ID code: '1VBX' 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' U B 100 beta 4 10 7 29 C1' G B 101 beta 24 30 27 52 C1' G B 102 beta 47 53 50 75 C1' C B 103 beta 70 76 73 95 C1' C B 104 beta 90 96 93 115 C1' G B 105 beta 110 116 113 138 C1' G B 106 beta 133 139 136 161 C1' C B 107 beta 156 162 159 181 C1' A B 108 beta 176 182 179 203 C1' U B 109 beta 198 204 201 223 C1' G B 110 beta 218 224 221 246 C1' G B 111 beta 241 247 244 269 C1' U B 112 beta 264 270 267 289 C1' C B 113 beta 284 290 287 309 C1' C B 114 beta 304 310 307 329 C1' C B 115 beta 324 330 327 349 C1' A B 116 beta 344 350 347 371 C1' G B 117 beta 366 372 369 394 C1' C B 118 beta 389 395 392 414 C1' C B 119 beta 409 415 412 434 C1' U B 120 beta 429 435 432 454 C1' C B 121 beta 449 455 452 474 C1' C B 122 beta 469 475 472 494 C1' U B 123 beta 489 495 492 514 C1' C B 124 beta 509 515 512 534 C1' G B 125 beta 529 535 532 557 C1' C B 126 beta 552 558 555 577 C1' U B 127 beta 572 578 575 597 C1' G B 128 beta 592 598 595 620 C1' G B 129 beta 615 621 618 643 C1' C B 130 beta 638 644 641 663 C1' G B 131 beta 658 664 661 686 C1' C B 132 beta 681 687 684 706 C1' C B 133 beta 701 707 704 726 C1' G B 134 beta 721 727 724 749 C1' G B 135 beta 744 750 747 772 C1' C B 136 beta 767 773 770 792 C1' U B 137 beta 787 793 790 812 C1' G B 138 beta 807 813 810 835 C1' G B 139 beta 830 836 833 858 C1' G B 140 beta 853 859 856 881 C1' C B 141 beta 876 882 879 901 C1' A B 142 beta 896 902 899 923 C1' A B 143 beta 918 924 921 945 C1' C B 144 beta 940 946 943 965 C1' A B 145 beta 960 966 963 987 C1' C B 146 beta 982 988 985 1007 C1' C B 147 beta 1002 1008 1005 1027 C1' A B 148 beta 1022 1028 1025 1049 C1' U B 149 beta 1044 1050 1047 1069 C1' U B 150 beta 1064 1070 1067 1089 C1' G B 151 beta 1084 1090 1087 1112 C1' C B 152 beta 1107 1113 1110 1132 C1' A B 153 beta 1127 1133 1130 1154 C1' C B 154 beta 1149 1155 1152 1174 C1' U B 155 beta 1169 1175 1172 1194 C1' C B 156 beta 1189 1195 1192 1214 C1' C B 157 beta 1209 1215 1212 1234 C1' G B 158 beta 1229 1235 1232 1257 C1' G B 159 beta 1252 1258 1255 1280 C1' U B 160 beta 1275 1281 1278 1300 C1' G B 161 beta 1295 1301 1298 1323 C1' G B 162 beta 1318 1324 1321 1346 C1' U B 163 beta 1341 1347 1344 1366 C1' G B 164 beta 1361 1367 1364 1389 C1' A B 165 beta 1384 1390 1387 1411 C1' A B 166 beta 1406 1412 1409 1433 C1' U B 167 beta 1428 1434 1431 1453 C1' G B 168 beta 1448 1454 1451 1476 C1' G B 169 beta 1471 1477 1474 1499 C1' G B 170 beta 1494 1500 1497 1522 C1' A B 171 beta 1517 1523 1520 1544 C1' C B 172 beta 1539 1545 1542 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' U B 100 OK 9 5 8 27 C2' G B 101 OK 29 25 28 50 C2' G B 102 OK 52 48 51 73 C2' C B 103 OK 75 71 74 93 C2' C B 104 OK 95 91 94 113 C2' G B 105 OK 115 111 114 136 C2' G B 106 OK 138 134 137 159 C2' C B 107 OK 161 157 160 179 C2' A B 108 OK 181 177 180 201 C2' U B 109 OK 203 199 202 221 C2' G B 110 OK 223 219 222 244 C2' G B 111 OK 246 242 245 267 C2' U B 112 OK 269 265 268 287 C2' C B 113 OK 289 285 288 307 C2' C B 114 OK 309 305 308 327 C2' C B 115 OK 329 325 328 347 C2' A