ID code: '5CKI' 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' --------------------------------------------------------------------------------- 12 C1' G D -6 beta 7 13 10 35 C1' C D -5 beta 30 36 33 55 C1' A D -4 beta 50 56 53 77 C1' C D -3 beta 72 78 75 97 C1' U D -2 beta 92 98 95 117 C1' A D -1 beta 112 118 115 139 C1' G D 1 beta 134 140 137 162 C1' A D 2 beta 157 163 160 184 C1' U D 3 beta 179 185 182 204 C1' C D 4 beta 199 205 202 224 C1' G D 5 beta 219 225 222 247 C1' G D 6 beta 242 248 245 270 C1' A D 7 beta 265 271 268 292 C1' U D 8 beta 287 293 290 312 C1' G D 9 beta 307 313 310 335 C1' DA Y 1 beta 331 336 334 356 C1' DT Y 2 beta 352 357 355 376 C1' DC Y 3 beta 372 377 375 395 C1' DC Y 4 beta 391 396 394 414 C1' DG Y 5 beta 410 415 413 436 C1' DA Y 6 beta 432 437 435 457 C1' DT Y 7 beta 453 458 456 477 C1' DG Y 8 beta 473 478 476 499 C1' DG Y 9 beta 495 500 498 521 C1' DA Y 10 beta 517 522 520 542 C1' DT Y 11 beta 538 543 541 562 C1' DC Y 12 beta 558 563 561 581 C1' DA Y 13 beta 577 582 580 602 C1' DT Y 14 beta 598 603 601 622 C1' DA Y 15 beta 618 623 621 643 C1' DC Y 16 beta 639 644 642 662 C1' DG Y 17 beta 658 663 661 684 C1' DG Y 18 beta 680 685 683 706 C1' DT Y 19 beta 702 707 705 726 C1' DC Y 20 beta 722 727 725 745 C1' DG Y 21 beta 741 746 744 767 C1' DG Y 22 beta 763 768 766 789 C1' DA Y 23 beta 785 790 788 810 C1' DG Y 24 beta 806 811 809 832 C1' DG Y 25 beta 828 833 831 854 C1' DG Y 26 beta 850 855 853 876 C1' DG Y 27 beta 872 877 875 898 C1' DT Y 28 beta 894 899 897 918 C1' DT Y 29 beta 914 919 917 938 C1' DT Y 30 beta 934 939 937 958 C1' DG Y 31 beta 954 959 957 980 C1' DC Y 32 beta 976 981 979 999 C1' DC Y 33 beta 995 1000 998 1018 C1' DG Y 34 beta 1014 1019 1017 1040 C1' DT Y 35 beta 1036 1041 1039 1060 C1' DT Y 36 beta 1056 1061 1059 1080 C1' DT Y 37 beta 1076 1081 1079 1100 C1' DA Y 38 beta 1096 1101 1099 1121 C1' DA Y 39 beta 1117 1122 1120 1142 C1' DG Y 40 beta 1138 1143 1141 1164 C1' DT Y 41 beta 1160 1165 1163 1184 C1' DG Y 42 beta 1180 1185 1183 1206 C1' DC Y 43 beta 1202 1207 1205 1225 C1' DC Y 44 beta 1221 1226 1224 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' G D -6 OK 12 8 11 33 C2' C D -5 OK 35 31 34 53 C2' A D -4 OK 55 51 54 75 C2' C D -3 OK 77 73 76 95 C2' U D -2 OK 97 93 96 115 C2' A D -1 OK 117 113 116 137 C2' G D 1 OK 139 135 138 160 C2' A D 2 OK 162 158 161 182 C2' U D 3 OK 184 180 183 202 C2' C D 4 OK 204 200 203 222 C2' G D 5 OK 224 220 223 245 C2' G D 6 OK 247 243 246 268 C2' A D 7 OK 270 266 269 290 C2' U D 8 OK 292 288 291 310 C2' G D 9 OK 312 308 311 334 C2' DA Y 1 335 332 355 C2' DT Y 2 356 353 375 C2' DC Y 3 376 373 394 C2' DC Y 4 395 392 413 C2' DG Y 5 414 411 435 C2' DA Y 6 436 433 456 C2' DT Y 7 457 454 476 C2' DG Y 8 477 474 498 C2' DG Y 9 499 496 520 C2' DA Y 10 521 518 541 C2' DT Y 11 542 539 561 C2' DC Y 12 562 559 580 C2' DA Y 13 581 578 601 C2' DT Y 14 602 599 621 C2' DA Y 15 622 619 642 C2' DC Y 16 643 640 661 C2' DG Y 17 662 659 683 C2' DG Y 