ID code: '2NQP' 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' --------------------------------------------------------------------------------- 9 C1' C F 3 beta 4 10 7 22 C1' C F 4 beta 17 23 20 35 C1' G F 5 beta 30 36 33 58 C1' G F 6 beta 53 59 56 81 C1' A F 7 beta 76 82 79 103 C1' U F 8 beta 98 104 101 123 C1' G F 9 beta 118 124 121 146 C1' G F 10 beta 141 147 144 169 C1' U F 11 beta 164 170 167 189 C1' G F 12 beta 184 190 187 212 C1' G F 13 beta 207 213 210 235 C1' A F 14 beta 230 236 233 257 C1' A F 15 beta 252 258 255 279 C1' U F 16 beta 274 280 277 299 C1' C F 17 beta 294 300 297 319 C1' G F 18 beta 314 320 317 342 C1' G F 19 beta 337 343 340 365 C1' U F 20 beta 360 366 363 385 C1' A F 20 beta 380 386 383 407 C1' G F 21 beta 402 408 405 430 C1' A F 22 beta 425 431 428 452 C1' C F 23 beta 447 453 450 472 C1' A F 24 beta 467 473 470 494 C1' C F 25 beta 489 495 492 514 C1' A F 26 beta 509 515 512 536 C1' A F 27 beta 531 537 534 558 C1' G F 28 beta 553 559 556 581 C1' G F 29 beta 576 582 579 604 C1' G F 30 beta 599 605 602 627 C1' A F 31 beta 622 628 625 653 C1' A F 37 beta 648 654 651 675 C1' A F 38 beta 670 676 673 697 C1' U F 39 beta 692 698 695 717 C1' C F 40 beta 712 718 715 737 C1' C F 41 beta 732 738 735 757 C1' C F 42 beta 752 758 755 777 C1' U F 43 beta 772 778 775 797 C1' C F 44 beta 792 798 795 817 C1' G F 45 beta 812 818 815 840 C1' G F 45 beta 835 841 838 863 C1' C F 45 beta 858 864 861 883 C1' G F 45 beta 878 884 881 906 C1' U F 45 beta 901 907 904 926 C1' G F 46 beta 921 927 924 949 C1' C F 46 beta 944 950 947 969 C1' U F 46 beta 964 970 967 989 C1' G F 47 beta 984 990 987 1012 C1' U F 48 beta 1007 1013 1010 1032 C1' G F 49 beta 1027 1033 1030 1055 C1' C F 50 beta 1050 1056 1053 1075 C1' G F 51 beta 1070 1076 1073 1098 C1' G F 52 beta 1093 1099 1096 1121 C1' G F 53 beta 1116 1122 1119 1144 C1' U F 54 beta 1139 1145 1142 1164 C1' U F 55 beta 1159 1165 1162 1184 C1' C F 56 beta 1179 1185 1182 1204 C1' A F 57 beta 1199 1205 1202 1226 C1' A F 58 beta 1221 1227 1224 1248 C1' G F 59 beta 1243 1249 1246 1271 C1' U F 60 beta 1266 1272 1269 1291 C1' C F 61 beta 1286 1292 1289 1311 C1' C F 62 beta 1306 1312 1309 1331 C1' C F 63 beta 1326 1332 1329 1351 C1' G F 64 beta 1346 1352 1349 1374 C1' C F 65 1369 1372 1386 C1' U F 66 beta 1381 1387 1384 1406 C1' C F 67 beta 1401 1407 1404 1426 C1' C F 68 beta 1421 1427 1424 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' C F 3 OK 9 5 8 20 C2' C F 4 OK 22 18 21 33 C2' G F 5 OK 35 31 34 56 C2' G F 6 OK 58 54 57 79 C2' A F 7 OK 81 77 80 101 C2' U F 8 OK 103 99 102 121 C2' G F 9 OK 123 119 122 144 C2' G F 10 OK 146 142 145 167 C2' U F 11 OK 169 165 168 187 C2' G F 12 OK 189 185 188 210 C2' G F 13 OK 212 208 211 233 C2' A F 14 OK 235 231 234 255 C2' A F 15 OK 257 253 256 277 C2' U F 16 OK 279 