ID code: '3LA5' 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' --------------------------------------------------------------------------------- 12 C1' G A 13 beta 7 13 10 35 C1' G A 14 beta 30 36 33 58 C1' C A 15 beta 53 59 56 78 C1' U A 16 beta 73 79 76 98 C1' U A 17 beta 93 99 96 118 C1' C A 18 beta 113 119 116 138 C1' A A 19 beta 133 139 136 160 C1' U A 20 beta 155 161 158 180 C1' A A 21 beta 175 181 178 202 C1' U A 22 beta 197 203 200 222 C1' A A 23 beta 217 223 220 244 C1' A A 24 beta 239 245 242 266 C1' U A 25 beta 261 267 264 286 C1' C A 26 beta 281 287 284 306 C1' C A 27 beta 301 307 304 326 C1' G A 28 beta 321 327 324 349 C1' A A 29 beta 344 350 347 371 C1' A A 30 beta 366 372 369 393 C1' U A 31 beta 388 394 391 413 C1' G A 32 beta 408 414 411 436 C1' A A 33 beta 431 437 434 458 C1' U A 34 beta 453 459 456 478 C1' A A 35 beta 473 479 476 500 C1' U A 36 beta 495 501 498 520 C1' G A 37 beta 515 521 518 543 C1' G A 38 beta 538 544 541 566 C1' U A 39 beta 561 567 564 586 C1' U A 40 beta 581 587 584 606 C1' U A 41 beta 601 607 604 626 C1' C A 42 beta 621 627 624 646 C1' G A 43 beta 641 647 644 669 C1' G A 44 beta 664 670 667 692 C1' A A 45 beta 687 693 690 714 C1' G A 46 beta 709 715 712 737 C1' C A 47 beta 732 738 735 757 C1' U A 48 beta 752 758 755 777 C1' U A 49 beta 772 778 775 797 C1' C A 50 beta 792 798 795 817 C1' C A 51 beta 812 818 815 837 C1' A A 52 beta 832 838 835 859 C1' C A 53 beta 854 860 857 879 C1' C A 54 beta 874 880 877 899 C1' A A 55 beta 894 900 897 921 C1' A A 56 beta 916 922 919 943 C1' G A 57 beta 938 944 941 966 C1' A A 58 beta 961 967 964 988 C1' G A 59 beta 983 989 986 1011 C1' C A 60 beta 1006 1012 1009 1031 C1' C A 61 beta 1026 1032 1029 1051 C1' U A 62 beta 1046 1052 1049 1071 C1' U A 63 beta 1066 1072 1069 1091 C1' A A 64 beta 1086 1092 1089 1113 C1' A A 65 beta 1108 1114 1111 1135 C1' A A 66 beta 1130 1136 1133 1157 C1' C A 67 beta 1152 1158 1155 1177 C1' U A 68 beta 1172 1178 1175 1197 C1' C A 69 beta 1192 1198 1195 1217 C1' U A 70 beta 1212 1218 1215 1237 C1' U A 71 beta 1232 1238 1235 1257 C1' G A 72 beta 1252 1258 1255 1280 C1' A A 73 beta 1275 1281 1278 1302 C1' C A 74 beta 1297 1303 1300 1322 C1' U A 75 beta 1317 1323 1320 1342 C1' A A 76 beta 1337 1343 1340 1364 C1' U A 77 beta 1359 1365 1362 1384 C1' G A 78 beta 1379 1385 1382 1407 C1' G A 79 beta 1402 1408 1405 1430 C1' A A 80 beta 1425 1431 1428 1452 C1' G A 81 beta 1447 1453 1450 1475 C1' U A 82 beta 1470 1476 1473 1495 C1' C A 83 beta 1490 1496 1493 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' G A 13 OK 12 8 11 33 C2' G A 14 OK 35 31 34 56 C2' C A 15 OK 58 54 57 76 C2' U A 16 OK 78 74 77 96 C2' U A 17 OK 98 94 97 116 C2' C A 18 OK 118 114 117 136 C2' A A 19 OK 138 134 137 158 C2' U A 20 OK 160 156 159 178 C2' A A 21 OK 180 176 179 200 C2' U A 22 OK 202 198 201 220 C2' A A 23 OK 222 218 221 242 C2' A A 24 OK 244 240 243 264 C2' U A 25 OK 266 262 265 284 C2' C A 26 OK 286 