ID code: '1SJF' 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 B 99 beta 4 10 7 31 C1' U B 100 beta 26 32 29 51 C1' G B 101 beta 46 52 49 74 C1' G B 102 beta 69 75 72 97 C1' C B 103 beta 92 98 95 117 C1' C B 104 beta 112 118 115 137 C1' G B 105 beta 132 138 135 160 C1' G B 106 beta 155 161 158 183 C1' C B 107 beta 178 184 181 203 C1' A B 108 beta 198 204 201 225 C1' U B 109 beta 220 226 223 245 C1' G B 110 beta 240 246 243 268 C1' G B 111 beta 263 269 266 291 C1' U B 112 beta 286 292 289 311 C1' C B 113 beta 306 312 309 331 C1' C B 114 beta 326 332 329 351 C1' C B 115 beta 346 352 349 371 C1' A B 116 beta 366 372 369 393 C1' G B 117 beta 388 394 391 416 C1' C B 118 beta 411 417 414 436 C1' C B 119 beta 431 437 434 456 C1' U B 120 beta 451 457 454 476 C1' C B 121 beta 471 477 474 496 C1' C B 122 beta 491 497 494 516 C1' U B 123 beta 511 517 514 536 C1' C B 124 beta 531 537 534 556 C1' G B 125 beta 551 557 554 579 C1' C B 126 beta 574 580 577 599 C1' U B 127 beta 594 600 597 619 C1' G B 128 beta 614 620 617 642 C1' G B 129 beta 637 643 640 665 C1' C B 130 beta 660 666 663 685 C1' G B 131 beta 680 686 683 708 C1' C B 132 beta 703 709 706 728 C1' C B 133 beta 723 729 726 748 C1' G B 134 beta 743 749 746 771 C1' G B 135 beta 766 772 769 794 C1' C B 136 beta 789 795 792 814 C1' U B 137 beta 809 815 812 834 C1' G B 138 beta 829 835 832 857 C1' G B 139 beta 852 858 855 880 C1' G B 140 beta 875 881 878 903 C1' C B 141 beta 898 904 901 923 C1' A B 142 beta 918 924 921 945 C1' A B 143 beta 940 946 943 967 C1' C B 144 beta 962 968 965 987 C1' A B 145 beta 982 988 985 1009 C1' C B 146 beta 1004 1010 1007 1029 C1' C B 147 beta 1024 1030 1027 1049 C1' A B 148 beta 1044 1050 1047 1071 C1' U B 149 beta 1066 1072 1069 1091 C1' U B 150 beta 1086 1092 1089 1111 C1' G B 151 beta 1106 1112 1109 1134 C1' C B 152 beta 1129 1135 1132 1154 C1' A B 153 beta 1149 1155 1152 1176 C1' C B 154 beta 1171 1177 1174 1196 C1' U B 155 beta 1191 1197 1194 1216 C1' C B 156 beta 1211 1217 1214 1236 C1' C B 157 beta 1231 1237 1234 1256 C1' G B 158 beta 1251 1257 1254 1279 C1' G B 159 beta 1274 1280 1277 1302 C1' U B 160 beta 1297 1303 1300 1322 C1' G B 161 beta 1317 1323 1320 1345 C1' G B 162 beta 1340 1346 1343 1368 C1' U B 163 beta 1363 1369 1366 1388 C1' G B 164 beta 1383 1389 1386 1411 C1' A B 165 beta 1406 1412 1409 1433 C1' A B 166 beta 1428 1434 1431 1455 C1' U B 167 beta 1450 1456 1453 1475 C1' G B 168 beta 1470 1476 1473 1498 C1' G B 169 beta 1493 1499 1496 1521 C1' G B 170 beta 1516 1522 1519 1544 C1' A B 171 beta 1539 1545 1542 1566 C1' C B 172 beta 1561 1567 1564 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' A B 99 OK 9 5 8 29 C2' U B 100 OK 31 27 30 49 C2' G B 101 OK 51 47 50 72 C2' G B 102 OK 74 70 73 95 C2' C B 103 OK 97 93 96 115 C2' C B 104 OK 117 113 116 135 C2' G B 105 OK 137 133 136 158 C2' G B 106 OK 160 156 159 181 C2' C B 107 OK 183 179 182 201 C2' A B 108 OK 203 199 202 223 C2' U B 109 OK 225 221 224 243 C2' G B 110 OK 245 241 244 266 C2' G B 111 OK 268 264 267 289 C2' U B 112 OK 291 287 290 309 C2' C B 113 OK 311 307 310 329 C2' C B 114 OK 331 327 330 349 C2' C B 115 OK 351 