275 278 297 C2' C F 17 OK 299 295 298 317 C2' G F 18 OK 319 315 318 340 C2' G F 19 OK 342 338 341 363 C2' U F 20 OK 365 361 364 383 C2' A F 20 OK 385 381 384 405 C2' G F 21 OK 407 403 406 428 C2' A F 22 OK 430 426 429 450 C2' C F 23 OK 452 448 451 470 C2' A F 24 OK 472 468 471 492 C2' C F 25 OK 494 490 493 512 C2' A F 26 OK 514 510 513 534 C2' A F 27 OK 536 532 535 556 C2' G F 28 OK 558 554 557 579 C2' G F 29 OK 581 577 580 602 C2' G F 30 OK 604 600 603 625 C2' A F 31 OK 627 623 626 651 C2' A F 37 OK 653 649 652 673 C2' A F 38 OK 675 671 674 695 C2' U F 39 OK 697 693 696 715 C2' C F 40 OK 717 713 716 735 C2' C F 41 OK 737 733 736 755 C2' C F 42 OK 757 753 756 775 C2' U F 43 OK 777 773 776 795 C2' C F 44 OK 797 793 796 815 C2' G F 45 OK 817 813 816 838 C2' G F 45 OK 840 836 839 861 C2' C F 45 OK 863 859 862 881 C2' G F 45 OK 883 879 882 904 C2' U F 45 OK 906 902 905 924 C2' G F 46 OK 926 922 925 947 C2' C F 46 OK 949 945 948 967 C2' U F 46 OK 969 965 968 987 C2' G F 47 OK 989 985 988 1010 C2' U F 48 OK 1012 1008 1011 1030 C2' G F 49 OK 1032 1028 1031 1053 C2' C F 50 OK 1055 1051 1054 1073 C2' G F 51 OK 1075 1071 1074 1096 C2' G F 52 OK 1098 1094 1097 1119 C2' G F 53 OK 1121 1117 1120 1142 C2' U F 54 OK 1144 1140 1143 1162 C2' U F 55 OK 1164 1160 1163 1182 C2' C F 56 OK 1184 1180 1183 1202 C2' A F 57 OK 1204 1200 1203 1224 C2' A F 58 OK 1226 1222 1225 1246 C2' G F 59 OK 1248 1244 1247 1269 C2' U F 60 OK 1271 1267 1270 1289 C2' C F 61 OK 1291 1287 1290 1309 C2' C F 62 OK 1311 1307 1310 1329 C2' C F 63 OK 1331 1327 1330 1349 C2' G F 64 OK 1351 1347 1350 1372 C2' C F 65 OK 1374 1370 1373 1384 C2' U F 66 OK 1386 1382 1385 1404 C2' C F 67 OK 1406 1402 1405 1424 C2' C F 68 OK 1426 1422 1425 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' C F 3 OK 3 6 7 18 C3' C F 4 OK 16 19 20 31 C3' G F 5 OK 29 32 33 54 C3' G F 6 OK 52 55 56 77 C3' A F 7 OK 75 78 79 99 C3' U F 8 OK 97 100 101 119 C3' G F 9 OK 117 120 121 142 C3' G F 10 OK 140 143 144 165 C3' U F 11 OK 163 166 167 185 C3' G F 12 OK 183 186 187 208 C3' G F 13 OK 206 209 210 231 C3' A F 14 OK 229 232 233 253 C3' A F 15 OK 251 254 255 275 C3' U F 16 OK 273 276 277 295 C3' C F 17 OK 293 296 297 315 C3' G F 18 OK 313 316 317 338 C3' G F 19 OK 336 339 340 361 C3' U F 20 OK 359 362 363 381 C3' A F 20 OK 379 382 383 403 C3' G F 21 OK 401 404 405 426 C3' A F 22 OK 424 427 428 448 C3' C F 23 OK 446 449 450 468 C3' A F 24 OK 466 469 470 490 C3' C F 25 OK 488 491 492 510 C3' A F 26 OK 508 511 512 532 C3' A F 27 OK 530 533 534 554 C3' G F 28 OK 552 555 556 577 C3' G F 29 OK 575 578 579 600 C3' G F 30 OK 598 601 602 623 C3' A F 31 OK 621 624 625 649 C3' A F 37 OK 647 650 651 671 C3' A F 38 OK 669 672 673 693 C3' U F 39 OK 691 694 695 713 C3' C F 40 OK 711 714 715 733 C3' C F 41 OK 731 734 735 753 C3' C F 42 OK 