ID code: '2MTJ' 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' A A 3 alpha beta 73 95 79 76 111 C1' C A 4 alpha beta 106 126 112 109 142 C1' C A 5 alpha beta 137 157 143 140 173 C1' U A 6 alpha beta 168 188 174 171 203 C1' C A 7 alpha beta 198 218 204 201 234 C1' C A 8 alpha beta 229 249 235 232 265 C1' C A 9 alpha beta 260 280 266 263 296 C1' G A 10 alpha beta 291 314 297 294 330 C1' U A 11 alpha beta 325 345 331 328 360 C1' C A 12 alpha beta 355 375 361 358 391 C1' C A 13 alpha beta 386 406 392 389 422 C1' U A 14 alpha beta 417 437 423 420 452 C1' U A 15 alpha beta 447 467 453 450 482 C1' G A 16 alpha beta 477 500 483 480 516 C1' G A 17 alpha beta 511 534 517 514 550 C1' A A 18 alpha beta 545 567 551 548 583 C1' C A 19 alpha beta 578 598 584 581 614 C1' G A 20 alpha beta 609 632 615 612 648 C1' G A 21 alpha beta 643 666 649 646 682 C1' U A 22 alpha beta 677 697 683 680 712 C1' C A 23 alpha beta 707 727 713 710 743 C1' G A 24 alpha beta 738 761 744 741 777 C1' A A 25 alpha beta 772 794 778 775 810 C1' G A 26 alpha beta 805 828 811 808 844 C1' C A 27 alpha beta 839 859 845 842 875 C1' G A 28 alpha beta 870 893 876 873 909 C1' A A 29 alpha beta 904 926 910 907 942 C1' A A 30 alpha beta 937 959 943 940 975 C1' A A 31 alpha beta 970 992 976 973 1008 C1' G A 32 alpha beta 1003 1026 1009 1006 1042 C1' C A 33 alpha beta 1037 1057 1043 1040 1073 C1' U A 34 alpha beta 1068 1088 1074 1071 1103 C1' U A 35 alpha beta 1098 1118 1104 1101 1133 C1' G A 36 alpha beta 1128 1151 1134 1131 1167 C1' U A 37 alpha beta 1162 1182 1168 1165 1197 C1' G A 38 alpha beta 1192 1215 1198 1195 1231 C1' A A 39 alpha beta 1226 1248 1232 1229 1264 C1' U A 40 alpha beta 1259 1279 1265 1262 1294 C1' U A 41 alpha beta 1289 1309 1295 1292 1324 C1' G A 42 alpha beta 1319 1342 1325 1322 1358 C1' G A 43 alpha beta 1353 1376 1359 1356 1392 C1' U A 44 alpha beta 1387 1407 1393 1390 1422 C1' C A 45 alpha beta 1417 1437 1423 1420 1453 C1' C A 46 alpha beta 1448 1468 1454 1451 1484 C1' G A 47 alpha beta 1479 1503 1485 1482 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' A A 3 OK OK 78 74 93 77 109 C2' C A 4 OK OK 111 107 124 110 140 C2' C A 5 OK OK 142 138 155 141 171 C2' U A 6 OK OK 173 169 186 172 201 C2' C A 7 OK OK 203 199 216 202 232 C2' C A 8 OK OK 234 230 247 233 263 C2' C A 9 OK OK 265 261 278 264 294 C2' G A 10 OK OK 296 292 312 295 328 C2' U A 11 OK OK 330 326 343 329 358 C2' C A 12 OK OK 360 356 373 359 389 C2' C A 13 OK OK 391 387 404 390 420 C2' U A 14 OK OK 422 418 435 421 450 C2' U A 15 OK OK 452 448 465 451 480 C2' G A 16 OK OK 482 478 498 481 514 C2' G A 17 OK OK 516 512 532 515 548 C2' A A 18 OK OK 550 546 565 549 581 C2' C A 19 OK OK 583 579 596 582 612 C2' G A 20 OK OK 614 610 630 613 646 C2' G A 21 OK OK 648 644 664 647 680 C2' U A 22 OK OK 682 678 695 681 710 C2' C A 23 OK OK 712 708 725 711 741 C2' G A 24 OK OK 743 739 759 742 775 C2' A A 25 OK OK 777 