ID code: '2DU3' 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 D 901 beta 8 14 11 36 C1' C D 902 beta 31 37 34 56 C1' C D 903 beta 51 57 54 76 C1' A D 904 beta 71 77 74 98 C1' G D 905 beta 93 99 96 121 C1' G D 906 beta 116 122 119 144 C1' G D 907 beta 139 145 142 167 C1' U D 908 beta 162 168 165 187 C1' G D 909 beta 182 188 185 210 C1' G D 910 beta 205 211 208 233 C1' C D 911 beta 228 234 231 253 C1' A D 912 beta 248 254 251 275 C1' G D 913 beta 270 276 273 298 C1' A D 914 beta 293 299 296 320 C1' G D 915 beta 315 321 318 343 C1' G D 916 beta 338 344 341 366 C1' G D 917 beta 361 367 364 389 C1' G D 918 beta 384 390 387 412 C1' C D 919 beta 407 413 410 432 C1' U D 920 beta 427 433 430 452 C1' U D 921 beta 447 453 450 472 C1' U D 922 beta 467 473 470 492 C1' G D 923 beta 487 493 490 515 C1' C D 924 beta 510 516 513 535 C1' G D 925 beta 530 536 533 558 C1' G D 926 beta 553 559 556 581 C1' C D 927 beta 576 582 579 601 C1' G D 928 beta 596 602 599 624 C1' G D 929 beta 619 625 622 647 C1' A D 930 beta 642 648 645 669 C1' C D 931 beta 664 670 667 689 C1' U D 932 beta 684 690 687 709 C1' G D 933 beta 704 710 707 732 C1' C D 934 beta 727 733 730 752 C1' A D 935 beta 747 753 750 774 C1' G D 936 beta 769 775 772 797 C1' A D 937 beta 792 798 795 819 C1' U D 938 beta 814 820 817 839 C1' C D 939 beta 834 840 837 859 C1' C D 940 beta 854 860 857 879 C1' G D 941 beta 874 880 877 902 C1' C D 942 beta 897 903 900 922 C1' U D 943 beta 917 923 920 942 C1' U D 944 beta 937 943 940 962 C1' U D 945 beta 957 963 960 982 C1' A D 946 beta 977 983 980 1004 C1' C D 947 beta 999 1005 1002 1024 C1' C D 948 beta 1019 1025 1022 1044 C1' C D 949 beta 1039 1045 1042 1064 C1' C D 950 beta 1059 1065 1062 1084 C1' G D 951 beta 1079 1085 1082 1107 C1' G D 952 beta 1102 1108 1105 1130 C1' U D 953 beta 1125 1131 1128 1150 C1' U D 954 beta 1145 1151 1148 1170 C1' C D 955 beta 1165 1171 1168 1190 C1' G D 956 beta 1185 1191 1188 1213 C1' A D 957 beta 1208 1214 1211 1235 C1' A D 958 beta 1230 1236 1233 1257 C1' U D 959 beta 1252 1258 1255 1277 C1' C D 960 beta 1272 1278 1275 1297 C1' C D 961 beta 1292 1298 1295 1317 C1' G D 962 beta 1312 1318 1315 1340 C1' G D 963 beta 1335 1341 1338 1363 C1' G D 964 beta 1358 1364 1361 1386 C1' C D 965 beta 1381 1387 1384 1406 C1' C D 966 beta 1401 1407 1404 1426 C1' C D 967 beta 1421 1427 1424 1446 C1' U D 968 beta 1441 1447 1444 1466 C1' G D 969 beta 1461 1467 1464 1489 C1' G D 970 beta 1484 1490 1487 1512 C1' C D 971 beta 1507 1513 1510 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 11 C2' G D 901 OK 13 9 12 34 C2' C D 902 OK 36 32 35 54 C2' C D 903 OK 56 52 55 74 C2' A D 904 OK 76 72 75 96 C2' G D 905 OK 98 94 97 119 C2' G D 906 OK 121 117 120 142 C2' G D 907 OK 144 140 143 165 C2' U D 908 OK 167 163 166 185 C2' G D 909 OK 187 183 186 208 C2' G D 910 OK 210 206 209 231 C2' C D 911 OK 233 229 232 251 C2' A D 912 OK 253 249 252 273 C2' G D 913 OK 275 271 274 296 C2' A D 914 OK 298 294 297 318 C2' G D 915 OK 320 316 319 341 C2' G D 916 OK 343 339 342 364 C2' G D 