ID code: '4PQV' 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 A 1 beta 7 13 10 35 C1' G A 2 beta 30 36 33 58 C1' G A 3 beta 53 59 56 81 C1' U A 4 beta 76 82 79 101 C1' C A 5 beta 96 102 99 121 C1' A A 6 beta 116 122 119 143 C1' G A 7 beta 138 144 141 166 C1' A A 8 beta 161 167 164 188 C1' U A 9 beta 183 189 186 208 C1' C A 10 beta 203 209 206 228 C1' G A 11 beta 223 229 226 251 C1' G A 12 beta 246 252 249 274 C1' C A 13 beta 269 275 272 294 C1' G A 14 beta 289 295 292 317 C1' A A 15 beta 312 318 315 339 C1' A A 16 beta 334 340 337 361 C1' A A 17 beta 356 362 359 383 C1' G A 18 beta 378 384 381 406 C1' U A 19 beta 401 407 404 426 C1' C A 20 beta 421 427 424 446 C1' G A 21 beta 441 447 444 469 C1' C A 22 beta 464 470 467 489 C1' C A 23 beta 484 490 487 509 C1' A A 24 beta 504 510 507 531 C1' C A 25 beta 526 532 529 551 C1' U A 26 beta 546 552 549 571 C1' U A 27 beta 566 572 569 591 C1' C A 28 beta 586 592 589 611 C1' G A 29 beta 606 612 609 634 C1' C A 30 beta 629 635 632 654 C1' C A 31 beta 649 655 652 674 C1' G A 32 beta 669 675 672 697 C1' A A 33 beta 692 698 695 719 C1' G A 34 beta 714 720 717 742 C1' G A 35 beta 737 743 740 765 C1' A A 36 beta 760 766 763 787 C1' G A 37 beta 782 788 785 810 C1' U A 38 beta 805 811 808 830 C1' G A 39 beta 825 831 828 853 C1' C A 40 beta 848 854 851 873 C1' A A 41 beta 868 874 871 895 C1' A A 42 beta 890 896 893 917 C1' U A 43 beta 912 918 915 937 C1' C A 44 beta 932 938 935 957 C1' U A 45 beta 952 958 955 977 C1' G A 46 beta 972 978 975 1000 C1' U A 47 beta 995 1001 998 1020 C1' G A 48 beta 1015 1021 1018 1043 C1' A A 49 beta 1038 1044 1041 1065 C1' G A 50 beta 1060 1066 1063 1088 C1' G A 51 beta 1083 1089 1086 1111 C1' C A 52 beta 1106 1112 1109 1131 C1' C A 53 beta 1126 1132 1129 1151 C1' C A 54 beta 1146 1152 1149 1171 C1' C A 55 beta 1166 1172 1169 1191 C1' A A 56 beta 1186 1192 1189 1213 C1' G A 57 beta 1208 1214 1211 1236 C1' G A 58 beta 1231 1237 1234 1259 C1' A A 59 beta 1254 1260 1257 1281 C1' G A 60 beta 1276 1282 1279 1304 C1' G A 61 beta 1299 1305 1302 1327 C1' A A 62 beta 1322 1328 1325 1349 C1' C A 63 beta 1344 1350 1347 1369 C1' U A 64 beta 1364 1370 1367 1389 C1' G A 65 beta 1384 1390 1387 1412 C1' G A 66 beta 1407 1413 1410 1435 C1' G A 67 beta 1430 1436 1433 1458 C1' U A 68 beta 1453 1459 1456 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' G A 1 OK 12 8 11 33 C2' G A 2 OK 35 31 34 56 C2' G A 3 OK 58 54 57 79 C2' U A 4 OK 81 77 80 99 C2' C A 5 OK 101 97 100 119 C2' A A 6 OK 121 117 120 141 C2' G A 7 OK 143 139 142 164 C2' A A 8 OK 166 162 165 186 C2' U A 9 OK 188 184 187 206 C2' C A 10 OK 208 204 207 226 C2' G A 11 OK 228 224 227 249 C2' G A 12 OK 251 247 250 272 C2' C A 13 OK 274 270 273 292 C2' G A 14 OK 294 290 293 315 C2' A A 15 OK 317 313 316 337 C2' A A 16 