ID code: '1A60' 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 A 1 alpha beta 4 27 10 7 44 C1' G A 2 alpha beta 39 62 45 42 78 C1' G A 3 alpha beta 73 96 79 76 112 C1' A A 4 alpha beta 107 129 113 110 145 C1' G A 5 alpha beta 140 163 146 143 179 C1' C A 6 alpha beta 174 194 180 177 210 C1' U A 7 alpha beta 205 225 211 208 240 C1' C A 8 alpha beta 235 255 241 238 271 C1' A A 9 alpha beta 266 288 272 269 304 C1' A A 10 alpha beta 299 321 305 302 337 C1' C A 11 alpha beta 332 352 338 335 368 C1' U A 12 alpha beta 363 383 369 366 398 C1' C A 13 alpha beta 393 413 399 396 429 C1' U A 14 alpha beta 424 444 430 427 459 C1' C A 15 alpha beta 454 474 460 457 490 C1' C A 16 alpha beta 485 505 491 488 521 C1' C A 17 alpha beta 516 536 522 519 552 C1' C A 18 alpha beta 547 567 553 550 583 C1' C A 19 alpha beta 578 598 584 581 614 C1' C A 20 alpha beta 609 629 615 612 645 C1' C A 21 alpha beta 640 660 646 643 676 C1' U A 22 alpha beta 671 691 677 674 706 C1' U A 23 alpha beta 701 721 707 704 736 C1' U A 24 alpha beta 731 751 737 734 766 C1' U A 25 alpha beta 761 781 767 764 796 C1' C A 26 alpha beta 791 811 797 794 827 C1' C A 27 alpha beta 822 842 828 825 858 C1' G A 28 alpha beta 853 876 859 856 892 C1' A A 29 alpha beta 887 909 893 890 925 C1' G A 30 alpha beta 920 943 926 923 959 C1' G A 31 alpha beta 954 977 960 957 993 C1' G A 32 alpha beta 988 1011 994 991 1027 C1' U A 33 alpha beta 1022 1042 1028 1025 1057 C1' C A 34 alpha beta 1052 1072 1058 1055 1088 C1' A A 35 alpha beta 1083 1105 1089 1086 1121 C1' U A 36 alpha beta 1116 1136 1122 1119 1151 C1' C A 37 alpha beta 1146 1166 1152 1149 1182 C1' G A 38 alpha beta 1177 1200 1183 1180 1216 C1' G A 39 alpha beta 1211 1234 1217 1214 1250 C1' A A 40 alpha beta 1245 1267 1251 1248 1283 C1' A A 41 alpha beta 1278 1300 1284 1281 1316 C1' C A 42 alpha beta 1311 1331 1317 1314 1347 C1' C A 43 alpha beta 1342 1362 1348 1345 1378 C1' A A 44 alpha beta 1373 1396 1379 1376 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G A 1 OK OK 9 5 25 8 42 C2' G A 2 OK OK 44 40 60 43 76 C2' G A 3 OK OK 78 74 94 77 110 C2' A A 4 OK OK 112 108 127 111 143 C2' G A 5 OK OK 145 141 161 144 177 C2' C A 6 OK OK 179 175 192 178 208 C2' U A 7 OK OK 210 206 223 209 238 C2' C A 8 OK OK 240 236 253 239 269 C2' A A 9 OK OK 271 267 286 270 302 C2' A A 10 OK OK 304 300 319 303 335 C2' C A 11 OK OK 337 333 350 336 366 C2' U A 12 OK OK 368 364 381 367 396 C2' C A 13 OK OK 398 394 411 397 427 C2' U A 14 OK OK 429 425 442 428 457 C2' C A 15 OK OK 459 455 472 458 488 C2' C A 16 OK OK 490 486 503 489 519 C2' C A 17 OK OK 521 517 534 520 550 C2' C A 18 OK OK 552 548 565 551 581 C2' C A 19 OK OK 583 579 596 582 612 C2' C A 20 OK OK 614 610 627 613 643 C2' C A 21 OK OK 645 641 658 644 674 C2' U A 22 OK