6 beta 1283 1288 1286 1309 C1' G B 7 beta 1305 1310 1308 1331 C1' G B 8 beta 1327 1332 1330 1353 C1' C B 9 beta 1349 1354 1352 1372 C1' G B 10 beta 1368 1373 1371 1394 C1' T B 11 beta 1390 1395 1393 1412 C1' T C 51 beta 1408 1413 1411 1432 C1' A C 52 beta 1428 1433 1431 1453 C1' C C 53 beta 1449 1454 1452 1472 C1' G C 54 beta 1468 1473 1471 1494 C1' C C 55 beta 1490 1495 1493 1513 C1' C C 56 beta 1509 1514 1512 1532 C1' C C 57 beta 1528 1533 1531 1551 C1' A C 58 beta 1547 1552 1550 1572 C1' C C 59 beta 1568 1573 1571 1591 C1' G C 60 beta 1587 1592 1590 1613 C1' C C 61 beta 1609 1614 1612 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 1182 C2' A B 1 1183 1180 1203 C2' G B 2 1204 1201 1225 C2' C B 3 1226 1223 1244 C2' G B 4 1245 1242 1266 C2' T B 5 1267 1264 1286 C2' G B 6 1287 1284 1308 C2' G B 7 1309 1306 1330 C2' G B 8 1331 1328 1352 C2' C B 9 1353 1350 1371 C2' G B 10 1372 1369 1393 C2' T B 11 1394 1391 1411 C2' T C 51 1412 1409 1431 C2' A C 52 1432 1429 1452 C2' C C 53 1453 1450 1471 C2' G C 54 1472 1469 1493 C2' C C 55 1494 1491 1512 C2' C C 56 1513 1510 1531 C2' C C 57 1532 1529 1550 C2' A C 58 1551 1548 1571 C2' C C 59 1572 1569 1590 C2' G C 60 1591 1588 1612 C2' C C 61 1613 1610 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 1180 C3' A B 1 OK 1178 1181 1182 1201 C3' G B 2 OK 1199 1202 1203 1223 C3' C B 3 OK 1221 1224 1225 1242 C3' G B 4 OK 1240 1243 1244 1264 C3' T B 5 OK 1262 1265 1266 1284 C3' G B 6 OK 1282 1285 1286 1306 C3' G B 7 OK 1304 1307 1308 1328 C3' G B 8 OK 1326 1329 1330 1350 C3' C B 9 OK 1348 1351 1352 1369 C3' G B 10 OK 1367 1370 1371 1391 C3' T B 11 OK 1389 1392 1393 1409 C3' T C 51 OK 1407 1410 1411 1429 C3' A C 52 OK 1427 1430 1431 1450 C3' C C 53 OK 1448 1451 1452 1469 C3' G C 54 OK 1467 1470 1471 1491 C3' C C 55 OK 1489 1492 1493 1510 C3' C C 56 OK 1508 1511 1512 1529 C3' C C 57 OK 1527 1530 1531 1548 C3' A C 58 OK 1546 1549 1550 1569 C3' C C 59 OK 1567 1570 1571 1588 C3' G C 60 OK 1586 1589 1590 1610 C3' C C 61 OK 1608 1611 1612 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 1178 C4' A B 1 OK 1180 1177 1179 1199 C4' G B 2 OK 1201 1198 1200 1221 C4' C B 3 OK 1223 1220 1222 1240 C4' G B 4 OK 1242 1239 1241 1262 C4' T B 5 OK 1264 1261 1263 1282 C4' G B 6 OK 1284 1281 1283 1304 C4' G B 7 OK 1306 1303 1305 1326 C4' G B 8 OK 1328 1325 1327 1348 C4' C B 9 OK 1350 1347 1349 1367 C4' G B 10 OK 1369 1366 1368 1389 C4' T B 11 OK 1391 1388 1390 1407 C4' T C 51 OK 1409 1406 1408 1427 C4' A C 52 OK 1429 1426 1428 1448 C4' C C 53 OK 1450 1447 1449 1467 C4' G C 54 OK 1469 1466 1468 1489 C4' C C 55 OK 1491 1488 1490 1508 C4' C C 56 OK 1510 1507 1509 1527 C4' C C 57 OK 1529 1526 1528 1546 C4' A C 58 OK 1548 1545 1547 1567 C4' C C 59 OK 1569 1566 1568 1586 C4' G C 60 OK 1588 1585 1587 1608 C4' C C 61 OK 1610 1607 1609 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 1177 C5' A B 1 1176 1178 1198 C5' G B 2 1197 1199 1220 C5' C B 3 1219 1221 1239 C5' G B 4 1238 1240 1261 C5' T B 5 1260 1262 1281 C5' G B 6 1280 1282 1303 C5' G B 7 1302 1304 1325 C5' G B 8 1324 1326 1347 C5' C B 9 1346 1348 1366 C5' G B 10 1365 1367 1388 C5' T B 11 1387 1389 1406 C5' T C 51 1405 1407 1426 C5' A C 52 1425 1427 1447 C5' C C 53 1446 1448 1466 C5' G C 54 1465 1467 1488 C5' C C 55 1487 1489 1507 C5' C C 56 1506 1508 1526 C5' C C 57 1525 1527 1545 C5' A C 58 1544 1546 1566 C5' C C 59 1565 1567 1585 C5' G C 60 1584 1586 1607 C5' C C 61 1606 1608 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1194 P G B 2 distorted distorted 1181 1195 1196 1197 1216 P C B 3 distorted distorted 1202 1217 1218 1219 1235 P G B 4 distorted distorted 1224 1236 1237 1238 1257 P T B 5 distorted distorted 1243 1258 1259 1260 1277 P G B 6 distorted distorted 1265 1278 1279 1280 1299 P G B 7 distorted distorted 1285 1300 1301 1302 1321 P G B 8 distorted distorted 1307 1322 1323 1324 1343 P C B 9 distorted distorted 1329 1344 1345 1346 1362 P G B 10 distorted distorted 1351 1363 1364 1365 1384 P T B 11 distorted distorted 1370 1385 1386 1387 1422 P A C 52 distorted distorted 1410 1423 1424 1425 1443 P C C 53 distorted distorted 1430 1444 1445 1446 1462 P G C 54 distorted distorted 1451 1463 1464 1465 1484 P C C 55 distorted distorted 1470 1485 1486 1487 1503 P C C 56 distorted distorted 1492 1504 1505 1506 1522 P C C 57 distorted distorted 1511 1523 1524 1525 1541 P A C 58 distorted distorted 1530 1542 1543 1544 1562 P C C 59 distorted distorted 1549 1563 1564 1565 1581 P G C 60 distorted distorted 1570 1582 1583 1584 1603 P C C 61 distorted distorted 1589 1604 1605 1606 ---------------------------------------------------------------------------------