ID code: '3DKN' 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' C D 53 beta 7 13 10 32 C1' G D 54 beta 27 33 30 55 C1' U D 55 beta 50 56 53 75 C1' G D 56 beta 70 76 73 98 C1' C D 57 beta 93 99 96 118 C1' C D 58 beta 113 119 116 138 C1' A D 59 beta 133 139 136 160 C1' A D 60 beta 155 161 158 182 C1' G D 61 beta 177 183 180 205 C1' C D 62 beta 200 206 203 225 C1' U D 63 beta 220 226 223 245 C1' G D 64 beta 240 246 243 268 C1' C D 65 beta 263 269 266 288 C1' G D 66 beta 283 289 286 311 C1' A D 67 beta 306 312 309 333 C1' U D 68 beta 328 334 331 353 C1' A D 69 beta 348 354 351 375 C1' A D 70 beta 370 376 373 397 C1' G D 71 beta 392 398 395 420 C1' C D 72 beta 415 421 418 441 C1' A E 80 beta 436 442 439 463 C1' G E 81 beta 458 464 461 486 C1' C E 82 beta 481 487 484 506 C1' C E 83 beta 501 507 504 526 C1' G E 84 beta 521 527 524 549 C1' C E 85 beta 544 550 547 569 C1' A E 86 beta 564 570 567 591 C1' C E 87 beta 586 592 589 611 C1' G E 88 beta 606 612 609 634 C1' G E 89 beta 629 635 632 657 C1' A E 90 beta 652 658 655 679 C1' G E 91 beta 674 680 677 702 C1' G E 92 beta 697 703 700 725 C1' C E 93 beta 720 726 723 745 C1' G E 94 beta 740 746 743 768 C1' A E 95 beta 763 769 766 790 C1' A E 96 beta 785 791 788 813 C1' G F1415 beta 808 814 811 836 C1' G F1416 beta 831 837 834 859 C1' G F1417 beta 854 860 857 882 C1' U F1418 beta 877 883 880 902 C1' U F1419 beta 897 903 900 922 C1' C F1420 beta 917 923 920 942 C1' C F1421 beta 937 943 940 962 C1' U F1422 beta 957 963 960 982 C1' C F1423 beta 977 983 980 1002 C1' A F1424 beta 997 1003 1000 1024 C1' G F1425 beta 1019 1025 1022 1047 C1' C F1426 beta 1042 1048 1045 1067 C1' A F1427 beta 1062 1068 1065 1089 C1' C F1428 beta 1084 1090 1087 1109 C1' U F1429 beta 1104 1110 1107 1129 C1' G F1430 beta 1124 1130 1127 1152 C1' C F1431 beta 1147 1153 1150 1172 C1' U F1432 beta 1167 1173 1170 1192 C1' G F1433 beta 1187 1193 1190 1215 C1' A F1434 beta 1210 1216 1213 1237 C1' U F1435 beta 1232 1238 1235 1257 C1' C F1436 beta 1252 1258 1255 1277 C1' A F1437 beta 1272 1278 1275 1299 C1' G F1438 beta 1294 1300 1297 1322 C1' C F1439 beta 1317 1323 1320 1342 C1' U F1440 beta 1337 1343 1340 1362 C1' G F1441 beta 1357 1363 1360 1385 C1' A F1442 beta 1380 1386 1383 1407 C1' G F1443 beta 1402 1408 1405 1430 C1' G F1444 beta 1425 1431 1428 1453 C1' G F1445 beta 1448 1454 1451 1476 C1' U F1446 beta 1471 1477 1474 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' C D 53 OK 12 8 11 30 C2' G D 54 OK 32 28 31 53 C2' U D 55 OK 55 51 54 73 C2' G D 56 OK 75 71 74 96 C2' C D 57 OK 98 94 97 116 C2' C D 58 OK 118 114 117 136 C2' A D 59 OK 138 134 137 158 C2' A D 60 OK 160 156 159 180 C2' G D 61 OK 182 178 181 203 C2' C D 62 OK 205 201 204 223 C2' U D 63 OK 225 221 224 243 C2' G D 64 OK 245 241 244 266 C2' C D 65 OK 268 264 267 286 C2' G D 66 OK 288 284 287 309 C2' A D 67 OK 311 307 310 331 C2' U D 68 