ID code: '2NUF' 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' --------------------------------------------------------------------------------- 13 C1' C C 1 beta 8 14 11 33 C1' A C 2 beta 28 34 31 55 C1' A C 3 beta 50 56 53 77 C1' G C 4 beta 72 78 75 100 C1' G C 5 beta 95 101 98 123 C1' U C 6 beta 118 124 121 143 C1' C C 7 beta 138 144 141 163 C1' A C 8 beta 158 164 161 185 C1' U C 9 beta 180 186 183 205 C1' U C 10 beta 200 206 203 225 C1' C C 11 beta 220 226 223 245 C1' G C 12 beta 240 246 243 268 C1' C C 13 beta 263 269 266 288 C1' A C 14 beta 283 289 286 310 C1' A C 15 beta 305 311 308 332 C1' G C 16 beta 327 333 330 355 C1' A C 17 beta 350 356 353 377 C1' G C 18 beta 372 378 375 400 C1' U C 19 beta 395 401 398 420 C1' G C 20 beta 415 421 418 443 C1' G C 21 beta 438 444 441 466 C1' C C 22 beta 461 467 464 486 C1' C C 23 beta 481 487 484 506 C1' U C 24 beta 501 507 504 526 C1' U C 25 beta 521 527 524 546 C1' G C 26 beta 541 547 544 569 C1' C C 27 beta 564 570 567 589 C1' G C 28 beta 584 590 587 614 C1' C D 1 beta 609 615 612 634 C1' A D 2 beta 629 635 632 656 C1' A D 3 beta 651 657 654 678 C1' G D 4 beta 673 679 676 701 C1' G D 5 beta 696 702 699 724 C1' U D 6 beta 719 725 722 744 C1' C D 7 beta 739 745 742 764 C1' A D 8 beta 759 765 762 786 C1' U D 9 beta 781 787 784 806 C1' U D 10 beta 801 807 804 826 C1' C D 11 beta 821 827 824 846 C1' G D 12 beta 841 847 844 869 C1' C D 13 beta 864 870 867 889 C1' A D 14 beta 884 890 887 911 C1' A D 15 beta 906 912 909 933 C1' G D 16 beta 928 934 931 956 C1' A D 17 beta 951 957 954 978 C1' G D 18 beta 973 979 976 1001 C1' U D 19 beta 996 1002 999 1021 C1' G D 20 beta 1016 1022 1019 1044 C1' G D 21 beta 1039 1045 1042 1067 C1' C D 22 beta 1062 1068 1065 1087 C1' C D 23 beta 1082 1088 1085 1107 C1' U D 24 beta 1102 1108 1105 1127 C1' U D 25 beta 1122 1128 1125 1147 C1' G D 26 beta 1142 1148 1145 1170 C1' C D 27 beta 1165 1171 1168 1190 C1' G D 28 beta 1185 1191 1188 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 11 C2' C C 1 OK 13 9 12 31 C2' A C 2 OK 33 29 32 53 C2' A C 3 OK 55 51 54 75 C2' G C 4 OK 77 73 76 98 C2' G C 5 OK 100 96 99 121 C2' U C 6 OK 123 119 122 141 C2' C C 7 OK 143 139 142 161 C2' A C 8 OK 163 159 162 183 C2' U C 9 OK 185 181 184 203 C2' U C 10 OK 205 201 204 223 C2' C C 11 OK 225 221 224 243 C2' G C 12 OK 245 241 244 266 C2' C C 13 OK 268 264 267 286 C2' A C 14 OK 288 284 287 308 C2' A C 15 OK 310 306 309 330 C2' G C 16 OK 332 328 331 353 C2' A C 17 OK 355 351 354 375 C2' G C 18 OK 377 373 376 398 C2' U C 19 OK 400 396 399 418 C2' G C 20 OK 420 416 419 441 C2' G C 21 OK 443 439 442 464 C2' C C 22 OK 466 462 465 484 C2' C C 23 OK 486 482 485 504 C2' U C 24 OK 506 502 505 524 C2' U C 25 OK 526 522 525 544 C2' G C 26 OK 546 542 545 567 C2' C C 27 OK 569 565 568 587 C2' G C 28 OK 589 585 588 612 C2' C D 1 OK 