OK 676 672 689 675 704 C2' U A 23 OK OK 706 702 719 705 734 C2' U A 24 OK OK 736 732 749 735 764 C2' U A 25 OK OK 766 762 779 765 794 C2' C A 26 OK OK 796 792 809 795 825 C2' C A 27 OK OK 827 823 840 826 856 C2' G A 28 OK OK 858 854 874 857 890 C2' A A 29 OK OK 892 888 907 891 923 C2' G A 30 OK OK 925 921 941 924 957 C2' G A 31 OK OK 959 955 975 958 991 C2' G A 32 OK OK 993 989 1009 992 1025 C2' U A 33 OK OK 1027 1023 1040 1026 1055 C2' C A 34 OK OK 1057 1053 1070 1056 1086 C2' A A 35 OK OK 1088 1084 1103 1087 1119 C2' U A 36 OK OK 1121 1117 1134 1120 1149 C2' C A 37 OK OK 1151 1147 1164 1150 1180 C2' G A 38 OK OK 1182 1178 1198 1181 1214 C2' G A 39 OK OK 1216 1212 1232 1215 1248 C2' A A 40 OK OK 1250 1246 1265 1249 1281 C2' A A 41 OK OK 1283 1279 1298 1282 1314 C2' C A 42 OK OK 1316 1312 1329 1315 1345 C2' C A 43 OK OK 1347 1343 1360 1346 1376 C2' A A 44 OK OK 1378 1374 1394 1377 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK OK 3 24 6 7 40 C3' G A 2 OK OK 38 59 41 42 74 C3' G A 3 OK OK 72 93 75 76 108 C3' A A 4 OK OK 106 126 109 110 141 C3' G A 5 OK OK 139 160 142 143 175 C3' C A 6 OK OK 173 191 176 177 206 C3' U A 7 OK OK 204 222 207 208 236 C3' C A 8 OK OK 234 252 237 238 267 C3' A A 9 OK OK 265 285 268 269 300 C3' A A 10 OK OK 298 318 301 302 333 C3' C A 11 OK OK 331 349 334 335 364 C3' U A 12 OK OK 362 380 365 366 394 C3' C A 13 OK OK 392 410 395 396 425 C3' U A 14 OK OK 423 441 426 427 455 C3' C A 15 OK OK 453 471 456 457 486 C3' C A 16 OK OK 484 502 487 488 517 C3' C A 17 OK OK 515 533 518 519 548 C3' C A 18 OK OK 546 564 549 550 579 C3' C A 19 OK OK 577 595 580 581 610 C3' C A 20 OK OK 608 626 611 612 641 C3' C A 21 OK OK 639 657 642 643 672 C3' U A 22 OK OK 670 688 673 674 702 C3' U A 23 OK OK 700 718 703 704 732 C3' U A 24 OK OK 730 748 733 734 762 C3' U A 25 OK OK 760 778 763 764 792 C3' C A 26 OK OK 790 808 793 794 823 C3' C A 27 OK OK 821 839 824 825 854 C3' G A 28 OK OK 852 873 855 856 888 C3' A A 29 OK OK 886 906 889 890 921 C3' G A 30 OK OK 919 940 922 923 955 C3' G A 31 OK OK 953 974 956 957 989 C3' G A 32 OK OK 987 1008 990 991 1023 C3' U A 33 OK OK 1021 1039 1024 1025 1053 C3' C A 34 OK OK 1051 1069 1054 1055 1084 C3' A A 35 OK OK 1082 1102 1085 1086 1117 C3' U A 36 OK OK 1115 1133 1118 1119 1147 C3' C A 37 OK OK 1145 1163 1148 1149 1178 C3' G A 38 OK OK 1176 1197 1179 1180 1212 C3' G A 39 OK OK 1210 1231 1213 1214 1246 C3' A A 40 OK OK 1244 1264 1247 1248 1279 C3' A A 41 OK OK 1277 1297 1280 1281 1312 C3' C A 42 OK OK 1310 1328 1313 1314 1343 C3' C A 43 OK OK 1341 1359 1344 1345 1374 C3' A A 44 OK OK 1372 1392 1375 1376 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK OK 5 23 2 4 38 C4' G A 2 OK OK 40 58 37 39 72 C4' G A 3 OK OK 74 92 71 73 106 C4' A A 4 OK OK 108 125 105 107 