ID code: '2F4X' 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 A 1 alpha beta 8 32 14 11 48 C1' G A 2 alpha beta 43 66 49 46 82 C1' U A 3 alpha beta 77 97 83 80 112 C1' U A 4 alpha beta 107 127 113 110 142 C1' G A 5 alpha beta 137 160 143 140 176 C1' C A 6 alpha beta 171 191 177 174 207 C1' U A 7 alpha beta 202 222 208 205 237 C1' G A 8 alpha beta 232 255 238 235 271 C1' A A 9 alpha beta 266 288 272 269 304 C1' A A 10 alpha beta 299 321 305 302 337 C1' G A 11 alpha beta 332 355 338 335 371 C1' C A 12 alpha beta 366 386 372 369 402 C1' G A 13 alpha beta 397 420 403 400 436 C1' C A 14 alpha beta 431 451 437 434 467 C1' G A 15 alpha beta 462 485 468 465 501 C1' C A 16 alpha beta 496 516 502 499 532 C1' A A 17 alpha beta 527 549 533 530 565 C1' C A 18 alpha beta 560 580 566 563 596 C1' G A 19 alpha beta 591 614 597 594 630 C1' G A 20 alpha beta 625 648 631 628 664 C1' C A 21 alpha beta 659 679 665 662 695 C1' A A 22 alpha beta 690 712 696 693 728 C1' A A 23 alpha beta 723 745 729 726 761 C1' C A 24 alpha beta 756 777 762 759 795 C1' G B 25 alpha beta 790 814 796 793 830 C1' G B 26 alpha beta 825 848 831 828 864 C1' U B 27 alpha beta 859 879 865 862 894 C1' U B 28 alpha beta 889 909 895 892 924 C1' G B 29 alpha beta 919 942 925 922 958 C1' C B 30 alpha beta 953 973 959 956 989 C1' U B 31 alpha beta 984 1004 990 987 1019 C1' G B 32 alpha beta 1014 1037 1020 1017 1053 C1' A B 33 alpha beta 1048 1070 1054 1051 1086 C1' A B 34 alpha beta 1081 1103 1087 1084 1119 C1' G B 35 alpha beta 1114 1137 1120 1117 1153 C1' C B 36 alpha beta 1148 1168 1154 1151 1184 C1' G B 37 alpha beta 1179 1202 1185 1182 1218 C1' C B 38 alpha beta 1213 1233 1219 1216 1249 C1' G B 39 alpha beta 1244 1267 1250 1247 1283 C1' C B 40 alpha beta 1278 1298 1284 1281 1314 C1' A B 41 alpha beta 1309 1331 1315 1312 1347 C1' C B 42 alpha beta 1342 1362 1348 1345 1378 C1' G B 43 alpha beta 1373 1396 1379 1376 1412 C1' G B 44 alpha beta 1407 1430 1413 1410 1446 C1' C B 45 alpha beta 1441 1461 1447 1444 1477 C1' A B 46 alpha beta 1472 1494 1478 1475 1510 C1' A B 47 alpha beta 1505 1527 1511 1508 1543 C1' C B 48 alpha beta 1538 1559 1544 1541 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 11 C2' G A 1 OK OK 13 9 30 12 46 C2' G A 2 OK OK 48 44 64 47 80 C2' U A 3 OK OK 82 78 95 81 110 C2' U A 4 OK OK 112 108 125 111 140 C2' G A 5 OK OK 142 138 158 141 174 C2' C A 6 OK OK 176 172 189 175 205 C2' U A 7 OK OK 207 203 220 206 235 C2' G A 8 OK OK 237 233 253 236 269 C2' A A 9 OK OK 271 267 286 270 302 C2' A A 10 OK OK 304 300 319 303 335 C2' G A 11 OK OK 337 333 353 336 369 C2' C A 12 OK OK 371 367 384 370 400 C2' G A 13 OK OK 402 398 418 401 434 C2' C A 14 OK OK 436 432 449 435 465 C2' G A 15 OK OK 467 463 483 466 499 C2' C A 16 OK OK 501 497 514 500 530 C2' A A 17 OK OK 532 528 547 531 563 C2' C A 18 OK OK 565 561 578 564 594 C2' G A 19 OK OK 596 592 612 595 628 C2' G A 20 OK OK 630 626 646 629 662 C2' C A 21 OK OK 664 660 677 663 693 C2' A A 22 OK OK 695 691 710 694 726 C2' A A 23 OK OK 728 724 743 727 759 C2' C A 24 OK OK 761 757 775 760 