B 116 OK 349 345 348 369 C2' G B 117 OK 371 367 370 392 C2' C B 118 OK 394 390 393 412 C2' C B 119 OK 414 410 413 432 C2' U B 120 OK 434 430 433 452 C2' C B 121 OK 454 450 453 472 C2' C B 122 OK 474 470 473 492 C2' U B 123 OK 494 490 493 512 C2' C B 124 OK 514 510 513 532 C2' G B 125 OK 534 530 533 555 C2' C B 126 OK 557 553 556 575 C2' U B 127 OK 577 573 576 595 C2' G B 128 OK 597 593 596 618 C2' G B 129 OK 620 616 619 641 C2' C B 130 OK 643 639 642 661 C2' G B 131 OK 663 659 662 684 C2' C B 132 OK 686 682 685 704 C2' C B 133 OK 706 702 705 724 C2' G B 134 OK 726 722 725 747 C2' G B 135 OK 749 745 748 770 C2' C B 136 OK 772 768 771 790 C2' U B 137 OK 792 788 791 810 C2' G B 138 OK 812 808 811 833 C2' G B 139 OK 835 831 834 856 C2' G B 140 OK 858 854 857 879 C2' C B 141 OK 881 877 880 899 C2' A B 142 OK 901 897 900 921 C2' A B 143 OK 923 919 922 943 C2' C B 144 OK 945 941 944 963 C2' A B 145 OK 965 961 964 985 C2' C B 146 OK 987 983 986 1005 C2' C B 147 OK 1007 1003 1006 1025 C2' A B 148 OK 1027 1023 1026 1047 C2' U B 149 OK 1049 1045 1048 1067 C2' U B 150 OK 1069 1065 1068 1087 C2' G B 151 OK 1089 1085 1088 1110 C2' C B 152 OK 1112 1108 1111 1130 C2' A B 153 OK 1132 1128 1131 1152 C2' C B 154 OK 1154 1150 1153 1172 C2' U B 155 OK 1174 1170 1173 1192 C2' C B 156 OK 1194 1190 1193 1212 C2' C B 157 OK 1214 1210 1213 1232 C2' G B 158 OK 1234 1230 1233 1255 C2' G B 159 OK 1257 1253 1256 1278 C2' U B 160 OK 1280 1276 1279 1298 C2' G B 161 OK 1300 1296 1299 1321 C2' G B 162 OK 1323 1319 1322 1344 C2' U B 163 OK 1346 1342 1345 1364 C2' G B 164 OK 1366 1362 1365 1387 C2' A B 165 OK 1389 1385 1388 1409 C2' A B 166 OK 1411 1407 1410 1431 C2' U B 167 OK 1433 1429 1432 1451 C2' G B 168 OK 1453 1449 1452 1474 C2' G B 169 OK 1476 1472 1475 1497 C2' G B 170 OK 1499 1495 1498 1520 C2' A B 171 OK 1522 1518 1521 1542 C2' C B 172 OK 1544 1540 1543 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' U B 100 OK 3 6 7 25 C3' G B 101 OK 23 26 27 48 C3' G B 102 OK 46 49 50 71 C3' C B 103 OK 69 72 73 91 C3' C B 104 OK 89 92 93 111 C3' G B 105 OK 109 112 113 134 C3' G B 106 OK 132 135 136 157 C3' C B 107 OK 155 158 159 177 C3' A B 108 OK 175 178 179 199 C3' U B 109 OK 197 200 201 219 C3' G B 110 OK 217 220 221 242 C3' G B 111 OK 240 243 244 265 C3' U B 112 OK 263 266 267 285 C3' C B 113 OK 283 286 287 305 C3' C B 114 OK 303 306 307 325 C3' C B 115 OK 323 326 327 345 C3' A B 116 OK 343 346 347 367 C3' G B 117 OK 365 368 369 390 C3' C B 118 OK 388 391 392 410 C3' C B 119 OK 408 411 412 430 C3' U B 120 OK 428 431 432 450 C3' C B 121 OK 448 451 452 470 C3' C B 122 OK 468 471 472 490 C3' U B 123 OK 488 491 492 510 C3' C B 124 OK 508 511 512 530 C3' G B 125 OK 528 531 532 553 C3' C B 126 OK 551 554 555 573 C3' U B 127 OK 571 574 575 593 C3' G B 128 OK 591 594 595 616 C3' G B 129 OK 614 617 618 639 C3' C B 130 OK 637 640 641 659 C3' G B 131 OK 657 660 661 682 C3' C B 132 OK 680 683 684 702 C3' C B 133 OK 700 703 704 722 C3' G B 134 OK 720 723 724 745 C3' G B 135 OK 743 746 747 768 C3' C B 136 OK 766 769 770 788 C3' U B 137 OK 786 789 790 808 C3' G B 138 OK 806 