18 684 681 705 C2' DT Y 19 706 703 725 C2' DC Y 20 726 723 744 C2' DG Y 21 745 742 766 C2' DG Y 22 767 764 788 C2' DA Y 23 789 786 809 C2' DG Y 24 810 807 831 C2' DG Y 25 832 829 853 C2' DG Y 26 854 851 875 C2' DG Y 27 876 873 897 C2' DT Y 28 898 895 917 C2' DT Y 29 918 915 937 C2' DT Y 30 938 935 957 C2' DG Y 31 958 955 979 C2' DC Y 32 980 977 998 C2' DC Y 33 999 996 1017 C2' DG Y 34 1018 1015 1039 C2' DT Y 35 1040 1037 1059 C2' DT Y 36 1060 1057 1079 C2' DT Y 37 1080 1077 1099 C2' DA Y 38 1100 1097 1120 C2' DA Y 39 1121 1118 1141 C2' DG Y 40 1142 1139 1163 C2' DT Y 41 1164 1161 1183 C2' DG Y 42 1184 1181 1205 C2' DC Y 43 1206 1203 1224 C2' DC Y 44 1225 1222 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' G D -6 OK 6 9 10 31 C3' C D -5 OK 29 32 33 51 C3' A D -4 OK 49 52 53 73 C3' C D -3 OK 71 74 75 93 C3' U D -2 OK 91 94 95 113 C3' A D -1 OK 111 114 115 135 C3' G D 1 OK 133 136 137 158 C3' A D 2 OK 156 159 160 180 C3' U D 3 OK 178 181 182 200 C3' C D 4 OK 198 201 202 220 C3' G D 5 OK 218 221 222 243 C3' G D 6 OK 241 244 245 266 C3' A D 7 OK 264 267 268 288 C3' U D 8 OK 286 289 290 308 C3' G D 9 OK 306 309 310 332 C3' DA Y 1 OK 330 333 334 353 C3' DT Y 2 OK 351 354 355 373 C3' DC Y 3 OK 371 374 375 392 C3' DC Y 4 OK 390 393 394 411 C3' DG Y 5 OK 409 412 413 433 C3' DA Y 6 OK 431 434 435 454 C3' DT Y 7 OK 452 455 456 474 C3' DG Y 8 OK 472 475 476 496 C3' DG Y 9 OK 494 497 498 518 C3' DA Y 10 OK 516 519 520 539 C3' DT Y 11 OK 537 540 541 559 C3' DC Y 12 OK 557 560 561 578 C3' DA Y 13 OK 576 579 580 599 C3' DT Y 14 OK 597 600 601 619 C3' DA Y 15 OK 617 620 621 640 C3' DC Y 16 OK 638 641 642 659 C3' DG Y 17 OK 657 660 661 681 C3' DG Y 18 OK 679 682 683 703 C3' DT Y 19 OK 701 704 705 723 C3' DC Y 20 OK 721 724 725 742 C3' DG Y 21 OK 740 743 744 764 C3' DG Y 22 OK 762 765 766 786 C3' DA Y 23 OK 784 787 788 807 C3' DG Y 24 OK 805 808 809 829 C3' DG Y 25 OK 827 830 831 851 C3' DG Y 26 OK 849 852 853 873 C3' DG Y 27 OK 871 874 875 895 C3' DT Y 28 OK 893 896 897 915 C3' DT Y 29 OK 913 916 917 935 C3' DT Y 30 OK 933 936 937 955 C3' DG Y 31 OK 953 956 957 977 C3' DC Y 32 OK 975 978 979 996 C3' DC Y 33 OK 994 997 998 1015 C3' DG Y 34 OK 1013 1016 1017 1037 C3' DT Y 35 OK 1035 1038 1039 1057 C3' DT Y 36 OK 1055 1058 1059 1077 C3' DT Y 37 OK 1075 1078 1079 1097 C3' DA Y 38 OK 1095 1098 1099 1118 C3' DA Y 39 OK 1116 1119 1120 1139 C3' DG Y 40 OK 1137 1140 1141 1161 C3' DT Y 41 OK 1159 1162 1163 1181 C3' DG Y 42 OK 1179 1182 1183 1203 C3' DC Y 43 OK 1201 1204 1205 1222 C3' DC Y 44 OK 1220 1223 1224 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' G D -6 OK 8 5 7 29 C4' C D -5 OK 31 28 30 49 C4' A D -4 OK 51 48 50 71 C4' C D -3 OK 73 70 72 91 C4' U D -2 OK 93 90 92 111 C4' A D -1 OK 113 110 112 133 C4' G D 1 OK 135 132 134 156 C4' A D 2 OK 158 155 157 178 C4' U D 3 OK 180 177 179 198 C4' C D 4 OK 200 197 199 218 C4' G D 5 OK 220 217 219 241 C4' G D 6 OK 243 240 242 264 C4' A D 7 OK 266 263 265 286 C4' U D 8 OK 288 285 287 