ID code: '2AVJ' 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 1 beta 4 9 7 30 C1' DG A 2 beta 26 31 29 52 C1' DG A 3 beta 48 53 51 74 C1' DG A 4 beta 70 75 73 95 C1' BRU A 5 beta 100 86 96 116 C1' DT A 6 beta 112 117 115 136 C1' DT A 7 beta 132 137 135 156 C1' DG A 8 beta 152 157 155 178 C1' DG A 9 beta 174 179 177 200 C1' DG A 10 beta 196 201 199 222 C1' DG A 11 beta 218 223 221 242 C1' DG B 12 beta 238 243 241 264 C1' DG B 13 beta 260 265 263 286 C1' DG B 14 beta 282 287 285 308 C1' DG B 15 beta 304 309 307 329 C1' BRU B 16 beta 334 320 330 350 C1' DT B 17 beta 346 351 349 370 C1' DT B 18 beta 366 371 369 390 C1' DG B 19 beta 386 391 389 412 C1' DG B 20 beta 408 413 411 434 C1' DG B 21 beta 430 435 433 456 C1' DG B 22 beta 452 457 455 476 C1' DG C 23 beta 472 477 475 498 C1' DG C 24 beta 494 499 497 520 C1' DG C 25 beta 516 521 519 542 C1' DG C 26 beta 538 543 541 563 C1' BRU C 27 beta 568 554 564 584 C1' DT C 28 beta 580 585 583 604 C1' DT C 29 beta 600 605 603 624 C1' DG C 30 beta 620 625 623 646 C1' DG C 31 beta 642 647 645 668 C1' DG C 32 beta 664 669 667 690 C1' DG C 33 beta 686 691 689 710 C1' DG D 34 beta 706 711 709 732 C1' DG D 35 beta 728 733 731 754 C1' DG D 36 beta 750 755 753 776 C1' DG D 37 beta 772 777 775 797 C1' BRU D 38 beta 802 788 798 818 C1' DT D 39 beta 814 819 817 838 C1' DT D 40 beta 834 839 837 858 C1' DG D 41 beta 854 859 857 880 C1' DG D 42 beta 876 881 879 902 C1' DG D 43 beta 898 903 901 924 C1' DG D 44 beta 920 925 923 944 C1' DG E 45 beta 940 945 943 966 C1' DG E 46 beta 962 967 965 988 C1' DG E 47 beta 984 989 987 1010 C1' DG E 48 beta 1006 1011 1009 1031 C1' BRU E 49 beta 1036 1022 1032 1052 C1' DT E 50 beta 1048 1053 1051 1072 C1' DT E 51 beta 1068 1073 1071 1092 C1' DG E 52 beta 1088 1093 1091 1114 C1' DG E 53 beta 1110 1115 1113 1136 C1' DG E 54 beta 1132 1137 1135 1158 C1' DG E 55 beta 1154 1159 1157 1178 C1' DG F 56 beta 1174 1179 1177 1200 C1' DG F 57 beta 1196 1201 1199 1222 C1' DG F 58 beta 1218 1223 1221 1244 C1' DG F 59 beta 1240 1245 1243 1265 C1' BRU F 60 beta 1270 1256 1266 1286 C1' DT F 61 beta 1282 1287 1285 1306 C1' DT F 62 beta 1302 1307 1305 1326 C1' DG F 63 beta 1322 1327 1325 1348 C1' DG F 64 beta 1344 1349 1347 1370 C1' DG F 65 beta 1366 1371 1369 1392 C1' DG F 66 beta 1388 1393 1391 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' DG A 1 8 5 29 C2' DG A 2 30 27 51 C2' DG A 3 52 49 73 C2' DG A 4 74 71 96 C2' BRU A 5 95 97 115 C2' DT A 6 116 113 135 C2' DT A 7 136 133 155 C2' DG A 8 156 153 177 C2' DG A 9 178 175 199 C2' DG A 10 200 197 221 C2' DG A 11 222 219 241 C2' DG B 12 242 239 263 C2' DG B 13 264 261 285 