ID code: '3NKB' 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' --------------------------------------------------------------------------------- 8 C1' DG A 2 beta 4 9 7 30 C1' DG A 3 beta 26 31 29 53 C1' C A 4 beta 48 54 51 73 C1' U A 5 beta 68 74 71 93 C1' U A 6 beta 88 94 91 113 C1' G A 7 beta 108 114 111 136 C1' C A 8 beta 131 137 134 156 C1' A A 9 beta 151 157 154 180 C1' G B 10 beta 175 181 178 203 C1' G B 11 beta 198 204 201 226 C1' U B 12 beta 221 227 224 246 C1' C B 13 beta 241 247 244 266 C1' C B 14 beta 261 267 264 286 C1' G B 15 beta 281 287 284 309 C1' C B 16 beta 304 310 307 329 C1' A B 17 beta 324 330 327 351 C1' G B 18 beta 346 352 349 374 C1' C B 19 beta 369 375 372 394 C1' C B 20 beta 389 395 392 414 C1' U B 21 beta 409 415 412 434 C1' C B 22 beta 429 435 432 454 C1' C B 23 beta 449 455 452 474 C1' U B 24 beta 469 475 472 494 C1' C B 25 beta 489 495 492 514 C1' G B 26 beta 509 515 512 537 C1' C B 27 beta 532 538 535 557 C1' G B 28 beta 552 558 555 580 C1' G B 29 beta 575 581 578 603 C1' C B 30 beta 598 604 601 623 C1' G B 31 beta 618 624 621 646 C1' C B 32 beta 641 647 644 666 C1' A B 33 beta 661 667 664 688 C1' A B 34 beta 683 689 686 710 C1' G B 35 beta 705 711 708 733 C1' C B 36 beta 728 734 731 753 C1' U B 37 beta 748 754 751 773 C1' G B 38 beta 768 774 771 796 C1' G B 39 beta 791 797 794 819 C1' G B 40 beta 814 820 817 842 C1' C B 41 beta 837 843 840 862 C1' A B 42 beta 857 863 860 884 C1' A B 43 beta 879 885 882 906 C1' C B 44 beta 901 907 904 926 C1' A B 45 beta 921 927 924 948 C1' U B 46 beta 943 949 946 968 C1' U B 47 beta 963 969 966 988 C1' C B 48 beta 983 989 986 1008 C1' C B 49 beta 1003 1009 1006 1028 C1' G B 50 beta 1023 1029 1026 1051 C1' A B 51 beta 1046 1052 1049 1073 C1' A B 52 beta 1068 1074 1071 1095 C1' A B 53 beta 1090 1096 1093 1117 C1' G B 54 beta 1112 1118 1115 1140 C1' G B 55 beta 1135 1141 1138 1163 C1' U B 56 beta 1158 1164 1161 1183 C1' A B 57 beta 1178 1184 1181 1205 C1' A B 58 beta 1200 1206 1203 1227 C1' U B 59 beta 1222 1228 1225 1247 C1' G B 60 beta 1242 1248 1245 1270 C1' G B 61 beta 1265 1271 1268 1293 C1' C B 62 beta 1288 1294 1291 1313 C1' G B 63 beta 1308 1314 1311 1336 C1' A B 64 beta 1331 1337 1334 1358 C1' A B 65 beta 1353 1359 1356 1380 C1' U B 66 beta 1375 1381 1378 1400 C1' G B 67 beta 1395 1401 1398 1423 C1' C B 68 beta 1418 1424 1421 1443 C1' G B 69 beta 1438 1444 1441 1466 C1' G B 70 beta 1461 1467 1464 1489 C1' A B 71 beta 1484 1490 1487 1511 C1' C B 72 beta 1506 1512 1509 1531 C1' C B 73 beta 1526 1532 1529 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' DG A 2 8 5 29 C2' DG A 3 30 27 51 C2' C A 4 OK 53 49 52 71 C2' U A 5 OK 73 69 72 91 C2' U A 6 OK 93 89 92 111 C2' G A 7 OK 113 109 112 134 C2' C A 8 OK 136 132 135 154 C2' A A 9 OK 156 152 155 178 C2' G B 10 OK 180 176 179 201 C2' G B 11 OK 203 199 202 224 C2' U B 12 OK 226 222 225 244 C2' C B 13 OK 246 242 245 264 C2' C B 14 OK 266 262 265 284 C2' G B 15 OK 286 282 285 307 C2' C