282 285 304 C2' C A 27 OK 306 302 305 324 C2' G A 28 OK 326 322 325 347 C2' A A 29 OK 349 345 348 369 C2' A A 30 OK 371 367 370 391 C2' U A 31 OK 393 389 392 411 C2' G A 32 OK 413 409 412 434 C2' A A 33 OK 436 432 435 456 C2' U A 34 OK 458 454 457 476 C2' A A 35 OK 478 474 477 498 C2' U A 36 OK 500 496 499 518 C2' G A 37 OK 520 516 519 541 C2' G A 38 OK 543 539 542 564 C2' U A 39 OK 566 562 565 584 C2' U A 40 OK 586 582 585 604 C2' U A 41 OK 606 602 605 624 C2' C A 42 OK 626 622 625 644 C2' G A 43 OK 646 642 645 667 C2' G A 44 OK 669 665 668 690 C2' A A 45 OK 692 688 691 712 C2' G A 46 OK 714 710 713 735 C2' C A 47 OK 737 733 736 755 C2' U A 48 OK 757 753 756 775 C2' U A 49 OK 777 773 776 795 C2' C A 50 OK 797 793 796 815 C2' C A 51 OK 817 813 816 835 C2' A A 52 OK 837 833 836 857 C2' C A 53 OK 859 855 858 877 C2' C A 54 OK 879 875 878 897 C2' A A 55 OK 899 895 898 919 C2' A A 56 OK 921 917 920 941 C2' G A 57 OK 943 939 942 964 C2' A A 58 OK 966 962 965 986 C2' G A 59 OK 988 984 987 1009 C2' C A 60 OK 1011 1007 1010 1029 C2' C A 61 OK 1031 1027 1030 1049 C2' U A 62 OK 1051 1047 1050 1069 C2' U A 63 OK 1071 1067 1070 1089 C2' A A 64 OK 1091 1087 1090 1111 C2' A A 65 OK 1113 1109 1112 1133 C2' A A 66 OK 1135 1131 1134 1155 C2' C A 67 OK 1157 1153 1156 1175 C2' U A 68 OK 1177 1173 1176 1195 C2' C A 69 OK 1197 1193 1196 1215 C2' U A 70 OK 1217 1213 1216 1235 C2' U A 71 OK 1237 1233 1236 1255 C2' G A 72 OK 1257 1253 1256 1278 C2' A A 73 OK 1280 1276 1279 1300 C2' C A 74 OK 1302 1298 1301 1320 C2' U A 75 OK 1322 1318 1321 1340 C2' A A 76 OK 1342 1338 1341 1362 C2' U A 77 OK 1364 1360 1363 1382 C2' G A 78 OK 1384 1380 1383 1405 C2' G A 79 OK 1407 1403 1406 1428 C2' A A 80 OK 1430 1426 1429 1450 C2' G A 81 OK 1452 1448 1451 1473 C2' U A 82 OK 1475 1471 1474 1493 C2' C A 83 OK 1495 1491 1494 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' G A 13 OK 6 9 10 31 C3' G A 14 OK 29 32 33 54 C3' C A 15 OK 52 55 56 74 C3' U A 16 OK 72 75 76 94 C3' U A 17 OK 92 95 96 114 C3' C A 18 OK 112 115 116 134 C3' A A 19 OK 132 135 136 156 C3' U A 20 OK 154 157 158 176 C3' A A 21 OK 174 177 178 198 C3' U A 22 OK 196 199 200 218 C3' A A 23 OK 216 219 220 240 C3' A A 24 OK 238 241 242 262 C3' U A 25 OK 260 263 264 282 C3' C A 26 OK 280 283 284 302 C3' C A 27 OK 300 303 304 322 C3' G A 28 OK 320 323 324 345 C3' A A 29 OK 343 346 347 367 C3' A A 30 OK 365 368 369 389 C3' U A 31 OK 387 390 391 409 C3' G A 32 OK 407 410 411 432 C3' A A 33 OK 430 433 434 454 C3' U A 34 OK 452 455 456 474 C3' A A 35 OK 472 475 476 496 C3' U A 36 OK 494 497 498 516 C3' G A 37 OK 514 517 518 539 C3' G A 38 OK 537 540 541 562 C3' U A 39 OK 560 563 564 582 C3' U A 40 OK 580 583 584 602 C3' U A 41 OK 600 603 604 622 C3' C A 42 OK 620 623 624 642 C3' G A 43 OK 640 643 644 665 C3' G A 44 OK 663 666 667 688 C3' A A 45 OK 686 689 690 710 C3' G A 46 OK 708 711 712 733 C3' C A 47 OK 731 734 735 753 C3' U A 48 OK 751 754 755 773 C3' U A 49 