809 810 831 C3' G B 139 OK 829 832 833 854 C3' G B 140 OK 852 855 856 877 C3' C B 141 OK 875 878 879 897 C3' A B 142 OK 895 898 899 919 C3' A B 143 OK 917 920 921 941 C3' C B 144 OK 939 942 943 961 C3' A B 145 OK 959 962 963 983 C3' C B 146 OK 981 984 985 1003 C3' C B 147 OK 1001 1004 1005 1023 C3' A B 148 OK 1021 1024 1025 1045 C3' U B 149 OK 1043 1046 1047 1065 C3' U B 150 OK 1063 1066 1067 1085 C3' G B 151 OK 1083 1086 1087 1108 C3' C B 152 OK 1106 1109 1110 1128 C3' A B 153 OK 1126 1129 1130 1150 C3' C B 154 OK 1148 1151 1152 1170 C3' U B 155 OK 1168 1171 1172 1190 C3' C B 156 OK 1188 1191 1192 1210 C3' C B 157 OK 1208 1211 1212 1230 C3' G B 158 OK 1228 1231 1232 1253 C3' G B 159 OK 1251 1254 1255 1276 C3' U B 160 OK 1274 1277 1278 1296 C3' G B 161 OK 1294 1297 1298 1319 C3' G B 162 OK 1317 1320 1321 1342 C3' U B 163 OK 1340 1343 1344 1362 C3' G B 164 OK 1360 1363 1364 1385 C3' A B 165 OK 1383 1386 1387 1407 C3' A B 166 OK 1405 1408 1409 1429 C3' U B 167 OK 1427 1430 1431 1449 C3' G B 168 OK 1447 1450 1451 1472 C3' G B 169 OK 1470 1473 1474 1495 C3' G B 170 OK 1493 1496 1497 1518 C3' A B 171 OK 1516 1519 1520 1540 C3' C B 172 OK 1538 1541 1542 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' U B 100 OK 5 2 4 23 C4' G B 101 OK 25 22 24 46 C4' G B 102 OK 48 45 47 69 C4' C B 103 OK 71 68 70 89 C4' C B 104 OK 91 88 90 109 C4' G B 105 OK 111 108 110 132 C4' G B 106 OK 134 131 133 155 C4' C B 107 OK 157 154 156 175 C4' A B 108 OK 177 174 176 197 C4' U B 109 OK 199 196 198 217 C4' G B 110 OK 219 216 218 240 C4' G B 111 OK 242 239 241 263 C4' U B 112 OK 265 262 264 283 C4' C B 113 OK 285 282 284 303 C4' C B 114 OK 305 302 304 323 C4' C B 115 OK 325 322 324 343 C4' A B 116 OK 345 342 344 365 C4' G B 117 OK 367 364 366 388 C4' C B 118 OK 390 387 389 408 C4' C B 119 OK 410 407 409 428 C4' U B 120 OK 430 427 429 448 C4' C B 121 OK 450 447 449 468 C4' C B 122 OK 470 467 469 488 C4' U B 123 OK 490 487 489 508 C4' C B 124 OK 510 507 509 528 C4' G B 125 OK 530 527 529 551 C4' C B 126 OK 553 550 552 571 C4' U B 127 OK 573 570 572 591 C4' G B 128 OK 593 590 592 614 C4' G B 129 OK 616 613 615 637 C4' C B 130 OK 639 636 638 657 C4' G B 131 OK 659 656 658 680 C4' C B 132 OK 682 679 681 700 C4' C B 133 OK 702 699 701 720 C4' G B 134 OK 722 719 721 743 C4' G B 135 OK 745 742 744 766 C4' C B 136 OK 768 765 767 786 C4' U B 137 OK 788 785 787 806 C4' G B 138 OK 808 805 807 829 C4' G B 139 OK 831 828 830 852 C4' G B 140 OK 854 851 853 875 C4' C B 141 OK 877 874 876 895 C4' A B 142 OK 897 894 896 917 C4' A B 143 OK 919 916 918 939 C4' C B 144 OK 941 938 940 959 C4' A B 145 OK 961 958 960 981 C4' C B 146 OK 983 980 982 1001 C4' C B 147 OK 1003 1000 1002 1021 C4' A B 148 OK 1023 1020 1022 1043 C4' U B 149 OK 1045 1042 1044 1063 C4' U B 150 OK 1065 1062 1064 1083 C4' G B 151 OK 1085 1082 1084 1106 C4' C B 152 OK 1108 1105 1107 1126 C4' A B 153 OK 1128 1125 1127 1148 C4' C B 154 OK 1150 1147 1149 1168 C4' U B 155 OK 1170 1167 1169 1188 C4' C B 156 OK 1190 1187 1189 1208 C4' C B 157 OK 1210 1207 1209 1228 C4' G B 158 OK 1230 1227 1229 1251 C4' G B 159 