B 16 OK 309 305 308 327 C2' A B 17 OK 329 325 328 349 C2' G B 18 OK 351 347 350 372 C2' C B 19 OK 374 370 373 392 C2' C B 20 OK 394 390 393 412 C2' U B 21 OK 414 410 413 432 C2' C B 22 OK 434 430 433 452 C2' C B 23 OK 454 450 453 472 C2' U B 24 OK 474 470 473 492 C2' C B 25 OK 494 490 493 512 C2' G B 26 OK 514 510 513 535 C2' C B 27 OK 537 533 536 555 C2' G B 28 OK 557 553 556 578 C2' G B 29 OK 580 576 579 601 C2' C B 30 OK 603 599 602 621 C2' G B 31 OK 623 619 622 644 C2' C B 32 OK 646 642 645 664 C2' A B 33 OK 666 662 665 686 C2' A B 34 OK 688 684 687 708 C2' G B 35 OK 710 706 709 731 C2' C B 36 OK 733 729 732 751 C2' U B 37 OK 753 749 752 771 C2' G B 38 OK 773 769 772 794 C2' G B 39 OK 796 792 795 817 C2' G B 40 OK 819 815 818 840 C2' C B 41 OK 842 838 841 860 C2' A B 42 OK 862 858 861 882 C2' A B 43 OK 884 880 883 904 C2' C B 44 OK 906 902 905 924 C2' A B 45 OK 926 922 925 946 C2' U B 46 OK 948 944 947 966 C2' U B 47 OK 968 964 967 986 C2' C B 48 OK 988 984 987 1006 C2' C B 49 OK 1008 1004 1007 1026 C2' G B 50 OK 1028 1024 1027 1049 C2' A B 51 OK 1051 1047 1050 1071 C2' A B 52 OK 1073 1069 1072 1093 C2' A B 53 OK 1095 1091 1094 1115 C2' G B 54 OK 1117 1113 1116 1138 C2' G B 55 OK 1140 1136 1139 1161 C2' U B 56 OK 1163 1159 1162 1181 C2' A B 57 OK 1183 1179 1182 1203 C2' A B 58 OK 1205 1201 1204 1225 C2' U B 59 OK 1227 1223 1226 1245 C2' G B 60 OK 1247 1243 1246 1268 C2' G B 61 OK 1270 1266 1269 1291 C2' C B 62 OK 1293 1289 1292 1311 C2' G B 63 OK 1313 1309 1312 1334 C2' A B 64 OK 1336 1332 1335 1356 C2' A B 65 OK 1358 1354 1357 1378 C2' U B 66 OK 1380 1376 1379 1398 C2' G B 67 OK 1400 1396 1399 1421 C2' C B 68 OK 1423 1419 1422 1441 C2' G B 69 OK 1443 1439 1442 1464 C2' G B 70 OK 1466 1462 1465 1487 C2' A B 71 OK 1489 1485 1488 1509 C2' C B 72 OK 1511 1507 1510 1529 C2' C B 73 OK 1531 1527 1530 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' DG A 2 OK 3 6 7 27 C3' DG A 3 OK 25 28 29 49 C3' C A 4 OK 47 50 51 69 C3' U A 5 OK 67 70 71 89 C3' U A 6 OK 87 90 91 109 C3' G A 7 OK 107 110 111 132 C3' C A 8 OK 130 133 134 152 C3' A A 9 OK 150 153 154 176 C3' G B 10 OK 174 177 178 199 C3' G B 11 OK 197 200 201 222 C3' U B 12 OK 220 223 224 242 C3' C B 13 OK 240 243 244 262 C3' C B 14 OK 260 263 264 282 C3' G B 15 OK 280 283 284 305 C3' C B 16 OK 303 306 307 325 C3' A B 17 OK 323 326 327 347 C3' G B 18 OK 345 348 349 370 C3' C B 19 OK 368 371 372 390 C3' C B 20 OK 388 391 392 410 C3' U B 21 OK 408 411 412 430 C3' C B 22 OK 428 431 432 450 C3' C B 23 OK 448 451 452 470 C3' U B 24 OK 468 471 472 490 C3' C B 25 OK 488 491 492 510 C3' G B 26 OK 508 511 512 533 C3' C B 27 OK 531 534 535 553 C3' G B 28 OK 551 554 555 576 C3' G B 29 OK 574 577 578 599 C3' C B 30 OK 597 600 601 619 C3' G B 31 OK 617 620 621 642 C3' C B 32 OK 640 643 644 662 C3' A B 33 OK 660 663 664 684 C3' A B 34 OK 682 685 686 706 C3' G B 35 OK 704 707 708 729 C3' C B 36 OK 727 730 731 749 C3' U B 37 OK 747 750 751 769 C3' G B 38 OK 767 770 771 