ID code: '3L0U' 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' --------------------------------------------------------------------------------- 13 C1' G A 1 beta 8 14 11 36 C1' C A 2 beta 31 37 34 56 C1' G A 3 beta 51 57 54 79 C1' C A 4 beta 74 80 77 99 C1' G A 5 beta 94 100 97 122 C1' G A 6 beta 117 123 120 145 C1' A A 7 beta 140 146 143 167 C1' U A 8 beta 162 168 165 187 C1' A A 9 beta 182 188 185 209 C1' G A 10 beta 204 210 207 232 C1' C A 11 beta 227 233 230 252 C1' U A 12 beta 247 253 250 272 C1' C A 13 beta 267 273 270 292 C1' A A 14 beta 287 293 290 314 C1' G A 15 beta 309 315 312 337 C1' U A 16 beta 332 338 335 357 C1' C A 17 beta 352 358 355 377 C1' G A 18 beta 372 378 375 400 C1' G A 19 beta 395 401 398 423 C1' U A 20 beta 418 424 421 443 C1' A A 21 beta 438 444 441 465 C1' G A 22 beta 460 466 463 488 C1' A A 23 beta 483 489 486 510 C1' G A 24 beta 505 511 508 533 C1' C A 25 beta 528 534 531 553 C1' A A 26 beta 548 554 551 575 C1' G A 27 beta 570 576 573 598 C1' G A 28 beta 593 599 596 621 C1' G A 29 beta 616 622 619 644 C1' G A 30 beta 639 645 642 667 C1' A A 31 beta 662 668 665 689 C1' U A 32 beta 684 690 687 709 C1' U A 33 beta 704 710 707 729 C1' G A 34 beta 724 730 727 752 C1' A A 35 beta 747 753 750 774 C1' A A 36 beta 769 775 772 796 C1' A A 37 beta 791 797 794 818 C1' A A 38 beta 813 819 816 840 C1' U A 39 beta 835 841 838 860 C1' C A 40 beta 855 861 858 880 C1' C A 41 beta 875 881 878 900 C1' C A 42 beta 895 901 898 920 C1' C A 43 beta 915 921 918 940 C1' G A 44 beta 935 941 938 963 C1' U A 45 beta 958 964 961 983 C1' G A 46 beta 978 984 981 1006 C1' U A 47 beta 1001 1007 1004 1026 C1' C A 48 beta 1021 1027 1024 1046 C1' C A 49 beta 1041 1047 1044 1066 C1' U A 50 beta 1061 1067 1064 1086 C1' U A 51 beta 1081 1087 1084 1106 C1' G A 52 beta 1101 1107 1104 1129 C1' G A 53 beta 1124 1130 1127 1152 C1' U A 54 beta 1147 1153 1150 1172 C1' U A 55 beta 1167 1173 1170 1192 C1' C A 56 beta 1187 1193 1190 1212 C1' G A 57 beta 1207 1213 1210 1235 C1' A A 58 beta 1230 1236 1233 1257 C1' U A 59 beta 1252 1258 1255 1277 C1' U A 60 beta 1272 1278 1275 1297 C1' C A 61 beta 1292 1298 1295 1317 C1' C A 62 beta 1312 1318 1315 1337 C1' G A 63 beta 1332 1338 1335 1360 C1' A A 64 beta 1355 1361 1358 1382 C1' G A 65 beta 1377 1383 1380 1405 C1' U A 66 beta 1400 1406 1403 1425 C1' C A 67 beta 1420 1426 1423 1445 C1' C A 68 beta 1440 1446 1443 1465 C1' G A 69 beta 1460 1466 1463 1488 C1' C A 70 beta 1483 1489 1486 1508 C1' G A 71 beta 1503 1509 1506 1531 C1' C A 72 beta 1526 1532 1529 1551 C1' A A 73 beta 1546 1552 1549 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 11 C2' G A 1 OK 13 9 12 34 C2' C A 2 OK 36 32 35 54 C2' G A 3 OK 56 52 55 77 C2' C A 4 OK 79 75 78 97 C2' G A 5 OK 99 95 98 120 C2' G A 6 OK 122 118 121 143 C2' A A 7 OK 145 141 144 165 C2' U A 8 OK 167 163 166 185 C2' A A 9 OK 187 183 186 207 C2' G A 10 OK 209 205 208 230 C2' C A 11 OK 232 228 231 250 C2' U A 12 OK 252 248 251 270 C2' C A 13 OK 272 268 271 290 C2' A A 14 OK 292 288 291 312 C2' G