OK 339 335 338 359 C2' A A 17 OK 361 357 360 381 C2' G A 18 OK 383 379 382 404 C2' U A 19 OK 406 402 405 424 C2' C A 20 OK 426 422 425 444 C2' G A 21 OK 446 442 445 467 C2' C A 22 OK 469 465 468 487 C2' C A 23 OK 489 485 488 507 C2' A A 24 OK 509 505 508 529 C2' C A 25 OK 531 527 530 549 C2' U A 26 OK 551 547 550 569 C2' U A 27 OK 571 567 570 589 C2' C A 28 OK 591 587 590 609 C2' G A 29 OK 611 607 610 632 C2' C A 30 OK 634 630 633 652 C2' C A 31 OK 654 650 653 672 C2' G A 32 OK 674 670 673 695 C2' A A 33 OK 697 693 696 717 C2' G A 34 OK 719 715 718 740 C2' G A 35 OK 742 738 741 763 C2' A A 36 OK 765 761 764 785 C2' G A 37 OK 787 783 786 808 C2' U A 38 OK 810 806 809 828 C2' G A 39 OK 830 826 829 851 C2' C A 40 OK 853 849 852 871 C2' A A 41 OK 873 869 872 893 C2' A A 42 OK 895 891 894 915 C2' U A 43 OK 917 913 916 935 C2' C A 44 OK 937 933 936 955 C2' U A 45 OK 957 953 956 975 C2' G A 46 OK 977 973 976 998 C2' U A 47 OK 1000 996 999 1018 C2' G A 48 OK 1020 1016 1019 1041 C2' A A 49 OK 1043 1039 1042 1063 C2' G A 50 OK 1065 1061 1064 1086 C2' G A 51 OK 1088 1084 1087 1109 C2' C A 52 OK 1111 1107 1110 1129 C2' C A 53 OK 1131 1127 1130 1149 C2' C A 54 OK 1151 1147 1150 1169 C2' C A 55 OK 1171 1167 1170 1189 C2' A A 56 OK 1191 1187 1190 1211 C2' G A 57 OK 1213 1209 1212 1234 C2' G A 58 OK 1236 1232 1235 1257 C2' A A 59 OK 1259 1255 1258 1279 C2' G A 60 OK 1281 1277 1280 1302 C2' G A 61 OK 1304 1300 1303 1325 C2' A A 62 OK 1327 1323 1326 1347 C2' C A 63 OK 1349 1345 1348 1367 C2' U A 64 OK 1369 1365 1368 1387 C2' G A 65 OK 1389 1385 1388 1410 C2' G A 66 OK 1412 1408 1411 1433 C2' G A 67 OK 1435 1431 1434 1456 C2' U A 68 OK 1458 1454 1457 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' G A 1 OK 6 9 10 31 C3' G A 2 OK 29 32 33 54 C3' G A 3 OK 52 55 56 77 C3' U A 4 OK 75 78 79 97 C3' C A 5 OK 95 98 99 117 C3' A A 6 OK 115 118 119 139 C3' G A 7 OK 137 140 141 162 C3' A A 8 OK 160 163 164 184 C3' U A 9 OK 182 185 186 204 C3' C A 10 OK 202 205 206 224 C3' G A 11 OK 222 225 226 247 C3' G A 12 OK 245 248 249 270 C3' C A 13 OK 268 271 272 290 C3' G A 14 OK 288 291 292 313 C3' A A 15 OK 311 314 315 335 C3' A A 16 OK 333 336 337 357 C3' A A 17 OK 355 358 359 379 C3' G A 18 OK 377 380 381 402 C3' U A 19 OK 400 403 404 422 C3' C A 20 OK 420 423 424 442 C3' G A 21 OK 440 443 444 465 C3' C A 22 OK 463 466 467 485 C3' C A 23 OK 483 486 487 505 C3' A A 24 OK 503 506 507 527 C3' C A 25 OK 525 528 529 547 C3' U A 26 OK 545 548 549 567 C3' U A 27 OK 565 568 569 587 C3' C A 28 OK 585 588 589 607 C3' G A 29 OK 605 608 609 630 C3' C A 30 OK 628 631 632 650 C3' C A 31 OK 648 651 652 670 C3' G A 32 OK 668 671 672 693 C3' A A 33 OK 691 694 695 715 C3' G A 34 OK 713 716 717 738 C3' G A 35 OK 736 739 740 761 C3' A A 36 OK 759 762 763 783 C3' G A 37 OK 781 