ID code: '2OEU' 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' --------------------------------------------------------------------------------- 21 C1' GTP A 1 beta 16 22 19 44 C1' G A 2 beta 39 45 42 67 C1' A A 3 beta 62 68 65 89 C1' U A 4 beta 84 90 87 109 C1' G A 5 beta 104 110 107 132 C1' U A 6 beta 127 133 130 152 C1' A A 7 beta 147 153 150 174 C1' C A 8 beta 169 175 172 194 C1' U A 9 beta 189 195 192 214 C1' A A 10 beta 209 215 212 236 C1' C A 11 beta 231 237 234 256 C1' C A 12 beta 251 257 254 276 C1' A A 13 beta 271 277 274 298 C1' G A 14 beta 293 299 296 321 C1' C A 15 beta 316 322 319 341 C1' U A 16 beta 336 342 339 361 C1' G A 17 beta 356 362 359 384 C1' A A 18 beta 379 385 382 406 C1' U A 19 beta 401 407 404 426 C1' G A 20 beta 421 427 424 449 C1' A A 21 beta 444 450 447 471 C1' G A 22 beta 466 472 469 494 C1' U A 23 beta 489 495 492 514 C1' C A 24 beta 509 515 512 534 C1' C A 25 beta 529 535 532 554 C1' C A 26 beta 549 555 552 574 C1' A A 27 beta 569 575 572 596 C1' A A 28 beta 591 597 594 618 C1' A A 29 beta 613 619 616 640 C1' U A 30 beta 635 641 638 660 C1' A A 31 beta 655 661 658 682 C1' G A 32 beta 677 683 680 705 C1' G A 33 beta 700 706 703 728 C1' A A 34 beta 723 729 726 750 C1' C A 35 beta 745 751 748 770 C1' G A 36 beta 765 771 768 793 C1' A A 37 beta 788 794 791 815 C1' A A 38 beta 810 816 813 837 C1' A A 39 beta 832 838 835 859 C1' C A 40 beta 854 860 857 879 C1' G A 41 beta 874 880 877 902 C1' C A 42 beta 897 903 900 922 C1' C A 43 beta 917 923 920 940 C1' G B 1 beta 935 941 938 963 C1' G B 2 beta 958 964 961 986 C1' C B 3 beta 981 987 984 1006 C1' G B 4 beta 1001 1007 1004 1029 C1' U B 5 beta 1024 1030 1027 1046 C1' OMC B 6 beta 1052 1038 1047 1070 C1' C B 7 beta 1065 1071 1068 1090 C1' U B 8 beta 1085 1091 1088 1110 C1' G B 9 beta 1105 1111 1108 1133 C1' G B 10 beta 1128 1134 1131 1156 C1' 5BU B 11 beta 1151 1157 1154 1177 C1' A B 12 beta 1172 1178 1175 1199 C1' U B 13 beta 1194 1200 1197 1219 C1' C B 14 beta 1214 1220 1217 1239 C1' C B 15 beta 1234 1240 1237 1259 C1' A B 16 beta 1254 1260 1257 1281 C1' A B 17 beta 1276 1282 1279 1303 C1' U B 18 beta 1298 1304 1301 1323 C1' C B 19 beta 1318 1324 1321 1342 C1' DC B 20 beta 1338 1343 1341 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 19 C2' GTP A 1 OK 21 17 20 42 C2' G A 2 OK 44 40 43 65 C2' A A 3 OK 67 63 66 87 C2' U A 4 OK 89 85 88 107 C2' G A 5 OK 109 105 108 130 C2' U A 6 OK 132 128 131 150 C2' A A 7 OK 152 148 151 172 C2' C A 8 OK 174 170 173 192 C2' U A 9 OK 194 190 193 212 C2' A A 10 OK 214 210 213 234 C2' C A 11 OK 236 232 235 254 C2' C A 12 OK 256 252 255 274 C2' A A 13 OK 276 272 275 296 C2' G A 14 OK 298 294 297 319 C2' C A 15 OK 321 317 320 339 C2' U A 16 OK 341 337 340 359 C2' G A 17 OK 361 357 360 382 C2' A A 18 OK 384 380 383 404 C2' U A 19 OK 406 402 405 424 C2' G A 20 OK 426 422 425 447 C2' A A 21 OK 449 445 448 469 C2' G A 22 OK 471 467 470 492 C2' U A 23 OK 494 490 493 512 C2' C A 24 OK 514 510 513 532 C2' C A 25 OK 534 530 533 552 C2' C A 26 OK 554 550 553 572 C2' A A 27 OK 574 570 573 594 C2' A A 28 OK 596 592 595 616 C2' A A 29 OK 618 614 617 638 C2' U A 30 OK 640 636 639 658 C2' A A 31 OK 660 656 659 680 C2' G A 32 OK 682 678 681 703 C2' G A 