347 350 369 C2' A B 116 OK 371 367 370 391 C2' G B 117 OK 393 389 392 414 C2' C B 118 OK 416 412 415 434 C2' C B 119 OK 436 432 435 454 C2' U B 120 OK 456 452 455 474 C2' C B 121 OK 476 472 475 494 C2' C B 122 OK 496 492 495 514 C2' U B 123 OK 516 512 515 534 C2' C B 124 OK 536 532 535 554 C2' G B 125 OK 556 552 555 577 C2' C B 126 OK 579 575 578 597 C2' U B 127 OK 599 595 598 617 C2' G B 128 OK 619 615 618 640 C2' G B 129 OK 642 638 641 663 C2' C B 130 OK 665 661 664 683 C2' G B 131 OK 685 681 684 706 C2' C B 132 OK 708 704 707 726 C2' C B 133 OK 728 724 727 746 C2' G B 134 OK 748 744 747 769 C2' G B 135 OK 771 767 770 792 C2' C B 136 OK 794 790 793 812 C2' U B 137 OK 814 810 813 832 C2' G B 138 OK 834 830 833 855 C2' G B 139 OK 857 853 856 878 C2' G B 140 OK 880 876 879 901 C2' C B 141 OK 903 899 902 921 C2' A B 142 OK 923 919 922 943 C2' A B 143 OK 945 941 944 965 C2' C B 144 OK 967 963 966 985 C2' A B 145 OK 987 983 986 1007 C2' C B 146 OK 1009 1005 1008 1027 C2' C B 147 OK 1029 1025 1028 1047 C2' A B 148 OK 1049 1045 1048 1069 C2' U B 149 OK 1071 1067 1070 1089 C2' U B 150 OK 1091 1087 1090 1109 C2' G B 151 OK 1111 1107 1110 1132 C2' C B 152 OK 1134 1130 1133 1152 C2' A B 153 OK 1154 1150 1153 1174 C2' C B 154 OK 1176 1172 1175 1194 C2' U B 155 OK 1196 1192 1195 1214 C2' C B 156 OK 1216 1212 1215 1234 C2' C B 157 OK 1236 1232 1235 1254 C2' G B 158 OK 1256 1252 1255 1277 C2' G B 159 OK 1279 1275 1278 1300 C2' U B 160 OK 1302 1298 1301 1320 C2' G B 161 OK 1322 1318 1321 1343 C2' G B 162 OK 1345 1341 1344 1366 C2' U B 163 OK 1368 1364 1367 1386 C2' G B 164 OK 1388 1384 1387 1409 C2' A B 165 OK 1411 1407 1410 1431 C2' A B 166 OK 1433 1429 1432 1453 C2' U B 167 OK 1455 1451 1454 1473 C2' G B 168 OK 1475 1471 1474 1496 C2' G B 169 OK 1498 1494 1497 1519 C2' G B 170 OK 1521 1517 1520 1542 C2' A B 171 OK 1544 1540 1543 1564 C2' C B 172 OK 1566 1562 1565 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' A B 99 OK 3 6 7 27 C3' U B 100 OK 25 28 29 47 C3' G B 101 OK 45 48 49 70 C3' G B 102 OK 68 71 72 93 C3' C B 103 OK 91 94 95 113 C3' C B 104 OK 111 114 115 133 C3' G B 105 OK 131 134 135 156 C3' G B 106 OK 154 157 158 179 C3' C B 107 OK 177 180 181 199 C3' A B 108 OK 197 200 201 221 C3' U B 109 OK 219 222 223 241 C3' G B 110 OK 239 242 243 264 C3' G B 111 OK 262 265 266 287 C3' U B 112 OK 285 288 289 307 C3' C B 113 OK 305 308 309 327 C3' C B 114 OK 325 328 329 347 C3' C B 115 OK 345 348 349 367 C3' A B 116 OK 365 368 369 389 C3' G B 117 OK 387 390 391 412 C3' C B 118 OK 410 413 414 432 C3' C B 119 OK 430 433 434 452 C3' U B 120 OK 450 453 454 472 C3' C B 121 OK 470 473 474 492 C3' C B 122 OK 490 493 494 512 C3' U B 123 OK 510 513 514 532 C3' C B 124 OK 530 533 534 552 C3' G B 125 OK 550 553 554 575 C3' C B 126 OK 573 576 577 595 C3' U B 127 OK 593 596 597 615 C3' G B 128 OK 613 616 617 638 C3' G B 129 OK 636 639 640 661 C3' C B 130 OK 659 662 663 681 C3' G B 131 OK 679 682 683 704 C3' C B 132 OK 702 705 706 724 C3' C B 133 OK 722 725 726 744 C3' G B 134 OK 742 745 746 767 C3' G B 135 OK 765 768 769 790 C3' C B 136 OK 788 791 792 810 C3' U B 137 OK 808 811 812 830 C3' G B 