784 785 806 C3' U A 38 OK 804 807 808 826 C3' G A 39 OK 824 827 828 849 C3' C A 40 OK 847 850 851 869 C3' A A 41 OK 867 870 871 891 C3' A A 42 OK 889 892 893 913 C3' U A 43 OK 911 914 915 933 C3' C A 44 OK 931 934 935 953 C3' U A 45 OK 951 954 955 973 C3' G A 46 OK 971 974 975 996 C3' U A 47 OK 994 997 998 1016 C3' G A 48 OK 1014 1017 1018 1039 C3' A A 49 OK 1037 1040 1041 1061 C3' G A 50 OK 1059 1062 1063 1084 C3' G A 51 OK 1082 1085 1086 1107 C3' C A 52 OK 1105 1108 1109 1127 C3' C A 53 OK 1125 1128 1129 1147 C3' C A 54 OK 1145 1148 1149 1167 C3' C A 55 OK 1165 1168 1169 1187 C3' A A 56 OK 1185 1188 1189 1209 C3' G A 57 OK 1207 1210 1211 1232 C3' G A 58 OK 1230 1233 1234 1255 C3' A A 59 OK 1253 1256 1257 1277 C3' G A 60 OK 1275 1278 1279 1300 C3' G A 61 OK 1298 1301 1302 1323 C3' A A 62 OK 1321 1324 1325 1345 C3' C A 63 OK 1343 1346 1347 1365 C3' U A 64 OK 1363 1366 1367 1385 C3' G A 65 OK 1383 1386 1387 1408 C3' G A 66 OK 1406 1409 1410 1431 C3' G A 67 OK 1429 1432 1433 1454 C3' U A 68 OK 1452 1455 1456 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' G A 1 OK 8 5 7 29 C4' G A 2 OK 31 28 30 52 C4' G A 3 OK 54 51 53 75 C4' U A 4 OK 77 74 76 95 C4' C A 5 OK 97 94 96 115 C4' A A 6 OK 117 114 116 137 C4' G A 7 OK 139 136 138 160 C4' A A 8 OK 162 159 161 182 C4' U A 9 OK 184 181 183 202 C4' C A 10 OK 204 201 203 222 C4' G A 11 OK 224 221 223 245 C4' G A 12 OK 247 244 246 268 C4' C A 13 OK 270 267 269 288 C4' G A 14 OK 290 287 289 311 C4' A A 15 OK 313 310 312 333 C4' A A 16 OK 335 332 334 355 C4' A A 17 OK 357 354 356 377 C4' G A 18 OK 379 376 378 400 C4' U A 19 OK 402 399 401 420 C4' C A 20 OK 422 419 421 440 C4' G A 21 OK 442 439 441 463 C4' C A 22 OK 465 462 464 483 C4' C A 23 OK 485 482 484 503 C4' A A 24 OK 505 502 504 525 C4' C A 25 OK 527 524 526 545 C4' U A 26 OK 547 544 546 565 C4' U A 27 OK 567 564 566 585 C4' C A 28 OK 587 584 586 605 C4' G A 29 OK 607 604 606 628 C4' C A 30 OK 630 627 629 648 C4' C A 31 OK 650 647 649 668 C4' G A 32 OK 670 667 669 691 C4' A A 33 OK 693 690 692 713 C4' G A 34 OK 715 712 714 736 C4' G A 35 OK 738 735 737 759 C4' A A 36 OK 761 758 760 781 C4' G A 37 OK 783 780 782 804 C4' U A 38 OK 806 803 805 824 C4' G A 39 OK 826 823 825 847 C4' C A 40 OK 849 846 848 867 C4' A A 41 OK 869 866 868 889 C4' A A 42 OK 891 888 890 911 C4' U A 43 OK 913 910 912 931 C4' C A 44 OK 933 930 932 951 C4' U A 45 OK 953 950 952 971 C4' G A 46 OK 973 970 972 994 C4' U A 47 OK 996 993 995 1014 C4' G A 48 OK 1016 1013 1015 1037 C4' A A 49 OK 1039 1036 1038 1059 C4' G A 50 OK 1061 1058 1060 1082 C4' G A 51 OK 1084 1081 1083 1105 C4' C A 52 OK 1107 1104 1106 1125 C4' C A 53 OK 1127 1124 1126 1145 C4' C A 54 OK 1147 1144 1146 1165 C4' C A 55 OK 1167 1164 1166 1185 C4' A A 56 OK 1187 1184 1186 1207 C4' G A 57 OK 1209 