ID code: '3GES' 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' U A 22 beta 156 162 159 181 C1' A A 23 beta 176 182 179 203 C1' A A 24 beta 198 204 201 225 C1' U A 25 beta 220 226 223 245 C1' C A 26 beta 240 246 243 265 C1' G A 27 beta 260 266 263 288 C1' C A 28 beta 283 289 286 308 C1' G A 29 beta 303 309 306 331 C1' U A 30 beta 326 332 329 351 C1' G A 31 beta 346 352 349 374 C1' G A 32 beta 369 375 372 397 C1' A A 33 beta 392 398 395 419 C1' U A 34 beta 414 420 417 439 C1' A A 35 beta 434 440 437 461 C1' U A 36 beta 456 462 459 481 C1' G A 37 beta 476 482 479 504 C1' G A 38 beta 499 505 502 527 C1' C A 39 beta 522 528 525 547 C1' A A 40 beta 542 548 545 569 C1' C A 41 beta 564 570 567 589 C1' G A 42 beta 584 590 587 612 C1' C A 43 beta 607 613 610 632 C1' A A 44 beta 627 633 630 654 C1' A A 45 beta 649 655 652 676 C1' G A 46 beta 671 677 674 699 C1' U A 47 beta 694 700 697 719 C1' U A 48 beta 714 720 717 739 C1' U A 49 beta 734 740 737 759 C1' C A 50 beta 754 760 757 779 C1' U A 51 beta 774 780 777 799 C1' A A 52 beta 794 800 797 821 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' U 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' U A 22 OK 161 157 160 179 C2' A A 23 OK 181 177 180 201 C2' A A 24 OK 203 199 202 223 C2' U A 25 OK 225 221 224 243 C2' C A 26 OK 245 241 244 263 C2' G A 27 OK 265 261 264 286 C2' C A 28 OK 288 284 287 306 C2' G A 29 OK 308 304 307 329 C2' U A 30 OK 331 327 330 349 C2' G A 31 OK 351 347 350 372 C2' G A 32 OK 374 370 373 395 C2' A A 33 OK 397 393 396 417 C2' U A 34 OK 419 415 418 437 C2' A A 35 OK 439 435 438 459 C2' U A 36 OK 461 457 460 479 C2' G A 37 OK 481 477 480 502 C2' G A 38 OK 504 500 503 525 C2' C A 39 OK 527 523 526 545 C2' A A 40 OK 547 543 546 567 C2' C A 41 OK 569 565 568 587 C2' G A 42 OK 589 585 588 610 C2' C A 43 OK 612 608 611 630 C2' A A 44 OK 632 628 631 652 C2' A A 45 OK 654 650 653 674 C2' G A 46 OK 676 672 675 697 C2' U A 47 OK 699 695 698 717 C2' U A 48 OK 719 715 718 737 C2' U A 49 OK 739 735 738 757 C2' C A 50 OK 759 755 758 777 C2' U A 51 OK 779 775 778 797 C2' A A 52 OK 799 795 798 819 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' U 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' U A 22 OK 155 158 159 177 C3' A A 23 OK 175 178 179 199 C3' A A 24 OK 197 200 201 221 C3' U A 25 OK 219 222 223 241 C3' C A 26 OK 239 242 243 261 C3' G A 27 OK 259 262 263 284 C3' C A 28 OK 282 285 286 304 C3' G A 29 OK 302 305 306 327 C3' U A 30 OK 325 328 329 347 C3' G A 31 OK 345 348 349 370 C3' G A 32 OK 368 371 372 393 C3' A A 33 OK 391 394 395 415 C3' U A 34 OK 413 416 417 435 C3' A A 35 OK 433 436 437 457 C3' U A 36 OK 455 458 459 477 C3' G A 37 OK 475 478 479 500 C3' G A 38 OK 498 501 502 523 C3' C A 39 OK 521 524 525 543 C3' A A 40 OK 541 544 545 565 C3' C A 41 OK 563 566 567 585 C3' G A 42 OK 583 586 587 608 C3' C A 43 OK 606 609 610 628 C3' A A 44 OK 626 629 630 650 C3' A A 45 OK 648 651 652 672 C3' G A 46 OK 670 673 674 695 C3' U A 47 OK 693 696 697 715 C3' U A 48 OK 713 716 717 735 C3' U A 49 OK 733 736 737 755 C3' C A 50 OK 753 756 757 775 C3' U A 51 OK 773 776 777 795 C3' A A 52 OK 793 796 797 817 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' U 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' U A 22 OK 157 154 156 175 C4' A A 23 OK 177 174 176 197 C4' A A 24 OK 199 196 198 219 C4' U A 25 OK 221 218 220 239 C4' C A 26 OK 241 238 240 259 C4' G A 27 OK 261 258 260 282 C4' C A 