ID code: '2AKE' 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 B 1 beta 8 14 11 36 C1' A B 2 beta 31 37 34 58 C1' C B 3 beta 53 59 56 78 C1' C B 4 beta 73 79 76 98 C1' U B 5 beta 93 99 96 118 C1' C B 6 beta 113 119 116 138 C1' G B 7 beta 133 139 136 161 C1' U B 8 beta 156 162 159 181 C1' G B 9 beta 176 182 179 204 C1' G B 10 beta 199 205 202 227 C1' C B 11 beta 222 228 225 247 C1' G B 12 beta 242 248 245 270 C1' C B 13 beta 265 271 268 290 C1' A B 14 beta 285 291 288 312 C1' A B 15 beta 307 313 310 334 C1' U B 16 beta 329 335 332 354 C1' G B 18 beta 349 355 352 377 C1' G B 19 beta 372 378 375 400 C1' U B 20 beta 395 401 398 420 C1' A B 21 beta 415 421 418 442 C1' G B 22 beta 437 443 440 465 C1' C B 23 beta 460 466 463 485 C1' G B 24 beta 480 486 483 508 C1' C B 25 beta 503 509 506 528 C1' G B 26 beta 523 529 526 551 C1' U B 27 beta 546 552 549 571 C1' C B 28 beta 566 572 569 591 C1' U B 29 beta 586 592 589 611 C1' G B 30 beta 606 612 609 634 C1' A B 31 beta 629 635 632 656 C1' C B 32 beta 651 657 654 676 C1' U B 33 beta 671 677 674 696 C1' C B 34 beta 691 697 694 716 C1' C B 35 beta 711 717 714 736 C1' A B 36 beta 731 737 734 758 C1' G B 37 beta 753 759 756 781 C1' A B 38 beta 776 782 779 803 C1' U B 39 beta 798 804 801 823 C1' C B 40 beta 818 824 821 843 C1' A B 41 beta 838 844 841 865 C1' G B 42 beta 860 866 863 888 C1' A B 43 beta 883 889 886 910 C1' A B 44 beta 905 911 908 932 C1' G B 45 beta 927 933 930 955 C1' G B 46 beta 950 956 953 978 C1' U B 47 beta 973 979 976 998 C1' U B 48 beta 993 999 996 1018 C1' G B 49 beta 1013 1019 1016 1041 C1' C B 50 beta 1036 1042 1039 1061 C1' G B 51 beta 1056 1062 1059 1084 C1' U B 52 beta 1079 1085 1082 1104 C1' G B 53 beta 1099 1105 1102 1127 C1' U B 54 beta 1122 1128 1125 1147 C1' U B 55 beta 1142 1148 1145 1167 C1' C B 56 beta 1162 1168 1165 1187 C1' G B 57 beta 1182 1188 1185 1210 C1' A B 58 beta 1205 1211 1208 1232 C1' A B 59 beta 1227 1233 1230 1254 C1' U B 60 beta 1249 1255 1252 1274 C1' C B 61 beta 1269 1275 1272 1294 C1' A B 62 beta 1289 1295 1292 1316 C1' C B 63 beta 1311 1317 1314 1336 C1' G B 64 beta 1331 1337 1334 1359 C1' U B 65 beta 1354 1360 1357 1379 C1' C B 66 beta 1374 1380 1377 1399 C1' G B 67 beta 1394 1400 1397 1422 C1' G B 68 beta 1417 1423 1420 1445 C1' G B 69 beta 1440 1446 1443 1468 C1' G B 70 beta 1463 1469 1466 1491 C1' U B 71 beta 1486 1492 1489 1511 C1' C B 72 beta 1506 1512 1509 1531 C1' A B 73 beta 1526 1532 1529 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 11 C2' G B 1 OK 13 9 12 34 C2' A B 2 OK 36 32 35 56 C2' C B 3 OK 58 54 57 76 C2' C B 4 OK 78 74 77 96 C2' U B 5 OK 98 94 97 116 C2' C B 6 OK 118 114 117 136 C2' G B 7 OK 138 134 137 159 C2' U B 8 OK 161 157 160 179 C2' G B 9 OK 181 177 180 202 C2' G B 10 OK 204 200 203 225 C2' C B 11 OK 227 223 226 245 C2' G B 12 OK 247 243 246 268 C2' C B 13 OK 270 266 269 288 C2' A B 14 OK 290 286 289 310 C2' A B 15 OK 312 308 311 332 C2' U B 16 OK 334 330 333 352 C2' G B 18 OK 