ID code: '1G70' 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' --------------------------------------------------------------------------------- 263 C1' G A 41 alpha beta 258 281 264 261 298 C1' G A 42 alpha beta 293 316 299 296 332 C1' U A 43 alpha beta 327 347 333 330 362 C1' C A 44 alpha beta 357 377 363 360 393 C1' U A 45 alpha beta 388 408 394 391 423 C1' G A 46 alpha beta 418 441 424 421 457 C1' G A 47 alpha beta 452 475 458 455 491 C1' G A 48 alpha beta 486 509 492 489 525 C1' C A 49 alpha beta 520 540 526 523 556 C1' G A 50 alpha beta 551 574 557 554 590 C1' C A 51 alpha beta 585 605 591 588 621 C1' A A 52 alpha beta 616 638 622 619 654 C1' C A 54 alpha beta 649 669 655 652 685 C1' U A 60 alpha beta 680 700 686 683 715 C1' U A 61 alpha beta 710 730 716 713 745 C1' C A 62 alpha beta 740 760 746 743 776 C1' G A 63 alpha beta 771 794 777 774 810 C1' G A 64 alpha beta 805 828 811 808 844 C1' U A 66 alpha beta 839 859 845 842 874 C1' G A 67 alpha beta 869 892 875 872 908 C1' A A 68 alpha beta 903 925 909 906 941 C1' C A 69 alpha beta 936 956 942 939 972 C1' G A 70 alpha beta 967 990 973 970 1006 C1' G A 71 alpha beta 1001 1024 1007 1004 1040 C1' U A 72 alpha beta 1035 1055 1041 1038 1070 C1' A A 73 alpha beta 1065 1087 1071 1068 1103 C1' C A 74 alpha beta 1098 1118 1104 1101 1134 C1' A A 75 alpha beta 1129 1151 1135 1132 1167 C1' G A 76 alpha beta 1162 1185 1168 1165 1201 C1' G A 77 alpha beta 1196 1219 1202 1199 1235 C1' C A 78 alpha beta 1230 1250 1236 1233 1266 C1' C A 79 alpha beta 1261 1282 1267 1264 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 261 C2' G A 41 OK OK 263 259 279 262 296 C2' G A 42 OK OK 298 294 314 297 330 C2' U A 43 OK OK 332 328 345 331 360 C2' C A 44 OK OK 362 358 375 361 391 C2' U A 45 OK OK 393 389 406 392 421 C2' G A 46 OK OK 423 419 439 422 455 C2' G A 47 OK OK 457 453 473 456 489 C2' G A 48 OK OK 491 487 507 490 523 C2' C A 49 OK OK 525 521 538 524 554 C2' G A 50 OK OK 556 552 572 555 588 C2' C A 51 OK OK 590 586 603 589 619 C2' A A 52 OK OK 621 617 636 620 652 C2' C A 54 OK OK 654 650 667 653 683 C2' U A 60 OK OK 685 681 698 684 713 C2' U A 61 OK OK 715 711 728 714 743 C2' C A 62 OK OK 745 741 758 744 774 C2' G A 63 OK OK 776 772 792 775 808 C2' G A 64 OK OK 810 806 826 809 842 C2' U A 66 OK OK 844 840 857 843 872 C2' G A 67 OK OK 874 870 890 873 906 C2' A A 68 OK OK 908 904 923 907 939 C2' C A 69 OK OK 941 937 954 940 970 C2' G A 70 OK OK 972 968 988 971 1004 C2' G A 71 OK OK 1006 1002 1022 1005 1038 C2' U A 72 OK OK 1040 1036 1053 1039 1068 C2' A A 73 OK OK 1070 1066 1085 1069 1101 C2' C A 74 OK OK 1103 1099 1116 1102 1132 C2' A A 75 OK OK 1134 1130 1149 1133 1165 C2' G A 76 OK OK 1167 1163 1183 1166 1199 C2' G A 77 OK OK 1201 1197 1217 1200 1233 C2' C A 78 OK OK 1235 1231 1248 