ID code: '5D8H' 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' --------------------------------------------------------------------------------- 13 C1' G A1151 beta 8 14 11 36 C1' C A1152 beta 31 37 34 56 C1' C A1153 beta 51 57 54 76 C1' U A1154 beta 71 77 74 96 C1' A A1155 beta 91 97 94 118 C1' A A1156 beta 113 119 116 140 C1' G A1157 beta 135 141 138 163 C1' A A1158 beta 158 164 161 185 C1' C A1159 beta 180 186 183 205 C1' A A1160 beta 200 206 203 227 C1' G A1161 beta 222 228 225 250 C1' C A1162 beta 245 251 248 270 C1' G A1163 beta 265 271 268 293 C1' G A1164 beta 288 294 291 316 C1' G A1165 beta 311 317 314 339 C1' G A1166 beta 334 340 337 362 C1' A A1167 beta 357 363 360 384 C1' G A1168 beta 379 385 382 407 C1' G A1169 beta 402 408 405 430 C1' U A1170 beta 425 431 428 450 C1' U A1171 beta 445 451 448 470 C1' G A1172 beta 465 471 468 493 C1' G A1173 beta 488 494 491 516 C1' C A1174 beta 511 517 514 536 C1' U A1175 beta 531 537 534 556 C1' U A1176 beta 551 557 554 576 C1' A A1177 beta 571 577 574 598 C1' G A1178 beta 593 599 596 621 C1' A A1179 beta 616 622 619 643 C1' A A1180 beta 638 644 641 665 C1' G A1181 beta 660 666 663 688 C1' C A1182 beta 683 689 686 708 C1' A A1183 beta 703 709 706 730 C1' G A1184 beta 725 731 728 753 C1' C A1185 beta 748 754 751 773 C1' C A1186 beta 768 774 771 793 C1' A A1187 beta 788 794 791 815 C1' U A1188 beta 810 816 813 835 C1' C A1189 beta 830 836 833 855 C1' C A1190 beta 850 856 853 875 C1' U A1191 beta 870 876 873 895 C1' U A1192 beta 890 896 893 915 C1' U A1193 beta 910 916 913 935 C1' A A1194 beta 930 936 933 957 C1' A A1195 beta 952 958 955 979 C1' A A1196 beta 974 980 977 1001 C1' G A1197 beta 996 1002 999 1024 C1' A A1198 beta 1019 1025 1022 1046 C1' G A1199 beta 1041 1047 1044 1069 C1' U A1200 beta 1064 1070 1067 1089 C1' G A1201 beta 1084 1090 1087 1112 C1' C A1202 beta 1107 1113 1110 1132 C1' G A1203 beta 1127 1133 1130 1155 C1' U A1204 beta 1150 1156 1153 1175 C1' A A1205 beta 1170 1176 1173 1197 C1' A A1206 beta 1192 1198 1195 1219 C1' C A1207 beta 1214 1220 1217 1239 C1' A A1208 beta 1234 1240 1237 1261 C1' G A1209 beta 1256 1262 1259 1284 C1' C A1210 beta 1279 1285 1282 1304 C1' U A1211 beta 1299 1305 1302 1324 C1' C A1212 beta 1319 1325 1322 1344 C1' A A1213 beta 1339 1345 1342 1366 C1' C A1214 beta 1361 1367 1364 1386 C1' C A1215 beta 1381 1387 1384 1406 C1' C A1216 beta 1401 1407 1404 1426 C1' G A1217 beta 1421 1427 1424 1449 C1' U A1218 beta 1444 1450 1447 1469 C1' C A1219 beta 1464 1470 1467 1489 C1' G A1220 beta 1484 1490 1487 1512 C1' A A1221 beta 1507 1513 1510 1534 C1' G A1222 beta 1529 1535 1532 1557 C1' G A1223 beta 1552 1558 1555 1580 C1' C A1224 beta 1575 1581 1578 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 11 C2' G A1151 OK 13 9 12 34 C2' C A1152 OK 36 32 35 54 C2' C A1153 OK 56 52 55 74 C2' U A1154 OK 76 72 75 94 C2' A A1155 OK 96 92 95 116 C2' A A1156 OK 118 114 117 138 C2' G A1157 OK 140 136 139 161 C2' A A1158 OK 163 159 162 183 C2' C A1159 OK 185 181 184 203 C2' A A1160 OK 205 201 204 225 C2' G A1161 OK 227 223 226 248 C2' C A1162 OK 250 246 249 268 C2' G A1163 OK 270 266 269 291 C2' G A1164 OK 293 289 292 314 C2' G