ID code: '2AWS' 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' --------------------------------------------------------------------------------- 371 C1' G C 1 beta 367 372 370 393 C1' T C 2 beta 389 394 392 413 C1' A C 3 beta 409 414 412 435 C1' T D 1 beta 431 436 434 455 C1' A D 2 beta 451 456 454 476 C1' C D 3 beta 472 477 475 496 C1' G E 1 beta 492 497 495 518 C1' T E 2 beta 514 519 517 538 C1' A E 3 beta 534 539 537 560 C1' T F 1 beta 556 561 559 580 C1' A F 2 beta 576 581 579 601 C1' C F 3 beta 597 602 600 621 C1' G I 1 beta 617 622 620 643 C1' T I 2 beta 639 644 642 663 C1' A I 3 beta 659 664 662 685 C1' T J 1 beta 681 686 684 705 C1' A J 2 beta 701 706 704 726 C1' C J 3 beta 722 727 725 746 C1' G K 1 beta 742 747 745 768 C1' T K 2 beta 764 769 767 789 C1' A L 1 beta 785 790 788 810 C1' C L 2 beta 806 811 809 830 C1' G M 1 beta 826 831 829 852 C1' T M 2 beta 848 853 851 872 C1' A M 3 beta 868 873 871 893 C1' C M 4 beta 889 894 892 913 C1' G N 1 beta 909 914 912 935 C1' T N 2 beta 931 936 934 955 C1' A N 3 beta 951 956 954 976 C1' C N 4 beta 972 977 975 996 C1' G O 1 beta 992 997 995 1018 C1' T O 2 beta 1014 1019 1017 1038 C1' A O 3 beta 1034 1039 1037 1060 C1' T P 1 beta 1056 1061 1059 1080 C1' A P 2 beta 1076 1081 1079 1101 C1' C P 3 beta 1097 1102 1100 1120 C1' G P 4 beta 1116 1121 1119 1143 C1' G S 1 beta 1139 1144 1142 1165 C1' T S 2 beta 1161 1166 1164 1185 C1' A S 3 beta 1181 1186 1184 1206 C1' C S 4 beta 1202 1207 1205 1226 C1' T T 1 beta 1222 1227 1225 1246 C1' A T 2 beta 1242 1247 1245 1267 C1' C T 3 beta 1263 1268 1266 1287 C1' G U 1 beta 1283 1288 1286 1309 C1' T U 2 beta 1305 1310 1308 1329 C1' A U 3 beta 1325 1330 1328 1351 C1' T V 1 beta 1347 1352 1350 1371 C1' A V 2 beta 1367 1372 1370 1392 C1' C V 3 beta 1388 1393 1391 1411 C1' G V 4 beta 1407 1412 1410 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 370 C2' G C 1 371 368 392 C2' T C 2 393 390 412 C2' A C 3 413 410 434 C2' T D 1 435 432 454 C2' A D 2 455 452 475 C2' C D 3 476 473 495 C2' G E 1 496 493 517 C2' T E 2 518 515 537 C2' A E 3 538 535 559 C2' T F 1 560 557 579 C2' A F 2 580 577 600 C2' C F 3 601 598 620 C2' G I 1 621 618 642 C2' T I 2 643 640 662 C2' A I 3 663 660 684 C2' T J 1 685 682 704 C2' A J 2 705 702 725 C2' C J 3 726 723 745 C2' G K 1 746 743 767 C2' T K 2 768 765 788 C2' A L 1 789 786 809 C2' C L 2 810 807 829 C2' G M 1 830 827 851 C2' T M 2 852 849 871 C2' A M 3 872 869 892 C2' C M 4 893 890 912 C2' G N 1 913 910 934 C2' T N 2 935 932 954 C2' A N 3 955 952 975 C2' C N 4 976 973 995 C2' G O 1 996 993 1017 C2' T O 2 1018 1015 1037 C2' A O 3 1038 1035 1059 C2' T P 1 1060 1057 1079 C2' A P 2 1080 1077 1100 C2' C P 3 1101 1098 1119 C2' G P 4 1120 1117 1142 C2' G S 1 1143 1140 1164 C2' T S 2 1165 1162 1184 C2' A S 3 1185 1182 1205 C2' C S 4 1206 1203 1225 C2' T T 1 1226 1223 1245 C2' A T 2 1246 1243 1266 C2' C T 3 1267 1264 1286 C2' G U 1 1287 1284 1308 C2' T U 2 1309 1306 1328 C2' A U 3 1329 1326 1350 C2' T V 1 1351 1348 1370 C2' A V 2 1371 1368 1391 C2' C V 3 1392 1389 1410 C2' G V 4 1411 1408 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 368 C3' G C 1 OK 366 369 370 390 C3' T C 2 OK 388 391 392 410 C3' A C 3 OK 408 411 412 432 C3' T D 1 OK 430 433 434 452 C3' A D 2 OK 450 453 454 473 C3' C D 3 OK 471 474 475 493 C3' G E 1 OK 491 