ID code: '1F5U' 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 1 alpha beta 4 27 10 7 44 C1' G A 2 alpha beta 39 62 45 42 78 C1' U A 3 alpha beta 73 93 79 76 108 C1' G A 4 alpha beta 103 126 109 106 142 C1' G A 5 alpha beta 137 160 143 140 176 C1' G A 6 alpha beta 171 194 177 174 210 C1' A A 7 alpha beta 205 227 211 208 243 C1' G A 8 alpha beta 238 261 244 241 277 C1' A A 9 alpha beta 272 294 278 275 310 C1' C A 10 alpha beta 305 325 311 308 341 C1' G A 11 alpha beta 336 359 342 339 375 C1' U A 12 alpha beta 370 390 376 373 405 C1' C A 13 alpha beta 400 420 406 403 436 C1' C A 14 alpha beta 431 451 437 434 467 C1' C A 15 alpha beta 462 482 468 465 498 C1' A A 16 alpha beta 493 515 499 496 531 C1' C A 17 alpha beta 526 546 532 529 562 C1' C A 18 alpha beta 557 577 563 560 591 C1' G B 1 alpha beta 586 609 592 589 626 C1' G B 2 alpha beta 621 644 627 624 660 C1' U B 3 alpha beta 655 675 661 658 690 C1' G B 4 alpha beta 685 708 691 688 724 C1' G B 5 alpha beta 719 742 725 722 758 C1' G B 6 alpha beta 753 776 759 756 792 C1' A B 7 alpha beta 787 809 793 790 825 C1' G B 8 alpha beta 820 843 826 823 859 C1' A B 9 alpha beta 854 876 860 857 892 C1' C B 10 alpha beta 887 907 893 890 923 C1' G B 11 alpha beta 918 941 924 921 957 C1' U B 12 alpha beta 952 972 958 955 987 C1' C B 13 alpha beta 982 1002 988 985 1018 C1' C B 14 alpha beta 1013 1033 1019 1016 1049 C1' C B 15 alpha beta 1044 1064 1050 1047 1080 C1' A B 16 alpha beta 1075 1097 1081 1078 1113 C1' C B 17 alpha beta 1108 1128 1114 1111 1144 C1' C B 18 alpha beta 1139 1159 1145 1142 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G A 1 OK OK 9 5 25 8 42 C2' G A 2 OK OK 44 40 60 43 76 C2' U A 3 OK OK 78 74 91 77 106 C2' G A 4 OK OK 108 104 124 107 140 C2' G A 5 OK OK 142 138 158 141 174 C2' G A 6 OK OK 176 172 192 175 208 C2' A A 7 OK OK 210 206 225 209 241 C2' G A 8 OK OK 243 239 259 242 275 C2' A A 9 OK OK 277 273 292 276 308 C2' C A 10 OK OK 310 306 323 309 339 C2' G A 11 OK OK 341 337 357 340 373 C2' U A 12 OK OK 375 371 388 374 403 C2' C A 13 OK OK 405 401 418 404 434 C2' C A 14 OK OK 436 432 449 435 465 C2' C A 15 OK OK 467 463 480 466 496 C2' A A 16 OK OK 498 494 513 497 529 C2' C A 17 OK OK 531 527 544 530 560 C2' C A 18 OK OK 562 558 575 561 589 C2' G B 1 OK OK 591 587 607 590 624 C2' G B 2 OK OK 626 622 642 625 658 C2' U B 3 OK OK 660 656 673 659 688 C2' G B 4 OK OK 690 686 706 689 722 C2' G B 5 OK OK 724 720 740 723 756 C2' G B 6 OK OK 758 754 774 757 790 C2' A B 7 OK OK 792 788 807 791 823 C2' G B 8 OK OK 825 821 841 824 857 C2' A B 9 OK OK 859 855 874 858 890 C2' C B 10 OK OK 892 888 905 891 921 C2' G B 11 OK OK 923 919 939 922 955 C2' U B 12 OK OK 957 953 970 956 985 C2' C B 13 OK OK 987 983 1000 986 1016 