ID code: '1BAU' 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 1 alpha beta 4 27 10 7 44 C1' G A 2 alpha beta 39 62 45 42 78 C1' C A 3 alpha beta 73 93 79 76 109 C1' A A 4 alpha beta 104 126 110 107 142 C1' A A 5 alpha beta 137 159 143 140 175 C1' U A 6 alpha beta 170 190 176 173 205 C1' G A 7 alpha beta 200 223 206 203 239 C1' A A 8 alpha beta 234 256 240 237 272 C1' A A 9 alpha beta 267 289 273 270 305 C1' G A 10 alpha beta 300 323 306 303 339 C1' C A 11 alpha beta 334 354 340 337 370 C1' G A 12 alpha beta 365 388 371 368 404 C1' C A 13 alpha beta 399 419 405 402 435 C1' G A 14 alpha beta 430 453 436 433 469 C1' C A 15 alpha beta 464 484 470 467 500 C1' A A 16 alpha beta 495 517 501 498 533 C1' C A 17 alpha beta 528 548 534 531 564 C1' G A 18 alpha beta 559 582 565 562 598 C1' U A 19 alpha beta 593 613 599 596 628 C1' U A 20 alpha beta 623 643 629 626 658 C1' G A 21 alpha beta 653 676 659 656 692 C1' C A 22 alpha beta 687 707 693 690 723 C1' C A 23 alpha beta 718 739 724 721 753 C1' G B 1 alpha beta 748 771 754 751 788 C1' G B 2 alpha beta 783 806 789 786 822 C1' C B 3 alpha beta 817 837 823 820 853 C1' A B 4 alpha beta 848 870 854 851 886 C1' A B 5 alpha beta 881 903 887 884 919 C1' U B 6 alpha beta 914 934 920 917 949 C1' G B 7 alpha beta 944 967 950 947 983 C1' A B 8 alpha beta 978 1000 984 981 1016 C1' A B 9 alpha beta 1011 1033 1017 1014 1049 C1' G B 10 alpha beta 1044 1067 1050 1047 1083 C1' C B 11 alpha beta 1078 1098 1084 1081 1114 C1' G B 12 alpha beta 1109 1132 1115 1112 1148 C1' C B 13 alpha beta 1143 1163 1149 1146 1179 C1' G B 14 alpha beta 1174 1197 1180 1177 1213 C1' C B 15 alpha beta 1208 1228 1214 1211 1244 C1' A B 16 alpha beta 1239 1261 1245 1242 1277 C1' C B 17 alpha beta 1272 1292 1278 1275 1308 C1' G B 18 alpha beta 1303 1326 1309 1306 1342 C1' U B 19 alpha beta 1337 1357 1343 1340 1372 C1' U B 20 alpha beta 1367 1387 1373 1370 1402 C1' G B 21 alpha beta 1397 1420 1403 1400 1436 C1' C B 22 alpha beta 1431 1451 1437 1434 1467 C1' C B 23 alpha beta 1462 1483 1468 1465 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G A 1 OK OK 9 5 25 8 42 C2' G A 2 OK OK 44 40 60 43 76 C2' C A 3 OK OK 78 74 91 77 107 C2' A A 4 OK OK 109 105 124 108 140 C2' A A 5 OK OK 142 138 157 141 173 C2' U A 6 OK OK 175 171 188 174 203 C2' G A 7 OK OK 205 201 221 204 237 C2' A A 8 OK OK 239 235 254 238 270 C2' A A 9 OK OK 272 268 287 271 303 C2' G A 10 OK OK 305 301 321 304 337 C2' C A 11 OK OK 339 335 352 338 368 C2' G A 12 OK OK 370 366 386 369 402 C2' C A 13 OK OK 404 400 417 403 433 C2' G A 14 OK OK 435 431 451 434 467 C2' C A 15 OK OK 469 465 482 468 498 C2' A A 16 OK OK 500 496 515 499 531 C2' C A 17 OK OK 533 529 546 532 562 C2' G A 18 OK OK 564 560 580 563 596 C2' U A 19 OK OK 598 594 611 597 626 C2' U A 20 OK OK 628 624 641 627 656 C2' G A 21 OK OK 658 654 674 657 690 C2' C A 22 OK OK 692 688 705 691 721 C2' C