ID code: '2K96' 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 93 alpha beta 4 27 10 7 43 C1' G A 94 alpha beta 38 61 44 41 77 C1' G A 95 alpha beta 72 95 78 75 111 C1' C A 96 alpha beta 106 126 112 109 142 C1' U A 97 alpha beta 137 157 143 140 172 C1' G A 98 alpha beta 167 190 173 170 206 C1' U A 99 alpha beta 201 221 207 204 236 C1' U A 100 alpha beta 231 251 237 234 266 C1' U A 101 alpha beta 261 281 267 264 296 C1' U A 102 alpha beta 291 311 297 294 326 C1' U A 103 alpha beta 321 341 327 324 356 C1' C A 104 alpha beta 351 371 357 354 387 C1' U A 105 alpha beta 382 402 388 385 417 C1' C A 106 alpha beta 412 432 418 415 448 C1' G A 107 alpha beta 443 466 449 446 482 C1' C A 108 alpha beta 477 497 483 480 513 C1' U A 109 alpha beta 508 528 514 511 543 C1' G A 110 alpha beta 538 561 544 541 577 C1' A A 111 alpha beta 572 594 578 575 610 C1' C A 112 alpha beta 605 625 611 608 641 C1' U A 113 alpha beta 636 656 642 639 671 C1' U A 114 alpha beta 666 686 672 669 701 C1' U A 115 alpha beta 696 716 702 699 731 C1' C A 116 alpha beta 726 746 732 729 762 C1' A A 117 alpha beta 757 779 763 760 795 C1' G A 118 alpha beta 790 813 796 793 829 C1' C A 119 alpha beta 824 844 830 827 860 C1' C A 120 alpha beta 855 875 861 858 891 C1' C A 121 alpha beta 886 906 892 889 922 C1' C A 166 alpha beta 917 937 923 920 953 C1' A A 167 alpha beta 948 970 954 951 986 C1' A A 168 alpha beta 981 1003 987 984 1019 C1' A A 169 alpha beta 1014 1036 1020 1017 1052 C1' C A 170 alpha beta 1047 1067 1053 1050 1083 C1' A A 171 alpha beta 1078 1100 1084 1081 1116 C1' A A 172 alpha beta 1111 1133 1117 1114 1149 C1' A A 173 alpha beta 1144 1166 1150 1147 1182 C1' A A 174 alpha beta 1177 1199 1183 1180 1215 C1' A A 175 alpha beta 1210 1232 1216 1213 1248 C1' A A 176 alpha beta 1243 1265 1249 1246 1281 C1' G A 178 alpha beta 1276 1299 1282 1279 1315 C1' U A 179 alpha beta 1310 1330 1316 1313 1345 C1' C A 180 alpha beta 1340 1360 1346 1343 1376 C1' A A 181 alpha beta 1371 1393 1377 1374 1409 C1' G A 182 alpha beta 1404 1427 1410 1407 1443 C1' C A 183 alpha beta 1438 1458 1444 1441 1474 C1' A A 184 alpha beta 1469 1491 1475 1472 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G A 93 OK OK 9 5 25 8 41 C2' G A 94 OK OK 43 39 59 42 75 C2' G A 95 OK OK 77 73 93 76 109 C2' C A 96 OK OK 111 107 124 110 140 C2' U A 97 OK OK 142 138 155 141 170 C2' G A 98 OK OK 172 168 188 171 204 C2' U A 99 OK OK 206 202 219 205 234 C2' U A 100 OK OK 236 232 249 235 264 C2' U A 101 OK OK 266 262 279 265 294 C2' U A 102 OK OK 296 292 309 295 324 C2' U A 103 OK OK 326 322 339 325 354 C2' C A 104 OK OK 356 352 369 355 385 C2' U A 105 OK OK 387 383 400 386 415 C2' C A 106 OK OK 417 413 430 416 446 C2' G A 107 OK OK 448 444 464 447 480 C2' C A 108 OK OK 482 478 495 481 511 C2' U A 109 OK OK 513 509 526 512 541 C2' G A 110 OK OK 543 539 559 542 575 C2' A A 111 OK OK 577 573 592 576 608 C2' C A 112 OK OK 610 606 623 609 639 C2' U A 113 OK OK 641 637 654 640 669 C2' U A 114 OK OK 671 667 684 670 699 C2' U A 115 OK OK 701 697 714 700 729 C2' C