C2' DG B 14 286 283 307 C2' DG B 15 308 305 330 C2' BRU B 16 329 331 349 C2' DT B 17 350 347 369 C2' DT B 18 370 367 389 C2' DG B 19 390 387 411 C2' DG B 20 412 409 433 C2' DG B 21 434 431 455 C2' DG B 22 456 453 475 C2' DG C 23 476 473 497 C2' DG C 24 498 495 519 C2' DG C 25 520 517 541 C2' DG C 26 542 539 564 C2' BRU C 27 563 565 583 C2' DT C 28 584 581 603 C2' DT C 29 604 601 623 C2' DG C 30 624 621 645 C2' DG C 31 646 643 667 C2' DG C 32 668 665 689 C2' DG C 33 690 687 709 C2' DG D 34 710 707 731 C2' DG D 35 732 729 753 C2' DG D 36 754 751 775 C2' DG D 37 776 773 798 C2' BRU D 38 797 799 817 C2' DT D 39 818 815 837 C2' DT D 40 838 835 857 C2' DG D 41 858 855 879 C2' DG D 42 880 877 901 C2' DG D 43 902 899 923 C2' DG D 44 924 921 943 C2' DG E 45 944 941 965 C2' DG E 46 966 963 987 C2' DG E 47 988 985 1009 C2' DG E 48 1010 1007 1032 C2' BRU E 49 1031 1033 1051 C2' DT E 50 1052 1049 1071 C2' DT E 51 1072 1069 1091 C2' DG E 52 1092 1089 1113 C2' DG E 53 1114 1111 1135 C2' DG E 54 1136 1133 1157 C2' DG E 55 1158 1155 1177 C2' DG F 56 1178 1175 1199 C2' DG F 57 1200 1197 1221 C2' DG F 58 1222 1219 1243 C2' DG F 59 1244 1241 1266 C2' BRU F 60 1265 1267 1285 C2' DT F 61 1286 1283 1305 C2' DT F 62 1306 1303 1325 C2' DG F 63 1326 1323 1347 C2' DG F 64 1348 1345 1369 C2' DG F 65 1370 1367 1391 C2' DG F 66 1392 1389 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' DG A 1 OK 3 6 7 27 C3' DG A 2 OK 25 28 29 49 C3' DG A 3 OK 47 50 51 71 C3' DG A 4 OK 69 72 73 97 C3' BRU A 5 OK 98 99 96 113 C3' DT A 6 OK 111 114 115 133 C3' DT A 7 OK 131 134 135 153 C3' DG A 8 OK 151 154 155 175 C3' DG A 9 OK 173 176 177 197 C3' DG A 10 OK 195 198 199 219 C3' DG A 11 OK 217 220 221 239 C3' DG B 12 OK 237 240 241 261 C3' DG B 13 OK 259 262 263 283 C3' DG B 14 OK 281 284 285 305 C3' DG B 15 OK 303 306 307 331 C3' BRU B 16 OK 332 333 330 347 C3' DT B 17 OK 345 348 349 367 C3' DT B 18 OK 365 368 369 387 C3' DG B 19 OK 385 388 389 409 C3' DG B 20 OK 407 410 411 431 C3' DG B 21 OK 429 432 433 453 C3' DG B 22 OK 451 454 455 473 C3' DG C 23 OK 471 474 475 495 C3' DG C 24 OK 493 496 497 517 C3' DG C 25 OK 515 518 519 539 C3' DG C 26 OK 537 540 541 565 C3' BRU C 27 OK 566 567 564 581 C3' DT C 28 OK 579 582 583 601 C3' DT C 29 OK 599 602 603 621 C3' DG C 30 OK 619 622 623 643 C3' DG C 31 OK 641 644 645 665 C3' DG C 32 OK 663 666 667 687 C3' DG C 33 OK 685 688 689 707 C3' DG D 34 OK 705 708 709 729 C3' DG D 35 OK 727 730 731 751 C3' DG D 36 OK 749 752 753 773 C3' DG D 37 OK 771 774 775 799 C3' BRU D 38 OK 800 801 798 815 C3' DT D 39 OK 813 816 817 835 C3' DT D 40 OK 833 836 837 855 C3' DG D 41 OK 853 856 857 