A 23 OK OK 723 719 737 722 751 C2' G B 1 OK OK 753 749 769 752 786 C2' G B 2 OK OK 788 784 804 787 820 C2' C B 3 OK OK 822 818 835 821 851 C2' A B 4 OK OK 853 849 868 852 884 C2' A B 5 OK OK 886 882 901 885 917 C2' U B 6 OK OK 919 915 932 918 947 C2' G B 7 OK OK 949 945 965 948 981 C2' A B 8 OK OK 983 979 998 982 1014 C2' A B 9 OK OK 1016 1012 1031 1015 1047 C2' G B 10 OK OK 1049 1045 1065 1048 1081 C2' C B 11 OK OK 1083 1079 1096 1082 1112 C2' G B 12 OK OK 1114 1110 1130 1113 1146 C2' C B 13 OK OK 1148 1144 1161 1147 1177 C2' G B 14 OK OK 1179 1175 1195 1178 1211 C2' C B 15 OK OK 1213 1209 1226 1212 1242 C2' A B 16 OK OK 1244 1240 1259 1243 1275 C2' C B 17 OK OK 1277 1273 1290 1276 1306 C2' G B 18 OK OK 1308 1304 1324 1307 1340 C2' U B 19 OK OK 1342 1338 1355 1341 1370 C2' U B 20 OK OK 1372 1368 1385 1371 1400 C2' G B 21 OK OK 1402 1398 1418 1401 1434 C2' C B 22 OK OK 1436 1432 1449 1435 1465 C2' C B 23 OK OK 1467 1463 1481 1466 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK OK 3 24 6 7 40 C3' G A 2 OK OK 38 59 41 42 74 C3' C A 3 OK OK 72 90 75 76 105 C3' A A 4 OK OK 103 123 106 107 138 C3' A A 5 OK OK 136 156 139 140 171 C3' U A 6 OK OK 169 187 172 173 201 C3' G A 7 OK OK 199 220 202 203 235 C3' A A 8 OK OK 233 253 236 237 268 C3' A A 9 OK OK 266 286 269 270 301 C3' G A 10 OK OK 299 320 302 303 335 C3' C A 11 OK OK 333 351 336 337 366 C3' G A 12 OK OK 364 385 367 368 400 C3' C A 13 OK OK 398 416 401 402 431 C3' G A 14 OK OK 429 450 432 433 465 C3' C A 15 OK OK 463 481 466 467 496 C3' A A 16 OK OK 494 514 497 498 529 C3' C A 17 OK OK 527 545 530 531 560 C3' G A 18 OK OK 558 579 561 562 594 C3' U A 19 OK OK 592 610 595 596 624 C3' U A 20 OK OK 622 640 625 626 654 C3' G A 21 OK OK 652 673 655 656 688 C3' C A 22 OK OK 686 704 689 690 719 C3' C A 23 OK OK 717 735 720 721 749 C3' G B 1 OK OK 747 768 750 751 784 C3' G B 2 OK OK 782 803 785 786 818 C3' C B 3 OK OK 816 834 819 820 849 C3' A B 4 OK OK 847 867 850 851 882 C3' A B 5 OK OK 880 900 883 884 915 C3' U B 6 OK OK 913 931 916 917 945 C3' G B 7 OK OK 943 964 946 947 979 C3' A B 8 OK OK 977 997 980 981 1012 C3' A B 9 OK OK 1010 1030 1013 1014 1045 C3' G B 10 OK OK 1043 1064 1046 1047 1079 C3' C B 11 OK OK 1077 1095 1080 1081 1110 C3' G B 12 OK OK 1108 1129 1111 1112 1144 C3' C B 13 OK OK 1142 1160 1145 1146 1175 C3' G B 14 OK OK 1173 1194 1176 1177 1209 C3' C B 15 OK OK 1207 1225 1210 1211 1240 C3' A B 16 OK OK 1238 1258 1241 1242 1273 C3' C B 17 OK OK 1271 1289 1274 1275 1304 C3' G B 18 OK OK 1302 1323 1305 1306 1338 C3' U B 19 OK OK 1336 1354 1339 1340 1368 C3' U B 20 OK OK 1366 1384 1369 1370 1398 C3' G B 21 OK OK 1396 1417 1399 1400 1432 C3' C B 22 OK OK 1430 1448 1433 1434 1463 C3' C B 23 OK OK 1461 1479 1464 1465 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK OK 5 23 2 4 38 C4' G A 2 OK OK 40 58 37 39 72 C4' C A 3 OK OK 74 89 71 73 103 C4' A A 4 OK