306 C4' G D 9 OK 308 305 307 330 C4' DA Y 1 OK 332 329 331 351 C4' DT Y 2 OK 353 350 352 371 C4' DC Y 3 OK 373 370 372 390 C4' DC Y 4 OK 392 389 391 409 C4' DG Y 5 OK 411 408 410 431 C4' DA Y 6 OK 433 430 432 452 C4' DT Y 7 OK 454 451 453 472 C4' DG Y 8 OK 474 471 473 494 C4' DG Y 9 OK 496 493 495 516 C4' DA Y 10 OK 518 515 517 537 C4' DT Y 11 OK 539 536 538 557 C4' DC Y 12 OK 559 556 558 576 C4' DA Y 13 OK 578 575 577 597 C4' DT Y 14 OK 599 596 598 617 C4' DA Y 15 OK 619 616 618 638 C4' DC Y 16 OK 640 637 639 657 C4' DG Y 17 OK 659 656 658 679 C4' DG Y 18 OK 681 678 680 701 C4' DT Y 19 OK 703 700 702 721 C4' DC Y 20 OK 723 720 722 740 C4' DG Y 21 OK 742 739 741 762 C4' DG Y 22 OK 764 761 763 784 C4' DA Y 23 OK 786 783 785 805 C4' DG Y 24 OK 807 804 806 827 C4' DG Y 25 OK 829 826 828 849 C4' DG Y 26 OK 851 848 850 871 C4' DG Y 27 OK 873 870 872 893 C4' DT Y 28 OK 895 892 894 913 C4' DT Y 29 OK 915 912 914 933 C4' DT Y 30 OK 935 932 934 953 C4' DG Y 31 OK 955 952 954 975 C4' DC Y 32 OK 977 974 976 994 C4' DC Y 33 OK 996 993 995 1013 C4' DG Y 34 OK 1015 1012 1014 1035 C4' DT Y 35 OK 1037 1034 1036 1055 C4' DT Y 36 OK 1057 1054 1056 1075 C4' DT Y 37 OK 1077 1074 1076 1095 C4' DA Y 38 OK 1097 1094 1096 1116 C4' DA Y 39 OK 1118 1115 1117 1137 C4' DG Y 40 OK 1139 1136 1138 1159 C4' DT Y 41 OK 1161 1158 1160 1179 C4' DG Y 42 OK 1181 1178 1180 1201 C4' DC Y 43 OK 1203 1200 1202 1220 C4' DC Y 44 OK 1222 1219 1221 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' G D -6 4 6 28 C5' C D -5 27 29 48 C5' A D -4 47 49 70 C5' C D -3 69 71 90 C5' U D -2 89 91 110 C5' A D -1 109 111 132 C5' G D 1 131 133 155 C5' A D 2 154 156 177 C5' U D 3 176 178 197 C5' C D 4 196 198 217 C5' G D 5 216 218 240 C5' G D 6 239 241 263 C5' A D 7 262 264 285 C5' U D 8 284 286 305 C5' G D 9 304 306 329 C5' DA Y 1 328 330 350 C5' DT Y 2 349 351 370 C5' DC Y 3 369 371 389 C5' DC Y 4 388 390 408 C5' DG Y 5 407 409 430 C5' DA Y 6 429 431 451 C5' DT Y 7 450 452 471 C5' DG Y 8 470 472 493 C5' DG Y 9 492 494 515 C5' DA Y 10 514 516 536 C5' DT Y 11 535 537 556 C5' DC Y 12 555 557 575 C5' DA Y 13 574 576 596 C5' DT Y 14 595 597 616 C5' DA Y 15 615 617 637 C5' DC Y 16 636 638 656 C5' DG Y 17 655 657 678 C5' DG Y 18 677 679 700 C5' DT Y 19 699 701 720 C5' DC Y 20 719 721 739 C5' DG Y 21 738 740 761 C5' DG Y 22 760 762 783 C5' DA Y 23 782 784 804 C5' DG Y 24 803 805 826 C5' DG Y 25 825 827 848 C5' DG Y 26 847 849 870 C5' DG Y 27 869 871 892 C5' DT Y 28 891 893 912 C5' DT Y 29 911 913 932 C5' DT Y 30 931 933 952 C5' DG Y 31 951 953 974 C5' DC Y 32 973 975 993 C5' DC Y 33 992 994 1012 C5' DG Y 34 1011 1013 1034 C5' DT Y 35 1033 1035 1054 C5' DT Y 36 1053 1055 1074 C5' DT Y 37 1073 1075 1094 C5' DA Y 38 1093 1095 1115 C5' DA Y 39 1114 1116 1136 C5' DG Y 40 1135 1137 1158 C5' DT Y 41 1157 1159 1178 C5' DG Y 42 1177 1179 1200 C5' DC Y 43 1199 1201 1219 C5' DC Y 44 1218 1220 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P G D -6 distorted distorted 2 3 4 24 P C