773 792 776 808 C2' G A 26 OK OK 810 806 826 809 842 C2' C A 27 OK OK 844 840 857 843 873 C2' G A 28 OK OK 875 871 891 874 907 C2' A A 29 OK OK 909 905 924 908 940 C2' A A 30 OK OK 942 938 957 941 973 C2' A A 31 OK OK 975 971 990 974 1006 C2' G A 32 OK OK 1008 1004 1024 1007 1040 C2' C A 33 OK OK 1042 1038 1055 1041 1071 C2' U A 34 OK OK 1073 1069 1086 1072 1101 C2' U A 35 OK OK 1103 1099 1116 1102 1131 C2' G A 36 OK OK 1133 1129 1149 1132 1165 C2' U A 37 OK OK 1167 1163 1180 1166 1195 C2' G A 38 OK OK 1197 1193 1213 1196 1229 C2' A A 39 OK OK 1231 1227 1246 1230 1262 C2' U A 40 OK OK 1264 1260 1277 1263 1292 C2' U A 41 OK OK 1294 1290 1307 1293 1322 C2' G A 42 OK OK 1324 1320 1340 1323 1356 C2' G A 43 OK OK 1358 1354 1374 1357 1390 C2' U A 44 OK OK 1392 1388 1405 1391 1420 C2' C A 45 OK OK 1422 1418 1435 1421 1451 C2' C A 46 OK OK 1453 1449 1466 1452 1482 C2' G A 47 OK OK 1484 1480 1501 1483 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' A A 3 OK OK 72 92 75 76 107 C3' C A 4 OK OK 105 123 108 109 138 C3' C A 5 OK OK 136 154 139 140 169 C3' U A 6 OK OK 167 185 170 171 199 C3' C A 7 OK OK 197 215 200 201 230 C3' C A 8 OK OK 228 246 231 232 261 C3' C A 9 OK OK 259 277 262 263 292 C3' G A 10 OK OK 290 311 293 294 326 C3' U A 11 OK OK 324 342 327 328 356 C3' C A 12 OK OK 354 372 357 358 387 C3' C A 13 OK OK 385 403 388 389 418 C3' U A 14 OK OK 416 434 419 420 448 C3' U A 15 OK OK 446 464 449 450 478 C3' G A 16 OK OK 476 497 479 480 512 C3' G A 17 OK OK 510 531 513 514 546 C3' A A 18 OK OK 544 564 547 548 579 C3' C A 19 OK OK 577 595 580 581 610 C3' G A 20 OK OK 608 629 611 612 644 C3' G A 21 OK OK 642 663 645 646 678 C3' U A 22 OK OK 676 694 679 680 708 C3' C A 23 OK OK 706 724 709 710 739 C3' G A 24 OK OK 737 758 740 741 773 C3' A A 25 OK OK 771 791 774 775 806 C3' G A 26 OK OK 804 825 807 808 840 C3' C A 27 OK OK 838 856 841 842 871 C3' G A 28 OK OK 869 890 872 873 905 C3' A A 29 OK OK 903 923 906 907 938 C3' A A 30 OK OK 936 956 939 940 971 C3' A A 31 OK OK 969 989 972 973 1004 C3' G A 32 OK OK 1002 1023 1005 1006 1038 C3' C A 33 OK OK 1036 1054 1039 1040 1069 C3' U A 34 OK OK 1067 1085 1070 1071 1099 C3' U A 35 OK OK 1097 1115 1100 1101 1129 C3' G A 36 OK OK 1127 1148 1130 1131 1163 C3' U A 37 OK OK 1161 1179 1164 1165 1193 C3' G A 38 OK OK 1191 1212 1194 1195 1227 C3' A A 39 OK OK 1225 1245 1228 1229 1260 C3' U A 40 OK OK 1258 1276 1261 1262 1290 C3' U A 41 OK OK 1288 1306 1291 1292 1320 C3' G A 42 OK OK 1318 1339 1321 1322 1354 C3' G A 43 OK OK 1352 1373 1355 1356 1388 C3' U A 44 OK OK 1386 1404 1389 1390 1418 C3' C A 45 OK OK 1416 1434 1419 1420 1449 C3' C A 46 OK OK 1447 1465 1450 1451 1480 C3' G A 47 OK OK 1478 1499 1481 1482 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' A A 3 OK OK 74 91 71 73 105 C4' C A 4 OK OK 107 122 104 106 136 C4' C A 5 OK OK 138 153 135 137 167 C4' U A 6 OK OK 169 184 166 168 197 C4' C A 7 OK OK 