ID code: '5K7E' 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' C A 1 beta 7 13 10 32 C1' G A 2 beta 27 33 30 55 C1' U A 3 beta 50 56 53 75 C1' G A 4 beta 70 76 73 98 C1' G A 5 beta 93 99 96 121 C1' U A 6 beta 116 122 119 141 C1' U A 7 beta 136 142 139 161 C1' A A 8 beta 156 162 159 183 C1' G A 9 beta 178 184 181 206 C1' G A 10 beta 201 207 204 229 C1' G A 11 beta 224 230 227 252 C1' C A 12 beta 247 253 250 272 C1' C A 13 beta 267 273 270 292 C1' A A 14 beta 287 293 290 314 C1' C A 15 beta 309 315 312 334 C1' G A 16 beta 329 335 332 357 C1' U A 17 beta 352 358 355 377 C1' U A 18 beta 372 378 375 397 C1' A A 19 beta 392 398 395 419 C1' A A 20 beta 414 420 417 441 C1' A A 21 beta 436 442 439 463 C1' U A 22 beta 458 464 461 483 C1' A A 23 beta 478 484 481 505 C1' G A 24 beta 500 506 503 528 C1' U A 25 beta 523 529 526 548 C1' U A 26 beta 543 549 546 568 C1' G A 27 beta 563 569 566 591 C1' C A 28 beta 586 592 589 611 C1' U A 29 beta 606 612 609 631 C1' U A 30 beta 626 632 629 651 C1' A A 31 beta 646 652 649 673 C1' A A 32 beta 668 674 671 695 C1' G A 33 beta 690 696 693 718 C1' C A 34 beta 713 719 716 738 C1' C A 35 beta 733 739 736 758 C1' C A 36 beta 753 759 756 778 C1' U A 37 beta 773 779 776 798 C1' A A 38 beta 793 799 796 820 C1' A A 39 beta 815 821 818 842 C1' G A 40 beta 837 843 840 865 C1' C A 41 beta 860 866 863 885 C1' G A 42 beta 880 886 883 908 C1' U A 43 beta 903 909 906 928 C1' U A 44 beta 923 929 926 948 C1' G A 45 beta 943 949 946 971 C1' A A 46 beta 966 972 969 993 C1' U A 47 beta 988 994 991 1014 C1' A B 48 beta 1009 1015 1012 1036 C1' U B 49 beta 1031 1037 1034 1056 C1' C B 50 beta 1051 1057 1054 1076 C1' A B 51 beta 1071 1077 1074 1098 C1' G B 52 beta 1093 1099 1096 1120 C1' DG B 53 beta 1116 1121 1119 1143 C1' U B 54 beta 1138 1144 1141 1163 C1' G B 55 beta 1158 1164 1161 1186 C1' C B 56 beta 1181 1187 1184 1206 C1' A B 57 beta 1201 1207 1204 1228 C1' A B 58 beta 1223 1229 1226 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' C A 1 OK 12 8 11 30 C2' G A 2 OK 32 28 31 53 C2' U A 3 OK 55 51 54 73 C2' G A 4 OK 75 71 74 96 C2' G A 5 OK 98 94 97 119 C2' U A 6 OK 121 117 120 139 C2' U A 7 OK 141 137 140 159 C2' A A 8 OK 161 157 160 181 C2' G A 9 OK 183 179 182 204 C2' G A 10 OK 206 202 205 227 C2' G A 11 OK 229 225 228 250 C2' C A 12 OK 252 248 251 270 C2' C A 13 OK 272 268 271 290 C2' A A 14 OK 292 288 291 312 C2' C A 15 OK 314 310 313 332 C2' G A 16 OK 334 330 333 355 C2' U A 17 OK 357 353 356 375 C2' U A 18 OK 377 373 376 395 C2' A A 19 OK 397 393 396 417 C2' A A 20 OK 419 415 418 439 C2' A A 21 OK 441 437 440 461 C2' U A 22 OK 463 459 462 481 C2' A A 23 OK 483 479 482 503 C2' G A 24 OK 505 501 504 526 C2' U A 25 OK 528 524 527 546 C2' U A 26 OK 548 544 547 566 C2' G A 27 OK 568 564 567 589 C2' C A 28 OK 591 587 590 609 C2' U A 29 OK 611 607 610 629 C2' U A 30 OK 631 627 630 649 C2' A A 31 OK 651 647 650 671 C2' A A 32 OK 673 669 672 693 