ID code: '2EEU' 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 15 beta 4 10 7 32 C1' G A 16 beta 27 33 30 55 C1' A A 17 beta 50 56 53 77 C1' C A 18 beta 72 78 75 97 C1' A A 19 beta 92 98 95 119 C1' U A 20 beta 114 120 117 139 C1' A A 21 beta 134 140 137 161 C1' A A 22 beta 156 162 159 183 C1' A A 23 beta 178 184 181 205 C1' A A 24 beta 200 206 203 227 C1' U A 25 beta 222 228 225 247 C1' C A 26 beta 242 248 245 267 C1' G A 27 beta 262 268 265 290 C1' C A 28 beta 285 291 288 310 C1' G A 29 beta 305 311 308 333 C1' U A 30 beta 328 334 331 353 C1' G A 31 beta 348 354 351 376 C1' G A 32 beta 371 377 374 399 C1' A A 33 beta 394 400 397 421 C1' U A 34 beta 416 422 419 441 C1' A A 35 beta 436 442 439 463 C1' U A 36 beta 458 464 461 483 C1' G A 37 beta 478 484 481 506 C1' G A 38 beta 501 507 504 529 C1' C A 39 beta 524 530 527 549 C1' A A 40 beta 544 550 547 571 C1' C A 41 beta 566 572 569 591 C1' G A 42 beta 586 592 589 614 C1' C A 43 beta 609 615 612 634 C1' A A 44 beta 629 635 632 656 C1' A A 45 beta 651 657 654 678 C1' G A 46 beta 673 679 676 701 C1' U A 47 beta 696 702 699 721 C1' U A 48 beta 716 722 719 741 C1' U A 49 beta 736 742 739 761 C1' C A 50 beta 756 762 759 781 C1' U A 51 beta 776 782 779 801 C1' U A 52 beta 796 802 799 821 C1' C A 53 beta 816 822 819 841 C1' C A 54 beta 836 842 839 861 C1' G A 55 beta 856 862 859 884 C1' G A 56 beta 879 885 882 907 C1' G A 57 beta 902 908 905 930 C1' C A 58 beta 925 931 928 950 C1' A A 59 beta 945 951 948 972 C1' C A 60 beta 967 973 970 992 C1' C A 61 beta 987 993 990 1012 C1' G A 62 beta 1007 1013 1010 1035 C1' U A 63 beta 1030 1036 1033 1055 C1' A A 64 beta 1050 1056 1053 1077 C1' A A 65 beta 1072 1078 1075 1099 C1' A A 66 beta 1094 1100 1097 1121 C1' U A 67 beta 1116 1122 1119 1141 C1' G A 68 beta 1136 1142 1139 1164 C1' U A 69 beta 1159 1165 1162 1184 C1' C A 70 beta 1179 1185 1182 1204 C1' C A 71 beta 1199 1205 1202 1224 C1' G A 72 beta 1219 1225 1222 1247 C1' A A 73 beta 1242 1248 1245 1269 C1' C A 74 beta 1264 1270 1267 1289 C1' U A 75 beta 1284 1290 1287 1309 C1' A A 76 beta 1304 1310 1307 1331 C1' U A 77 beta 1326 1332 1329 1351 C1' G A 78 beta 1346 1352 1349 1374 C1' U A 79 beta 1369 1375 1372 1394 C1' C A 80 beta 1389 1395 1392 1414 C1' C A 81 beta 1409 1415 1412 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G A 15 OK 9 5 8 30 C2' G A 16 OK 32 28 31 53 C2' A A 17 OK 55 51 54 75 C2' C A 18 OK 77 73 76 95 C2' A A 19 OK 97 93 96 117 C2' U A 20 OK 119 115 118 137 C2' A A 21 OK 139 135 138 159 C2' A A 22 OK 161 157 160 181 C2' A A 23 OK 183 179 182 203 C2' A A 24 OK 205 201 204 225 C2' U A 25 OK 227 223 226 245 C2' C A 26 OK 247 243 246 265 C2' G A 27 OK 267 263 266 288 C2' C A 28 OK 290 286 289 308 C2' G A 29 OK 310 306 309 