ID code: '2OZB' 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' A C 20 beta 4 10 7 31 C1' U C 21 beta 26 32 29 51 C1' C C 22 beta 46 52 49 71 C1' G C 23 beta 66 72 69 94 C1' U C 24 beta 89 95 92 114 C1' A C 25 beta 109 115 112 136 C1' G C 26 beta 131 137 134 159 C1' C C 27 beta 154 160 157 179 C1' C C 28 beta 174 180 177 199 C1' A C 29 beta 194 200 197 221 C1' A C 30 beta 216 222 219 243 C1' U C 31 beta 238 244 241 263 C1' G C 32 beta 258 264 261 286 C1' A C 33 beta 281 287 284 308 C1' G C 34 beta 303 309 306 331 C1' G C 35 beta 326 332 329 354 C1' U C 36 beta 349 355 352 374 C1' U C 37 beta 369 375 372 394 C1' U C 38 beta 389 395 392 414 C1' A C 39 beta 409 415 412 436 C1' U C 40 beta 431 437 434 456 C1' C C 41 beta 451 457 454 476 C1' C C 42 beta 471 477 474 496 C1' G C 43 beta 491 497 494 519 C1' A C 44 beta 514 520 517 541 C1' G C 45 beta 536 542 539 564 C1' G C 46 beta 559 565 562 587 C1' C C 47 beta 582 588 585 607 C1' G C 48 beta 602 608 605 630 C1' C C 49 beta 625 631 628 650 C1' G C 50 beta 645 651 648 673 C1' A C 51 beta 668 674 671 695 C1' U C 52 beta 690 696 693 713 C1' A F 20 beta 708 714 711 735 C1' U F 21 beta 730 736 733 755 C1' C F 22 beta 750 756 753 775 C1' G F 23 beta 770 776 773 798 C1' U F 24 beta 793 799 796 818 C1' A F 25 beta 813 819 816 840 C1' G F 26 beta 835 841 838 863 C1' C F 27 beta 858 864 861 883 C1' C F 28 beta 878 884 881 903 C1' A F 29 beta 898 904 901 925 C1' A F 30 beta 920 926 923 947 C1' U F 31 beta 942 948 945 967 C1' G F 32 beta 962 968 965 990 C1' A F 33 beta 985 991 988 1012 C1' G F 34 beta 1007 1013 1010 1035 C1' G F 35 beta 1030 1036 1033 1058 C1' U F 36 beta 1053 1059 1056 1078 C1' U F 37 beta 1073 1079 1076 1098 C1' U F 38 beta 1093 1099 1096 1118 C1' A F 39 beta 1113 1119 1116 1140 C1' U F 40 beta 1135 1141 1138 1160 C1' C F 41 beta 1155 1161 1158 1180 C1' C F 42 beta 1175 1181 1178 1200 C1' G F 43 beta 1195 1201 1198 1223 C1' A F 44 beta 1218 1224 1221 1245 C1' G F 45 beta 1240 1246 1243 1268 C1' G F 46 beta 1263 1269 1266 1291 C1' C F 47 beta 1286 1292 1289 1311 C1' G F 48 beta 1306 1312 1309 1334 C1' C F 49 beta 1329 1335 1332 1354 C1' G F 50 beta 1349 1355 1352 1377 C1' A F 51 beta 1372 1378 1375 1399 C1' U F 52 beta 1394 1400 1397 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' A C 20 OK 9 5 8 29 C2' U C 21 OK 31 27 30 49 C2' C C 22 OK 51 47 50 69 C2' G C 23 OK 71 67 70 92 C2' U C 24 OK 94 90 93 112 C2' A C 25 OK 114 110 113 134 C2' G C 26 OK 136 132 135 157 C2' C C 27 OK 159 155 158 177 C2' C C 28 OK 179 175 178 197 C2' A C 29 OK 199 195 198 219 C2' A C 30 OK 221 217 220 241 C2' U C 31 OK 243 239 242 261 C2' G C 32 OK 263 259 262 284 C2' A C 33 OK 286 282 285 306 C2' G