494 495 515 C3' T E 2 OK 513 516 517 535 C3' A E 3 OK 533 536 537 557 C3' T F 1 OK 555 558 559 577 C3' A F 2 OK 575 578 579 598 C3' C F 3 OK 596 599 600 618 C3' G I 1 OK 616 619 620 640 C3' T I 2 OK 638 641 642 660 C3' A I 3 OK 658 661 662 682 C3' T J 1 OK 680 683 684 702 C3' A J 2 OK 700 703 704 723 C3' C J 3 OK 721 724 725 743 C3' G K 1 OK 741 744 745 765 C3' T K 2 OK 763 766 767 786 C3' A L 1 OK 784 787 788 807 C3' C L 2 OK 805 808 809 827 C3' G M 1 OK 825 828 829 849 C3' T M 2 OK 847 850 851 869 C3' A M 3 OK 867 870 871 890 C3' C M 4 OK 888 891 892 910 C3' G N 1 OK 908 911 912 932 C3' T N 2 OK 930 933 934 952 C3' A N 3 OK 950 953 954 973 C3' C N 4 OK 971 974 975 993 C3' G O 1 OK 991 994 995 1015 C3' T O 2 OK 1013 1016 1017 1035 C3' A O 3 OK 1033 1036 1037 1057 C3' T P 1 OK 1055 1058 1059 1077 C3' A P 2 OK 1075 1078 1079 1098 C3' C P 3 OK 1096 1099 1100 1117 C3' G P 4 OK 1115 1118 1119 1140 C3' G S 1 OK 1138 1141 1142 1162 C3' T S 2 OK 1160 1163 1164 1182 C3' A S 3 OK 1180 1183 1184 1203 C3' C S 4 OK 1201 1204 1205 1223 C3' T T 1 OK 1221 1224 1225 1243 C3' A T 2 OK 1241 1244 1245 1264 C3' C T 3 OK 1262 1265 1266 1284 C3' G U 1 OK 1282 1285 1286 1306 C3' T U 2 OK 1304 1307 1308 1326 C3' A U 3 OK 1324 1327 1328 1348 C3' T V 1 OK 1346 1349 1350 1368 C3' A V 2 OK 1366 1369 1370 1389 C3' C V 3 OK 1387 1390 1391 1408 C3' G V 4 OK 1406 1409 1410 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 366 C4' G C 1 OK 368 365 367 388 C4' T C 2 OK 390 387 389 408 C4' A C 3 OK 410 407 409 430 C4' T D 1 OK 432 429 431 450 C4' A D 2 OK 452 449 451 471 C4' C D 3 OK 473 470 472 491 C4' G E 1 OK 493 490 492 513 C4' T E 2 OK 515 512 514 533 C4' A E 3 OK 535 532 534 555 C4' T F 1 OK 557 554 556 575 C4' A F 2 OK 577 574 576 596 C4' C F 3 OK 598 595 597 616 C4' G I 1 OK 618 615 617 638 C4' T I 2 OK 640 637 639 658 C4' A I 3 OK 660 657 659 680 C4' T J 1 OK 682 679 681 700 C4' A J 2 OK 702 699 701 721 C4' C J 3 OK 723 720 722 741 C4' G K 1 OK 743 740 742 763 C4' T K 2 OK 765 762 764 784 C4' A L 1 OK 786 783 785 805 C4' C L 2 OK 807 804 806 825 C4' G M 1 OK 827 824 826 847 C4' T M 2 OK 849 846 848 867 C4' A M 3 OK 869 866 868 888 C4' C M 4 OK 890 887 889 908 C4' G N 1 OK 910 907 909 930 C4' T N 2 OK 932 929 931 950 C4' A N 3 OK 952 949 951 971 C4' C N 4 OK 973 970 972 991 C4' G O 1 OK 993 990 992 1013 C4' T O 2 OK 1015 1012 1014 1033 C4' A O 3 OK 1035 1032 1034 1055 C4' T P 1 OK 1057 1054 1056 1075 C4' A P 2 OK 1077 1074 1076 1096 C4' C P 3 OK 1098 1095 1097 1115 C4' G P 4 OK 1117 1114 1116 1138 C4' G S 1 OK 1140 1137 1139 1160 C4' T S 2 OK 1162 1159 1161 1180 C4' A S 3 OK 1182 1179 1181 1201 C4' C S 4 OK 1203 1200 1202 1221 C4' T T 1 OK 1223 1220 1222 1241 C4' A T 2 OK 1243 1240 1242 1262 C4' C T 3 OK 1264 1261 1263 1282 C4' G U 1 OK 1284 1281 1283 1304 C4' T U 2 OK 1306 1303 1305 1324 C4' A U 3 OK 1326 1323 1325 1346 C4' T V 1 OK 1348 1345 1347 1366 C4' A V 2 OK 1368 1365 1367 1387 C4' C V 3 OK 1389 1386 1388 1406 C4' G V 4 OK 1408 1405 1407 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 365 C5' G C 1 364 366 387 C5' T C 2 386 388 407 C5' A C 3 406 408 429 C5' T D 1 428 430 449 C5' A D 2 448 450 470 C5' C D 3 469 471 490 C5' G E 1 489 491 512 C5' T E 2 511 513 532 C5' A E 3 531 533 554 C5' T F 1 553 555 574 C5' A F 2 573 575 595 C5' C F 3 594 596 615 