ID code: '2DU6' 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 D 901 beta 8 14 11 36 C1' C D 902 beta 31 37 34 56 C1' C D 903 beta 51 57 54 76 C1' A D 904 beta 71 77 74 98 C1' G D 905 beta 93 99 96 121 C1' G D 906 beta 116 122 119 144 C1' G D 907 beta 139 145 142 167 C1' U D 908 beta 162 168 165 187 C1' G D 909 beta 182 188 185 210 C1' G D 910 beta 205 211 208 233 C1' C D 911 beta 228 234 231 253 C1' A D 912 beta 248 254 251 275 C1' G D 913 beta 270 276 273 298 C1' A D 914 beta 293 299 296 320 C1' G D 915 beta 315 321 318 343 C1' G D 916 beta 338 344 341 366 C1' G D 917 beta 361 367 364 389 C1' G D 918 beta 384 390 387 412 C1' C D 919 beta 407 413 410 432 C1' U D 920 beta 427 433 430 452 C1' U D 921 beta 447 453 450 472 C1' U D 922 beta 467 473 470 492 C1' G D 923 beta 487 493 490 515 C1' C D 924 beta 510 516 513 535 C1' G D 925 beta 530 536 533 558 C1' G D 926 beta 553 559 556 581 C1' C D 927 beta 576 582 579 601 C1' G D 928 beta 596 602 599 624 C1' G D 929 beta 619 625 622 647 C1' A D 930 beta 642 648 645 669 C1' C D 931 beta 664 670 667 689 C1' U D 932 beta 684 690 687 709 C1' C D 933 beta 704 710 707 729 C1' U D 934 beta 724 730 727 749 C1' A D 935 beta 744 750 747 771 C1' G D 936 beta 766 772 769 794 C1' A D 937 beta 789 795 792 816 C1' U D 938 beta 811 817 814 836 C1' C D 939 beta 831 837 834 856 C1' C D 940 beta 851 857 854 876 C1' G D 941 beta 871 877 874 899 C1' C D 942 beta 894 900 897 919 C1' U D 943 beta 914 920 917 939 C1' U D 944 beta 934 940 937 959 C1' U D 945 beta 954 960 957 979 C1' A D 946 beta 974 980 977 1001 C1' C D 947 beta 996 1002 999 1021 C1' C D 948 beta 1016 1022 1019 1041 C1' C D 949 beta 1036 1042 1039 1061 C1' C D 950 beta 1056 1062 1059 1081 C1' G D 951 beta 1076 1082 1079 1104 C1' G D 952 beta 1099 1105 1102 1127 C1' U D 953 beta 1122 1128 1125 1147 C1' U D 954 beta 1142 1148 1145 1167 C1' C D 955 beta 1162 1168 1165 1187 C1' G D 956 beta 1182 1188 1185 1210 C1' A D 957 beta 1205 1211 1208 1232 C1' A D 958 beta 1227 1233 1230 1254 C1' U D 959 beta 1249 1255 1252 1274 C1' C D 960 beta 1269 1275 1272 1294 C1' C D 961 beta 1289 1295 1292 1314 C1' G D 962 beta 1309 1315 1312 1337 C1' G D 963 beta 1332 1338 1335 1360 C1' G D 964 beta 1355 1361 1358 1383 C1' C D 965 beta 1378 1384 1381 1403 C1' C D 966 beta 1398 1404 1401 1423 C1' C D 967 beta 1418 1424 1421 1443 C1' U D 968 beta 1438 1444 1441 1463 C1' G D 969 beta 1458 1464 1461 1486 C1' G D 970 beta 1481 1487 1484 1509 C1' C D 971 beta 1504 1510 1507 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 11 C2' G D 901 OK 13 9 12 34 C2' C D 902 OK 36 32 35 54 C2' C D 903 OK 56 52 55 74 C2' A D 904 OK 76 72 75 96 C2' G D 905 OK 98 94 97 119 C2' G D 906 OK 121 117 120 142 C2' G D 907 OK 144 140 143 165 C2' U D 908 OK 167 163 166 185 C2' G D 909 OK 187 183 186 208 C2' G D 910 OK 210 206 209 231 C2' C D 911 OK 233 229 232 251 C2' A D 912 OK 253 249 252 273 C2' G D 913 OK 275 271 274 296 C2' A D 914 OK 298 294 297 318 C2' G D 915 OK 320 316 319 341 C2' G D 916 OK 343 339 342 364 C2' G