751 754 755 773 C3' U F 43 OK 771 774 775 793 C3' C F 44 OK 791 794 795 813 C3' G F 45 OK 811 814 815 836 C3' G F 45 OK 834 837 838 859 C3' C F 45 OK 857 860 861 879 C3' G F 45 OK 877 880 881 902 C3' U F 45 OK 900 903 904 922 C3' G F 46 OK 920 923 924 945 C3' C F 46 OK 943 946 947 965 C3' U F 46 OK 963 966 967 985 C3' G F 47 OK 983 986 987 1008 C3' U F 48 OK 1006 1009 1010 1028 C3' G F 49 OK 1026 1029 1030 1051 C3' C F 50 OK 1049 1052 1053 1071 C3' G F 51 OK 1069 1072 1073 1094 C3' G F 52 OK 1092 1095 1096 1117 C3' G F 53 OK 1115 1118 1119 1140 C3' U F 54 OK 1138 1141 1142 1160 C3' U F 55 OK 1158 1161 1162 1180 C3' C F 56 OK 1178 1181 1182 1200 C3' A F 57 OK 1198 1201 1202 1222 C3' A F 58 OK 1220 1223 1224 1244 C3' G F 59 OK 1242 1245 1246 1267 C3' U F 60 OK 1265 1268 1269 1287 C3' C F 61 OK 1285 1288 1289 1307 C3' C F 62 OK 1305 1308 1309 1327 C3' C F 63 OK 1325 1328 1329 1347 C3' G F 64 OK 1345 1348 1349 1370 C3' C F 65 OK 1368 1371 1372 1382 C3' U F 66 OK 1380 1383 1384 1402 C3' C F 67 OK 1400 1403 1404 1422 C3' C F 68 OK 1420 1423 1424 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' C F 3 OK 5 2 4 16 C4' C F 4 OK 18 15 17 29 C4' G F 5 OK 31 28 30 52 C4' G F 6 OK 54 51 53 75 C4' A F 7 OK 77 74 76 97 C4' U F 8 OK 99 96 98 117 C4' G F 9 OK 119 116 118 140 C4' G F 10 OK 142 139 141 163 C4' U F 11 OK 165 162 164 183 C4' G F 12 OK 185 182 184 206 C4' G F 13 OK 208 205 207 229 C4' A F 14 OK 231 228 230 251 C4' A F 15 OK 253 250 252 273 C4' U F 16 OK 275 272 274 293 C4' C F 17 OK 295 292 294 313 C4' G F 18 OK 315 312 314 336 C4' G F 19 OK 338 335 337 359 C4' U F 20 OK 361 358 360 379 C4' A F 20 OK 381 378 380 401 C4' G F 21 OK 403 400 402 424 C4' A F 22 OK 426 423 425 446 C4' C F 23 OK 448 445 447 466 C4' A F 24 OK 468 465 467 488 C4' C F 25 OK 490 487 489 508 C4' A F 26 OK 510 507 509 530 C4' A F 27 OK 532 529 531 552 C4' G F 28 OK 554 551 553 575 C4' G F 29 OK 577 574 576 598 C4' G F 30 OK 600 597 599 621 C4' A F 31 OK 623 620 622 647 C4' A F 37 OK 649 646 648 669 C4' A F 38 OK 671 668 670 691 C4' U F 39 OK 693 690 692 711 C4' C F 40 OK 713 710 712 731 C4' C F 41 OK 733 730 732 751 C4' C F 42 OK 753 750 752 771 C4' U F 43 OK 773 770 772 791 C4' C F 44 OK 793 790 792 811 C4' G F 45 OK 813 810 812 834 C4' G F 45 OK 836 833 835 857 C4' C F 45 OK 859 856 858 877 C4' G F 45 OK 879 876 878 900 C4' U F 45 OK 902 899 901 920 C4' G F 46 OK 922 919 921 943 C4' C F 46 OK 945 942 944 963 C4' U F 46 OK 965 962 964 983 C4' G F 47 OK 985 982 984 1006 C4' U F 48 OK 1008 1005 1007 1026 C4' G F 49 OK 1028 1025 1027 1049 C4' C F 50 OK 1051 1048 1050 1069 C4' G F 51 OK 1071 1068 1070 1092 C4' G F 52 OK 1094 1091 1093 1115 C4' G F 53 OK 1117 1114 1116 1138 C4' U F 54 OK 1140 1137 1139 1158 C4' U F 55 OK 1160 1157 1159 1178 C4' C F 56 OK 1180 1177 1179 1198 C4' A F 57 