ID code: '2OIH' 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' --------------------------------------------------------------------------------- 12 C1' U B 100 beta 7 13 10 32 C1' G B 101 beta 27 33 30 55 C1' G B 102 beta 50 56 53 78 C1' C B 103 beta 73 79 76 98 C1' C B 104 beta 93 99 96 118 C1' G B 105 beta 113 119 116 141 C1' G B 106 beta 136 142 139 164 C1' C B 107 beta 159 165 162 184 C1' A B 108 beta 179 185 182 206 C1' U B 109 beta 201 207 204 226 C1' G B 110 beta 221 227 224 249 C1' G B 111 beta 244 250 247 272 C1' U B 112 beta 267 273 270 292 C1' C B 113 beta 287 293 290 312 C1' C B 114 beta 307 313 310 332 C1' C B 115 beta 327 333 330 352 C1' A B 116 beta 347 353 350 374 C1' G B 117 beta 369 375 372 397 C1' C B 118 beta 392 398 395 417 C1' C B 119 beta 412 418 415 437 C1' U B 120 beta 432 438 435 457 C1' C B 121 beta 452 458 455 477 C1' C B 122 beta 472 478 475 497 C1' U B 123 beta 492 498 495 517 C1' C B 124 beta 512 518 515 537 C1' G B 125 beta 532 538 535 560 C1' C B 126 beta 555 561 558 580 C1' U B 127 beta 575 581 578 600 C1' G B 128 beta 595 601 598 623 C1' G B 129 beta 618 624 621 646 C1' C B 130 beta 641 647 644 666 C1' G B 131 beta 661 667 664 689 C1' C B 132 beta 684 690 687 709 C1' C B 133 beta 704 710 707 729 C1' G B 134 beta 724 730 727 752 C1' G B 135 beta 747 753 750 775 C1' C B 136 beta 770 776 773 795 C1' U B 137 beta 790 796 793 815 C1' G B 138 beta 810 816 813 838 C1' G B 139 beta 833 839 836 861 C1' G B 140 beta 856 862 859 884 C1' C B 141 beta 879 885 882 904 C1' A B 142 beta 899 905 902 926 C1' A B 143 beta 921 927 924 948 C1' C B 144 beta 943 949 946 968 C1' A B 145 beta 963 969 966 990 C1' C B 146 beta 985 991 988 1010 C1' C B 147 beta 1005 1011 1008 1030 C1' A B 148 beta 1025 1031 1028 1052 C1' U B 149 beta 1047 1053 1050 1072 C1' U B 150 beta 1067 1073 1070 1092 C1' G B 151 beta 1087 1093 1090 1115 C1' C B 152 beta 1110 1116 1113 1135 C1' A B 153 beta 1130 1136 1133 1157 C1' C B 154 beta 1152 1158 1155 1177 C1' U B 155 beta 1172 1178 1175 1197 C1' C B 156 beta 1192 1198 1195 1217 C1' C B 157 beta 1212 1218 1215 1237 C1' G B 158 beta 1232 1238 1235 1260 C1' G B 159 beta 1255 1261 1258 1283 C1' U B 160 beta 1278 1284 1281 1303 C1' G B 161 beta 1298 1304 1301 1326 C1' G B 162 beta 1321 1327 1324 1349 C1' U B 163 beta 1344 1350 1347 1369 C1' G B 164 beta 1364 1370 1367 1392 C1' A B 165 beta 1387 1393 1390 1414 C1' A B 166 beta 1409 1415 1412 1436 C1' U B 167 beta 1431 1437 1434 1456 C1' G B 168 beta 1451 1457 1454 1479 C1' G B 169 beta 1474 1480 1477 1502 C1' G B 170 beta 1497 1503 1500 1525 C1' A B 171 beta 1520 1526 1523 1547 C1' C B 172 beta 1542 1548 1545 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' U B 100 OK 12 8 11 30 C2' G B 101 OK 32 28 31 53 C2' G B 102 OK 55 51 54 76 C2' C B 103 OK 78 74 77 96 C2' C B 104 OK 98 94 97 116 C2' G B 105 OK 118 114 117 139 C2' G B 106 OK 141 137 140 162 C2' C B 107 OK 164 160 163 182 C2' A B 108 OK 184 180 183 204 C2' U B 109 OK 206 202 205 224 C2' G B 110 OK 226 222 225 247 C2' G B 111 OK 249 245 248 270 C2' U B 112 OK 272 268 271 290 C2' C B 113 OK 292 288 291 310 