ID code: '1ZJW' 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' --------------------------------------------------------------------------------- 9 C1' G B 902 beta 4 10 7 32 C1' G B 903 beta 27 33 30 55 C1' G B 904 beta 50 56 53 78 C1' G B 905 beta 73 79 76 101 C1' U B 906 beta 96 102 99 121 C1' A B 907 beta 116 122 119 143 C1' U B 908 beta 138 144 141 163 C1' C B 909 beta 158 164 161 183 C1' G B 910 beta 178 184 181 206 C1' C B 911 beta 201 207 204 226 C1' C B 912 beta 221 227 224 246 C1' A B 913 beta 241 247 244 268 C1' A B 914 beta 263 269 266 290 C1' G B 915 beta 285 291 288 313 C1' C B 916 beta 308 314 311 333 C1' G B 918 beta 328 334 331 356 C1' G B 919 beta 351 357 354 379 C1' U B 920 beta 374 380 377 399 C1' A B 921 beta 394 400 397 421 C1' A B 922 beta 416 422 419 443 C1' G B 923 beta 438 444 441 466 C1' G B 924 beta 461 467 464 489 C1' C B 925 beta 484 490 487 509 C1' A B 926 beta 504 510 507 531 C1' C B 927 beta 526 532 529 551 C1' C B 928 beta 546 552 549 571 C1' G B 929 beta 566 572 569 594 C1' G B 930 beta 589 595 592 617 C1' A B 931 beta 612 618 615 639 C1' U B 932 beta 634 640 637 659 C1' U B 933 beta 654 660 657 679 C1' C B 934 beta 674 680 677 699 C1' U B 935 beta 694 700 697 719 C1' G B 936 beta 714 720 717 742 C1' A B 937 beta 737 743 740 764 C1' U B 938 beta 759 765 762 784 C1' U B 939 beta 779 785 782 804 C1' C B 940 beta 799 805 802 824 C1' C B 941 beta 819 825 822 844 C1' G B 942 beta 839 845 842 867 C1' G B 943 beta 862 868 865 890 C1' C B 944 beta 885 891 888 910 C1' A B 945 beta 905 911 908 932 C1' U B 946 beta 927 933 930 952 C1' U B 947 beta 947 953 950 972 C1' C B 948 beta 967 973 970 992 C1' C B 949 beta 987 993 990 1012 C1' G B 950 beta 1007 1013 1010 1035 C1' A B 951 beta 1030 1036 1033 1057 C1' G B 952 beta 1052 1058 1055 1080 C1' G B 953 beta 1075 1081 1078 1103 C1' U B 954 beta 1098 1104 1101 1123 C1' U B 955 beta 1118 1124 1121 1143 C1' C B 956 beta 1138 1144 1141 1163 C1' G B 957 beta 1158 1164 1161 1186 C1' A B 958 beta 1181 1187 1184 1208 C1' A B 959 beta 1203 1209 1206 1230 C1' U B 960 beta 1225 1231 1228 1250 C1' C B 961 beta 1245 1251 1248 1270 C1' C B 962 beta 1265 1271 1268 1290 C1' U B 963 beta 1285 1291 1288 1310 C1' C B 964 beta 1305 1311 1308 1330 C1' G B 965 beta 1325 1331 1328 1353 C1' U B 966 beta 1348 1354 1351 1373 C1' A B 967 beta 1368 1374 1371 1395 C1' C B 968 beta 1390 1396 1393 1415 C1' C B 969 beta 1410 1416 1413 1435 C1' C B 970 beta 1430 1436 1433 1455 C1' C B 971 beta 1450 1456 1453 1475 C1' A B 972 beta 1470 1476 1473 1497 C1' G B 973 beta 1492 1498 1495 1520 C1' C B 974 beta 1515 1521 1518 1540 C1' C B 975 beta 1535 1541 1538 1559 C1' A B 976 beta 1555 1560 1558 5873 C1' AMP A 998 beta 5868 5874 5871 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G B 902 OK 9 5 8 30 C2' G B 903 OK 32 28 31 53 C2' G B 904 OK 55 51 54 76 C2' G B 905 OK 78 74 77 99 C2' U B 906 OK 101 97 100 119 C2' A B 907 OK 121 117 120 141 C2' U B 908 OK 143 139 142 161 C2' C B 909 OK 163 159 162 181 C2' G B 910 OK 183 179 182 204 C2' C B 911 OK 206 202 205 224 C2' C B 912 OK 226 222 225 244 C2' A B 913 OK 246 242 245 266 C2' A B 914 OK 268 264 267 288 C2' G B 915 OK 290 286 289 311 C2' C B 