614 610 613 632 C2' A D 2 OK 634 630 633 654 C2' A D 3 OK 656 652 655 676 C2' G D 4 OK 678 674 677 699 C2' G D 5 OK 701 697 700 722 C2' U D 6 OK 724 720 723 742 C2' C D 7 OK 744 740 743 762 C2' A D 8 OK 764 760 763 784 C2' U D 9 OK 786 782 785 804 C2' U D 10 OK 806 802 805 824 C2' C D 11 OK 826 822 825 844 C2' G D 12 OK 846 842 845 867 C2' C D 13 OK 869 865 868 887 C2' A D 14 OK 889 885 888 909 C2' A D 15 OK 911 907 910 931 C2' G D 16 OK 933 929 932 954 C2' A D 17 OK 956 952 955 976 C2' G D 18 OK 978 974 977 999 C2' U D 19 OK 1001 997 1000 1019 C2' G D 20 OK 1021 1017 1020 1042 C2' G D 21 OK 1044 1040 1043 1065 C2' C D 22 OK 1067 1063 1066 1085 C2' C D 23 OK 1087 1083 1086 1105 C2' U D 24 OK 1107 1103 1106 1125 C2' U D 25 OK 1127 1123 1126 1145 C2' G D 26 OK 1147 1143 1146 1168 C2' C D 27 OK 1170 1166 1169 1188 C2' G D 28 OK 1190 1186 1189 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 9 C3' C C 1 OK 7 10 11 29 C3' A C 2 OK 27 30 31 51 C3' A C 3 OK 49 52 53 73 C3' G C 4 OK 71 74 75 96 C3' G C 5 OK 94 97 98 119 C3' U C 6 OK 117 120 121 139 C3' C C 7 OK 137 140 141 159 C3' A C 8 OK 157 160 161 181 C3' U C 9 OK 179 182 183 201 C3' U C 10 OK 199 202 203 221 C3' C C 11 OK 219 222 223 241 C3' G C 12 OK 239 242 243 264 C3' C C 13 OK 262 265 266 284 C3' A C 14 OK 282 285 286 306 C3' A C 15 OK 304 307 308 328 C3' G C 16 OK 326 329 330 351 C3' A C 17 OK 349 352 353 373 C3' G C 18 OK 371 374 375 396 C3' U C 19 OK 394 397 398 416 C3' G C 20 OK 414 417 418 439 C3' G C 21 OK 437 440 441 462 C3' C C 22 OK 460 463 464 482 C3' C C 23 OK 480 483 484 502 C3' U C 24 OK 500 503 504 522 C3' U C 25 OK 520 523 524 542 C3' G C 26 OK 540 543 544 565 C3' C C 27 OK 563 566 567 585 C3' G C 28 OK 583 586 587 610 C3' C D 1 OK 608 611 612 630 C3' A D 2 OK 628 631 632 652 C3' A D 3 OK 650 653 654 674 C3' G D 4 OK 672 675 676 697 C3' G D 5 OK 695 698 699 720 C3' U D 6 OK 718 721 722 740 C3' C D 7 OK 738 741 742 760 C3' A D 8 OK 758 761 762 782 C3' U D 9 OK 780 783 784 802 C3' U D 10 OK 800 803 804 822 C3' C D 11 OK 820 823 824 842 C3' G D 12 OK 840 843 844 865 C3' C D 13 OK 863 866 867 885 C3' A D 14 OK 883 886 887 907 C3' A D 15 OK 905 908 909 929 C3' G D 16 OK 927 930 931 952 C3' A D 17 OK 950 953 954 974 C3' G D 18 OK 972 975 976 997 C3' U D 19 OK 995 998 999 1017 C3' G D 20 OK 1015 1018 1019 1040 C3' G D 21 OK 1038 1041 1042 1063 C3' C D 22 OK 1061 1064 1065 1083 C3' C D 23 OK 1081 1084 1085 1103 C3' U D 24 OK 1101 1104 1105 1123 C3' U D 25 OK 1121 1124 1125 1143 C3' G D 26 OK 1141 1144 1145 1166 C3' C D 27 OK 1164 1167 1168 1186 C3' G D 28 OK 1184 1187 1188 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 7 C4' C C 1 OK 9 6 8 27 C4' A C 2 OK 29 26 28 49 C4' A C 3 OK 51 48 50 71 C4' G C 4 OK 73 70 72 94 C4' G C 5 OK 96 93 95 117 C4' U C 6 OK 119 116 118 137 C4' C C 7 OK 139 136 138 157 C4' A C 