A 15 OK 314 310 313 335 C2' U A 16 OK 337 333 336 355 C2' C A 17 OK 357 353 356 375 C2' G A 18 OK 377 373 376 398 C2' G A 19 OK 400 396 399 421 C2' U A 20 OK 423 419 422 441 C2' A A 21 OK 443 439 442 463 C2' G A 22 OK 465 461 464 486 C2' A A 23 OK 488 484 487 508 C2' G A 24 OK 510 506 509 531 C2' C A 25 OK 533 529 532 551 C2' A A 26 OK 553 549 552 573 C2' G A 27 OK 575 571 574 596 C2' G A 28 OK 598 594 597 619 C2' G A 29 OK 621 617 620 642 C2' G A 30 OK 644 640 643 665 C2' A A 31 OK 667 663 666 687 C2' U A 32 OK 689 685 688 707 C2' U A 33 OK 709 705 708 727 C2' G A 34 OK 729 725 728 750 C2' A A 35 OK 752 748 751 772 C2' A A 36 OK 774 770 773 794 C2' A A 37 OK 796 792 795 816 C2' A A 38 OK 818 814 817 838 C2' U A 39 OK 840 836 839 858 C2' C A 40 OK 860 856 859 878 C2' C A 41 OK 880 876 879 898 C2' C A 42 OK 900 896 899 918 C2' C A 43 OK 920 916 919 938 C2' G A 44 OK 940 936 939 961 C2' U A 45 OK 963 959 962 981 C2' G A 46 OK 983 979 982 1004 C2' U A 47 OK 1006 1002 1005 1024 C2' C A 48 OK 1026 1022 1025 1044 C2' C A 49 OK 1046 1042 1045 1064 C2' U A 50 OK 1066 1062 1065 1084 C2' U A 51 OK 1086 1082 1085 1104 C2' G A 52 OK 1106 1102 1105 1127 C2' G A 53 OK 1129 1125 1128 1150 C2' U A 54 OK 1152 1148 1151 1170 C2' U A 55 OK 1172 1168 1171 1190 C2' C A 56 OK 1192 1188 1191 1210 C2' G A 57 OK 1212 1208 1211 1233 C2' A A 58 OK 1235 1231 1234 1255 C2' U A 59 OK 1257 1253 1256 1275 C2' U A 60 OK 1277 1273 1276 1295 C2' C A 61 OK 1297 1293 1296 1315 C2' C A 62 OK 1317 1313 1316 1335 C2' G A 63 OK 1337 1333 1336 1358 C2' A A 64 OK 1360 1356 1359 1380 C2' G A 65 OK 1382 1378 1381 1403 C2' U A 66 OK 1405 1401 1404 1423 C2' C A 67 OK 1425 1421 1424 1443 C2' C A 68 OK 1445 1441 1444 1463 C2' G A 69 OK 1465 1461 1464 1486 C2' C A 70 OK 1488 1484 1487 1506 C2' G A 71 OK 1508 1504 1507 1529 C2' C A 72 OK 1531 1527 1530 1549 C2' A A 73 OK 1551 1547 1550 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 9 C3' G A 1 OK 7 10 11 32 C3' C A 2 OK 30 33 34 52 C3' G A 3 OK 50 53 54 75 C3' C A 4 OK 73 76 77 95 C3' G A 5 OK 93 96 97 118 C3' G A 6 OK 116 119 120 141 C3' A A 7 OK 139 142 143 163 C3' U A 8 OK 161 164 165 183 C3' A A 9 OK 181 184 185 205 C3' G A 10 OK 203 206 207 228 C3' C A 11 OK 226 229 230 248 C3' U A 12 OK 246 249 250 268 C3' C A 13 OK 266 269 270 288 C3' A A 14 OK 286 289 290 310 C3' G A 15 OK 308 311 312 333 C3' U A 16 OK 331 334 335 353 C3' C A 17 OK 351 354 355 373 C3' G A 18 OK 371 374 375 396 C3' G A 19 OK 394 397 398 419 C3' U A 20 OK 417 420 421 439 C3' A A 21 OK 437 440 441 461 C3' G A 22 OK 459 462 463 484 C3' A A 23 OK 482 485 486 506 C3' G A 24 OK 504 507 508 529 C3' C A 25 OK 527 530 531 549 C3' A A 26 OK 547 550 551 571 C3' G A 27 OK 569 572 573 594 C3' G A 28 OK 592 595 596 617 C3' G A 29 OK 615 618 619 640 C3' G A 30 OK 638 641 642 663 C3' A A 31 OK 661 664 665 685 C3' U A 32 OK 683 686 687 705 C3' U A 33 OK 703 706 707 725 C3' G A 34 OK 723 726 727 748 C3' A A 35 OK 746 749 750 770 C3' A A 36 OK 768 771 772 792 C3' A A 37 OK 790 793 794 814 C3' A A 38 OK 