ID code: '1LWS' 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' --------------------------------------------------------------------------------- 11 C1' T B 2 beta 7 12 10 31 C1' C B 3 beta 27 32 30 50 C1' T B 4 beta 46 51 49 70 C1' A B 5 beta 66 71 69 91 C1' T B 6 beta 87 92 90 111 C1' G B 7 beta 107 112 110 133 C1' T B 8 beta 129 134 132 153 C1' C B 9 beta 149 154 152 172 C1' G B 10 beta 168 173 171 194 C1' G B 11 beta 190 195 193 216 C1' G B 12 beta 212 217 215 238 C1' T B 13 beta 234 239 237 258 C1' G B 14 beta 254 259 257 280 C1' C B 15 beta 276 281 279 299 C1' G B 16 beta 295 300 298 321 C1' G B 17 beta 317 322 320 343 C1' A B 18 beta 339 344 342 364 C1' G B 19 beta 360 365 363 386 C1' A B 20 beta 382 387 385 407 C1' A B 21 beta 403 408 406 428 C1' A B 22 beta 424 429 427 449 C1' G B 23 beta 445 450 448 471 C1' A B 24 beta 467 472 470 492 C1' G B 25 beta 488 493 491 514 C1' G B 26 beta 510 515 513 536 C1' T B 27 beta 532 537 535 556 C1' A B 28 beta 552 557 555 577 C1' A B 29 beta 573 578 576 598 C1' T B 30 beta 594 599 597 618 C1' G B 31 beta 614 619 617 640 C1' A B 32 beta 636 641 639 661 C1' A B 33 beta 657 662 660 682 C1' A B 34 beta 678 683 681 703 C1' T B 35 beta 699 704 702 724 C1' A C 4 beta 720 725 723 745 C1' T C 5 beta 741 746 744 765 C1' T C 6 beta 761 766 764 785 C1' T C 7 beta 781 786 784 805 C1' C C 8 beta 801 806 804 824 C1' A C 9 beta 820 825 823 845 C1' T C 10 beta 841 846 844 865 C1' T C 11 beta 861 866 864 885 C1' A C 12 beta 881 886 884 906 C1' C C 13 beta 902 907 905 925 C1' C C 14 beta 921 926 924 944 C1' T C 15 beta 940 945 943 964 C1' C C 16 beta 960 965 963 983 C1' T C 17 beta 979 984 982 1003 C1' T C 18 beta 999 1004 1002 1023 C1' T C 19 beta 1019 1024 1022 1043 C1' C C 20 beta 1039 1044 1042 1062 C1' T C 21 beta 1058 1063 1061 1082 C1' C C 22 beta 1078 1083 1081 1101 C1' C C 23 beta 1097 1102 1100 1120 C1' G C 24 beta 1116 1121 1119 1142 C1' C C 25 beta 1138 1143 1141 1161 C1' A C 26 beta 1157 1162 1160 1182 C1' C C 27 beta 1178 1183 1181 1201 C1' C C 28 beta 1197 1202 1200 1220 C1' C C 29 beta 1216 1221 1219 1239 C1' G C 30 beta 1235 1240 1238 1261 C1' A C 31 beta 1257 1262 1260 1282 C1' C C 32 beta 1278 1283 1281 1301 C1' A C 33 beta 1297 1302 1300 1322 C1' T C 34 beta 1318 1323 1321 1342 C1' A C 35 beta 1338 1343 1341 1363 C1' G C 36 beta 1359 1364 1362 1385 C1' A C 37 beta 1381 1386 1384 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' T B 2 11 8 30 C2' C B 3 31 28 49 C2' T B 4 50 47 69 C2' A B 5 70 67 90 C2' T B 6 91 88 110 C2' G B 7 111 108 132 C2' T B 8 133 130 152 C2' C B 9 153 150 171 C2' G B 10 172 169 193 C2' G B 11 194 191 215 C2' G B 12 216 213 237 C2' T B 13 238 235 257 C2' G