ID code: '2PJP' 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' --------------------------------------------------------------------------------- 995 C1' G B 12 beta 990 996 993 1018 C1' G B 13 beta 1013 1019 1016 1041 C1' C B 14 beta 1036 1042 1039 1061 C1' G B 15 beta 1056 1062 1059 1084 C1' G B 16 beta 1079 1085 1082 1107 C1' U B 17 beta 1102 1108 1105 1127 C1' U B 18 beta 1122 1128 1125 1147 C1' G B 19 beta 1142 1148 1145 1170 C1' C B 20 beta 1165 1171 1168 1190 C1' A B 21 beta 1185 1191 1188 1212 C1' G B 22 beta 1207 1213 1210 1235 C1' G B 23 beta 1230 1236 1233 1258 C1' U B 24 beta 1253 1259 1256 1278 C1' C B 25 beta 1273 1279 1276 1298 C1' U B 26 beta 1293 1299 1296 1318 C1' G B 27 beta 1313 1319 1316 1341 C1' C B 28 beta 1336 1342 1339 1361 C1' A B 29 beta 1356 1362 1359 1383 C1' C B 30 beta 1378 1384 1381 1403 C1' C B 31 beta 1398 1404 1401 1423 C1' G B 32 beta 1418 1424 1421 1446 C1' C B 33 beta 1441 1447 1444 1466 C1' C B 34 beta 1461 1467 1464 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 993 C2' G B 12 OK 995 991 994 1016 C2' G B 13 OK 1018 1014 1017 1039 C2' C B 14 OK 1041 1037 1040 1059 C2' G B 15 OK 1061 1057 1060 1082 C2' G B 16 OK 1084 1080 1083 1105 C2' U B 17 OK 1107 1103 1106 1125 C2' U B 18 OK 1127 1123 1126 1145 C2' G B 19 OK 1147 1143 1146 1168 C2' C B 20 OK 1170 1166 1169 1188 C2' A B 21 OK 1190 1186 1189 1210 C2' G B 22 OK 1212 1208 1211 1233 C2' G B 23 OK 1235 1231 1234 1256 C2' U B 24 OK 1258 1254 1257 1276 C2' C B 25 OK 1278 1274 1277 1296 C2' U B 26 OK 1298 1294 1297 1316 C2' G B 27 OK 1318 1314 1317 1339 C2' C B 28 OK 1341 1337 1340 1359 C2' A B 29 OK 1361 1357 1360 1381 C2' C B 30 OK 1383 1379 1382 1401 C2' C B 31 OK 1403 1399 1402 1421 C2' G B 32 OK 1423 1419 1422 1444 C2' C B 33 OK 1446 1442 1445 1464 C2' C B 34 OK 1466 1462 1465 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 991 C3' G B 12 OK 989 992 993 1014 C3' G B 13 OK 1012 1015 1016 1037 C3' C B 14 OK 1035 1038 1039 1057 C3' G B 15 OK 1055 1058 1059 1080 C3' G B 16 OK 1078 1081 1082 1103 C3' U B 17 OK 1101 1104 1105 1123 C3' U B 18 OK 1121 1124 1125 1143 C3' G B 19 OK 1141 1144 1145 1166 C3' C B 20 OK 1164 1167 1168 1186 C3' A B 21 OK 1184 1187 1188 1208 C3' G B 22 OK 1206 1209 1210 1231 C3' G B 23 OK 1229 1232 1233 1254 C3' U B 24 OK 1252 1255 1256 1274 C3' C B 25 OK 1272 1275 1276 1294 C3' U B 26 OK 1292 1295 1296 1314 C3' G B 27 OK 1312 1315 1316 1337 C3' C B 28 OK 1335 1338 1339 1357 C3' A B 29 OK 1355 1358 1359 1379 C3' C B 30 OK 1377 1380 1381 1399 C3' C B 31 OK 1397 1400 1401 1419 C3' G B 32 OK 1417 1420 1421 1442 C3' C B 33 OK 1440 1443 1444 1462 C3' C B 34 OK 1460 1463 1464 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 989 C4' G B 12 OK 991 988 990 1012 C4' G B 13 OK 