ID code: '1YMO' 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' C A 4 alpha beta 107 127 113 110 143 C1' U A 5 alpha beta 138 158 144 141 173 C1' G A 6 alpha beta 168 191 174 171 207 C1' U A 7 alpha beta 202 222 208 205 237 C1' U A 8 alpha beta 232 252 238 235 267 C1' U A 9 alpha beta 262 282 268 265 297 C1' U A 10 alpha beta 292 312 298 295 327 C1' U A 11 alpha beta 322 342 328 325 357 C1' C A 12 alpha beta 352 372 358 355 388 C1' U A 13 alpha beta 383 403 389 386 418 C1' C A 14 alpha beta 413 433 419 416 449 C1' G A 15 alpha beta 444 467 450 447 483 C1' C A 16 alpha beta 478 498 484 481 514 C1' U A 17 alpha beta 509 529 515 512 544 C1' G A 18 alpha beta 539 562 545 542 578 C1' A A 19 alpha beta 573 595 579 576 611 C1' C A 20 alpha beta 606 626 612 609 642 C1' U A 21 alpha beta 637 657 643 640 672 C1' U A 22 alpha beta 667 687 673 670 702 C1' U A 23 alpha beta 697 717 703 700 732 C1' C A 24 alpha beta 727 747 733 730 763 C1' A A 25 alpha beta 758 780 764 761 796 C1' G A 26 alpha beta 791 814 797 794 830 C1' C A 27 alpha beta 825 845 831 828 861 C1' C A 28 alpha beta 856 876 862 859 892 C1' C A 29 alpha beta 887 907 893 890 923 C1' C A 30 alpha beta 918 938 924 921 954 C1' A A 31 alpha beta 949 971 955 952 987 C1' A A 32 alpha beta 982 1004 988 985 1020 C1' A A 33 alpha beta 1015 1037 1021 1018 1053 C1' C A 34 alpha beta 1048 1068 1054 1051 1084 C1' A A 35 alpha beta 1079 1101 1085 1082 1117 C1' A A 36 alpha beta 1112 1134 1118 1115 1150 C1' A A 37 alpha beta 1145 1167 1151 1148 1183 C1' A A 38 alpha beta 1178 1200 1184 1181 1216 C1' A A 39 alpha beta 1211 1233 1217 1214 1249 C1' A A 40 alpha beta 1244 1266 1250 1247 1282 C1' G A 41 alpha beta 1277 1300 1283 1280 1316 C1' U A 42 alpha beta 1311 1331 1317 1314 1346 C1' C A 43 alpha beta 1341 1361 1347 1344 1377 C1' A A 44 alpha beta 1372 1394 1378 1375 1410 C1' G A 45 alpha beta 1405 1428 1411 1408 1444 C1' C A 46 alpha beta 1439 1459 1445 1442 1475 C1' A A 47 alpha beta 1470 1493 1476 1473 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' C A 4 OK OK 112 108 125 111 141 C2' U A 5 OK OK 143 139 156 142 171 C2' G A 6 OK OK 173 169 189 172 205 C2' U A 7 OK OK 207 203 220 206 235 C2' U A 8 OK OK 237 233 250 236 265 C2' U A 9 OK OK 267 263 280 266 295 C2' U A 10 OK OK 297 293 310 296 325 C2' U A 11 OK OK 327 323 340 326 355 C2' C A 12 OK OK 357 353 370 356 386 C2' U A 13 OK OK 388 384 401 387 416 C2' C A 14 OK OK 418 414 431 417 447 C2' G A 15 OK OK 449 445 465 448 481 C2' C A 16 OK OK 483 479 496 482 512 C2' U A 17 OK OK 514 510 527 513 542 C2' G A 18 OK OK 544 540 560 543 576 C2' A A 19 OK OK 578 574 593 577 609 C2' C A 20 OK OK 611 607 624 610 640 C2' U A 21 OK OK 642 638 655 641 670 C2' U A 22 OK OK 672 668 685 671 700 C2' U A 23 OK OK 702 698 715 701 730 C2' C A 24 OK OK 732 728 745 731 761 C2' A A 25 OK OK 763 759 