877 C3' DG D 42 OK 875 878 879 899 C3' DG D 43 OK 897 900 901 921 C3' DG D 44 OK 919 922 923 941 C3' DG E 45 OK 939 942 943 963 C3' DG E 46 OK 961 964 965 985 C3' DG E 47 OK 983 986 987 1007 C3' DG E 48 OK 1005 1008 1009 1033 C3' BRU E 49 OK 1034 1035 1032 1049 C3' DT E 50 OK 1047 1050 1051 1069 C3' DT E 51 OK 1067 1070 1071 1089 C3' DG E 52 OK 1087 1090 1091 1111 C3' DG E 53 OK 1109 1112 1113 1133 C3' DG E 54 OK 1131 1134 1135 1155 C3' DG E 55 OK 1153 1156 1157 1175 C3' DG F 56 OK 1173 1176 1177 1197 C3' DG F 57 OK 1195 1198 1199 1219 C3' DG F 58 OK 1217 1220 1221 1241 C3' DG F 59 OK 1239 1242 1243 1267 C3' BRU F 60 OK 1268 1269 1266 1283 C3' DT F 61 OK 1281 1284 1285 1303 C3' DT F 62 OK 1301 1304 1305 1323 C3' DG F 63 OK 1321 1324 1325 1345 C3' DG F 64 OK 1343 1346 1347 1367 C3' DG F 65 OK 1365 1368 1369 1389 C3' DG F 66 OK 1387 1390 1391 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' DG A 1 OK 5 2 4 25 C4' DG A 2 OK 27 24 26 47 C4' DG A 3 OK 49 46 48 69 C4' DG A 4 OK 71 68 70 98 C4' BRU A 5 OK 97 101 100 111 C4' DT A 6 OK 113 110 112 131 C4' DT A 7 OK 133 130 132 151 C4' DG A 8 OK 153 150 152 173 C4' DG A 9 OK 175 172 174 195 C4' DG A 10 OK 197 194 196 217 C4' DG A 11 OK 219 216 218 237 C4' DG B 12 OK 239 236 238 259 C4' DG B 13 OK 261 258 260 281 C4' DG B 14 OK 283 280 282 303 C4' DG B 15 OK 305 302 304 332 C4' BRU B 16 OK 331 335 334 345 C4' DT B 17 OK 347 344 346 365 C4' DT B 18 OK 367 364 366 385 C4' DG B 19 OK 387 384 386 407 C4' DG B 20 OK 409 406 408 429 C4' DG B 21 OK 431 428 430 451 C4' DG B 22 OK 453 450 452 471 C4' DG C 23 OK 473 470 472 493 C4' DG C 24 OK 495 492 494 515 C4' DG C 25 OK 517 514 516 537 C4' DG C 26 OK 539 536 538 566 C4' BRU C 27 OK 565 569 568 579 C4' DT C 28 OK 581 578 580 599 C4' DT C 29 OK 601 598 600 619 C4' DG C 30 OK 621 618 620 641 C4' DG C 31 OK 643 640 642 663 C4' DG C 32 OK 665 662 664 685 C4' DG C 33 OK 687 684 686 705 C4' DG D 34 OK 707 704 706 727 C4' DG D 35 OK 729 726 728 749 C4' DG D 36 OK 751 748 750 771 C4' DG D 37 OK 773 770 772 800 C4' BRU D 38 OK 799 803 802 813 C4' DT D 39 OK 815 812 814 833 C4' DT D 40 OK 835 832 834 853 C4' DG D 41 OK 855 852 854 875 C4' DG D 42 OK 877 874 876 897 C4' DG D 43 OK 899 896 898 919 C4' DG D 44 OK 921 918 920 939 C4' DG E 45 OK 941 938 940 961 C4' DG E 46 OK 963 960 962 983 C4' DG E 47 OK 985 982 984 1005 C4' DG E 48 OK 1007 1004 1006 1034 C4' BRU E 49 OK 1033 1037 1036 1047 C4' DT E 50 OK 1049 1046 1048 1067 C4' DT E 51 OK 1069 1066 1068 1087 C4' DG E 52 OK 1089 1086 1088 1109 C4' DG E 53 OK 1111 1108 1110 1131 C4' DG E 54 OK 1133 1130 1132 1153 C4' DG E 55 OK 1155 1152 1154 1173 C4' DG