C5' G I 1 614 616 637 C5' T I 2 636 638 657 C5' A I 3 656 658 679 C5' T J 1 678 680 699 C5' A J 2 698 700 720 C5' C J 3 719 721 740 C5' G K 1 739 741 762 C5' T K 2 761 763 783 C5' A L 1 782 784 804 C5' C L 2 803 805 824 C5' G M 1 823 825 846 C5' T M 2 845 847 866 C5' A M 3 865 867 887 C5' C M 4 886 888 907 C5' G N 1 906 908 929 C5' T N 2 928 930 949 C5' A N 3 948 950 970 C5' C N 4 969 971 990 C5' G O 1 989 991 1012 C5' T O 2 1011 1013 1032 C5' A O 3 1031 1033 1054 C5' T P 1 1053 1055 1074 C5' A P 2 1073 1075 1095 C5' C P 3 1094 1096 1114 C5' G P 4 1113 1115 1137 C5' G S 1 1136 1138 1159 C5' T S 2 1158 1160 1179 C5' A S 3 1178 1180 1200 C5' C S 4 1199 1201 1220 C5' T T 1 1219 1221 1240 C5' A T 2 1239 1241 1261 C5' C T 3 1260 1262 1281 C5' G U 1 1280 1282 1303 C5' T U 2 1302 1304 1323 C5' A U 3 1322 1324 1345 C5' T V 1 1344 1346 1365 C5' A V 2 1364 1366 1386 C5' C V 3 1385 1387 1405 C5' G V 4 1404 1406 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 361 P G C 1 OK OK 362 363 364 383 P T C 2 distorted distorted 369 384 385 386 403 P A C 3 distorted distorted 391 404 405 406 425 P T D 1 OK OK 426 427 428 445 P A D 2 distorted distorted 433 446 447 448 466 P C D 3 distorted distorted 453 467 468 469 486 P G E 1 OK OK 487 488 489 508 P T E 2 distorted distorted 494 509 510 511 528 P A E 3 distorted distorted 516 529 530 531 550 P T F 1 OK OK 551 552 553 570 P A F 2 distorted distorted 558 571 572 573 591 P C F 3 distorted distorted 578 592 593 594 611 P G I 1 OK OK 612 613 614 633 P T I 2 distorted distorted 619 634 635 636 653 P A I 3 distorted distorted 641 654 655 656 675 P T J 1 OK OK 676 677 678 695 P A J 2 distorted distorted 683 696 697 698 716 P C J 3 distorted distorted 703 717 718 719 736 P G K 1 OK OK 737 738 739 758 P T K 2 distorted distorted 744 759 760 761 779 P A L 1 OK OK 780 781 782 800 P C L 2 distorted distorted 787 801 802 803 820 P G M 1 OK OK 821 822 823 842 P T M 2 distorted distorted 828 843 844 845 862 P A M 3 distorted distorted 850 863 864 865 883 P C M 4 distorted distorted 870 884 885 886 903 P G N 1 OK OK 904 905 906 925 P T N 2 distorted distorted 911 926 927 928 945 P A N 3 distorted distorted 933 946 947 948 966 P C N 4 distorted distorted 953 967 968 969 986 P G O 1 OK OK 987 988 989 1008 P T O 2 distorted distorted 994 1009 1010 1011 1028 P A O 3 distorted distorted 1016 1029 1030 1031 1050 P T P 1 OK OK 1051 1052 1053 1070 P A P 2 distorted distorted 1058 1071 1072 1073 1091 P C P 3 distorted distorted 1078 1092 1093 1094 1110 P G P 4 distorted distorted 1099 1111 1112 1113 1133 P G S 1 OK OK 1134 1135 1136 1155 P T S 2 distorted distorted 1141 1156 1157 1158 1175 P A S 3 distorted distorted 1163 1176 1177 1178 1196 P C S 4 distorted distorted 1183 1197 1198 1199 1216 P T T 1 OK OK 1217 1218 1219 1236 P A T 2 distorted distorted 1224 1237 1238 1239 1257 P C T 3 distorted distorted 1244 1258 1259 1260 1277 P G U 1 OK OK 1278 1279 1280 1299 P T U 2 distorted distorted 1285 1300 1301 1302 1319 P A U 3 distorted distorted 1307 1320 1321 1322 1341 P T V 1 OK OK 1342 1343 1344 1361 P A V 2 distorted distorted 1349 1362 1363 1364 1382 P C V 3 distorted distorted 1369 1383 1384 1385 1401 P G V 4 distorted distorted 1390 1402 1403 1404 ---------------------------------------------------------------------------------