ID code: '2EES' 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' U A 21 beta 134 140 137 159 C1' U A 22 beta 154 160 157 179 C1' A A 23 beta 174 180 177 201 C1' A A 24 beta 196 202 199 223 C1' U A 25 beta 218 224 221 243 C1' C A 26 beta 238 244 241 263 C1' G A 27 beta 258 264 261 286 C1' C A 28 beta 281 287 284 306 C1' G A 29 beta 301 307 304 329 C1' U A 30 beta 324 330 327 349 C1' G A 31 beta 344 350 347 372 C1' G A 32 beta 367 373 370 395 C1' A A 33 beta 390 396 393 417 C1' U A 34 beta 412 418 415 437 C1' A A 35 beta 432 438 435 459 C1' U A 36 beta 454 460 457 479 C1' G A 37 beta 474 480 477 502 C1' G A 38 beta 497 503 500 525 C1' C A 39 beta 520 526 523 545 C1' A A 40 beta 540 546 543 567 C1' C A 41 beta 562 568 565 587 C1' G A 42 beta 582 588 585 610 C1' C A 43 beta 605 611 608 630 C1' A A 44 beta 625 631 628 652 C1' A A 45 beta 647 653 650 674 C1' G A 46 beta 669 675 672 697 C1' U A 47 beta 692 698 695 717 C1' U A 48 beta 712 718 715 737 C1' U A 49 beta 732 738 735 757 C1' C A 50 beta 752 758 755 777 C1' U A 51 beta 772 778 775 797 C1' A A 52 beta 792 798 795 819 C1' C A 53 beta 814 820 817 839 C1' C A 54 beta 834 840 837 859 C1' G A 55 beta 854 860 857 882 C1' G A 56 beta 877 883 880 905 C1' G A 57 beta 900 906 903 928 C1' C A 58 beta 923 929 926 948 C1' A A 59 beta 943 949 946 970 C1' C A 60 beta 965 971 968 990 C1' C A 61 beta 985 991 988 1010 C1' G A 62 beta 1005 1011 1008 1033 C1' U A 63 beta 1028 1034 1031 1053 C1' A A 64 beta 1048 1054 1051 1075 C1' A A 65 beta 1070 1076 1073 1097 C1' A A 66 beta 1092 1098 1095 1119 C1' U A 67 beta 1114 1120 1117 1139 C1' G A 68 beta 1134 1140 1137 1162 C1' U A 69 beta 1157 1163 1160 1182 C1' C A 70 beta 1177 1183 1180 1202 C1' C A 71 beta 1197 1203 1200 1222 C1' G A 72 beta 1217 1223 1220 1245 C1' A A 73 beta 1240 1246 1243 1267 C1' C A 74 beta 1262 1268 1265 1287 C1' A A 75 beta 1282 1288 1285 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' U A 21 OK 139 135 138 157 C2' U A 22 OK 159 155 158 177 C2' A A 23 OK 179 175 178 199 C2' A A 24 OK 201 197 200 221 C2' U A 25 OK 223 219 222 241 C2' C A 26 OK 243 239 242 261 C2' G A 27 OK 263 259 262 284 C2' C A 28 OK 286 282 285 304 C2' G A 29 OK 306 302 305 327 C2' U A 30 OK 329 325 328 347 C2' G A 31 OK 349 345 348 370 C2' G A 32 OK 372 368 371 393 C2' A A 33 OK 395 391 394 415 C2' U A 34 OK 417 413 416 435 C2' A A 35 OK 437 433 436 457 C2' U A 36 OK 459 455 458 477 C2' G A 37 OK 479 475 478 500 C2' G A 38 OK 502 498 501 523 C2' C A 39 OK 525 521 524 543 C2' A A 40 OK 545 541 544 565 C2' C A 41 OK 567 563 566 585 C2' G A 42 OK 587 583 586 608 C2' C A 43 OK 610 606 609 628 C2' A A 44 OK 630 626 629 650 C2' A A 45 OK 652 648 651 672 C2' G A 46 OK 674 670 673 695 C2' U A 47 OK 697 693 696 715 C2' U A 48 OK 717 713 716 735 C2' U A 49 OK 737 733 736 755 C2' C A 50 OK 757 753 756 775 C2' U A 51 OK 777 773 776 795 C2' A A 