793 C2' G B 25 OK OK 795 791 812 794 828 C2' G B 26 OK OK 830 826 846 829 862 C2' U B 27 OK OK 864 860 877 863 892 C2' U B 28 OK OK 894 890 907 893 922 C2' G B 29 OK OK 924 920 940 923 956 C2' C B 30 OK OK 958 954 971 957 987 C2' U B 31 OK OK 989 985 1002 988 1017 C2' G B 32 OK OK 1019 1015 1035 1018 1051 C2' A B 33 OK OK 1053 1049 1068 1052 1084 C2' A B 34 OK OK 1086 1082 1101 1085 1117 C2' G B 35 OK OK 1119 1115 1135 1118 1151 C2' C B 36 OK OK 1153 1149 1166 1152 1182 C2' G B 37 OK OK 1184 1180 1200 1183 1216 C2' C B 38 OK OK 1218 1214 1231 1217 1247 C2' G B 39 OK OK 1249 1245 1265 1248 1281 C2' C B 40 OK OK 1283 1279 1296 1282 1312 C2' A B 41 OK OK 1314 1310 1329 1313 1345 C2' C B 42 OK OK 1347 1343 1360 1346 1376 C2' G B 43 OK OK 1378 1374 1394 1377 1410 C2' G B 44 OK OK 1412 1408 1428 1411 1444 C2' C B 45 OK OK 1446 1442 1459 1445 1475 C2' A B 46 OK OK 1477 1473 1492 1476 1508 C2' A B 47 OK OK 1510 1506 1525 1509 1541 C2' C B 48 OK OK 1543 1539 1557 1542 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 9 C3' G A 1 OK OK 7 29 10 11 44 C3' G A 2 OK OK 42 63 45 46 78 C3' U A 3 OK OK 76 94 79 80 108 C3' U A 4 OK OK 106 124 109 110 138 C3' G A 5 OK OK 136 157 139 140 172 C3' C A 6 OK OK 170 188 173 174 203 C3' U A 7 OK OK 201 219 204 205 233 C3' G A 8 OK OK 231 252 234 235 267 C3' A A 9 OK OK 265 285 268 269 300 C3' A A 10 OK OK 298 318 301 302 333 C3' G A 11 OK OK 331 352 334 335 367 C3' C A 12 OK OK 365 383 368 369 398 C3' G A 13 OK OK 396 417 399 400 432 C3' C A 14 OK OK 430 448 433 434 463 C3' G A 15 OK OK 461 482 464 465 497 C3' C A 16 OK OK 495 513 498 499 528 C3' A A 17 OK OK 526 546 529 530 561 C3' C A 18 OK OK 559 577 562 563 592 C3' G A 19 OK OK 590 611 593 594 626 C3' G A 20 OK OK 624 645 627 628 660 C3' C A 21 OK OK 658 676 661 662 691 C3' A A 22 OK OK 689 709 692 693 724 C3' A A 23 OK OK 722 742 725 726 757 C3' C A 24 OK OK 755 773 758 759 791 C3' G B 25 OK OK 789 811 792 793 826 C3' G B 26 OK OK 824 845 827 828 860 C3' U B 27 OK OK 858 876 861 862 890 C3' U B 28 OK OK 888 906 891 892 920 C3' G B 29 OK OK 918 939 921 922 954 C3' C B 30 OK OK 952 970 955 956 985 C3' U B 31 OK OK 983 1001 986 987 1015 C3' G B 32 OK OK 1013 1034 1016 1017 1049 C3' A B 33 OK OK 1047 1067 1050 1051 1082 C3' A B 34 OK OK 1080 1100 1083 1084 1115 C3' G B 35 OK OK 1113 1134 1116 1117 1149 C3' C B 36 OK OK 1147 1165 1150 1151 1180 C3' G B 37 OK OK 1178 1199 1181 1182 1214 C3' C B 38 OK OK 1212 1230 1215 1216 1245 C3' G B 39 OK OK 1243 1264 1246 1247 1279 C3' C B 40 OK OK 1277 1295 1280 1281 1310 C3' A B 41 OK OK 1308 1328 1311 1312 1343 C3' C B 42 OK OK 1341 1359 1344 1345 1374 C3' G B 43 OK OK 1372 1393 1375 1376 1408 C3' G B 44 OK OK 1406 1427 1409 1410 1442 C3' C B 45 OK OK 1440 1458 1443 1444 1473 C3' A B 46 OK OK 1471 1491 1474 1475 1506 C3' A B 47 OK OK 1504 1524 1507 1508 1539 C3' C B 48 OK OK 1537 1555 1540 1541 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 7 C4' G A 1 OK OK 9 28 6 8 42 C4' G A 2 OK OK 44 62 41 43 76 C4' U A 3 OK OK 78 93 75 77 106 C4' U A 4 OK OK 108 123 105 107 136 C4' G