C2' C B 114 OK 312 308 311 330 C2' C B 115 OK 332 328 331 350 C2' A B 116 OK 352 348 351 372 C2' G B 117 OK 374 370 373 395 C2' C B 118 OK 397 393 396 415 C2' C B 119 OK 417 413 416 435 C2' U B 120 OK 437 433 436 455 C2' C B 121 OK 457 453 456 475 C2' C B 122 OK 477 473 476 495 C2' U B 123 OK 497 493 496 515 C2' C B 124 OK 517 513 516 535 C2' G B 125 OK 537 533 536 558 C2' C B 126 OK 560 556 559 578 C2' U B 127 OK 580 576 579 598 C2' G B 128 OK 600 596 599 621 C2' G B 129 OK 623 619 622 644 C2' C B 130 OK 646 642 645 664 C2' G B 131 OK 666 662 665 687 C2' C B 132 OK 689 685 688 707 C2' C B 133 OK 709 705 708 727 C2' G B 134 OK 729 725 728 750 C2' G B 135 OK 752 748 751 773 C2' C B 136 OK 775 771 774 793 C2' U B 137 OK 795 791 794 813 C2' G B 138 OK 815 811 814 836 C2' G B 139 OK 838 834 837 859 C2' G B 140 OK 861 857 860 882 C2' C B 141 OK 884 880 883 902 C2' A B 142 OK 904 900 903 924 C2' A B 143 OK 926 922 925 946 C2' C B 144 OK 948 944 947 966 C2' A B 145 OK 968 964 967 988 C2' C B 146 OK 990 986 989 1008 C2' C B 147 OK 1010 1006 1009 1028 C2' A B 148 OK 1030 1026 1029 1050 C2' U B 149 OK 1052 1048 1051 1070 C2' U B 150 OK 1072 1068 1071 1090 C2' G B 151 OK 1092 1088 1091 1113 C2' C B 152 OK 1115 1111 1114 1133 C2' A B 153 OK 1135 1131 1134 1155 C2' C B 154 OK 1157 1153 1156 1175 C2' U B 155 OK 1177 1173 1176 1195 C2' C B 156 OK 1197 1193 1196 1215 C2' C B 157 OK 1217 1213 1216 1235 C2' G B 158 OK 1237 1233 1236 1258 C2' G B 159 OK 1260 1256 1259 1281 C2' U B 160 OK 1283 1279 1282 1301 C2' G B 161 OK 1303 1299 1302 1324 C2' G B 162 OK 1326 1322 1325 1347 C2' U B 163 OK 1349 1345 1348 1367 C2' G B 164 OK 1369 1365 1368 1390 C2' A B 165 OK 1392 1388 1391 1412 C2' A B 166 OK 1414 1410 1413 1434 C2' U B 167 OK 1436 1432 1435 1454 C2' G B 168 OK 1456 1452 1455 1477 C2' G B 169 OK 1479 1475 1478 1500 C2' G B 170 OK 1502 1498 1501 1523 C2' A B 171 OK 1525 1521 1524 1545 C2' C B 172 OK 1547 1543 1546 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' U B 100 OK 6 9 10 28 C3' G B 101 OK 26 29 30 51 C3' G B 102 OK 49 52 53 74 C3' C B 103 OK 72 75 76 94 C3' C B 104 OK 92 95 96 114 C3' G B 105 OK 112 115 116 137 C3' G B 106 OK 135 138 139 160 C3' C B 107 OK 158 161 162 180 C3' A B 108 OK 178 181 182 202 C3' U B 109 OK 200 203 204 222 C3' G B 110 OK 220 223 224 245 C3' G B 111 OK 243 246 247 268 C3' U B 112 OK 266 269 270 288 C3' C B 113 OK 286 289 290 308 C3' C B 114 OK 306 309 310 328 C3' C B 115 OK 326 329 330 348 C3' A B 116 OK 346 349 350 370 C3' G B 117 OK 368 371 372 393 C3' C B 118 OK 391 394 395 413 C3' C B 119 OK 411 414 415 433 C3' U B 120 OK 431 434 435 453 C3' C B 121 OK 451 454 455 473 C3' C B 122 OK 471 474 475 493 C3' U B 123 OK 491 494 495 513 C3' C B 124 OK 511 514 515 533 C3' G B 125 OK 531 534 535 556 C3' C B 126 OK 554 557 558 576 C3' U B 127 OK 574 577 578 596 C3' G B 128 OK 594 597 598 619 C3' G B 129 OK 617 620 621 642 C3' C B 130 OK 640 643 644 662 C3' G B 131 OK 660 663 664 685 C3' C B 132 OK 683 686 687 705 C3' C B 133 OK 703 706 707 725 C3' G B 134 OK 723 726 727 748 C3' G B 135 OK 746 749 750 771 C3' C B 136 OK 769 772 773 791 