139 C4' G A 5 OK OK 141 159 138 140 173 C4' C A 6 OK OK 175 190 172 174 204 C4' U A 7 OK OK 206 221 203 205 234 C4' C A 8 OK OK 236 251 233 235 265 C4' A A 9 OK OK 267 284 264 266 298 C4' A A 10 OK OK 300 317 297 299 331 C4' C A 11 OK OK 333 348 330 332 362 C4' U A 12 OK OK 364 379 361 363 392 C4' C A 13 OK OK 394 409 391 393 423 C4' U A 14 OK OK 425 440 422 424 453 C4' C A 15 OK OK 455 470 452 454 484 C4' C A 16 OK OK 486 501 483 485 515 C4' C A 17 OK OK 517 532 514 516 546 C4' C A 18 OK OK 548 563 545 547 577 C4' C A 19 OK OK 579 594 576 578 608 C4' C A 20 OK OK 610 625 607 609 639 C4' C A 21 OK OK 641 656 638 640 670 C4' U A 22 OK OK 672 687 669 671 700 C4' U A 23 OK OK 702 717 699 701 730 C4' U A 24 OK OK 732 747 729 731 760 C4' U A 25 OK OK 762 777 759 761 790 C4' C A 26 OK OK 792 807 789 791 821 C4' C A 27 OK OK 823 838 820 822 852 C4' G A 28 OK OK 854 872 851 853 886 C4' A A 29 OK OK 888 905 885 887 919 C4' G A 30 OK OK 921 939 918 920 953 C4' G A 31 OK OK 955 973 952 954 987 C4' G A 32 OK OK 989 1007 986 988 1021 C4' U A 33 OK OK 1023 1038 1020 1022 1051 C4' C A 34 OK OK 1053 1068 1050 1052 1082 C4' A A 35 OK OK 1084 1101 1081 1083 1115 C4' U A 36 OK OK 1117 1132 1114 1116 1145 C4' C A 37 OK OK 1147 1162 1144 1146 1176 C4' G A 38 OK OK 1178 1196 1175 1177 1210 C4' G A 39 OK OK 1212 1230 1209 1211 1244 C4' A A 40 OK OK 1246 1263 1243 1245 1277 C4' A A 41 OK OK 1279 1296 1276 1278 1310 C4' C A 42 OK OK 1312 1327 1309 1311 1341 C4' C A 43 OK OK 1343 1358 1340 1342 1372 C4' A A 44 OK OK 1374 1391 1371 1373 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 1 OK OK 1 21 22 3 37 C5' G A 2 OK OK 36 56 57 38 71 C5' G A 3 OK OK 70 90 91 72 105 C5' A A 4 OK OK 104 123 124 106 138 C5' G A 5 OK OK 137 157 158 139 172 C5' C A 6 OK OK 171 188 189 173 203 C5' U A 7 OK OK 202 219 220 204 233 C5' C A 8 OK OK 232 249 250 234 264 C5' A A 9 OK OK 263 282 283 265 297 C5' A A 10 OK OK 296 315 316 298 330 C5' C A 11 OK OK 329 346 347 331 361 C5' U A 12 OK OK 360 377 378 362 391 C5' C A 13 OK OK 390 407 408 392 422 C5' U A 14 OK OK 421 438 439 423 452 C5' C A 15 OK OK 451 468 469 453 483 C5' C A 16 OK OK 482 499 500 484 514 C5' C A 17 OK OK 513 530 531 515 545 C5' C A 18 OK OK 544 561 562 546 576 C5' C A 19 OK OK 575 592 593 577 607 C5' C A 20 OK OK 606 623 624 608 638 C5' C A 21 OK OK 637 654 655 639 669 C5' U A 22 OK OK 668 685 686 670 699 C5' U A 23 OK OK 698 715 716 700 729 C5' U A 24 OK OK 728 745 746 730 759 C5' U A 25 OK OK 758 775 776 760 789 C5' C A 26 OK OK 788 805 806 790 820 C5' C A 27 OK OK 819 836 837 821 851 C5' G A 28 OK OK 850 870 871 852 885 C5' A A 29 OK OK 884 903 904 886 918 C5' G A 30 OK OK 917 937 938 919 952 C5' G A 31 OK OK 951 971 972 953 986 C5' G A 32 OK OK 985 1005 1006 987 1020 C5' U A 33 OK