792 C3' G B 39 OK 790 793 794 815 C3' G B 40 OK 813 816 817 838 C3' C B 41 OK 836 839 840 858 C3' A B 42 OK 856 859 860 880 C3' A B 43 OK 878 881 882 902 C3' C B 44 OK 900 903 904 922 C3' A B 45 OK 920 923 924 944 C3' U B 46 OK 942 945 946 964 C3' U B 47 OK 962 965 966 984 C3' C B 48 OK 982 985 986 1004 C3' C B 49 OK 1002 1005 1006 1024 C3' G B 50 OK 1022 1025 1026 1047 C3' A B 51 OK 1045 1048 1049 1069 C3' A B 52 OK 1067 1070 1071 1091 C3' A B 53 OK 1089 1092 1093 1113 C3' G B 54 OK 1111 1114 1115 1136 C3' G B 55 OK 1134 1137 1138 1159 C3' U B 56 OK 1157 1160 1161 1179 C3' A B 57 OK 1177 1180 1181 1201 C3' A B 58 OK 1199 1202 1203 1223 C3' U B 59 OK 1221 1224 1225 1243 C3' G B 60 OK 1241 1244 1245 1266 C3' G B 61 OK 1264 1267 1268 1289 C3' C B 62 OK 1287 1290 1291 1309 C3' G B 63 OK 1307 1310 1311 1332 C3' A B 64 OK 1330 1333 1334 1354 C3' A B 65 OK 1352 1355 1356 1376 C3' U B 66 OK 1374 1377 1378 1396 C3' G B 67 OK 1394 1397 1398 1419 C3' C B 68 OK 1417 1420 1421 1439 C3' G B 69 OK 1437 1440 1441 1462 C3' G B 70 OK 1460 1463 1464 1485 C3' A B 71 OK 1483 1486 1487 1507 C3' C B 72 OK 1505 1508 1509 1527 C3' C B 73 OK 1525 1528 1529 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' DG A 2 OK 5 2 4 25 C4' DG A 3 OK 27 24 26 47 C4' C A 4 OK 49 46 48 67 C4' U A 5 OK 69 66 68 87 C4' U A 6 OK 89 86 88 107 C4' G A 7 OK 109 106 108 130 C4' C A 8 OK 132 129 131 150 C4' A A 9 OK 152 149 151 174 C4' G B 10 OK 176 173 175 197 C4' G B 11 OK 199 196 198 220 C4' U B 12 OK 222 219 221 240 C4' C B 13 OK 242 239 241 260 C4' C B 14 OK 262 259 261 280 C4' G B 15 OK 282 279 281 303 C4' C B 16 OK 305 302 304 323 C4' A B 17 OK 325 322 324 345 C4' G B 18 OK 347 344 346 368 C4' C B 19 OK 370 367 369 388 C4' C B 20 OK 390 387 389 408 C4' U B 21 OK 410 407 409 428 C4' C B 22 OK 430 427 429 448 C4' C B 23 OK 450 447 449 468 C4' U B 24 OK 470 467 469 488 C4' C B 25 OK 490 487 489 508 C4' G B 26 OK 510 507 509 531 C4' C B 27 OK 533 530 532 551 C4' G B 28 OK 553 550 552 574 C4' G B 29 OK 576 573 575 597 C4' C B 30 OK 599 596 598 617 C4' G B 31 OK 619 616 618 640 C4' C B 32 OK 642 639 641 660 C4' A B 33 OK 662 659 661 682 C4' A B 34 OK 684 681 683 704 C4' G B 35 OK 706 703 705 727 C4' C B 36 OK 729 726 728 747 C4' U B 37 OK 749 746 748 767 C4' G B 38 OK 769 766 768 790 C4' G B 39 OK 792 789 791 813 C4' G B 40 OK 815 812 814 836 C4' C B 41 OK 838 835 837 856 C4' A B 42 OK 858 855 857 878 C4' A B 43 OK 880 877 879 900 C4' C B 44 OK 902 899 901 920 C4' A B 45 OK 922 919 921 942 C4' U B 46 OK 944 941 943 962 C4' U B 47 OK 964 961 963 982 C4' C B 48 OK 984 981 983 1002 C4' C B 49 OK 1004 1001 1003 1022 C4' G B 50 OK 1024 1021 1023 1045 C4' A B 51 OK 1047 1044 1046 1067 C4' A B 52 OK 1069 1066 1068 1089 C4' A B 53 OK 1091 1088 1090 1111 C4' G B 54 OK 1113 1110 1112 1134 C4' G B 55 OK 1136 1133 1135 1157 C4' U B 56 OK 1159 1156 1158 1177 C4' A B 57 OK 1179 1176 1178 1199 C4' A B 58 OK 1201 1198 1200 1221 C4' U B 59 OK 1223 1220 1222 1241 C4' G