ID code: '2A04' 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 2 beta 4 10 7 32 C1' U A 3 beta 27 33 30 52 C1' G A 4 beta 47 53 50 75 C1' G A 5 beta 70 76 73 98 C1' U A 6 beta 93 99 96 118 C1' G A 7 beta 113 119 116 141 C1' A A 8 beta 136 142 139 163 C1' A A 9 beta 158 164 161 185 C1' G A 10 beta 180 186 183 208 C1' U A 11 beta 203 209 206 228 C1' C A 12 beta 223 229 226 248 C1' G A 13 beta 243 249 246 271 C1' C A 14 beta 266 272 269 291 C1' G A 15 beta 286 292 289 314 C1' G A 16 beta 309 315 312 335 C1' C B 21 beta 330 336 333 355 C1' G B 22 beta 350 356 353 378 C1' C B 23 beta 373 379 376 398 C1' G B 24 beta 393 399 396 421 C1' U B 25 beta 416 422 419 441 C1' C B 26 beta 436 442 439 461 C1' A B 27 beta 456 462 459 483 C1' C B 28 beta 478 484 481 503 C1' A B 29 beta 498 504 501 525 C1' C B 30 beta 520 526 523 545 C1' C B 31 beta 540 546 543 565 C1' A B 32 beta 560 566 563 587 C1' C B 33 beta 582 588 585 607 C1' C B 34 beta 602 608 605 625 C1' G C 2 beta 620 626 623 648 C1' U C 3 beta 643 649 646 668 C1' G C 4 beta 663 669 666 691 C1' G C 5 beta 686 692 689 714 C1' U C 6 beta 709 715 712 734 C1' G C 7 beta 729 735 732 757 C1' A C 8 beta 752 758 755 779 C1' A C 9 beta 774 780 777 801 C1' G C 10 beta 796 802 799 824 C1' U C 11 beta 819 825 822 844 C1' C C 12 beta 839 845 842 864 C1' G C 13 beta 859 865 862 887 C1' C C 14 beta 882 888 885 907 C1' G C 15 beta 902 908 905 930 C1' G C 16 beta 925 931 928 951 C1' C D 21 beta 946 952 949 971 C1' G D 22 beta 966 972 969 994 C1' C D 23 beta 989 995 992 1014 C1' G D 24 beta 1009 1015 1012 1037 C1' U D 25 beta 1032 1038 1035 1057 C1' C D 26 beta 1052 1058 1055 1077 C1' A D 27 beta 1072 1078 1075 1099 C1' C D 28 beta 1094 1100 1097 1119 C1' A D 29 beta 1114 1120 1117 1141 C1' C D 30 beta 1136 1142 1139 1161 C1' C D 31 beta 1156 1162 1159 1181 C1' A D 32 beta 1176 1182 1179 1203 C1' C D 33 beta 1198 1204 1201 1223 C1' C D 34 beta 1218 1224 1221 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G A 2 OK 9 5 8 30 C2' U A 3 OK 32 28 31 50 C2' G A 4 OK 52 48 51 73 C2' G A 5 OK 75 71 74 96 C2' U A 6 OK 98 94 97 116 C2' G A 7 OK 118 114 117 139 C2' A A 8 OK 141 137 140 161 C2' A A 9 OK 163 159 162 183 C2' G A 10 OK 185 181 184 206 C2' U A 11 OK 208 204 207 226 C2' C A 12 OK 228 224 227 246 C2' G A 13 OK 248 244 247 269 C2' C A 14 OK 271 267 270 289 C2' G A 15 OK 291 287 290 312 C2' G A 16 OK 314 310 313 333 C2' C B 21 OK 335 331 334 353 C2' G B 22 OK 355 351 354 376 C2' C B 23 OK 378 374 377 396 C2' G B 24 OK 398 394 397 419 C2' U B 25 OK 421 417 420 439 C2' C B 26 OK 441 437 440 459 C2' A B 27 OK 461 457 460 481 C2' C B 28 OK 483 479 482 501 C2' A B 29 OK 503 499 502 523 C2' C B 30 OK 525 521 524 543 C2' C B 31 OK 545 541 544 563 C2' A B 32 OK 565 561 564 585 C2' C B 33 OK 587 583 586 605 C2' C B 34 OK 607 603 606 623 C2' G C 2 OK 625 621 624 646 C2' U C 3 OK 648 644 647 