ID code: '1CQL' 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' G A 1 alpha beta 4 27 10 7 44 C1' G A 2 alpha beta 39 62 45 42 78 C1' C A 3 alpha beta 73 93 79 76 109 C1' G A 4 alpha beta 104 127 110 107 143 C1' U A 5 alpha beta 138 158 144 141 173 C1' U A 6 alpha beta 168 188 174 171 203 C1' U A 7 alpha beta 198 218 204 201 233 C1' A A 8 alpha beta 228 250 234 231 266 C1' C A 9 alpha beta 261 281 267 264 297 C1' C A 10 alpha beta 292 312 298 295 328 C1' A A 11 alpha beta 323 345 329 326 361 C1' G A 12 alpha beta 356 379 362 359 395 C1' G A 13 alpha beta 390 413 396 393 429 C1' U A 14 alpha beta 424 444 430 427 459 C1' C A 15 alpha beta 454 474 460 457 490 C1' A A 16 alpha beta 485 507 491 488 523 C1' G A 17 alpha beta 518 541 524 521 557 C1' G A 18 alpha beta 552 575 558 555 591 C1' U A 19 alpha beta 586 606 592 589 621 C1' C A 20 alpha beta 616 636 622 619 652 C1' C A 21 alpha beta 647 667 653 650 683 C1' G A 22 alpha beta 678 701 684 681 717 C1' G A 23 alpha beta 712 735 718 715 751 C1' A A 24 alpha beta 746 768 752 749 784 C1' A A 25 alpha beta 779 801 785 782 817 C1' G A 26 alpha beta 812 835 818 815 851 C1' G A 27 alpha beta 846 869 852 849 885 C1' A A 28 alpha beta 880 902 886 883 918 C1' A A 29 alpha beta 913 935 919 916 951 C1' G A 30 alpha beta 946 969 952 949 985 C1' C A 31 alpha beta 980 1000 986 983 1016 C1' A A 32 alpha beta 1011 1033 1017 1014 1049 C1' G A 33 alpha beta 1044 1067 1050 1047 1083 C1' C A 34 alpha beta 1078 1098 1084 1081 1114 C1' C A 35 alpha beta 1109 1129 1115 1112 1145 C1' A A 36 alpha beta 1140 1162 1146 1143 1178 C1' A A 37 alpha beta 1173 1195 1179 1176 1211 C1' G A 38 alpha beta 1206 1229 1212 1209 1245 C1' G A 39 alpha beta 1240 1263 1246 1243 1279 C1' C A 40 alpha beta 1274 1294 1280 1277 1310 C1' G A 41 alpha beta 1305 1328 1311 1308 1344 C1' C A 42 alpha beta 1339 1359 1345 1342 1375 C1' C A 43 alpha beta 1370 1391 1376 1373 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G A 1 OK OK 9 5 25 8 42 C2' G A 2 OK OK 44 40 60 43 76 C2' C A 3 OK OK 78 74 91 77 107 C2' G A 4 OK OK 109 105 125 108 141 C2' U A 5 OK OK 143 139 156 142 171 C2' U A 6 OK OK 173 169 186 172 201 C2' U A 7 OK OK 203 199 216 202 231 C2' A A 8 OK OK 233 229 248 232 264 C2' C A 9 OK OK 266 262 279 265 295 C2' C A 10 OK OK 297 293 310 296 326 C2' A A 11 OK OK 328 324 343 327 359 C2' G A 12 OK OK 361 357 377 360 393 C2' G A 13 OK OK 395 391 411 394 427 C2' U A 14 OK OK 429 425 442 428 457 C2' C A 15 OK OK 459 455 472 458 488 C2' A A 16 OK OK 490 486 505 489 521 C2' G A 17 OK OK 523 519 539 522 555 C2' G A 18 OK OK 557 553 573 556 589 C2' U A 19 OK OK 591 587 604 590 619 C2' C A 20 OK OK 621 617 634 620 650 C2' C A 21 OK OK 652 648 665 