917 OK 366 362 365 387 C2' G D 918 OK 389 385 388 410 C2' C D 919 OK 412 408 411 430 C2' U D 920 OK 432 428 431 450 C2' U D 921 OK 452 448 451 470 C2' U D 922 OK 472 468 471 490 C2' G D 923 OK 492 488 491 513 C2' C D 924 OK 515 511 514 533 C2' G D 925 OK 535 531 534 556 C2' G D 926 OK 558 554 557 579 C2' C D 927 OK 581 577 580 599 C2' G D 928 OK 601 597 600 622 C2' G D 929 OK 624 620 623 645 C2' A D 930 OK 647 643 646 667 C2' C D 931 OK 669 665 668 687 C2' U D 932 OK 689 685 688 707 C2' G D 933 OK 709 705 708 730 C2' C D 934 OK 732 728 731 750 C2' A D 935 OK 752 748 751 772 C2' G D 936 OK 774 770 773 795 C2' A D 937 OK 797 793 796 817 C2' U D 938 OK 819 815 818 837 C2' C D 939 OK 839 835 838 857 C2' C D 940 OK 859 855 858 877 C2' G D 941 OK 879 875 878 900 C2' C D 942 OK 902 898 901 920 C2' U D 943 OK 922 918 921 940 C2' U D 944 OK 942 938 941 960 C2' U D 945 OK 962 958 961 980 C2' A D 946 OK 982 978 981 1002 C2' C D 947 OK 1004 1000 1003 1022 C2' C D 948 OK 1024 1020 1023 1042 C2' C D 949 OK 1044 1040 1043 1062 C2' C D 950 OK 1064 1060 1063 1082 C2' G D 951 OK 1084 1080 1083 1105 C2' G D 952 OK 1107 1103 1106 1128 C2' U D 953 OK 1130 1126 1129 1148 C2' U D 954 OK 1150 1146 1149 1168 C2' C D 955 OK 1170 1166 1169 1188 C2' G D 956 OK 1190 1186 1189 1211 C2' A D 957 OK 1213 1209 1212 1233 C2' A D 958 OK 1235 1231 1234 1255 C2' U D 959 OK 1257 1253 1256 1275 C2' C D 960 OK 1277 1273 1276 1295 C2' C D 961 OK 1297 1293 1296 1315 C2' G D 962 OK 1317 1313 1316 1338 C2' G D 963 OK 1340 1336 1339 1361 C2' G D 964 OK 1363 1359 1362 1384 C2' C D 965 OK 1386 1382 1385 1404 C2' C D 966 OK 1406 1402 1405 1424 C2' C D 967 OK 1426 1422 1425 1444 C2' U D 968 OK 1446 1442 1445 1464 C2' G D 969 OK 1466 1462 1465 1487 C2' G D 970 OK 1489 1485 1488 1510 C2' C D 971 OK 1512 1508 1511 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 9 C3' G D 901 OK 7 10 11 32 C3' C D 902 OK 30 33 34 52 C3' C D 903 OK 50 53 54 72 C3' A D 904 OK 70 73 74 94 C3' G D 905 OK 92 95 96 117 C3' G D 906 OK 115 118 119 140 C3' G D 907 OK 138 141 142 163 C3' U D 908 OK 161 164 165 183 C3' G D 909 OK 181 184 185 206 C3' G D 910 OK 204 207 208 229 C3' C D 911 OK 227 230 231 249 C3' A D 912 OK 247 250 251 271 C3' G D 913 OK 269 272 273 294 C3' A D 914 OK 292 295 296 316 C3' G D 915 OK 314 317 318 339 C3' G D 916 OK 337 340 341 362 C3' G D 917 OK 360 363 364 385 C3' G D 918 OK 383 386 387 408 C3' C D 919 OK 406 409 410 428 C3' U D 920 OK 426 429 430 448 C3' U D 921 OK 446 449 450 468 C3' U D 922 OK 466 469 470 488 C3' G D 923 OK 486 489 490 511 C3' C D 924 OK 509 512 513 531 C3' G D 925 OK 529 532 533 554 C3' G D 926 OK 552 555 556 577 C3' C D 927 OK 575 578 579 597 C3' G D 928 OK 595 598 599 620 C3' G D 929 OK 618 621 622 643 C3' A D 930 OK 641 644 645 665 C3' C D 931 OK 663 666 667 685 C3' U D 932 OK 683 686 687 705 C3' G D 933 OK 703 706 707 728 C3' C D 934 OK 726 729 730 748 C3' A D 935 OK 746 749 750 770 C3' G D 936 OK 768 771 772 793 C3' A D 937 OK 791 794 795 815 C3' U D 938 OK 813 816 817 835 C3' C D 939 OK 