ID code: '2G7T' 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' --------------------------------------------------------------------------------- 1185 C1' A B 1 beta 1181 1186 1184 1206 C1' G B 2 beta 1202 1207 1205 1228 C1' C B 3 beta 1224 1229 1227 1247 C1' G B 4 beta 1243 1248 1246 1269 C1' T B 5 beta 1265 1270 1268 1289 C1' G B 6 beta 1285 1290 1288 1311 C1' G B 7 beta 1307 1312 1310 1333 C1' G B 8 beta 1329 1334 1332 1355 C1' C B 9 beta 1351 1356 1354 1374 C1' G B 10 beta 1370 1375 1373 1396 C1' T B 11 beta 1392 1397 1395 1414 C1' T C 51 beta 1410 1415 1413 1434 C1' A C 52 beta 1430 1435 1433 1455 C1' C C 53 beta 1451 1456 1454 1474 C1' G C 54 beta 1470 1475 1473 1496 C1' C C 55 beta 1492 1497 1495 1515 C1' C C 56 beta 1511 1516 1514 1534 C1' C C 57 beta 1530 1535 1533 1553 C1' A C 58 beta 1549 1554 1552 1574 C1' C C 59 beta 1570 1575 1573 1593 C1' G C 60 beta 1589 1594 1592 1615 C1' C C 61 beta 1611 1616 1614 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 1184 C2' A B 1 1185 1182 1205 C2' G B 2 1206 1203 1227 C2' C B 3 1228 1225 1246 C2' G B 4 1247 1244 1268 C2' T B 5 1269 1266 1288 C2' G B 6 1289 1286 1310 C2' G B 7 1311 1308 1332 C2' G B 8 1333 1330 1354 C2' C B 9 1355 1352 1373 C2' G B 10 1374 1371 1395 C2' T B 11 1396 1393 1413 C2' T C 51 1414 1411 1433 C2' A C 52 1434 1431 1454 C2' C C 53 1455 1452 1473 C2' G C 54 1474 1471 1495 C2' C C 55 1496 1493 1514 C2' C C 56 1515 1512 1533 C2' C C 57 1534 1531 1552 C2' A C 58 1553 1550 1573 C2' C C 59 1574 1571 1592 C2' G C 60 1593 1590 1614 C2' C C 61 1615 1612 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 1182 C3' A B 1 OK 1180 1183 1184 1203 C3' G B 2 OK 1201 1204 1205 1225 C3' C B 3 OK 1223 1226 1227 1244 C3' G B 4 OK 1242 1245 1246 1266 C3' T B 5 OK 1264 1267 1268 1286 C3' G B 6 OK 1284 1287 1288 1308 C3' G B 7 OK 1306 1309 1310 1330 C3' G B 8 OK 1328 1331 1332 1352 C3' C B 9 OK 1350 1353 1354 1371 C3' G B 10 OK 1369 1372 1373 1393 C3' T B 11 OK 1391 1394 1395 1411 C3' T C 51 OK 1409 1412 1413 1431 C3' A C 52 OK 1429 1432 1433 1452 C3' C C 53 OK 1450 1453 1454 1471 C3' G C 54 OK 1469 1472 1473 1493 C3' C C 55 OK 1491 1494 1495 1512 C3' C C 56 OK 1510 1513 1514 1531 C3' C C 57 OK 1529 1532 1533 1550 C3' A C 58 OK 1548 1551 1552 1571 C3' C C 59 OK 1569 1572 1573 1590 C3' G C 60 OK 1588 1591 1592 1612 C3' C C 61 OK 1610 1613 1614 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 1180 C4' A B 1 OK 1182 1179 1181 1201 C4' G B 2 OK 1203 1200 1202 1223 C4' C B 3 OK 1225 1222 1224 1242 C4' G B 4 OK 1244 1241 1243 1264 C4' T B 5 OK 1266 1263 1265 1284 C4' G B 6 OK 1286 1283 1285 1306 C4' G B 7 OK 1308 1305 1307 1328 C4' G B 8 OK 1330 1327 1329 1350 C4' C B 9 OK 1352 1349 1351 1369 C4' G B 10 OK 1371 1368 1370 1391 C4' T B 11 OK 1393 1390 1392 1409 C4' T C 51 OK 1411 1408 1410 1429 C4' A C 52 OK 1431 1428 1430 1450 C4' C C 53 OK 1452 1449 1451 1469 C4' G C 54 OK 1471 1468 1470 1491 C4' C C 55 OK 1493 1490 1492 1510 C4' C C 56 OK 1512 1509 1511 1529 C4' C C 57 OK 1531 1528 1530 1548 C4' A C 58 OK 1550 1547 1549 1569 C4' C C 59 OK 1571 1568 1570 1588 C4' G C 60 OK 1590 1587 1589 1610 C4' C C 61 OK 1612 1609 1611 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 1179 C5' A B 1 1178 1180 1200 C5' G B 2 1199 1201 1222 C5' C B 3 1221 1223 1241 C5' G B 4 1240 1242 1263 C5' T B 5 1262 1264 1283 C5' G B 6 1282 1284 1305 C5' G B 7 1304 1306 1327 C5' G B 8 1326 1328 1349 C5' C B 9 1348 1350 1368 C5' G B 10 1367 1369 1390 C5' T B 11 1389 1391 1408 C5' T C 51 1407 1409 1428 C5' A C 52 1427 1429 1449 C5' C C 53 1448 1450 1468 C5' G C 54 1467 1469 1490 C5' C C 55 1489 1491 1509 C5' C C 56 1508 1510 1528 C5' C C 57 1527 1529 1547 C5' A C 58 1546 1548 1568 C5' C C 59 1567 1569 1587 C5' G C 60 1586 1588 1609 C5' C C 61 1608 1610 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1196 P G B 2 distorted distorted 1183 1197 1198 1199 1218 P C B 3 distorted distorted 1204 1219 1220 1221 1237 P G B 4 distorted distorted 1226 1238 1239 1240 1259 P T B 5 distorted distorted 1245 1260 1261 1262 1279 P G B 6 distorted distorted 1267 1280 1281 1282 1301 P G B 7 distorted distorted 1287 1302 1303 1304 1323 P G B 8 distorted distorted 1309 1324 1325 1326 1345 P C B 9 distorted distorted 1331 1346 1347 1348 1364 P G B 10 distorted distorted 1353 1365 1366 1367 1386 P T B 11 distorted distorted 1372 1387 1388 1389 1424 P A C 52 distorted distorted 1412 1425 1426 1427 1445 P C C 53 distorted distorted 1432 1446 1447 1448 1464 P G C 54 distorted distorted 1453 1465 1466 1467 1486 P C C 55 distorted distorted 1472 1487 1488 1489 1505 P C C 56 distorted distorted 1494 1506 1507 1508 1524 P C C 57 distorted distorted 1513 1525 1526 1527 1543 P A C 58 distorted distorted 1532 1544 1545 1546 1564 P C C 59 distorted distorted 1551 1565 1566 1567 1583 P G C 60 distorted distorted 1572 1584 1585 1586 1605 P C C 61 distorted distorted 1591 1606 1607 1608 ---------------------------------------------------------------------------------