331 C2' U A 30 OK 333 329 332 351 C2' G A 31 OK 353 349 352 374 C2' G A 32 OK 376 372 375 397 C2' A A 33 OK 399 395 398 419 C2' U A 34 OK 421 417 420 439 C2' A A 35 OK 441 437 440 461 C2' U A 36 OK 463 459 462 481 C2' G A 37 OK 483 479 482 504 C2' G A 38 OK 506 502 505 527 C2' C A 39 OK 529 525 528 547 C2' A A 40 OK 549 545 548 569 C2' C A 41 OK 571 567 570 589 C2' G A 42 OK 591 587 590 612 C2' C A 43 OK 614 610 613 632 C2' A A 44 OK 634 630 633 654 C2' A A 45 OK 656 652 655 676 C2' G A 46 OK 678 674 677 699 C2' U A 47 OK 701 697 700 719 C2' U A 48 OK 721 717 720 739 C2' U A 49 OK 741 737 740 759 C2' C A 50 OK 761 757 760 779 C2' U A 51 OK 781 777 780 799 C2' U A 52 OK 801 797 800 819 C2' C A 53 OK 821 817 820 839 C2' C A 54 OK 841 837 840 859 C2' G A 55 OK 861 857 860 882 C2' G A 56 OK 884 880 883 905 C2' G A 57 OK 907 903 906 928 C2' C A 58 OK 930 926 929 948 C2' A A 59 OK 950 946 949 970 C2' C A 60 OK 972 968 971 990 C2' C A 61 OK 992 988 991 1010 C2' G A 62 OK 1012 1008 1011 1033 C2' U A 63 OK 1035 1031 1034 1053 C2' A A 64 OK 1055 1051 1054 1075 C2' A A 65 OK 1077 1073 1076 1097 C2' A A 66 OK 1099 1095 1098 1119 C2' U A 67 OK 1121 1117 1120 1139 C2' G A 68 OK 1141 1137 1140 1162 C2' U A 69 OK 1164 1160 1163 1182 C2' C A 70 OK 1184 1180 1183 1202 C2' C A 71 OK 1204 1200 1203 1222 C2' G A 72 OK 1224 1220 1223 1245 C2' A A 73 OK 1247 1243 1246 1267 C2' C A 74 OK 1269 1265 1268 1287 C2' U A 75 OK 1289 1285 1288 1307 C2' A A 76 OK 1309 1305 1308 1329 C2' U A 77 OK 1331 1327 1330 1349 C2' G A 78 OK 1351 1347 1350 1372 C2' U A 79 OK 1374 1370 1373 1392 C2' C A 80 OK 1394 1390 1393 1412 C2' C A 81 OK 1414 1410 1413 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 15 OK 3 6 7 28 C3' G A 16 OK 26 29 30 51 C3' A A 17 OK 49 52 53 73 C3' C A 18 OK 71 74 75 93 C3' A A 19 OK 91 94 95 115 C3' U A 20 OK 113 116 117 135 C3' A A 21 OK 133 136 137 157 C3' A A 22 OK 155 158 159 179 C3' A A 23 OK 177 180 181 201 C3' A A 24 OK 199 202 203 223 C3' U A 25 OK 221 224 225 243 C3' C A 26 OK 241 244 245 263 C3' G A 27 OK 261 264 265 286 C3' C A 28 OK 284 287 288 306 C3' G A 29 OK 304 307 308 329 C3' U A 30 OK 327 330 331 349 C3' G A 31 OK 347 350 351 372 C3' G A 32 OK 370 373 374 395 C3' A A 33 OK 393 396 397 417 C3' U A 34 OK 415 418 419 437 C3' A A 35 OK 435 438 439 459 C3' U A 36 OK 457 460 461 479 C3' G A 37 OK 477 480 481 502 C3' G A 38 OK 500 503 504 525 C3' C A 39 OK 523 526 527 545 C3' A A 40 OK 543 546 547 567 C3' C A 41 OK 565 568 569 587 C3' G A 42 OK 585 588 589 610 C3' C A 43 OK 608 611 612 630 C3' A A 44 OK 628 631 632 652 C3' A A 45 OK 650 653 654 674 C3' G A 46 OK 672 675 676 697 C3' U A 47 OK 695 698 699 717 C3' U A 48 OK 715 718 719 737 C3' U A 49 OK 735 738 739 757 C3' C A 50 OK 755 