833 836 837 855 C3' C D 940 OK 853 856 857 875 C3' G D 941 OK 873 876 877 898 C3' C D 942 OK 896 899 900 918 C3' U D 943 OK 916 919 920 938 C3' U D 944 OK 936 939 940 958 C3' U D 945 OK 956 959 960 978 C3' A D 946 OK 976 979 980 1000 C3' C D 947 OK 998 1001 1002 1020 C3' C D 948 OK 1018 1021 1022 1040 C3' C D 949 OK 1038 1041 1042 1060 C3' C D 950 OK 1058 1061 1062 1080 C3' G D 951 OK 1078 1081 1082 1103 C3' G D 952 OK 1101 1104 1105 1126 C3' U D 953 OK 1124 1127 1128 1146 C3' U D 954 OK 1144 1147 1148 1166 C3' C D 955 OK 1164 1167 1168 1186 C3' G D 956 OK 1184 1187 1188 1209 C3' A D 957 OK 1207 1210 1211 1231 C3' A D 958 OK 1229 1232 1233 1253 C3' U D 959 OK 1251 1254 1255 1273 C3' C D 960 OK 1271 1274 1275 1293 C3' C D 961 OK 1291 1294 1295 1313 C3' G D 962 OK 1311 1314 1315 1336 C3' G D 963 OK 1334 1337 1338 1359 C3' G D 964 OK 1357 1360 1361 1382 C3' C D 965 OK 1380 1383 1384 1402 C3' C D 966 OK 1400 1403 1404 1422 C3' C D 967 OK 1420 1423 1424 1442 C3' U D 968 OK 1440 1443 1444 1462 C3' G D 969 OK 1460 1463 1464 1485 C3' G D 970 OK 1483 1486 1487 1508 C3' C D 971 OK 1506 1509 1510 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 7 C4' G D 901 OK 9 6 8 30 C4' C D 902 OK 32 29 31 50 C4' C D 903 OK 52 49 51 70 C4' A D 904 OK 72 69 71 92 C4' G D 905 OK 94 91 93 115 C4' G D 906 OK 117 114 116 138 C4' G D 907 OK 140 137 139 161 C4' U D 908 OK 163 160 162 181 C4' G D 909 OK 183 180 182 204 C4' G D 910 OK 206 203 205 227 C4' C D 911 OK 229 226 228 247 C4' A D 912 OK 249 246 248 269 C4' G D 913 OK 271 268 270 292 C4' A D 914 OK 294 291 293 314 C4' G D 915 OK 316 313 315 337 C4' G D 916 OK 339 336 338 360 C4' G D 917 OK 362 359 361 383 C4' G D 918 OK 385 382 384 406 C4' C D 919 OK 408 405 407 426 C4' U D 920 OK 428 425 427 446 C4' U D 921 OK 448 445 447 466 C4' U D 922 OK 468 465 467 486 C4' G D 923 OK 488 485 487 509 C4' C D 924 OK 511 508 510 529 C4' G D 925 OK 531 528 530 552 C4' G D 926 OK 554 551 553 575 C4' C D 927 OK 577 574 576 595 C4' G D 928 OK 597 594 596 618 C4' G D 929 OK 620 617 619 641 C4' A D 930 OK 643 640 642 663 C4' C D 931 OK 665 662 664 683 C4' U D 932 OK 685 682 684 703 C4' G D 933 OK 705 702 704 726 C4' C D 934 OK 728 725 727 746 C4' A D 935 OK 748 745 747 768 C4' G D 936 OK 770 767 769 791 C4' A D 937 OK 793 790 792 813 C4' U D 938 OK 815 812 814 833 C4' C D 939 OK 835 832 834 853 C4' C D 940 OK 855 852 854 873 C4' G D 941 OK 875 872 874 896 C4' C D 942 OK 898 895 897 916 C4' U D 943 OK 918 915 917 936 C4' U D 944 OK 938 935 937 956 C4' U D 945 OK 958 955 957 976 C4' A D 946 OK 978 975 977 998 C4' C D 947 OK 1000 997 999 1018 C4' C D 948 OK 1020 1017 1019 1038 C4' C D 949 OK 1040 1037 1039 1058 C4' C D 950 OK 1060 1057 1059 1078 C4' G D 951 OK 1080 1077 1079 1101 C4' G D 952 OK 1103 1100 1102 1124 C4' U D 953 OK 1126 1123 1125 1144 C4' U D 954 OK 1146 1143 1145 1164 C4' C D 955 OK 1166 1163 1165 1184 C4' G D 956 OK 1186 1183 1185 1207 C4' A D 957 OK 1209 1206 1208 1229 C4' A D 958 OK 1231 1228 1230 1251 C4' U D 959 OK 1253 1250 1252 1271 C4' C