354 350 353 375 C2' G B 19 OK 377 373 376 398 C2' U B 20 OK 400 396 399 418 C2' A B 21 OK 420 416 419 440 C2' G B 22 OK 442 438 441 463 C2' C B 23 OK 465 461 464 483 C2' G B 24 OK 485 481 484 506 C2' C B 25 OK 508 504 507 526 C2' G B 26 OK 528 524 527 549 C2' U B 27 OK 551 547 550 569 C2' C B 28 OK 571 567 570 589 C2' U B 29 OK 591 587 590 609 C2' G B 30 OK 611 607 610 632 C2' A B 31 OK 634 630 633 654 C2' C B 32 OK 656 652 655 674 C2' U B 33 OK 676 672 675 694 C2' C B 34 OK 696 692 695 714 C2' C B 35 OK 716 712 715 734 C2' A B 36 OK 736 732 735 756 C2' G B 37 OK 758 754 757 779 C2' A B 38 OK 781 777 780 801 C2' U B 39 OK 803 799 802 821 C2' C B 40 OK 823 819 822 841 C2' A B 41 OK 843 839 842 863 C2' G B 42 OK 865 861 864 886 C2' A B 43 OK 888 884 887 908 C2' A B 44 OK 910 906 909 930 C2' G B 45 OK 932 928 931 953 C2' G B 46 OK 955 951 954 976 C2' U B 47 OK 978 974 977 996 C2' U B 48 OK 998 994 997 1016 C2' G B 49 OK 1018 1014 1017 1039 C2' C B 50 OK 1041 1037 1040 1059 C2' G B 51 OK 1061 1057 1060 1082 C2' U B 52 OK 1084 1080 1083 1102 C2' G B 53 OK 1104 1100 1103 1125 C2' U B 54 OK 1127 1123 1126 1145 C2' U B 55 OK 1147 1143 1146 1165 C2' C B 56 OK 1167 1163 1166 1185 C2' G B 57 OK 1187 1183 1186 1208 C2' A B 58 OK 1210 1206 1209 1230 C2' A B 59 OK 1232 1228 1231 1252 C2' U B 60 OK 1254 1250 1253 1272 C2' C B 61 OK 1274 1270 1273 1292 C2' A B 62 OK 1294 1290 1293 1314 C2' C B 63 OK 1316 1312 1315 1334 C2' G B 64 OK 1336 1332 1335 1357 C2' U B 65 OK 1359 1355 1358 1377 C2' C B 66 OK 1379 1375 1378 1397 C2' G B 67 OK 1399 1395 1398 1420 C2' G B 68 OK 1422 1418 1421 1443 C2' G B 69 OK 1445 1441 1444 1466 C2' G B 70 OK 1468 1464 1467 1489 C2' U B 71 OK 1491 1487 1490 1509 C2' C B 72 OK 1511 1507 1510 1529 C2' A B 73 OK 1531 1527 1530 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 9 C3' G B 1 OK 7 10 11 32 C3' A B 2 OK 30 33 34 54 C3' C B 3 OK 52 55 56 74 C3' C B 4 OK 72 75 76 94 C3' U B 5 OK 92 95 96 114 C3' C B 6 OK 112 115 116 134 C3' G B 7 OK 132 135 136 157 C3' U B 8 OK 155 158 159 177 C3' G B 9 OK 175 178 179 200 C3' G B 10 OK 198 201 202 223 C3' C B 11 OK 221 224 225 243 C3' G B 12 OK 241 244 245 266 C3' C B 13 OK 264 267 268 286 C3' A B 14 OK 284 287 288 308 C3' A B 15 OK 306 309 310 330 C3' U B 16 OK 328 331 332 350 C3' G B 18 OK 348 351 352 373 C3' G B 19 OK 371 374 375 396 C3' U B 20 OK 394 397 398 416 C3' A B 21 OK 414 417 418 438 C3' G B 22 OK 436 439 440 461 C3' C B 23 OK 459 462 463 481 C3' G B 24 OK 479 482 483 504 C3' C B 25 OK 502 505 506 524 C3' G B 26 OK 522 525 526 547 C3' U B 27 OK 545 548 549 567 C3' C B 28 OK 565 568 569 587 C3' U B 29 OK 585 588 589 607 C3' G B 30 OK 605 608 609 630 C3' A B 31 OK 628 631 632 652 C3' C B 32 OK 650 653 654 672 C3' U B 33 OK 670 673 674 692 C3' C B 34 OK 690 693 694 712 C3' C B 35 OK 710 713 714 732 C3' A B 36 OK 730 733 734 754 C3' G B 37 OK 752 755 756 777 C3' A B 38 OK 775 778 779 799 C3' U B 39 OK 797 800 801 819 C3' C B 40 OK 817 820 821 