ID code: '1YUJ' 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' --------------------------------------------------------------------------------- 896 C1' G B 101 beta 892 897 895 929 C1' C B 102 beta 925 930 928 959 C1' C B 103 beta 955 960 958 989 C1' G B 104 beta 985 990 988 1022 C1' A B 105 beta 1018 1023 1021 1054 C1' G B 106 beta 1050 1055 1053 1087 C1' A B 107 beta 1083 1088 1086 1119 C1' G B 108 beta 1115 1120 1118 1152 C1' T B 109 beta 1148 1153 1151 1184 C1' A B 110 beta 1180 1185 1183 1216 C1' C B 111 beta 1212 1217 1215 1243 C1' G B 112 beta 1239 1244 1242 1276 C1' T B 113 beta 1272 1277 1275 1308 C1' A B 114 beta 1304 1309 1307 1340 C1' C B 115 beta 1336 1341 1339 1370 C1' T B 116 beta 1366 1371 1369 1402 C1' C B 117 beta 1398 1403 1401 1432 C1' T B 118 beta 1428 1433 1431 1464 C1' C B 119 beta 1460 1465 1463 1494 C1' G B 120 beta 1490 1495 1493 1527 C1' G B 121 beta 1523 1528 1526 1560 C1' C B 122 beta 1556 1561 1559 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 895 C2' G B 101 896 893 928 C2' C B 102 929 926 958 C2' C B 103 959 956 988 C2' G B 104 989 986 1021 C2' A B 105 1022 1019 1053 C2' G B 106 1054 1051 1086 C2' A B 107 1087 1084 1118 C2' G B 108 1119 1116 1151 C2' T B 109 1152 1149 1183 C2' A B 110 1184 1181 1215 C2' C B 111 1216 1213 1242 C2' G B 112 1243 1240 1275 C2' T B 113 1276 1273 1307 C2' A B 114 1308 1305 1339 C2' C B 115 1340 1337 1369 C2' T B 116 1370 1367 1401 C2' C B 117 1402 1399 1431 C2' T B 118 1432 1429 1463 C2' C B 119 1464 1461 1493 C2' G B 120 1494 1491 1526 C2' G B 121 1527 1524 1559 C2' C B 122 1560 1557 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 893 C3' G B 101 OK 891 894 895 926 C3' C B 102 OK 924 927 928 956 C3' C B 103 OK 954 957 958 986 C3' G B 104 OK 984 987 988 1019 C3' A B 105 OK 1017 1020 1021 1051 C3' G B 106 OK 1049 1052 1053 1084 C3' A B 107 OK 1082 1085 1086 1116 C3' G B 108 OK 1114 1117 1118 1149 C3' T B 109 OK 1147 1150 1151 1181 C3' A B 110 OK 1179 1182 1183 1213 C3' C B 111 OK 1211 1214 1215 1240 C3' G B 112 OK 1238 1241 1242 1273 C3' T B 113 OK 1271 1274 1275 1305 C3' A B 114 OK 1303 1306 1307 1337 C3' C B 115 OK 1335 1338 1339 1367 C3' T B 116 OK 1365 1368 1369 1399 C3' C B 117 OK 1397 1400 1401 1429 C3' T B 118 OK 1427 1430 1431 1461 C3' C B 119 OK 1459 1462 1463 1491 C3' G B 120 OK 1489 1492 1493 1524 C3' G B 121 OK 1522 1525 1526 1557 C3' C B 122 OK 1555 1558 1559 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 891 C4' G B 101 OK 893 890 892 924 C4' C B 102 OK 926 923 925 954 C4' C B 103 OK 956 953 955 984 C4' G B 104 OK 986 983 985 1017 C4' A B 105 OK 1019 1016 1018 1049 C4' G B 106 OK 1051 1048 1050 1082 C4' A B 107 OK 1084 1081 1083 1114 C4' G B 108 OK 1116 1113 1115 1147 C4' T B 109 OK 1149 1146 1148 1179 C4' A B 110 OK 1181 1178 1180 1211 C4' C B 111 OK 1213 1210 1212 1238 C4' G B 112 OK 1240 1237 1239 1271 C4' T B 113 OK 1273 1270 1272 1303 C4' A B 114 OK 1305 1302 1304 1335 C4' C B 115 OK 1337 1334 1336 1365 C4' T B 116 OK 1367 1364 1366 1397 C4' C B 117 OK 1399 1396 1398 1427 C4' T B 118 OK 1429 1426 1428 1459 C4' C B 119 OK 1461 1458 1460 1489 C4' G B 120 OK 1491 1488 1490 1522 C4' G B 121 OK 1524 1521 1523 1555 C4' C B 122 OK 1557 1554 1556 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 890 C5' G B 101 889 891 923 C5' C B 102 922 924 953 C5' C B 103 952 954 983 C5' G B 104 982 984 1016 C5' A B 105 1015 1017 1048 C5' G B 106 1047 1049 1081 C5' A B 107 1080 1082 1113 C5' G B 108 1112 1114 1146 C5' T B 109 1145 1147 1178 C5' A B 110 1177 1179 1210 C5' C B 111 1209 1211 1237 C5' G B 112 1236 1238 1270 C5' T B 113 1269 1271 1302 C5' A B 114 1301 1303 1334 C5' C B 115 1333 1335 1364 C5' T B 116 1363 1365 1396 C5' C B 117 1395 1397 1426 C5' T B 118 1425 1427 1458 C5' C B 119 1457 1459 1488 C5' G B 120 1487 1489 1521 C5' G B 121 1520 1522 1554 C5' C B 122 1553 1555 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 919 P C B 102 OK OK 894 920 921 922 949 P C B 103 OK OK 927 950 951 952 979 P G B 104 OK OK 957 980 981 982 1012 P A B 105 OK OK 987 1013 1014 1015 1044 P G B 106 OK OK 1020 1045 1046 1047 1077 P A B 107 OK OK 1052 1078 1079 1080 1109 P G B 108 OK OK 1085 1110 1111 1112 1142 P T B 109 OK OK 1117 1143 1144 1145 1174 P A B 110 OK OK 1150 1175 1176 1177 1206 P C B 111 OK OK 1182 1207 1208 1209 1266 P T B 113 OK OK 1241 1267 1268 1269 1298 P A B 114 OK OK 1274 1299 1300 1301 1330 P C B 115 OK OK 1306 1331 1332 1333 1360 P T B 116 OK OK 1338 1361 1362 1363 1392 P C B 117 OK OK 1368 1393 1394 1395 1422 P T B 118 OK OK 1400 1423 1424 1425 1454 P C B 119 OK OK 1430 1455 1456 1457 1484 P G B 120 OK OK 1462 1485 1486 1487 1517 P G B 121 OK OK 1492 1518 1519 1520 1550 P C B 122 OK OK 1525 1551 1552 1553 ---------------------------------------------------------------------------------