ID code: '1P5M' 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 43 C1' G A 2 alpha beta 38 61 44 41 77 C1' C A 3 alpha beta 72 92 78 75 108 C1' U A 4 alpha beta 103 123 109 106 138 C1' G A 5 alpha beta 133 156 139 136 172 C1' U A 6 alpha beta 167 187 173 170 202 C1' G A 7 alpha beta 197 220 203 200 236 C1' A A 8 alpha beta 231 253 237 234 269 C1' G A 9 alpha beta 264 287 270 267 303 C1' G A 10 alpha beta 298 321 304 301 337 C1' A A 11 alpha beta 332 354 338 335 370 C1' A A 12 alpha beta 365 387 371 368 403 C1' C A 13 alpha beta 398 418 404 401 434 C1' U A 14 alpha beta 429 449 435 432 464 C1' A A 15 alpha beta 459 481 465 462 497 C1' C A 16 alpha beta 492 512 498 495 528 C1' U A 17 alpha beta 523 543 529 526 558 C1' G A 18 alpha beta 553 576 559 556 592 C1' U A 19 alpha beta 587 607 593 590 622 C1' C A 20 alpha beta 617 637 623 620 653 C1' U A 21 alpha beta 648 668 654 651 683 C1' U A 22 alpha beta 678 698 684 681 713 C1' C A 23 alpha beta 708 728 714 711 744 C1' A A 24 alpha beta 739 761 745 742 777 C1' C A 25 alpha beta 772 792 778 775 808 C1' G A 26 alpha beta 803 826 809 806 842 C1' C A 27 alpha beta 837 857 843 840 873 C1' C A 28 alpha beta 868 888 874 871 904 C1' U A 29 alpha beta 899 919 905 902 934 C1' U A 30 alpha beta 929 949 935 932 964 C1' C A 31 alpha beta 959 979 965 962 995 C1' G A 32 alpha beta 990 1013 996 993 1029 C1' G A 33 alpha beta 1024 1047 1030 1027 1063 C1' G A 34 alpha beta 1058 1081 1064 1061 1097 C1' A A 35 alpha beta 1092 1114 1098 1095 1130 C1' G A 36 alpha beta 1125 1148 1131 1128 1164 C1' U A 37 alpha beta 1159 1179 1165 1162 1194 C1' G A 38 alpha beta 1189 1212 1195 1192 1228 C1' U A 39 alpha beta 1223 1243 1229 1226 1258 C1' C A 40 alpha beta 1253 1273 1259 1256 1289 C1' G A 41 alpha beta 1284 1307 1290 1287 1323 C1' U A 42 alpha beta 1318 1338 1324 1321 1353 C1' G A 43 alpha beta 1348 1371 1354 1351 1387 C1' C A 44 alpha beta 1382 1402 1388 1385 1418 C1' A A 45 alpha beta 1413 1435 1419 1416 1451 C1' G A 46 alpha beta 1446 1469 1452 1449 1485 C1' C A 47 alpha beta 1480 1500 1486 1483 1516 C1' C A 48 alpha beta 1511 1531 1517 1514 1547 C1' U A 49 alpha beta 1542 1562 1548 1545 1577 C1' C A 50 alpha beta 1572 1592 1578 1575 1608 C1' C A 51 alpha beta 1603 1623 1609 1606 1639 C1' A A 52 alpha beta 1634 1656 1640 1637 1672 C1' G A 53 alpha beta 1667 1690 1673 1670 1706 C1' C A 54 alpha beta 1701 1721 1707 1704 1737 C1' C A 55 alpha beta 1732 1753 1738 1735 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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 41 C2' G A 2 OK OK 43 39 59 42 75 C2' C A 3 OK OK 77 73 90 76 106 C2' U A 4 OK OK 108 104 121 107 136 C2' G A 5 OK OK 138 134 154 137 170 C2' U A 6 OK OK 172 168 185 171 200 C2' G A 7 OK OK 202 198 218 201 234 C2' A A 8 OK OK 236 232 251 235 267 C2' G A 