OK 333 329 332 351 C2' A D 69 OK 353 349 352 373 C2' A D 70 OK 375 371 374 395 C2' G D 71 OK 397 393 396 418 C2' C D 72 OK 420 416 419 439 C2' A E 80 OK 441 437 440 461 C2' G E 81 OK 463 459 462 484 C2' C E 82 OK 486 482 485 504 C2' C E 83 OK 506 502 505 524 C2' G E 84 OK 526 522 525 547 C2' C E 85 OK 549 545 548 567 C2' A E 86 OK 569 565 568 589 C2' C E 87 OK 591 587 590 609 C2' G E 88 OK 611 607 610 632 C2' G E 89 OK 634 630 633 655 C2' A E 90 OK 657 653 656 677 C2' G E 91 OK 679 675 678 700 C2' G E 92 OK 702 698 701 723 C2' C E 93 OK 725 721 724 743 C2' G E 94 OK 745 741 744 766 C2' A E 95 OK 768 764 767 788 C2' A E 96 OK 790 786 789 811 C2' G F1415 OK 813 809 812 834 C2' G F1416 OK 836 832 835 857 C2' G F1417 OK 859 855 858 880 C2' U F1418 OK 882 878 881 900 C2' U F1419 OK 902 898 901 920 C2' C F1420 OK 922 918 921 940 C2' C F1421 OK 942 938 941 960 C2' U F1422 OK 962 958 961 980 C2' C F1423 OK 982 978 981 1000 C2' A F1424 OK 1002 998 1001 1022 C2' G F1425 OK 1024 1020 1023 1045 C2' C F1426 OK 1047 1043 1046 1065 C2' A F1427 OK 1067 1063 1066 1087 C2' C F1428 OK 1089 1085 1088 1107 C2' U F1429 OK 1109 1105 1108 1127 C2' G F1430 OK 1129 1125 1128 1150 C2' C F1431 OK 1152 1148 1151 1170 C2' U F1432 OK 1172 1168 1171 1190 C2' G F1433 OK 1192 1188 1191 1213 C2' A F1434 OK 1215 1211 1214 1235 C2' U F1435 OK 1237 1233 1236 1255 C2' C F1436 OK 1257 1253 1256 1275 C2' A F1437 OK 1277 1273 1276 1297 C2' G F1438 OK 1299 1295 1298 1320 C2' C F1439 OK 1322 1318 1321 1340 C2' U F1440 OK 1342 1338 1341 1360 C2' G F1441 OK 1362 1358 1361 1383 C2' A F1442 OK 1385 1381 1384 1405 C2' G F1443 OK 1407 1403 1406 1428 C2' G F1444 OK 1430 1426 1429 1451 C2' G F1445 OK 1453 1449 1452 1474 C2' U F1446 OK 1476 1472 1475 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' C D 53 OK 6 9 10 28 C3' G D 54 OK 26 29 30 51 C3' U D 55 OK 49 52 53 71 C3' G D 56 OK 69 72 73 94 C3' C D 57 OK 92 95 96 114 C3' C D 58 OK 112 115 116 134 C3' A D 59 OK 132 135 136 156 C3' A D 60 OK 154 157 158 178 C3' G D 61 OK 176 179 180 201 C3' C D 62 OK 199 202 203 221 C3' U D 63 OK 219 222 223 241 C3' G D 64 OK 239 242 243 264 C3' C D 65 OK 262 265 266 284 C3' G D 66 OK 282 285 286 307 C3' A D 67 OK 305 308 309 329 C3' U D 68 OK 327 330 331 349 C3' A D 69 OK 347 350 351 371 C3' A D 70 OK 369 372 373 393 C3' G D 71 OK 391 394 395 416 C3' C D 72 OK 414 417 418 437 C3' A E 80 OK 435 438 439 459 C3' G E 81 OK 457 460 461 482 C3' C E 82 OK 480 483 484 502 C3' C E 83 OK 500 503 504 522 C3' G E 84 OK 520 523 524 545 C3' C E 85 OK 543 546 547 565 C3' A E 86 OK 563 566 567 587 C3' C E 87 OK 585 588 589 607 C3' G E 88 OK 605 608 609 630 C3' G E 89 OK 628 631 632 653 C3' A E 90 OK 651 654 655 675 C3' G E 91 OK 673 676 677 698 C3' G E 92 OK 696 699 700 721 C3' C E 93 OK 719 722 723 741 C3' G E 94 OK 739 742 743 764 C3' A E 95 OK 762 765 766 786 C3' A E 96 OK 784 787 788 