651 681 C2' G A 22 OK OK 683 679 699 682 715 C2' G A 23 OK OK 717 713 733 716 749 C2' A A 24 OK OK 751 747 766 750 782 C2' A A 25 OK OK 784 780 799 783 815 C2' G A 26 OK OK 817 813 833 816 849 C2' G A 27 OK OK 851 847 867 850 883 C2' A A 28 OK OK 885 881 900 884 916 C2' A A 29 OK OK 918 914 933 917 949 C2' G A 30 OK OK 951 947 967 950 983 C2' C A 31 OK OK 985 981 998 984 1014 C2' A A 32 OK OK 1016 1012 1031 1015 1047 C2' G A 33 OK OK 1049 1045 1065 1048 1081 C2' C A 34 OK OK 1083 1079 1096 1082 1112 C2' C A 35 OK OK 1114 1110 1127 1113 1143 C2' A A 36 OK OK 1145 1141 1160 1144 1176 C2' A A 37 OK OK 1178 1174 1193 1177 1209 C2' G A 38 OK OK 1211 1207 1227 1210 1243 C2' G A 39 OK OK 1245 1241 1261 1244 1277 C2' C A 40 OK OK 1279 1275 1292 1278 1308 C2' G A 41 OK OK 1310 1306 1326 1309 1342 C2' C A 42 OK OK 1344 1340 1357 1343 1373 C2' C A 43 OK OK 1375 1371 1389 1374 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK OK 3 24 6 7 40 C3' G A 2 OK OK 38 59 41 42 74 C3' C A 3 OK OK 72 90 75 76 105 C3' G A 4 OK OK 103 124 106 107 139 C3' U A 5 OK OK 137 155 140 141 169 C3' U A 6 OK OK 167 185 170 171 199 C3' U A 7 OK OK 197 215 200 201 229 C3' A A 8 OK OK 227 247 230 231 262 C3' C A 9 OK OK 260 278 263 264 293 C3' C A 10 OK OK 291 309 294 295 324 C3' A A 11 OK OK 322 342 325 326 357 C3' G A 12 OK OK 355 376 358 359 391 C3' G A 13 OK OK 389 410 392 393 425 C3' U A 14 OK OK 423 441 426 427 455 C3' C A 15 OK OK 453 471 456 457 486 C3' A A 16 OK OK 484 504 487 488 519 C3' G A 17 OK OK 517 538 520 521 553 C3' G A 18 OK OK 551 572 554 555 587 C3' U A 19 OK OK 585 603 588 589 617 C3' C A 20 OK OK 615 633 618 619 648 C3' C A 21 OK OK 646 664 649 650 679 C3' G A 22 OK OK 677 698 680 681 713 C3' G A 23 OK OK 711 732 714 715 747 C3' A A 24 OK OK 745 765 748 749 780 C3' A A 25 OK OK 778 798 781 782 813 C3' G A 26 OK OK 811 832 814 815 847 C3' G A 27 OK OK 845 866 848 849 881 C3' A A 28 OK OK 879 899 882 883 914 C3' A A 29 OK OK 912 932 915 916 947 C3' G A 30 OK OK 945 966 948 949 981 C3' C A 31 OK OK 979 997 982 983 1012 C3' A A 32 OK OK 1010 1030 1013 1014 1045 C3' G A 33 OK OK 1043 1064 1046 1047 1079 C3' C A 34 OK OK 1077 1095 1080 1081 1110 C3' C A 35 OK OK 1108 1126 1111 1112 1141 C3' A A 36 OK OK 1139 1159 1142 1143 1174 C3' A A 37 OK OK 1172 1192 1175 1176 1207 C3' G A 38 OK OK 1205 1226 1208 1209 1241 C3' G A 39 OK OK 1239 1260 1242 1243 1275 C3' C A 40 OK OK 1273 1291 1276 1277 1306 C3' G A 41 OK OK 1304 1325 1307 1308 1340 C3' C A 42 OK OK 1338 1356 1341 1342 1371 C3' C A 43 OK OK 1369 1387 1372 1373 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK OK 5 23 2 4 38 C4' G A 2 OK OK 40 58 37 39 72 C4' C A 3 OK OK 74 89 71 73 103 C4' G A 4 OK OK 105 123 