758 759 777 C3' U A 51 OK 775 778 779 797 C3' U A 52 OK 795 798 799 817 C3' C A 53 OK 815 818 819 837 C3' C A 54 OK 835 838 839 857 C3' G A 55 OK 855 858 859 880 C3' G A 56 OK 878 881 882 903 C3' G A 57 OK 901 904 905 926 C3' C A 58 OK 924 927 928 946 C3' A A 59 OK 944 947 948 968 C3' C A 60 OK 966 969 970 988 C3' C A 61 OK 986 989 990 1008 C3' G A 62 OK 1006 1009 1010 1031 C3' U A 63 OK 1029 1032 1033 1051 C3' A A 64 OK 1049 1052 1053 1073 C3' A A 65 OK 1071 1074 1075 1095 C3' A A 66 OK 1093 1096 1097 1117 C3' U A 67 OK 1115 1118 1119 1137 C3' G A 68 OK 1135 1138 1139 1160 C3' U A 69 OK 1158 1161 1162 1180 C3' C A 70 OK 1178 1181 1182 1200 C3' C A 71 OK 1198 1201 1202 1220 C3' G A 72 OK 1218 1221 1222 1243 C3' A A 73 OK 1241 1244 1245 1265 C3' C A 74 OK 1263 1266 1267 1285 C3' U A 75 OK 1283 1286 1287 1305 C3' A A 76 OK 1303 1306 1307 1327 C3' U A 77 OK 1325 1328 1329 1347 C3' G A 78 OK 1345 1348 1349 1370 C3' U A 79 OK 1368 1371 1372 1390 C3' C A 80 OK 1388 1391 1392 1410 C3' C A 81 OK 1408 1411 1412 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 15 OK 5 2 4 26 C4' G A 16 OK 28 25 27 49 C4' A A 17 OK 51 48 50 71 C4' C A 18 OK 73 70 72 91 C4' A A 19 OK 93 90 92 113 C4' U A 20 OK 115 112 114 133 C4' A A 21 OK 135 132 134 155 C4' A A 22 OK 157 154 156 177 C4' A A 23 OK 179 176 178 199 C4' A A 24 OK 201 198 200 221 C4' U A 25 OK 223 220 222 241 C4' C A 26 OK 243 240 242 261 C4' G A 27 OK 263 260 262 284 C4' C A 28 OK 286 283 285 304 C4' G A 29 OK 306 303 305 327 C4' U A 30 OK 329 326 328 347 C4' G A 31 OK 349 346 348 370 C4' G A 32 OK 372 369 371 393 C4' A A 33 OK 395 392 394 415 C4' U A 34 OK 417 414 416 435 C4' A A 35 OK 437 434 436 457 C4' U A 36 OK 459 456 458 477 C4' G A 37 OK 479 476 478 500 C4' G A 38 OK 502 499 501 523 C4' C A 39 OK 525 522 524 543 C4' A A 40 OK 545 542 544 565 C4' C A 41 OK 567 564 566 585 C4' G A 42 OK 587 584 586 608 C4' C A 43 OK 610 607 609 628 C4' A A 44 OK 630 627 629 650 C4' A A 45 OK 652 649 651 672 C4' G A 46 OK 674 671 673 695 C4' U A 47 OK 697 694 696 715 C4' U A 48 OK 717 714 716 735 C4' U A 49 OK 737 734 736 755 C4' C A 50 OK 757 754 756 775 C4' U A 51 OK 777 774 776 795 C4' U A 52 OK 797 794 796 815 C4' C A 53 OK 817 814 816 835 C4' C A 54 OK 837 834 836 855 C4' G A 55 OK 857 854 856 878 C4' G A 56 OK 880 877 879 901 C4' G A 57 OK 903 900 902 924 C4' C A 58 OK 926 923 925 944 C4' A A 59 OK 946 943 945 966 C4' C A 60 OK 968 965 967 986 C4' C A 61 OK 988 985 987 1006 C4' G A 62 OK 1008 1005 1007 1029 C4' U A 63 OK 1031 1028 1030 1049 C4' A A 64 OK 1051 1048 1050 1071 C4' A A 65 OK 1073 1070 1072 1093 C4' A A 66 OK 1095 1092 1094 1115 C4' U A 67 OK 1117 1114 1116 1135 C4' G A 68 OK 1137 1134 1136 1158 C4' U A 69 OK 1160 1157 1159 1178 C4' C A 