839 C3' A B 41 OK 837 840 841 861 C3' G B 42 OK 859 862 863 884 C3' A B 43 OK 882 885 886 906 C3' A B 44 OK 904 907 908 928 C3' G B 45 OK 926 929 930 951 C3' G B 46 OK 949 952 953 974 C3' U B 47 OK 972 975 976 994 C3' U B 48 OK 992 995 996 1014 C3' G B 49 OK 1012 1015 1016 1037 C3' C B 50 OK 1035 1038 1039 1057 C3' G B 51 OK 1055 1058 1059 1080 C3' U B 52 OK 1078 1081 1082 1100 C3' G B 53 OK 1098 1101 1102 1123 C3' U B 54 OK 1121 1124 1125 1143 C3' U B 55 OK 1141 1144 1145 1163 C3' C B 56 OK 1161 1164 1165 1183 C3' G B 57 OK 1181 1184 1185 1206 C3' A B 58 OK 1204 1207 1208 1228 C3' A B 59 OK 1226 1229 1230 1250 C3' U B 60 OK 1248 1251 1252 1270 C3' C B 61 OK 1268 1271 1272 1290 C3' A B 62 OK 1288 1291 1292 1312 C3' C B 63 OK 1310 1313 1314 1332 C3' G B 64 OK 1330 1333 1334 1355 C3' U B 65 OK 1353 1356 1357 1375 C3' C B 66 OK 1373 1376 1377 1395 C3' G B 67 OK 1393 1396 1397 1418 C3' G B 68 OK 1416 1419 1420 1441 C3' G B 69 OK 1439 1442 1443 1464 C3' G B 70 OK 1462 1465 1466 1487 C3' U B 71 OK 1485 1488 1489 1507 C3' C B 72 OK 1505 1508 1509 1527 C3' A B 73 OK 1525 1528 1529 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 7 C4' G B 1 OK 9 6 8 30 C4' A B 2 OK 32 29 31 52 C4' C B 3 OK 54 51 53 72 C4' C B 4 OK 74 71 73 92 C4' U B 5 OK 94 91 93 112 C4' C B 6 OK 114 111 113 132 C4' G B 7 OK 134 131 133 155 C4' U B 8 OK 157 154 156 175 C4' G B 9 OK 177 174 176 198 C4' G B 10 OK 200 197 199 221 C4' C B 11 OK 223 220 222 241 C4' G B 12 OK 243 240 242 264 C4' C B 13 OK 266 263 265 284 C4' A B 14 OK 286 283 285 306 C4' A B 15 OK 308 305 307 328 C4' U B 16 OK 330 327 329 348 C4' G B 18 OK 350 347 349 371 C4' G B 19 OK 373 370 372 394 C4' U B 20 OK 396 393 395 414 C4' A B 21 OK 416 413 415 436 C4' G B 22 OK 438 435 437 459 C4' C B 23 OK 461 458 460 479 C4' G B 24 OK 481 478 480 502 C4' C B 25 OK 504 501 503 522 C4' G B 26 OK 524 521 523 545 C4' U B 27 OK 547 544 546 565 C4' C B 28 OK 567 564 566 585 C4' U B 29 OK 587 584 586 605 C4' G B 30 OK 607 604 606 628 C4' A B 31 OK 630 627 629 650 C4' C B 32 OK 652 649 651 670 C4' U B 33 OK 672 669 671 690 C4' C B 34 OK 692 689 691 710 C4' C B 35 OK 712 709 711 730 C4' A B 36 OK 732 729 731 752 C4' G B 37 OK 754 751 753 775 C4' A B 38 OK 777 774 776 797 C4' U B 39 OK 799 796 798 817 C4' C B 40 OK 819 816 818 837 C4' A B 41 OK 839 836 838 859 C4' G B 42 OK 861 858 860 882 C4' A B 43 OK 884 881 883 904 C4' A B 44 OK 906 903 905 926 C4' G B 45 OK 928 925 927 949 C4' G B 46 OK 951 948 950 972 C4' U B 47 OK 974 971 973 992 C4' U B 48 OK 994 991 993 1012 C4' G B 49 OK 1014 1011 1013 1035 C4' C B 50 OK 1037 1034 1036 1055 C4' G B 51 OK 1057 1054 1056 1078 C4' U B 52 OK 1080 1077 1079 1098 C4' G B 53 OK 1100 1097 1099 1121 C4' U B 54 OK 1123 1120 1122 1141 C4' U B 55 OK 1143 1140 1142 1161 C4' C B 56 OK 1163 1160 1162 1181 C4' G B 57 OK 1183 1180 1182 1204 C4' A B 58 OK 1206 1203 1205 1226 C4' A B 59 OK 1228 1225 1227 1248 C4' U B 60 OK 1250 1247 1249 1268 C4' C B 61 OK 1270 1267 