OK 1253 1250 1252 1274 C4' U B 160 OK 1276 1273 1275 1294 C4' G B 161 OK 1296 1293 1295 1317 C4' G B 162 OK 1319 1316 1318 1340 C4' U B 163 OK 1342 1339 1341 1360 C4' G B 164 OK 1362 1359 1361 1383 C4' A B 165 OK 1385 1382 1384 1405 C4' A B 166 OK 1407 1404 1406 1427 C4' U B 167 OK 1429 1426 1428 1447 C4' G B 168 OK 1449 1446 1448 1470 C4' G B 169 OK 1472 1469 1471 1493 C4' G B 170 OK 1495 1492 1494 1516 C4' A B 171 OK 1518 1515 1517 1538 C4' C B 172 OK 1540 1537 1539 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' U B 100 1 3 22 C5' G B 101 21 23 45 C5' G B 102 44 46 68 C5' C B 103 67 69 88 C5' C B 104 87 89 108 C5' G B 105 107 109 131 C5' G B 106 130 132 154 C5' C B 107 153 155 174 C5' A B 108 173 175 196 C5' U B 109 195 197 216 C5' G B 110 215 217 239 C5' G B 111 238 240 262 C5' U B 112 261 263 282 C5' C B 113 281 283 302 C5' C B 114 301 303 322 C5' C B 115 321 323 342 C5' A B 116 341 343 364 C5' G B 117 363 365 387 C5' C B 118 386 388 407 C5' C B 119 406 408 427 C5' U B 120 426 428 447 C5' C B 121 446 448 467 C5' C B 122 466 468 487 C5' U B 123 486 488 507 C5' C B 124 506 508 527 C5' G B 125 526 528 550 C5' C B 126 549 551 570 C5' U B 127 569 571 590 C5' G B 128 589 591 613 C5' G B 129 612 614 636 C5' C B 130 635 637 656 C5' G B 131 655 657 679 C5' C B 132 678 680 699 C5' C B 133 698 700 719 C5' G B 134 718 720 742 C5' G B 135 741 743 765 C5' C B 136 764 766 785 C5' U B 137 784 786 805 C5' G B 138 804 806 828 C5' G B 139 827 829 851 C5' G B 140 850 852 874 C5' C B 141 873 875 894 C5' A B 142 893 895 916 C5' A B 143 915 917 938 C5' C B 144 937 939 958 C5' A B 145 957 959 980 C5' C B 146 979 981 1000 C5' C B 147 999 1001 1020 C5' A B 148 1019 1021 1042 C5' U B 149 1041 1043 1062 C5' U B 150 1061 1063 1082 C5' G B 151 1081 1083 1105 C5' C B 152 1104 1106 1125 C5' A B 153 1124 1126 1147 C5' C B 154 1146 1148 1167 C5' U B 155 1166 1168 1187 C5' C B 156 1186 1188 1207 C5' C B 157 1206 1208 1227 C5' G B 158 1226 1228 1250 C5' G B 159 1249 1251 1273 C5' U B 160 1272 1274 1293 C5' G B 161 1292 1294 1316 C5' G B 162 1315 1317 1339 C5' U B 163 1338 1340 1359 C5' G B 164 1358 1360 1382 C5' A B 165 1381 1383 1404 C5' A B 166 1403 1405 1426 C5' U B 167 1425 1427 1446 C5' G B 168 1445 1447 1469 C5' G B 169 1468 1470 1492 C5' G B 170 1491 1493 1515 C5' A B 171 1514 1516 1537 C5' C B 172 1536 1538 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 18 P G B 101 distorted distorted 6 19 20 21 41 P G B 102 distorted distorted 26 42 43 44 64 P C B 103 distorted distorted 49 65 66 67 84 P C B 104 distorted distorted 72 85 86 87 104 P G B 105 distorted distorted 92 105 106 107 127 P G B 106 distorted distorted 112 128 129 130 150 P C B 107 distorted distorted 135 151 152 153 170 P A B 108 distorted distorted 158 171 172 173 192 P U B 109 distorted distorted 178 193 194 195 212 P G B 110 distorted distorted 200 213 214 215 235 P G B 111 distorted distorted 220 236 237 238 258 P U B 112 distorted distorted 243 259 260 261 278 P C B 113 distorted distorted 266 279 280 281 298 P C B 114 distorted distorted 286 299 300 301 318 P C B 115 distorted