138 OK 828 831 832 853 C3' G B 139 OK 851 854 855 876 C3' G B 140 OK 874 877 878 899 C3' C B 141 OK 897 900 901 919 C3' A B 142 OK 917 920 921 941 C3' A B 143 OK 939 942 943 963 C3' C B 144 OK 961 964 965 983 C3' A B 145 OK 981 984 985 1005 C3' C B 146 OK 1003 1006 1007 1025 C3' C B 147 OK 1023 1026 1027 1045 C3' A B 148 OK 1043 1046 1047 1067 C3' U B 149 OK 1065 1068 1069 1087 C3' U B 150 OK 1085 1088 1089 1107 C3' G B 151 OK 1105 1108 1109 1130 C3' C B 152 OK 1128 1131 1132 1150 C3' A B 153 OK 1148 1151 1152 1172 C3' C B 154 OK 1170 1173 1174 1192 C3' U B 155 OK 1190 1193 1194 1212 C3' C B 156 OK 1210 1213 1214 1232 C3' C B 157 OK 1230 1233 1234 1252 C3' G B 158 OK 1250 1253 1254 1275 C3' G B 159 OK 1273 1276 1277 1298 C3' U B 160 OK 1296 1299 1300 1318 C3' G B 161 OK 1316 1319 1320 1341 C3' G B 162 OK 1339 1342 1343 1364 C3' U B 163 OK 1362 1365 1366 1384 C3' G B 164 OK 1382 1385 1386 1407 C3' A B 165 OK 1405 1408 1409 1429 C3' A B 166 OK 1427 1430 1431 1451 C3' U B 167 OK 1449 1452 1453 1471 C3' G B 168 OK 1469 1472 1473 1494 C3' G B 169 OK 1492 1495 1496 1517 C3' G B 170 OK 1515 1518 1519 1540 C3' A B 171 OK 1538 1541 1542 1562 C3' C B 172 OK 1560 1563 1564 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' A B 99 OK 5 2 4 25 C4' U B 100 OK 27 24 26 45 C4' G B 101 OK 47 44 46 68 C4' G B 102 OK 70 67 69 91 C4' C B 103 OK 93 90 92 111 C4' C B 104 OK 113 110 112 131 C4' G B 105 OK 133 130 132 154 C4' G B 106 OK 156 153 155 177 C4' C B 107 OK 179 176 178 197 C4' A B 108 OK 199 196 198 219 C4' U B 109 OK 221 218 220 239 C4' G B 110 OK 241 238 240 262 C4' G B 111 OK 264 261 263 285 C4' U B 112 OK 287 284 286 305 C4' C B 113 OK 307 304 306 325 C4' C B 114 OK 327 324 326 345 C4' C B 115 OK 347 344 346 365 C4' A B 116 OK 367 364 366 387 C4' G B 117 OK 389 386 388 410 C4' C B 118 OK 412 409 411 430 C4' C B 119 OK 432 429 431 450 C4' U B 120 OK 452 449 451 470 C4' C B 121 OK 472 469 471 490 C4' C B 122 OK 492 489 491 510 C4' U B 123 OK 512 509 511 530 C4' C B 124 OK 532 529 531 550 C4' G B 125 OK 552 549 551 573 C4' C B 126 OK 575 572 574 593 C4' U B 127 OK 595 592 594 613 C4' G B 128 OK 615 612 614 636 C4' G B 129 OK 638 635 637 659 C4' C B 130 OK 661 658 660 679 C4' G B 131 OK 681 678 680 702 C4' C B 132 OK 704 701 703 722 C4' C B 133 OK 724 721 723 742 C4' G B 134 OK 744 741 743 765 C4' G B 135 OK 767 764 766 788 C4' C B 136 OK 790 787 789 808 C4' U B 137 OK 810 807 809 828 C4' G B 138 OK 830 827 829 851 C4' G B 139 OK 853 850 852 874 C4' G B 140 OK 876 873 875 897 C4' C B 141 OK 899 896 898 917 C4' A B 142 OK 919 916 918 939 C4' A B 143 OK 941 938 940 961 C4' C B 144 OK 963 960 962 981 C4' A B 145 OK 983 980 982 1003 C4' C B 146 OK 1005 1002 1004 1023 C4' C B 147 OK 1025 1022 1024 1043 C4' A B 148 OK 1045 1042 1044 1065 C4' U B 149 OK 1067 1064 1066 1085 C4' U B 150 OK 1087 1084 1086 1105 C4' G B 151 OK 1107 1104 1106 1128 C4' C B 152 OK 1130 1127 1129 1148 C4' A B 153 OK 1150 1147 1149 1170 C4' C B 154 OK 1172 1169 1171 1190 C4' U B 155 OK 1192 1189 1191 1210 C4' C B 156 OK 1212 1209 1211 1230 C4' C B 157 OK 1232 1229 1231 1250 C4' G B 158 OK 1252 1249 1251 1273 C4' G B 