9 OK OK 269 265 285 268 301 C2' G A 10 OK OK 303 299 319 302 335 C2' A A 11 OK OK 337 333 352 336 368 C2' A A 12 OK OK 370 366 385 369 401 C2' C A 13 OK OK 403 399 416 402 432 C2' U A 14 OK OK 434 430 447 433 462 C2' A A 15 OK OK 464 460 479 463 495 C2' C A 16 OK OK 497 493 510 496 526 C2' U A 17 OK OK 528 524 541 527 556 C2' G A 18 OK OK 558 554 574 557 590 C2' U A 19 OK OK 592 588 605 591 620 C2' C A 20 OK OK 622 618 635 621 651 C2' U A 21 OK OK 653 649 666 652 681 C2' U A 22 OK OK 683 679 696 682 711 C2' C A 23 OK OK 713 709 726 712 742 C2' A A 24 OK OK 744 740 759 743 775 C2' C A 25 OK OK 777 773 790 776 806 C2' G A 26 OK OK 808 804 824 807 840 C2' C A 27 OK OK 842 838 855 841 871 C2' C A 28 OK OK 873 869 886 872 902 C2' U A 29 OK OK 904 900 917 903 932 C2' U A 30 OK OK 934 930 947 933 962 C2' C A 31 OK OK 964 960 977 963 993 C2' G A 32 OK OK 995 991 1011 994 1027 C2' G A 33 OK OK 1029 1025 1045 1028 1061 C2' G A 34 OK OK 1063 1059 1079 1062 1095 C2' A A 35 OK OK 1097 1093 1112 1096 1128 C2' G A 36 OK OK 1130 1126 1146 1129 1162 C2' U A 37 OK OK 1164 1160 1177 1163 1192 C2' G A 38 OK OK 1194 1190 1210 1193 1226 C2' U A 39 OK OK 1228 1224 1241 1227 1256 C2' C A 40 OK OK 1258 1254 1271 1257 1287 C2' G A 41 OK OK 1289 1285 1305 1288 1321 C2' U A 42 OK OK 1323 1319 1336 1322 1351 C2' G A 43 OK OK 1353 1349 1369 1352 1385 C2' C A 44 OK OK 1387 1383 1400 1386 1416 C2' A A 45 OK OK 1418 1414 1433 1417 1449 C2' G A 46 OK OK 1451 1447 1467 1450 1483 C2' C A 47 OK OK 1485 1481 1498 1484 1514 C2' C A 48 OK OK 1516 1512 1529 1515 1545 C2' U A 49 OK OK 1547 1543 1560 1546 1575 C2' C A 50 OK OK 1577 1573 1590 1576 1606 C2' C A 51 OK OK 1608 1604 1621 1607 1637 C2' A A 52 OK OK 1639 1635 1654 1638 1670 C2' G A 53 OK OK 1672 1668 1688 1671 1704 C2' C A 54 OK OK 1706 1702 1719 1705 1735 C2' C A 55 OK OK 1737 1733 1751 1736 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK OK 3 24 6 7 39 C3' G A 2 OK OK 37 58 40 41 73 C3' C A 3 OK OK 71 89 74 75 104 C3' U A 4 OK OK 102 120 105 106 134 C3' G A 5 OK OK 132 153 135 136 168 C3' U A 6 OK OK 166 184 169 170 198 C3' G A 7 OK OK 196 217 199 200 232 C3' A A 8 OK OK 230 250 233 234 265 C3' G A 9 OK OK 263 284 266 267 299 C3' G A 10 OK OK 297 318 300 301 333 C3' A A 11 OK OK 331 351 334 335 366 C3' A A 12 OK OK 364 384 367 368 399 C3' C A 13 OK OK 397 415 400 401 430 C3' U A 14 OK OK 428 446 431 432 460 C3' A A 15 OK OK 458 478 461 462 493 C3' C A 16 OK OK 491 509 494 495 524 C3' U A 17 OK OK 522 540 525 526 554 C3' G A 18 OK OK 552 573 555 556 588 C3' U A 19 OK OK 586 604 589 590 618 C3' C A 20 OK OK 616 634 619 620 649 C3' U A 21 OK OK 647 665 650 651 679 C3' U A 22 OK OK 677 695 680 681 709 C3' C A 23 OK OK 707 725 710 711 740 C3' A A 24 OK OK 738 758 741 742 773 C3' C A 25 OK OK 771 789 774 775 804 C3' G A 26 OK