ID code: '3B58' 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' --------------------------------------------------------------------------------- 46 C1' C A 2 beta 41 47 44 66 C1' C A 3 beta 61 67 64 86 C1' C A 4 beta 81 87 84 105 C1' A A 5 beta 101 106 103 127 C1' G A 6 beta 122 128 125 150 C1' U A 7 beta 145 151 148 170 C1' C A 8 beta 165 171 168 190 C1' C A 9 beta 185 191 188 210 C1' A A 10 beta 205 211 208 232 C1' C A 11 beta 227 233 230 252 C1' C A 12 beta 247 253 250 272 C1' G A 13 beta 267 273 270 293 C1' C B 2 beta 288 294 291 313 C1' G B 3 beta 308 314 311 336 C1' G B 4 beta 331 337 334 359 C1' U B 5 beta 354 360 357 379 C1' G B 6 beta 374 380 377 402 C1' A B 7 beta 397 403 400 424 C1' G B 8 beta 419 425 422 447 C1' A B 9 beta 442 448 445 469 C1' A B 10 beta 464 470 467 491 C1' G B 11 beta 486 492 489 514 C1' G B 12 beta 509 515 512 537 C1' G B 13 beta 532 538 535 573 C1' G B 15 beta 568 574 571 596 C1' G B 16 beta 591 597 594 619 C1' C B 17 beta 614 620 617 639 C1' A B 18 beta 634 640 637 661 C1' G B 19 beta 656 662 659 684 C1' A B 20 beta 679 685 682 706 C1' G B 21 beta 701 707 704 729 C1' A B 22 beta 724 730 727 751 C1' A B 23 beta 746 752 749 773 C1' A B 24 beta 768 774 771 795 C1' C B 25 beta 790 796 793 815 C1' A B 26 beta 810 816 813 837 C1' C B 27 beta 832 838 835 857 C1' A B 28 beta 852 858 855 879 C1' C B 29 beta 874 880 877 899 C1' G B 30 beta 894 900 897 922 C1' A B 31 beta 917 923 920 942 C1' U C 31 beta 937 943 940 962 C1' C C 32 beta 957 963 960 982 C1' G C 33 beta 977 983 980 1005 C1' U C 34 beta 1000 1006 1003 1025 C1' G C 35 beta 1020 1026 1023 1048 C1' G C 36 beta 1043 1049 1046 1197 C1' A C 40 beta 1192 1198 1195 1219 C1' U C 41 beta 1214 1220 1217 1239 C1' U C 42 beta 1234 1240 1237 1259 C1' A C 43 beta 1254 1260 1257 1281 C1' C C 44 beta 1276 1282 1279 1301 C1' C C 45 beta 1296 1302 1299 1321 C1' U C 46 beta 1316 1322 1319 1341 C1' G C 47 beta 1336 1342 1339 1364 C1' C C 48 beta 1359 1365 1362 1384 C1' C C 49 beta 1379 1385 1382 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 44 C2' C A 2 OK 46 42 45 64 C2' C A 3 OK 66 62 65 84 C2' C A 4 OK 86 82 85 103 C2' A A 5 OK 105 102 104 125 C2' G A 6 OK 127 123 126 148 C2' U A 7 OK 150 146 149 168 C2' C A 8 OK 170 166 169 188 C2' C A 9 OK 190 186 189 208 C2' A A 10 OK 210 206 209 230 C2' C A 11 OK 232 228 231 250 C2' C A 12 OK 252 248 251 270 C2' G A 13 OK 272 268 271 291 C2' C B 2 OK 293 289 292 311 C2' G B 3 OK 313 309 312 334 C2' G B 4 OK 336 332 335 357 C2' U B 5 OK 359 355 358 377 C2' G B 6 OK 379 375 378 400 C2' A B 7 OK 402 398 401 422 C2' G B 8 OK 424 420 423 445 C2' A B 9 OK 447 443 446 467 C2' A B 10 OK 469 465 468 489 C2' G B 11 OK 491 487 490 512 C2' G B 12 OK 514 510 513 535 C2' G B 13 OK 537 533 536 571 C2' G B 15 OK 573 569 572 594 C2' G B 16 OK 596 592 595 617 C2' C B 17 OK 619 615 618 637 C2' A B 18 OK 639 635 638 659 C2' G B 19 OK 661 657 660 682 C2' A B 20 OK 684 680 