8 OK 159 156 158 179 C4' U C 9 OK 181 178 180 199 C4' U C 10 OK 201 198 200 219 C4' C C 11 OK 221 218 220 239 C4' G C 12 OK 241 238 240 262 C4' C C 13 OK 264 261 263 282 C4' A C 14 OK 284 281 283 304 C4' A C 15 OK 306 303 305 326 C4' G C 16 OK 328 325 327 349 C4' A C 17 OK 351 348 350 371 C4' G C 18 OK 373 370 372 394 C4' U C 19 OK 396 393 395 414 C4' G C 20 OK 416 413 415 437 C4' G C 21 OK 439 436 438 460 C4' C C 22 OK 462 459 461 480 C4' C C 23 OK 482 479 481 500 C4' U C 24 OK 502 499 501 520 C4' U C 25 OK 522 519 521 540 C4' G C 26 OK 542 539 541 563 C4' C C 27 OK 565 562 564 583 C4' G C 28 OK 585 582 584 608 C4' C D 1 OK 610 607 609 628 C4' A D 2 OK 630 627 629 650 C4' A D 3 OK 652 649 651 672 C4' G D 4 OK 674 671 673 695 C4' G D 5 OK 697 694 696 718 C4' U D 6 OK 720 717 719 738 C4' C D 7 OK 740 737 739 758 C4' A D 8 OK 760 757 759 780 C4' U D 9 OK 782 779 781 800 C4' U D 10 OK 802 799 801 820 C4' C D 11 OK 822 819 821 840 C4' G D 12 OK 842 839 841 863 C4' C D 13 OK 865 862 864 883 C4' A D 14 OK 885 882 884 905 C4' A D 15 OK 907 904 906 927 C4' G D 16 OK 929 926 928 950 C4' A D 17 OK 952 949 951 972 C4' G D 18 OK 974 971 973 995 C4' U D 19 OK 997 994 996 1015 C4' G D 20 OK 1017 1014 1016 1038 C4' G D 21 OK 1040 1037 1039 1061 C4' C D 22 OK 1063 1060 1062 1081 C4' C D 23 OK 1083 1080 1082 1101 C4' U D 24 OK 1103 1100 1102 1121 C4' U D 25 OK 1123 1120 1122 1141 C4' G D 26 OK 1143 1140 1142 1164 C4' C D 27 OK 1166 1163 1165 1184 C4' G D 28 OK 1186 1183 1185 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 6 C5' C C 1 5 7 26 C5' A C 2 25 27 48 C5' A C 3 47 49 70 C5' G C 4 69 71 93 C5' G C 5 92 94 116 C5' U C 6 115 117 136 C5' C C 7 135 137 156 C5' A C 8 155 157 178 C5' U C 9 177 179 198 C5' U C 10 197 199 218 C5' C C 11 217 219 238 C5' G C 12 237 239 261 C5' C C 13 260 262 281 C5' A C 14 280 282 303 C5' A C 15 302 304 325 C5' G C 16 324 326 348 C5' A C 17 347 349 370 C5' G C 18 369 371 393 C5' U C 19 392 394 413 C5' G C 20 412 414 436 C5' G C 21 435 437 459 C5' C C 22 458 460 479 C5' C C 23 478 480 499 C5' U C 24 498 500 519 C5' U C 25 518 520 539 C5' G C 26 538 540 562 C5' C C 27 561 563 582 C5' G C 28 581 583 607 C5' C D 1 606 608 627 C5' A D 2 626 628 649 C5' A D 3 648 650 671 C5' G D 4 670 672 694 C5' G D 5 693 695 717 C5' U D 6 716 718 737 C5' C D 7 736 738 757 C5' A D 8 756 758 779 C5' U D 9 778 780 799 C5' U D 10 798 800 819 C5' C D 11 818 820 839 C5' G D 12 838 840 862 C5' C D 13 861 863 882 C5' A D 14 881 883 904 C5' A D 15 903 905 926 C5' G D 16 925 927 949 C5' A D 17 948 950 971 C5' G D 18 970 972 994 C5' U D 19 993 995 1014 C5' G D 20 1013 1015 1037 C5' G D 21 1036 1038 1060 C5' C D 22 1059 1061 1080 C5' C D 23 1079 1081 1100 C5' U D 24 1099 1101 1120 C5' U D 25 1119 1121 1140 C5' G D 26 1139 1141 1163 C5' C D 27 1162 1164 1183 C5' G D 28 1182 1184 