ID code: '2EZ6' 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' A C 1 beta 8 14 11 35 C1' A C 2 beta 30 36 33 57 C1' A C 3 beta 52 58 55 79 C1' G C 4 beta 74 80 77 102 C1' G C 5 beta 97 103 100 125 C1' U C 6 beta 120 126 123 145 C1' C C 7 beta 140 146 143 165 C1' A C 8 beta 160 166 163 187 C1' U C 9 beta 182 188 185 207 C1' U C 10 beta 202 208 205 227 C1' C C 11 beta 222 228 225 247 C1' G C 12 beta 242 248 245 270 C1' C C 13 beta 265 271 268 290 C1' A C 14 beta 285 291 288 312 C1' A C 15 beta 307 313 310 334 C1' G C 16 beta 329 335 332 357 C1' A C 17 beta 352 358 355 379 C1' G C 18 beta 374 380 377 402 C1' U C 19 beta 397 403 400 422 C1' G C 20 beta 417 423 420 445 C1' G C 21 beta 440 446 443 468 C1' C C 22 beta 463 469 466 488 C1' C C 23 beta 483 489 486 508 C1' U C 24 beta 503 509 506 528 C1' U C 25 beta 523 529 526 548 C1' U C 26 beta 543 549 546 568 C1' A C 27 beta 563 569 566 590 C1' U C 28 beta 585 591 588 612 C1' A D 1 beta 607 613 610 634 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' U D 26 beta 1142 1148 1145 1167 C1' A D 27 beta 1162 1168 1165 1189 C1' U D 28 beta 1184 1190 1187 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 11 C2' A C 1 OK 13 9 12 33 C2' A C 2 OK 35 31 34 55 C2' A C 3 OK 57 53 56 77 C2' G C 4 OK 79 75 78 100 C2' G C 5 OK 102 98 101 123 C2' U C 6 OK 125 121 124 143 C2' C C 7 OK 145 141 144 163 C2' A C 8 OK 165 161 164 185 C2' U C 9 OK 187 183 186 205 C2' U C 10 OK 207 203 206 225 C2' C C 11 OK 227 223 226 245 C2' G C 12 OK 247 243 246 268 C2' C C 13 OK 270 266 269 288 C2' A C 14 OK 290 286 289 310 C2' A C 15 OK 312 308 311 332 C2' G C 16 OK 334 330 333 355 C2' A C 17 OK 357 353 356 377 C2' G C 18 OK 379 375 378 400 C2' U C 19 OK 402 398 401 420 C2' G C 20 OK 422 418 421 443 C2' G C 21 OK 445 441 444 466 C2' C C 22 OK 468 464 467 486 C2' C C 23 OK 488 484 487 506 C2' U C 24 OK 508 504 507 526 C2' U C 25 OK 528 524 527 546 C2' U C 26 OK 548 544 547 566 C2' A C 27 OK 568 564 567 588 C2' U C 28 OK 590 586 589 610 C2' A D 1 OK 612 608 611 632 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' U D 26 OK 1147 1143 1146 1165 C2' A D 27 OK 1167 1163 1166 1187 C2' U D 28 OK 1189 1185 1188 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 9 C3' A C 1 OK 7 10 11 31 C3' A C 2 OK 29 32 33 53 C3' A C 3 OK 51 54 55 75 C3' G C 4 OK 73 76 77 98 C3' G C 5 OK 96 99 100 121 C3' U C 6 OK 119 122 123 141 C3' C C 7 OK 139 142 143 161 C3' A C 8 OK 159 162 163 183 C3' U C 9 OK 181 184 185 203 C3' U C 10 OK 201 204 205 223 C3' C C 11 OK 221 224 225 243 C3' G C 12 OK 241 244 245 266 C3' C C 13 OK 264 267 268 286 C3' A C 14 OK 284 287 288 308 C3' A C 15 OK 306 309 310 330 C3' G C 16 OK 328 331 332 353 C3' A C 17 OK 351 354 355 375 C3' G C 18 OK 373 376 377 398 C3' U C 19 OK 396 399 400 418 C3' G C 20 OK 416 419 420 441 C3' G C 21 OK 439 442 443 464 C3' C C 22 OK 462 465 466 484 C3' C C 23 OK 482 485 486 504 C3' U C 24 OK 502 505 506 524 C3' U C 25 OK 522 525 526 544 C3' U C 26 OK 542 545 546 564 C3' A C 27 OK 562 565 566 586 C3' U C 28 OK 584 587 588 608 C3' A D 1 OK 606 609 610 630 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' U D 26 OK 1141 1144 1145 1163 C3' A D 27 OK 1161 1164 1165 1185 C3' U D 28 OK 1183 1186 1187 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 7 C4' A C 1 OK 9 6 8 29 C4' A C 2 OK 31 28 30 51 C4' A C 3 OK 53 50 52 73 C4' G C 4 OK 75 72 74 96 C4' G C 5 OK 98 95 97 119 C4' U C 6 OK 121 