916 OK 313 309 312 331 C2' G B 918 OK 333 329 332 354 C2' G B 919 OK 356 352 355 377 C2' U B 920 OK 379 375 378 397 C2' A B 921 OK 399 395 398 419 C2' A B 922 OK 421 417 420 441 C2' G B 923 OK 443 439 442 464 C2' G B 924 OK 466 462 465 487 C2' C B 925 OK 489 485 488 507 C2' A B 926 OK 509 505 508 529 C2' C B 927 OK 531 527 530 549 C2' C B 928 OK 551 547 550 569 C2' G B 929 OK 571 567 570 592 C2' G B 930 OK 594 590 593 615 C2' A B 931 OK 617 613 616 637 C2' U B 932 OK 639 635 638 657 C2' U B 933 OK 659 655 658 677 C2' C B 934 OK 679 675 678 697 C2' U B 935 OK 699 695 698 717 C2' G B 936 OK 719 715 718 740 C2' A B 937 OK 742 738 741 762 C2' U B 938 OK 764 760 763 782 C2' U B 939 OK 784 780 783 802 C2' C B 940 OK 804 800 803 822 C2' C B 941 OK 824 820 823 842 C2' G B 942 OK 844 840 843 865 C2' G B 943 OK 867 863 866 888 C2' C B 944 OK 890 886 889 908 C2' A B 945 OK 910 906 909 930 C2' U B 946 OK 932 928 931 950 C2' U B 947 OK 952 948 951 970 C2' C B 948 OK 972 968 971 990 C2' C B 949 OK 992 988 991 1010 C2' G B 950 OK 1012 1008 1011 1033 C2' A B 951 OK 1035 1031 1034 1055 C2' G B 952 OK 1057 1053 1056 1078 C2' G B 953 OK 1080 1076 1079 1101 C2' U B 954 OK 1103 1099 1102 1121 C2' U B 955 OK 1123 1119 1122 1141 C2' C B 956 OK 1143 1139 1142 1161 C2' G B 957 OK 1163 1159 1162 1184 C2' A B 958 OK 1186 1182 1185 1206 C2' A B 959 OK 1208 1204 1207 1228 C2' U B 960 OK 1230 1226 1229 1248 C2' C B 961 OK 1250 1246 1249 1268 C2' C B 962 OK 1270 1266 1269 1288 C2' U B 963 OK 1290 1286 1289 1308 C2' C B 964 OK 1310 1306 1309 1328 C2' G B 965 OK 1330 1326 1329 1351 C2' U B 966 OK 1353 1349 1352 1371 C2' A B 967 OK 1373 1369 1372 1393 C2' C B 968 OK 1395 1391 1394 1413 C2' C B 969 OK 1415 1411 1414 1433 C2' C B 970 OK 1435 1431 1434 1453 C2' C B 971 OK 1455 1451 1454 1473 C2' A B 972 OK 1475 1471 1474 1495 C2' G B 973 OK 1497 1493 1496 1518 C2' C B 974 OK 1520 1516 1519 1538 C2' C B 975 OK 1540 1536 1539 1558 C2' A B 976 1559 1556 5871 C2' AMP A 998 OK 5873 5869 5872 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G B 902 OK 3 6 7 28 C3' G B 903 OK 26 29 30 51 C3' G B 904 OK 49 52 53 74 C3' G B 905 OK 72 75 76 97 C3' U B 906 OK 95 98 99 117 C3' A B 907 OK 115 118 119 139 C3' U B 908 OK 137 140 141 159 C3' C B 909 OK 157 160 161 179 C3' G B 910 OK 177 180 181 202 C3' C B 911 OK 200 203 204 222 C3' C B 912 OK 220 223 224 242 C3' A B 913 OK 240 243 244 264 C3' A B 914 OK 262 265 266 286 C3' G B 915 OK 284 287 288 309 C3' C B 916 OK 307 310 311 329 C3' G B 918 OK 327 330 331 352 C3' G B 919 OK 350 353 354 375 C3' U B 920 OK 373 376 377 395 C3' A B 921 OK 393 396 397 417 C3' A B 922 OK 415 418 419 439 C3' G B 923 OK 437 440 441 462 C3' G B 924 OK 460 463 464 485 C3' C B 925 OK 483 486 487 505 C3' A B 926 OK 503 506 507 527 C3' C B 927 OK 525 528 529 547 C3' C B 928 OK 545 548 549 567 C3' G B 929 OK 565 568 569 590 C3' G B 930 OK 588 591 592 613 C3' A B 931 OK 611 614 615 635 C3' U B 932 OK 633 636 637 655 C3' U B 933 OK 653 656 657 675 C3' C B 934 OK 673 676 677 695 C3' U B 935 OK 693 696 697 715 C3' G B 936 OK 713 716 717 738 C3' A B 937 OK 736 739 740 760 C3' U B 938 OK 758 761 762 780 C3' U B 939 OK 778 781 782 800 C3' C B 940 OK 798 801 802 820 C3' C