F 56 OK 1175 1172 1174 1195 C4' DG F 57 OK 1197 1194 1196 1217 C4' DG F 58 OK 1219 1216 1218 1239 C4' DG F 59 OK 1241 1238 1240 1268 C4' BRU F 60 OK 1267 1271 1270 1281 C4' DT F 61 OK 1283 1280 1282 1301 C4' DT F 62 OK 1303 1300 1302 1321 C4' DG F 63 OK 1323 1320 1322 1343 C4' DG F 64 OK 1345 1342 1344 1365 C4' DG F 65 OK 1367 1364 1366 1387 C4' DG F 66 OK 1389 1386 1388 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' DG A 1 1 3 24 C5' DG A 2 23 25 46 C5' DG A 3 45 47 68 C5' DG A 4 67 69 101 C5' BRU A 5 102 98 110 C5' DT A 6 109 111 130 C5' DT A 7 129 131 150 C5' DG A 8 149 151 172 C5' DG A 9 171 173 194 C5' DG A 10 193 195 216 C5' DG A 11 215 217 236 C5' DG B 12 235 237 258 C5' DG B 13 257 259 280 C5' DG B 14 279 281 302 C5' DG B 15 301 303 335 C5' BRU B 16 336 332 344 C5' DT B 17 343 345 364 C5' DT B 18 363 365 384 C5' DG B 19 383 385 406 C5' DG B 20 405 407 428 C5' DG B 21 427 429 450 C5' DG B 22 449 451 470 C5' DG C 23 469 471 492 C5' DG C 24 491 493 514 C5' DG C 25 513 515 536 C5' DG C 26 535 537 569 C5' BRU C 27 570 566 578 C5' DT C 28 577 579 598 C5' DT C 29 597 599 618 C5' DG C 30 617 619 640 C5' DG C 31 639 641 662 C5' DG C 32 661 663 684 C5' DG C 33 683 685 704 C5' DG D 34 703 705 726 C5' DG D 35 725 727 748 C5' DG D 36 747 749 770 C5' DG D 37 769 771 803 C5' BRU D 38 804 800 812 C5' DT D 39 811 813 832 C5' DT D 40 831 833 852 C5' DG D 41 851 853 874 C5' DG D 42 873 875 896 C5' DG D 43 895 897 918 C5' DG D 44 917 919 938 C5' DG E 45 937 939 960 C5' DG E 46 959 961 982 C5' DG E 47 981 983 1004 C5' DG E 48 1003 1005 1037 C5' BRU E 49 1038 1034 1046 C5' DT E 50 1045 1047 1066 C5' DT E 51 1065 1067 1086 C5' DG E 52 1085 1087 1108 C5' DG E 53 1107 1109 1130 C5' DG E 54 1129 1131 1152 C5' DG E 55 1151 1153 1172 C5' DG F 56 1171 1173 1194 C5' DG F 57 1193 1195 1216 C5' DG F 58 1215 1217 1238 C5' DG F 59 1237 1239 1271 C5' BRU F 60 1272 1268 1280 C5' DT F 61 1279 1281 1300 C5' DT F 62 1299 1301 1320 C5' DG F 63 1319 1321 1342 C5' DG F 64 1341 1343 1364 C5' DG F 65 1363 1365 1386 C5' DG F 66 1385 1387 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 20 P DG A 2 distorted distorted 6 21 22 23 42 P DG A 3 distorted distorted 28 43 44 45 64 P DG A 4 distorted distorted 50 65 66 67 103 P BRU A 5 distorted distorted 72 104 105 102 106 P DT A 6 distorted distorted 99 107 108 109 126 P DT A 7 distorted distorted 114 127 128 129 146 P DG A 8 distorted distorted 134 147 148 149 168 P DG A 9 distorted distorted 154 169 170 171 190 P DG A 10 distorted distorted 176 191 192 193 212 P DG A 11 distorted distorted 198 213 214 215 254 P DG B 13 distorted distorted 240 255 256 257 