A1165 OK 316 312 315 337 C2' G A1166 OK 339 335 338 360 C2' A A1167 OK 362 358 361 382 C2' G A1168 OK 384 380 383 405 C2' G A1169 OK 407 403 406 428 C2' U A1170 OK 430 426 429 448 C2' U A1171 OK 450 446 449 468 C2' G A1172 OK 470 466 469 491 C2' G A1173 OK 493 489 492 514 C2' C A1174 OK 516 512 515 534 C2' U A1175 OK 536 532 535 554 C2' U A1176 OK 556 552 555 574 C2' A A1177 OK 576 572 575 596 C2' G A1178 OK 598 594 597 619 C2' A A1179 OK 621 617 620 641 C2' A A1180 OK 643 639 642 663 C2' G A1181 OK 665 661 664 686 C2' C A1182 OK 688 684 687 706 C2' A A1183 OK 708 704 707 728 C2' G A1184 OK 730 726 729 751 C2' C A1185 OK 753 749 752 771 C2' C A1186 OK 773 769 772 791 C2' A A1187 OK 793 789 792 813 C2' U A1188 OK 815 811 814 833 C2' C A1189 OK 835 831 834 853 C2' C A1190 OK 855 851 854 873 C2' U A1191 OK 875 871 874 893 C2' U A1192 OK 895 891 894 913 C2' U A1193 OK 915 911 914 933 C2' A A1194 OK 935 931 934 955 C2' A A1195 OK 957 953 956 977 C2' A A1196 OK 979 975 978 999 C2' G A1197 OK 1001 997 1000 1022 C2' A A1198 OK 1024 1020 1023 1044 C2' G A1199 OK 1046 1042 1045 1067 C2' U A1200 OK 1069 1065 1068 1087 C2' G A1201 OK 1089 1085 1088 1110 C2' C A1202 OK 1112 1108 1111 1130 C2' G A1203 OK 1132 1128 1131 1153 C2' U A1204 OK 1155 1151 1154 1173 C2' A A1205 OK 1175 1171 1174 1195 C2' A A1206 OK 1197 1193 1196 1217 C2' C A1207 OK 1219 1215 1218 1237 C2' A A1208 OK 1239 1235 1238 1259 C2' G A1209 OK 1261 1257 1260 1282 C2' C A1210 OK 1284 1280 1283 1302 C2' U A1211 OK 1304 1300 1303 1322 C2' C A1212 OK 1324 1320 1323 1342 C2' A A1213 OK 1344 1340 1343 1364 C2' C A1214 OK 1366 1362 1365 1384 C2' C A1215 OK 1386 1382 1385 1404 C2' C A1216 OK 1406 1402 1405 1424 C2' G A1217 OK 1426 1422 1425 1447 C2' U A1218 OK 1449 1445 1448 1467 C2' C A1219 OK 1469 1465 1468 1487 C2' G A1220 OK 1489 1485 1488 1510 C2' A A1221 OK 1512 1508 1511 1532 C2' G A1222 OK 1534 1530 1533 1555 C2' G A1223 OK 1557 1553 1556 1578 C2' C A1224 OK 1580 1576 1579 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 9 C3' G A1151 OK 7 10 11 32 C3' C A1152 OK 30 33 34 52 C3' C A1153 OK 50 53 54 72 C3' U A1154 OK 70 73 74 92 C3' A A1155 OK 90 93 94 114 C3' A A1156 OK 112 115 116 136 C3' G A1157 OK 134 137 138 159 C3' A A1158 OK 157 160 161 181 C3' C A1159 OK 179 182 183 201 C3' A A1160 OK 199 202 203 223 C3' G A1161 OK 221 224 225 246 C3' C A1162 OK 244 247 248 266 C3' G A1163 OK 264 267 268 289 C3' G A1164 OK 287 290 291 312 C3' G A1165 OK 310 313 314 335 C3' G A1166 OK 333 336 337 358 C3' A A1167 OK 356 359 360 380 C3' G A1168 OK 378 381 382 403 C3' G A1169 OK 401 404 405 426 C3' U A1170 OK 424 427 428 446 C3' U A1171 OK 444 447 448 466 C3' G A1172 OK 464 467 468 489 C3' G A1173 OK 487 490 491 512 C3' C A1174 OK 510 513 514 532 C3' U A1175 OK 530 533 534 552 C3' U A1176 OK 550 553 554 572 C3' A A1177 OK 570 573 574 594 C3' G A1178 OK 592 595 596 617 C3' A A1179 OK 615 618 619 639 C3' A A1180 OK 637 640 641 661 C3' G A1181 OK 659 662 663 684 C3' C A1182 OK 682 685 686 704 C3' A A1183 OK 702 705 706 726 C3' G A1184 OK 724 727 728 749 C3' C A1185 OK 747 750 751 769 C3' C A1186 OK 767 770 771 789 C3' A A1187 OK 787 790 791 811 C3' U A1188 OK 809 812 