OK 105 122 102 104 136 C4' A A 5 OK OK 138 155 135 137 169 C4' U A 6 OK OK 171 186 168 170 199 C4' G A 7 OK OK 201 219 198 200 233 C4' A A 8 OK OK 235 252 232 234 266 C4' A A 9 OK OK 268 285 265 267 299 C4' G A 10 OK OK 301 319 298 300 333 C4' C A 11 OK OK 335 350 332 334 364 C4' G A 12 OK OK 366 384 363 365 398 C4' C A 13 OK OK 400 415 397 399 429 C4' G A 14 OK OK 431 449 428 430 463 C4' C A 15 OK OK 465 480 462 464 494 C4' A A 16 OK OK 496 513 493 495 527 C4' C A 17 OK OK 529 544 526 528 558 C4' G A 18 OK OK 560 578 557 559 592 C4' U A 19 OK OK 594 609 591 593 622 C4' U A 20 OK OK 624 639 621 623 652 C4' G A 21 OK OK 654 672 651 653 686 C4' C A 22 OK OK 688 703 685 687 717 C4' C A 23 OK OK 719 734 716 718 747 C4' G B 1 OK OK 749 767 746 748 782 C4' G B 2 OK OK 784 802 781 783 816 C4' C B 3 OK OK 818 833 815 817 847 C4' A B 4 OK OK 849 866 846 848 880 C4' A B 5 OK OK 882 899 879 881 913 C4' U B 6 OK OK 915 930 912 914 943 C4' G B 7 OK OK 945 963 942 944 977 C4' A B 8 OK OK 979 996 976 978 1010 C4' A B 9 OK OK 1012 1029 1009 1011 1043 C4' G B 10 OK OK 1045 1063 1042 1044 1077 C4' C B 11 OK OK 1079 1094 1076 1078 1108 C4' G B 12 OK OK 1110 1128 1107 1109 1142 C4' C B 13 OK OK 1144 1159 1141 1143 1173 C4' G B 14 OK OK 1175 1193 1172 1174 1207 C4' C B 15 OK OK 1209 1224 1206 1208 1238 C4' A B 16 OK OK 1240 1257 1237 1239 1271 C4' C B 17 OK OK 1273 1288 1270 1272 1302 C4' G B 18 OK OK 1304 1322 1301 1303 1336 C4' U B 19 OK OK 1338 1353 1335 1337 1366 C4' U B 20 OK OK 1368 1383 1365 1367 1396 C4' G B 21 OK OK 1398 1416 1395 1397 1430 C4' C B 22 OK OK 1432 1447 1429 1431 1461 C4' C B 23 OK OK 1463 1478 1460 1462 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 1 OK OK 1 21 22 3 37 C5' G A 2 OK OK 36 56 57 38 71 C5' C A 3 OK OK 70 87 88 72 102 C5' A A 4 OK OK 101 120 121 103 135 C5' A A 5 OK OK 134 153 154 136 168 C5' U A 6 OK OK 167 184 185 169 198 C5' G A 7 OK OK 197 217 218 199 232 C5' A A 8 OK OK 231 250 251 233 265 C5' A A 9 OK OK 264 283 284 266 298 C5' G A 10 OK OK 297 317 318 299 332 C5' C A 11 OK OK 331 348 349 333 363 C5' G A 12 OK OK 362 382 383 364 397 C5' C A 13 OK OK 396 413 414 398 428 C5' G A 14 OK OK 427 447 448 429 462 C5' C A 15 OK OK 461 478 479 463 493 C5' A A 16 OK OK 492 511 512 494 526 C5' C A 17 OK OK 525 542 543 527 557 C5' G A 18 OK OK 556 576 577 558 591 C5' U A 19 OK OK 590 607 608 592 621 C5' U A 20 OK OK 620 637 638 622 651 C5' G A 21 OK OK 650 670 671 652 685 C5' C A 22 OK OK 684 701 702 686 716 C5' C A 23 OK OK 715 732 733 717 746 C5' G B 1 OK OK 745 765 766 747 781 C5' G B 2 OK OK 780 800 801 782 815 C5' C B 3 OK OK 814 831 832 816 846 C5' A B 4 OK OK 845 864 865 847 879 C5' A B 5 OK OK 878 897 898 880 912 C5' U B 6 OK OK 911 928 929 913 942 C5' G B 7 OK OK 941 961 962 943 976 C5' A B 8 OK OK 975 994 995 977 1009 C5' A B 9 OK OK 1008 1027 1028 1010 1042 C5' G B 10 OK OK 1041 1061 1062 1043 