A 116 OK OK 731 727 744 730 760 C2' A A 117 OK OK 762 758 777 761 793 C2' G A 118 OK OK 795 791 811 794 827 C2' C A 119 OK OK 829 825 842 828 858 C2' C A 120 OK OK 860 856 873 859 889 C2' C A 121 OK OK 891 887 904 890 920 C2' C A 166 OK OK 922 918 935 921 951 C2' A A 167 OK OK 953 949 968 952 984 C2' A A 168 OK OK 986 982 1001 985 1017 C2' A A 169 OK OK 1019 1015 1034 1018 1050 C2' C A 170 OK OK 1052 1048 1065 1051 1081 C2' A A 171 OK OK 1083 1079 1098 1082 1114 C2' A A 172 OK OK 1116 1112 1131 1115 1147 C2' A A 173 OK OK 1149 1145 1164 1148 1180 C2' A A 174 OK OK 1182 1178 1197 1181 1213 C2' A A 175 OK OK 1215 1211 1230 1214 1246 C2' A A 176 OK OK 1248 1244 1263 1247 1279 C2' G A 178 OK OK 1281 1277 1297 1280 1313 C2' U A 179 OK OK 1315 1311 1328 1314 1343 C2' C A 180 OK OK 1345 1341 1358 1344 1374 C2' A A 181 OK OK 1376 1372 1391 1375 1407 C2' G A 182 OK OK 1409 1405 1425 1408 1441 C2' C A 183 OK OK 1443 1439 1456 1442 1472 C2' A A 184 OK OK 1474 1470 1489 1473 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 93 OK OK 3 24 6 7 39 C3' G A 94 OK OK 37 58 40 41 73 C3' G A 95 OK OK 71 92 74 75 107 C3' C A 96 OK OK 105 123 108 109 138 C3' U A 97 OK OK 136 154 139 140 168 C3' G A 98 OK OK 166 187 169 170 202 C3' U A 99 OK OK 200 218 203 204 232 C3' U A 100 OK OK 230 248 233 234 262 C3' U A 101 OK OK 260 278 263 264 292 C3' U A 102 OK OK 290 308 293 294 322 C3' U A 103 OK OK 320 338 323 324 352 C3' C A 104 OK OK 350 368 353 354 383 C3' U A 105 OK OK 381 399 384 385 413 C3' C A 106 OK OK 411 429 414 415 444 C3' G A 107 OK OK 442 463 445 446 478 C3' C A 108 OK OK 476 494 479 480 509 C3' U A 109 OK OK 507 525 510 511 539 C3' G A 110 OK OK 537 558 540 541 573 C3' A A 111 OK OK 571 591 574 575 606 C3' C A 112 OK OK 604 622 607 608 637 C3' U A 113 OK OK 635 653 638 639 667 C3' U A 114 OK OK 665 683 668 669 697 C3' U A 115 OK OK 695 713 698 699 727 C3' C A 116 OK OK 725 743 728 729 758 C3' A A 117 OK OK 756 776 759 760 791 C3' G A 118 OK OK 789 810 792 793 825 C3' C A 119 OK OK 823 841 826 827 856 C3' C A 120 OK OK 854 872 857 858 887 C3' C A 121 OK OK 885 903 888 889 918 C3' C A 166 OK OK 916 934 919 920 949 C3' A A 167 OK OK 947 967 950 951 982 C3' A A 168 OK OK 980 1000 983 984 1015 C3' A A 169 OK OK 1013 1033 1016 1017 1048 C3' C A 170 OK OK 1046 1064 1049 1050 1079 C3' A A 171 OK OK 1077 1097 1080 1081 1112 C3' A A 172 OK OK 1110 1130 1113 1114 1145 C3' A A 173 OK OK 1143 1163 1146 1147 1178 C3' A A 174 OK OK 1176 1196 1179 1180 1211 C3' A A 175 OK OK 1209 1229 1212 1213 1244 C3' A A 176 OK OK 1242 1262 1245 1246 1277 C3' G A 178 OK OK 1275 1296 1278 1279 1311 C3' U A 179 OK OK 1309 1327 1312 1313 1341 C3' C A 180 OK OK 1339 1357 1342 1343 1372 C3' A A 181 OK OK 1370 1390 1373 1374 1405 C3' G A 182 OK OK 1403 1424 1406 1407 1439 C3' C A 183 OK OK 1437 1455 1440 1441 1470 C3' A A 184 OK OK 1468 1488 1471 1472 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 93 OK OK 5 23 2 4 37 C4' G A 94 OK OK 39 57 36 38 71 C4' G A 95 OK OK 73 91 70 72 105 C4' C A 96 OK OK 107 122 104 106 136 