ID code: '4XNR' 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' --------------------------------------------------------------------------------- 12 C1' G X 13 beta 7 13 10 35 C1' G X 14 beta 30 36 33 58 C1' G X 15 beta 53 59 56 81 C1' A X 16 beta 76 82 79 103 C1' A X 17 beta 98 104 101 125 C1' G X 18 beta 120 126 123 148 C1' A X 19 beta 143 149 146 170 C1' U X 20 beta 165 171 168 190 C1' A X 21 beta 185 191 188 212 C1' U X 22 beta 207 213 210 232 C1' A X 23 beta 227 233 230 254 C1' A X 24 beta 249 255 252 276 C1' U X 25 beta 271 277 274 296 C1' C X 26 beta 291 297 294 316 C1' C X 27 beta 311 317 314 336 C1' U X 28 beta 331 337 334 356 C1' A X 29 beta 351 357 354 378 C1' A X 30 beta 373 379 376 400 C1' U X 31 beta 395 401 398 420 C1' G X 32 beta 415 421 418 443 C1' A X 33 beta 438 444 441 465 C1' U X 34 beta 460 466 463 485 C1' A X 35 beta 480 486 483 507 C1' U X 36 beta 502 508 505 527 C1' G X 37 beta 522 528 525 550 C1' G X 38 beta 545 551 548 573 C1' U X 39 beta 568 574 571 593 C1' U X 40 beta 588 594 591 613 C1' U X 41 beta 608 614 611 633 C1' G X 42 beta 628 634 631 656 C1' G X 43 beta 651 657 654 679 C1' G X 44 beta 674 680 677 702 C1' A X 45 beta 697 703 700 724 C1' G X 46 beta 719 725 722 747 C1' U X 47 beta 742 748 745 767 C1' U X 48 beta 762 768 765 787 C1' U X 49 beta 782 788 785 807 C1' C X 50 beta 802 808 805 827 C1' U X 51 beta 822 828 825 847 C1' A X 52 beta 842 848 845 869 C1' C X 53 beta 864 870 867 889 C1' C X 54 beta 884 890 887 909 C1' A X 55 beta 904 910 907 931 C1' A X 56 beta 926 932 929 953 C1' G X 57 beta 948 954 951 976 C1' A X 58 beta 971 977 974 998 C1' G X 59 beta 993 999 996 1021 C1' C X 60 beta 1016 1022 1019 1041 C1' C X 61 beta 1036 1042 1039 1061 C1' U X 62 beta 1056 1062 1059 1081 C1' U X 63 beta 1076 1082 1079 1101 C1' A X 64 beta 1096 1102 1099 1123 C1' A X 65 beta 1118 1124 1121 1145 C1' A X 66 beta 1140 1146 1143 1167 C1' C X 67 beta 1162 1168 1165 1187 C1' U X 68 beta 1182 1188 1185 1207 C1' C X 69 beta 1202 1208 1205 1227 C1' U X 70 beta 1222 1228 1225 1247 C1' U X 71 beta 1242 1248 1245 1267 C1' G X 72 beta 1262 1268 1265 1290 C1' A X 73 beta 1285 1291 1288 1312 C1' U X 74 beta 1307 1313 1310 1332 C1' U X 75 beta 1327 1333 1330 1352 C1' A X 76 beta 1347 1353 1350 1374 C1' U X 77 beta 1369 1375 1372 1394 C1' C X 78 beta 1389 1395 1392 1414 C1' U X 79 beta 1409 1415 1412 1434 C1' U X 80 beta 1429 1435 1432 1454 C1' C X 81 beta 1449 1455 1452 1474 C1' C X 82 beta 1469 1475 1472 1494 C1' C X 83 beta 1489 1495 1492 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' G X 13 OK 12 8 11 33 C2' G X 14 OK 35 31 34 56 C2' G X 15 OK 58 54 57 79 C2' A X 16 OK 81 77 80 101 C2' A X 17 OK 103 99 102 123 C2' G X 18 OK 125 121 124 146 C2' A X 19 OK 148 144 147 168 C2' U X 20 OK 170 166 169 188 C2' A X 21 OK 190 186 189 210 C2' U X 22 OK 212 208 211 230 C2' A X 23 OK 232 228 231 252 C2' A X 24 OK 254 250 253 274 C2' U X 25 OK 276 272 275 294 C2' C X 26 