1076 C5' C B 11 OK OK 1075 1092 1093 1077 1107 C5' G B 12 OK OK 1106 1126 1127 1108 1141 C5' C B 13 OK OK 1140 1157 1158 1142 1172 C5' G B 14 OK OK 1171 1191 1192 1173 1206 C5' C B 15 OK OK 1205 1222 1223 1207 1237 C5' A B 16 OK OK 1236 1255 1256 1238 1270 C5' C B 17 OK OK 1269 1286 1287 1271 1301 C5' G B 18 OK OK 1300 1320 1321 1302 1335 C5' U B 19 OK OK 1334 1351 1352 1336 1365 C5' U B 20 OK OK 1364 1381 1382 1366 1395 C5' G B 21 OK OK 1394 1414 1415 1396 1429 C5' C B 22 OK OK 1428 1445 1446 1430 1460 C5' C B 23 OK OK 1459 1476 1477 1461 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 2 distorted distorted 6 34 35 36 67 P C A 3 distorted distorted 41 68 69 70 98 P A A 4 distorted distorted 75 99 100 101 131 P A A 5 distorted distorted 106 132 133 134 164 P U A 6 distorted distorted 139 165 166 167 194 P G A 7 distorted distorted 172 195 196 197 228 P A A 8 distorted distorted 202 229 230 231 261 P A A 9 distorted distorted 236 262 263 264 294 P G A 10 distorted distorted 269 295 296 297 328 P C A 11 distorted distorted 302 329 330 331 359 P G A 12 distorted distorted 336 360 361 362 393 P C A 13 distorted distorted 367 394 395 396 424 P G A 14 distorted distorted 401 425 426 427 458 P C A 15 distorted distorted 432 459 460 461 489 P A A 16 distorted distorted 466 490 491 492 522 P C A 17 distorted distorted 497 523 524 525 553 P G A 18 distorted distorted 530 554 555 556 587 P U A 19 distorted distorted 561 588 589 590 617 P U A 20 distorted distorted 595 618 619 620 647 P G A 21 distorted distorted 625 648 649 650 681 P C A 22 distorted distorted 655 682 683 684 712 P C A 23 distorted distorted 689 713 714 715 777 P G B 2 distorted distorted 750 778 779 780 811 P C B 3 distorted distorted 785 812 813 814 842 P A B 4 distorted distorted 819 843 844 845 875 P A B 5 distorted distorted 850 876 877 878 908 P U B 6 distorted distorted 883 909 910 911 938 P G B 7 distorted distorted 916 939 940 941 972 P A B 8 distorted distorted 946 973 974 975 1005 P A B 9 distorted distorted 980 1006 1007 1008 1038 P G B 10 distorted distorted 1013 1039 1040 1041 1072 P C B 11 distorted distorted 1046 1073 1074 1075 1103 P G B 12 distorted distorted 1080 1104 1105 1106 1137 P C B 13 distorted distorted 1111 1138 1139 1140 1168 P G B 14 distorted distorted 1145 1169 1170 1171 1202 P C B 15 distorted distorted 1176 1203 1204 1205 1233 P A B 16 distorted distorted 1210 1234 1235 1236 1266 P C B 17 distorted distorted 1241 1267 1268 1269 1297 P G B 18 distorted distorted 1274 1298 1299 1300 1331 P U B 19 distorted distorted 1305 1332 1333 1334 1361 P U B 20 distorted distorted 1339 1362 1363 1364 1391 P G B 21 distorted distorted 1369 1392 1393 1394 1425 P C B 22 distorted distorted 1399 1426 1427 1428 1456 P C B 23 distorted distorted 1433 1457 1458 1459 ---------------------------------------------------------------------------------