52 OK 797 793 796 817 C2' C A 53 OK 819 815 818 837 C2' C A 54 OK 839 835 838 857 C2' G A 55 OK 859 855 858 880 C2' G A 56 OK 882 878 881 903 C2' G A 57 OK 905 901 904 926 C2' C A 58 OK 928 924 927 946 C2' A A 59 OK 948 944 947 968 C2' C A 60 OK 970 966 969 988 C2' C A 61 OK 990 986 989 1008 C2' G A 62 OK 1010 1006 1009 1031 C2' U A 63 OK 1033 1029 1032 1051 C2' A A 64 OK 1053 1049 1052 1073 C2' A A 65 OK 1075 1071 1074 1095 C2' A A 66 OK 1097 1093 1096 1117 C2' U A 67 OK 1119 1115 1118 1137 C2' G A 68 OK 1139 1135 1138 1160 C2' U A 69 OK 1162 1158 1161 1180 C2' C A 70 OK 1182 1178 1181 1200 C2' C A 71 OK 1202 1198 1201 1220 C2' G A 72 OK 1222 1218 1221 1243 C2' A A 73 OK 1245 1241 1244 1265 C2' C A 74 OK 1267 1263 1266 1285 C2' A A 75 OK 1287 1283 1286 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' U A 21 OK 133 136 137 155 C3' U A 22 OK 153 156 157 175 C3' A A 23 OK 173 176 177 197 C3' A A 24 OK 195 198 199 219 C3' U A 25 OK 217 220 221 239 C3' C A 26 OK 237 240 241 259 C3' G A 27 OK 257 260 261 282 C3' C A 28 OK 280 283 284 302 C3' G A 29 OK 300 303 304 325 C3' U A 30 OK 323 326 327 345 C3' G A 31 OK 343 346 347 368 C3' G A 32 OK 366 369 370 391 C3' A A 33 OK 389 392 393 413 C3' U A 34 OK 411 414 415 433 C3' A A 35 OK 431 434 435 455 C3' U A 36 OK 453 456 457 475 C3' G A 37 OK 473 476 477 498 C3' G A 38 OK 496 499 500 521 C3' C A 39 OK 519 522 523 541 C3' A A 40 OK 539 542 543 563 C3' C A 41 OK 561 564 565 583 C3' G A 42 OK 581 584 585 606 C3' C A 43 OK 604 607 608 626 C3' A A 44 OK 624 627 628 648 C3' A A 45 OK 646 649 650 670 C3' G A 46 OK 668 671 672 693 C3' U A 47 OK 691 694 695 713 C3' U A 48 OK 711 714 715 733 C3' U A 49 OK 731 734 735 753 C3' C A 50 OK 751 754 755 773 C3' U A 51 OK 771 774 775 793 C3' A A 52 OK 791 794 795 815 C3' C A 53 OK 813 816 817 835 C3' C A 54 OK 833 836 837 855 C3' G A 55 OK 853 856 857 878 C3' G A 56 OK 876 879 880 901 C3' G A 57 OK 899 902 903 924 C3' C A 58 OK 922 925 926 944 C3' A A 59 OK 942 945 946 966 C3' C A 60 OK 964 967 968 986 C3' C A 61 OK 984 987 988 1006 C3' G A 62 OK 1004 1007 1008 1029 C3' U A 63 OK 1027 1030 1031 1049 C3' A A 64 OK 1047 1050 1051 1071 C3' A A 65 OK 1069 1072 1073 1093 C3' A A 66 OK 1091 1094 1095 1115 C3' U A 67 OK 1113 1116 1117 1135 C3' G A 68 OK 1133 1136 1137 1158 C3' U A 69 OK 1156 1159 1160 1178 C3' C A 70 OK 1176 1179 1180 1198 C3' C A 71 OK 1196 1199 1200 1218 C3' G A 72 OK 1216 1219 1220 1241 C3' A A 73 OK 1239 1242 1243 1263 C3' C A 74 OK 1261 1264 1265 1283 C3' A A 75 OK 1281 1284 1285 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' U A 21 OK 135 132 134 153 C4' U A 22 OK 155 152 154 173 C4' A A 23 OK 175 172 174 195 C4' A A 24 OK 197 194 196 217 C4' U A 25 OK 219 216 218 237 C4' C A 26 OK 239 236 238 257 C4' G A 27 OK 259 256 258 280 C4' C A 28 OK 282 279 281 300 C4' G A 29 OK 302 299 301 323 C4' U A 30 OK 325 322 324 343 