OK 802 823 805 806 838 C3' C A 27 OK OK 836 854 839 840 869 C3' C A 28 OK OK 867 885 870 871 900 C3' U A 29 OK OK 898 916 901 902 930 C3' U A 30 OK OK 928 946 931 932 960 C3' C A 31 OK OK 958 976 961 962 991 C3' G A 32 OK OK 989 1010 992 993 1025 C3' G A 33 OK OK 1023 1044 1026 1027 1059 C3' G A 34 OK OK 1057 1078 1060 1061 1093 C3' A A 35 OK OK 1091 1111 1094 1095 1126 C3' G A 36 OK OK 1124 1145 1127 1128 1160 C3' U A 37 OK OK 1158 1176 1161 1162 1190 C3' G A 38 OK OK 1188 1209 1191 1192 1224 C3' U A 39 OK OK 1222 1240 1225 1226 1254 C3' C A 40 OK OK 1252 1270 1255 1256 1285 C3' G A 41 OK OK 1283 1304 1286 1287 1319 C3' U A 42 OK OK 1317 1335 1320 1321 1349 C3' G A 43 OK OK 1347 1368 1350 1351 1383 C3' C A 44 OK OK 1381 1399 1384 1385 1414 C3' A A 45 OK OK 1412 1432 1415 1416 1447 C3' G A 46 OK OK 1445 1466 1448 1449 1481 C3' C A 47 OK OK 1479 1497 1482 1483 1512 C3' C A 48 OK OK 1510 1528 1513 1514 1543 C3' U A 49 OK OK 1541 1559 1544 1545 1573 C3' C A 50 OK OK 1571 1589 1574 1575 1604 C3' C A 51 OK OK 1602 1620 1605 1606 1635 C3' A A 52 OK OK 1633 1653 1636 1637 1668 C3' G A 53 OK OK 1666 1687 1669 1670 1702 C3' C A 54 OK OK 1700 1718 1703 1704 1733 C3' C A 55 OK OK 1731 1749 1734 1735 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK OK 5 23 2 4 37 C4' G A 2 OK OK 39 57 36 38 71 C4' C A 3 OK OK 73 88 70 72 102 C4' U A 4 OK OK 104 119 101 103 132 C4' G A 5 OK OK 134 152 131 133 166 C4' U A 6 OK OK 168 183 165 167 196 C4' G A 7 OK OK 198 216 195 197 230 C4' A A 8 OK OK 232 249 229 231 263 C4' G A 9 OK OK 265 283 262 264 297 C4' G A 10 OK OK 299 317 296 298 331 C4' A A 11 OK OK 333 350 330 332 364 C4' A A 12 OK OK 366 383 363 365 397 C4' C A 13 OK OK 399 414 396 398 428 C4' U A 14 OK OK 430 445 427 429 458 C4' A A 15 OK OK 460 477 457 459 491 C4' C A 16 OK OK 493 508 490 492 522 C4' U A 17 OK OK 524 539 521 523 552 C4' G A 18 OK OK 554 572 551 553 586 C4' U A 19 OK OK 588 603 585 587 616 C4' C A 20 OK OK 618 633 615 617 647 C4' U A 21 OK OK 649 664 646 648 677 C4' U A 22 OK OK 679 694 676 678 707 C4' C A 23 OK OK 709 724 706 708 738 C4' A A 24 OK OK 740 757 737 739 771 C4' C A 25 OK OK 773 788 770 772 802 C4' G A 26 OK OK 804 822 801 803 836 C4' C A 27 OK OK 838 853 835 837 867 C4' C A 28 OK OK 869 884 866 868 898 C4' U A 29 OK OK 900 915 897 899 928 C4' U A 30 OK OK 930 945 927 929 958 C4' C A 31 OK OK 960 975 957 959 989 C4' G A 32 OK OK 991 1009 988 990 1023 C4' G A 33 OK OK 1025 1043 1022 1024 1057 C4' G A 34 OK OK 1059 1077 1056 1058 1091 C4' A A 35 OK OK 1093 1110 1090 1092 1124 C4' G A 36 OK OK 1126 1144 1123 1125 1158 C4' U A 37 OK OK 1160 1175 1157 1159 1188 C4' G A 38 OK OK 1190 1208 1187 1189 1222 C4' U A 39 OK OK 1224 1239 1221 1223 1252 C4' C A 40 OK OK 1254 1269 1251 1253 1283 C4' G A 41 OK OK 1285 1303 1282 1284 1317 C4' U A 42 