D 917 OK 366 362 365 387 C2' G D 918 OK 389 385 388 410 C2' C D 919 OK 412 408 411 430 C2' U D 920 OK 432 428 431 450 C2' U D 921 OK 452 448 451 470 C2' U D 922 OK 472 468 471 490 C2' G D 923 OK 492 488 491 513 C2' C D 924 OK 515 511 514 533 C2' G D 925 OK 535 531 534 556 C2' G D 926 OK 558 554 557 579 C2' C D 927 OK 581 577 580 599 C2' G D 928 OK 601 597 600 622 C2' G D 929 OK 624 620 623 645 C2' A D 930 OK 647 643 646 667 C2' C D 931 OK 669 665 668 687 C2' U D 932 OK 689 685 688 707 C2' C D 933 OK 709 705 708 727 C2' U D 934 OK 729 725 728 747 C2' A D 935 OK 749 745 748 769 C2' G D 936 OK 771 767 770 792 C2' A D 937 OK 794 790 793 814 C2' U D 938 OK 816 812 815 834 C2' C D 939 OK 836 832 835 854 C2' C D 940 OK 856 852 855 874 C2' G D 941 OK 876 872 875 897 C2' C D 942 OK 899 895 898 917 C2' U D 943 OK 919 915 918 937 C2' U D 944 OK 939 935 938 957 C2' U D 945 OK 959 955 958 977 C2' A D 946 OK 979 975 978 999 C2' C D 947 OK 1001 997 1000 1019 C2' C D 948 OK 1021 1017 1020 1039 C2' C D 949 OK 1041 1037 1040 1059 C2' C D 950 OK 1061 1057 1060 1079 C2' G D 951 OK 1081 1077 1080 1102 C2' G D 952 OK 1104 1100 1103 1125 C2' U D 953 OK 1127 1123 1126 1145 C2' U D 954 OK 1147 1143 1146 1165 C2' C D 955 OK 1167 1163 1166 1185 C2' G D 956 OK 1187 1183 1186 1208 C2' A D 957 OK 1210 1206 1209 1230 C2' A D 958 OK 1232 1228 1231 1252 C2' U D 959 OK 1254 1250 1253 1272 C2' C D 960 OK 1274 1270 1273 1292 C2' C D 961 OK 1294 1290 1293 1312 C2' G D 962 OK 1314 1310 1313 1335 C2' G D 963 OK 1337 1333 1336 1358 C2' G D 964 OK 1360 1356 1359 1381 C2' C D 965 OK 1383 1379 1382 1401 C2' C D 966 OK 1403 1399 1402 1421 C2' C D 967 OK 1423 1419 1422 1441 C2' U D 968 OK 1443 1439 1442 1461 C2' G D 969 OK 1463 1459 1462 1484 C2' G D 970 OK 1486 1482 1485 1507 C2' C D 971 OK 1509 1505 1508 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 9 C3' G D 901 OK 7 10 11 32 C3' C D 902 OK 30 33 34 52 C3' C D 903 OK 50 53 54 72 C3' A D 904 OK 70 73 74 94 C3' G D 905 OK 92 95 96 117 C3' G D 906 OK 115 118 119 140 C3' G D 907 OK 138 141 142 163 C3' U D 908 OK 161 164 165 183 C3' G D 909 OK 181 184 185 206 C3' G D 910 OK 204 207 208 229 C3' C D 911 OK 227 230 231 249 C3' A D 912 OK 247 250 251 271 C3' G D 913 OK 269 272 273 294 C3' A D 914 OK 292 295 296 316 C3' G D 915 OK 314 317 318 339 C3' G D 916 OK 337 340 341 362 C3' G D 917 OK 360 363 364 385 C3' G D 918 OK 383 386 387 408 C3' C D 919 OK 406 409 410 428 C3' U D 920 OK 426 429 430 448 C3' U D 921 OK 446 449 450 468 C3' U D 922 OK 466 469 470 488 C3' G D 923 OK 486 489 490 511 C3' C D 924 OK 509 512 513 531 C3' G D 925 OK 529 532 533 554 C3' G D 926 OK 552 555 556 577 C3' C D 927 OK 575 578 579 597 C3' G D 928 OK 595 598 599 620 C3' G D 929 OK 618 621 622 643 C3' A D 930 OK 641 644 645 665 C3' C D 931 OK 663 666 667 685 C3' U D 932 OK 683 686 687 705 C3' C D 933 OK 703 706 707 725 C3' U D 934 OK 723 726 727 745 C3' A D 935 OK 743 746 747 767 C3' G D 936 OK 765 768 769 790 C3' A D 937 OK 788 791 792 812 C3' U D 938 OK 810 813 814 832 C3' C D 939 OK 