OK 771 774 775 793 C3' C A 50 OK 791 794 795 813 C3' C A 51 OK 811 814 815 833 C3' A A 52 OK 831 834 835 855 C3' C A 53 OK 853 856 857 875 C3' C A 54 OK 873 876 877 895 C3' A A 55 OK 893 896 897 917 C3' A A 56 OK 915 918 919 939 C3' G A 57 OK 937 940 941 962 C3' A A 58 OK 960 963 964 984 C3' G A 59 OK 982 985 986 1007 C3' C A 60 OK 1005 1008 1009 1027 C3' C A 61 OK 1025 1028 1029 1047 C3' U A 62 OK 1045 1048 1049 1067 C3' U A 63 OK 1065 1068 1069 1087 C3' A A 64 OK 1085 1088 1089 1109 C3' A A 65 OK 1107 1110 1111 1131 C3' A A 66 OK 1129 1132 1133 1153 C3' C A 67 OK 1151 1154 1155 1173 C3' U A 68 OK 1171 1174 1175 1193 C3' C A 69 OK 1191 1194 1195 1213 C3' U A 70 OK 1211 1214 1215 1233 C3' U A 71 OK 1231 1234 1235 1253 C3' G A 72 OK 1251 1254 1255 1276 C3' A A 73 OK 1274 1277 1278 1298 C3' C A 74 OK 1296 1299 1300 1318 C3' U A 75 OK 1316 1319 1320 1338 C3' A A 76 OK 1336 1339 1340 1360 C3' U A 77 OK 1358 1361 1362 1380 C3' G A 78 OK 1378 1381 1382 1403 C3' G A 79 OK 1401 1404 1405 1426 C3' A A 80 OK 1424 1427 1428 1448 C3' G A 81 OK 1446 1449 1450 1471 C3' U A 82 OK 1469 1472 1473 1491 C3' C A 83 OK 1489 1492 1493 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' G A 13 OK 8 5 7 29 C4' G A 14 OK 31 28 30 52 C4' C A 15 OK 54 51 53 72 C4' U A 16 OK 74 71 73 92 C4' U A 17 OK 94 91 93 112 C4' C A 18 OK 114 111 113 132 C4' A A 19 OK 134 131 133 154 C4' U A 20 OK 156 153 155 174 C4' A A 21 OK 176 173 175 196 C4' U A 22 OK 198 195 197 216 C4' A A 23 OK 218 215 217 238 C4' A A 24 OK 240 237 239 260 C4' U A 25 OK 262 259 261 280 C4' C A 26 OK 282 279 281 300 C4' C A 27 OK 302 299 301 320 C4' G A 28 OK 322 319 321 343 C4' A A 29 OK 345 342 344 365 C4' A A 30 OK 367 364 366 387 C4' U A 31 OK 389 386 388 407 C4' G A 32 OK 409 406 408 430 C4' A A 33 OK 432 429 431 452 C4' U A 34 OK 454 451 453 472 C4' A A 35 OK 474 471 473 494 C4' U A 36 OK 496 493 495 514 C4' G A 37 OK 516 513 515 537 C4' G A 38 OK 539 536 538 560 C4' U A 39 OK 562 559 561 580 C4' U A 40 OK 582 579 581 600 C4' U A 41 OK 602 599 601 620 C4' C A 42 OK 622 619 621 640 C4' G A 43 OK 642 639 641 663 C4' G A 44 OK 665 662 664 686 C4' A A 45 OK 688 685 687 708 C4' G A 46 OK 710 707 709 731 C4' C A 47 OK 733 730 732 751 C4' U A 48 OK 753 750 752 771 C4' U A 49 OK 773 770 772 791 C4' C A 50 OK 793 790 792 811 C4' C A 51 OK 813 810 812 831 C4' A A 52 OK 833 830 832 853 C4' C A 53 OK 855 852 854 873 C4' C A 54 OK 875 872 874 893 C4' A A 55 OK 895 892 894 915 C4' A A 56 OK 917 914 916 937 C4' G A 57 OK 939 936 938 960 C4' A A 58 OK 962 959 961 982 C4' G A 59 OK 984 981 983 1005 C4' C A 60 OK 1007 1004 1006 1025 C4' C A 61 OK 1027 1024 1026 1045 C4' U A 62 OK 1047 1044 1046 1065 C4' U A 63 OK 1067 1064 1066 1085 C4' A A 64 OK 1087 1084 1086 1107 C4' A A 65 OK 1109 1106 1108 1129 C4' A A 66 OK 1131 1128 1130 1151 C4' C A 67 OK 1153 1150 1152 1171 C4' U A 68 OK 1173 1170 1172 1191 C4' C A 69 OK 1193 1190 1192 1211 C4' U A 70 OK 1213 1210 1212 