1269 1288 C4' A B 62 OK 1290 1287 1289 1310 C4' C B 63 OK 1312 1309 1311 1330 C4' G B 64 OK 1332 1329 1331 1353 C4' U B 65 OK 1355 1352 1354 1373 C4' C B 66 OK 1375 1372 1374 1393 C4' G B 67 OK 1395 1392 1394 1416 C4' G B 68 OK 1418 1415 1417 1439 C4' G B 69 OK 1441 1438 1440 1462 C4' G B 70 OK 1464 1461 1463 1485 C4' U B 71 OK 1487 1484 1486 1505 C4' C B 72 OK 1507 1504 1506 1525 C4' A B 73 OK 1527 1524 1526 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 6 C5' G B 1 5 7 29 C5' A B 2 28 30 51 C5' C B 3 50 52 71 C5' C B 4 70 72 91 C5' U B 5 90 92 111 C5' C B 6 110 112 131 C5' G B 7 130 132 154 C5' U B 8 153 155 174 C5' G B 9 173 175 197 C5' G B 10 196 198 220 C5' C B 11 219 221 240 C5' G B 12 239 241 263 C5' C B 13 262 264 283 C5' A B 14 282 284 305 C5' A B 15 304 306 327 C5' U B 16 326 328 347 C5' G B 18 346 348 370 C5' G B 19 369 371 393 C5' U B 20 392 394 413 C5' A B 21 412 414 435 C5' G B 22 434 436 458 C5' C B 23 457 459 478 C5' G B 24 477 479 501 C5' C B 25 500 502 521 C5' G B 26 520 522 544 C5' U B 27 543 545 564 C5' C B 28 563 565 584 C5' U B 29 583 585 604 C5' G B 30 603 605 627 C5' A B 31 626 628 649 C5' C B 32 648 650 669 C5' U B 33 668 670 689 C5' C B 34 688 690 709 C5' C B 35 708 710 729 C5' A B 36 728 730 751 C5' G B 37 750 752 774 C5' A B 38 773 775 796 C5' U B 39 795 797 816 C5' C B 40 815 817 836 C5' A B 41 835 837 858 C5' G B 42 857 859 881 C5' A B 43 880 882 903 C5' A B 44 902 904 925 C5' G B 45 924 926 948 C5' G B 46 947 949 971 C5' U B 47 970 972 991 C5' U B 48 990 992 1011 C5' G B 49 1010 1012 1034 C5' C B 50 1033 1035 1054 C5' G B 51 1053 1055 1077 C5' U B 52 1076 1078 1097 C5' G B 53 1096 1098 1120 C5' U B 54 1119 1121 1140 C5' U B 55 1139 1141 1160 C5' C B 56 1159 1161 1180 C5' G B 57 1179 1181 1203 C5' A B 58 1202 1204 1225 C5' A B 59 1224 1226 1247 C5' U B 60 1246 1248 1267 C5' C B 61 1266 1268 1287 C5' A B 62 1286 1288 1309 C5' C B 63 1308 1310 1329 C5' G B 64 1328 1330 1352 C5' U B 65 1351 1353 1372 C5' C B 66 1371 1373 1392 C5' G B 67 1391 1393 1415 C5' G B 68 1414 1416 1438 C5' G B 69 1437 1439 1461 C5' G B 70 1460 1462 1484 C5' U B 71 1483 1485 1504 C5' C B 72 1503 1505 1524 C5' A B 73 1523 1525 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2 P G B 1 distorted distorted 3 4 5 25 P A B 2 distorted distorted 10 26 27 28 47 P C B 3 distorted distorted 33 48 49 50 67 P C B 4 distorted distorted 55 68 69 70 87 P U B 5 distorted distorted 75 88 89 90 107 P C B 6 distorted distorted 95 108 109 110 127 P G B 7 distorted distorted 115 128 129 130 150 P U B 8 distorted distorted 135 151 152 153 170 P G B 9 distorted distorted 158 171 172 173 193 P G B 10 distorted distorted 178 194 195 196 216 P C B 11 distorted distorted 201 217 218 219 236 P G B 12 distorted distorted 224 237 238 239 259 P C B 13 distorted distorted 244 260 261 262 279 P A B 14 distorted distorted 267 280 281 282 301 P A B 15 distorted distorted 287 302 303 304 323 P U B 16 distorted distorted 309 324 