830 833 834 852 C3' C D 940 OK 850 853 854 872 C3' G D 941 OK 870 873 874 895 C3' C D 942 OK 893 896 897 915 C3' U D 943 OK 913 916 917 935 C3' U D 944 OK 933 936 937 955 C3' U D 945 OK 953 956 957 975 C3' A D 946 OK 973 976 977 997 C3' C D 947 OK 995 998 999 1017 C3' C D 948 OK 1015 1018 1019 1037 C3' C D 949 OK 1035 1038 1039 1057 C3' C D 950 OK 1055 1058 1059 1077 C3' G D 951 OK 1075 1078 1079 1100 C3' G D 952 OK 1098 1101 1102 1123 C3' U D 953 OK 1121 1124 1125 1143 C3' U D 954 OK 1141 1144 1145 1163 C3' C D 955 OK 1161 1164 1165 1183 C3' G D 956 OK 1181 1184 1185 1206 C3' A D 957 OK 1204 1207 1208 1228 C3' A D 958 OK 1226 1229 1230 1250 C3' U D 959 OK 1248 1251 1252 1270 C3' C D 960 OK 1268 1271 1272 1290 C3' C D 961 OK 1288 1291 1292 1310 C3' G D 962 OK 1308 1311 1312 1333 C3' G D 963 OK 1331 1334 1335 1356 C3' G D 964 OK 1354 1357 1358 1379 C3' C D 965 OK 1377 1380 1381 1399 C3' C D 966 OK 1397 1400 1401 1419 C3' C D 967 OK 1417 1420 1421 1439 C3' U D 968 OK 1437 1440 1441 1459 C3' G D 969 OK 1457 1460 1461 1482 C3' G D 970 OK 1480 1483 1484 1505 C3' C D 971 OK 1503 1506 1507 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 7 C4' G D 901 OK 9 6 8 30 C4' C D 902 OK 32 29 31 50 C4' C D 903 OK 52 49 51 70 C4' A D 904 OK 72 69 71 92 C4' G D 905 OK 94 91 93 115 C4' G D 906 OK 117 114 116 138 C4' G D 907 OK 140 137 139 161 C4' U D 908 OK 163 160 162 181 C4' G D 909 OK 183 180 182 204 C4' G D 910 OK 206 203 205 227 C4' C D 911 OK 229 226 228 247 C4' A D 912 OK 249 246 248 269 C4' G D 913 OK 271 268 270 292 C4' A D 914 OK 294 291 293 314 C4' G D 915 OK 316 313 315 337 C4' G D 916 OK 339 336 338 360 C4' G D 917 OK 362 359 361 383 C4' G D 918 OK 385 382 384 406 C4' C D 919 OK 408 405 407 426 C4' U D 920 OK 428 425 427 446 C4' U D 921 OK 448 445 447 466 C4' U D 922 OK 468 465 467 486 C4' G D 923 OK 488 485 487 509 C4' C D 924 OK 511 508 510 529 C4' G D 925 OK 531 528 530 552 C4' G D 926 OK 554 551 553 575 C4' C D 927 OK 577 574 576 595 C4' G D 928 OK 597 594 596 618 C4' G D 929 OK 620 617 619 641 C4' A D 930 OK 643 640 642 663 C4' C D 931 OK 665 662 664 683 C4' U D 932 OK 685 682 684 703 C4' C D 933 OK 705 702 704 723 C4' U D 934 OK 725 722 724 743 C4' A D 935 OK 745 742 744 765 C4' G D 936 OK 767 764 766 788 C4' A D 937 OK 790 787 789 810 C4' U D 938 OK 812 809 811 830 C4' C D 939 OK 832 829 831 850 C4' C D 940 OK 852 849 851 870 C4' G D 941 OK 872 869 871 893 C4' C D 942 OK 895 892 894 913 C4' U D 943 OK 915 912 914 933 C4' U D 944 OK 935 932 934 953 C4' U D 945 OK 955 952 954 973 C4' A D 946 OK 975 972 974 995 C4' C D 947 OK 997 994 996 1015 C4' C D 948 OK 1017 1014 1016 1035 C4' C D 949 OK 1037 1034 1036 1055 C4' C D 950 OK 1057 1054 1056 1075 C4' G D 951 OK 1077 1074 1076 1098 C4' G D 952 OK 1100 1097 1099 1121 C4' U D 953 OK 1123 1120 1122 1141 C4' U D 954 OK 1143 1140 1142 1161 C4' C D 955 OK 1163 1160 1162 1181 C4' G D 956 OK 1183 1180 1182 1204 C4' A D 957 OK 1206 1203 1205 1226 C4' A D 958 OK 1228 1225 1227 1248 C4' U D 959 OK 1250 1247 1249 1268 C4' C D 