683 704 C2' G B 21 OK 706 702 705 727 C2' A B 22 OK 729 725 728 749 C2' A B 23 OK 751 747 750 771 C2' A B 24 OK 773 769 772 793 C2' C B 25 OK 795 791 794 813 C2' A B 26 OK 815 811 814 835 C2' C B 27 OK 837 833 836 855 C2' A B 28 OK 857 853 856 877 C2' C B 29 OK 879 875 878 897 C2' G B 30 OK 899 895 898 920 C2' A B 31 OK 922 918 921 940 C2' U C 31 OK 942 938 941 960 C2' C C 32 OK 962 958 961 980 C2' G C 33 OK 982 978 981 1003 C2' U C 34 OK 1005 1001 1004 1023 C2' G C 35 OK 1025 1021 1024 1046 C2' G C 36 OK 1048 1044 1047 1195 C2' A C 40 OK 1197 1193 1196 1217 C2' U C 41 OK 1219 1215 1218 1237 C2' U C 42 OK 1239 1235 1238 1257 C2' A C 43 OK 1259 1255 1258 1279 C2' C C 44 OK 1281 1277 1280 1299 C2' C C 45 OK 1301 1297 1300 1319 C2' U C 46 OK 1321 1317 1320 1339 C2' G C 47 OK 1341 1337 1340 1362 C2' C C 48 OK 1364 1360 1363 1382 C2' C C 49 OK 1384 1380 1383 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 42 C3' C A 2 OK 40 43 44 62 C3' C A 3 OK 60 63 64 82 C3' C A 4 OK 80 83 84 102 C3' A A 5 100 103 123 C3' G A 6 OK 121 124 125 146 C3' U A 7 OK 144 147 148 166 C3' C A 8 OK 164 167 168 186 C3' C A 9 OK 184 187 188 206 C3' A A 10 OK 204 207 208 228 C3' C A 11 OK 226 229 230 248 C3' C A 12 OK 246 249 250 268 C3' G A 13 OK 266 269 270 289 C3' C B 2 OK 287 290 291 309 C3' G B 3 OK 307 310 311 332 C3' G B 4 OK 330 333 334 355 C3' U B 5 OK 353 356 357 375 C3' G B 6 OK 373 376 377 398 C3' A B 7 OK 396 399 400 420 C3' G B 8 OK 418 421 422 443 C3' A B 9 OK 441 444 445 465 C3' A B 10 OK 463 466 467 487 C3' G B 11 OK 485 488 489 510 C3' G B 12 OK 508 511 512 533 C3' G B 13 OK 531 534 535 569 C3' G B 15 OK 567 570 571 592 C3' G B 16 OK 590 593 594 615 C3' C B 17 OK 613 616 617 635 C3' A B 18 OK 633 636 637 657 C3' G B 19 OK 655 658 659 680 C3' A B 20 OK 678 681 682 702 C3' G B 21 OK 700 703 704 725 C3' A B 22 OK 723 726 727 747 C3' A B 23 OK 745 748 749 769 C3' A B 24 OK 767 770 771 791 C3' C B 25 OK 789 792 793 811 C3' A B 26 OK 809 812 813 833 C3' C B 27 OK 831 834 835 853 C3' A B 28 OK 851 854 855 875 C3' C B 29 OK 873 876 877 895 C3' G B 30 OK 893 896 897 918 C3' A B 31 OK 916 919 920 938 C3' U C 31 OK 936 939 940 958 C3' C C 32 OK 956 959 960 978 C3' G C 33 OK 976 979 980 1001 C3' U C 34 OK 999 1002 1003 1021 C3' G C 35 OK 1019 1022 1023 1044 C3' G C 36 OK 1042 1045 1046 1193 C3' A C 40 OK 1191 1194 1195 1215 C3' U C 41 OK 1213 1216 1217 1235 C3' U C 42 OK 1233 1236 1237 1255 C3' A C 43 OK 1253 1256 1257 1277 C3' C C 44 OK 1275 1278 1279 1297 C3' C C 45 OK 1295 1298 1299 1317 C3' U C 46 OK 1315 1318 1319 1337 C3' G C 47 OK 1335 1338 1339 1360 C3' C C 48 OK 1358 1361 1362 1380 C3' C C 49 OK 1378 1381 1382 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 40 C4' C A 2 OK 42 39 41 60 C4' C A 3 OK 62 59 61 80 C4' C A 4 OK 82 79 81 100 C4' A A 5 OK 102 99 101 121 C4' G A 6 OK 123 120 122 144 C4' U A 7 OK 146 143 145 164 C4' C A 8 OK 166 163 165 184 C4' C A 9 OK 186 183 185 