C 34 OK 308 304 307 329 C2' G C 35 OK 331 327 330 352 C2' U C 36 OK 354 350 353 372 C2' U C 37 OK 374 370 373 392 C2' U C 38 OK 394 390 393 412 C2' A C 39 OK 414 410 413 434 C2' U C 40 OK 436 432 435 454 C2' C C 41 OK 456 452 455 474 C2' C C 42 OK 476 472 475 494 C2' G C 43 OK 496 492 495 517 C2' A C 44 OK 519 515 518 539 C2' G C 45 OK 541 537 540 562 C2' G C 46 OK 564 560 563 585 C2' C C 47 OK 587 583 586 605 C2' G C 48 OK 607 603 606 628 C2' C C 49 OK 630 626 629 648 C2' G C 50 OK 650 646 649 671 C2' A C 51 OK 673 669 672 693 C2' U C 52 OK 695 691 694 711 C2' A F 20 OK 713 709 712 733 C2' U F 21 OK 735 731 734 753 C2' C F 22 OK 755 751 754 773 C2' G F 23 OK 775 771 774 796 C2' U F 24 OK 798 794 797 816 C2' A F 25 OK 818 814 817 838 C2' G F 26 OK 840 836 839 861 C2' C F 27 OK 863 859 862 881 C2' C F 28 OK 883 879 882 901 C2' A F 29 OK 903 899 902 923 C2' A F 30 OK 925 921 924 945 C2' U F 31 OK 947 943 946 965 C2' G F 32 OK 967 963 966 988 C2' A F 33 OK 990 986 989 1010 C2' G F 34 OK 1012 1008 1011 1033 C2' G F 35 OK 1035 1031 1034 1056 C2' U F 36 OK 1058 1054 1057 1076 C2' U F 37 OK 1078 1074 1077 1096 C2' U F 38 OK 1098 1094 1097 1116 C2' A F 39 OK 1118 1114 1117 1138 C2' U F 40 OK 1140 1136 1139 1158 C2' C F 41 OK 1160 1156 1159 1178 C2' C F 42 OK 1180 1176 1179 1198 C2' G F 43 OK 1200 1196 1199 1221 C2' A F 44 OK 1223 1219 1222 1243 C2' G F 45 OK 1245 1241 1244 1266 C2' G F 46 OK 1268 1264 1267 1289 C2' C F 47 OK 1291 1287 1290 1309 C2' G F 48 OK 1311 1307 1310 1332 C2' C F 49 OK 1334 1330 1333 1352 C2' G F 50 OK 1354 1350 1353 1375 C2' A F 51 OK 1377 1373 1376 1397 C2' U F 52 OK 1399 1395 1398 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' A C 20 OK 3 6 7 27 C3' U C 21 OK 25 28 29 47 C3' C C 22 OK 45 48 49 67 C3' G C 23 OK 65 68 69 90 C3' U C 24 OK 88 91 92 110 C3' A C 25 OK 108 111 112 132 C3' G C 26 OK 130 133 134 155 C3' C C 27 OK 153 156 157 175 C3' C C 28 OK 173 176 177 195 C3' A C 29 OK 193 196 197 217 C3' A C 30 OK 215 218 219 239 C3' U C 31 OK 237 240 241 259 C3' G C 32 OK 257 260 261 282 C3' A C 33 OK 280 283 284 304 C3' G C 34 OK 302 305 306 327 C3' G C 35 OK 325 328 329 350 C3' U C 36 OK 348 351 352 370 C3' U C 37 OK 368 371 372 390 C3' U C 38 OK 388 391 392 410 C3' A C 39 OK 408 411 412 432 C3' U C 40 OK 430 433 434 452 C3' C C 41 OK 450 453 454 472 C3' C C 42 OK 470 473 474 492 C3' G C 43 OK 490 493 494 515 C3' A C 44 OK 513 516 517 537 C3' G C 45 OK 535 538 539 560 C3' G C 46 OK 558 561 562 583 C3' C C 47 OK 581 584 585 603 C3' G C 48 OK 601 604 605 626 C3' C C 49 OK 624 627 628 646 C3' G C 50 OK 644 647 648 669 C3' A C 51 OK 667 670 671 691 C3' U C 52 OK 689 692 693 709 C3' A F 20 OK 707 710 711 731 C3' U F 