809 C3' G F1415 OK 807 810 811 832 C3' G F1416 OK 830 833 834 855 C3' G F1417 OK 853 856 857 878 C3' U F1418 OK 876 879 880 898 C3' U F1419 OK 896 899 900 918 C3' C F1420 OK 916 919 920 938 C3' C F1421 OK 936 939 940 958 C3' U F1422 OK 956 959 960 978 C3' C F1423 OK 976 979 980 998 C3' A F1424 OK 996 999 1000 1020 C3' G F1425 OK 1018 1021 1022 1043 C3' C F1426 OK 1041 1044 1045 1063 C3' A F1427 OK 1061 1064 1065 1085 C3' C F1428 OK 1083 1086 1087 1105 C3' U F1429 OK 1103 1106 1107 1125 C3' G F1430 OK 1123 1126 1127 1148 C3' C F1431 OK 1146 1149 1150 1168 C3' U F1432 OK 1166 1169 1170 1188 C3' G F1433 OK 1186 1189 1190 1211 C3' A F1434 OK 1209 1212 1213 1233 C3' U F1435 OK 1231 1234 1235 1253 C3' C F1436 OK 1251 1254 1255 1273 C3' A F1437 OK 1271 1274 1275 1295 C3' G F1438 OK 1293 1296 1297 1318 C3' C F1439 OK 1316 1319 1320 1338 C3' U F1440 OK 1336 1339 1340 1358 C3' G F1441 OK 1356 1359 1360 1381 C3' A F1442 OK 1379 1382 1383 1403 C3' G F1443 OK 1401 1404 1405 1426 C3' G F1444 OK 1424 1427 1428 1449 C3' G F1445 OK 1447 1450 1451 1472 C3' U F1446 OK 1470 1473 1474 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' C D 53 OK 8 5 7 26 C4' G D 54 OK 28 25 27 49 C4' U D 55 OK 51 48 50 69 C4' G D 56 OK 71 68 70 92 C4' C D 57 OK 94 91 93 112 C4' C D 58 OK 114 111 113 132 C4' A D 59 OK 134 131 133 154 C4' A D 60 OK 156 153 155 176 C4' G D 61 OK 178 175 177 199 C4' C D 62 OK 201 198 200 219 C4' U D 63 OK 221 218 220 239 C4' G D 64 OK 241 238 240 262 C4' C D 65 OK 264 261 263 282 C4' G D 66 OK 284 281 283 305 C4' A D 67 OK 307 304 306 327 C4' U D 68 OK 329 326 328 347 C4' A D 69 OK 349 346 348 369 C4' A D 70 OK 371 368 370 391 C4' G D 71 OK 393 390 392 414 C4' C D 72 OK 416 413 415 435 C4' A E 80 OK 437 434 436 457 C4' G E 81 OK 459 456 458 480 C4' C E 82 OK 482 479 481 500 C4' C E 83 OK 502 499 501 520 C4' G E 84 OK 522 519 521 543 C4' C E 85 OK 545 542 544 563 C4' A E 86 OK 565 562 564 585 C4' C E 87 OK 587 584 586 605 C4' G E 88 OK 607 604 606 628 C4' G E 89 OK 630 627 629 651 C4' A E 90 OK 653 650 652 673 C4' G E 91 OK 675 672 674 696 C4' G E 92 OK 698 695 697 719 C4' C E 93 OK 721 718 720 739 C4' G E 94 OK 741 738 740 762 C4' A E 95 OK 764 761 763 784 C4' A E 96 OK 786 783 785 807 C4' G F1415 OK 809 806 808 830 C4' G F1416 OK 832 829 831 853 C4' G F1417 OK 855 852 854 876 C4' U F1418 OK 878 875 877 896 C4' U F1419 OK 898 895 897 916 C4' C F1420 OK 918 915 917 936 C4' C F1421 OK 938 935 937 956 C4' U F1422 OK 958 955 957 976 C4' C F1423 OK 978 975 977 996 C4' A F1424 OK 998 995 997 1018 C4' G F1425 OK 1020 1017 1019 1041 C4' C F1426 OK 1043 1040 1042 1061 C4' A F1427 OK 1063 1060 1062 1083 C4' C F1428 OK 1085 1082 1084 1103 C4' U F1429 OK 1105 1102 1104 1123 C4' G F1430 OK 1125 1122 1124 1146 C4' C F1431 OK 1148 1145 1147 1166 C4' U F1432 OK 1168 1165 1167 1186 C4' G F1433 OK 1188 1185 1187 1209 C4' A F1434 OK 1211 