B 60 OK 1243 1240 1242 1264 C4' G B 61 OK 1266 1263 1265 1287 C4' C B 62 OK 1289 1286 1288 1307 C4' G B 63 OK 1309 1306 1308 1330 C4' A B 64 OK 1332 1329 1331 1352 C4' A B 65 OK 1354 1351 1353 1374 C4' U B 66 OK 1376 1373 1375 1394 C4' G B 67 OK 1396 1393 1395 1417 C4' C B 68 OK 1419 1416 1418 1437 C4' G B 69 OK 1439 1436 1438 1460 C4' G B 70 OK 1462 1459 1461 1483 C4' A B 71 OK 1485 1482 1484 1505 C4' C B 72 OK 1507 1504 1506 1525 C4' C B 73 OK 1527 1524 1526 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' DG A 2 1 3 24 C5' DG A 3 23 25 46 C5' C A 4 45 47 66 C5' U A 5 65 67 86 C5' U A 6 85 87 106 C5' G A 7 105 107 129 C5' C A 8 128 130 149 C5' A A 9 148 150 173 C5' G B 10 172 174 196 C5' G B 11 195 197 219 C5' U B 12 218 220 239 C5' C B 13 238 240 259 C5' C B 14 258 260 279 C5' G B 15 278 280 302 C5' C B 16 301 303 322 C5' A B 17 321 323 344 C5' G B 18 343 345 367 C5' C B 19 366 368 387 C5' C B 20 386 388 407 C5' U B 21 406 408 427 C5' C B 22 426 428 447 C5' C B 23 446 448 467 C5' U B 24 466 468 487 C5' C B 25 486 488 507 C5' G B 26 506 508 530 C5' C B 27 529 531 550 C5' G B 28 549 551 573 C5' G B 29 572 574 596 C5' C B 30 595 597 616 C5' G B 31 615 617 639 C5' C B 32 638 640 659 C5' A B 33 658 660 681 C5' A B 34 680 682 703 C5' G B 35 702 704 726 C5' C B 36 725 727 746 C5' U B 37 745 747 766 C5' G B 38 765 767 789 C5' G B 39 788 790 812 C5' G B 40 811 813 835 C5' C B 41 834 836 855 C5' A B 42 854 856 877 C5' A B 43 876 878 899 C5' C B 44 898 900 919 C5' A B 45 918 920 941 C5' U B 46 940 942 961 C5' U B 47 960 962 981 C5' C B 48 980 982 1001 C5' C B 49 1000 1002 1021 C5' G B 50 1020 1022 1044 C5' A B 51 1043 1045 1066 C5' A B 52 1065 1067 1088 C5' A B 53 1087 1089 1110 C5' G B 54 1109 1111 1133 C5' G B 55 1132 1134 1156 C5' U B 56 1155 1157 1176 C5' A B 57 1175 1177 1198 C5' A B 58 1197 1199 1220 C5' U B 59 1219 1221 1240 C5' G B 60 1239 1241 1263 C5' G B 61 1262 1264 1286 C5' C B 62 1285 1287 1306 C5' G B 63 1305 1307 1329 C5' A B 64 1328 1330 1351 C5' A B 65 1350 1352 1373 C5' U B 66 1372 1374 1393 C5' G B 67 1392 1394 1416 C5' C B 68 1415 1417 1436 C5' G B 69 1435 1437 1459 C5' G B 70 1458 1460 1482 C5' A B 71 1481 1483 1504 C5' C B 72 1503 1505 1524 C5' C B 73 1523 1525 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 20 P DG A 3 distorted distorted 6 21 22 23 42 P C A 4 distorted distorted 28 43 44 45 62 P U A 5 distorted distorted 50 63 64 65 82 P U A 6 distorted distorted 70 83 84 85 102 P G A 7 distorted distorted 90 103 104 105 125 P C A 8 distorted distorted 110 126 127 128 145 P A A 9 distorted distorted 133 146 147 148 169 P G B 10 distorted distorted 170 171 172 192 P G B 11 distorted distorted 177 193 194 195 215 P U B 12 distorted distorted 200 216 217 218 235 P C B 13 distorted distorted 223 236 237 238 255 P C B 14 distorted distorted 243 256 257 258 275 P G B 15 distorted distorted 263 276 277 278 298 P C B 16 distorted distorted 283 299 300 301 318 P A B 17 distorted distorted 