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2 P C C 1 OK OK 3 4 5 22 P A C 2 distorted distorted 10 23 24 25 44 P A C 3 distorted distorted 30 45 46 47 66 P G C 4 distorted distorted 52 67 68 69 89 P G C 5 distorted distorted 74 90 91 92 112 P U C 6 distorted distorted 97 113 114 115 132 P C C 7 distorted distorted 120 133 134 135 152 P A C 8 distorted distorted 140 153 154 155 174 P U C 9 distorted distorted 160 175 176 177 194 P U C 10 distorted distorted 182 195 196 197 214 P C C 11 distorted distorted 202 215 216 217 234 P G C 12 distorted distorted 222 235 236 237 257 P C C 13 distorted distorted 242 258 259 260 277 P A C 14 distorted distorted 265 278 279 280 299 P A C 15 distorted distorted 285 300 301 302 321 P G C 16 distorted distorted 307 322 323 324 344 P A C 17 distorted distorted 329 345 346 347 366 P G C 18 distorted distorted 352 367 368 369 389 P U C 19 distorted distorted 374 390 391 392 409 P G C 20 distorted distorted 397 410 411 412 432 P G C 21 distorted distorted 417 433 434 435 455 P C C 22 distorted distorted 440 456 457 458 475 P C C 23 distorted distorted 463 476 477 478 495 P U C 24 distorted distorted 483 496 497 498 515 P U C 25 distorted distorted 503 516 517 518 535 P G C 26 distorted distorted 523 536 537 538 558 P C C 27 distorted distorted 543 559 560 561 578 P G C 28 distorted distorted 566 579 580 581 603 P C D 1 OK OK 604 605 606 623 P A D 2 distorted distorted 611 624 625 626 645 P A D 3 distorted distorted 631 646 647 648 667 P G D 4 distorted distorted 653 668 669 670 690 P G D 5 distorted distorted 675 691 692 693 713 P U D 6 distorted distorted 698 714 715 716 733 P C D 7 distorted distorted 721 734 735 736 753 P A D 8 distorted distorted 741 754 755 756 775 P U D 9 distorted distorted 761 776 777 778 795 P U D 10 distorted distorted 783 796 797 798 815 P C D 11 distorted distorted 803 816 817 818 835 P G D 12 distorted distorted 823 836 837 838 858 P C D 13 distorted distorted 843 859 860 861 878 P A D 14 distorted distorted 866 879 880 881 900 P A D 15 distorted distorted 886 901 902 903 922 P G D 16 distorted distorted 908 923 924 925 945 P A D 17 distorted distorted 930 946 947 948 967 P G D 18 distorted distorted 953 968 969 970 990 P U D 19 distorted distorted 975 991 992 993 1010 P G D 20 distorted distorted 998 1011 1012 1013 1033 P G D 21 distorted distorted 1018 1034 1035 1036 1056 P C D 22 distorted distorted 1041 1057 1058 1059 1076 P C D 23 distorted distorted 1064 1077 1078 1079 1096 P U D 24 distorted distorted 1084 1097 1098 1099 1116 P U D 25 distorted distorted 1104 1117 1118 1119 1136 P G D 26 distorted distorted 1124 1137 1138 1139 1159 P C D 27 distorted distorted 1144 1160 1161 1162 1179 P G D 28 distorted distorted 1167 1180 1181 1182 ---------------------------------------------------------------------------------