C2' G A 33 OK 695 691 694 716 C2' C A 34 OK 718 714 717 736 C2' C A 35 OK 738 734 737 756 C2' C A 36 OK 758 754 757 776 C2' U A 37 OK 778 774 777 796 C2' A A 38 OK 798 794 797 818 C2' A A 39 OK 820 816 819 840 C2' G A 40 OK 842 838 841 863 C2' C A 41 OK 865 861 864 883 C2' G A 42 OK 885 881 884 906 C2' U A 43 OK 908 904 907 926 C2' U A 44 OK 928 924 927 946 C2' G A 45 OK 948 944 947 969 C2' A A 46 OK 971 967 970 991 C2' U A 47 OK 993 989 992 1012 C2' A B 48 OK 1014 1010 1013 1034 C2' U B 49 OK 1036 1032 1035 1054 C2' C B 50 OK 1056 1052 1055 1074 C2' A B 51 OK 1076 1072 1075 1096 C2' G B 52 OK 1098 1094 1097 1119 C2' DG B 53 1120 1117 1141 C2' U B 54 OK 1143 1139 1142 1161 C2' G B 55 OK 1163 1159 1162 1184 C2' C B 56 OK 1186 1182 1185 1204 C2' A B 57 OK 1206 1202 1205 1226 C2' A B 58 OK 1228 1224 1227 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' C A 1 OK 6 9 10 28 C3' G A 2 OK 26 29 30 51 C3' U A 3 OK 49 52 53 71 C3' G A 4 OK 69 72 73 94 C3' G A 5 OK 92 95 96 117 C3' U A 6 OK 115 118 119 137 C3' U A 7 OK 135 138 139 157 C3' A A 8 OK 155 158 159 179 C3' G A 9 OK 177 180 181 202 C3' G A 10 OK 200 203 204 225 C3' G A 11 OK 223 226 227 248 C3' C A 12 OK 246 249 250 268 C3' C A 13 OK 266 269 270 288 C3' A A 14 OK 286 289 290 310 C3' C A 15 OK 308 311 312 330 C3' G A 16 OK 328 331 332 353 C3' U A 17 OK 351 354 355 373 C3' U A 18 OK 371 374 375 393 C3' A A 19 OK 391 394 395 415 C3' A A 20 OK 413 416 417 437 C3' A A 21 OK 435 438 439 459 C3' U A 22 OK 457 460 461 479 C3' A A 23 OK 477 480 481 501 C3' G A 24 OK 499 502 503 524 C3' U A 25 OK 522 525 526 544 C3' U A 26 OK 542 545 546 564 C3' G A 27 OK 562 565 566 587 C3' C A 28 OK 585 588 589 607 C3' U A 29 OK 605 608 609 627 C3' U A 30 OK 625 628 629 647 C3' A A 31 OK 645 648 649 669 C3' A A 32 OK 667 670 671 691 C3' G A 33 OK 689 692 693 714 C3' C A 34 OK 712 715 716 734 C3' C A 35 OK 732 735 736 754 C3' C A 36 OK 752 755 756 774 C3' U A 37 OK 772 775 776 794 C3' A A 38 OK 792 795 796 816 C3' A A 39 OK 814 817 818 838 C3' G A 40 OK 836 839 840 861 C3' C A 41 OK 859 862 863 881 C3' G A 42 OK 879 882 883 904 C3' U A 43 OK 902 905 906 924 C3' U A 44 OK 922 925 926 944 C3' G A 45 OK 942 945 946 967 C3' A A 46 OK 965 968 969 989 C3' U A 47 OK 987 990 991 1010 C3' A B 48 OK 1008 1011 1012 1032 C3' U B 49 OK 1030 1033 1034 1052 C3' C B 50 OK 1050 1053 1054 1072 C3' A B 51 OK 1070 1073 1074 1094 C3' G B 52 OK 1092 1095 1096 1117 C3' DG B 53 OK 1115 1118 1119 1139 C3' U B 54 OK 1137 1140 1141 1159 C3' G B 55 OK 1157 1160 1161 1182 C3' C B 56 OK 1180 1183 1184 1202 C3' A B 57 OK 1200 1203 1204 1224 C3' A B 58 OK 1222 1225 1226 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' C A 1 OK 8 5 7 26 C4' G A 2 OK 28 25 27 49 C4' U A 3 OK 51 48 50 69 C4' G A 4 OK 71 68 70 92 C4' G A 5 OK 94 91 93 115 C4' U A 6 OK 117 114 116 135 C4' U A 7 OK 137 134 136 155 C4' A A 8 OK 157 154 156 177 C4' G A 9 OK 179 176 178 200 C4' G A 10 OK 202 