1208 1210 1231 C4' U F1435 OK 1233 1230 1232 1251 C4' C F1436 OK 1253 1250 1252 1271 C4' A F1437 OK 1273 1270 1272 1293 C4' G F1438 OK 1295 1292 1294 1316 C4' C F1439 OK 1318 1315 1317 1336 C4' U F1440 OK 1338 1335 1337 1356 C4' G F1441 OK 1358 1355 1357 1379 C4' A F1442 OK 1381 1378 1380 1401 C4' G F1443 OK 1403 1400 1402 1424 C4' G F1444 OK 1426 1423 1425 1447 C4' G F1445 OK 1449 1446 1448 1470 C4' U F1446 OK 1472 1469 1471 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' C D 53 4 6 25 C5' G D 54 24 26 48 C5' U D 55 47 49 68 C5' G D 56 67 69 91 C5' C D 57 90 92 111 C5' C D 58 110 112 131 C5' A D 59 130 132 153 C5' A D 60 152 154 175 C5' G D 61 174 176 198 C5' C D 62 197 199 218 C5' U D 63 217 219 238 C5' G D 64 237 239 261 C5' C D 65 260 262 281 C5' G D 66 280 282 304 C5' A D 67 303 305 326 C5' U D 68 325 327 346 C5' A D 69 345 347 368 C5' A D 70 367 369 390 C5' G D 71 389 391 413 C5' C D 72 412 414 434 C5' A E 80 433 435 456 C5' G E 81 455 457 479 C5' C E 82 478 480 499 C5' C E 83 498 500 519 C5' G E 84 518 520 542 C5' C E 85 541 543 562 C5' A E 86 561 563 584 C5' C E 87 583 585 604 C5' G E 88 603 605 627 C5' G E 89 626 628 650 C5' A E 90 649 651 672 C5' G E 91 671 673 695 C5' G E 92 694 696 718 C5' C E 93 717 719 738 C5' G E 94 737 739 761 C5' A E 95 760 762 783 C5' A E 96 782 784 806 C5' G F1415 805 807 829 C5' G F1416 828 830 852 C5' G F1417 851 853 875 C5' U F1418 874 876 895 C5' U F1419 894 896 915 C5' C F1420 914 916 935 C5' C F1421 934 936 955 C5' U F1422 954 956 975 C5' C F1423 974 976 995 C5' A F1424 994 996 1017 C5' G F1425 1016 1018 1040 C5' C F1426 1039 1041 1060 C5' A F1427 1059 1061 1082 C5' C F1428 1081 1083 1102 C5' U F1429 1101 1103 1122 C5' G F1430 1121 1123 1145 C5' C F1431 1144 1146 1165 C5' U F1432 1164 1166 1185 C5' G F1433 1184 1186 1208 C5' A F1434 1207 1209 1230 C5' U F1435 1229 1231 1250 C5' C F1436 1249 1251 1270 C5' A F1437 1269 1271 1292 C5' G F1438 1291 1293 1315 C5' C F1439 1314 1316 1335 C5' U F1440 1334 1336 1355 C5' G F1441 1354 1356 1378 C5' A F1442 1377 1379 1400 C5' G F1443 1399 1401 1423 C5' G F1444 1422 1424 1446 C5' G F1445 1445 1447 1469 C5' U F1446 1468 1470 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P C D 53 distorted distorted 2 3 4 21 P G D 54 distorted distorted 9 22 23 24 44 P U D 55 distorted distorted 29 45 46 47 64 P G D 56 distorted distorted 52 65 66 67 87 P C D 57 distorted distorted 72 88 89 90 107 P C D 58 distorted distorted 95 108 109 110 127 P A D 59 distorted distorted 115 128 129 130 149 P A D 60 distorted distorted 135 150 151 152 171 P G D 61 distorted distorted 157 172 173 174 194 P C D 62 distorted distorted 179 195 196 197 214 P U D 63 distorted distorted 202 215 216 217 234 P G D 64 distorted distorted 222 235 236 237 257 P C D 65 distorted distorted 242 258 259 260 277 P G D 66 distorted distorted 265 278 279 280 300 P A D 67 