33 OK 705 701 704 726 C2' A A 34 OK 728 724 727 748 C2' C A 35 OK 750 746 749 768 C2' G A 36 OK 770 766 769 791 C2' A A 37 OK 793 789 792 813 C2' A A 38 OK 815 811 814 835 C2' A A 39 OK 837 833 836 857 C2' C A 40 OK 859 855 858 877 C2' G A 41 OK 879 875 878 900 C2' C A 42 OK 902 898 901 920 C2' C A 43 OK 922 918 921 938 C2' G B 1 OK 940 936 939 961 C2' G B 2 OK 963 959 962 984 C2' C B 3 OK 986 982 985 1004 C2' G B 4 OK 1006 1002 1005 1027 C2' U B 5 OK 1029 1025 1028 1047 C2' OMC B 6 OK 1046 1050 1048 1068 C2' C B 7 OK 1070 1066 1069 1088 C2' U B 8 OK 1090 1086 1089 1108 C2' G B 9 OK 1110 1106 1109 1131 C2' G B 10 OK 1133 1129 1132 1154 C2' 5BU B 11 OK 1156 1152 1155 1175 C2' A B 12 OK 1177 1173 1176 1197 C2' U B 13 OK 1199 1195 1198 1217 C2' C B 14 OK 1219 1215 1218 1237 C2' C B 15 OK 1239 1235 1238 1257 C2' A B 16 OK 1259 1255 1258 1279 C2' A B 17 OK 1281 1277 1280 1301 C2' U B 18 OK 1303 1299 1302 1321 C2' C B 19 OK 1323 1319 1322 1341 C2' DC B 20 1342 1339 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 17 C3' GTP A 1 OK 15 18 19 40 C3' G A 2 OK 38 41 42 63 C3' A A 3 OK 61 64 65 85 C3' U A 4 OK 83 86 87 105 C3' G A 5 OK 103 106 107 128 C3' U A 6 OK 126 129 130 148 C3' A A 7 OK 146 149 150 170 C3' C A 8 OK 168 171 172 190 C3' U A 9 OK 188 191 192 210 C3' A A 10 OK 208 211 212 232 C3' C A 11 OK 230 233 234 252 C3' C A 12 OK 250 253 254 272 C3' A A 13 OK 270 273 274 294 C3' G A 14 OK 292 295 296 317 C3' C A 15 OK 315 318 319 337 C3' U A 16 OK 335 338 339 357 C3' G A 17 OK 355 358 359 380 C3' A A 18 OK 378 381 382 402 C3' U A 19 OK 400 403 404 422 C3' G A 20 OK 420 423 424 445 C3' A A 21 OK 443 446 447 467 C3' G A 22 OK 465 468 469 490 C3' U A 23 OK 488 491 492 510 C3' C A 24 OK 508 511 512 530 C3' C A 25 OK 528 531 532 550 C3' C A 26 OK 548 551 552 570 C3' A A 27 OK 568 571 572 592 C3' A A 28 OK 590 593 594 614 C3' A A 29 OK 612 615 616 636 C3' U A 30 OK 634 637 638 656 C3' A A 31 OK 654 657 658 678 C3' G A 32 OK 676 679 680 701 C3' G A 33 OK 699 702 703 724 C3' A A 34 OK 722 725 726 746 C3' C A 35 OK 744 747 748 766 C3' G A 36 OK 764 767 768 789 C3' A A 37 OK 787 790 791 811 C3' A A 38 OK 809 812 813 833 C3' A A 39 OK 831 834 835 855 C3' C A 40 OK 853 856 857 875 C3' G A 41 OK 873 876 877 898 C3' C A 42 OK 896 899 900 918 C3' C A 43 OK 916 919 920 936 C3' G B 1 OK 934 937 938 959 C3' G B 2 OK 957 960 961 982 C3' C B 3 OK 980 983 984 1002 C3' G B 4 OK 1000 1003 1004 1025 C3' U B 5 OK 1023 1026 1027 1050 C3' OMC B 6 OK 1051 1053 1047 1066 C3' C B 7 OK 1064 1067 1068 1086 C3' U B 8 OK 1084 1087 1088 1106 C3' G B 9 OK 1104 1107 1108 1129 C3' G B 10 OK 1127 1130 1131 1152 C3' 5BU B 11 OK 1150 1153 1154 1173 C3' A B 12 OK 1171 1174 1175 1195 C3' U B 13 OK 1193 1196 1197 1215 C3' C B 14 OK 1213 1216 1217 1235 C3' C B 15 OK 1233 1236 1237 1255 C3' A B 16 OK 1253 1256 1257 1277 C3' A B 17 OK 1275 1278 1279 1299 C3' U B 18 OK 1297 1300 1301 1319 C3' C B 19 OK 1317 1320 1321 1339 C3' DC B 20 OK 1337 1340 1341 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 15 C4' GTP A 1 OK 17 14 16 38 C4' G A 2 OK 40 37 39 61 C4' A A 3 OK 63 60 62 83 C4' U A 4 OK 85 82 84 103 C4' G A 5 OK 105 102 104 126 C4' U A 6 OK 128 125 127 146 C4' A A 7 OK 148 145 147 168 C4' C