distorted 306 319 320 321 338 P A B 116 distorted distorted 326 339 340 341 360 P G B 117 distorted distorted 346 361 362 363 383 P C B 118 distorted distorted 368 384 385 386 403 P C B 119 distorted distorted 391 404 405 406 423 P U B 120 distorted distorted 411 424 425 426 443 P C B 121 distorted distorted 431 444 445 446 463 P C B 122 distorted distorted 451 464 465 466 483 P U B 123 distorted distorted 471 484 485 486 503 P C B 124 distorted distorted 491 504 505 506 523 P G B 125 distorted distorted 511 524 525 526 546 P C B 126 distorted distorted 531 547 548 549 566 P U B 127 distorted distorted 554 567 568 569 586 P G B 128 distorted distorted 574 587 588 589 609 P G B 129 distorted distorted 594 610 611 612 632 P C B 130 distorted distorted 617 633 634 635 652 P G B 131 distorted distorted 640 653 654 655 675 P C B 132 distorted distorted 660 676 677 678 695 P C B 133 distorted distorted 683 696 697 698 715 P G B 134 distorted distorted 703 716 717 718 738 P G B 135 distorted distorted 723 739 740 741 761 P C B 136 distorted distorted 746 762 763 764 781 P U B 137 distorted distorted 769 782 783 784 801 P G B 138 distorted distorted 789 802 803 804 824 P G B 139 distorted distorted 809 825 826 827 847 P G B 140 distorted distorted 832 848 849 850 870 P C B 141 distorted distorted 855 871 872 873 890 P A B 142 distorted distorted 878 891 892 893 912 P A B 143 distorted distorted 898 913 914 915 934 P C B 144 distorted distorted 920 935 936 937 954 P A B 145 distorted distorted 942 955 956 957 976 P C B 146 distorted distorted 962 977 978 979 996 P C B 147 distorted distorted 984 997 998 999 1016 P A B 148 distorted distorted 1004 1017 1018 1019 1038 P U B 149 distorted distorted 1024 1039 1040 1041 1058 P U B 150 distorted distorted 1046 1059 1060 1061 1078 P G B 151 distorted distorted 1066 1079 1080 1081 1101 P C B 152 distorted distorted 1086 1102 1103 1104 1121 P A B 153 distorted distorted 1109 1122 1123 1124 1143 P C B 154 distorted distorted 1129 1144 1145 1146 1163 P U B 155 distorted distorted 1151 1164 1165 1166 1183 P C B 156 distorted distorted 1171 1184 1185 1186 1203 P C B 157 distorted distorted 1191 1204 1205 1206 1223 P G B 158 distorted distorted 1211 1224 1225 1226 1246 P G B 159 distorted distorted 1231 1247 1248 1249 1269 P U B 160 distorted distorted 1254 1270 1271 1272 1289 P G B 161 distorted distorted 1277 1290 1291 1292 1312 P G B 162 distorted distorted 1297 1313 1314 1315 1335 P U B 163 distorted distorted 1320 1336 1337 1338 1355 P G B 164 distorted distorted 1343 1356 1357 1358 1378 P A B 165 distorted distorted 1363 1379 1380 1381 1400 P A B 166 distorted distorted 1386 1401 1402 1403 1422 P U B 167 distorted distorted 1408 1423 1424 1425 1442 P G B 168 distorted distorted 1430 1443 1444 1445 1465 P G B 169 distorted distorted 1450 1466 1467 1468 1488 P G B 170 distorted distorted 1473 1489 1490 1491 1511 P A B 171 distorted distorted 1496 1512 1513 1514 1533 P C B 172 distorted distorted 1519 1534 1535 1536 ---------------------------------------------------------------------------------