199 214 196 198 228 C4' C A 8 OK OK 230 245 227 229 259 C4' C A 9 OK OK 261 276 258 260 290 C4' G A 10 OK OK 292 310 289 291 324 C4' U A 11 OK OK 326 341 323 325 354 C4' C A 12 OK OK 356 371 353 355 385 C4' C A 13 OK OK 387 402 384 386 416 C4' U A 14 OK OK 418 433 415 417 446 C4' U A 15 OK OK 448 463 445 447 476 C4' G A 16 OK OK 478 496 475 477 510 C4' G A 17 OK OK 512 530 509 511 544 C4' A A 18 OK OK 546 563 543 545 577 C4' C A 19 OK OK 579 594 576 578 608 C4' G A 20 OK OK 610 628 607 609 642 C4' G A 21 OK OK 644 662 641 643 676 C4' U A 22 OK OK 678 693 675 677 706 C4' C A 23 OK OK 708 723 705 707 737 C4' G A 24 OK OK 739 757 736 738 771 C4' A A 25 OK OK 773 790 770 772 804 C4' G A 26 OK OK 806 824 803 805 838 C4' C A 27 OK OK 840 855 837 839 869 C4' G A 28 OK OK 871 889 868 870 903 C4' A A 29 OK OK 905 922 902 904 936 C4' A A 30 OK OK 938 955 935 937 969 C4' A A 31 OK OK 971 988 968 970 1002 C4' G A 32 OK OK 1004 1022 1001 1003 1036 C4' C A 33 OK OK 1038 1053 1035 1037 1067 C4' U A 34 OK OK 1069 1084 1066 1068 1097 C4' U A 35 OK OK 1099 1114 1096 1098 1127 C4' G A 36 OK OK 1129 1147 1126 1128 1161 C4' U A 37 OK OK 1163 1178 1160 1162 1191 C4' G A 38 OK OK 1193 1211 1190 1192 1225 C4' A A 39 OK OK 1227 1244 1224 1226 1258 C4' U A 40 OK OK 1260 1275 1257 1259 1288 C4' U A 41 OK OK 1290 1305 1287 1289 1318 C4' G A 42 OK OK 1320 1338 1317 1319 1352 C4' G A 43 OK OK 1354 1372 1351 1353 1386 C4' U A 44 OK OK 1388 1403 1385 1387 1416 C4' C A 45 OK OK 1418 1433 1415 1417 1447 C4' C A 46 OK OK 1449 1464 1446 1448 1478 C4' G A 47 OK OK 1480 1498 1477 1479 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' A A 3 OK OK 70 89 90 72 104 C5' C A 4 OK OK 103 120 121 105 135 C5' C A 5 OK OK 134 151 152 136 166 C5' U A 6 OK OK 165 182 183 167 196 C5' C A 7 OK OK 195 212 213 197 227 C5' C A 8 OK OK 226 243 244 228 258 C5' C A 9 OK OK 257 274 275 259 289 C5' G A 10 OK OK 288 308 309 290 323 C5' U A 11 OK OK 322 339 340 324 353 C5' C A 12 OK OK 352 369 370 354 384 C5' C A 13 OK OK 383 400 401 385 415 C5' U A 14 OK OK 414 431 432 416 445 C5' U A 15 OK OK 444 461 462 446 475 C5' G A 16 OK OK 474 494 495 476 509 C5' G A 17 OK OK 508 528 529 510 543 C5' A A 18 OK OK 542 561 562 544 576 C5' C A 19 OK OK 575 592 593 577 607 C5' G A 20 OK OK 606 626 627 608 641 C5' G A 21 OK OK 640 660 661 642 675 C5' U A 22 OK OK 674 691 692 676 705 C5' C A 23 OK OK 704 721 722 706 736 C5' G A 24 OK OK 735 755 756 737 770 C5' A A 25 OK OK 769 788 789 771 803 C5' G A 26 OK OK 802 822 823 804 837 C5' C A 27 OK OK 836 853 854 838 868 C5' G A 28 OK OK 867 887 888 869 902 C5' A A 29 OK OK 901 920 921 903 935 C5' A A 30 OK OK 934 953 954 936 968 C5' A A 31 OK OK 967 986 987 969 1001 C5' G A 32 OK OK 1000 1020 1021 1002 1035 C5' C A 33 OK OK 1034 1051 1052 1036 1066 C5' U A 34 OK OK 1065 1082 1083 1067 1096 C5' U A 35 OK OK 1095 1112 1113 1097 1126 C5' G A 36 OK OK 1125 1145 1146 1127 