OK 296 292 295 314 C2' C X 27 OK 316 312 315 334 C2' U X 28 OK 336 332 335 354 C2' A X 29 OK 356 352 355 376 C2' A X 30 OK 378 374 377 398 C2' U X 31 OK 400 396 399 418 C2' G X 32 OK 420 416 419 441 C2' A X 33 OK 443 439 442 463 C2' U X 34 OK 465 461 464 483 C2' A X 35 OK 485 481 484 505 C2' U X 36 OK 507 503 506 525 C2' G X 37 OK 527 523 526 548 C2' G X 38 OK 550 546 549 571 C2' U X 39 OK 573 569 572 591 C2' U X 40 OK 593 589 592 611 C2' U X 41 OK 613 609 612 631 C2' G X 42 OK 633 629 632 654 C2' G X 43 OK 656 652 655 677 C2' G X 44 OK 679 675 678 700 C2' A X 45 OK 702 698 701 722 C2' G X 46 OK 724 720 723 745 C2' U X 47 OK 747 743 746 765 C2' U X 48 OK 767 763 766 785 C2' U X 49 OK 787 783 786 805 C2' C X 50 OK 807 803 806 825 C2' U X 51 OK 827 823 826 845 C2' A X 52 OK 847 843 846 867 C2' C X 53 OK 869 865 868 887 C2' C X 54 OK 889 885 888 907 C2' A X 55 OK 909 905 908 929 C2' A X 56 OK 931 927 930 951 C2' G X 57 OK 953 949 952 974 C2' A X 58 OK 976 972 975 996 C2' G X 59 OK 998 994 997 1019 C2' C X 60 OK 1021 1017 1020 1039 C2' C X 61 OK 1041 1037 1040 1059 C2' U X 62 OK 1061 1057 1060 1079 C2' U X 63 OK 1081 1077 1080 1099 C2' A X 64 OK 1101 1097 1100 1121 C2' A X 65 OK 1123 1119 1122 1143 C2' A X 66 OK 1145 1141 1144 1165 C2' C X 67 OK 1167 1163 1166 1185 C2' U X 68 OK 1187 1183 1186 1205 C2' C X 69 OK 1207 1203 1206 1225 C2' U X 70 OK 1227 1223 1226 1245 C2' U X 71 OK 1247 1243 1246 1265 C2' G X 72 OK 1267 1263 1266 1288 C2' A X 73 OK 1290 1286 1289 1310 C2' U X 74 OK 1312 1308 1311 1330 C2' U X 75 OK 1332 1328 1331 1350 C2' A X 76 OK 1352 1348 1351 1372 C2' U X 77 OK 1374 1370 1373 1392 C2' C X 78 OK 1394 1390 1393 1412 C2' U X 79 OK 1414 1410 1413 1432 C2' U X 80 OK 1434 1430 1433 1452 C2' C X 81 OK 1454 1450 1453 1472 C2' C X 82 OK 1474 1470 1473 1492 C2' C X 83 OK 1494 1490 1493 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' G X 13 OK 6 9 10 31 C3' G X 14 OK 29 32 33 54 C3' G X 15 OK 52 55 56 77 C3' A X 16 OK 75 78 79 99 C3' A X 17 OK 97 100 101 121 C3' G X 18 OK 119 122 123 144 C3' A X 19 OK 142 145 146 166 C3' U X 20 OK 164 167 168 186 C3' A X 21 OK 184 187 188 208 C3' U X 22 OK 206 209 210 228 C3' A X 23 OK 226 229 230 250 C3' A X 24 OK 248 251 252 272 C3' U X 25 OK 270 273 274 292 C3' C X 26 OK 290 293 294 312 C3' C X 27 OK 310 313 314 332 C3' U X 28 OK 330 333 334 352 C3' A X 29 OK 350 353 354 374 C3' A X 30 OK 372 375 376 396 C3' U X 31 OK 394 397 398 416 C3' G X 32 OK 414 417 418 439 C3' A X 33 OK 437 440 441 461 C3' U X 34 OK 459 462 463 481 C3' A X 35 OK 479 482 483 503 C3' U X 36 OK 501 504 505 523 C3' G X 37 OK 521 524 525 546 C3' G X 38 OK 544 547 548 569 C3' U X 39 OK 567 570 571 589 C3' U X 40 OK 587 590 591 609 C3' U X 41 OK 607 610 611 629 C3' G X 42 OK 627 630 631 652 C3' G X 43 OK 650 653 654 675 C3' G X 44 OK 673 676 677 698 C3' A X 45 OK 696 699 700 720 C3' G X 46 OK 718 721 722 743 C3' U X 47 OK 741 744 745 763 C3' U X 48 OK 761 764 765 783 C3' U X 