813 831 C3' C A1189 OK 829 832 833 851 C3' C A1190 OK 849 852 853 871 C3' U A1191 OK 869 872 873 891 C3' U A1192 OK 889 892 893 911 C3' U A1193 OK 909 912 913 931 C3' A A1194 OK 929 932 933 953 C3' A A1195 OK 951 954 955 975 C3' A A1196 OK 973 976 977 997 C3' G A1197 OK 995 998 999 1020 C3' A A1198 OK 1018 1021 1022 1042 C3' G A1199 OK 1040 1043 1044 1065 C3' U A1200 OK 1063 1066 1067 1085 C3' G A1201 OK 1083 1086 1087 1108 C3' C A1202 OK 1106 1109 1110 1128 C3' G A1203 OK 1126 1129 1130 1151 C3' U A1204 OK 1149 1152 1153 1171 C3' A A1205 OK 1169 1172 1173 1193 C3' A A1206 OK 1191 1194 1195 1215 C3' C A1207 OK 1213 1216 1217 1235 C3' A A1208 OK 1233 1236 1237 1257 C3' G A1209 OK 1255 1258 1259 1280 C3' C A1210 OK 1278 1281 1282 1300 C3' U A1211 OK 1298 1301 1302 1320 C3' C A1212 OK 1318 1321 1322 1340 C3' A A1213 OK 1338 1341 1342 1362 C3' C A1214 OK 1360 1363 1364 1382 C3' C A1215 OK 1380 1383 1384 1402 C3' C A1216 OK 1400 1403 1404 1422 C3' G A1217 OK 1420 1423 1424 1445 C3' U A1218 OK 1443 1446 1447 1465 C3' C A1219 OK 1463 1466 1467 1485 C3' G A1220 OK 1483 1486 1487 1508 C3' A A1221 OK 1506 1509 1510 1530 C3' G A1222 OK 1528 1531 1532 1553 C3' G A1223 OK 1551 1554 1555 1576 C3' C A1224 OK 1574 1577 1578 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 7 C4' G A1151 OK 9 6 8 30 C4' C A1152 OK 32 29 31 50 C4' C A1153 OK 52 49 51 70 C4' U A1154 OK 72 69 71 90 C4' A A1155 OK 92 89 91 112 C4' A A1156 OK 114 111 113 134 C4' G A1157 OK 136 133 135 157 C4' A A1158 OK 159 156 158 179 C4' C A1159 OK 181 178 180 199 C4' A A1160 OK 201 198 200 221 C4' G A1161 OK 223 220 222 244 C4' C A1162 OK 246 243 245 264 C4' G A1163 OK 266 263 265 287 C4' G A1164 OK 289 286 288 310 C4' G A1165 OK 312 309 311 333 C4' G A1166 OK 335 332 334 356 C4' A A1167 OK 358 355 357 378 C4' G A1168 OK 380 377 379 401 C4' G A1169 OK 403 400 402 424 C4' U A1170 OK 426 423 425 444 C4' U A1171 OK 446 443 445 464 C4' G A1172 OK 466 463 465 487 C4' G A1173 OK 489 486 488 510 C4' C A1174 OK 512 509 511 530 C4' U A1175 OK 532 529 531 550 C4' U A1176 OK 552 549 551 570 C4' A A1177 OK 572 569 571 592 C4' G A1178 OK 594 591 593 615 C4' A A1179 OK 617 614 616 637 C4' A A1180 OK 639 636 638 659 C4' G A1181 OK 661 658 660 682 C4' C A1182 OK 684 681 683 702 C4' A A1183 OK 704 701 703 724 C4' G A1184 OK 726 723 725 747 C4' C A1185 OK 749 746 748 767 C4' C A1186 OK 769 766 768 787 C4' A A1187 OK 789 786 788 809 C4' U A1188 OK 811 808 810 829 C4' C A1189 OK 831 828 830 849 C4' C A1190 OK 851 848 850 869 C4' U A1191 OK 871 868 870 889 C4' U A1192 OK 891 888 890 909 C4' U A1193 OK 911 908 910 929 C4' A A1194 OK 931 928 930 951 C4' A A1195 OK 953 950 952 973 C4' A A1196 OK 975 972 974 995 C4' G A1197 OK 997 994 996 1018 C4' A A1198 OK 1020 1017 1019 1040 C4' G A1199 OK 1042 1039 1041 1063 C4' U A1200 OK 1065 1062 1064 1083 C4' G A1201 OK 1085 1082 1084 1106 C4' C A1202 OK 1108 1105 1107 1126 C4' G A1203 OK 1128 1125 1127 1149 C4' U A1204 OK 1151 1148 1150 1169 C4' A A1205 OK 1171 1168 1170 1191 C4' A A1206 OK 1193 1190 1192 1213 C4' C A1207 OK 1215 1212 1214 1233 C4' A A1208 OK 1235 1232 1234 1255 C4' G A1209 OK 1257 1254 1256 1278 C4' C A1210 OK 1280 