B 941 OK 818 821 822 840 C3' G B 942 OK 838 841 842 863 C3' G B 943 OK 861 864 865 886 C3' C B 944 OK 884 887 888 906 C3' A B 945 OK 904 907 908 928 C3' U B 946 OK 926 929 930 948 C3' U B 947 OK 946 949 950 968 C3' C B 948 OK 966 969 970 988 C3' C B 949 OK 986 989 990 1008 C3' G B 950 OK 1006 1009 1010 1031 C3' A B 951 OK 1029 1032 1033 1053 C3' G B 952 OK 1051 1054 1055 1076 C3' G B 953 OK 1074 1077 1078 1099 C3' U B 954 OK 1097 1100 1101 1119 C3' U B 955 OK 1117 1120 1121 1139 C3' C B 956 OK 1137 1140 1141 1159 C3' G B 957 OK 1157 1160 1161 1182 C3' A B 958 OK 1180 1183 1184 1204 C3' A B 959 OK 1202 1205 1206 1226 C3' U B 960 OK 1224 1227 1228 1246 C3' C B 961 OK 1244 1247 1248 1266 C3' C B 962 OK 1264 1267 1268 1286 C3' U B 963 OK 1284 1287 1288 1306 C3' C B 964 OK 1304 1307 1308 1326 C3' G B 965 OK 1324 1327 1328 1349 C3' U B 966 OK 1347 1350 1351 1369 C3' A B 967 OK 1367 1370 1371 1391 C3' C B 968 OK 1389 1392 1393 1411 C3' C B 969 OK 1409 1412 1413 1431 C3' C B 970 OK 1429 1432 1433 1451 C3' C B 971 OK 1449 1452 1453 1471 C3' A B 972 OK 1469 1472 1473 1493 C3' G B 973 OK 1491 1494 1495 1516 C3' C B 974 OK 1514 1517 1518 1536 C3' C B 975 OK 1534 1537 1538 1556 C3' A B 976 OK 1554 1557 1558 5869 C3' AMP A 998 OK 5867 5870 5871 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G B 902 OK 5 2 4 26 C4' G B 903 OK 28 25 27 49 C4' G B 904 OK 51 48 50 72 C4' G B 905 OK 74 71 73 95 C4' U B 906 OK 97 94 96 115 C4' A B 907 OK 117 114 116 137 C4' U B 908 OK 139 136 138 157 C4' C B 909 OK 159 156 158 177 C4' G B 910 OK 179 176 178 200 C4' C B 911 OK 202 199 201 220 C4' C B 912 OK 222 219 221 240 C4' A B 913 OK 242 239 241 262 C4' A B 914 OK 264 261 263 284 C4' G B 915 OK 286 283 285 307 C4' C B 916 OK 309 306 308 327 C4' G B 918 OK 329 326 328 350 C4' G B 919 OK 352 349 351 373 C4' U B 920 OK 375 372 374 393 C4' A B 921 OK 395 392 394 415 C4' A B 922 OK 417 414 416 437 C4' G B 923 OK 439 436 438 460 C4' G B 924 OK 462 459 461 483 C4' C B 925 OK 485 482 484 503 C4' A B 926 OK 505 502 504 525 C4' C B 927 OK 527 524 526 545 C4' C B 928 OK 547 544 546 565 C4' G B 929 OK 567 564 566 588 C4' G B 930 OK 590 587 589 611 C4' A B 931 OK 613 610 612 633 C4' U B 932 OK 635 632 634 653 C4' U B 933 OK 655 652 654 673 C4' C B 934 OK 675 672 674 693 C4' U B 935 OK 695 692 694 713 C4' G B 936 OK 715 712 714 736 C4' A B 937 OK 738 735 737 758 C4' U B 938 OK 760 757 759 778 C4' U B 939 OK 780 777 779 798 C4' C B 940 OK 800 797 799 818 C4' C B 941 OK 820 817 819 838 C4' G B 942 OK 840 837 839 861 C4' G B 943 OK 863 860 862 884 C4' C B 944 OK 886 883 885 904 C4' A B 945 OK 906 903 905 926 C4' U B 946 OK 928 925 927 946 C4' U B 947 OK 948 945 947 966 C4' C B 948 OK 968 965 967 986 C4' C B 949 OK 988 985 987 1006 C4' G B 950 OK 1008 1005 1007 1029 C4' A B 951 OK 1031 1028 1030 1051 C4' G B 952 OK 1053 1050 1052 1074 C4' G B 953 OK 1076 1073 1075 1097 C4' U B 954 OK 1099 1096 1098 1117 C4' U B 955 OK 1119 1116 1118 1137 C4' C B 956 OK 1139 1136 1138 1157 C4' G B 957 OK 1159 1156 1158 1180 C4' A B 958 OK 1182 1179 1181 1202 C4' A B 959 OK 1204 1201 1203 1224 C4' U B 960 OK 1226 1223 1225 1244 C4' C B 961 OK 1246 1243 1245 1264 C4' C B 962 OK 1266 1263 1265 1284 