159 OK 1275 1272 1274 1296 C4' U B 160 OK 1298 1295 1297 1316 C4' G B 161 OK 1318 1315 1317 1339 C4' G B 162 OK 1341 1338 1340 1362 C4' U B 163 OK 1364 1361 1363 1382 C4' G B 164 OK 1384 1381 1383 1405 C4' A B 165 OK 1407 1404 1406 1427 C4' A B 166 OK 1429 1426 1428 1449 C4' U B 167 OK 1451 1448 1450 1469 C4' G B 168 OK 1471 1468 1470 1492 C4' G B 169 OK 1494 1491 1493 1515 C4' G B 170 OK 1517 1514 1516 1538 C4' A B 171 OK 1540 1537 1539 1560 C4' C B 172 OK 1562 1559 1561 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' A B 99 1 3 24 C5' U B 100 23 25 44 C5' G B 101 43 45 67 C5' G B 102 66 68 90 C5' C B 103 89 91 110 C5' C B 104 109 111 130 C5' G B 105 129 131 153 C5' G B 106 152 154 176 C5' C B 107 175 177 196 C5' A B 108 195 197 218 C5' U B 109 217 219 238 C5' G B 110 237 239 261 C5' G B 111 260 262 284 C5' U B 112 283 285 304 C5' C B 113 303 305 324 C5' C B 114 323 325 344 C5' C B 115 343 345 364 C5' A B 116 363 365 386 C5' G B 117 385 387 409 C5' C B 118 408 410 429 C5' C B 119 428 430 449 C5' U B 120 448 450 469 C5' C B 121 468 470 489 C5' C B 122 488 490 509 C5' U B 123 508 510 529 C5' C B 124 528 530 549 C5' G B 125 548 550 572 C5' C B 126 571 573 592 C5' U B 127 591 593 612 C5' G B 128 611 613 635 C5' G B 129 634 636 658 C5' C B 130 657 659 678 C5' G B 131 677 679 701 C5' C B 132 700 702 721 C5' C B 133 720 722 741 C5' G B 134 740 742 764 C5' G B 135 763 765 787 C5' C B 136 786 788 807 C5' U B 137 806 808 827 C5' G B 138 826 828 850 C5' G B 139 849 851 873 C5' G B 140 872 874 896 C5' C B 141 895 897 916 C5' A B 142 915 917 938 C5' A B 143 937 939 960 C5' C B 144 959 961 980 C5' A B 145 979 981 1002 C5' C B 146 1001 1003 1022 C5' C B 147 1021 1023 1042 C5' A B 148 1041 1043 1064 C5' U B 149 1063 1065 1084 C5' U B 150 1083 1085 1104 C5' G B 151 1103 1105 1127 C5' C B 152 1126 1128 1147 C5' A B 153 1146 1148 1169 C5' C B 154 1168 1170 1189 C5' U B 155 1188 1190 1209 C5' C B 156 1208 1210 1229 C5' C B 157 1228 1230 1249 C5' G B 158 1248 1250 1272 C5' G B 159 1271 1273 1295 C5' U B 160 1294 1296 1315 C5' G B 161 1314 1316 1338 C5' G B 162 1337 1339 1361 C5' U B 163 1360 1362 1381 C5' G B 164 1380 1382 1404 C5' A B 165 1403 1405 1426 C5' A B 166 1425 1427 1448 C5' U B 167 1447 1449 1468 C5' G B 168 1467 1469 1491 C5' G B 169 1490 1492 1514 C5' G B 170 1513 1515 1537 C5' A B 171 1536 1538 1559 C5' C B 172 1558 1560 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 20 P U B 100 distorted distorted 6 21 22 23 40 P G B 101 distorted distorted 28 41 42 43 63 P G B 102 distorted distorted 48 64 65 66 86 P C B 103 distorted distorted 71 87 88 89 106 P C B 104 distorted distorted 94 107 108 109 126 P G B 105 distorted distorted 114 127 128 129 149 P G B 106 distorted distorted 134 150 151 152 172 P C B 107 distorted distorted 157 173 174 175 192 P A B 108 distorted distorted 180 193 194 195 214 P U B 109 distorted distorted 200 215 216 217 234 P G B 110 distorted distorted 222 235 236 237 257 P G B 111 distorted distorted 242 258 259 260 280 P U B 112 distorted distorted 265 281 282 283 300 P C B 113 distorted distorted 288 301 302 303 320 P C B 114 distorted distorted 