1231 C4' U A 71 OK 1233 1230 1232 1251 C4' G A 72 OK 1253 1250 1252 1274 C4' A A 73 OK 1276 1273 1275 1296 C4' C A 74 OK 1298 1295 1297 1316 C4' U A 75 OK 1318 1315 1317 1336 C4' A A 76 OK 1338 1335 1337 1358 C4' U A 77 OK 1360 1357 1359 1378 C4' G A 78 OK 1380 1377 1379 1401 C4' G A 79 OK 1403 1400 1402 1424 C4' A A 80 OK 1426 1423 1425 1446 C4' G A 81 OK 1448 1445 1447 1469 C4' U A 82 OK 1471 1468 1470 1489 C4' C A 83 OK 1491 1488 1490 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' G A 13 4 6 28 C5' G A 14 27 29 51 C5' C A 15 50 52 71 C5' U A 16 70 72 91 C5' U A 17 90 92 111 C5' C A 18 110 112 131 C5' A A 19 130 132 153 C5' U A 20 152 154 173 C5' A A 21 172 174 195 C5' U A 22 194 196 215 C5' A A 23 214 216 237 C5' A A 24 236 238 259 C5' U A 25 258 260 279 C5' C A 26 278 280 299 C5' C A 27 298 300 319 C5' G A 28 318 320 342 C5' A A 29 341 343 364 C5' A A 30 363 365 386 C5' U A 31 385 387 406 C5' G A 32 405 407 429 C5' A A 33 428 430 451 C5' U A 34 450 452 471 C5' A A 35 470 472 493 C5' U A 36 492 494 513 C5' G A 37 512 514 536 C5' G A 38 535 537 559 C5' U A 39 558 560 579 C5' U A 40 578 580 599 C5' U A 41 598 600 619 C5' C A 42 618 620 639 C5' G A 43 638 640 662 C5' G A 44 661 663 685 C5' A A 45 684 686 707 C5' G A 46 706 708 730 C5' C A 47 729 731 750 C5' U A 48 749 751 770 C5' U A 49 769 771 790 C5' C A 50 789 791 810 C5' C A 51 809 811 830 C5' A A 52 829 831 852 C5' C A 53 851 853 872 C5' C A 54 871 873 892 C5' A A 55 891 893 914 C5' A A 56 913 915 936 C5' G A 57 935 937 959 C5' A A 58 958 960 981 C5' G A 59 980 982 1004 C5' C A 60 1003 1005 1024 C5' C A 61 1023 1025 1044 C5' U A 62 1043 1045 1064 C5' U A 63 1063 1065 1084 C5' A A 64 1083 1085 1106 C5' A A 65 1105 1107 1128 C5' A A 66 1127 1129 1150 C5' C A 67 1149 1151 1170 C5' U A 68 1169 1171 1190 C5' C A 69 1189 1191 1210 C5' U A 70 1209 1211 1230 C5' U A 71 1229 1231 1250 C5' G A 72 1249 1251 1273 C5' A A 73 1272 1274 1295 C5' C A 74 1294 1296 1315 C5' U A 75 1314 1316 1335 C5' A A 76 1334 1336 1357 C5' U A 77 1356 1358 1377 C5' G A 78 1376 1378 1400 C5' G A 79 1399 1401 1423 C5' A A 80 1422 1424 1445 C5' G A 81 1444 1446 1468 C5' U A 82 1467 1469 1488 C5' C A 83 1487 1489 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P G A 13 distorted distorted 2 3 4 24 P G A 14 distorted distorted 9 25 26 27 47 P C A 15 distorted distorted 32 48 49 50 67 P U A 16 distorted distorted 55 68 69 70 87 P U A 17 distorted distorted 75 88 89 90 107 P C A 18 distorted distorted 95 108 109 110 127 P A A 19 distorted distorted 115 128 129 130 149 P U A 20 distorted distorted 135 150 151 152 169 P A A 21 distorted distorted 157 170 171 172 191 P U A 22 distorted distorted 177 192 193 194 211 P A A 23 distorted distorted 199 212 213 214 233 P A A 24 distorted distorted 219 234 235 236 255 P U A 25 distorted distorted 241 256 257 258 275 P C A 26 distorted distorted 263 276 277 278 295 P C A 27 distorted distorted 283 296 297 298 315 P