276 P DG B 14 distorted distorted 262 277 278 279 298 P DG B 15 distorted distorted 284 299 300 301 337 P BRU B 16 distorted distorted 306 338 339 336 340 P DT B 17 distorted distorted 333 341 342 343 360 P DT B 18 distorted distorted 348 361 362 363 380 P DG B 19 distorted distorted 368 381 382 383 402 P DG B 20 distorted distorted 388 403 404 405 424 P DG B 21 distorted distorted 410 425 426 427 446 P DG B 22 distorted distorted 432 447 448 449 488 P DG C 24 distorted distorted 474 489 490 491 510 P DG C 25 distorted distorted 496 511 512 513 532 P DG C 26 distorted distorted 518 533 534 535 571 P BRU C 27 distorted distorted 540 572 573 570 574 P DT C 28 distorted distorted 567 575 576 577 594 P DT C 29 distorted distorted 582 595 596 597 614 P DG C 30 distorted distorted 602 615 616 617 636 P DG C 31 distorted distorted 622 637 638 639 658 P DG C 32 distorted distorted 644 659 660 661 680 P DG C 33 distorted distorted 666 681 682 683 722 P DG D 35 distorted distorted 708 723 724 725 744 P DG D 36 distorted distorted 730 745 746 747 766 P DG D 37 distorted distorted 752 767 768 769 805 P BRU D 38 distorted distorted 774 806 807 804 808 P DT D 39 distorted distorted 801 809 810 811 828 P DT D 40 distorted distorted 816 829 830 831 848 P DG D 41 distorted distorted 836 849 850 851 870 P DG D 42 distorted distorted 856 871 872 873 892 P DG D 43 distorted distorted 878 893 894 895 914 P DG D 44 distorted distorted 900 915 916 917 956 P DG E 46 distorted distorted 942 957 958 959 978 P DG E 47 distorted distorted 964 979 980 981 1000 P DG E 48 distorted distorted 986 1001 1002 1003 1039 P BRU E 49 distorted distorted 1008 1040 1041 1038 1042 P DT E 50 distorted distorted 1035 1043 1044 1045 1062 P DT E 51 distorted distorted 1050 1063 1064 1065 1082 P DG E 52 distorted distorted 1070 1083 1084 1085 1104 P DG E 53 distorted distorted 1090 1105 1106 1107 1126 P DG E 54 distorted distorted 1112 1127 1128 1129 1148 P DG E 55 distorted distorted 1134 1149 1150 1151 1190 P DG F 57 distorted distorted 1176 1191 1192 1193 1212 P DG F 58 distorted distorted 1198 1213 1214 1215 1234 P DG F 59 distorted distorted 1220 1235 1236 1237 1273 P BRU F 60 distorted distorted 1242 1274 1275 1272 1276 P DT F 61 distorted distorted 1269 1277 1278 1279 1296 P DT F 62 distorted distorted 1284 1297 1298 1299 1316 P DG F 63 distorted distorted 1304 1317 1318 1319 1338 P DG F 64 distorted distorted 1324 1339 1340 1341 1360 P DG F 65 distorted distorted 1346 1361 1362 1363 1382 P DG F 66 distorted distorted 1368 1383 1384 1385 ---------------------------------------------------------------------------------