B 14 258 255 279 C2' C B 15 280 277 298 C2' G B 16 299 296 320 C2' G B 17 321 318 342 C2' A B 18 343 340 363 C2' G B 19 364 361 385 C2' A B 20 386 383 406 C2' A B 21 407 404 427 C2' A B 22 428 425 448 C2' G B 23 449 446 470 C2' A B 24 471 468 491 C2' G B 25 492 489 513 C2' G B 26 514 511 535 C2' T B 27 536 533 555 C2' A B 28 556 553 576 C2' A B 29 577 574 597 C2' T B 30 598 595 617 C2' G B 31 618 615 639 C2' A B 32 640 637 660 C2' A B 33 661 658 681 C2' A B 34 682 679 702 C2' T B 35 703 700 723 C2' A C 4 724 721 744 C2' T C 5 745 742 764 C2' T C 6 765 762 784 C2' T C 7 785 782 804 C2' C C 8 805 802 823 C2' A C 9 824 821 844 C2' T C 10 845 842 864 C2' T C 11 865 862 884 C2' A C 12 885 882 905 C2' C C 13 906 903 924 C2' C C 14 925 922 943 C2' T C 15 944 941 963 C2' C C 16 964 961 982 C2' T C 17 983 980 1002 C2' T C 18 1003 1000 1022 C2' T C 19 1023 1020 1042 C2' C C 20 1043 1040 1061 C2' T C 21 1062 1059 1081 C2' C C 22 1082 1079 1100 C2' C C 23 1101 1098 1119 C2' G C 24 1120 1117 1141 C2' C C 25 1142 1139 1160 C2' A C 26 1161 1158 1181 C2' C C 27 1182 1179 1200 C2' C C 28 1201 1198 1219 C2' C C 29 1220 1217 1238 C2' G C 30 1239 1236 1260 C2' A C 31 1261 1258 1281 C2' C C 32 1282 1279 1300 C2' A C 33 1301 1298 1321 C2' T C 34 1322 1319 1341 C2' A C 35 1342 1339 1362 C2' G C 36 1363 1360 1384 C2' A C 37 1385 1382 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' T B 2 OK 6 9 10 28 C3' C B 3 OK 26 29 30 47 C3' T B 4 OK 45 48 49 67 C3' A B 5 OK 65 68 69 88 C3' T B 6 OK 86 89 90 108 C3' G B 7 OK 106 109 110 130 C3' T B 8 OK 128 131 132 150 C3' C B 9 OK 148 151 152 169 C3' G B 10 OK 167 170 171 191 C3' G B 11 OK 189 192 193 213 C3' G B 12 OK 211 214 215 235 C3' T B 13 OK 233 236 237 255 C3' G B 14 OK 253 256 257 277 C3' C B 15 OK 275 278 279 296 C3' G B 16 OK 294 297 298 318 C3' G B 17 OK 316 319 320 340 C3' A B 18 OK 338 341 342 361 C3' G B 19 OK 359 362 363 383 C3' A B 20 OK 381 384 385 404 C3' A B 21 OK 402 405 406 425 C3' A B 22 OK 423 426 427 446 C3' G B 23 OK 444 447 448 468 C3' A B 24 OK 466 469 470 489 C3' G B 25 OK 487 490 491 511 C3' G B 26 OK 509 512 513 533 C3' T B 27 OK 531 534 535 553 C3' A B 28 OK 551 554 555 574 C3' A B 29 OK 572 575 576 595 C3' T B 30 OK 593 596 597 615 C3' G B 31 OK 613 616 617 637 C3' A B 32 OK 635 638 639 658 C3' A B 33 OK 656 659 660 679 C3' A B 34 OK 677 680 681 700 C3' T B 35 OK 698 701 702 721 C3' A C 4 OK 719 722 723 742 C3' T C 5 OK 740 743 744 762 C3' T C 6 OK 760 763 764 782 C3' T C 7 OK 780 783 784 802 C3' C C 8 OK 800 803 804 821 C3' A C 9 OK 819 822 823 842 C3' T C 10 OK 840 843 844 862 C3' T C 11 OK 860 863 864 882 C3' A C 12 OK 880 883 884 903 C3' C C 13 OK 901 904 905 922 C3' C C 14 