49 OK 781 784 785 803 C3' C X 50 OK 801 804 805 823 C3' U X 51 OK 821 824 825 843 C3' A X 52 OK 841 844 845 865 C3' C X 53 OK 863 866 867 885 C3' C X 54 OK 883 886 887 905 C3' A X 55 OK 903 906 907 927 C3' A X 56 OK 925 928 929 949 C3' G X 57 OK 947 950 951 972 C3' A X 58 OK 970 973 974 994 C3' G X 59 OK 992 995 996 1017 C3' C X 60 OK 1015 1018 1019 1037 C3' C X 61 OK 1035 1038 1039 1057 C3' U X 62 OK 1055 1058 1059 1077 C3' U X 63 OK 1075 1078 1079 1097 C3' A X 64 OK 1095 1098 1099 1119 C3' A X 65 OK 1117 1120 1121 1141 C3' A X 66 OK 1139 1142 1143 1163 C3' C X 67 OK 1161 1164 1165 1183 C3' U X 68 OK 1181 1184 1185 1203 C3' C X 69 OK 1201 1204 1205 1223 C3' U X 70 OK 1221 1224 1225 1243 C3' U X 71 OK 1241 1244 1245 1263 C3' G X 72 OK 1261 1264 1265 1286 C3' A X 73 OK 1284 1287 1288 1308 C3' U X 74 OK 1306 1309 1310 1328 C3' U X 75 OK 1326 1329 1330 1348 C3' A X 76 OK 1346 1349 1350 1370 C3' U X 77 OK 1368 1371 1372 1390 C3' C X 78 OK 1388 1391 1392 1410 C3' U X 79 OK 1408 1411 1412 1430 C3' U X 80 OK 1428 1431 1432 1450 C3' C X 81 OK 1448 1451 1452 1470 C3' C X 82 OK 1468 1471 1472 1490 C3' C X 83 OK 1488 1491 1492 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' G X 13 OK 8 5 7 29 C4' G X 14 OK 31 28 30 52 C4' G X 15 OK 54 51 53 75 C4' A X 16 OK 77 74 76 97 C4' A X 17 OK 99 96 98 119 C4' G X 18 OK 121 118 120 142 C4' A X 19 OK 144 141 143 164 C4' U X 20 OK 166 163 165 184 C4' A X 21 OK 186 183 185 206 C4' U X 22 OK 208 205 207 226 C4' A X 23 OK 228 225 227 248 C4' A X 24 OK 250 247 249 270 C4' U X 25 OK 272 269 271 290 C4' C X 26 OK 292 289 291 310 C4' C X 27 OK 312 309 311 330 C4' U X 28 OK 332 329 331 350 C4' A X 29 OK 352 349 351 372 C4' A X 30 OK 374 371 373 394 C4' U X 31 OK 396 393 395 414 C4' G X 32 OK 416 413 415 437 C4' A X 33 OK 439 436 438 459 C4' U X 34 OK 461 458 460 479 C4' A X 35 OK 481 478 480 501 C4' U X 36 OK 503 500 502 521 C4' G X 37 OK 523 520 522 544 C4' G X 38 OK 546 543 545 567 C4' U X 39 OK 569 566 568 587 C4' U X 40 OK 589 586 588 607 C4' U X 41 OK 609 606 608 627 C4' G X 42 OK 629 626 628 650 C4' G X 43 OK 652 649 651 673 C4' G X 44 OK 675 672 674 696 C4' A X 45 OK 698 695 697 718 C4' G X 46 OK 720 717 719 741 C4' U X 47 OK 743 740 742 761 C4' U X 48 OK 763 760 762 781 C4' U X 49 OK 783 780 782 801 C4' C X 50 OK 803 800 802 821 C4' U X 51 OK 823 820 822 841 C4' A X 52 OK 843 840 842 863 C4' C X 53 OK 865 862 864 883 C4' C X 54 OK 885 882 884 903 C4' A X 55 OK 905 902 904 925 C4' A X 56 OK 927 924 926 947 C4' G X 57 OK 949 946 948 970 C4' A X 58 OK 972 969 971 992 C4' G X 59 OK 994 991 993 1015 C4' C X 60 OK 1017 1014 1016 1035 C4' C X 61 OK 1037 1034 1036 1055 C4' U X 62 OK 1057 1054 1056 1075 C4' U X 63 OK 1077 1074 1076 1095 C4' A X 64 OK 1097 1094 1096 1117 C4' A X 65 OK 1119 1116 1118 1139 C4' A X 66 OK 1141 1138 1140 1161 C4' C X 67 OK 1163 1160 1162 1181 C4' U X 68 OK 1183 1180 1182 1201 C4' C X 69 OK 1203 1200 1202 1221 C4' U X 70 OK 1223 1220 