A 8 OK 170 167 169 188 C4' U A 9 OK 190 187 189 208 C4' A A 10 OK 210 207 209 230 C4' C A 11 OK 232 229 231 250 C4' C A 12 OK 252 249 251 270 C4' A A 13 OK 272 269 271 292 C4' G A 14 OK 294 291 293 315 C4' C A 15 OK 317 314 316 335 C4' U A 16 OK 337 334 336 355 C4' G A 17 OK 357 354 356 378 C4' A A 18 OK 380 377 379 400 C4' U A 19 OK 402 399 401 420 C4' G A 20 OK 422 419 421 443 C4' A A 21 OK 445 442 444 465 C4' G A 22 OK 467 464 466 488 C4' U A 23 OK 490 487 489 508 C4' C A 24 OK 510 507 509 528 C4' C A 25 OK 530 527 529 548 C4' C A 26 OK 550 547 549 568 C4' A A 27 OK 570 567 569 590 C4' A A 28 OK 592 589 591 612 C4' A A 29 OK 614 611 613 634 C4' U A 30 OK 636 633 635 654 C4' A A 31 OK 656 653 655 676 C4' G A 32 OK 678 675 677 699 C4' G A 33 OK 701 698 700 722 C4' A A 34 OK 724 721 723 744 C4' C A 35 OK 746 743 745 764 C4' G A 36 OK 766 763 765 787 C4' A A 37 OK 789 786 788 809 C4' A A 38 OK 811 808 810 831 C4' A A 39 OK 833 830 832 853 C4' C A 40 OK 855 852 854 873 C4' G A 41 OK 875 872 874 896 C4' C A 42 OK 898 895 897 916 C4' C A 43 OK 918 915 917 934 C4' G B 1 OK 936 933 935 957 C4' G B 2 OK 959 956 958 980 C4' C B 3 OK 982 979 981 1000 C4' G B 4 OK 1002 999 1001 1023 C4' U B 5 OK 1025 1022 1024 1051 C4' OMC B 6 OK 1050 1054 1052 1064 C4' C B 7 OK 1066 1063 1065 1084 C4' U B 8 OK 1086 1083 1085 1104 C4' G B 9 OK 1106 1103 1105 1127 C4' G B 10 OK 1129 1126 1128 1150 C4' 5BU B 11 OK 1152 1149 1151 1171 C4' A B 12 OK 1173 1170 1172 1193 C4' U B 13 OK 1195 1192 1194 1213 C4' C B 14 OK 1215 1212 1214 1233 C4' C B 15 OK 1235 1232 1234 1253 C4' A B 16 OK 1255 1252 1254 1275 C4' A B 17 OK 1277 1274 1276 1297 C4' U B 18 OK 1299 1296 1298 1317 C4' C B 19 OK 1319 1316 1318 1337 C4' DC B 20 OK 1339 1336 1338 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 14 C5' GTP A 1 13 15 37 C5' G A 2 36 38 60 C5' A A 3 59 61 82 C5' U A 4 81 83 102 C5' G A 5 101 103 125 C5' U A 6 124 126 145 C5' A A 7 144 146 167 C5' C A 8 166 168 187 C5' U A 9 186 188 207 C5' A A 10 206 208 229 C5' C A 11 228 230 249 C5' C A 12 248 250 269 C5' A A 13 268 270 291 C5' G A 14 290 292 314 C5' C A 15 313 315 334 C5' U A 16 333 335 354 C5' G A 17 353 355 377 C5' A A 18 376 378 399 C5' U A 19 398 400 419 C5' G A 20 418 420 442 C5' A A 21 441 443 464 C5' G A 22 463 465 487 C5' U A 23 486 488 507 C5' C A 24 506 508 527 C5' C A 25 526 528 547 C5' C A 26 546 548 567 C5' A A 27 566 568 589 C5' A A 28 588 590 611 C5' A A 29 610 612 633 C5' U A 30 632 634 653 C5' A A 31 652 654 675 C5' G A 32 674 676 698 C5' G A 33 697 699 721 C5' A A 34 720 722 743 C5' C A 35 742 744 763 C5' G A 36 762 764 786 C5' A A 37 785 787 808 C5' A A 38 807 809 830 C5' A A 39 829 831 852 C5' C A 40 851 853 872 C5' G A 41 871 873 895 C5' C A 42 894 896 915 C5' C A 43 914 916 933 C5' G B 1 932 934 956 C5' G B 2 955 957 979 C5' C B 3 978 980 999 C5' G B 4 998 1000 1022 C5' U B 5 1021 1023 1054 C5' OMC B 6 1055 1051 1063 C5' C B 7 1062 1064 1083 C5' U B 8 1082 1084 1103 C5' G B 9 1102 1104 1126 C5' G B 10 1125 1127 1149 C5' 5BU B 11 1148 1150 1170 C5' A B 12 1169 1171 1192 C5' U B 13 1191 1193 1212 C5' C B 14 1211 1213 1232 C5' C B 15 1231 1233 1252 C5' A B 16 1251 1253 1274 C5' A B 17 1273 1275 1296 C5' U B 18 1295 1297 1316 