204 C4' A A 10 OK 206 203 205 226 C4' C A 11 OK 228 225 227 246 C4' C A 12 OK 248 245 247 266 C4' G A 13 OK 268 265 267 287 C4' C B 2 OK 289 286 288 307 C4' G B 3 OK 309 306 308 330 C4' G B 4 OK 332 329 331 353 C4' U B 5 OK 355 352 354 373 C4' G B 6 OK 375 372 374 396 C4' A B 7 OK 398 395 397 418 C4' G B 8 OK 420 417 419 441 C4' A B 9 OK 443 440 442 463 C4' A B 10 OK 465 462 464 485 C4' G B 11 OK 487 484 486 508 C4' G B 12 OK 510 507 509 531 C4' G B 13 OK 533 530 532 567 C4' G B 15 OK 569 566 568 590 C4' G B 16 OK 592 589 591 613 C4' C B 17 OK 615 612 614 633 C4' A B 18 OK 635 632 634 655 C4' G B 19 OK 657 654 656 678 C4' A B 20 OK 680 677 679 700 C4' G B 21 OK 702 699 701 723 C4' A B 22 OK 725 722 724 745 C4' A B 23 OK 747 744 746 767 C4' A B 24 OK 769 766 768 789 C4' C B 25 OK 791 788 790 809 C4' A B 26 OK 811 808 810 831 C4' C B 27 OK 833 830 832 851 C4' A B 28 OK 853 850 852 873 C4' C B 29 OK 875 872 874 893 C4' G B 30 OK 895 892 894 916 C4' A B 31 OK 918 915 917 936 C4' U C 31 OK 938 935 937 956 C4' C C 32 OK 958 955 957 976 C4' G C 33 OK 978 975 977 999 C4' U C 34 OK 1001 998 1000 1019 C4' G C 35 OK 1021 1018 1020 1042 C4' G C 36 OK 1044 1041 1043 1191 C4' A C 40 OK 1193 1190 1192 1213 C4' U C 41 OK 1215 1212 1214 1233 C4' U C 42 OK 1235 1232 1234 1253 C4' A C 43 OK 1255 1252 1254 1275 C4' C C 44 OK 1277 1274 1276 1295 C4' C C 45 OK 1297 1294 1296 1315 C4' U C 46 OK 1317 1314 1316 1335 C4' G C 47 OK 1337 1334 1336 1358 C4' C C 48 OK 1360 1357 1359 1378 C4' C C 49 OK 1380 1377 1379 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 39 C5' C A 2 38 40 59 C5' C A 3 58 60 79 C5' C A 4 78 80 99 C5' A A 5 98 100 120 C5' G A 6 119 121 143 C5' U A 7 142 144 163 C5' C A 8 162 164 183 C5' C A 9 182 184 203 C5' A A 10 202 204 225 C5' C A 11 224 226 245 C5' C A 12 244 246 265 C5' G A 13 264 266 286 C5' C B 2 285 287 306 C5' G B 3 305 307 329 C5' G B 4 328 330 352 C5' U B 5 351 353 372 C5' G B 6 371 373 395 C5' A B 7 394 396 417 C5' G B 8 416 418 440 C5' A B 9 439 441 462 C5' A B 10 461 463 484 C5' G B 11 483 485 507 C5' G B 12 506 508 530 C5' G B 13 529 531 566 C5' G B 15 565 567 589 C5' G B 16 588 590 612 C5' C B 17 611 613 632 C5' A B 18 631 633 654 C5' G B 19 653 655 677 C5' A B 20 676 678 699 C5' G B 21 698 700 722 C5' A B 22 721 723 744 C5' A B 23 743 745 766 C5' A B 24 765 767 788 C5' C B 25 787 789 808 C5' A B 26 807 809 830 C5' C B 27 829 831 850 C5' A B 28 849 851 872 C5' C B 29 871 873 892 C5' G B 30 891 893 915 C5' A B 31 914 916 935 C5' U C 31 934 936 955 C5' C C 32 954 956 975 C5' G C 33 974 976 998 C5' U C 34 997 999 1018 C5' G C 35 1017 1019 1041 C5' G C 36 1040 1042 1190 C5' A C 40 1189 1191 1212 C5' U C 41 1211 1213 1232 C5' U C 42 1231 1233 1252 C5' A C 43 1251 1253 1274 C5' C C 44 1273 1275 1294 C5' C C 45 1293 1295 1314 C5' U C 46 1313 1315 1334 C5' G C 47 1333 1335 1357 C5' C C 48 1356 1358 1377 C5' C C 49 1376 1378 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 