21 OK 729 732 733 751 C3' C F 22 OK 749 752 753 771 C3' G F 23 OK 769 772 773 794 C3' U F 24 OK 792 795 796 814 C3' A F 25 OK 812 815 816 836 C3' G F 26 OK 834 837 838 859 C3' C F 27 OK 857 860 861 879 C3' C F 28 OK 877 880 881 899 C3' A F 29 OK 897 900 901 921 C3' A F 30 OK 919 922 923 943 C3' U F 31 OK 941 944 945 963 C3' G F 32 OK 961 964 965 986 C3' A F 33 OK 984 987 988 1008 C3' G F 34 OK 1006 1009 1010 1031 C3' G F 35 OK 1029 1032 1033 1054 C3' U F 36 OK 1052 1055 1056 1074 C3' U F 37 OK 1072 1075 1076 1094 C3' U F 38 OK 1092 1095 1096 1114 C3' A F 39 OK 1112 1115 1116 1136 C3' U F 40 OK 1134 1137 1138 1156 C3' C F 41 OK 1154 1157 1158 1176 C3' C F 42 OK 1174 1177 1178 1196 C3' G F 43 OK 1194 1197 1198 1219 C3' A F 44 OK 1217 1220 1221 1241 C3' G F 45 OK 1239 1242 1243 1264 C3' G F 46 OK 1262 1265 1266 1287 C3' C F 47 OK 1285 1288 1289 1307 C3' G F 48 OK 1305 1308 1309 1330 C3' C F 49 OK 1328 1331 1332 1350 C3' G F 50 OK 1348 1351 1352 1373 C3' A F 51 OK 1371 1374 1375 1395 C3' U F 52 OK 1393 1396 1397 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' A C 20 OK 5 2 4 25 C4' U C 21 OK 27 24 26 45 C4' C C 22 OK 47 44 46 65 C4' G C 23 OK 67 64 66 88 C4' U C 24 OK 90 87 89 108 C4' A C 25 OK 110 107 109 130 C4' G C 26 OK 132 129 131 153 C4' C C 27 OK 155 152 154 173 C4' C C 28 OK 175 172 174 193 C4' A C 29 OK 195 192 194 215 C4' A C 30 OK 217 214 216 237 C4' U C 31 OK 239 236 238 257 C4' G C 32 OK 259 256 258 280 C4' A C 33 OK 282 279 281 302 C4' G C 34 OK 304 301 303 325 C4' G C 35 OK 327 324 326 348 C4' U C 36 OK 350 347 349 368 C4' U C 37 OK 370 367 369 388 C4' U C 38 OK 390 387 389 408 C4' A C 39 OK 410 407 409 430 C4' U C 40 OK 432 429 431 450 C4' C C 41 OK 452 449 451 470 C4' C C 42 OK 472 469 471 490 C4' G C 43 OK 492 489 491 513 C4' A C 44 OK 515 512 514 535 C4' G C 45 OK 537 534 536 558 C4' G C 46 OK 560 557 559 581 C4' C C 47 OK 583 580 582 601 C4' G C 48 OK 603 600 602 624 C4' C C 49 OK 626 623 625 644 C4' G C 50 OK 646 643 645 667 C4' A C 51 OK 669 666 668 689 C4' U C 52 OK 691 688 690 707 C4' A F 20 OK 709 706 708 729 C4' U F 21 OK 731 728 730 749 C4' C F 22 OK 751 748 750 769 C4' G F 23 OK 771 768 770 792 C4' U F 24 OK 794 791 793 812 C4' A F 25 OK 814 811 813 834 C4' G F 26 OK 836 833 835 857 C4' C F 27 OK 859 856 858 877 C4' C F 28 OK 879 876 878 897 C4' A F 29 OK 899 896 898 919 C4' A F 30 OK 921 918 920 941 C4' U F 31 OK 943 940 942 961 C4' G F 32 OK 963 960 962 984 C4' A F 33 OK 986 983 985 1006 C4' G F 34 OK 1008 1005 1007 1029 C4' G F 35 OK 1031 1028 1030 1052 C4' U F 36 OK 1054 1051 1053 1072 C4' U F 37 OK 1074 1071 1073 1092 C4' U F 38 OK 1094 1091 1093 1112 C4' A F 39 OK 1114 1111 1113 1134 C4' U F 40 OK 1136 