D -5 distorted distorted 9 25 26 27 44 P A D -4 distorted distorted 32 45 46 47 66 P C D -3 distorted distorted 52 67 68 69 86 P U D -2 distorted distorted 74 87 88 89 106 P A D -1 distorted distorted 94 107 108 109 128 P G D 1 distorted distorted 114 129 130 131 151 P A D 2 distorted distorted 136 152 153 154 173 P U D 3 distorted distorted 159 174 175 176 193 P C D 4 distorted distorted 181 194 195 196 213 P G D 5 distorted distorted 201 214 215 216 236 P G D 6 distorted distorted 221 237 238 239 259 P A D 7 distorted distorted 244 260 261 262 281 P U D 8 distorted distorted 267 282 283 284 301 P G D 9 distorted distorted 289 302 303 304 325 P DA Y 1 distorted distorted 326 327 328 346 P DT Y 2 distorted distorted 333 347 348 349 366 P DC Y 3 distorted distorted 354 367 368 369 385 P DC Y 4 distorted distorted 374 386 387 388 404 P DG Y 5 distorted distorted 393 405 406 407 426 P DA Y 6 distorted distorted 412 427 428 429 447 P DT Y 7 distorted distorted 434 448 449 450 467 P DG Y 8 distorted distorted 455 468 469 470 489 P DG Y 9 distorted distorted 475 490 491 492 511 P DA Y 10 distorted distorted 497 512 513 514 532 P DT Y 11 distorted distorted 519 533 534 535 552 P DC Y 12 distorted distorted 540 553 554 555 571 P DA Y 13 distorted distorted 560 572 573 574 592 P DT Y 14 distorted distorted 579 593 594 595 612 P DA Y 15 distorted distorted 600 613 614 615 633 P DC Y 16 distorted distorted 620 634 635 636 652 P DG Y 17 distorted distorted 641 653 654 655 674 P DG Y 18 distorted distorted 660 675 676 677 696 P DT Y 19 distorted distorted 682 697 698 699 716 P DC Y 20 distorted distorted 704 717 718 719 735 P DG Y 21 distorted distorted 724 736 737 738 757 P DG Y 22 distorted distorted 743 758 759 760 779 P DA Y 23 distorted distorted 765 780 781 782 800 P DG Y 24 distorted distorted 787 801 802 803 822 P DG Y 25 distorted distorted 808 823 824 825 844 P DG Y 26 distorted distorted 830 845 846 847 866 P DG Y 27 distorted distorted 852 867 868 869 888 P DT Y 28 distorted distorted 874 889 890 891 908 P DT Y 29 distorted distorted 896 909 910 911 928 P DT Y 30 distorted distorted 916 929 930 931 948 P DG Y 31 distorted distorted 936 949 950 951 970 P DC Y 32 distorted distorted 956 971 972 973 989 P DC Y 33 distorted distorted 978 990 991 992 1008 P DG Y 34 distorted distorted 997 1009 1010 1011 1030 P DT Y 35 distorted distorted 1016 1031 1032 1033 1050 P DT Y 36 distorted distorted 1038 1051 1052 1053 1070 P DT Y 37 distorted distorted 1058 1071 1072 1073 1090 P DA Y 38 distorted distorted 1078 1091 1092 1093 1111 P DA Y 39 distorted distorted 1098 1112 1113 1114 1132 P DG Y 40 distorted distorted 1119 1133 1134 1135 1154 P DT Y 41 distorted distorted 1140 1155 1156 1157 1174 P DG Y 42 distorted distorted 1162 1175 1176 1177 1196 P DC Y 43 distorted distorted 1182 1197 1198 1199 1215 P DC Y 44 distorted distorted 1204 1216 1217 1218 ---------------------------------------------------------------------------------