35 P C A 2 distorted distorted 36 37 38 55 P C A 3 distorted distorted 43 56 57 58 75 P C A 4 distorted distorted 63 76 77 78 95 P A A 5 distorted distorted 83 96 97 98 116 P G A 6 OK OK 117 118 119 139 P U A 7 distorted distorted 124 140 141 142 159 P C A 8 distorted distorted 147 160 161 162 179 P C A 9 distorted distorted 167 180 181 182 199 P A A 10 distorted distorted 187 200 201 202 221 P C A 11 distorted distorted 207 222 223 224 241 P C A 12 distorted distorted 229 242 243 244 261 P G A 13 distorted distorted 249 262 263 264 302 P G B 3 distorted distorted 290 303 304 305 325 P G B 4 distorted distorted 310 326 327 328 348 P U B 5 distorted distorted 333 349 350 351 368 P G B 6 distorted distorted 356 369 370 371 391 P A B 7 distorted distorted 376 392 393 394 413 P G B 8 distorted distorted 399 414 415 416 436 P A B 9 distorted distorted 421 437 438 439 458 P A B 10 distorted distorted 444 459 460 461 480 P G B 11 distorted distorted 466 481 482 483 503 P G B 12 distorted distorted 488 504 505 506 526 P G B 13 distorted distorted 511 527 528 529 549 P S9L B 14 OK OK 534 550 551 552 562 P G B 15 distorted distorted 561 563 564 565 585 P G B 16 distorted distorted 570 586 587 588 608 P C B 17 distorted distorted 593 609 610 611 628 P A B 18 distorted distorted 616 629 630 631 650 P G B 19 distorted distorted 636 651 652 653 673 P A B 20 distorted distorted 658 674 675 676 695 P G B 21 distorted distorted 681 696 697 698 718 P A B 22 distorted distorted 703 719 720 721 740 P A B 23 distorted distorted 726 741 742 743 762 P A B 24 distorted distorted 748 763 764 765 784 P C B 25 distorted distorted 770 785 786 787 804 P A B 26 distorted distorted 792 805 806 807 826 P C B 27 distorted distorted 812 827 828 829 846 P A B 28 distorted distorted 834 847 848 849 868 P C B 29 distorted distorted 854 869 870 871 888 P G B 30 distorted distorted 876 889 890 891 911 P A B 31 distorted distorted 896 912 913 914 951 P C C 32 distorted distorted 939 952 953 954 971 P G C 33 distorted distorted 959 972 973 974 994 P U C 34 distorted distorted 979 995 996 997 1014 P G C 35 distorted distorted 1002 1015 1016 1017 1037 P G C 36 distorted distorted 1022 1038 1039 1040 1060 P U C 37 1045 1061 P U C 37 1045 1100 P G C 38 1101 P G C 38 1146 P C C 39 1147 P C C 39 1186 P A C 40 distorted distorted 1187 1188 1189 1208 P U C 41 distorted distorted 1194 1209 1210 1211 1228 P U C 42 distorted distorted 1216 1229 1230 1231 1248 P A C 43 distorted distorted 1236 1249 1250 1251 1270 P C C 44 distorted distorted 1256 1271 1272 1273 1290 P C C 45 distorted distorted 1278 1291 1292 1293 1310 P U C 46 distorted distorted 1298 1311 1312 1313 1330 P G C 47 distorted distorted 1318 1331 1332 1333 1353 P C C 48 distorted distorted 1338 1354 1355 1356 1373 P C C 49 distorted distorted 1361 1374 1375 1376 ---------------------------------------------------------------------------------