70 OK 1180 1177 1179 1198 C4' C A 71 OK 1200 1197 1199 1218 C4' G A 72 OK 1220 1217 1219 1241 C4' A A 73 OK 1243 1240 1242 1263 C4' C A 74 OK 1265 1262 1264 1283 C4' U A 75 OK 1285 1282 1284 1303 C4' A A 76 OK 1305 1302 1304 1325 C4' U A 77 OK 1327 1324 1326 1345 C4' G A 78 OK 1347 1344 1346 1368 C4' U A 79 OK 1370 1367 1369 1388 C4' C A 80 OK 1390 1387 1389 1408 C4' C A 81 OK 1410 1407 1409 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 15 1 3 25 C5' G A 16 24 26 48 C5' A A 17 47 49 70 C5' C A 18 69 71 90 C5' A A 19 89 91 112 C5' U A 20 111 113 132 C5' A A 21 131 133 154 C5' A A 22 153 155 176 C5' A A 23 175 177 198 C5' A A 24 197 199 220 C5' U A 25 219 221 240 C5' C A 26 239 241 260 C5' G A 27 259 261 283 C5' C A 28 282 284 303 C5' G A 29 302 304 326 C5' U A 30 325 327 346 C5' G A 31 345 347 369 C5' G A 32 368 370 392 C5' A A 33 391 393 414 C5' U A 34 413 415 434 C5' A A 35 433 435 456 C5' U A 36 455 457 476 C5' G A 37 475 477 499 C5' G A 38 498 500 522 C5' C A 39 521 523 542 C5' A A 40 541 543 564 C5' C A 41 563 565 584 C5' G A 42 583 585 607 C5' C A 43 606 608 627 C5' A A 44 626 628 649 C5' A A 45 648 650 671 C5' G A 46 670 672 694 C5' U A 47 693 695 714 C5' U A 48 713 715 734 C5' U A 49 733 735 754 C5' C A 50 753 755 774 C5' U A 51 773 775 794 C5' U A 52 793 795 814 C5' C A 53 813 815 834 C5' C A 54 833 835 854 C5' G A 55 853 855 877 C5' G A 56 876 878 900 C5' G A 57 899 901 923 C5' C A 58 922 924 943 C5' A A 59 942 944 965 C5' C A 60 964 966 985 C5' C A 61 984 986 1005 C5' G A 62 1004 1006 1028 C5' U A 63 1027 1029 1048 C5' A A 64 1047 1049 1070 C5' A A 65 1069 1071 1092 C5' A A 66 1091 1093 1114 C5' U A 67 1113 1115 1134 C5' G A 68 1133 1135 1157 C5' U A 69 1156 1158 1177 C5' C A 70 1176 1178 1197 C5' C A 71 1196 1198 1217 C5' G A 72 1216 1218 1240 C5' A A 73 1239 1241 1262 C5' C A 74 1261 1263 1282 C5' U A 75 1281 1283 1302 C5' A A 76 1301 1303 1324 C5' U A 77 1323 1325 1344 C5' G A 78 1343 1345 1367 C5' U A 79 1366 1368 1387 C5' C A 80 1386 1388 1407 C5' C A 81 1406 1408 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 21 P G A 16 distorted distorted 6 22 23 24 44 P A A 17 distorted distorted 29 45 46 47 66 P C A 18 distorted distorted 52 67 68 69 86 P A A 19 distorted distorted 74 87 88 89 108 P U A 20 distorted distorted 94 109 110 111 128 P A A 21 distorted distorted 116 129 130 131 150 P A A 22 distorted distorted 136 151 152 153 172 P A A 23 distorted distorted 158 173 174 175 194 P A A 24 distorted distorted 180 195 196 197 216 P U A 25 distorted distorted 202 217 218 219 236 P C A 26 distorted distorted 224 237 238 239 256 P G A 27 distorted distorted 244 257 258 259 279 P C A 28 distorted distorted 264 280 281 282 299 P G A 29 distorted distorted 287 300 301 