A 5 OK OK 138 156 135 137 170 C4' C A 6 OK OK 172 187 169 171 201 C4' U A 7 OK OK 203 218 200 202 231 C4' G A 8 OK OK 233 251 230 232 265 C4' A A 9 OK OK 267 284 264 266 298 C4' A A 10 OK OK 300 317 297 299 331 C4' G A 11 OK OK 333 351 330 332 365 C4' C A 12 OK OK 367 382 364 366 396 C4' G A 13 OK OK 398 416 395 397 430 C4' C A 14 OK OK 432 447 429 431 461 C4' G A 15 OK OK 463 481 460 462 495 C4' C A 16 OK OK 497 512 494 496 526 C4' A A 17 OK OK 528 545 525 527 559 C4' C A 18 OK OK 561 576 558 560 590 C4' G A 19 OK OK 592 610 589 591 624 C4' G A 20 OK OK 626 644 623 625 658 C4' C A 21 OK OK 660 675 657 659 689 C4' A A 22 OK OK 691 708 688 690 722 C4' A A 23 OK OK 724 741 721 723 755 C4' C A 24 OK OK 757 772 754 756 789 C4' G B 25 OK OK 791 810 788 790 824 C4' G B 26 OK OK 826 844 823 825 858 C4' U B 27 OK OK 860 875 857 859 888 C4' U B 28 OK OK 890 905 887 889 918 C4' G B 29 OK OK 920 938 917 919 952 C4' C B 30 OK OK 954 969 951 953 983 C4' U B 31 OK OK 985 1000 982 984 1013 C4' G B 32 OK OK 1015 1033 1012 1014 1047 C4' A B 33 OK OK 1049 1066 1046 1048 1080 C4' A B 34 OK OK 1082 1099 1079 1081 1113 C4' G B 35 OK OK 1115 1133 1112 1114 1147 C4' C B 36 OK OK 1149 1164 1146 1148 1178 C4' G B 37 OK OK 1180 1198 1177 1179 1212 C4' C B 38 OK OK 1214 1229 1211 1213 1243 C4' G B 39 OK OK 1245 1263 1242 1244 1277 C4' C B 40 OK OK 1279 1294 1276 1278 1308 C4' A B 41 OK OK 1310 1327 1307 1309 1341 C4' C B 42 OK OK 1343 1358 1340 1342 1372 C4' G B 43 OK OK 1374 1392 1371 1373 1406 C4' G B 44 OK OK 1408 1426 1405 1407 1440 C4' C B 45 OK OK 1442 1457 1439 1441 1471 C4' A B 46 OK OK 1473 1490 1470 1472 1504 C4' A B 47 OK OK 1506 1523 1503 1505 1537 C4' C B 48 OK OK 1539 1554 1536 1538 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 6 C5' G A 1 OK OK 5 26 27 7 41 C5' G A 2 OK OK 40 60 61 42 75 C5' U A 3 OK OK 74 91 92 76 105 C5' U A 4 OK OK 104 121 122 106 135 C5' G A 5 OK OK 134 154 155 136 169 C5' C A 6 OK OK 168 185 186 170 200 C5' U A 7 OK OK 199 216 217 201 230 C5' G A 8 OK OK 229 249 250 231 264 C5' A A 9 OK OK 263 282 283 265 297 C5' A A 10 OK OK 296 315 316 298 330 C5' G A 11 OK OK 329 349 350 331 364 C5' C A 12 OK OK 363 380 381 365 395 C5' G A 13 OK OK 394 414 415 396 429 C5' C A 14 OK OK 428 445 446 430 460 C5' G A 15 OK OK 459 479 480 461 494 C5' C A 16 OK OK 493 510 511 495 525 C5' A A 17 OK OK 524 543 544 526 558 C5' C A 18 OK OK 557 574 575 559 589 C5' G A 19 OK OK 588 608 609 590 623 C5' G A 20 OK OK 622 642 643 624 657 C5' C A 21 OK OK 656 673 674 658 688 C5' A A 22 OK OK 687 706 707 689 721 C5' A A 23 OK OK 720 739 740 722 754 C5' C A 24 OK OK 753 770 771 755 788 C5' G B 25 OK OK 787 808 809 789 823 C5' G B 26 OK OK 822 842 843 824 857 C5' U B 27 OK OK 856 873 874 858 887 C5' U B 28 OK OK 886 903 904 888 917 C5' G B 29 OK OK 916 936 937 918 951 C5' C B 30 OK OK 950 967 968 952 982 C5' U B 31 OK OK 981 998 999 983 1012 C5' G B 32 OK OK 1011 1031 1032 1013 1046 C5' A B 33 OK OK 1045 1064 1065 1047 1079 C5' A B 34 OK OK 1078 1097 1098 1080 1112 C5' G B 35 OK OK 1111 1131 1132 1113 1146 C5' C B 