C4' G A 31 OK 345 342 344 366 C4' G A 32 OK 368 365 367 389 C4' A A 33 OK 391 388 390 411 C4' U A 34 OK 413 410 412 431 C4' A A 35 OK 433 430 432 453 C4' U A 36 OK 455 452 454 473 C4' G A 37 OK 475 472 474 496 C4' G A 38 OK 498 495 497 519 C4' C A 39 OK 521 518 520 539 C4' A A 40 OK 541 538 540 561 C4' C A 41 OK 563 560 562 581 C4' G A 42 OK 583 580 582 604 C4' C A 43 OK 606 603 605 624 C4' A A 44 OK 626 623 625 646 C4' A A 45 OK 648 645 647 668 C4' G A 46 OK 670 667 669 691 C4' U A 47 OK 693 690 692 711 C4' U A 48 OK 713 710 712 731 C4' U A 49 OK 733 730 732 751 C4' C A 50 OK 753 750 752 771 C4' U A 51 OK 773 770 772 791 C4' A A 52 OK 793 790 792 813 C4' C A 53 OK 815 812 814 833 C4' C A 54 OK 835 832 834 853 C4' G A 55 OK 855 852 854 876 C4' G A 56 OK 878 875 877 899 C4' G A 57 OK 901 898 900 922 C4' C A 58 OK 924 921 923 942 C4' A A 59 OK 944 941 943 964 C4' C A 60 OK 966 963 965 984 C4' C A 61 OK 986 983 985 1004 C4' G A 62 OK 1006 1003 1005 1027 C4' U A 63 OK 1029 1026 1028 1047 C4' A A 64 OK 1049 1046 1048 1069 C4' A A 65 OK 1071 1068 1070 1091 C4' A A 66 OK 1093 1090 1092 1113 C4' U A 67 OK 1115 1112 1114 1133 C4' G A 68 OK 1135 1132 1134 1156 C4' U A 69 OK 1158 1155 1157 1176 C4' C A 70 OK 1178 1175 1177 1196 C4' C A 71 OK 1198 1195 1197 1216 C4' G A 72 OK 1218 1215 1217 1239 C4' A A 73 OK 1241 1238 1240 1261 C4' C A 74 OK 1263 1260 1262 1281 C4' A A 75 OK 1283 1280 1282 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' U A 21 131 133 152 C5' U A 22 151 153 172 C5' A A 23 171 173 194 C5' A A 24 193 195 216 C5' U A 25 215 217 236 C5' C A 26 235 237 256 C5' G A 27 255 257 279 C5' C A 28 278 280 299 C5' G A 29 298 300 322 C5' U A 30 321 323 342 C5' G A 31 341 343 365 C5' G A 32 364 366 388 C5' A A 33 387 389 410 C5' U A 34 409 411 430 C5' A A 35 429 431 452 C5' U A 36 451 453 472 C5' G A 37 471 473 495 C5' G A 38 494 496 518 C5' C A 39 517 519 538 C5' A A 40 537 539 560 C5' C A 41 559 561 580 C5' G A 42 579 581 603 C5' C A 43 602 604 623 C5' A A 44 622 624 645 C5' A A 45 644 646 667 C5' G A 46 666 668 690 C5' U A 47 689 691 710 C5' U A 48 709 711 730 C5' U A 49 729 731 750 C5' C A 50 749 751 770 C5' U A 51 769 771 790 C5' A A 52 789 791 812 C5' C A 53 811 813 832 C5' C A 54 831 833 852 C5' G A 55 851 853 875 C5' G A 56 874 876 898 C5' G A 57 897 899 921 C5' C A 58 920 922 941 C5' A A 59 940 942 963 C5' C A 60 962 964 983 C5' C A 61 982 984 1003 C5' G A 62 1002 1004 1026 C5' U A 63 1025 1027 1046 C5' A A 64 1045 1047 1068 C5' A A 65 1067 1069 1090 C5' A A 66 1089 1091 1112 C5' U A 67 1111 1113 1132 C5' G A 68 1131 1133 1155 C5' U A 69 1154 1156 1175 C5' C A 70 1174 1176 1195 C5' C A 71 1194 1196 1215 C5' G A 72 1214 1216 1238 C5' A A 73 1237 1239 1260 C5' C A 74 1259 1261 1280 C5' A A 75 1279 1281 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 U A 21 distorted distorted 116 129 130 131 148 P U A 22 distorted