1206 1208 1230 C4' G A 58 OK 1232 1229 1231 1253 C4' A A 59 OK 1255 1252 1254 1275 C4' G A 60 OK 1277 1274 1276 1298 C4' G A 61 OK 1300 1297 1299 1321 C4' A A 62 OK 1323 1320 1322 1343 C4' C A 63 OK 1345 1342 1344 1363 C4' U A 64 OK 1365 1362 1364 1383 C4' G A 65 OK 1385 1382 1384 1406 C4' G A 66 OK 1408 1405 1407 1429 C4' G A 67 OK 1431 1428 1430 1452 C4' U A 68 OK 1454 1451 1453 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' G A 1 4 6 28 C5' G A 2 27 29 51 C5' G A 3 50 52 74 C5' U A 4 73 75 94 C5' C A 5 93 95 114 C5' A A 6 113 115 136 C5' G A 7 135 137 159 C5' A A 8 158 160 181 C5' U A 9 180 182 201 C5' C A 10 200 202 221 C5' G A 11 220 222 244 C5' G A 12 243 245 267 C5' C A 13 266 268 287 C5' G A 14 286 288 310 C5' A A 15 309 311 332 C5' A A 16 331 333 354 C5' A A 17 353 355 376 C5' G A 18 375 377 399 C5' U A 19 398 400 419 C5' C A 20 418 420 439 C5' G A 21 438 440 462 C5' C A 22 461 463 482 C5' C A 23 481 483 502 C5' A A 24 501 503 524 C5' C A 25 523 525 544 C5' U A 26 543 545 564 C5' U A 27 563 565 584 C5' C A 28 583 585 604 C5' G A 29 603 605 627 C5' C A 30 626 628 647 C5' C A 31 646 648 667 C5' G A 32 666 668 690 C5' A A 33 689 691 712 C5' G A 34 711 713 735 C5' G A 35 734 736 758 C5' A A 36 757 759 780 C5' G A 37 779 781 803 C5' U A 38 802 804 823 C5' G A 39 822 824 846 C5' C A 40 845 847 866 C5' A A 41 865 867 888 C5' A A 42 887 889 910 C5' U A 43 909 911 930 C5' C A 44 929 931 950 C5' U A 45 949 951 970 C5' G A 46 969 971 993 C5' U A 47 992 994 1013 C5' G A 48 1012 1014 1036 C5' A A 49 1035 1037 1058 C5' G A 50 1057 1059 1081 C5' G A 51 1080 1082 1104 C5' C A 52 1103 1105 1124 C5' C A 53 1123 1125 1144 C5' C A 54 1143 1145 1164 C5' C A 55 1163 1165 1184 C5' A A 56 1183 1185 1206 C5' G A 57 1205 1207 1229 C5' G A 58 1228 1230 1252 C5' A A 59 1251 1253 1274 C5' G A 60 1273 1275 1297 C5' G A 61 1296 1298 1320 C5' A A 62 1319 1321 1342 C5' C A 63 1341 1343 1362 C5' U A 64 1361 1363 1382 C5' G A 65 1381 1383 1405 C5' G A 66 1404 1406 1428 C5' G A 67 1427 1429 1451 C5' U A 68 1450 1452 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P G A 1 distorted distorted 2 3 4 24 P G A 2 distorted distorted 9 25 26 27 47 P G A 3 distorted distorted 32 48 49 50 70 P U A 4 distorted distorted 55 71 72 73 90 P C A 5 distorted distorted 78 91 92 93 110 P A A 6 distorted distorted 98 111 112 113 132 P G A 7 distorted distorted 118 133 134 135 155 P A A 8 distorted distorted 140 156 157 158 177 P U A 9 distorted distorted 163 178 179 180 197 P C A 10 distorted distorted 185 198 199 200 217 P G A 11 distorted distorted 205 218 219 220 240 P G A 12 distorted distorted 225 241 242 243 263 P C A 13 distorted distorted 248 264 265 266 283 P G A 14 distorted distorted 271 284 285 286 306 P A A 15 distorted distorted 291 307 308 309 328 