666 C2' G C 4 OK 668 664 667 689 C2' G C 5 OK 691 687 690 712 C2' U C 6 OK 714 710 713 732 C2' G C 7 OK 734 730 733 755 C2' A C 8 OK 757 753 756 777 C2' A C 9 OK 779 775 778 799 C2' G C 10 OK 801 797 800 822 C2' U C 11 OK 824 820 823 842 C2' C C 12 OK 844 840 843 862 C2' G C 13 OK 864 860 863 885 C2' C C 14 OK 887 883 886 905 C2' G C 15 OK 907 903 906 928 C2' G C 16 OK 930 926 929 949 C2' C D 21 OK 951 947 950 969 C2' G D 22 OK 971 967 970 992 C2' C D 23 OK 994 990 993 1012 C2' G D 24 OK 1014 1010 1013 1035 C2' U D 25 OK 1037 1033 1036 1055 C2' C D 26 OK 1057 1053 1056 1075 C2' A D 27 OK 1077 1073 1076 1097 C2' C D 28 OK 1099 1095 1098 1117 C2' A D 29 OK 1119 1115 1118 1139 C2' C D 30 OK 1141 1137 1140 1159 C2' C D 31 OK 1161 1157 1160 1179 C2' A D 32 OK 1181 1177 1180 1201 C2' C D 33 OK 1203 1199 1202 1221 C2' C D 34 OK 1223 1219 1222 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 2 OK 3 6 7 28 C3' U A 3 OK 26 29 30 48 C3' G A 4 OK 46 49 50 71 C3' G A 5 OK 69 72 73 94 C3' U A 6 OK 92 95 96 114 C3' G A 7 OK 112 115 116 137 C3' A A 8 OK 135 138 139 159 C3' A A 9 OK 157 160 161 181 C3' G A 10 OK 179 182 183 204 C3' U A 11 OK 202 205 206 224 C3' C A 12 OK 222 225 226 244 C3' G A 13 OK 242 245 246 267 C3' C A 14 OK 265 268 269 287 C3' G A 15 OK 285 288 289 310 C3' G A 16 OK 308 311 312 331 C3' C B 21 OK 329 332 333 351 C3' G B 22 OK 349 352 353 374 C3' C B 23 OK 372 375 376 394 C3' G B 24 OK 392 395 396 417 C3' U B 25 OK 415 418 419 437 C3' C B 26 OK 435 438 439 457 C3' A B 27 OK 455 458 459 479 C3' C B 28 OK 477 480 481 499 C3' A B 29 OK 497 500 501 521 C3' C B 30 OK 519 522 523 541 C3' C B 31 OK 539 542 543 561 C3' A B 32 OK 559 562 563 583 C3' C B 33 OK 581 584 585 603 C3' C B 34 OK 601 604 605 621 C3' G C 2 OK 619 622 623 644 C3' U C 3 OK 642 645 646 664 C3' G C 4 OK 662 665 666 687 C3' G C 5 OK 685 688 689 710 C3' U C 6 OK 708 711 712 730 C3' G C 7 OK 728 731 732 753 C3' A C 8 OK 751 754 755 775 C3' A C 9 OK 773 776 777 797 C3' G C 10 OK 795 798 799 820 C3' U C 11 OK 818 821 822 840 C3' C C 12 OK 838 841 842 860 C3' G C 13 OK 858 861 862 883 C3' C C 14 OK 881 884 885 903 C3' G C 15 OK 901 904 905 926 C3' G C 16 OK 924 927 928 947 C3' C D 21 OK 945 948 949 967 C3' G D 22 OK 965 968 969 990 C3' C D 23 OK 988 991 992 1010 C3' G D 24 OK 1008 1011 1012 1033 C3' U D 25 OK 1031 1034 1035 1053 C3' C D 26 OK 1051 1054 1055 1073 C3' A D 27 OK 1071 1074 1075 1095 C3' C D 28 OK 1093 1096 1097 1115 C3' A D 29 OK 1113 1116 1117 1137 C3' C D 30 OK 1135 1138 1139 1157 C3' C D 31 OK 1155 1158 1159 1177 C3' A D 32 OK 1175 1178 1179 1199 C3' C D 33 OK 1197 1200 1201 1219 C3' C D 34 OK 1217 1220 1221 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 2 OK 5 2 4 26 C4' U A 3 OK 28 25 27 46 C4' G A 4 OK 48 45 47 69 C4' G A 5 OK 71 68 70 92 C4' U A 6 OK 94 91 93 112 C4' G A 7 OK 114 111 113 135 C4' A A 8 OK 137 134 136 157 C4' A