D 960 OK 1273 1270 1272 1291 C4' C D 961 OK 1293 1290 1292 1311 C4' G D 962 OK 1313 1310 1312 1334 C4' G D 963 OK 1336 1333 1335 1357 C4' G D 964 OK 1359 1356 1358 1380 C4' C D 965 OK 1382 1379 1381 1400 C4' C D 966 OK 1402 1399 1401 1420 C4' C D 967 OK 1422 1419 1421 1440 C4' U D 968 OK 1442 1439 1441 1460 C4' G D 969 OK 1462 1459 1461 1483 C4' G D 970 OK 1485 1482 1484 1506 C4' C D 971 OK 1508 1505 1507 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 6 C5' G D 901 5 7 29 C5' C D 902 28 30 49 C5' C D 903 48 50 69 C5' A D 904 68 70 91 C5' G D 905 90 92 114 C5' G D 906 113 115 137 C5' G D 907 136 138 160 C5' U D 908 159 161 180 C5' G D 909 179 181 203 C5' G D 910 202 204 226 C5' C D 911 225 227 246 C5' A D 912 245 247 268 C5' G D 913 267 269 291 C5' A D 914 290 292 313 C5' G D 915 312 314 336 C5' G D 916 335 337 359 C5' G D 917 358 360 382 C5' G D 918 381 383 405 C5' C D 919 404 406 425 C5' U D 920 424 426 445 C5' U D 921 444 446 465 C5' U D 922 464 466 485 C5' G D 923 484 486 508 C5' C D 924 507 509 528 C5' G D 925 527 529 551 C5' G D 926 550 552 574 C5' C D 927 573 575 594 C5' G D 928 593 595 617 C5' G D 929 616 618 640 C5' A D 930 639 641 662 C5' C D 931 661 663 682 C5' U D 932 681 683 702 C5' G D 933 701 703 725 C5' C D 934 724 726 745 C5' A D 935 744 746 767 C5' G D 936 766 768 790 C5' A D 937 789 791 812 C5' U D 938 811 813 832 C5' C D 939 831 833 852 C5' C D 940 851 853 872 C5' G D 941 871 873 895 C5' C D 942 894 896 915 C5' U D 943 914 916 935 C5' U D 944 934 936 955 C5' U D 945 954 956 975 C5' A D 946 974 976 997 C5' C D 947 996 998 1017 C5' C D 948 1016 1018 1037 C5' C D 949 1036 1038 1057 C5' C D 950 1056 1058 1077 C5' G D 951 1076 1078 1100 C5' G D 952 1099 1101 1123 C5' U D 953 1122 1124 1143 C5' U D 954 1142 1144 1163 C5' C D 955 1162 1164 1183 C5' G D 956 1182 1184 1206 C5' A D 957 1205 1207 1228 C5' A D 958 1227 1229 1250 C5' U D 959 1249 1251 1270 C5' C D 960 1269 1271 1290 C5' C D 961 1289 1291 1310 C5' G D 962 1309 1311 1333 C5' G D 963 1332 1334 1356 C5' G D 964 1355 1357 1379 C5' C D 965 1378 1380 1399 C5' C D 966 1398 1400 1419 C5' C D 967 1418 1420 1439 C5' U D 968 1438 1440 1459 C5' G D 969 1458 1460 1482 C5' G D 970 1481 1483 1505 C5' C D 971 1504 1506 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2 P G D 901 distorted distorted 3 4 5 25 P C D 902 distorted distorted 10 26 27 28 45 P C D 903 distorted distorted 33 46 47 48 65 P A D 904 distorted distorted 53 66 67 68 87 P G D 905 distorted distorted 73 88 89 90 110 P G D 906 distorted distorted 95 111 112 113 133 P G D 907 distorted distorted 118 134 135 136 156 P U D 908 distorted distorted 141 157 158 159 176 P G D 909 distorted distorted 164 177 178 179 199 P G D 910 distorted distorted 184 200 201 202 222 P C D 911 distorted distorted 207 223 224 225 242 P A D 912 distorted distorted 230 243 244 245 264 P G D 913 distorted distorted 250 265 266 267 287 P A D 914 distorted distorted 272 288 289 290 309 P G D 915 distorted distorted 295 310 311 312 332 P G D 916 distorted distorted 