C4' U A 97 OK OK 138 153 135 137 166 C4' G A 98 OK OK 168 186 165 167 200 C4' U A 99 OK OK 202 217 199 201 230 C4' U A 100 OK OK 232 247 229 231 260 C4' U A 101 OK OK 262 277 259 261 290 C4' U A 102 OK OK 292 307 289 291 320 C4' U A 103 OK OK 322 337 319 321 350 C4' C A 104 OK OK 352 367 349 351 381 C4' U A 105 OK OK 383 398 380 382 411 C4' C A 106 OK OK 413 428 410 412 442 C4' G A 107 OK OK 444 462 441 443 476 C4' C A 108 OK OK 478 493 475 477 507 C4' U A 109 OK OK 509 524 506 508 537 C4' G A 110 OK OK 539 557 536 538 571 C4' A A 111 OK OK 573 590 570 572 604 C4' C A 112 OK OK 606 621 603 605 635 C4' U A 113 OK OK 637 652 634 636 665 C4' U A 114 OK OK 667 682 664 666 695 C4' U A 115 OK OK 697 712 694 696 725 C4' C A 116 OK OK 727 742 724 726 756 C4' A A 117 OK OK 758 775 755 757 789 C4' G A 118 OK OK 791 809 788 790 823 C4' C A 119 OK OK 825 840 822 824 854 C4' C A 120 OK OK 856 871 853 855 885 C4' C A 121 OK OK 887 902 884 886 916 C4' C A 166 OK OK 918 933 915 917 947 C4' A A 167 OK OK 949 966 946 948 980 C4' A A 168 OK OK 982 999 979 981 1013 C4' A A 169 OK OK 1015 1032 1012 1014 1046 C4' C A 170 OK OK 1048 1063 1045 1047 1077 C4' A A 171 OK OK 1079 1096 1076 1078 1110 C4' A A 172 OK OK 1112 1129 1109 1111 1143 C4' A A 173 OK OK 1145 1162 1142 1144 1176 C4' A A 174 OK OK 1178 1195 1175 1177 1209 C4' A A 175 OK OK 1211 1228 1208 1210 1242 C4' A A 176 OK OK 1244 1261 1241 1243 1275 C4' G A 178 OK OK 1277 1295 1274 1276 1309 C4' U A 179 OK OK 1311 1326 1308 1310 1339 C4' C A 180 OK OK 1341 1356 1338 1340 1370 C4' A A 181 OK OK 1372 1389 1369 1371 1403 C4' G A 182 OK OK 1405 1423 1402 1404 1437 C4' C A 183 OK OK 1439 1454 1436 1438 1468 C4' A A 184 OK OK 1470 1487 1467 1469 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 93 OK OK 1 21 22 3 36 C5' G A 94 OK OK 35 55 56 37 70 C5' G A 95 OK OK 69 89 90 71 104 C5' C A 96 OK OK 103 120 121 105 135 C5' U A 97 OK OK 134 151 152 136 165 C5' G A 98 OK OK 164 184 185 166 199 C5' U A 99 OK OK 198 215 216 200 229 C5' U A 100 OK OK 228 245 246 230 259 C5' U A 101 OK OK 258 275 276 260 289 C5' U A 102 OK OK 288 305 306 290 319 C5' U A 103 OK OK 318 335 336 320 349 C5' C A 104 OK OK 348 365 366 350 380 C5' U A 105 OK OK 379 396 397 381 410 C5' C A 106 OK OK 409 426 427 411 441 C5' G A 107 OK OK 440 460 461 442 475 C5' C A 108 OK OK 474 491 492 476 506 C5' U A 109 OK OK 505 522 523 507 536 C5' G A 110 OK OK 535 555 556 537 570 C5' A A 111 OK OK 569 588 589 571 603 C5' C A 112 OK OK 602 619 620 604 634 C5' U A 113 OK OK 633 650 651 635 664 C5' U A 114 OK OK 663 680 681 665 694 C5' U A 115 OK OK 693 710 711 695 724 C5' C A 116 OK OK 723 740 741 725 755 C5' A A 117 OK OK 754 773 774 756 788 C5' G A 118 OK OK 787 807 808 789 822 C5' C A 119 OK OK 821 838 839 823 853 C5' C A 120 OK OK 852 869 870 854 884 C5' C A 121 OK OK 883 900 901 885 915 C5' C A 166 OK OK 914 931 932 916 946 C5' A A 167 OK OK 945 964 965 947 979 C5' A A 168 OK OK 978 997 998 980 1012 C5' A A 169 OK OK 1011 1030 1031 1013 1045 C5' C A 170 OK OK 1044 1061 1062 1046 1076 C5' A A 