C3' U B 137 OK 789 792 793 811 C3' G B 138 OK 809 812 813 834 C3' G B 139 OK 832 835 836 857 C3' G B 140 OK 855 858 859 880 C3' C B 141 OK 878 881 882 900 C3' A B 142 OK 898 901 902 922 C3' A B 143 OK 920 923 924 944 C3' C B 144 OK 942 945 946 964 C3' A B 145 OK 962 965 966 986 C3' C B 146 OK 984 987 988 1006 C3' C B 147 OK 1004 1007 1008 1026 C3' A B 148 OK 1024 1027 1028 1048 C3' U B 149 OK 1046 1049 1050 1068 C3' U B 150 OK 1066 1069 1070 1088 C3' G B 151 OK 1086 1089 1090 1111 C3' C B 152 OK 1109 1112 1113 1131 C3' A B 153 OK 1129 1132 1133 1153 C3' C B 154 OK 1151 1154 1155 1173 C3' U B 155 OK 1171 1174 1175 1193 C3' C B 156 OK 1191 1194 1195 1213 C3' C B 157 OK 1211 1214 1215 1233 C3' G B 158 OK 1231 1234 1235 1256 C3' G B 159 OK 1254 1257 1258 1279 C3' U B 160 OK 1277 1280 1281 1299 C3' G B 161 OK 1297 1300 1301 1322 C3' G B 162 OK 1320 1323 1324 1345 C3' U B 163 OK 1343 1346 1347 1365 C3' G B 164 OK 1363 1366 1367 1388 C3' A B 165 OK 1386 1389 1390 1410 C3' A B 166 OK 1408 1411 1412 1432 C3' U B 167 OK 1430 1433 1434 1452 C3' G B 168 OK 1450 1453 1454 1475 C3' G B 169 OK 1473 1476 1477 1498 C3' G B 170 OK 1496 1499 1500 1521 C3' A B 171 OK 1519 1522 1523 1543 C3' C B 172 OK 1541 1544 1545 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' U B 100 OK 8 5 7 26 C4' G B 101 OK 28 25 27 49 C4' G B 102 OK 51 48 50 72 C4' C B 103 OK 74 71 73 92 C4' C B 104 OK 94 91 93 112 C4' G B 105 OK 114 111 113 135 C4' G B 106 OK 137 134 136 158 C4' C B 107 OK 160 157 159 178 C4' A B 108 OK 180 177 179 200 C4' U B 109 OK 202 199 201 220 C4' G B 110 OK 222 219 221 243 C4' G B 111 OK 245 242 244 266 C4' U B 112 OK 268 265 267 286 C4' C B 113 OK 288 285 287 306 C4' C B 114 OK 308 305 307 326 C4' C B 115 OK 328 325 327 346 C4' A B 116 OK 348 345 347 368 C4' G B 117 OK 370 367 369 391 C4' C B 118 OK 393 390 392 411 C4' C B 119 OK 413 410 412 431 C4' U B 120 OK 433 430 432 451 C4' C B 121 OK 453 450 452 471 C4' C B 122 OK 473 470 472 491 C4' U B 123 OK 493 490 492 511 C4' C B 124 OK 513 510 512 531 C4' G B 125 OK 533 530 532 554 C4' C B 126 OK 556 553 555 574 C4' U B 127 OK 576 573 575 594 C4' G B 128 OK 596 593 595 617 C4' G B 129 OK 619 616 618 640 C4' C B 130 OK 642 639 641 660 C4' G B 131 OK 662 659 661 683 C4' C B 132 OK 685 682 684 703 C4' C B 133 OK 705 702 704 723 C4' G B 134 OK 725 722 724 746 C4' G B 135 OK 748 745 747 769 C4' C B 136 OK 771 768 770 789 C4' U B 137 OK 791 788 790 809 C4' G B 138 OK 811 808 810 832 C4' G B 139 OK 834 831 833 855 C4' G B 140 OK 857 854 856 878 C4' C B 141 OK 880 877 879 898 C4' A B 142 OK 900 897 899 920 C4' A B 143 OK 922 919 921 942 C4' C B 144 OK 944 941 943 962 C4' A B 145 OK 964 961 963 984 C4' C B 146 OK 986 983 985 1004 C4' C B 147 OK 1006 1003 1005 1024 C4' A B 148 OK 1026 1023 1025 1046 C4' U B 149 OK 1048 1045 1047 1066 C4' U B 150 OK 1068 1065 1067 1086 C4' G B 151 OK 1088 1085 1087 1109 C4' C B 152 OK 1111 1108 1110 1129 C4' A B 153 OK 1131 1128 1130 1151 C4' C B 154 OK 1153 1150 1152 1171 C4' U B 155 OK 1173 1170 1172 1191 C4' C B 156 OK 1193 1190 1192 1211 C4' C B 157 OK 1213 1210 1212 1231 C4' G B 158 OK 1233 1230 