812 815 816 836 C3' U A 39 OK 834 837 838 856 C3' C A 40 OK 854 857 858 876 C3' C A 41 OK 874 877 878 896 C3' C A 42 OK 894 897 898 916 C3' C A 43 OK 914 917 918 936 C3' G A 44 OK 934 937 938 959 C3' U A 45 OK 957 960 961 979 C3' G A 46 OK 977 980 981 1002 C3' U A 47 OK 1000 1003 1004 1022 C3' C A 48 OK 1020 1023 1024 1042 C3' C A 49 OK 1040 1043 1044 1062 C3' U A 50 OK 1060 1063 1064 1082 C3' U A 51 OK 1080 1083 1084 1102 C3' G A 52 OK 1100 1103 1104 1125 C3' G A 53 OK 1123 1126 1127 1148 C3' U A 54 OK 1146 1149 1150 1168 C3' U A 55 OK 1166 1169 1170 1188 C3' C A 56 OK 1186 1189 1190 1208 C3' G A 57 OK 1206 1209 1210 1231 C3' A A 58 OK 1229 1232 1233 1253 C3' U A 59 OK 1251 1254 1255 1273 C3' U A 60 OK 1271 1274 1275 1293 C3' C A 61 OK 1291 1294 1295 1313 C3' C A 62 OK 1311 1314 1315 1333 C3' G A 63 OK 1331 1334 1335 1356 C3' A A 64 OK 1354 1357 1358 1378 C3' G A 65 OK 1376 1379 1380 1401 C3' U A 66 OK 1399 1402 1403 1421 C3' C A 67 OK 1419 1422 1423 1441 C3' C A 68 OK 1439 1442 1443 1461 C3' G A 69 OK 1459 1462 1463 1484 C3' C A 70 OK 1482 1485 1486 1504 C3' G A 71 OK 1502 1505 1506 1527 C3' C A 72 OK 1525 1528 1529 1547 C3' A A 73 OK 1545 1548 1549 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 7 C4' G A 1 OK 9 6 8 30 C4' C A 2 OK 32 29 31 50 C4' G A 3 OK 52 49 51 73 C4' C A 4 OK 75 72 74 93 C4' G A 5 OK 95 92 94 116 C4' G A 6 OK 118 115 117 139 C4' A A 7 OK 141 138 140 161 C4' U A 8 OK 163 160 162 181 C4' A A 9 OK 183 180 182 203 C4' G A 10 OK 205 202 204 226 C4' C A 11 OK 228 225 227 246 C4' U A 12 OK 248 245 247 266 C4' C A 13 OK 268 265 267 286 C4' A A 14 OK 288 285 287 308 C4' G A 15 OK 310 307 309 331 C4' U A 16 OK 333 330 332 351 C4' C A 17 OK 353 350 352 371 C4' G A 18 OK 373 370 372 394 C4' G A 19 OK 396 393 395 417 C4' U A 20 OK 419 416 418 437 C4' A A 21 OK 439 436 438 459 C4' G A 22 OK 461 458 460 482 C4' A A 23 OK 484 481 483 504 C4' G A 24 OK 506 503 505 527 C4' C A 25 OK 529 526 528 547 C4' A A 26 OK 549 546 548 569 C4' G A 27 OK 571 568 570 592 C4' G A 28 OK 594 591 593 615 C4' G A 29 OK 617 614 616 638 C4' G A 30 OK 640 637 639 661 C4' A A 31 OK 663 660 662 683 C4' U A 32 OK 685 682 684 703 C4' U A 33 OK 705 702 704 723 C4' G A 34 OK 725 722 724 746 C4' A A 35 OK 748 745 747 768 C4' A A 36 OK 770 767 769 790 C4' A A 37 OK 792 789 791 812 C4' A A 38 OK 814 811 813 834 C4' U A 39 OK 836 833 835 854 C4' C A 40 OK 856 853 855 874 C4' C A 41 OK 876 873 875 894 C4' C A 42 OK 896 893 895 914 C4' C A 43 OK 916 913 915 934 C4' G A 44 OK 936 933 935 957 C4' U A 45 OK 959 956 958 977 C4' G A 46 OK 979 976 978 1000 C4' U A 47 OK 1002 999 1001 1020 C4' C A 48 OK 1022 1019 1021 1040 C4' C A 49 OK 1042 1039 1041 1060 C4' U A 50 OK 1062 1059 1061 1080 C4' U A 51 OK 1082 1079 1081 1100 C4' G A 52 OK 1102 1099 1101 1123 C4' G A 53 OK 1125 1122 1124 1146 C4' U A 54 OK 1148 1145 1147 1166 C4' U A 55 OK 1168 1165 1167 1186 C4' C A 56 OK 1188 1185 1187 1206 C4' G A 57 OK 1208 1205 1207 1229 C4' A A 58 OK 1231 1228 1230 1251 C4' U A 59 OK 1253 1250 1252 1271 