36 OK OK 1145 1162 1163 1147 1177 C5' G B 37 OK OK 1176 1196 1197 1178 1211 C5' C B 38 OK OK 1210 1227 1228 1212 1242 C5' G B 39 OK OK 1241 1261 1262 1243 1276 C5' C B 40 OK OK 1275 1292 1293 1277 1307 C5' A B 41 OK OK 1306 1325 1326 1308 1340 C5' C B 42 OK OK 1339 1356 1357 1341 1371 C5' G B 43 OK OK 1370 1390 1391 1372 1405 C5' G B 44 OK OK 1404 1424 1425 1406 1439 C5' C B 45 OK OK 1438 1455 1456 1440 1470 C5' A B 46 OK OK 1469 1488 1489 1471 1503 C5' A B 47 OK OK 1502 1521 1522 1504 1536 C5' C B 48 OK OK 1535 1552 1553 1537 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2 P G A 1 OK OK 3 4 5 37 P G A 2 distorted distorted 10 38 39 40 71 P U A 3 distorted distorted 45 72 73 74 101 P U A 4 distorted distorted 79 102 103 104 131 P G A 5 distorted distorted 109 132 133 134 165 P C A 6 distorted distorted 139 166 167 168 196 P U A 7 distorted distorted 173 197 198 199 226 P G A 8 distorted distorted 204 227 228 229 260 P A A 9 distorted distorted 234 261 262 263 293 P A A 10 distorted distorted 268 294 295 296 326 P G A 11 distorted distorted 301 327 328 329 360 P C A 12 distorted distorted 334 361 362 363 391 P G A 13 distorted distorted 368 392 393 394 425 P C A 14 distorted distorted 399 426 427 428 456 P G A 15 distorted distorted 433 457 458 459 490 P C A 16 distorted distorted 464 491 492 493 521 P A A 17 distorted distorted 498 522 523 524 554 P C A 18 distorted distorted 529 555 556 557 585 P G A 19 distorted distorted 562 586 587 588 619 P G A 20 distorted distorted 593 620 621 622 653 P C A 21 distorted distorted 627 654 655 656 684 P A A 22 distorted distorted 661 685 686 687 717 P A A 23 distorted distorted 692 718 719 720 750 P C A 24 distorted distorted 725 751 752 753 784 P G B 25 distorted distorted 785 786 787 819 P G B 26 distorted distorted 792 820 821 822 853 P U B 27 distorted distorted 827 854 855 856 883 P U B 28 distorted distorted 861 884 885 886 913 P G B 29 distorted distorted 891 914 915 916 947 P C B 30 distorted distorted 921 948 949 950 978 P U B 31 distorted distorted 955 979 980 981 1008 P G B 32 distorted distorted 986 1009 1010 1011 1042 P A B 33 distorted distorted 1016 1043 1044 1045 1075 P A B 34 distorted distorted 1050 1076 1077 1078 1108 P G B 35 distorted distorted 1083 1109 1110 1111 1142 P C B 36 distorted distorted 1116 1143 1144 1145 1173 P G B 37 distorted distorted 1150 1174 1175 1176 1207 P C B 38 distorted distorted 1181 1208 1209 1210 1238 P G B 39 distorted distorted 1215 1239 1240 1241 1272 P C B 40 distorted distorted 1246 1273 1274 1275 1303 P A B 41 distorted distorted 1280 1304 1305 1306 1336 P C B 42 distorted distorted 1311 1337 1338 1339 1367 P G B 43 distorted distorted 1344 1368 1369 1370 1401 P G B 44 distorted distorted 1375 1402 1403 1404 1435 P C B 45 distorted distorted 1409 1436 1437 1438 1466 P A B 46 distorted distorted 1443 1467 1468 1469 1499 P A B 47 distorted distorted 1474 1500 1501 1502 1532 P C B 48 distorted distorted 1507 1533 1534 1535 ---------------------------------------------------------------------------------