306 319 320 321 340 P G B 18 distorted distorted 326 341 342 343 363 P C B 19 distorted distorted 348 364 365 366 383 P C B 20 distorted distorted 371 384 385 386 403 P U B 21 distorted distorted 391 404 405 406 423 P C B 22 distorted distorted 411 424 425 426 443 P C B 23 distorted distorted 431 444 445 446 463 P U B 24 distorted distorted 451 464 465 466 483 P C B 25 distorted distorted 471 484 485 486 503 P G B 26 distorted distorted 491 504 505 506 526 P C B 27 distorted distorted 511 527 528 529 546 P G B 28 distorted distorted 534 547 548 549 569 P G B 29 distorted distorted 554 570 571 572 592 P C B 30 distorted distorted 577 593 594 595 612 P G B 31 distorted distorted 600 613 614 615 635 P C B 32 distorted distorted 620 636 637 638 655 P A B 33 distorted distorted 643 656 657 658 677 P A B 34 distorted distorted 663 678 679 680 699 P G B 35 distorted distorted 685 700 701 702 722 P C B 36 distorted distorted 707 723 724 725 742 P U B 37 distorted distorted 730 743 744 745 762 P G B 38 distorted distorted 750 763 764 765 785 P G B 39 distorted distorted 770 786 787 788 808 P G B 40 distorted distorted 793 809 810 811 831 P C B 41 distorted distorted 816 832 833 834 851 P A B 42 distorted distorted 839 852 853 854 873 P A B 43 distorted distorted 859 874 875 876 895 P C B 44 distorted distorted 881 896 897 898 915 P A B 45 distorted distorted 903 916 917 918 937 P U B 46 distorted distorted 923 938 939 940 957 P U B 47 distorted distorted 945 958 959 960 977 P C B 48 distorted distorted 965 978 979 980 997 P C B 49 distorted distorted 985 998 999 1000 1017 P G B 50 distorted distorted 1005 1018 1019 1020 1040 P A B 51 distorted distorted 1025 1041 1042 1043 1062 P A B 52 distorted distorted 1048 1063 1064 1065 1084 P A B 53 distorted distorted 1070 1085 1086 1087 1106 P G B 54 distorted distorted 1092 1107 1108 1109 1129 P G B 55 distorted distorted 1114 1130 1131 1132 1152 P U B 56 distorted distorted 1137 1153 1154 1155 1172 P A B 57 distorted distorted 1160 1173 1174 1175 1194 P A B 58 distorted distorted 1180 1195 1196 1197 1216 P U B 59 distorted distorted 1202 1217 1218 1219 1236 P G B 60 distorted distorted 1224 1237 1238 1239 1259 P G B 61 distorted distorted 1244 1260 1261 1262 1282 P C B 62 distorted distorted 1267 1283 1284 1285 1302 P G B 63 distorted distorted 1290 1303 1304 1305 1325 P A B 64 distorted distorted 1310 1326 1327 1328 1347 P A B 65 distorted distorted 1333 1348 1349 1350 1369 P U B 66 distorted distorted 1355 1370 1371 1372 1389 P G B 67 distorted distorted 1377 1390 1391 1392 1412 P C B 68 distorted distorted 1397 1413 1414 1415 1432 P G B 69 distorted distorted 1420 1433 1434 1435 1455 P G B 70 distorted distorted 1440 1456 1457 1458 1478 P A B 71 distorted distorted 1463 1479 1480 1481 1500 P C B 72 distorted distorted 1486 1501 1502 1503 1520 P C B 73 distorted distorted 1508 1521 1522 1523 ---------------------------------------------------------------------------------