C4' U A 60 OK 1273 1270 1272 1291 C4' C A 61 OK 1293 1290 1292 1311 C4' C A 62 OK 1313 1310 1312 1331 C4' G A 63 OK 1333 1330 1332 1354 C4' A A 64 OK 1356 1353 1355 1376 C4' G A 65 OK 1378 1375 1377 1399 C4' U A 66 OK 1401 1398 1400 1419 C4' C A 67 OK 1421 1418 1420 1439 C4' C A 68 OK 1441 1438 1440 1459 C4' G A 69 OK 1461 1458 1460 1482 C4' C A 70 OK 1484 1481 1483 1502 C4' G A 71 OK 1504 1501 1503 1525 C4' C A 72 OK 1527 1524 1526 1545 C4' A A 73 OK 1547 1544 1546 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 6 C5' G A 1 5 7 29 C5' C A 2 28 30 49 C5' G A 3 48 50 72 C5' C A 4 71 73 92 C5' G A 5 91 93 115 C5' G A 6 114 116 138 C5' A A 7 137 139 160 C5' U A 8 159 161 180 C5' A A 9 179 181 202 C5' G A 10 201 203 225 C5' C A 11 224 226 245 C5' U A 12 244 246 265 C5' C A 13 264 266 285 C5' A A 14 284 286 307 C5' G A 15 306 308 330 C5' U A 16 329 331 350 C5' C A 17 349 351 370 C5' G A 18 369 371 393 C5' G A 19 392 394 416 C5' U A 20 415 417 436 C5' A A 21 435 437 458 C5' G A 22 457 459 481 C5' A A 23 480 482 503 C5' G A 24 502 504 526 C5' C A 25 525 527 546 C5' A A 26 545 547 568 C5' G A 27 567 569 591 C5' G A 28 590 592 614 C5' G A 29 613 615 637 C5' G A 30 636 638 660 C5' A A 31 659 661 682 C5' U A 32 681 683 702 C5' U A 33 701 703 722 C5' G A 34 721 723 745 C5' A A 35 744 746 767 C5' A A 36 766 768 789 C5' A A 37 788 790 811 C5' A A 38 810 812 833 C5' U A 39 832 834 853 C5' C A 40 852 854 873 C5' C A 41 872 874 893 C5' C A 42 892 894 913 C5' C A 43 912 914 933 C5' G A 44 932 934 956 C5' U A 45 955 957 976 C5' G A 46 975 977 999 C5' U A 47 998 1000 1019 C5' C A 48 1018 1020 1039 C5' C A 49 1038 1040 1059 C5' U A 50 1058 1060 1079 C5' U A 51 1078 1080 1099 C5' G A 52 1098 1100 1122 C5' G A 53 1121 1123 1145 C5' U A 54 1144 1146 1165 C5' U A 55 1164 1166 1185 C5' C A 56 1184 1186 1205 C5' G A 57 1204 1206 1228 C5' A A 58 1227 1229 1250 C5' U A 59 1249 1251 1270 C5' U A 60 1269 1271 1290 C5' C A 61 1289 1291 1310 C5' C A 62 1309 1311 1330 C5' G A 63 1329 1331 1353 C5' A A 64 1352 1354 1375 C5' G A 65 1374 1376 1398 C5' U A 66 1397 1399 1418 C5' C A 67 1417 1419 1438 C5' C A 68 1437 1439 1458 C5' G A 69 1457 1459 1481 C5' C A 70 1480 1482 1501 C5' G A 71 1500 1502 1524 C5' C A 72 1523 1525 1544 C5' A A 73 1543 1545 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2 P G A 1 OK OK 3 4 5 25 P C A 2 distorted distorted 10 26 27 28 45 P G A 3 distorted distorted 33 46 47 48 68 P C A 4 distorted distorted 53 69 70 71 88 P G A 5 distorted distorted 76 89 90 91 111 P G A 6 distorted distorted 96 112 113 114 134 P A A 7 distorted distorted 119 135 136 137 156 P U A 8 distorted distorted 142 157 158 159 176 P A A 9 distorted distorted 164 177 178 179 198 P G A 10 distorted distorted 184 199 200 201 221 P C A 11 distorted distorted 206 222 223 224 241 P U A 12 distorted distorted 229 242 243 244 261 P C A 13 distorted distorted 249 262 263 264 281 P A A 14 distorted distorted 269 282 283 284 303 P G A 15 distorted distorted 289 304 305 306 326 P U A 16 distorted distorted 