102 104 137 C4' U A 5 OK OK 139 154 136 138 167 C4' U A 6 OK OK 169 184 166 168 197 C4' U A 7 OK OK 199 214 196 198 227 C4' A A 8 OK OK 229 246 226 228 260 C4' C A 9 OK OK 262 277 259 261 291 C4' C A 10 OK OK 293 308 290 292 322 C4' A A 11 OK OK 324 341 321 323 355 C4' G A 12 OK OK 357 375 354 356 389 C4' G A 13 OK OK 391 409 388 390 423 C4' U A 14 OK OK 425 440 422 424 453 C4' C A 15 OK OK 455 470 452 454 484 C4' A A 16 OK OK 486 503 483 485 517 C4' G A 17 OK OK 519 537 516 518 551 C4' G A 18 OK OK 553 571 550 552 585 C4' U A 19 OK OK 587 602 584 586 615 C4' C A 20 OK OK 617 632 614 616 646 C4' C A 21 OK OK 648 663 645 647 677 C4' G A 22 OK OK 679 697 676 678 711 C4' G A 23 OK OK 713 731 710 712 745 C4' A A 24 OK OK 747 764 744 746 778 C4' A A 25 OK OK 780 797 777 779 811 C4' G A 26 OK OK 813 831 810 812 845 C4' G A 27 OK OK 847 865 844 846 879 C4' A A 28 OK OK 881 898 878 880 912 C4' A A 29 OK OK 914 931 911 913 945 C4' G A 30 OK OK 947 965 944 946 979 C4' C A 31 OK OK 981 996 978 980 1010 C4' A A 32 OK OK 1012 1029 1009 1011 1043 C4' G A 33 OK OK 1045 1063 1042 1044 1077 C4' C A 34 OK OK 1079 1094 1076 1078 1108 C4' C A 35 OK OK 1110 1125 1107 1109 1139 C4' A A 36 OK OK 1141 1158 1138 1140 1172 C4' A A 37 OK OK 1174 1191 1171 1173 1205 C4' G A 38 OK OK 1207 1225 1204 1206 1239 C4' G A 39 OK OK 1241 1259 1238 1240 1273 C4' C A 40 OK OK 1275 1290 1272 1274 1304 C4' G A 41 OK OK 1306 1324 1303 1305 1338 C4' C A 42 OK OK 1340 1355 1337 1339 1369 C4' C A 43 OK OK 1371 1386 1368 1370 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 1 OK OK 1 21 22 3 37 C5' G A 2 OK OK 36 56 57 38 71 C5' C A 3 OK OK 70 87 88 72 102 C5' G A 4 OK OK 101 121 122 103 136 C5' U A 5 OK OK 135 152 153 137 166 C5' U A 6 OK OK 165 182 183 167 196 C5' U A 7 OK OK 195 212 213 197 226 C5' A A 8 OK OK 225 244 245 227 259 C5' C A 9 OK OK 258 275 276 260 290 C5' C A 10 OK OK 289 306 307 291 321 C5' A A 11 OK OK 320 339 340 322 354 C5' G A 12 OK OK 353 373 374 355 388 C5' G A 13 OK OK 387 407 408 389 422 C5' U A 14 OK OK 421 438 439 423 452 C5' C A 15 OK OK 451 468 469 453 483 C5' A A 16 OK OK 482 501 502 484 516 C5' G A 17 OK OK 515 535 536 517 550 C5' G A 18 OK OK 549 569 570 551 584 C5' U A 19 OK OK 583 600 601 585 614 C5' C A 20 OK OK 613 630 631 615 645 C5' C A 21 OK OK 644 661 662 646 676 C5' G A 22 OK OK 675 695 696 677 710 C5' G A 23 OK OK 709 729 730 711 744 C5' A A 24 OK OK 743 762 763 745 777 C5' A A 25 OK OK 776 795 796 778 810 C5' G A 26 OK OK 809 829 830 811 844 C5' G A 27 OK OK 843 863 864 845 878 C5' A A 28 OK OK 877 896 897 879 911 C5' A A 29 OK OK 910 929 930 912 944 C5' G A 30 OK OK 943 963 964 945 978 C5' C A 31 OK OK 977 994 995 979 1009 C5' A A 32 OK OK 1008 