1277 1279 1298 C4' U A1211 OK 1300 1297 1299 1318 C4' C A1212 OK 1320 1317 1319 1338 C4' A A1213 OK 1340 1337 1339 1360 C4' C A1214 OK 1362 1359 1361 1380 C4' C A1215 OK 1382 1379 1381 1400 C4' C A1216 OK 1402 1399 1401 1420 C4' G A1217 OK 1422 1419 1421 1443 C4' U A1218 OK 1445 1442 1444 1463 C4' C A1219 OK 1465 1462 1464 1483 C4' G A1220 OK 1485 1482 1484 1506 C4' A A1221 OK 1508 1505 1507 1528 C4' G A1222 OK 1530 1527 1529 1551 C4' G A1223 OK 1553 1550 1552 1574 C4' C A1224 OK 1576 1573 1575 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 6 C5' G A1151 5 7 29 C5' C A1152 28 30 49 C5' C A1153 48 50 69 C5' U A1154 68 70 89 C5' A A1155 88 90 111 C5' A A1156 110 112 133 C5' G A1157 132 134 156 C5' A A1158 155 157 178 C5' C A1159 177 179 198 C5' A A1160 197 199 220 C5' G A1161 219 221 243 C5' C A1162 242 244 263 C5' G A1163 262 264 286 C5' G A1164 285 287 309 C5' G A1165 308 310 332 C5' G A1166 331 333 355 C5' A A1167 354 356 377 C5' G A1168 376 378 400 C5' G A1169 399 401 423 C5' U A1170 422 424 443 C5' U A1171 442 444 463 C5' G A1172 462 464 486 C5' G A1173 485 487 509 C5' C A1174 508 510 529 C5' U A1175 528 530 549 C5' U A1176 548 550 569 C5' A A1177 568 570 591 C5' G A1178 590 592 614 C5' A A1179 613 615 636 C5' A A1180 635 637 658 C5' G A1181 657 659 681 C5' C A1182 680 682 701 C5' A A1183 700 702 723 C5' G A1184 722 724 746 C5' C A1185 745 747 766 C5' C A1186 765 767 786 C5' A A1187 785 787 808 C5' U A1188 807 809 828 C5' C A1189 827 829 848 C5' C A1190 847 849 868 C5' U A1191 867 869 888 C5' U A1192 887 889 908 C5' U A1193 907 909 928 C5' A A1194 927 929 950 C5' A A1195 949 951 972 C5' A A1196 971 973 994 C5' G A1197 993 995 1017 C5' A A1198 1016 1018 1039 C5' G A1199 1038 1040 1062 C5' U A1200 1061 1063 1082 C5' G A1201 1081 1083 1105 C5' C A1202 1104 1106 1125 C5' G A1203 1124 1126 1148 C5' U A1204 1147 1149 1168 C5' A A1205 1167 1169 1190 C5' A A1206 1189 1191 1212 C5' C A1207 1211 1213 1232 C5' A A1208 1231 1233 1254 C5' G A1209 1253 1255 1277 C5' C A1210 1276 1278 1297 C5' U A1211 1296 1298 1317 C5' C A1212 1316 1318 1337 C5' A A1213 1336 1338 1359 C5' C A1214 1358 1360 1379 C5' C A1215 1378 1380 1399 C5' C A1216 1398 1400 1419 C5' G A1217 1418 1420 1442 C5' U A1218 1441 1443 1462 C5' C A1219 1461 1463 1482 C5' G A1220 1481 1483 1505 C5' A A1221 1504 1506 1527 C5' G A1222 1526 1528 1550 C5' G A1223 1549 1551 1573 C5' C A1224 1572 1574 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2 P G A1151 distorted distorted 3 4 5 25 P C A1152 distorted distorted 10 26 27 28 45 P C A1153 distorted distorted 33 46 47 48 65 P U A1154 distorted distorted 53 66 67 68 85 P A A1155 distorted distorted 73 86 87 88 107 P A A1156 distorted distorted 93 108 109 110 129 P G A1157 distorted distorted 115 130 131 132 152 P A A1158 distorted distorted 137 153 154 155 174 P C A1159 distorted distorted 160 175 176 177 194 P A A1160 distorted distorted 182 195 196 197 216 P G A1161 distorted distorted 202 217 218 219 239 P C A1162 distorted distorted 224 240 241 242 259 P G A1163 distorted distorted 247 260 261 262 282 P G A1164 distorted distorted 267 283 284 285 305 P G A1165 distorted distorted 290 306 307 308 