OK 920 923 924 941 C3' T C 15 OK 939 942 943 961 C3' C C 16 OK 959 962 963 980 C3' T C 17 OK 978 981 982 1000 C3' T C 18 OK 998 1001 1002 1020 C3' T C 19 OK 1018 1021 1022 1040 C3' C C 20 OK 1038 1041 1042 1059 C3' T C 21 OK 1057 1060 1061 1079 C3' C C 22 OK 1077 1080 1081 1098 C3' C C 23 OK 1096 1099 1100 1117 C3' G C 24 OK 1115 1118 1119 1139 C3' C C 25 OK 1137 1140 1141 1158 C3' A C 26 OK 1156 1159 1160 1179 C3' C C 27 OK 1177 1180 1181 1198 C3' C C 28 OK 1196 1199 1200 1217 C3' C C 29 OK 1215 1218 1219 1236 C3' G C 30 OK 1234 1237 1238 1258 C3' A C 31 OK 1256 1259 1260 1279 C3' C C 32 OK 1277 1280 1281 1298 C3' A C 33 OK 1296 1299 1300 1319 C3' T C 34 OK 1317 1320 1321 1339 C3' A C 35 OK 1337 1340 1341 1360 C3' G C 36 OK 1358 1361 1362 1382 C3' A C 37 OK 1380 1383 1384 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' T B 2 OK 8 5 7 26 C4' C B 3 OK 28 25 27 45 C4' T B 4 OK 47 44 46 65 C4' A B 5 OK 67 64 66 86 C4' T B 6 OK 88 85 87 106 C4' G B 7 OK 108 105 107 128 C4' T B 8 OK 130 127 129 148 C4' C B 9 OK 150 147 149 167 C4' G B 10 OK 169 166 168 189 C4' G B 11 OK 191 188 190 211 C4' G B 12 OK 213 210 212 233 C4' T B 13 OK 235 232 234 253 C4' G B 14 OK 255 252 254 275 C4' C B 15 OK 277 274 276 294 C4' G B 16 OK 296 293 295 316 C4' G B 17 OK 318 315 317 338 C4' A B 18 OK 340 337 339 359 C4' G B 19 OK 361 358 360 381 C4' A B 20 OK 383 380 382 402 C4' A B 21 OK 404 401 403 423 C4' A B 22 OK 425 422 424 444 C4' G B 23 OK 446 443 445 466 C4' A B 24 OK 468 465 467 487 C4' G B 25 OK 489 486 488 509 C4' G B 26 OK 511 508 510 531 C4' T B 27 OK 533 530 532 551 C4' A B 28 OK 553 550 552 572 C4' A B 29 OK 574 571 573 593 C4' T B 30 OK 595 592 594 613 C4' G B 31 OK 615 612 614 635 C4' A B 32 OK 637 634 636 656 C4' A B 33 OK 658 655 657 677 C4' A B 34 OK 679 676 678 698 C4' T B 35 OK 700 697 699 719 C4' A C 4 OK 721 718 720 740 C4' T C 5 OK 742 739 741 760 C4' T C 6 OK 762 759 761 780 C4' T C 7 OK 782 779 781 800 C4' C C 8 OK 802 799 801 819 C4' A C 9 OK 821 818 820 840 C4' T C 10 OK 842 839 841 860 C4' T C 11 OK 862 859 861 880 C4' A C 12 OK 882 879 881 901 C4' C C 13 OK 903 900 902 920 C4' C C 14 OK 922 919 921 939 C4' T C 15 OK 941 938 940 959 C4' C C 16 OK 961 958 960 978 C4' T C 17 OK 980 977 979 998 C4' T C 18 OK 1000 997 999 1018 C4' T C 19 OK 1020 1017 1019 1038 C4' C C 20 OK 1040 1037 1039 1057 C4' T C 21 OK 1059 1056 1058 1077 C4' C C 22 OK 1079 1076 1078 1096 C4' C C 23 OK 1098 1095 1097 1115 C4' G C 24 OK 1117 1114 1116 1137 C4' C C 25 OK 1139 1136 1138 1156 C4' A C 26 OK 1158 1155 1157 1177 C4' C C 27 OK 1179 1176 1178 1196 C4' C C 28 OK 1198 1195 1197 1215 C4' C C 29 OK 1217 1214 1216 1234 C4' G C 30 OK 1236 1233 1235 1256 