OK 1019 1036 1037 1021 1050 C5' C A 34 OK OK 1049 1066 1067 1051 1081 C5' A A 35 OK OK 1080 1099 1100 1082 1114 C5' U A 36 OK OK 1113 1130 1131 1115 1144 C5' C A 37 OK OK 1143 1160 1161 1145 1175 C5' G A 38 OK OK 1174 1194 1195 1176 1209 C5' G A 39 OK OK 1208 1228 1229 1210 1243 C5' A A 40 OK OK 1242 1261 1262 1244 1276 C5' A A 41 OK OK 1275 1294 1295 1277 1309 C5' C A 42 OK OK 1308 1325 1326 1310 1340 C5' C A 43 OK OK 1339 1356 1357 1341 1371 C5' A A 44 OK OK 1370 1389 1390 1372 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 2 distorted distorted 6 34 35 36 67 P G A 3 distorted distorted 41 68 69 70 101 P A A 4 distorted distorted 75 102 103 104 134 P G A 5 distorted distorted 109 135 136 137 168 P C A 6 distorted distorted 142 169 170 171 199 P U A 7 distorted distorted 176 200 201 202 229 P C A 8 distorted distorted 207 230 231 232 260 P A A 9 distorted distorted 237 261 262 263 293 P A A 10 distorted distorted 268 294 295 296 326 P C A 11 distorted distorted 301 327 328 329 357 P U A 12 distorted distorted 334 358 359 360 387 P C A 13 distorted distorted 365 388 389 390 418 P U A 14 distorted distorted 395 419 420 421 448 P C A 15 distorted distorted 426 449 450 451 479 P C A 16 distorted distorted 456 480 481 482 510 P C A 17 distorted distorted 487 511 512 513 541 P C A 18 distorted distorted 518 542 543 544 572 P C A 19 distorted distorted 549 573 574 575 603 P C A 20 distorted distorted 580 604 605 606 634 P C A 21 distorted distorted 611 635 636 637 665 P U A 22 distorted distorted 642 666 667 668 695 P U A 23 distorted distorted 673 696 697 698 725 P U A 24 distorted distorted 703 726 727 728 755 P U A 25 distorted distorted 733 756 757 758 785 P C A 26 distorted distorted 763 786 787 788 816 P C A 27 distorted distorted 793 817 818 819 847 P G A 28 distorted distorted 824 848 849 850 881 P A A 29 distorted distorted 855 882 883 884 914 P G A 30 distorted distorted 889 915 916 917 948 P G A 31 distorted distorted 922 949 950 951 982 P G A 32 distorted distorted 956 983 984 985 1016 P U A 33 distorted distorted 990 1017 1018 1019 1046 P C A 34 distorted distorted 1024 1047 1048 1049 1077 P A A 35 distorted distorted 1054 1078 1079 1080 1110 P U A 36 distorted distorted 1085 1111 1112 1113 1140 P C A 37 distorted distorted 1118 1141 1142 1143 1171 P G A 38 distorted distorted 1148 1172 1173 1174 1205 P G A 39 distorted distorted 1179 1206 1207 1208 1239 P A A 40 distorted distorted 1213 1240 1241 1242 1272 P A A 41 distorted distorted 1247 1273 1274 1275 1305 P C A 42 distorted distorted 1280 1306 1307 1308 1336 P C A 43 distorted distorted 1313 1337 1338 1339 1367 P A A 44 distorted distorted 1344 1368 1369 1370 ---------------------------------------------------------------------------------