C4' U B 963 OK 1286 1283 1285 1304 C4' C B 964 OK 1306 1303 1305 1324 C4' G B 965 OK 1326 1323 1325 1347 C4' U B 966 OK 1349 1346 1348 1367 C4' A B 967 OK 1369 1366 1368 1389 C4' C B 968 OK 1391 1388 1390 1409 C4' C B 969 OK 1411 1408 1410 1429 C4' C B 970 OK 1431 1428 1430 1449 C4' C B 971 OK 1451 1448 1450 1469 C4' A B 972 OK 1471 1468 1470 1491 C4' G B 973 OK 1493 1490 1492 1514 C4' C B 974 OK 1516 1513 1515 1534 C4' C B 975 OK 1536 1533 1535 1554 C4' A B 976 OK 1556 1553 1555 5867 C4' AMP A 998 OK 5869 5866 5868 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G B 902 1 3 25 C5' G B 903 24 26 48 C5' G B 904 47 49 71 C5' G B 905 70 72 94 C5' U B 906 93 95 114 C5' A B 907 113 115 136 C5' U B 908 135 137 156 C5' C B 909 155 157 176 C5' G B 910 175 177 199 C5' C B 911 198 200 219 C5' C B 912 218 220 239 C5' A B 913 238 240 261 C5' A B 914 260 262 283 C5' G B 915 282 284 306 C5' C B 916 305 307 326 C5' G B 918 325 327 349 C5' G B 919 348 350 372 C5' U B 920 371 373 392 C5' A B 921 391 393 414 C5' A B 922 413 415 436 C5' G B 923 435 437 459 C5' G B 924 458 460 482 C5' C B 925 481 483 502 C5' A B 926 501 503 524 C5' C B 927 523 525 544 C5' C B 928 543 545 564 C5' G B 929 563 565 587 C5' G B 930 586 588 610 C5' A B 931 609 611 632 C5' U B 932 631 633 652 C5' U B 933 651 653 672 C5' C B 934 671 673 692 C5' U B 935 691 693 712 C5' G B 936 711 713 735 C5' A B 937 734 736 757 C5' U B 938 756 758 777 C5' U B 939 776 778 797 C5' C B 940 796 798 817 C5' C B 941 816 818 837 C5' G B 942 836 838 860 C5' G B 943 859 861 883 C5' C B 944 882 884 903 C5' A B 945 902 904 925 C5' U B 946 924 926 945 C5' U B 947 944 946 965 C5' C B 948 964 966 985 C5' C B 949 984 986 1005 C5' G B 950 1004 1006 1028 C5' A B 951 1027 1029 1050 C5' G B 952 1049 1051 1073 C5' G B 953 1072 1074 1096 C5' U B 954 1095 1097 1116 C5' U B 955 1115 1117 1136 C5' C B 956 1135 1137 1156 C5' G B 957 1155 1157 1179 C5' A B 958 1178 1180 1201 C5' A B 959 1200 1202 1223 C5' U B 960 1222 1224 1243 C5' C B 961 1242 1244 1263 C5' C B 962 1262 1264 1283 C5' U B 963 1282 1284 1303 C5' C B 964 1302 1304 1323 C5' G B 965 1322 1324 1346 C5' U B 966 1345 1347 1366 C5' A B 967 1365 1367 1388 C5' C B 968 1387 1389 1408 C5' C B 969 1407 1409 1428 C5' C B 970 1427 1429 1448 C5' C B 971 1447 1449 1468 C5' A B 972 1467 1469 1490 C5' G B 973 1489 1491 1513 C5' C B 974 1512 1514 1533 C5' C B 975 1532 1534 1553 C5' A B 976 1552 1554 5866 C5' AMP A 998 5865 5867 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 21 P G B 903 distorted distorted 6 22 23 24 44 P G B 904 distorted distorted 29 45 46 47 67 P G B 905 distorted distorted 52 68 69 70 90 P U B 906 distorted distorted 75 91 92 93 110 P A B 907 distorted distorted 98 111 112 113 132 P U B 908 distorted distorted 118 133 134 135 152 P C B 909 distorted distorted 140 153 154 155 172 P G B 910 distorted distorted 160 173 174 175 195 P C B 911 distorted distorted 180 196 197 198 215 P C B 912 distorted distorted 203 216 217 218 235 P A B 913 distorted distorted 223 236 237 238 257 P A B 914 distorted distorted 243 258 259 260 279 P G B 915 distorted distorted 265 280 281 282 302 P C B 916 distorted distorted 287 303 304 305 322 P G B 918 distorted