C4' A C 31 OK 1258 1255 1257 1277 C4' C C 32 OK 1279 1276 1278 1296 C4' A C 33 OK 1298 1295 1297 1317 C4' T C 34 OK 1319 1316 1318 1337 C4' A C 35 OK 1339 1336 1338 1358 C4' G C 36 OK 1360 1357 1359 1380 C4' A C 37 OK 1382 1379 1381 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' T B 2 4 6 25 C5' C B 3 24 26 44 C5' T B 4 43 45 64 C5' A B 5 63 65 85 C5' T B 6 84 86 105 C5' G B 7 104 106 127 C5' T B 8 126 128 147 C5' C B 9 146 148 166 C5' G B 10 165 167 188 C5' G B 11 187 189 210 C5' G B 12 209 211 232 C5' T B 13 231 233 252 C5' G B 14 251 253 274 C5' C B 15 273 275 293 C5' G B 16 292 294 315 C5' G B 17 314 316 337 C5' A B 18 336 338 358 C5' G B 19 357 359 380 C5' A B 20 379 381 401 C5' A B 21 400 402 422 C5' A B 22 421 423 443 C5' G B 23 442 444 465 C5' A B 24 464 466 486 C5' G B 25 485 487 508 C5' G B 26 507 509 530 C5' T B 27 529 531 550 C5' A B 28 549 551 571 C5' A B 29 570 572 592 C5' T B 30 591 593 612 C5' G B 31 611 613 634 C5' A B 32 633 635 655 C5' A B 33 654 656 676 C5' A B 34 675 677 697 C5' T B 35 696 698 718 C5' A C 4 717 719 739 C5' T C 5 738 740 759 C5' T C 6 758 760 779 C5' T C 7 778 780 799 C5' C C 8 798 800 818 C5' A C 9 817 819 839 C5' T C 10 838 840 859 C5' T C 11 858 860 879 C5' A C 12 878 880 900 C5' C C 13 899 901 919 C5' C C 14 918 920 938 C5' T C 15 937 939 958 C5' C C 16 957 959 977 C5' T C 17 976 978 997 C5' T C 18 996 998 1017 C5' T C 19 1016 1018 1037 C5' C C 20 1036 1038 1056 C5' T C 21 1055 1057 1076 C5' C C 22 1075 1077 1095 C5' C C 23 1094 1096 1114 C5' G C 24 1113 1115 1136 C5' C C 25 1135 1137 1155 C5' A C 26 1154 1156 1176 C5' C C 27 1175 1177 1195 C5' C C 28 1194 1196 1214 C5' C C 29 1213 1215 1233 C5' G C 30 1232 1234 1255 C5' A C 31 1254 1256 1276 C5' C C 32 1275 1277 1295 C5' A C 33 1294 1296 1316 C5' T C 34 1315 1317 1336 C5' A C 35 1335 1337 1357 C5' G C 36 1356 1358 1379 C5' A C 37 1378 1380 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P T B 2 distorted distorted 2 3 4 21 P C B 3 distorted distorted 9 22 23 24 40 P T B 4 distorted distorted 29 41 42 43 60 P A B 5 distorted distorted 48 61 62 63 81 P T B 6 distorted distorted 68 82 83 84 101 P G B 7 distorted distorted 89 102 103 104 123 P T B 8 distorted distorted 109 124 125 126 143 P C B 9 distorted distorted 131 144 145 146 162 P G B 10 distorted distorted 151 163 164 165 184 P G B 11 distorted distorted 170 185 186 187 206 P G B 12 distorted distorted 192 207 208 209 228 P T B 13 distorted distorted 214 229 230 231 248 P G B 14 distorted distorted 236 249 250 251 270 P C B 15 distorted distorted 256 271 272 273 289 P G B 16 distorted distorted 278 290 291 292 311 P G B 17 distorted distorted 297 312 313 314 333 P A B 18 distorted