1014 1011 1013 1035 C4' C B 14 OK 1037 1034 1036 1055 C4' G B 15 OK 1057 1054 1056 1078 C4' G B 16 OK 1080 1077 1079 1101 C4' U B 17 OK 1103 1100 1102 1121 C4' U B 18 OK 1123 1120 1122 1141 C4' G B 19 OK 1143 1140 1142 1164 C4' C B 20 OK 1166 1163 1165 1184 C4' A B 21 OK 1186 1183 1185 1206 C4' G B 22 OK 1208 1205 1207 1229 C4' G B 23 OK 1231 1228 1230 1252 C4' U B 24 OK 1254 1251 1253 1272 C4' C B 25 OK 1274 1271 1273 1292 C4' U B 26 OK 1294 1291 1293 1312 C4' G B 27 OK 1314 1311 1313 1335 C4' C B 28 OK 1337 1334 1336 1355 C4' A B 29 OK 1357 1354 1356 1377 C4' C B 30 OK 1379 1376 1378 1397 C4' C B 31 OK 1399 1396 1398 1417 C4' G B 32 OK 1419 1416 1418 1440 C4' C B 33 OK 1442 1439 1441 1460 C4' C B 34 OK 1462 1459 1461 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 988 C5' G B 12 987 989 1011 C5' G B 13 1010 1012 1034 C5' C B 14 1033 1035 1054 C5' G B 15 1053 1055 1077 C5' G B 16 1076 1078 1100 C5' U B 17 1099 1101 1120 C5' U B 18 1119 1121 1140 C5' G B 19 1139 1141 1163 C5' C B 20 1162 1164 1183 C5' A B 21 1182 1184 1205 C5' G B 22 1204 1206 1228 C5' G B 23 1227 1229 1251 C5' U B 24 1250 1252 1271 C5' C B 25 1270 1272 1291 C5' U B 26 1290 1292 1311 C5' G B 27 1310 1312 1334 C5' C B 28 1333 1335 1354 C5' A B 29 1353 1355 1376 C5' C B 30 1375 1377 1396 C5' C B 31 1395 1397 1416 C5' G B 32 1415 1417 1439 C5' C B 33 1438 1440 1459 C5' C B 34 1458 1460 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 984 P G B 12 distorted distorted 985 986 987 1007 P G B 13 distorted distorted 992 1008 1009 1010 1030 P C B 14 distorted distorted 1015 1031 1032 1033 1050 P G B 15 distorted distorted 1038 1051 1052 1053 1073 P G B 16 distorted distorted 1058 1074 1075 1076 1096 P U B 17 distorted distorted 1081 1097 1098 1099 1116 P U B 18 distorted distorted 1104 1117 1118 1119 1136 P G B 19 distorted distorted 1124 1137 1138 1139 1159 P C B 20 distorted distorted 1144 1160 1161 1162 1179 P A B 21 distorted distorted 1167 1180 1181 1182 1201 P G B 22 distorted distorted 1187 1202 1203 1204 1224 P G B 23 distorted distorted 1209 1225 1226 1227 1247 P U B 24 distorted distorted 1232 1248 1249 1250 1267 P C B 25 distorted distorted 1255 1268 1269 1270 1287 P U B 26 distorted distorted 1275 1288 1289 1290 1307 P G B 27 distorted distorted 1295 1308 1309 1310 1330 P C B 28 distorted distorted 1315 1331 1332 1333 1350 P A B 29 distorted distorted 1338 1351 1352 1353 1372 P C B 30 distorted distorted 1358 1373 1374 1375 1392 P C B 31 distorted distorted 1380 1393 1394 1395 1412 P G B 32 distorted distorted 1400 1413 1414 1415 1435 P C B 33 distorted distorted 1420 1436 1437 1438 1455 P C B 34 distorted distorted 1443 1456 1457 1458 ---------------------------------------------------------------------------------