302 322 P U A 30 distorted distorted 307 323 324 325 342 P G A 31 distorted distorted 330 343 344 345 365 P G A 32 distorted distorted 350 366 367 368 388 P A A 33 distorted distorted 373 389 390 391 410 P U A 34 distorted distorted 396 411 412 413 430 P A A 35 distorted distorted 418 431 432 433 452 P U A 36 distorted distorted 438 453 454 455 472 P G A 37 distorted distorted 460 473 474 475 495 P G A 38 distorted distorted 480 496 497 498 518 P C A 39 distorted distorted 503 519 520 521 538 P A A 40 distorted distorted 526 539 540 541 560 P C A 41 distorted distorted 546 561 562 563 580 P G A 42 distorted distorted 568 581 582 583 603 P C A 43 distorted distorted 588 604 605 606 623 P A A 44 distorted distorted 611 624 625 626 645 P A A 45 distorted distorted 631 646 647 648 667 P G A 46 distorted distorted 653 668 669 670 690 P U A 47 distorted distorted 675 691 692 693 710 P U A 48 distorted distorted 698 711 712 713 730 P U A 49 distorted distorted 718 731 732 733 750 P C A 50 distorted distorted 738 751 752 753 770 P U A 51 distorted distorted 758 771 772 773 790 P U A 52 distorted distorted 778 791 792 793 810 P C A 53 distorted distorted 798 811 812 813 830 P C A 54 distorted distorted 818 831 832 833 850 P G A 55 distorted distorted 838 851 852 853 873 P G A 56 distorted distorted 858 874 875 876 896 P G A 57 distorted distorted 881 897 898 899 919 P C A 58 distorted distorted 904 920 921 922 939 P A A 59 distorted distorted 927 940 941 942 961 P C A 60 distorted distorted 947 962 963 964 981 P C A 61 distorted distorted 969 982 983 984 1001 P G A 62 distorted distorted 989 1002 1003 1004 1024 P U A 63 distorted distorted 1009 1025 1026 1027 1044 P A A 64 distorted distorted 1032 1045 1046 1047 1066 P A A 65 distorted distorted 1052 1067 1068 1069 1088 P A A 66 distorted distorted 1074 1089 1090 1091 1110 P U A 67 distorted distorted 1096 1111 1112 1113 1130 P G A 68 distorted distorted 1118 1131 1132 1133 1153 P U A 69 distorted distorted 1138 1154 1155 1156 1173 P C A 70 distorted distorted 1161 1174 1175 1176 1193 P C A 71 distorted distorted 1181 1194 1195 1196 1213 P G A 72 distorted distorted 1201 1214 1215 1216 1236 P A A 73 distorted distorted 1221 1237 1238 1239 1258 P C A 74 distorted distorted 1244 1259 1260 1261 1278 P U A 75 distorted distorted 1266 1279 1280 1281 1298 P A A 76 distorted distorted 1286 1299 1300 1301 1320 P U A 77 distorted distorted 1306 1321 1322 1323 1340 P G A 78 distorted distorted 1328 1341 1342 1343 1363 P U A 79 distorted distorted 1348 1364 1365 1366 1383 P C A 80 distorted distorted 1371 1384 1385 1386 1403 P C A 81 distorted distorted 1391 1404 1405 1406 ---------------------------------------------------------------------------------