distorted 319 334 335 336 354 P G B 19 distorted distorted 341 355 356 357 376 P A B 20 distorted distorted 362 377 378 379 397 P A B 21 distorted distorted 384 398 399 400 418 P A B 22 distorted distorted 405 419 420 421 439 P G B 23 distorted distorted 426 440 441 442 461 P A B 24 distorted distorted 447 462 463 464 482 P G B 25 distorted distorted 469 483 484 485 504 P G B 26 distorted distorted 490 505 506 507 526 P T B 27 distorted distorted 512 527 528 529 546 P A B 28 distorted distorted 534 547 548 549 567 P A B 29 distorted distorted 554 568 569 570 588 P T B 30 distorted distorted 575 589 590 591 608 P G B 31 distorted distorted 596 609 610 611 630 P A B 32 distorted distorted 616 631 632 633 651 P A B 33 distorted distorted 638 652 653 654 672 P A B 34 distorted distorted 659 673 674 675 693 P T B 35 distorted distorted 680 694 695 696 714 P A C 4 OK OK 715 716 717 735 P T C 5 distorted distorted 722 736 737 738 755 P T C 6 distorted distorted 743 756 757 758 775 P T C 7 distorted distorted 763 776 777 778 795 P C C 8 distorted distorted 783 796 797 798 814 P A C 9 distorted distorted 803 815 816 817 835 P T C 10 distorted distorted 822 836 837 838 855 P T C 11 distorted distorted 843 856 857 858 875 P A C 12 distorted distorted 863 876 877 878 896 P C C 13 distorted distorted 883 897 898 899 915 P C C 14 distorted distorted 904 916 917 918 934 P T C 15 distorted distorted 923 935 936 937 954 P C C 16 distorted distorted 942 955 956 957 973 P T C 17 distorted distorted 962 974 975 976 993 P T C 18 distorted distorted 981 994 995 996 1013 P T C 19 distorted distorted 1001 1014 1015 1016 1033 P C C 20 distorted distorted 1021 1034 1035 1036 1052 P T C 21 distorted distorted 1041 1053 1054 1055 1072 P C C 22 distorted distorted 1060 1073 1074 1075 1091 P C C 23 distorted distorted 1080 1092 1093 1094 1110 P G C 24 distorted distorted 1099 1111 1112 1113 1132 P C C 25 distorted distorted 1118 1133 1134 1135 1151 P A C 26 distorted distorted 1140 1152 1153 1154 1172 P C C 27 distorted distorted 1159 1173 1174 1175 1191 P C C 28 distorted distorted 1180 1192 1193 1194 1210 P C C 29 distorted distorted 1199 1211 1212 1213 1229 P G C 30 distorted distorted 1218 1230 1231 1232 1251 P A C 31 distorted distorted 1237 1252 1253 1254 1272 P C C 32 distorted distorted 1259 1273 1274 1275 1291 P A C 33 distorted distorted 1280 1292 1293 1294 1312 P T C 34 distorted distorted 1299 1313 1314 1315 1332 P A C 35 distorted distorted 1320 1333 1334 1335 1353 P G C 36 distorted distorted 1340 1354 1355 1356 1375 P A C 37 distorted distorted 1361 1376 1377 1378 ---------------------------------------------------------------------------------