28 OK 284 281 283 302 C4' G A 29 OK 304 301 303 325 C4' U A 30 OK 327 324 326 345 C4' G A 31 OK 347 344 346 368 C4' G A 32 OK 370 367 369 391 C4' A A 33 OK 393 390 392 413 C4' U A 34 OK 415 412 414 433 C4' A A 35 OK 435 432 434 455 C4' U A 36 OK 457 454 456 475 C4' G A 37 OK 477 474 476 498 C4' G A 38 OK 500 497 499 521 C4' C A 39 OK 523 520 522 541 C4' A A 40 OK 543 540 542 563 C4' C A 41 OK 565 562 564 583 C4' G A 42 OK 585 582 584 606 C4' C A 43 OK 608 605 607 626 C4' A A 44 OK 628 625 627 648 C4' A A 45 OK 650 647 649 670 C4' G A 46 OK 672 669 671 693 C4' U A 47 OK 695 692 694 713 C4' U A 48 OK 715 712 714 733 C4' U A 49 OK 735 732 734 753 C4' C A 50 OK 755 752 754 773 C4' U A 51 OK 775 772 774 793 C4' A A 52 OK 795 792 794 815 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' U 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' U A 22 153 155 174 C5' A A 23 173 175 196 C5' A A 24 195 197 218 C5' U A 25 217 219 238 C5' C A 26 237 239 258 C5' G A 27 257 259 281 C5' C A 28 280 282 301 C5' G A 29 300 302 324 C5' U A 30 323 325 344 C5' G A 31 343 345 367 C5' G A 32 366 368 390 C5' A A 33 389 391 412 C5' U A 34 411 413 432 C5' A A 35 431 433 454 C5' U A 36 453 455 474 C5' G A 37 473 475 497 C5' G A 38 496 498 520 C5' C A 39 519 521 540 C5' A A 40 539 541 562 C5' C A 41 561 563 582 C5' G A 42 581 583 605 C5' C A 43 604 606 625 C5' A A 44 624 626 647 C5' A A 45 646 648 669 C5' G A 46 668 670 692 C5' U A 47 691 693 712 C5' U A 48 711 713 732 C5' U A 49 731 733 752 C5' C A 50 751 753 772 C5' U A 51 771 773 792 C5' A A 52 791 793 814 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' U 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 U A 22 distorted distorted 136 151 152 153 170 P A A 23 distorted distorted 158 171 172 173 192 P A A 24 distorted distorted 178 193 194 195 214 P U A 25 distorted distorted 200 215 216 217 234 P C A 26 distorted distorted 222 235 236 237 254 P G A 27 distorted distorted 242 255 256 257 277 P C A 28 distorted distorted 262 278 279 280 297 P G A 29 distorted distorted 285 298 299 300 320 P U A 30 distorted distorted 305 321 322 323 340 P G A 31 distorted distorted 328 341 342 343 363 P G A 32 distorted distorted 348 364 365 366 386 P A A 33 distorted distorted 371 387 388 389 408 P U A 34 distorted distorted 394 409 410 411 428 P A A 35 distorted distorted 416 429 430 431 450 P U A 36 distorted distorted 436 451 452 453 470 P G A 37 distorted distorted 458 471 472 473 493 P G A 38 distorted distorted 478 494 495 496 516 P C A 39 distorted distorted 501 517 518 519 536 P A A 40 distorted distorted 524 537 538 539 558 P C A 41 distorted distorted 544 559 560 561 578 P G A 42 distorted distorted 566 579 580 581 601 P C A 43 distorted distorted 586 602 603 604 621 P A A 44 distorted distorted 609 622 623 624 643 P A A 45 distorted distorted 629 644 645 646 665 P G A 46 distorted distorted 651 666 667 668 688 P U A 47 distorted distorted 673 689 690 691 708 P U A 48 distorted distorted 696 709 710 711 728 P U A 49 distorted distorted 716 729 730 731 748 P C A 50 distorted distorted 736 749 750 751 768 P U A 51 distorted distorted 756 769 770 771 788 P A A 52 distorted distorted 776 789 790 791 810 P C A 53 distorted distorted 796 811 812 813 830 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 U 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 ---------------------------------------------------------------------------------