328 P G A1166 distorted distorted 313 329 330 331 351 P A A1167 distorted distorted 336 352 353 354 373 P G A1168 distorted distorted 359 374 375 376 396 P G A1169 distorted distorted 381 397 398 399 419 P U A1170 distorted distorted 404 420 421 422 439 P U A1171 distorted distorted 427 440 441 442 459 P G A1172 distorted distorted 447 460 461 462 482 P G A1173 distorted distorted 467 483 484 485 505 P C A1174 distorted distorted 490 506 507 508 525 P U A1175 distorted distorted 513 526 527 528 545 P U A1176 distorted distorted 533 546 547 548 565 P A A1177 distorted distorted 553 566 567 568 587 P G A1178 distorted distorted 573 588 589 590 610 P A A1179 distorted distorted 595 611 612 613 632 P A A1180 distorted distorted 618 633 634 635 654 P G A1181 distorted distorted 640 655 656 657 677 P C A1182 distorted distorted 662 678 679 680 697 P A A1183 distorted distorted 685 698 699 700 719 P G A1184 distorted distorted 705 720 721 722 742 P C A1185 distorted distorted 727 743 744 745 762 P C A1186 distorted distorted 750 763 764 765 782 P A A1187 distorted distorted 770 783 784 785 804 P U A1188 distorted distorted 790 805 806 807 824 P C A1189 distorted distorted 812 825 826 827 844 P C A1190 distorted distorted 832 845 846 847 864 P U A1191 distorted distorted 852 865 866 867 884 P U A1192 distorted distorted 872 885 886 887 904 P U A1193 distorted distorted 892 905 906 907 924 P A A1194 distorted distorted 912 925 926 927 946 P A A1195 distorted distorted 932 947 948 949 968 P A A1196 distorted distorted 954 969 970 971 990 P G A1197 distorted distorted 976 991 992 993 1013 P A A1198 distorted distorted 998 1014 1015 1016 1035 P G A1199 distorted distorted 1021 1036 1037 1038 1058 P U A1200 distorted distorted 1043 1059 1060 1061 1078 P G A1201 distorted distorted 1066 1079 1080 1081 1101 P C A1202 distorted distorted 1086 1102 1103 1104 1121 P G A1203 distorted distorted 1109 1122 1123 1124 1144 P U A1204 distorted distorted 1129 1145 1146 1147 1164 P A A1205 distorted distorted 1152 1165 1166 1167 1186 P A A1206 distorted distorted 1172 1187 1188 1189 1208 P C A1207 distorted distorted 1194 1209 1210 1211 1228 P A A1208 distorted distorted 1216 1229 1230 1231 1250 P G A1209 distorted distorted 1236 1251 1252 1253 1273 P C A1210 distorted distorted 1258 1274 1275 1276 1293 P U A1211 distorted distorted 1281 1294 1295 1296 1313 P C A1212 distorted distorted 1301 1314 1315 1316 1333 P A A1213 distorted distorted 1321 1334 1335 1336 1355 P C A1214 distorted distorted 1341 1356 1357 1358 1375 P C A1215 distorted distorted 1363 1376 1377 1378 1395 P C A1216 distorted distorted 1383 1396 1397 1398 1415 P G A1217 distorted distorted 1403 1416 1417 1418 1438 P U A1218 distorted distorted 1423 1439 1440 1441 1458 P C A1219 distorted distorted 1446 1459 1460 1461 1478 P G A1220 distorted distorted 1466 1479 1480 1481 1501 P A A1221 distorted distorted 1486 1502 1503 1504 1523 P G A1222 distorted distorted 1509 1524 1525 1526 1546 P G A1223 distorted distorted 1531 1547 1548 1549 1569 P C A1224 distorted distorted 1554 1570 1571 1572 ---------------------------------------------------------------------------------