G A 28 distorted distorted 303 316 317 318 338 P A A 29 distorted distorted 323 339 340 341 360 P A A 30 distorted distorted 346 361 362 363 382 P U A 31 distorted distorted 368 383 384 385 402 P G A 32 distorted distorted 390 403 404 405 425 P A A 33 distorted distorted 410 426 427 428 447 P U A 34 distorted distorted 433 448 449 450 467 P A A 35 distorted distorted 455 468 469 470 489 P U A 36 distorted distorted 475 490 491 492 509 P G A 37 distorted distorted 497 510 511 512 532 P G A 38 distorted distorted 517 533 534 535 555 P U A 39 distorted distorted 540 556 557 558 575 P U A 40 distorted distorted 563 576 577 578 595 P U A 41 distorted distorted 583 596 597 598 615 P C A 42 distorted distorted 603 616 617 618 635 P G A 43 distorted distorted 623 636 637 638 658 P G A 44 distorted distorted 643 659 660 661 681 P A A 45 distorted distorted 666 682 683 684 703 P G A 46 distorted distorted 689 704 705 706 726 P C A 47 distorted distorted 711 727 728 729 746 P U A 48 distorted distorted 734 747 748 749 766 P U A 49 distorted distorted 754 767 768 769 786 P C A 50 distorted distorted 774 787 788 789 806 P C A 51 distorted distorted 794 807 808 809 826 P A A 52 distorted distorted 814 827 828 829 848 P C A 53 distorted distorted 834 849 850 851 868 P C A 54 distorted distorted 856 869 870 871 888 P A A 55 distorted distorted 876 889 890 891 910 P A A 56 distorted distorted 896 911 912 913 932 P G A 57 distorted distorted 918 933 934 935 955 P A A 58 distorted distorted 940 956 957 958 977 P G A 59 distorted distorted 963 978 979 980 1000 P C A 60 distorted distorted 985 1001 1002 1003 1020 P C A 61 distorted distorted 1008 1021 1022 1023 1040 P U A 62 distorted distorted 1028 1041 1042 1043 1060 P U A 63 distorted distorted 1048 1061 1062 1063 1080 P A A 64 distorted distorted 1068 1081 1082 1083 1102 P A A 65 distorted distorted 1088 1103 1104 1105 1124 P A A 66 distorted distorted 1110 1125 1126 1127 1146 P C A 67 distorted distorted 1132 1147 1148 1149 1166 P U A 68 distorted distorted 1154 1167 1168 1169 1186 P C A 69 distorted distorted 1174 1187 1188 1189 1206 P U A 70 distorted distorted 1194 1207 1208 1209 1226 P U A 71 distorted distorted 1214 1227 1228 1229 1246 P G A 72 distorted distorted 1234 1247 1248 1249 1269 P A A 73 distorted distorted 1254 1270 1271 1272 1291 P C A 74 distorted distorted 1277 1292 1293 1294 1311 P U A 75 distorted distorted 1299 1312 1313 1314 1331 P A A 76 distorted distorted 1319 1332 1333 1334 1353 P U A 77 distorted distorted 1339 1354 1355 1356 1373 P G A 78 distorted distorted 1361 1374 1375 1376 1396 P G A 79 distorted distorted 1381 1397 1398 1399 1419 P A A 80 distorted distorted 1404 1420 1421 1422 1441 P G A 81 distorted distorted 1427 1442 1443 1444 1464 P U A 82 distorted distorted 1449 1465 1466 1467 1484 P C A 83 distorted distorted 1472 1485 1486 1487 ---------------------------------------------------------------------------------