distorted 310 323 324 325 345 P G B 919 distorted distorted 330 346 347 348 368 P U B 920 distorted distorted 353 369 370 371 388 P A B 921 distorted distorted 376 389 390 391 410 P A B 922 distorted distorted 396 411 412 413 432 P G B 923 distorted distorted 418 433 434 435 455 P G B 924 distorted distorted 440 456 457 458 478 P C B 925 distorted distorted 463 479 480 481 498 P A B 926 distorted distorted 486 499 500 501 520 P C B 927 distorted distorted 506 521 522 523 540 P C B 928 distorted distorted 528 541 542 543 560 P G B 929 distorted distorted 548 561 562 563 583 P G B 930 distorted distorted 568 584 585 586 606 P A B 931 distorted distorted 591 607 608 609 628 P U B 932 distorted distorted 614 629 630 631 648 P U B 933 distorted distorted 636 649 650 651 668 P C B 934 distorted distorted 656 669 670 671 688 P U B 935 distorted distorted 676 689 690 691 708 P G B 936 distorted distorted 696 709 710 711 731 P A B 937 distorted distorted 716 732 733 734 753 P U B 938 distorted distorted 739 754 755 756 773 P U B 939 distorted distorted 761 774 775 776 793 P C B 940 distorted distorted 781 794 795 796 813 P C B 941 distorted distorted 801 814 815 816 833 P G B 942 distorted distorted 821 834 835 836 856 P G B 943 distorted distorted 841 857 858 859 879 P C B 944 distorted distorted 864 880 881 882 899 P A B 945 distorted distorted 887 900 901 902 921 P U B 946 distorted distorted 907 922 923 924 941 P U B 947 distorted distorted 929 942 943 944 961 P C B 948 distorted distorted 949 962 963 964 981 P C B 949 distorted distorted 969 982 983 984 1001 P G B 950 distorted distorted 989 1002 1003 1004 1024 P A B 951 distorted distorted 1009 1025 1026 1027 1046 P G B 952 distorted distorted 1032 1047 1048 1049 1069 P G B 953 distorted distorted 1054 1070 1071 1072 1092 P U B 954 distorted distorted 1077 1093 1094 1095 1112 P U B 955 distorted distorted 1100 1113 1114 1115 1132 P C B 956 distorted distorted 1120 1133 1134 1135 1152 P G B 957 distorted distorted 1140 1153 1154 1155 1175 P A B 958 distorted distorted 1160 1176 1177 1178 1197 P A B 959 distorted distorted 1183 1198 1199 1200 1219 P U B 960 distorted distorted 1205 1220 1221 1222 1239 P C B 961 distorted distorted 1227 1240 1241 1242 1259 P C B 962 distorted distorted 1247 1260 1261 1262 1279 P U B 963 distorted distorted 1267 1280 1281 1282 1299 P C B 964 distorted distorted 1287 1300 1301 1302 1319 P G B 965 distorted distorted 1307 1320 1321 1322 1342 P U B 966 distorted distorted 1327 1343 1344 1345 1362 P A B 967 distorted distorted 1350 1363 1364 1365 1384 P C B 968 distorted distorted 1370 1385 1386 1387 1404 P C B 969 distorted distorted 1392 1405 1406 1407 1424 P C B 970 distorted distorted 1412 1425 1426 1427 1444 P C B 971 distorted distorted 1432 1445 1446 1447 1464 P A B 972 distorted distorted 1452 1465 1466 1467 1486 P G B 973 distorted distorted 1472 1487 1488 1489 1509 P C B 974 distorted distorted 1494 1510 1511 1512 1529 P C B 975 distorted distorted 1517 1530 1531 1532 1549 P A B 976 distorted distorted 1537 1550 1551 1552 5861 P AMP A 998 distorted distorted 5862 5863 5865 ---------------------------------------------------------------------------------