A 9 OK 159 156 158 179 C4' G A 10 OK 181 178 180 202 C4' U A 11 OK 204 201 203 222 C4' C A 12 OK 224 221 223 242 C4' G A 13 OK 244 241 243 265 C4' C A 14 OK 267 264 266 285 C4' G A 15 OK 287 284 286 308 C4' G A 16 OK 310 307 309 329 C4' C B 21 OK 331 328 330 349 C4' G B 22 OK 351 348 350 372 C4' C B 23 OK 374 371 373 392 C4' G B 24 OK 394 391 393 415 C4' U B 25 OK 417 414 416 435 C4' C B 26 OK 437 434 436 455 C4' A B 27 OK 457 454 456 477 C4' C B 28 OK 479 476 478 497 C4' A B 29 OK 499 496 498 519 C4' C B 30 OK 521 518 520 539 C4' C B 31 OK 541 538 540 559 C4' A B 32 OK 561 558 560 581 C4' C B 33 OK 583 580 582 601 C4' C B 34 OK 603 600 602 619 C4' G C 2 OK 621 618 620 642 C4' U C 3 OK 644 641 643 662 C4' G C 4 OK 664 661 663 685 C4' G C 5 OK 687 684 686 708 C4' U C 6 OK 710 707 709 728 C4' G C 7 OK 730 727 729 751 C4' A C 8 OK 753 750 752 773 C4' A C 9 OK 775 772 774 795 C4' G C 10 OK 797 794 796 818 C4' U C 11 OK 820 817 819 838 C4' C C 12 OK 840 837 839 858 C4' G C 13 OK 860 857 859 881 C4' C C 14 OK 883 880 882 901 C4' G C 15 OK 903 900 902 924 C4' G C 16 OK 926 923 925 945 C4' C D 21 OK 947 944 946 965 C4' G D 22 OK 967 964 966 988 C4' C D 23 OK 990 987 989 1008 C4' G D 24 OK 1010 1007 1009 1031 C4' U D 25 OK 1033 1030 1032 1051 C4' C D 26 OK 1053 1050 1052 1071 C4' A D 27 OK 1073 1070 1072 1093 C4' C D 28 OK 1095 1092 1094 1113 C4' A D 29 OK 1115 1112 1114 1135 C4' C D 30 OK 1137 1134 1136 1155 C4' C D 31 OK 1157 1154 1156 1175 C4' A D 32 OK 1177 1174 1176 1197 C4' C D 33 OK 1199 1196 1198 1217 C4' C D 34 OK 1219 1216 1218 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 2 1 3 25 C5' U A 3 24 26 45 C5' G A 4 44 46 68 C5' G A 5 67 69 91 C5' U A 6 90 92 111 C5' G A 7 110 112 134 C5' A A 8 133 135 156 C5' A A 9 155 157 178 C5' G A 10 177 179 201 C5' U A 11 200 202 221 C5' C A 12 220 222 241 C5' G A 13 240 242 264 C5' C A 14 263 265 284 C5' G A 15 283 285 307 C5' G A 16 306 308 328 C5' C B 21 327 329 348 C5' G B 22 347 349 371 C5' C B 23 370 372 391 C5' G B 24 390 392 414 C5' U B 25 413 415 434 C5' C B 26 433 435 454 C5' A B 27 453 455 476 C5' C B 28 475 477 496 C5' A B 29 495 497 518 C5' C B 30 517 519 538 C5' C B 31 537 539 558 C5' A B 32 557 559 580 C5' C B 33 579 581 600 C5' C B 34 599 601 618 C5' G C 2 617 619 641 C5' U C 3 640 642 661 C5' G C 4 660 662 684 C5' G C 5 683 685 707 C5' U C 6 706 708 727 C5' G C 7 726 728 750 C5' A C 8 749 751 772 C5' A C 9 771 773 794 C5' G C 10 793 795 817 C5' U C 11 816 818 837 C5' C C 12 836 838 857 C5' G C 13 856 858 880 C5' C C 14 879 881 900 C5' G C 15 899 901 923 C5' G C 16 922 924 944 C5' C D 21 943 945 964 C5' G D 22 963 965 987 C5' C D 23 986 988 1007 C5' G D 24 1006 1008 1030 C5' U D 25 1029 1031 1050 C5' C D 26 1049 1051 1070 C5' A D 27 1069 1071 1092 C5' C D 28 1091 1093 1112 C5' A D 29 1111 1113 1134 C5' C D 30 1133 1135 1154 C5' C D 31 1153 1155 1174 C5' A