1222 1241 C4' U X 71 OK 1243 1240 1242 1261 C4' G X 72 OK 1263 1260 1262 1284 C4' A X 73 OK 1286 1283 1285 1306 C4' U X 74 OK 1308 1305 1307 1326 C4' U X 75 OK 1328 1325 1327 1346 C4' A X 76 OK 1348 1345 1347 1368 C4' U X 77 OK 1370 1367 1369 1388 C4' C X 78 OK 1390 1387 1389 1408 C4' U X 79 OK 1410 1407 1409 1428 C4' U X 80 OK 1430 1427 1429 1448 C4' C X 81 OK 1450 1447 1449 1468 C4' C X 82 OK 1470 1467 1469 1488 C4' C X 83 OK 1490 1487 1489 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' G X 13 4 6 28 C5' G X 14 27 29 51 C5' G X 15 50 52 74 C5' A X 16 73 75 96 C5' A X 17 95 97 118 C5' G X 18 117 119 141 C5' A X 19 140 142 163 C5' U X 20 162 164 183 C5' A X 21 182 184 205 C5' U X 22 204 206 225 C5' A X 23 224 226 247 C5' A X 24 246 248 269 C5' U X 25 268 270 289 C5' C X 26 288 290 309 C5' C X 27 308 310 329 C5' U X 28 328 330 349 C5' A X 29 348 350 371 C5' A X 30 370 372 393 C5' U X 31 392 394 413 C5' G X 32 412 414 436 C5' A X 33 435 437 458 C5' U X 34 457 459 478 C5' A X 35 477 479 500 C5' U X 36 499 501 520 C5' G X 37 519 521 543 C5' G X 38 542 544 566 C5' U X 39 565 567 586 C5' U X 40 585 587 606 C5' U X 41 605 607 626 C5' G X 42 625 627 649 C5' G X 43 648 650 672 C5' G X 44 671 673 695 C5' A X 45 694 696 717 C5' G X 46 716 718 740 C5' U X 47 739 741 760 C5' U X 48 759 761 780 C5' U X 49 779 781 800 C5' C X 50 799 801 820 C5' U X 51 819 821 840 C5' A X 52 839 841 862 C5' C X 53 861 863 882 C5' C X 54 881 883 902 C5' A X 55 901 903 924 C5' A X 56 923 925 946 C5' G X 57 945 947 969 C5' A X 58 968 970 991 C5' G X 59 990 992 1014 C5' C X 60 1013 1015 1034 C5' C X 61 1033 1035 1054 C5' U X 62 1053 1055 1074 C5' U X 63 1073 1075 1094 C5' A X 64 1093 1095 1116 C5' A X 65 1115 1117 1138 C5' A X 66 1137 1139 1160 C5' C X 67 1159 1161 1180 C5' U X 68 1179 1181 1200 C5' C X 69 1199 1201 1220 C5' U X 70 1219 1221 1240 C5' U X 71 1239 1241 1260 C5' G X 72 1259 1261 1283 C5' A X 73 1282 1284 1305 C5' U X 74 1304 1306 1325 C5' U X 75 1324 1326 1345 C5' A X 76 1344 1346 1367 C5' U X 77 1366 1368 1387 C5' C X 78 1386 1388 1407 C5' U X 79 1406 1408 1427 C5' U X 80 1426 1428 1447 C5' C X 81 1446 1448 1467 C5' C X 82 1466 1468 1487 C5' C X 83 1486 1488 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P G X 13 distorted distorted 2 3 4 24 P G X 14 distorted distorted 9 25 26 27 47 P G X 15 distorted distorted 32 48 49 50 70 P A X 16 distorted distorted 55 71 72 73 92 P A X 17 distorted distorted 78 93 94 95 114 P G X 18 distorted distorted 100 115 116 117 137 P A X 19 distorted distorted 122 138 139 140 159 P U X 20 distorted distorted 145 160 161 162 179 P A X 21 distorted distorted 167 180 181 182 201 P U X 22 distorted distorted 187 202 203 204 221 P A X 23 distorted distorted 209 222 223 224 243 P A X 24 distorted distorted 229 244 245 246 265 P U X 25 distorted distorted 251 266 267 268 285 P C X 26 distorted distorted 273 286 287 288 305 P C X 27 distorted distorted 293 306 307 308 325 