OK 1200 1197 1199 1220 C4' A F 58 OK 1222 1219 1221 1242 C4' G F 59 OK 1244 1241 1243 1265 C4' U F 60 OK 1267 1264 1266 1285 C4' C F 61 OK 1287 1284 1286 1305 C4' C F 62 OK 1307 1304 1306 1325 C4' C F 63 OK 1327 1324 1326 1345 C4' G F 64 OK 1347 1344 1346 1368 C4' C F 65 OK 1370 1367 1369 1380 C4' U F 66 OK 1382 1379 1381 1400 C4' C F 67 OK 1402 1399 1401 1420 C4' C F 68 OK 1422 1419 1421 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' C F 3 1 3 15 C5' C F 4 14 16 28 C5' G F 5 27 29 51 C5' G F 6 50 52 74 C5' A F 7 73 75 96 C5' U F 8 95 97 116 C5' G F 9 115 117 139 C5' G F 10 138 140 162 C5' U F 11 161 163 182 C5' G F 12 181 183 205 C5' G F 13 204 206 228 C5' A F 14 227 229 250 C5' A F 15 249 251 272 C5' U F 16 271 273 292 C5' C F 17 291 293 312 C5' G F 18 311 313 335 C5' G F 19 334 336 358 C5' U F 20 357 359 378 C5' A F 20 377 379 400 C5' G F 21 399 401 423 C5' A F 22 422 424 445 C5' C F 23 444 446 465 C5' A F 24 464 466 487 C5' C F 25 486 488 507 C5' A F 26 506 508 529 C5' A F 27 528 530 551 C5' G F 28 550 552 574 C5' G F 29 573 575 597 C5' G F 30 596 598 620 C5' A F 31 619 621 646 C5' A F 37 645 647 668 C5' A F 38 667 669 690 C5' U F 39 689 691 710 C5' C F 40 709 711 730 C5' C F 41 729 731 750 C5' C F 42 749 751 770 C5' U F 43 769 771 790 C5' C F 44 789 791 810 C5' G F 45 809 811 833 C5' G F 45 832 834 856 C5' C F 45 855 857 876 C5' G F 45 875 877 899 C5' U F 45 898 900 919 C5' G F 46 918 920 942 C5' C F 46 941 943 962 C5' U F 46 961 963 982 C5' G F 47 981 983 1005 C5' U F 48 1004 1006 1025 C5' G F 49 1024 1026 1048 C5' C F 50 1047 1049 1068 C5' G F 51 1067 1069 1091 C5' G F 52 1090 1092 1114 C5' G F 53 1113 1115 1137 C5' U F 54 1136 1138 1157 C5' U F 55 1156 1158 1177 C5' C F 56 1176 1178 1197 C5' A F 57 1196 1198 1219 C5' A F 58 1218 1220 1241 C5' G F 59 1240 1242 1264 C5' U F 60 1263 1265 1284 C5' C F 61 1283 1285 1304 C5' C F 62 1303 1305 1324 C5' C F 63 1323 1325 1344 C5' G F 64 1343 1345 1367 C5' C F 65 1366 1368 1379 C5' U F 66 1378 1380 1399 C5' C F 67 1398 1400 1419 C5' C F 68 1418 1420 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 11 P C F 4 distorted distorted 6 12 13 14 24 P G F 5 distorted distorted 19 25 26 27 47 P G F 6 distorted distorted 32 48 49 50 70 P A F 7 distorted distorted 55 71 72 73 92 P U F 8 distorted distorted 78 93 94 95 112 P G F 9 distorted distorted 100 113 114 115 135 P G F 10 distorted distorted 120 136 137 138 158 P U F 11 distorted distorted 143 159 160 161 178 P G F 12 distorted distorted 166 179 180 181 201 P G F 13 distorted distorted 186 202 203 204 224 P A F 14 distorted distorted 209 225 226 227 246 P A F 15 distorted distorted 232 247 248 249 268 P U F 16 distorted distorted 254 269 270 271 288 P C F 17 distorted distorted 276 289 290 291 308 P G F 18 distorted distorted 296 309 310 311 