OK OK 1319 1334 1316 1318 1347 C4' G A 43 OK OK 1349 1367 1346 1348 1381 C4' C A 44 OK OK 1383 1398 1380 1382 1412 C4' A A 45 OK OK 1414 1431 1411 1413 1445 C4' G A 46 OK OK 1447 1465 1444 1446 1479 C4' C A 47 OK OK 1481 1496 1478 1480 1510 C4' C A 48 OK OK 1512 1527 1509 1511 1541 C4' U A 49 OK OK 1543 1558 1540 1542 1571 C4' C A 50 OK OK 1573 1588 1570 1572 1602 C4' C A 51 OK OK 1604 1619 1601 1603 1633 C4' A A 52 OK OK 1635 1652 1632 1634 1666 C4' G A 53 OK OK 1668 1686 1665 1667 1700 C4' C A 54 OK OK 1702 1717 1699 1701 1731 C4' C A 55 OK OK 1733 1748 1730 1732 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 36 C5' G A 2 OK OK 35 55 56 37 70 C5' C A 3 OK OK 69 86 87 71 101 C5' U A 4 OK OK 100 117 118 102 131 C5' G A 5 OK OK 130 150 151 132 165 C5' U A 6 OK OK 164 181 182 166 195 C5' G A 7 OK OK 194 214 215 196 229 C5' A A 8 OK OK 228 247 248 230 262 C5' G A 9 OK OK 261 281 282 263 296 C5' G A 10 OK OK 295 315 316 297 330 C5' A A 11 OK OK 329 348 349 331 363 C5' A A 12 OK OK 362 381 382 364 396 C5' C A 13 OK OK 395 412 413 397 427 C5' U A 14 OK OK 426 443 444 428 457 C5' A A 15 OK OK 456 475 476 458 490 C5' C A 16 OK OK 489 506 507 491 521 C5' U A 17 OK OK 520 537 538 522 551 C5' G A 18 OK OK 550 570 571 552 585 C5' U A 19 OK OK 584 601 602 586 615 C5' C A 20 OK OK 614 631 632 616 646 C5' U A 21 OK OK 645 662 663 647 676 C5' U A 22 OK OK 675 692 693 677 706 C5' C A 23 OK OK 705 722 723 707 737 C5' A A 24 OK OK 736 755 756 738 770 C5' C A 25 OK OK 769 786 787 771 801 C5' G A 26 OK OK 800 820 821 802 835 C5' C A 27 OK OK 834 851 852 836 866 C5' C A 28 OK OK 865 882 883 867 897 C5' U A 29 OK OK 896 913 914 898 927 C5' U A 30 OK OK 926 943 944 928 957 C5' C A 31 OK OK 956 973 974 958 988 C5' G A 32 OK OK 987 1007 1008 989 1022 C5' G A 33 OK OK 1021 1041 1042 1023 1056 C5' G A 34 OK OK 1055 1075 1076 1057 1090 C5' A A 35 OK OK 1089 1108 1109 1091 1123 C5' G A 36 OK OK 1122 1142 1143 1124 1157 C5' U A 37 OK OK 1156 1173 1174 1158 1187 C5' G A 38 OK OK 1186 1206 1207 1188 1221 C5' U A 39 OK OK 1220 1237 1238 1222 1251 C5' C A 40 OK OK 1250 1267 1268 1252 1282 C5' G A 41 OK OK 1281 1301 1302 1283 1316 C5' U A 42 OK OK 1315 1332 1333 1317 1346 C5' G A 43 OK OK 1345 1365 1366 1347 1380 C5' C A 44 OK OK 1379 1396 1397 1381 1411 C5' A A 45 OK OK 1410 1429 1430 1412 1444 C5' G A 46 OK OK 1443 1463 1464 1445 1478 C5' C A 47 OK OK 1477 1494 1495 1479 1509 C5' C A 48 OK OK 1508 1525 1526 1510 1540 C5' U A 49 OK OK 1539 1556 1557 1541 1570 C5' C A 50 OK OK 1569 1586 1587 1571 1601 C5' C A 51 OK OK 1600 1617 1618 1602 1632 C5' A A 52 OK OK 1631 1650 1651 1633 1665 C5' G A 53 OK OK 1664 1684 1685 1666 1699 C5' C A 54 OK OK 1698 1715 1716 1700 1730 C5' C A 55 OK OK 1729 1746 1747 1731 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 32 P G A 2 distorted