1133 1135 1154 C4' C F 41 OK 1156 1153 1155 1174 C4' C F 42 OK 1176 1173 1175 1194 C4' G F 43 OK 1196 1193 1195 1217 C4' A F 44 OK 1219 1216 1218 1239 C4' G F 45 OK 1241 1238 1240 1262 C4' G F 46 OK 1264 1261 1263 1285 C4' C F 47 OK 1287 1284 1286 1305 C4' G F 48 OK 1307 1304 1306 1328 C4' C F 49 OK 1330 1327 1329 1348 C4' G F 50 OK 1350 1347 1349 1371 C4' A F 51 OK 1373 1370 1372 1393 C4' U F 52 OK 1395 1392 1394 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' A C 20 1 3 24 C5' U C 21 23 25 44 C5' C C 22 43 45 64 C5' G C 23 63 65 87 C5' U C 24 86 88 107 C5' A C 25 106 108 129 C5' G C 26 128 130 152 C5' C C 27 151 153 172 C5' C C 28 171 173 192 C5' A C 29 191 193 214 C5' A C 30 213 215 236 C5' U C 31 235 237 256 C5' G C 32 255 257 279 C5' A C 33 278 280 301 C5' G C 34 300 302 324 C5' G C 35 323 325 347 C5' U C 36 346 348 367 C5' U C 37 366 368 387 C5' U C 38 386 388 407 C5' A C 39 406 408 429 C5' U C 40 428 430 449 C5' C C 41 448 450 469 C5' C C 42 468 470 489 C5' G C 43 488 490 512 C5' A C 44 511 513 534 C5' G C 45 533 535 557 C5' G C 46 556 558 580 C5' C C 47 579 581 600 C5' G C 48 599 601 623 C5' C C 49 622 624 643 C5' G C 50 642 644 666 C5' A C 51 665 667 688 C5' U C 52 687 689 706 C5' A F 20 705 707 728 C5' U F 21 727 729 748 C5' C F 22 747 749 768 C5' G F 23 767 769 791 C5' U F 24 790 792 811 C5' A F 25 810 812 833 C5' G F 26 832 834 856 C5' C F 27 855 857 876 C5' C F 28 875 877 896 C5' A F 29 895 897 918 C5' A F 30 917 919 940 C5' U F 31 939 941 960 C5' G F 32 959 961 983 C5' A F 33 982 984 1005 C5' G F 34 1004 1006 1028 C5' G F 35 1027 1029 1051 C5' U F 36 1050 1052 1071 C5' U F 37 1070 1072 1091 C5' U F 38 1090 1092 1111 C5' A F 39 1110 1112 1133 C5' U F 40 1132 1134 1153 C5' C F 41 1152 1154 1173 C5' C F 42 1172 1174 1193 C5' G F 43 1192 1194 1216 C5' A F 44 1215 1217 1238 C5' G F 45 1237 1239 1261 C5' G F 46 1260 1262 1284 C5' C F 47 1283 1285 1304 C5' G F 48 1303 1305 1327 C5' C F 49 1326 1328 1347 C5' G F 50 1346 1348 1370 C5' A F 51 1369 1371 1392 C5' U F 52 1391 1393 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 20 P U C 21 distorted distorted 6 21 22 23 40 P C C 22 distorted distorted 28 41 42 43 60 P G C 23 distorted distorted 48 61 62 63 83 P U C 24 distorted distorted 68 84 85 86 103 P A C 25 distorted distorted 91 104 105 106 125 P G C 26 distorted distorted 111 126 127 128 148 P C C 27 distorted distorted 133 149 150 151 168 P C C 28 distorted distorted 156 169 170 171 188 P A C 29 distorted distorted 176 189 190 191 210 P A C 30 distorted distorted 196 211 212 213 232 P U C 31 distorted distorted 218 233 234 235 252 P G C 32 distorted distorted 240 253 254 255 275 P A C 33 distorted distorted 260 