1232 1254 C4' G B 159 OK 1256 1253 1255 1277 C4' U B 160 OK 1279 1276 1278 1297 C4' G B 161 OK 1299 1296 1298 1320 C4' G B 162 OK 1322 1319 1321 1343 C4' U B 163 OK 1345 1342 1344 1363 C4' G B 164 OK 1365 1362 1364 1386 C4' A B 165 OK 1388 1385 1387 1408 C4' A B 166 OK 1410 1407 1409 1430 C4' U B 167 OK 1432 1429 1431 1450 C4' G B 168 OK 1452 1449 1451 1473 C4' G B 169 OK 1475 1472 1474 1496 C4' G B 170 OK 1498 1495 1497 1519 C4' A B 171 OK 1521 1518 1520 1541 C4' C B 172 OK 1543 1540 1542 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' U B 100 4 6 25 C5' G B 101 24 26 48 C5' G B 102 47 49 71 C5' C B 103 70 72 91 C5' C B 104 90 92 111 C5' G B 105 110 112 134 C5' G B 106 133 135 157 C5' C B 107 156 158 177 C5' A B 108 176 178 199 C5' U B 109 198 200 219 C5' G B 110 218 220 242 C5' G B 111 241 243 265 C5' U B 112 264 266 285 C5' C B 113 284 286 305 C5' C B 114 304 306 325 C5' C B 115 324 326 345 C5' A B 116 344 346 367 C5' G B 117 366 368 390 C5' C B 118 389 391 410 C5' C B 119 409 411 430 C5' U B 120 429 431 450 C5' C B 121 449 451 470 C5' C B 122 469 471 490 C5' U B 123 489 491 510 C5' C B 124 509 511 530 C5' G B 125 529 531 553 C5' C B 126 552 554 573 C5' U B 127 572 574 593 C5' G B 128 592 594 616 C5' G B 129 615 617 639 C5' C B 130 638 640 659 C5' G B 131 658 660 682 C5' C B 132 681 683 702 C5' C B 133 701 703 722 C5' G B 134 721 723 745 C5' G B 135 744 746 768 C5' C B 136 767 769 788 C5' U B 137 787 789 808 C5' G B 138 807 809 831 C5' G B 139 830 832 854 C5' G B 140 853 855 877 C5' C B 141 876 878 897 C5' A B 142 896 898 919 C5' A B 143 918 920 941 C5' C B 144 940 942 961 C5' A B 145 960 962 983 C5' C B 146 982 984 1003 C5' C B 147 1002 1004 1023 C5' A B 148 1022 1024 1045 C5' U B 149 1044 1046 1065 C5' U B 150 1064 1066 1085 C5' G B 151 1084 1086 1108 C5' C B 152 1107 1109 1128 C5' A B 153 1127 1129 1150 C5' C B 154 1149 1151 1170 C5' U B 155 1169 1171 1190 C5' C B 156 1189 1191 1210 C5' C B 157 1209 1211 1230 C5' G B 158 1229 1231 1253 C5' G B 159 1252 1254 1276 C5' U B 160 1275 1277 1296 C5' G B 161 1295 1297 1319 C5' G B 162 1318 1320 1342 C5' U B 163 1341 1343 1362 C5' G B 164 1361 1363 1385 C5' A B 165 1384 1386 1407 C5' A B 166 1406 1408 1429 C5' U B 167 1428 1430 1449 C5' G B 168 1448 1450 1472 C5' G B 169 1471 1473 1495 C5' G B 170 1494 1496 1518 C5' A B 171 1517 1519 1540 C5' C B 172 1539 1541 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P U B 100 OK OK 2 3 4 21 P G B 101 distorted distorted 9 22 23 24 44 P G B 102 distorted distorted 29 45 46 47 67 P C B 103 distorted distorted 52 68 69 70 87 P C B 104 distorted distorted 75 88 89 90 107 P G B 105 distorted distorted 95 108 109 110 130 P G B 106 distorted distorted 115 131 132 133 153 P C B 107 distorted distorted 138 154 155 156 173 P A B 108 distorted distorted 161 174 175 176 195 P U B 109 distorted distorted 181 196 197 198 215 P G B 110 distorted distorted 203 216 217 218 238 P G B 111 distorted distorted 223 239 240 241 261 P U B 112 distorted distorted 246 262 263 264 281 P C B 113 distorted distorted 269 282 283 284 301 P C B 114 distorted distorted 289 302 303 304 