1234 1264 C2' C A 79 OK OK 1266 1262 1280 1265 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 259 C3' G A 41 OK OK 257 278 260 261 294 C3' G A 42 OK OK 292 313 295 296 328 C3' U A 43 OK OK 326 344 329 330 358 C3' C A 44 OK OK 356 374 359 360 389 C3' U A 45 OK OK 387 405 390 391 419 C3' G A 46 OK OK 417 438 420 421 453 C3' G A 47 OK OK 451 472 454 455 487 C3' G A 48 OK OK 485 506 488 489 521 C3' C A 49 OK OK 519 537 522 523 552 C3' G A 50 OK OK 550 571 553 554 586 C3' C A 51 OK OK 584 602 587 588 617 C3' A A 52 OK OK 615 635 618 619 650 C3' C A 54 OK OK 648 666 651 652 681 C3' U A 60 OK OK 679 697 682 683 711 C3' U A 61 OK OK 709 727 712 713 741 C3' C A 62 OK OK 739 757 742 743 772 C3' G A 63 OK OK 770 791 773 774 806 C3' G A 64 OK OK 804 825 807 808 840 C3' U A 66 OK OK 838 856 841 842 870 C3' G A 67 OK OK 868 889 871 872 904 C3' A A 68 OK OK 902 922 905 906 937 C3' C A 69 OK OK 935 953 938 939 968 C3' G A 70 OK OK 966 987 969 970 1002 C3' G A 71 OK OK 1000 1021 1003 1004 1036 C3' U A 72 OK OK 1034 1052 1037 1038 1066 C3' A A 73 OK OK 1064 1084 1067 1068 1099 C3' C A 74 OK OK 1097 1115 1100 1101 1130 C3' A A 75 OK OK 1128 1148 1131 1132 1163 C3' G A 76 OK OK 1161 1182 1164 1165 1197 C3' G A 77 OK OK 1195 1216 1198 1199 1231 C3' C A 78 OK OK 1229 1247 1232 1233 1262 C3' C A 79 OK OK 1260 1278 1263 1264 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 257 C4' G A 41 OK OK 259 277 256 258 292 C4' G A 42 OK OK 294 312 291 293 326 C4' U A 43 OK OK 328 343 325 327 356 C4' C A 44 OK OK 358 373 355 357 387 C4' U A 45 OK OK 389 404 386 388 417 C4' G A 46 OK OK 419 437 416 418 451 C4' G A 47 OK OK 453 471 450 452 485 C4' G A 48 OK OK 487 505 484 486 519 C4' C A 49 OK OK 521 536 518 520 550 C4' G A 50 OK OK 552 570 549 551 584 C4' C A 51 OK OK 586 601 583 585 615 C4' A A 52 OK OK 617 634 614 616 648 C4' C A 54 OK OK 650 665 647 649 679 C4' U A 60 OK OK 681 696 678 680 709 C4' U A 61 OK OK 711 726 708 710 739 C4' C A 62 OK OK 741 756 738 740 770 C4' G A 63 OK OK 772 790 769 771 804 C4' G A 64 OK OK 806 824 803 805 838 C4' U A 66 OK OK 840 855 837 839 868 C4' G A 67 OK OK 870 888 867 869 902 C4' A A 68 OK OK 904 921 901 903 935 C4' C A 69 OK OK 937 952 934 936 966 C4' G A 70 OK OK 968 986 965 967 1000 C4' G A 71 OK OK 1002 1020 999 1001 1034 C4' U A 72 OK OK 1036 1051 1033 1035 1064 C4' A A 73 OK OK 1066 1083 1063 1065 1097 C4' C A 74 OK OK 1099 1114 1096 1098 1128 C4' A A 75 OK OK 1130 1147 1127 1129 1161 C4' G A 76 OK OK 1163 1181 1160 1162 1195 C4' G A 77 OK OK 1197 1215 1194 1196 1229 C4' C A 78 OK OK 1231 1246 1228 1230 1260 C4' C A 79 OK OK 1262 1277 1259 1261 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 256 C5' G A 41 OK OK 255 275 276 257 291 C5' G A 42 OK OK 290 310 311 292 325 C5' U A 43 OK OK 324 341 342 326 355 