D 32 1173 1175 1196 C5' C D 33 1195 1197 1216 C5' C D 34 1215 1217 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 21 P U A 3 distorted distorted 6 22 23 24 41 P G A 4 distorted distorted 29 42 43 44 64 P G A 5 distorted distorted 49 65 66 67 87 P U A 6 distorted distorted 72 88 89 90 107 P G A 7 distorted distorted 95 108 109 110 130 P A A 8 distorted distorted 115 131 132 133 152 P A A 9 distorted distorted 138 153 154 155 174 P G A 10 distorted distorted 160 175 176 177 197 P U A 11 distorted distorted 182 198 199 200 217 P C A 12 distorted distorted 205 218 219 220 237 P G A 13 distorted distorted 225 238 239 240 260 P C A 14 distorted distorted 245 261 262 263 280 P G A 15 distorted distorted 268 281 282 283 303 P G A 16 distorted distorted 288 304 305 306 344 P G B 22 distorted distorted 332 345 346 347 367 P C B 23 distorted distorted 352 368 369 370 387 P G B 24 distorted distorted 375 388 389 390 410 P U B 25 distorted distorted 395 411 412 413 430 P C B 26 distorted distorted 418 431 432 433 450 P A B 27 distorted distorted 438 451 452 453 472 P C B 28 distorted distorted 458 473 474 475 492 P A B 29 distorted distorted 480 493 494 495 514 P C B 30 distorted distorted 500 515 516 517 534 P C B 31 distorted distorted 522 535 536 537 554 P A B 32 distorted distorted 542 555 556 557 576 P C B 33 distorted distorted 562 577 578 579 596 P C B 34 distorted distorted 584 597 598 599 637 P U C 3 distorted distorted 622 638 639 640 657 P G C 4 distorted distorted 645 658 659 660 680 P G C 5 distorted distorted 665 681 682 683 703 P U C 6 distorted distorted 688 704 705 706 723 P G C 7 distorted distorted 711 724 725 726 746 P A C 8 distorted distorted 731 747 748 749 768 P A C 9 distorted distorted 754 769 770 771 790 P G C 10 distorted distorted 776 791 792 793 813 P U C 11 distorted distorted 798 814 815 816 833 P C C 12 distorted distorted 821 834 835 836 853 P G C 13 distorted distorted 841 854 855 856 876 P C C 14 distorted distorted 861 877 878 879 896 P G C 15 distorted distorted 884 897 898 899 919 P G C 16 distorted distorted 904 920 921 922 960 P G D 22 distorted distorted 948 961 962 963 983 P C D 23 distorted distorted 968 984 985 986 1003 P G D 24 distorted distorted 991 1004 1005 1006 1026 P U D 25 distorted distorted 1011 1027 1028 1029 1046 P C D 26 distorted distorted 1034 1047 1048 1049 1066 P A D 27 distorted distorted 1054 1067 1068 1069 1088 P C D 28 distorted distorted 1074 1089 1090 1091 1108 P A D 29 distorted distorted 1096 1109 1110 1111 1130 P C D 30 distorted distorted 1116 1131 1132 1133 1150 P C D 31 distorted distorted 1138 1151 1152 1153 1170 P A D 32 distorted distorted 1158 1171 1172 1173 1192 P C D 33 distorted distorted 1178 1193 1194 1195 1212 P C D 34 distorted distorted 1200 1213 1214 1215 ---------------------------------------------------------------------------------