1160 C5' U A 37 OK OK 1159 1176 1177 1161 1190 C5' G A 38 OK OK 1189 1209 1210 1191 1224 C5' A A 39 OK OK 1223 1242 1243 1225 1257 C5' U A 40 OK OK 1256 1273 1274 1258 1287 C5' U A 41 OK OK 1286 1303 1304 1288 1317 C5' G A 42 OK OK 1316 1336 1337 1318 1351 C5' G A 43 OK OK 1350 1370 1371 1352 1385 C5' U A 44 OK OK 1384 1401 1402 1386 1415 C5' C A 45 OK OK 1414 1431 1432 1416 1446 C5' C A 46 OK OK 1445 1462 1463 1447 1477 C5' G A 47 OK OK 1476 1496 1497 1478 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 2 distorted distorted 6 34 35 36 67 P A A 3 distorted distorted 41 68 69 70 100 P C A 4 distorted distorted 75 101 102 103 131 P C A 5 distorted distorted 108 132 133 134 162 P U A 6 distorted distorted 139 163 164 165 192 P C A 7 distorted distorted 170 193 194 195 223 P C A 8 distorted distorted 200 224 225 226 254 P C A 9 distorted distorted 231 255 256 257 285 P G A 10 distorted distorted 262 286 287 288 319 P U A 11 distorted distorted 293 320 321 322 349 P C A 12 distorted distorted 327 350 351 352 380 P C A 13 distorted distorted 357 381 382 383 411 P U A 14 distorted distorted 388 412 413 414 441 P U A 15 distorted distorted 419 442 443 444 471 P G A 16 distorted distorted 449 472 473 474 505 P G A 17 distorted distorted 479 506 507 508 539 P A A 18 distorted distorted 513 540 541 542 572 P C A 19 distorted distorted 547 573 574 575 603 P G A 20 distorted distorted 580 604 605 606 637 P G A 21 distorted distorted 611 638 639 640 671 P U A 22 distorted distorted 645 672 673 674 701 P C A 23 distorted distorted 679 702 703 704 732 P G A 24 distorted distorted 709 733 734 735 766 P A A 25 distorted distorted 740 767 768 769 799 P G A 26 distorted distorted 774 800 801 802 833 P C A 27 distorted distorted 807 834 835 836 864 P G A 28 distorted distorted 841 865 866 867 898 P A A 29 distorted distorted 872 899 900 901 931 P A A 30 distorted distorted 906 932 933 934 964 P A A 31 distorted distorted 939 965 966 967 997 P G A 32 distorted distorted 972 998 999 1000 1031 P C A 33 distorted distorted 1005 1032 1033 1034 1062 P U A 34 distorted distorted 1039 1063 1064 1065 1092 P U A 35 distorted distorted 1070 1093 1094 1095 1122 P G A 36 distorted distorted 1100 1123 1124 1125 1156 P U A 37 distorted distorted 1130 1157 1158 1159 1186 P G A 38 distorted distorted 1164 1187 1188 1189 1220 P A A 39 distorted distorted 1194 1221 1222 1223 1253 P U A 40 distorted distorted 1228 1254 1255 1256 1283 P U A 41 distorted distorted 1261 1284 1285 1286 1313 P G A 42 distorted distorted 1291 1314 1315 1316 1347 P G A 43 distorted distorted 1321 1348 1349 1350 1381 P U A 44 distorted distorted 1355 1382 1383 1384 1411 P C A 45 distorted distorted 1389 1412 1413 1414 1442 P C A 46 distorted distorted 1419 1443 1444 1445 1473 P G A 47 distorted distorted 1450 1474 1475 1476 ---------------------------------------------------------------------------------