321 P C B 115 distorted distorted 309 322 323 324 341 P A B 116 distorted distorted 329 342 343 344 363 P G B 117 distorted distorted 349 364 365 366 386 P C B 118 distorted distorted 371 387 388 389 406 P C B 119 distorted distorted 394 407 408 409 426 P U B 120 distorted distorted 414 427 428 429 446 P C B 121 distorted distorted 434 447 448 449 466 P C B 122 distorted distorted 454 467 468 469 486 P U B 123 distorted distorted 474 487 488 489 506 P C B 124 distorted distorted 494 507 508 509 526 P G B 125 distorted distorted 514 527 528 529 549 P C B 126 distorted distorted 534 550 551 552 569 P U B 127 distorted distorted 557 570 571 572 589 P G B 128 distorted distorted 577 590 591 592 612 P G B 129 distorted distorted 597 613 614 615 635 P C B 130 distorted distorted 620 636 637 638 655 P G B 131 distorted distorted 643 656 657 658 678 P C B 132 distorted distorted 663 679 680 681 698 P C B 133 distorted distorted 686 699 700 701 718 P G B 134 distorted distorted 706 719 720 721 741 P G B 135 distorted distorted 726 742 743 744 764 P C B 136 distorted distorted 749 765 766 767 784 P U B 137 distorted distorted 772 785 786 787 804 P G B 138 distorted distorted 792 805 806 807 827 P G B 139 distorted distorted 812 828 829 830 850 P G B 140 distorted distorted 835 851 852 853 873 P C B 141 distorted distorted 858 874 875 876 893 P A B 142 distorted distorted 881 894 895 896 915 P A B 143 distorted distorted 901 916 917 918 937 P C B 144 distorted distorted 923 938 939 940 957 P A B 145 distorted distorted 945 958 959 960 979 P C B 146 distorted distorted 965 980 981 982 999 P C B 147 distorted distorted 987 1000 1001 1002 1019 P A B 148 distorted distorted 1007 1020 1021 1022 1041 P U B 149 distorted distorted 1027 1042 1043 1044 1061 P U B 150 distorted distorted 1049 1062 1063 1064 1081 P G B 151 distorted distorted 1069 1082 1083 1084 1104 P C B 152 distorted distorted 1089 1105 1106 1107 1124 P A B 153 distorted distorted 1112 1125 1126 1127 1146 P C B 154 distorted distorted 1132 1147 1148 1149 1166 P U B 155 distorted distorted 1154 1167 1168 1169 1186 P C B 156 distorted distorted 1174 1187 1188 1189 1206 P C B 157 distorted distorted 1194 1207 1208 1209 1226 P G B 158 distorted distorted 1214 1227 1228 1229 1249 P G B 159 distorted distorted 1234 1250 1251 1252 1272 P U B 160 distorted distorted 1257 1273 1274 1275 1292 P G B 161 distorted distorted 1280 1293 1294 1295 1315 P G B 162 distorted distorted 1300 1316 1317 1318 1338 P U B 163 distorted distorted 1323 1339 1340 1341 1358 P G B 164 distorted distorted 1346 1359 1360 1361 1381 P A B 165 distorted distorted 1366 1382 1383 1384 1403 P A B 166 distorted distorted 1389 1404 1405 1406 1425 P U B 167 distorted distorted 1411 1426 1427 1428 1445 P G B 168 distorted distorted 1433 1446 1447 1448 1468 P G B 169 distorted distorted 1453 1469 1470 1471 1491 P G B 170 distorted distorted 1476 1492 1493 1494 1514 P A B 171 distorted distorted 1499 1515 1516 1517 1536 P C B 172 distorted distorted 1522 1537 1538 1539 ---------------------------------------------------------------------------------