778 762 794 C2' G A 26 OK OK 796 792 812 795 828 C2' C A 27 OK OK 830 826 843 829 859 C2' C A 28 OK OK 861 857 874 860 890 C2' C A 29 OK OK 892 888 905 891 921 C2' C A 30 OK OK 923 919 936 922 952 C2' A A 31 OK OK 954 950 969 953 985 C2' A A 32 OK OK 987 983 1002 986 1018 C2' A A 33 OK OK 1020 1016 1035 1019 1051 C2' C A 34 OK OK 1053 1049 1066 1052 1082 C2' A A 35 OK OK 1084 1080 1099 1083 1115 C2' A A 36 OK OK 1117 1113 1132 1116 1148 C2' A A 37 OK OK 1150 1146 1165 1149 1181 C2' A A 38 OK OK 1183 1179 1198 1182 1214 C2' A A 39 OK OK 1216 1212 1231 1215 1247 C2' A A 40 OK OK 1249 1245 1264 1248 1280 C2' G A 41 OK OK 1282 1278 1298 1281 1314 C2' U A 42 OK OK 1316 1312 1329 1315 1344 C2' C A 43 OK OK 1346 1342 1359 1345 1375 C2' A A 44 OK OK 1377 1373 1392 1376 1408 C2' G A 45 OK OK 1410 1406 1426 1409 1442 C2' C A 46 OK OK 1444 1440 1457 1443 1473 C2' A A 47 OK OK 1475 1471 1491 1474 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' C A 4 OK OK 106 124 109 110 139 C3' U A 5 OK OK 137 155 140 141 169 C3' G A 6 OK OK 167 188 170 171 203 C3' U A 7 OK OK 201 219 204 205 233 C3' U A 8 OK OK 231 249 234 235 263 C3' U A 9 OK OK 261 279 264 265 293 C3' U A 10 OK OK 291 309 294 295 323 C3' U A 11 OK OK 321 339 324 325 353 C3' C A 12 OK OK 351 369 354 355 384 C3' U A 13 OK OK 382 400 385 386 414 C3' C A 14 OK OK 412 430 415 416 445 C3' G A 15 OK OK 443 464 446 447 479 C3' C A 16 OK OK 477 495 480 481 510 C3' U A 17 OK OK 508 526 511 512 540 C3' G A 18 OK OK 538 559 541 542 574 C3' A A 19 OK OK 572 592 575 576 607 C3' C A 20 OK OK 605 623 608 609 638 C3' U A 21 OK OK 636 654 639 640 668 C3' U A 22 OK OK 666 684 669 670 698 C3' U A 23 OK OK 696 714 699 700 728 C3' C A 24 OK OK 726 744 729 730 759 C3' A A 25 OK OK 757 777 760 761 792 C3' G A 26 OK OK 790 811 793 794 826 C3' C A 27 OK OK 824 842 827 828 857 C3' C A 28 OK OK 855 873 858 859 888 C3' C A 29 OK OK 886 904 889 890 919 C3' C A 30 OK OK 917 935 920 921 950 C3' A A 31 OK OK 948 968 951 952 983 C3' A A 32 OK OK 981 1001 984 985 1016 C3' A A 33 OK OK 1014 1034 1017 1018 1049 C3' C A 34 OK OK 1047 1065 1050 1051 1080 C3' A A 35 OK OK 1078 1098 1081 1082 1113 C3' A A 36 OK OK 1111 1131 1114 1115 1146 C3' A A 37 OK OK 1144 1164 1147 1148 1179 C3' A A 38 OK OK 1177 1197 1180 1181 1212 C3' A A 39 OK OK 1210 1230 1213 1214 1245 C3' A A 40 OK OK 1243 1263 1246 1247 1278 C3' G A 41 OK OK 1276 1297 1279 1280 1312 C3' U A 42 OK OK 1310 1328 1313 1314 1342 C3' C A 43 OK OK 1340 1358 1343 1344 1373 C3' A A 44 OK OK 1371 1391 1374 1375 1406 C3' G A 45 OK OK 1404 1425 1407 1408 1440 C3' C A 46 OK OK 1438 1456 1441 1442 1471 C3' A A 47 OK OK 1469 1489 1472 1473 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' C A 4 OK OK 108 123 105 107 137 C4' U A 5 OK OK 139 154 136 138 167 C4' G A 6 OK OK 169 187 166 168 201 C4' U A 7 OK OK 203 218 