276 277 278 297 P G C 34 distorted distorted 283 298 299 300 320 P G C 35 distorted distorted 305 321 322 323 343 P U C 36 distorted distorted 328 344 345 346 363 P U C 37 distorted distorted 351 364 365 366 383 P U C 38 distorted distorted 371 384 385 386 403 P A C 39 distorted distorted 391 404 405 406 425 P U C 40 distorted distorted 411 426 427 428 445 P C C 41 distorted distorted 433 446 447 448 465 P C C 42 distorted distorted 453 466 467 468 485 P G C 43 distorted distorted 473 486 487 488 508 P A C 44 distorted distorted 493 509 510 511 530 P G C 45 distorted distorted 516 531 532 533 553 P G C 46 distorted distorted 538 554 555 556 576 P C C 47 distorted distorted 561 577 578 579 596 P G C 48 distorted distorted 584 597 598 599 619 P C C 49 distorted distorted 604 620 621 622 639 P G C 50 distorted distorted 627 640 641 642 662 P A C 51 distorted distorted 647 663 664 665 684 P U C 52 distorted distorted 670 685 686 687 724 P U F 21 distorted distorted 710 725 726 727 744 P C F 22 distorted distorted 732 745 746 747 764 P G F 23 distorted distorted 752 765 766 767 787 P U F 24 distorted distorted 772 788 789 790 807 P A F 25 distorted distorted 795 808 809 810 829 P G F 26 distorted distorted 815 830 831 832 852 P C F 27 distorted distorted 837 853 854 855 872 P C F 28 distorted distorted 860 873 874 875 892 P A F 29 distorted distorted 880 893 894 895 914 P A F 30 distorted distorted 900 915 916 917 936 P U F 31 distorted distorted 922 937 938 939 956 P G F 32 distorted distorted 944 957 958 959 979 P A F 33 distorted distorted 964 980 981 982 1001 P G F 34 distorted distorted 987 1002 1003 1004 1024 P G F 35 distorted distorted 1009 1025 1026 1027 1047 P U F 36 distorted distorted 1032 1048 1049 1050 1067 P U F 37 distorted distorted 1055 1068 1069 1070 1087 P U F 38 distorted distorted 1075 1088 1089 1090 1107 P A F 39 distorted distorted 1095 1108 1109 1110 1129 P U F 40 distorted distorted 1115 1130 1131 1132 1149 P C F 41 distorted distorted 1137 1150 1151 1152 1169 P C F 42 distorted distorted 1157 1170 1171 1172 1189 P G F 43 distorted distorted 1177 1190 1191 1192 1212 P A F 44 distorted distorted 1197 1213 1214 1215 1234 P G F 45 distorted distorted 1220 1235 1236 1237 1257 P G F 46 distorted distorted 1242 1258 1259 1260 1280 P C F 47 distorted distorted 1265 1281 1282 1283 1300 P G F 48 distorted distorted 1288 1301 1302 1303 1323 P C F 49 distorted distorted 1308 1324 1325 1326 1343 P G F 50 distorted distorted 1331 1344 1345 1346 1366 P A F 51 distorted distorted 1351 1367 1368 1369 1388 P U F 52 distorted distorted 1374 1389 1390 1391 ---------------------------------------------------------------------------------