308 321 322 323 340 P C B 115 distorted distorted 328 341 342 343 360 P A B 116 distorted distorted 348 361 362 363 382 P G B 117 distorted distorted 368 383 384 385 405 P C B 118 distorted distorted 390 406 407 408 425 P C B 119 distorted distorted 413 426 427 428 445 P U B 120 distorted distorted 433 446 447 448 465 P C B 121 distorted distorted 453 466 467 468 485 P C B 122 distorted distorted 473 486 487 488 505 P U B 123 distorted distorted 493 506 507 508 525 P C B 124 distorted distorted 513 526 527 528 545 P G B 125 distorted distorted 533 546 547 548 568 P C B 126 distorted distorted 553 569 570 571 588 P U B 127 distorted distorted 576 589 590 591 608 P G B 128 distorted distorted 596 609 610 611 631 P G B 129 distorted distorted 616 632 633 634 654 P C B 130 distorted distorted 639 655 656 657 674 P G B 131 distorted distorted 662 675 676 677 697 P C B 132 distorted distorted 682 698 699 700 717 P C B 133 distorted distorted 705 718 719 720 737 P G B 134 distorted distorted 725 738 739 740 760 P G B 135 distorted distorted 745 761 762 763 783 P C B 136 distorted distorted 768 784 785 786 803 P U B 137 distorted distorted 791 804 805 806 823 P G B 138 distorted distorted 811 824 825 826 846 P G B 139 distorted distorted 831 847 848 849 869 P G B 140 distorted distorted 854 870 871 872 892 P C B 141 distorted distorted 877 893 894 895 912 P A B 142 distorted distorted 900 913 914 915 934 P A B 143 distorted distorted 920 935 936 937 956 P C B 144 distorted distorted 942 957 958 959 976 P A B 145 distorted distorted 964 977 978 979 998 P C B 146 distorted distorted 984 999 1000 1001 1018 P C B 147 distorted distorted 1006 1019 1020 1021 1038 P A B 148 distorted distorted 1026 1039 1040 1041 1060 P U B 149 distorted distorted 1046 1061 1062 1063 1080 P U B 150 distorted distorted 1068 1081 1082 1083 1100 P G B 151 distorted distorted 1088 1101 1102 1103 1123 P C B 152 distorted distorted 1108 1124 1125 1126 1143 P A B 153 distorted distorted 1131 1144 1145 1146 1165 P C B 154 distorted distorted 1151 1166 1167 1168 1185 P U B 155 distorted distorted 1173 1186 1187 1188 1205 P C B 156 distorted distorted 1193 1206 1207 1208 1225 P C B 157 distorted distorted 1213 1226 1227 1228 1245 P G B 158 distorted distorted 1233 1246 1247 1248 1268 P G B 159 distorted distorted 1253 1269 1270 1271 1291 P U B 160 distorted distorted 1276 1292 1293 1294 1311 P G B 161 distorted distorted 1299 1312 1313 1314 1334 P G B 162 distorted distorted 1319 1335 1336 1337 1357 P U B 163 distorted distorted 1342 1358 1359 1360 1377 P G B 164 distorted distorted 1365 1378 1379 1380 1400 P A B 165 distorted distorted 1385 1401 1402 1403 1422 P A B 166 distorted distorted 1408 1423 1424 1425 1444 P U B 167 distorted distorted 1430 1445 1446 1447 1464 P G B 168 distorted distorted 1452 1465 1466 1467 1487 P G B 169 distorted distorted 1472 1488 1489 1490 1510 P G B 170 distorted distorted 1495 1511 1512 1513 1533 P A B 171 distorted distorted 1518 1534 1535 1536 1555 P C B 172 distorted distorted 1541 1556 1557 1558 ---------------------------------------------------------------------------------