200 202 231 C4' U A 8 OK OK 233 248 230 232 261 C4' U A 9 OK OK 263 278 260 262 291 C4' U A 10 OK OK 293 308 290 292 321 C4' U A 11 OK OK 323 338 320 322 351 C4' C A 12 OK OK 353 368 350 352 382 C4' U A 13 OK OK 384 399 381 383 412 C4' C A 14 OK OK 414 429 411 413 443 C4' G A 15 OK OK 445 463 442 444 477 C4' C A 16 OK OK 479 494 476 478 508 C4' U A 17 OK OK 510 525 507 509 538 C4' G A 18 OK OK 540 558 537 539 572 C4' A A 19 OK OK 574 591 571 573 605 C4' C A 20 OK OK 607 622 604 606 636 C4' U A 21 OK OK 638 653 635 637 666 C4' U A 22 OK OK 668 683 665 667 696 C4' U A 23 OK OK 698 713 695 697 726 C4' C A 24 OK OK 728 743 725 727 757 C4' A A 25 OK OK 759 776 756 758 790 C4' G A 26 OK OK 792 810 789 791 824 C4' C A 27 OK OK 826 841 823 825 855 C4' C A 28 OK OK 857 872 854 856 886 C4' C A 29 OK OK 888 903 885 887 917 C4' C A 30 OK OK 919 934 916 918 948 C4' A A 31 OK OK 950 967 947 949 981 C4' A A 32 OK OK 983 1000 980 982 1014 C4' A A 33 OK OK 1016 1033 1013 1015 1047 C4' C A 34 OK OK 1049 1064 1046 1048 1078 C4' A A 35 OK OK 1080 1097 1077 1079 1111 C4' A A 36 OK OK 1113 1130 1110 1112 1144 C4' A A 37 OK OK 1146 1163 1143 1145 1177 C4' A A 38 OK OK 1179 1196 1176 1178 1210 C4' A A 39 OK OK 1212 1229 1209 1211 1243 C4' A A 40 OK OK 1245 1262 1242 1244 1276 C4' G A 41 OK OK 1278 1296 1275 1277 1310 C4' U A 42 OK OK 1312 1327 1309 1311 1340 C4' C A 43 OK OK 1342 1357 1339 1341 1371 C4' A A 44 OK OK 1373 1390 1370 1372 1404 C4' G A 45 OK OK 1406 1424 1403 1405 1438 C4' C A 46 OK OK 1440 1455 1437 1439 1469 C4' A A 47 OK OK 1471 1488 1468 1470 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' C A 4 OK OK 104 121 122 106 136 C5' U A 5 OK OK 135 152 153 137 166 C5' G A 6 OK OK 165 185 186 167 200 C5' U A 7 OK OK 199 216 217 201 230 C5' U A 8 OK OK 229 246 247 231 260 C5' U A 9 OK OK 259 276 277 261 290 C5' U A 10 OK OK 289 306 307 291 320 C5' U A 11 OK OK 319 336 337 321 350 C5' C A 12 OK OK 349 366 367 351 381 C5' U A 13 OK OK 380 397 398 382 411 C5' C A 14 OK OK 410 427 428 412 442 C5' G A 15 OK OK 441 461 462 443 476 C5' C A 16 OK OK 475 492 493 477 507 C5' U A 17 OK OK 506 523 524 508 537 C5' G A 18 OK OK 536 556 557 538 571 C5' A A 19 OK OK 570 589 590 572 604 C5' C A 20 OK OK 603 620 621 605 635 C5' U A 21 OK OK 634 651 652 636 665 C5' U A 22 OK OK 664 681 682 666 695 C5' U A 23 OK OK 694 711 712 696 725 C5' C A 24 OK OK 724 741 742 726 756 C5' A A 25 OK OK 755 774 775 757 789 C5' G A 26 OK OK 788 808 809 790 823 C5' C A 27 OK OK 822 839 840 824 854 C5' C A 28 OK OK 853 870 871 855 885 C5' C A 29 OK OK 884 901 902 886 916 C5' C A 30 OK OK 915 932 933 917 947 C5' A A 31 OK OK 946 965 966 948 980 C5' A A 32 OK OK 979 998 999 981 1013 C5' A A 33 OK OK 1012 1031 1032 1014 1046 C5' C A 34 OK OK 1045 1062 1063 1047 1077 C5' A A 35 OK OK 1076 1095 1096 1078 1110 C5' A A 36 OK OK 1109 