960 OK 1270 1267 1269 1288 C4' C D 961 OK 1290 1287 1289 1308 C4' G D 962 OK 1310 1307 1309 1331 C4' G D 963 OK 1333 1330 1332 1354 C4' G D 964 OK 1356 1353 1355 1377 C4' C D 965 OK 1379 1376 1378 1397 C4' C D 966 OK 1399 1396 1398 1417 C4' C D 967 OK 1419 1416 1418 1437 C4' U D 968 OK 1439 1436 1438 1457 C4' G D 969 OK 1459 1456 1458 1480 C4' G D 970 OK 1482 1479 1481 1503 C4' C D 971 OK 1505 1502 1504 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 6 C5' G D 901 5 7 29 C5' C D 902 28 30 49 C5' C D 903 48 50 69 C5' A D 904 68 70 91 C5' G D 905 90 92 114 C5' G D 906 113 115 137 C5' G D 907 136 138 160 C5' U D 908 159 161 180 C5' G D 909 179 181 203 C5' G D 910 202 204 226 C5' C D 911 225 227 246 C5' A D 912 245 247 268 C5' G D 913 267 269 291 C5' A D 914 290 292 313 C5' G D 915 312 314 336 C5' G D 916 335 337 359 C5' G D 917 358 360 382 C5' G D 918 381 383 405 C5' C D 919 404 406 425 C5' U D 920 424 426 445 C5' U D 921 444 446 465 C5' U D 922 464 466 485 C5' G D 923 484 486 508 C5' C D 924 507 509 528 C5' G D 925 527 529 551 C5' G D 926 550 552 574 C5' C D 927 573 575 594 C5' G D 928 593 595 617 C5' G D 929 616 618 640 C5' A D 930 639 641 662 C5' C D 931 661 663 682 C5' U D 932 681 683 702 C5' C D 933 701 703 722 C5' U D 934 721 723 742 C5' A D 935 741 743 764 C5' G D 936 763 765 787 C5' A D 937 786 788 809 C5' U D 938 808 810 829 C5' C D 939 828 830 849 C5' C D 940 848 850 869 C5' G D 941 868 870 892 C5' C D 942 891 893 912 C5' U D 943 911 913 932 C5' U D 944 931 933 952 C5' U D 945 951 953 972 C5' A D 946 971 973 994 C5' C D 947 993 995 1014 C5' C D 948 1013 1015 1034 C5' C D 949 1033 1035 1054 C5' C D 950 1053 1055 1074 C5' G D 951 1073 1075 1097 C5' G D 952 1096 1098 1120 C5' U D 953 1119 1121 1140 C5' U D 954 1139 1141 1160 C5' C D 955 1159 1161 1180 C5' G D 956 1179 1181 1203 C5' A D 957 1202 1204 1225 C5' A D 958 1224 1226 1247 C5' U D 959 1246 1248 1267 C5' C D 960 1266 1268 1287 C5' C D 961 1286 1288 1307 C5' G D 962 1306 1308 1330 C5' G D 963 1329 1331 1353 C5' G D 964 1352 1354 1376 C5' C D 965 1375 1377 1396 C5' C D 966 1395 1397 1416 C5' C D 967 1415 1417 1436 C5' U D 968 1435 1437 1456 C5' G D 969 1455 1457 1479 C5' G D 970 1478 1480 1502 C5' C D 971 1501 1503 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2 P G D 901 distorted distorted 3 4 5 25 P C D 902 distorted distorted 10 26 27 28 45 P C D 903 distorted distorted 33 46 47 48 65 P A D 904 distorted distorted 53 66 67 68 87 P G D 905 distorted distorted 73 88 89 90 110 P G D 906 distorted distorted 95 111 112 113 133 P G D 907 distorted distorted 118 134 135 136 156 P U D 908 distorted distorted 141 157 158 159 176 P G D 909 distorted distorted 164 177 178 179 199 P G D 910 distorted distorted 184 200 201 202 222 P C D 911 distorted distorted 207 223 224 225 242 P A D 912 distorted distorted 230 243 244 245 264 P G D 913 distorted distorted 250 265 266 267 287 P A D 914 distorted distorted 272 288 289 290 309 P G D 915 distorted distorted 295 310 311 312 332 P G D 916 distorted distorted 