1027 1028 1010 1042 C5' G A 33 OK OK 1041 1061 1062 1043 1076 C5' C A 34 OK OK 1075 1092 1093 1077 1107 C5' C A 35 OK OK 1106 1123 1124 1108 1138 C5' A A 36 OK OK 1137 1156 1157 1139 1171 C5' A A 37 OK OK 1170 1189 1190 1172 1204 C5' G A 38 OK OK 1203 1223 1224 1205 1238 C5' G A 39 OK OK 1237 1257 1258 1239 1272 C5' C A 40 OK OK 1271 1288 1289 1273 1303 C5' G A 41 OK OK 1302 1322 1323 1304 1337 C5' C A 42 OK OK 1336 1353 1354 1338 1368 C5' C A 43 OK OK 1367 1384 1385 1369 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 2 distorted distorted 6 34 35 36 67 P C A 3 distorted distorted 41 68 69 70 98 P G A 4 distorted distorted 75 99 100 101 132 P U A 5 distorted distorted 106 133 134 135 162 P U A 6 distorted distorted 140 163 164 165 192 P U A 7 distorted distorted 170 193 194 195 222 P A A 8 distorted distorted 200 223 224 225 255 P C A 9 distorted distorted 230 256 257 258 286 P C A 10 distorted distorted 263 287 288 289 317 P A A 11 distorted distorted 294 318 319 320 350 P G A 12 distorted distorted 325 351 352 353 384 P G A 13 distorted distorted 358 385 386 387 418 P U A 14 distorted distorted 392 419 420 421 448 P C A 15 distorted distorted 426 449 450 451 479 P A A 16 distorted distorted 456 480 481 482 512 P G A 17 distorted distorted 487 513 514 515 546 P G A 18 distorted distorted 520 547 548 549 580 P U A 19 distorted distorted 554 581 582 583 610 P C A 20 distorted distorted 588 611 612 613 641 P C A 21 distorted distorted 618 642 643 644 672 P G A 22 distorted distorted 649 673 674 675 706 P G A 23 distorted distorted 680 707 708 709 740 P A A 24 distorted distorted 714 741 742 743 773 P A A 25 distorted distorted 748 774 775 776 806 P G A 26 distorted distorted 781 807 808 809 840 P G A 27 distorted distorted 814 841 842 843 874 P A A 28 distorted distorted 848 875 876 877 907 P A A 29 distorted distorted 882 908 909 910 940 P G A 30 distorted distorted 915 941 942 943 974 P C A 31 distorted distorted 948 975 976 977 1005 P A A 32 distorted distorted 982 1006 1007 1008 1038 P G A 33 distorted distorted 1013 1039 1040 1041 1072 P C A 34 distorted distorted 1046 1073 1074 1075 1103 P C A 35 distorted distorted 1080 1104 1105 1106 1134 P A A 36 distorted distorted 1111 1135 1136 1137 1167 P A A 37 distorted distorted 1142 1168 1169 1170 1200 P G A 38 distorted distorted 1175 1201 1202 1203 1234 P G A 39 distorted distorted 1208 1235 1236 1237 1268 P C A 40 distorted distorted 1242 1269 1270 1271 1299 P G A 41 distorted distorted 1276 1300 1301 1302 1333 P C A 42 distorted distorted 1307 1334 1335 1336 1364 P C A 43 distorted distorted 1341 1365 1366 1367 ---------------------------------------------------------------------------------