325 326 343 P G B 18 distorted distorted 331 344 345 346 366 P G B 19 distorted distorted 351 367 368 369 389 P U B 20 distorted distorted 374 390 391 392 409 P A B 21 distorted distorted 397 410 411 412 431 P G B 22 distorted distorted 417 432 433 434 454 P C B 23 distorted distorted 439 455 456 457 474 P G B 24 distorted distorted 462 475 476 477 497 P C B 25 distorted distorted 482 498 499 500 517 P G B 26 distorted distorted 505 518 519 520 540 P U B 27 distorted distorted 525 541 542 543 560 P C B 28 distorted distorted 548 561 562 563 580 P U B 29 distorted distorted 568 581 582 583 600 P G B 30 distorted distorted 588 601 602 603 623 P A B 31 distorted distorted 608 624 625 626 645 P C B 32 distorted distorted 631 646 647 648 665 P U B 33 distorted distorted 653 666 667 668 685 P C B 34 distorted distorted 673 686 687 688 705 P C B 35 distorted distorted 693 706 707 708 725 P A B 36 distorted distorted 713 726 727 728 747 P G B 37 distorted distorted 733 748 749 750 770 P A B 38 distorted distorted 755 771 772 773 792 P U B 39 distorted distorted 778 793 794 795 812 P C B 40 distorted distorted 800 813 814 815 832 P A B 41 distorted distorted 820 833 834 835 854 P G B 42 distorted distorted 840 855 856 857 877 P A B 43 distorted distorted 862 878 879 880 899 P A B 44 distorted distorted 885 900 901 902 921 P G B 45 distorted distorted 907 922 923 924 944 P G B 46 distorted distorted 929 945 946 947 967 P U B 47 distorted distorted 952 968 969 970 987 P U B 48 distorted distorted 975 988 989 990 1007 P G B 49 distorted distorted 995 1008 1009 1010 1030 P C B 50 distorted distorted 1015 1031 1032 1033 1050 P G B 51 distorted distorted 1038 1051 1052 1053 1073 P U B 52 distorted distorted 1058 1074 1075 1076 1093 P G B 53 distorted distorted 1081 1094 1095 1096 1116 P U B 54 distorted distorted 1101 1117 1118 1119 1136 P U B 55 distorted distorted 1124 1137 1138 1139 1156 P C B 56 distorted distorted 1144 1157 1158 1159 1176 P G B 57 distorted distorted 1164 1177 1178 1179 1199 P A B 58 distorted distorted 1184 1200 1201 1202 1221 P A B 59 distorted distorted 1207 1222 1223 1224 1243 P U B 60 distorted distorted 1229 1244 1245 1246 1263 P C B 61 distorted distorted 1251 1264 1265 1266 1283 P A B 62 distorted distorted 1271 1284 1285 1286 1305 P C B 63 distorted distorted 1291 1306 1307 1308 1325 P G B 64 distorted distorted 1313 1326 1327 1328 1348 P U B 65 distorted distorted 1333 1349 1350 1351 1368 P C B 66 distorted distorted 1356 1369 1370 1371 1388 P G B 67 distorted distorted 1376 1389 1390 1391 1411 P G B 68 distorted distorted 1396 1412 1413 1414 1434 P G B 69 distorted distorted 1419 1435 1436 1437 1457 P G B 70 distorted distorted 1442 1458 1459 1460 1480 P U B 71 distorted distorted 1465 1481 1482 1483 1500 P C B 72 distorted distorted 1488 1501 1502 1503 1520 P A B 73 distorted distorted 1508 1521 1522 1523 ---------------------------------------------------------------------------------