171 OK OK 1075 1094 1095 1077 1109 C5' A A 172 OK OK 1108 1127 1128 1110 1142 C5' A A 173 OK OK 1141 1160 1161 1143 1175 C5' A A 174 OK OK 1174 1193 1194 1176 1208 C5' A A 175 OK OK 1207 1226 1227 1209 1241 C5' A A 176 OK OK 1240 1259 1260 1242 1274 C5' G A 178 OK OK 1273 1293 1294 1275 1308 C5' U A 179 OK OK 1307 1324 1325 1309 1338 C5' C A 180 OK OK 1337 1354 1355 1339 1369 C5' A A 181 OK OK 1368 1387 1388 1370 1402 C5' G A 182 OK OK 1401 1421 1422 1403 1436 C5' C A 183 OK OK 1435 1452 1453 1437 1467 C5' A A 184 OK OK 1466 1485 1486 1468 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 32 P G A 94 distorted distorted 6 33 34 35 66 P G A 95 distorted distorted 40 67 68 69 100 P C A 96 distorted distorted 74 101 102 103 131 P U A 97 distorted distorted 108 132 133 134 161 P G A 98 distorted distorted 139 162 163 164 195 P U A 99 distorted distorted 169 196 197 198 225 P U A 100 distorted distorted 203 226 227 228 255 P U A 101 distorted distorted 233 256 257 258 285 P U A 102 distorted distorted 263 286 287 288 315 P U A 103 distorted distorted 293 316 317 318 345 P C A 104 distorted distorted 323 346 347 348 376 P U A 105 distorted distorted 353 377 378 379 406 P C A 106 distorted distorted 384 407 408 409 437 P G A 107 distorted distorted 414 438 439 440 471 P C A 108 distorted distorted 445 472 473 474 502 P U A 109 distorted distorted 479 503 504 505 532 P G A 110 distorted distorted 510 533 534 535 566 P A A 111 distorted distorted 540 567 568 569 599 P C A 112 distorted distorted 574 600 601 602 630 P U A 113 distorted distorted 607 631 632 633 660 P U A 114 distorted distorted 638 661 662 663 690 P U A 115 distorted distorted 668 691 692 693 720 P C A 116 distorted distorted 698 721 722 723 751 P A A 117 distorted distorted 728 752 753 754 784 P G A 118 distorted distorted 759 785 786 787 818 P C A 119 distorted distorted 792 819 820 821 849 P C A 120 distorted distorted 826 850 851 852 880 P C A 121 distorted distorted 857 881 882 883 911 P C A 166 distorted distorted 888 912 913 914 942 P A A 167 distorted distorted 919 943 944 945 975 P A A 168 distorted distorted 950 976 977 978 1008 P A A 169 distorted distorted 983 1009 1010 1011 1041 P C A 170 distorted distorted 1016 1042 1043 1044 1072 P A A 171 distorted distorted 1049 1073 1074 1075 1105 P A A 172 distorted distorted 1080 1106 1107 1108 1138 P A A 173 distorted distorted 1113 1139 1140 1141 1171 P A A 174 distorted distorted 1146 1172 1173 1174 1204 P A A 175 distorted distorted 1179 1205 1206 1207 1237 P A A 176 distorted distorted 1212 1238 1239 1240 1270 P G A 178 distorted distorted 1245 1271 1272 1273 1304 P U A 179 distorted distorted 1278 1305 1306 1307 1334 P C A 180 distorted distorted 1312 1335 1336 1337 1365 P A A 181 distorted distorted 1342 1366 1367 1368 1398 P G A 182 distorted distorted 1373 1399 1400 1401 1432 P C A 183 distorted distorted 1406 1433 1434 1435 1463 P A A 184 distorted distorted 1440 1464 1465 1466 ---------------------------------------------------------------------------------