118 120 139 C4' C C 7 OK 141 138 140 159 C4' A C 8 OK 161 158 160 181 C4' U C 9 OK 183 180 182 201 C4' U C 10 OK 203 200 202 221 C4' C C 11 OK 223 220 222 241 C4' G C 12 OK 243 240 242 264 C4' C C 13 OK 266 263 265 284 C4' A C 14 OK 286 283 285 306 C4' A C 15 OK 308 305 307 328 C4' G C 16 OK 330 327 329 351 C4' A C 17 OK 353 350 352 373 C4' G C 18 OK 375 372 374 396 C4' U C 19 OK 398 395 397 416 C4' G C 20 OK 418 415 417 439 C4' G C 21 OK 441 438 440 462 C4' C C 22 OK 464 461 463 482 C4' C C 23 OK 484 481 483 502 C4' U C 24 OK 504 501 503 522 C4' U C 25 OK 524 521 523 542 C4' U C 26 OK 544 541 543 562 C4' A C 27 OK 564 561 563 584 C4' U C 28 OK 586 583 585 606 C4' A D 1 OK 608 605 607 628 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' U D 26 OK 1143 1140 1142 1161 C4' A D 27 OK 1163 1160 1162 1183 C4' U D 28 OK 1185 1182 1184 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 6 C5' A C 1 5 7 28 C5' A C 2 27 29 50 C5' A C 3 49 51 72 C5' G C 4 71 73 95 C5' G C 5 94 96 118 C5' U C 6 117 119 138 C5' C C 7 137 139 158 C5' A C 8 157 159 180 C5' U C 9 179 181 200 C5' U C 10 199 201 220 C5' C C 11 219 221 240 C5' G C 12 239 241 263 C5' C C 13 262 264 283 C5' A C 14 282 284 305 C5' A C 15 304 306 327 C5' G C 16 326 328 350 C5' A C 17 349 351 372 C5' G C 18 371 373 395 C5' U C 19 394 396 415 C5' G C 20 414 416 438 C5' G C 21 437 439 461 C5' C C 22 460 462 481 C5' C C 23 480 482 501 C5' U C 24 500 502 521 C5' U C 25 520 522 541 C5' U C 26 540 542 561 C5' A C 27 560 562 583 C5' U C 28 582 584 605 C5' A D 1 604 606 627 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' U D 26 1139 1141 1160 C5' A D 27 1159 1161 1182 C5' U D 28 1181 1183 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2 P A C 1 OK OK 3 4 5 24 P A C 2 distorted distorted 10 25 26 27 46 P A C 3 distorted distorted 32 47 48 49 68 P G C 4 distorted distorted 54 69 70 71 91 P G C 5 distorted distorted 76 92 93 94 114 P U C 6 distorted distorted 99 115 116 117 134 P C C 7 distorted distorted 122 135 136 137 154 P A C 8 distorted distorted 142 155 156 157 176 P U C 9 distorted distorted 162 177 178 179 196 P U C 10 distorted distorted 184 197 198 199 216 P C C 11 distorted distorted 204 217 218 219 236 P G C 12 distorted distorted 224 237 238 239 259 P C C 13 distorted distorted 244 260 261 262 279 P A C 14 distorted distorted 267 280 281 282 301 P A C 15 distorted distorted 287 302 303 304 323 P G C 16 distorted distorted 309 324 325 326 346 P A C 17 distorted distorted 331 347 348 349 368 P G C 18 distorted distorted 354 369 370 371 391 P U C 19 distorted distorted 376 392 393 394 411 P G C 20 distorted distorted 399 412 413 414 434 P G C 21 distorted distorted 419 435 436 437 457 P C C 22 distorted distorted 442 458 459 460 477 P C C 23 distorted distorted 465 478 479 480 497 P U C 24 distorted distorted 485 498 499 500 517 P U C 25 distorted distorted 505 518 519 520 537 P U C 26 distorted distorted 525 538 539 540 557 P A C 27 distorted distorted 545 558 559 560 579 P U C 28 distorted distorted 565 580 581 582 601 P A D 1 OK OK 602 603 604 623 P A D 2 distorted distorted 609 624 625 626 645 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 U D 26 distorted distorted 1124 1137 1138 1139 1156 P A D 27 distorted distorted 1144 1157 1158 1159 1178 P U D 28 distorted distorted 1164 1179 1180 1181 ---------------------------------------------------------------------------------