331 P G F 19 distorted distorted 316 332 333 334 354 P U F 20 distorted distorted 339 355 356 357 374 P A F 20 distorted distorted 362 375 376 377 396 P G F 21 distorted distorted 382 397 398 399 419 P A F 22 distorted distorted 404 420 421 422 441 P C F 23 distorted distorted 427 442 443 444 461 P A F 24 distorted distorted 449 462 463 464 483 P C F 25 distorted distorted 469 484 485 486 503 P A F 26 distorted distorted 491 504 505 506 525 P A F 27 distorted distorted 511 526 527 528 547 P G F 28 distorted distorted 533 548 549 550 570 P G F 29 distorted distorted 555 571 572 573 593 P G F 30 distorted distorted 578 594 595 596 616 P A F 31 distorted distorted 601 617 618 619 638 P U F 32 distorted distorted 624 639 640 641 642 P A F 37 OK OK 643 644 645 664 P A F 38 distorted distorted 650 665 666 667 686 P U F 39 distorted distorted 672 687 688 689 706 P C F 40 distorted distorted 694 707 708 709 726 P C F 41 distorted distorted 714 727 728 729 746 P C F 42 distorted distorted 734 747 748 749 766 P U F 43 distorted distorted 754 767 768 769 786 P C F 44 distorted distorted 774 787 788 789 806 P G F 45 distorted distorted 794 807 808 809 829 P G F 45 distorted distorted 814 830 831 832 852 P C F 45 distorted distorted 837 853 854 855 872 P G F 45 distorted distorted 860 873 874 875 895 P U F 45 distorted distorted 880 896 897 898 915 P G F 46 OK OK 916 917 918 938 P C F 46 distorted distorted 923 939 940 941 958 P U F 46 distorted distorted 946 959 960 961 978 P G F 47 distorted distorted 966 979 980 981 1001 P U F 48 distorted distorted 986 1002 1003 1004 1021 P G F 49 distorted distorted 1009 1022 1023 1024 1044 P C F 50 distorted distorted 1029 1045 1046 1047 1064 P G F 51 distorted distorted 1052 1065 1066 1067 1087 P G F 52 distorted distorted 1072 1088 1089 1090 1110 P G F 53 distorted distorted 1095 1111 1112 1113 1133 P U F 54 distorted distorted 1118 1134 1135 1136 1153 P U F 55 distorted distorted 1141 1154 1155 1156 1173 P C F 56 distorted distorted 1161 1174 1175 1176 1193 P A F 57 distorted distorted 1181 1194 1195 1196 1215 P A F 58 distorted distorted 1201 1216 1217 1218 1237 P G F 59 distorted distorted 1223 1238 1239 1240 1260 P U F 60 distorted distorted 1245 1261 1262 1263 1280 P C F 61 distorted distorted 1268 1281 1282 1283 1300 P C F 62 distorted distorted 1288 1301 1302 1303 1320 P C F 63 distorted distorted 1308 1321 1322 1323 1340 P G F 64 distorted distorted 1328 1341 1342 1343 1363 P C F 65 distorted distorted 1348 1364 1365 1366 1375 P U F 66 distorted distorted 1371 1376 1377 1378 1395 P C F 67 distorted distorted 1383 1396 1397 1398 1415 P C F 68 distorted distorted 1403 1416 1417 1418 1435 P G F 69 distorted distorted 1423 1436 1437 1438 ---------------------------------------------------------------------------------