P U X 28 distorted distorted 313 326 327 328 345 P A X 29 distorted distorted 333 346 347 348 367 P A X 30 distorted distorted 353 368 369 370 389 P U X 31 distorted distorted 375 390 391 392 409 P G X 32 distorted distorted 397 410 411 412 432 P A X 33 distorted distorted 417 433 434 435 454 P U X 34 distorted distorted 440 455 456 457 474 P A X 35 distorted distorted 462 475 476 477 496 P U X 36 distorted distorted 482 497 498 499 516 P G X 37 distorted distorted 504 517 518 519 539 P G X 38 distorted distorted 524 540 541 542 562 P U X 39 distorted distorted 547 563 564 565 582 P U X 40 distorted distorted 570 583 584 585 602 P U X 41 distorted distorted 590 603 604 605 622 P G X 42 distorted distorted 610 623 624 625 645 P G X 43 distorted distorted 630 646 647 648 668 P G X 44 distorted distorted 653 669 670 671 691 P A X 45 distorted distorted 676 692 693 694 713 P G X 46 distorted distorted 699 714 715 716 736 P U X 47 distorted distorted 721 737 738 739 756 P U X 48 distorted distorted 744 757 758 759 776 P U X 49 distorted distorted 764 777 778 779 796 P C X 50 distorted distorted 784 797 798 799 816 P U X 51 distorted distorted 804 817 818 819 836 P A X 52 distorted distorted 824 837 838 839 858 P C X 53 distorted distorted 844 859 860 861 878 P C X 54 distorted distorted 866 879 880 881 898 P A X 55 distorted distorted 886 899 900 901 920 P A X 56 distorted distorted 906 921 922 923 942 P G X 57 distorted distorted 928 943 944 945 965 P A X 58 distorted distorted 950 966 967 968 987 P G X 59 distorted distorted 973 988 989 990 1010 P C X 60 distorted distorted 995 1011 1012 1013 1030 P C X 61 distorted distorted 1018 1031 1032 1033 1050 P U X 62 distorted distorted 1038 1051 1052 1053 1070 P U X 63 distorted distorted 1058 1071 1072 1073 1090 P A X 64 distorted distorted 1078 1091 1092 1093 1112 P A X 65 distorted distorted 1098 1113 1114 1115 1134 P A X 66 distorted distorted 1120 1135 1136 1137 1156 P C X 67 distorted distorted 1142 1157 1158 1159 1176 P U X 68 distorted distorted 1164 1177 1178 1179 1196 P C X 69 distorted distorted 1184 1197 1198 1199 1216 P U X 70 distorted distorted 1204 1217 1218 1219 1236 P U X 71 distorted distorted 1224 1237 1238 1239 1256 P G X 72 distorted distorted 1244 1257 1258 1259 1279 P A X 73 distorted distorted 1264 1280 1281 1282 1301 P U X 74 distorted distorted 1287 1302 1303 1304 1321 P U X 75 distorted distorted 1309 1322 1323 1324 1341 P A X 76 distorted distorted 1329 1342 1343 1344 1363 P U X 77 distorted distorted 1349 1364 1365 1366 1383 P C X 78 distorted distorted 1371 1384 1385 1386 1403 P U X 79 distorted distorted 1391 1404 1405 1406 1423 P U X 80 distorted distorted 1411 1424 1425 1426 1443 P C X 81 distorted distorted 1431 1444 1445 1446 1463 P C X 82 distorted distorted 1451 1464 1465 1466 1483 P C X 83 distorted distorted 1471 1484 1485 1486 ---------------------------------------------------------------------------------