distorted 136 149 150 151 168 P A A 23 distorted distorted 156 169 170 171 190 P A A 24 distorted distorted 176 191 192 193 212 P U A 25 distorted distorted 198 213 214 215 232 P C A 26 distorted distorted 220 233 234 235 252 P G A 27 distorted distorted 240 253 254 255 275 P C A 28 distorted distorted 260 276 277 278 295 P G A 29 distorted distorted 283 296 297 298 318 P U A 30 distorted distorted 303 319 320 321 338 P G A 31 distorted distorted 326 339 340 341 361 P G A 32 distorted distorted 346 362 363 364 384 P A A 33 distorted distorted 369 385 386 387 406 P U A 34 distorted distorted 392 407 408 409 426 P A A 35 distorted distorted 414 427 428 429 448 P U A 36 distorted distorted 434 449 450 451 468 P G A 37 distorted distorted 456 469 470 471 491 P G A 38 distorted distorted 476 492 493 494 514 P C A 39 distorted distorted 499 515 516 517 534 P A A 40 distorted distorted 522 535 536 537 556 P C A 41 distorted distorted 542 557 558 559 576 P G A 42 distorted distorted 564 577 578 579 599 P C A 43 distorted distorted 584 600 601 602 619 P A A 44 distorted distorted 607 620 621 622 641 P A A 45 distorted distorted 627 642 643 644 663 P G A 46 distorted distorted 649 664 665 666 686 P U A 47 distorted distorted 671 687 688 689 706 P U A 48 distorted distorted 694 707 708 709 726 P U A 49 distorted distorted 714 727 728 729 746 P C A 50 distorted distorted 734 747 748 749 766 P U A 51 distorted distorted 754 767 768 769 786 P A A 52 distorted distorted 774 787 788 789 808 P C A 53 distorted distorted 794 809 810 811 828 P C A 54 distorted distorted 816 829 830 831 848 P G A 55 distorted distorted 836 849 850 851 871 P G A 56 distorted distorted 856 872 873 874 894 P G A 57 distorted distorted 879 895 896 897 917 P C A 58 distorted distorted 902 918 919 920 937 P A A 59 distorted distorted 925 938 939 940 959 P C A 60 distorted distorted 945 960 961 962 979 P C A 61 distorted distorted 967 980 981 982 999 P G A 62 distorted distorted 987 1000 1001 1002 1022 P U A 63 distorted distorted 1007 1023 1024 1025 1042 P A A 64 distorted distorted 1030 1043 1044 1045 1064 P A A 65 distorted distorted 1050 1065 1066 1067 1086 P A A 66 distorted distorted 1072 1087 1088 1089 1108 P U A 67 distorted distorted 1094 1109 1110 1111 1128 P G A 68 distorted distorted 1116 1129 1130 1131 1151 P U A 69 distorted distorted 1136 1152 1153 1154 1171 P C A 70 distorted distorted 1159 1172 1173 1174 1191 P C A 71 distorted distorted 1179 1192 1193 1194 1211 P G A 72 distorted distorted 1199 1212 1213 1214 1234 P A A 73 distorted distorted 1219 1235 1236 1237 1256 P C A 74 distorted distorted 1242 1257 1258 1259 1276 P A A 75 distorted distorted 1264 1277 1278 1279 1298 P A A 76 distorted distorted 1284 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 ---------------------------------------------------------------------------------