317 333 334 335 355 P G D 917 distorted distorted 340 356 357 358 378 P G D 918 distorted distorted 363 379 380 381 401 P C D 919 distorted distorted 386 402 403 404 421 P U D 920 distorted distorted 409 422 423 424 441 P U D 921 distorted distorted 429 442 443 444 461 P U D 922 distorted distorted 449 462 463 464 481 P G D 923 distorted distorted 469 482 483 484 504 P C D 924 distorted distorted 489 505 506 507 524 P G D 925 distorted distorted 512 525 526 527 547 P G D 926 distorted distorted 532 548 549 550 570 P C D 927 distorted distorted 555 571 572 573 590 P G D 928 distorted distorted 578 591 592 593 613 P G D 929 distorted distorted 598 614 615 616 636 P A D 930 distorted distorted 621 637 638 639 658 P C D 931 distorted distorted 644 659 660 661 678 P U D 932 distorted distorted 666 679 680 681 698 P C D 933 distorted distorted 686 699 700 701 718 P U D 934 distorted distorted 706 719 720 721 738 P A D 935 distorted distorted 726 739 740 741 760 P G D 936 distorted distorted 746 761 762 763 783 P A D 937 distorted distorted 768 784 785 786 805 P U D 938 distorted distorted 791 806 807 808 825 P C D 939 distorted distorted 813 826 827 828 845 P C D 940 distorted distorted 833 846 847 848 865 P G D 941 distorted distorted 853 866 867 868 888 P C D 942 distorted distorted 873 889 890 891 908 P U D 943 distorted distorted 896 909 910 911 928 P U D 944 distorted distorted 916 929 930 931 948 P U D 945 distorted distorted 936 949 950 951 968 P A D 946 distorted distorted 956 969 970 971 990 P C D 947 distorted distorted 976 991 992 993 1010 P C D 948 distorted distorted 998 1011 1012 1013 1030 P C D 949 distorted distorted 1018 1031 1032 1033 1050 P C D 950 distorted distorted 1038 1051 1052 1053 1070 P G D 951 distorted distorted 1058 1071 1072 1073 1093 P G D 952 distorted distorted 1078 1094 1095 1096 1116 P U D 953 distorted distorted 1101 1117 1118 1119 1136 P U D 954 distorted distorted 1124 1137 1138 1139 1156 P C D 955 distorted distorted 1144 1157 1158 1159 1176 P G D 956 distorted distorted 1164 1177 1178 1179 1199 P A D 957 distorted distorted 1184 1200 1201 1202 1221 P A D 958 distorted distorted 1207 1222 1223 1224 1243 P U D 959 distorted distorted 1229 1244 1245 1246 1263 P C D 960 distorted distorted 1251 1264 1265 1266 1283 P C D 961 distorted distorted 1271 1284 1285 1286 1303 P G D 962 distorted distorted 1291 1304 1305 1306 1326 P G D 963 distorted distorted 1311 1327 1328 1329 1349 P G D 964 distorted distorted 1334 1350 1351 1352 1372 P C D 965 distorted distorted 1357 1373 1374 1375 1392 P C D 966 distorted distorted 1380 1393 1394 1395 1412 P C D 967 distorted distorted 1400 1413 1414 1415 1432 P U D 968 distorted distorted 1420 1433 1434 1435 1452 P G D 969 distorted distorted 1440 1453 1454 1455 1475 P G D 970 distorted distorted 1460 1476 1477 1478 1498 P C D 971 distorted distorted 1483 1499 1500 1501 9608 P SEP A1001 9609 9610 9619 P SEP A1002 9620 9621 ---------------------------------------------------------------------------------