C5' C B 19 1315 1317 1336 C5' DC B 20 1335 1337 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 2 distorted distorted 18 34 35 36 56 P A A 3 distorted distorted 41 57 58 59 78 P U A 4 distorted distorted 64 79 80 81 98 P G A 5 distorted distorted 86 99 100 101 121 P U A 6 distorted distorted 106 122 123 124 141 P A A 7 distorted distorted 129 142 143 144 163 P C A 8 distorted distorted 149 164 165 166 183 P U A 9 distorted distorted 171 184 185 186 203 P A A 10 distorted distorted 191 204 205 206 225 P C A 11 distorted distorted 211 226 227 228 245 P C A 12 distorted distorted 233 246 247 248 265 P A A 13 distorted distorted 253 266 267 268 287 P G A 14 distorted distorted 273 288 289 290 310 P C A 15 distorted distorted 295 311 312 313 330 P U A 16 distorted distorted 318 331 332 333 350 P G A 17 distorted distorted 338 351 352 353 373 P A A 18 distorted distorted 358 374 375 376 395 P U A 19 distorted distorted 381 396 397 398 415 P G A 20 distorted distorted 403 416 417 418 438 P A A 21 distorted distorted 423 439 440 441 460 P G A 22 distorted distorted 446 461 462 463 483 P U A 23 distorted distorted 468 484 485 486 503 P C A 24 distorted distorted 491 504 505 506 523 P C A 25 distorted distorted 511 524 525 526 543 P C A 26 distorted distorted 531 544 545 546 563 P A A 27 distorted distorted 551 564 565 566 585 P A A 28 distorted distorted 571 586 587 588 607 P A A 29 distorted distorted 593 608 609 610 629 P U A 30 distorted distorted 615 630 631 632 649 P A A 31 distorted distorted 637 650 651 652 671 P G A 32 distorted distorted 657 672 673 674 694 P G A 33 distorted distorted 679 695 696 697 717 P A A 34 distorted distorted 702 718 719 720 739 P C A 35 distorted distorted 725 740 741 742 759 P G A 36 distorted distorted 747 760 761 762 782 P A A 37 distorted distorted 767 783 784 785 804 P A A 38 distorted distorted 790 805 806 807 826 P A A 39 distorted distorted 812 827 828 829 848 P C A 40 distorted distorted 834 849 850 851 868 P G A 41 distorted distorted 856 869 870 871 891 P C A 42 distorted distorted 876 892 893 894 911 P C A 43 distorted distorted 899 912 913 914 952 P G B 2 distorted distorted 937 953 954 955 975 P C B 3 distorted distorted 960 976 977 978 995 P G B 4 distorted distorted 983 996 997 998 1018 P U B 5 distorted distorted 1003 1019 1020 1021 1056 P OMC B 6 distorted distorted 1026 1057 1058 1055 1059 P C B 7 distorted distorted 1053 1060 1061 1062 1079 P U B 8 distorted distorted 1067 1080 1081 1082 1099 P G B 9 distorted distorted 1087 1100 1101 1102 1122 P G B 10 distorted distorted 1107 1123 1124 1125 1145 P 5BU B 11 distorted distorted 1130 1146 1147 1148 1166 P A B 12 distorted distorted 1153 1167 1168 1169 1188 P U B 13 distorted distorted 1174 1189 1190 1191 1208 P C B 14 distorted distorted 1196 1209 1210 1211 1228 P C B 15 distorted distorted 1216 1229 1230 1231 1248 P A B 16 distorted distorted 1236 1249 1250 1251 1270 P A B 17 distorted distorted 1256 1271 1272 1273 1292 P U B 18 distorted distorted 1278 1293 1294 1295 1312 P C B 19 distorted distorted 1300 1313 1314 1315 1332 P DC B 20 distorted distorted 1320 1333 1334 1335 ---------------------------------------------------------------------------------