C5' C A 44 OK OK 354 371 372 356 386 C5' U A 45 OK OK 385 402 403 387 416 C5' G A 46 OK OK 415 435 436 417 450 C5' G A 47 OK OK 449 469 470 451 484 C5' G A 48 OK OK 483 503 504 485 518 C5' C A 49 OK OK 517 534 535 519 549 C5' G A 50 OK OK 548 568 569 550 583 C5' C A 51 OK OK 582 599 600 584 614 C5' A A 52 OK OK 613 632 633 615 647 C5' C A 54 OK OK 646 663 664 648 678 C5' U A 60 OK OK 677 694 695 679 708 C5' U A 61 OK OK 707 724 725 709 738 C5' C A 62 OK OK 737 754 755 739 769 C5' G A 63 OK OK 768 788 789 770 803 C5' G A 64 OK OK 802 822 823 804 837 C5' U A 66 OK OK 836 853 854 838 867 C5' G A 67 OK OK 866 886 887 868 901 C5' A A 68 OK OK 900 919 920 902 934 C5' C A 69 OK OK 933 950 951 935 965 C5' G A 70 OK OK 964 984 985 966 999 C5' G A 71 OK OK 998 1018 1019 1000 1033 C5' U A 72 OK OK 1032 1049 1050 1034 1063 C5' A A 73 OK OK 1062 1081 1082 1064 1096 C5' C A 74 OK OK 1095 1112 1113 1097 1127 C5' A A 75 OK OK 1126 1145 1146 1128 1160 C5' G A 76 OK OK 1159 1179 1180 1161 1194 C5' G A 77 OK OK 1193 1213 1214 1195 1228 C5' C A 78 OK OK 1227 1244 1245 1229 1259 C5' C A 79 OK OK 1258 1275 1276 1260 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 287 P G A 42 distorted distorted 260 288 289 290 321 P U A 43 distorted distorted 295 322 323 324 351 P C A 44 distorted distorted 329 352 353 354 382 P U A 45 distorted distorted 359 383 384 385 412 P G A 46 distorted distorted 390 413 414 415 446 P G A 47 distorted distorted 420 447 448 449 480 P G A 48 distorted distorted 454 481 482 483 514 P C A 49 distorted distorted 488 515 516 517 545 P G A 50 distorted distorted 522 546 547 548 579 P C A 51 distorted distorted 553 580 581 582 610 P A A 52 distorted distorted 587 611 612 613 643 P C A 54 distorted distorted 618 644 645 646 674 P U A 60 distorted distorted 651 675 676 677 704 P U A 61 distorted distorted 682 705 706 707 734 P C A 62 distorted distorted 712 735 736 737 765 P G A 63 distorted distorted 742 766 767 768 799 P G A 64 distorted distorted 773 800 801 802 833 P U A 66 distorted distorted 807 834 835 836 863 P G A 67 distorted distorted 841 864 865 866 897 P A A 68 distorted distorted 871 898 899 900 930 P C A 69 distorted distorted 905 931 932 933 961 P G A 70 distorted distorted 938 962 963 964 995 P G A 71 distorted distorted 969 996 997 998 1029 P U A 72 distorted distorted 1003 1030 1031 1032 1059 P A A 73 distorted distorted 1037 1060 1061 1062 1092 P C A 74 distorted distorted 1067 1093 1094 1095 1123 P A A 75 distorted distorted 1100 1124 1125 1126 1156 P G A 76 distorted distorted 1131 1157 1158 1159 1190 P G A 77 distorted distorted 1164 1191 1192 1193 1224 P C A 78 distorted distorted 1198 1225 1226 1227 1255 P C A 79 distorted distorted 1232 1256 1257 1258 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