distorted distorted 285 301 302 303 322 P U D 68 distorted distorted 308 323 324 325 342 P A D 69 distorted distorted 330 343 344 345 364 P A D 70 distorted distorted 350 365 366 367 386 P G D 71 distorted distorted 372 387 388 389 409 P C D 72 distorted distorted 394 410 411 412 430 P A E 80 distorted distorted 431 432 433 452 P G E 81 distorted distorted 438 453 454 455 475 P C E 82 distorted distorted 460 476 477 478 495 P C E 83 distorted distorted 483 496 497 498 515 P G E 84 distorted distorted 503 516 517 518 538 P C E 85 distorted distorted 523 539 540 541 558 P A E 86 distorted distorted 546 559 560 561 580 P C E 87 distorted distorted 566 581 582 583 600 P G E 88 distorted distorted 588 601 602 603 623 P G E 89 distorted distorted 608 624 625 626 646 P A E 90 distorted distorted 631 647 648 649 668 P G E 91 distorted distorted 654 669 670 671 691 P G E 92 distorted distorted 676 692 693 694 714 P C E 93 distorted distorted 699 715 716 717 734 P G E 94 distorted distorted 722 735 736 737 757 P A E 95 distorted distorted 742 758 759 760 779 P A E 96 distorted distorted 765 780 781 782 802 P G F1415 distorted distorted 803 804 805 825 P G F1416 distorted distorted 810 826 827 828 848 P G F1417 distorted distorted 833 849 850 851 871 P U F1418 distorted distorted 856 872 873 874 891 P U F1419 distorted distorted 879 892 893 894 911 P C F1420 distorted distorted 899 912 913 914 931 P C F1421 distorted distorted 919 932 933 934 951 P U F1422 distorted distorted 939 952 953 954 971 P C F1423 distorted distorted 959 972 973 974 991 P A F1424 distorted distorted 979 992 993 994 1013 P G F1425 distorted distorted 999 1014 1015 1016 1036 P C F1426 distorted distorted 1021 1037 1038 1039 1056 P A F1427 distorted distorted 1044 1057 1058 1059 1078 P C F1428 distorted distorted 1064 1079 1080 1081 1098 P U F1429 distorted distorted 1086 1099 1100 1101 1118 P G F1430 distorted distorted 1106 1119 1120 1121 1141 P C F1431 distorted distorted 1126 1142 1143 1144 1161 P U F1432 distorted distorted 1149 1162 1163 1164 1181 P G F1433 distorted distorted 1169 1182 1183 1184 1204 P A F1434 distorted distorted 1189 1205 1206 1207 1226 P U F1435 distorted distorted 1212 1227 1228 1229 1246 P C F1436 distorted distorted 1234 1247 1248 1249 1266 P A F1437 distorted distorted 1254 1267 1268 1269 1288 P G F1438 distorted distorted 1274 1289 1290 1291 1311 P C F1439 distorted distorted 1296 1312 1313 1314 1331 P U F1440 distorted distorted 1319 1332 1333 1334 1351 P G F1441 distorted distorted 1339 1352 1353 1354 1374 P A F1442 distorted distorted 1359 1375 1376 1377 1396 P G F1443 distorted distorted 1382 1397 1398 1399 1419 P G F1444 distorted distorted 1404 1420 1421 1422 1442 P G F1445 distorted distorted 1427 1443 1444 1445 1465 P U F1446 distorted distorted 1450 1466 1467 1468 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