311 327 328 329 346 P C A 17 distorted distorted 334 347 348 349 366 P G A 18 distorted distorted 354 367 368 369 389 P G A 19 distorted distorted 374 390 391 392 412 P U A 20 distorted distorted 397 413 414 415 432 P A A 21 distorted distorted 420 433 434 435 454 P G A 22 distorted distorted 440 455 456 457 477 P A A 23 distorted distorted 462 478 479 480 499 P G A 24 distorted distorted 485 500 501 502 522 P C A 25 distorted distorted 507 523 524 525 542 P A A 26 distorted distorted 530 543 544 545 564 P G A 27 distorted distorted 550 565 566 567 587 P G A 28 distorted distorted 572 588 589 590 610 P G A 29 distorted distorted 595 611 612 613 633 P G A 30 distorted distorted 618 634 635 636 656 P A A 31 distorted distorted 641 657 658 659 678 P U A 32 distorted distorted 664 679 680 681 698 P U A 33 distorted distorted 686 699 700 701 718 P G A 34 distorted distorted 706 719 720 721 741 P A A 35 distorted distorted 726 742 743 744 763 P A A 36 distorted distorted 749 764 765 766 785 P A A 37 distorted distorted 771 786 787 788 807 P A A 38 distorted distorted 793 808 809 810 829 P U A 39 distorted distorted 815 830 831 832 849 P C A 40 distorted distorted 837 850 851 852 869 P C A 41 distorted distorted 857 870 871 872 889 P C A 42 distorted distorted 877 890 891 892 909 P C A 43 distorted distorted 897 910 911 912 929 P G A 44 distorted distorted 917 930 931 932 952 P U A 45 distorted distorted 937 953 954 955 972 P G A 46 distorted distorted 960 973 974 975 995 P U A 47 distorted distorted 980 996 997 998 1015 P C A 48 distorted distorted 1003 1016 1017 1018 1035 P C A 49 distorted distorted 1023 1036 1037 1038 1055 P U A 50 distorted distorted 1043 1056 1057 1058 1075 P U A 51 distorted distorted 1063 1076 1077 1078 1095 P G A 52 distorted distorted 1083 1096 1097 1098 1118 P G A 53 distorted distorted 1103 1119 1120 1121 1141 P U A 54 distorted distorted 1126 1142 1143 1144 1161 P U A 55 distorted distorted 1149 1162 1163 1164 1181 P C A 56 distorted distorted 1169 1182 1183 1184 1201 P G A 57 distorted distorted 1189 1202 1203 1204 1224 P A A 58 distorted distorted 1209 1225 1226 1227 1246 P U A 59 distorted distorted 1232 1247 1248 1249 1266 P U A 60 distorted distorted 1254 1267 1268 1269 1286 P C A 61 distorted distorted 1274 1287 1288 1289 1306 P C A 62 distorted distorted 1294 1307 1308 1309 1326 P G A 63 distorted distorted 1314 1327 1328 1329 1349 P A A 64 distorted distorted 1334 1350 1351 1352 1371 P G A 65 distorted distorted 1357 1372 1373 1374 1394 P U A 66 distorted distorted 1379 1395 1396 1397 1414 P C A 67 distorted distorted 1402 1415 1416 1417 1434 P C A 68 distorted distorted 1422 1435 1436 1437 1454 P G A 69 distorted distorted 1442 1455 1456 1457 1477 P C A 70 distorted distorted 1462 1478 1479 1480 1497 P G A 71 distorted distorted 1485 1498 1499 1500 1520 P C A 72 distorted distorted 1505 1521 1522 1523 1540 P A A 73 distorted distorted 1528 1541 1542 1543 ---------------------------------------------------------------------------------