P A A 16 distorted distorted 314 329 330 331 350 P A A 17 distorted distorted 336 351 352 353 372 P G A 18 distorted distorted 358 373 374 375 395 P U A 19 distorted distorted 380 396 397 398 415 P C A 20 distorted distorted 403 416 417 418 435 P G A 21 distorted distorted 423 436 437 438 458 P C A 22 distorted distorted 443 459 460 461 478 P C A 23 distorted distorted 466 479 480 481 498 P A A 24 distorted distorted 486 499 500 501 520 P C A 25 distorted distorted 506 521 522 523 540 P U A 26 distorted distorted 528 541 542 543 560 P U A 27 distorted distorted 548 561 562 563 580 P C A 28 distorted distorted 568 581 582 583 600 P G A 29 distorted distorted 588 601 602 603 623 P C A 30 distorted distorted 608 624 625 626 643 P C A 31 distorted distorted 631 644 645 646 663 P G A 32 distorted distorted 651 664 665 666 686 P A A 33 distorted distorted 671 687 688 689 708 P G A 34 distorted distorted 694 709 710 711 731 P G A 35 distorted distorted 716 732 733 734 754 P A A 36 distorted distorted 739 755 756 757 776 P G A 37 distorted distorted 762 777 778 779 799 P U A 38 distorted distorted 784 800 801 802 819 P G A 39 distorted distorted 807 820 821 822 842 P C A 40 distorted distorted 827 843 844 845 862 P A A 41 distorted distorted 850 863 864 865 884 P A A 42 distorted distorted 870 885 886 887 906 P U A 43 distorted distorted 892 907 908 909 926 P C A 44 distorted distorted 914 927 928 929 946 P U A 45 distorted distorted 934 947 948 949 966 P G A 46 distorted distorted 954 967 968 969 989 P U A 47 distorted distorted 974 990 991 992 1009 P G A 48 distorted distorted 997 1010 1011 1012 1032 P A A 49 distorted distorted 1017 1033 1034 1035 1054 P G A 50 distorted distorted 1040 1055 1056 1057 1077 P G A 51 distorted distorted 1062 1078 1079 1080 1100 P C A 52 distorted distorted 1085 1101 1102 1103 1120 P C A 53 distorted distorted 1108 1121 1122 1123 1140 P C A 54 distorted distorted 1128 1141 1142 1143 1160 P C A 55 distorted distorted 1148 1161 1162 1163 1180 P A A 56 distorted distorted 1168 1181 1182 1183 1202 P G A 57 distorted distorted 1188 1203 1204 1205 1225 P G A 58 distorted distorted 1210 1226 1227 1228 1248 P A A 59 distorted distorted 1233 1249 1250 1251 1270 P G A 60 distorted distorted 1256 1271 1272 1273 1293 P G A 61 distorted distorted 1278 1294 1295 1296 1316 P A A 62 distorted distorted 1301 1317 1318 1319 1338 P C A 63 distorted distorted 1324 1339 1340 1341 1358 P U A 64 distorted distorted 1346 1359 1360 1361 1378 P G A 65 distorted distorted 1366 1379 1380 1381 1401 P G A 66 distorted distorted 1386 1402 1403 1404 1424 P G A 67 distorted distorted 1409 1425 1426 1427 1447 P U A 68 distorted distorted 1432 1448 1449 1450 ---------------------------------------------------------------------------------