1128 1129 1111 1143 C5' A A 37 OK OK 1142 1161 1162 1144 1176 C5' A A 38 OK OK 1175 1194 1195 1177 1209 C5' A A 39 OK OK 1208 1227 1228 1210 1242 C5' A A 40 OK OK 1241 1260 1261 1243 1275 C5' G A 41 OK OK 1274 1294 1295 1276 1309 C5' U A 42 OK OK 1308 1325 1326 1310 1339 C5' C A 43 OK OK 1338 1355 1356 1340 1370 C5' A A 44 OK OK 1369 1388 1389 1371 1403 C5' G A 45 OK OK 1402 1422 1423 1404 1437 C5' C A 46 OK OK 1436 1453 1454 1438 1468 C5' A A 47 OK OK 1467 1486 1487 1469 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 C A 4 distorted distorted 75 102 103 104 132 P U A 5 distorted distorted 109 133 134 135 162 P G A 6 distorted distorted 140 163 164 165 196 P U A 7 distorted distorted 170 197 198 199 226 P U A 8 distorted distorted 204 227 228 229 256 P U A 9 distorted distorted 234 257 258 259 286 P U A 10 distorted distorted 264 287 288 289 316 P U A 11 distorted distorted 294 317 318 319 346 P C A 12 distorted distorted 324 347 348 349 377 P U A 13 distorted distorted 354 378 379 380 407 P C A 14 distorted distorted 385 408 409 410 438 P G A 15 distorted distorted 415 439 440 441 472 P C A 16 distorted distorted 446 473 474 475 503 P U A 17 distorted distorted 480 504 505 506 533 P G A 18 distorted distorted 511 534 535 536 567 P A A 19 distorted distorted 541 568 569 570 600 P C A 20 distorted distorted 575 601 602 603 631 P U A 21 distorted distorted 608 632 633 634 661 P U A 22 distorted distorted 639 662 663 664 691 P U A 23 distorted distorted 669 692 693 694 721 P C A 24 distorted distorted 699 722 723 724 752 P A A 25 distorted distorted 729 753 754 755 785 P G A 26 distorted distorted 760 786 787 788 819 P C A 27 distorted distorted 793 820 821 822 850 P C A 28 distorted distorted 827 851 852 853 881 P C A 29 distorted distorted 858 882 883 884 912 P C A 30 distorted distorted 889 913 914 915 943 P A A 31 distorted distorted 920 944 945 946 976 P A A 32 distorted distorted 951 977 978 979 1009 P A A 33 distorted distorted 984 1010 1011 1012 1042 P C A 34 distorted distorted 1017 1043 1044 1045 1073 P A A 35 distorted distorted 1050 1074 1075 1076 1106 P A A 36 distorted distorted 1081 1107 1108 1109 1139 P A A 37 distorted distorted 1114 1140 1141 1142 1172 P A A 38 distorted distorted 1147 1173 1174 1175 1205 P A A 39 distorted distorted 1180 1206 1207 1208 1238 P A A 40 distorted distorted 1213 1239 1240 1241 1271 P G A 41 distorted distorted 1246 1272 1273 1274 1305 P U A 42 distorted distorted 1279 1306 1307 1308 1335 P C A 43 distorted distorted 1313 1336 1337 1338 1366 P A A 44 distorted distorted 1343 1367 1368 1369 1399 P G A 45 distorted distorted 1374 1400 1401 1402 1433 P C A 46 distorted distorted 1407 1434 1435 1436 1464 P A A 47 distorted distorted 1441 1465 1466 1467 ---------------------------------------------------------------------------------