199 201 223 C4' G A 11 OK 225 222 224 246 C4' C A 12 OK 248 245 247 266 C4' C A 13 OK 268 265 267 286 C4' A A 14 OK 288 285 287 308 C4' C A 15 OK 310 307 309 328 C4' G A 16 OK 330 327 329 351 C4' U A 17 OK 353 350 352 371 C4' U A 18 OK 373 370 372 391 C4' A A 19 OK 393 390 392 413 C4' A A 20 OK 415 412 414 435 C4' A A 21 OK 437 434 436 457 C4' U A 22 OK 459 456 458 477 C4' A A 23 OK 479 476 478 499 C4' G A 24 OK 501 498 500 522 C4' U A 25 OK 524 521 523 542 C4' U A 26 OK 544 541 543 562 C4' G A 27 OK 564 561 563 585 C4' C A 28 OK 587 584 586 605 C4' U A 29 OK 607 604 606 625 C4' U A 30 OK 627 624 626 645 C4' A A 31 OK 647 644 646 667 C4' A A 32 OK 669 666 668 689 C4' G A 33 OK 691 688 690 712 C4' C A 34 OK 714 711 713 732 C4' C A 35 OK 734 731 733 752 C4' C A 36 OK 754 751 753 772 C4' U A 37 OK 774 771 773 792 C4' A A 38 OK 794 791 793 814 C4' A A 39 OK 816 813 815 836 C4' G A 40 OK 838 835 837 859 C4' C A 41 OK 861 858 860 879 C4' G A 42 OK 881 878 880 902 C4' U A 43 OK 904 901 903 922 C4' U A 44 OK 924 921 923 942 C4' G A 45 OK 944 941 943 965 C4' A A 46 OK 967 964 966 987 C4' U A 47 OK 989 986 988 1008 C4' A B 48 OK 1010 1007 1009 1030 C4' U B 49 OK 1032 1029 1031 1050 C4' C B 50 OK 1052 1049 1051 1070 C4' A B 51 OK 1072 1069 1071 1092 C4' G B 52 OK 1094 1091 1093 1115 C4' DG B 53 OK 1117 1114 1116 1137 C4' U B 54 OK 1139 1136 1138 1157 C4' G B 55 OK 1159 1156 1158 1180 C4' C B 56 OK 1182 1179 1181 1200 C4' A B 57 OK 1202 1199 1201 1222 C4' A B 58 OK 1224 1221 1223 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' C A 1 4 6 25 C5' G A 2 24 26 48 C5' U A 3 47 49 68 C5' G A 4 67 69 91 C5' G A 5 90 92 114 C5' U A 6 113 115 134 C5' U A 7 133 135 154 C5' A A 8 153 155 176 C5' G A 9 175 177 199 C5' G A 10 198 200 222 C5' G A 11 221 223 245 C5' C A 12 244 246 265 C5' C A 13 264 266 285 C5' A A 14 284 286 307 C5' C A 15 306 308 327 C5' G A 16 326 328 350 C5' U A 17 349 351 370 C5' U A 18 369 371 390 C5' A A 19 389 391 412 C5' A A 20 411 413 434 C5' A A 21 433 435 456 C5' U A 22 455 457 476 C5' A A 23 475 477 498 C5' G A 24 497 499 521 C5' U A 25 520 522 541 C5' U A 26 540 542 561 C5' G A 27 560 562 584 C5' C A 28 583 585 604 C5' U A 29 603 605 624 C5' U A 30 623 625 644 C5' A A 31 643 645 666 C5' A A 32 665 667 688 C5' G A 33 687 689 711 C5' C A 34 710 712 731 C5' C A 35 730 732 751 C5' C A 36 750 752 771 C5' U A 37 770 772 791 C5' A A 38 790 792 813 C5' A A 39 812 814 835 C5' G A 40 834 836 858 C5' C A 41 857 859 878 C5' G A 42 877 879 901 C5' U A 43 900 902 921 C5' U A 44 920 922 941 C5' G A 45 940 942 964 C5' A A 46 963 965 986 C5' U A 47 985 987 1007 C5' A B 48 1006 1008 1029 C5' U B 49 1028 1030 1049 C5' C B 50 1048 1050 1069 C5' A B 51 1068 1070 1091 C5' G B 52 1090 1092 1114 C5' DG B 53 1113 1115 1136 C5' U B 54 1135 1137 1156 C5' G B 55 1155 1157 1179 C5' C B 56 1178 1180 1199 C5' A B 57 1198 1200 1221 C5' A B 58 1220 1222 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P