distorted 6 33 34 35 66 P C A 3 distorted distorted 40 67 68 69 97 P U A 4 distorted distorted 74 98 99 100 127 P G A 5 distorted distorted 105 128 129 130 161 P U A 6 distorted distorted 135 162 163 164 191 P G A 7 distorted distorted 169 192 193 194 225 P A A 8 distorted distorted 199 226 227 228 258 P G A 9 distorted distorted 233 259 260 261 292 P G A 10 distorted distorted 266 293 294 295 326 P A A 11 distorted distorted 300 327 328 329 359 P A A 12 distorted distorted 334 360 361 362 392 P C A 13 distorted distorted 367 393 394 395 423 P U A 14 distorted distorted 400 424 425 426 453 P A A 15 distorted distorted 431 454 455 456 486 P C A 16 distorted distorted 461 487 488 489 517 P U A 17 distorted distorted 494 518 519 520 547 P G A 18 distorted distorted 525 548 549 550 581 P U A 19 distorted distorted 555 582 583 584 611 P C A 20 distorted distorted 589 612 613 614 642 P U A 21 distorted distorted 619 643 644 645 672 P U A 22 distorted distorted 650 673 674 675 702 P C A 23 distorted distorted 680 703 704 705 733 P A A 24 distorted distorted 710 734 735 736 766 P C A 25 distorted distorted 741 767 768 769 797 P G A 26 distorted distorted 774 798 799 800 831 P C A 27 distorted distorted 805 832 833 834 862 P C A 28 distorted distorted 839 863 864 865 893 P U A 29 distorted distorted 870 894 895 896 923 P U A 30 distorted distorted 901 924 925 926 953 P C A 31 distorted distorted 931 954 955 956 984 P G A 32 distorted distorted 961 985 986 987 1018 P G A 33 distorted distorted 992 1019 1020 1021 1052 P G A 34 distorted distorted 1026 1053 1054 1055 1086 P A A 35 distorted distorted 1060 1087 1088 1089 1119 P G A 36 distorted distorted 1094 1120 1121 1122 1153 P U A 37 distorted distorted 1127 1154 1155 1156 1183 P G A 38 distorted distorted 1161 1184 1185 1186 1217 P U A 39 distorted distorted 1191 1218 1219 1220 1247 P C A 40 distorted distorted 1225 1248 1249 1250 1278 P G A 41 distorted distorted 1255 1279 1280 1281 1312 P U A 42 distorted distorted 1286 1313 1314 1315 1342 P G A 43 distorted distorted 1320 1343 1344 1345 1376 P C A 44 distorted distorted 1350 1377 1378 1379 1407 P A A 45 distorted distorted 1384 1408 1409 1410 1440 P G A 46 distorted distorted 1415 1441 1442 1443 1474 P C A 47 distorted distorted 1448 1475 1476 1477 1505 P C A 48 distorted distorted 1482 1506 1507 1508 1536 P U A 49 distorted distorted 1513 1537 1538 1539 1566 P C A 50 distorted distorted 1544 1567 1568 1569 1597 P C A 51 distorted distorted 1574 1598 1599 1600 1628 P A A 52 distorted distorted 1605 1629 1630 1631 1661 P G A 53 distorted distorted 1636 1662 1663 1664 1695 P C A 54 distorted distorted 1669 1696 1697 1698 1726 P C A 55 distorted distorted 1703 1727 1728 1729 ---------------------------------------------------------------------------------