317 333 334 335 355 P G D 917 distorted distorted 340 356 357 358 378 P G D 918 distorted distorted 363 379 380 381 401 P C D 919 distorted distorted 386 402 403 404 421 P U D 920 distorted distorted 409 422 423 424 441 P U D 921 distorted distorted 429 442 443 444 461 P U D 922 distorted distorted 449 462 463 464 481 P G D 923 distorted distorted 469 482 483 484 504 P C D 924 distorted distorted 489 505 506 507 524 P G D 925 distorted distorted 512 525 526 527 547 P G D 926 distorted distorted 532 548 549 550 570 P C D 927 distorted distorted 555 571 572 573 590 P G D 928 distorted distorted 578 591 592 593 613 P G D 929 distorted distorted 598 614 615 616 636 P A D 930 distorted distorted 621 637 638 639 658 P C D 931 distorted distorted 644 659 660 661 678 P U D 932 distorted distorted 666 679 680 681 698 P G D 933 distorted distorted 686 699 700 701 721 P C D 934 distorted distorted 706 722 723 724 741 P A D 935 distorted distorted 729 742 743 744 763 P G D 936 distorted distorted 749 764 765 766 786 P A D 937 distorted distorted 771 787 788 789 808 P U D 938 distorted distorted 794 809 810 811 828 P C D 939 distorted distorted 816 829 830 831 848 P C D 940 distorted distorted 836 849 850 851 868 P G D 941 distorted distorted 856 869 870 871 891 P C D 942 distorted distorted 876 892 893 894 911 P U D 943 distorted distorted 899 912 913 914 931 P U D 944 distorted distorted 919 932 933 934 951 P U D 945 distorted distorted 939 952 953 954 971 P A D 946 distorted distorted 959 972 973 974 993 P C D 947 distorted distorted 979 994 995 996 1013 P C D 948 distorted distorted 1001 1014 1015 1016 1033 P C D 949 distorted distorted 1021 1034 1035 1036 1053 P C D 950 distorted distorted 1041 1054 1055 1056 1073 P G D 951 distorted distorted 1061 1074 1075 1076 1096 P G D 952 distorted distorted 1081 1097 1098 1099 1119 P U D 953 distorted distorted 1104 1120 1121 1122 1139 P U D 954 distorted distorted 1127 1140 1141 1142 1159 P C D 955 distorted distorted 1147 1160 1161 1162 1179 P G D 956 distorted distorted 1167 1180 1181 1182 1202 P A D 957 distorted distorted 1187 1203 1204 1205 1224 P A D 958 distorted distorted 1210 1225 1226 1227 1246 P U D 959 distorted distorted 1232 1247 1248 1249 1266 P C D 960 distorted distorted 1254 1267 1268 1269 1286 P C D 961 distorted distorted 1274 1287 1288 1289 1306 P G D 962 distorted distorted 1294 1307 1308 1309 1329 P G D 963 distorted distorted 1314 1330 1331 1332 1352 P G D 964 distorted distorted 1337 1353 1354 1355 1375 P C D 965 distorted distorted 1360 1376 1377 1378 1395 P C D 966 distorted distorted 1383 1396 1397 1398 1415 P C D 967 distorted distorted 1403 1416 1417 1418 1435 P U D 968 distorted distorted 1423 1436 1437 1438 1455 P G D 969 distorted distorted 1443 1456 1457 1458 1478 P G D 970 distorted distorted 1463 1479 1480 1481 1501 P C D 971 distorted distorted 1486 1502 1503 1504 9615 P SEP A1001 9616 9617 9626 P SEP A1002 9627 9628 ---------------------------------------------------------------------------------