C A 1 OK OK 2 3 4 21 P G A 2 distorted distorted 9 22 23 24 44 P U A 3 distorted distorted 29 45 46 47 64 P G A 4 distorted distorted 52 65 66 67 87 P G A 5 distorted distorted 72 88 89 90 110 P U A 6 distorted distorted 95 111 112 113 130 P U A 7 distorted distorted 118 131 132 133 150 P A A 8 distorted distorted 138 151 152 153 172 P G A 9 distorted distorted 158 173 174 175 195 P G A 10 distorted distorted 180 196 197 198 218 P G A 11 distorted distorted 203 219 220 221 241 P C A 12 distorted distorted 226 242 243 244 261 P C A 13 distorted distorted 249 262 263 264 281 P A A 14 distorted distorted 269 282 283 284 303 P C A 15 distorted distorted 289 304 305 306 323 P G A 16 distorted distorted 311 324 325 326 346 P U A 17 distorted distorted 331 347 348 349 366 P U A 18 distorted distorted 354 367 368 369 386 P A A 19 distorted distorted 374 387 388 389 408 P A A 20 distorted distorted 394 409 410 411 430 P A A 21 distorted distorted 416 431 432 433 452 P U A 22 distorted distorted 438 453 454 455 472 P A A 23 distorted distorted 460 473 474 475 494 P G A 24 distorted distorted 480 495 496 497 517 P U A 25 distorted distorted 502 518 519 520 537 P U A 26 distorted distorted 525 538 539 540 557 P G A 27 distorted distorted 545 558 559 560 580 P C A 28 distorted distorted 565 581 582 583 600 P U A 29 distorted distorted 588 601 602 603 620 P U A 30 distorted distorted 608 621 622 623 640 P A A 31 distorted distorted 628 641 642 643 662 P A A 32 distorted distorted 648 663 664 665 684 P G A 33 distorted distorted 670 685 686 687 707 P C A 34 distorted distorted 692 708 709 710 727 P C A 35 distorted distorted 715 728 729 730 747 P C A 36 distorted distorted 735 748 749 750 767 P U A 37 distorted distorted 755 768 769 770 787 P A A 38 distorted distorted 775 788 789 790 809 P A A 39 distorted distorted 795 810 811 812 831 P G A 40 distorted distorted 817 832 833 834 854 P C A 41 distorted distorted 839 855 856 857 874 P G A 42 distorted distorted 862 875 876 877 897 P U A 43 distorted distorted 882 898 899 900 917 P U A 44 distorted distorted 905 918 919 920 937 P G A 45 distorted distorted 925 938 939 940 960 P A A 46 distorted distorted 945 961 962 963 982 P U A 47 distorted distorted 968 983 984 985 1003 P A B 48 OK OK 1004 1005 1006 1025 P U B 49 distorted distorted 1011 1026 1027 1028 1045 P C B 50 distorted distorted 1033 1046 1047 1048 1065 P A B 51 distorted distorted 1053 1066 1067 1068 1087 P G B 52 distorted distorted 1073 1088 1089 1090 1110 P DG B 53 distorted distorted 1095 1111 1112 1113 1132 P U B 54 distorted distorted 1118 1133 1134 1135 1152 P G B 55 distorted distorted 1140 1153 1154 1155 1175 P C B 56 distorted distorted 1160 1176 1177 1178 1195 P A B 57 distorted distorted 1183 1196 1197 1198 1217 P A B 58 distorted distorted 1203 1218 1219 1220 ---------------------------------------------------------------------------------