C2' C B 14 OK OK 1018 1014 1031 1017 1047 C2' C B 15 OK OK 1049 1045 1062 1048 1078 C2' A B 16 OK OK 1080 1076 1095 1079 1111 C2' C B 17 OK OK 1113 1109 1126 1112 1142 C2' C B 18 OK OK 1144 1140 1157 1143 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK OK 3 24 6 7 40 C3' G A 2 OK OK 38 59 41 42 74 C3' U A 3 OK OK 72 90 75 76 104 C3' G A 4 OK OK 102 123 105 106 138 C3' G A 5 OK OK 136 157 139 140 172 C3' G A 6 OK OK 170 191 173 174 206 C3' A A 7 OK OK 204 224 207 208 239 C3' G A 8 OK OK 237 258 240 241 273 C3' A A 9 OK OK 271 291 274 275 306 C3' C A 10 OK OK 304 322 307 308 337 C3' G A 11 OK OK 335 356 338 339 371 C3' U A 12 OK OK 369 387 372 373 401 C3' C A 13 OK OK 399 417 402 403 432 C3' C A 14 OK OK 430 448 433 434 463 C3' C A 15 OK OK 461 479 464 465 494 C3' A A 16 OK OK 492 512 495 496 527 C3' C A 17 OK OK 525 543 528 529 558 C3' C A 18 OK OK 556 574 559 560 587 C3' G B 1 OK OK 585 606 588 589 622 C3' G B 2 OK OK 620 641 623 624 656 C3' U B 3 OK OK 654 672 657 658 686 C3' G B 4 OK OK 684 705 687 688 720 C3' G B 5 OK OK 718 739 721 722 754 C3' G B 6 OK OK 752 773 755 756 788 C3' A B 7 OK OK 786 806 789 790 821 C3' G B 8 OK OK 819 840 822 823 855 C3' A B 9 OK OK 853 873 856 857 888 C3' C B 10 OK OK 886 904 889 890 919 C3' G B 11 OK OK 917 938 920 921 953 C3' U B 12 OK OK 951 969 954 955 983 C3' C B 13 OK OK 981 999 984 985 1014 C3' C B 14 OK OK 1012 1030 1015 1016 1045 C3' C B 15 OK OK 1043 1061 1046 1047 1076 C3' A B 16 OK OK 1074 1094 1077 1078 1109 C3' C B 17 OK OK 1107 1125 1110 1111 1140 C3' C B 18 OK OK 1138 1156 1141 1142 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK OK 5 23 2 4 38 C4' G A 2 OK OK 40 58 37 39 72 C4' U A 3 OK OK 74 89 71 73 102 C4' G A 4 OK OK 104 122 101 103 136 C4' G A 5 OK OK 138 156 135 137 170 C4' G A 6 OK OK 172 190 169 171 204 C4' A A 7 OK OK 206 223 203 205 237 C4' G A 8 OK OK 239 257 236 238 271 C4' A A 9 OK OK 273 290 270 272 304 C4' C A 10 OK OK 306 321 303 305 335 C4' G A 11 OK OK 337 355 334 336 369 C4' U A 12 OK OK 371 386 368 370 399 C4' C A 13 OK OK 401 416 398 400 430 C4' C A 14 OK OK 432 447 429 431 461 C4' C A 15 OK OK 463 478 460 462 492 C4' A A 16 OK OK 494 511 491 493 525 C4' C A 17 OK OK 527 542 524 526 556 C4' C A 18 OK OK 558 573 555 557 585 C4' G B 1 OK OK 587 605 584 586 620 C4' G B 2 OK OK 622 640 619 621 654 C4' U B 3 OK OK 656 671 653 655 684 C4' G B 4 OK OK 686 704 683 685 718 C4' G B 5 OK OK 720 738 717 719 752 C4' G B 6 OK OK 754 772 751 753 786 C4' A B 7 OK OK 788 805 785 787 819 C4' G B 8 OK OK 821 839 818 820 853 C4' A B 9 OK OK 855 872 852 854 886 C4' C B 10 OK OK 888 903 885 887 917 C4' G B 11 OK OK 919 937 916 918 951 C4' U B 12 OK OK 953 968 950 952 981 C4' C B 13 OK OK 983 998 980 982 1012 C4' C B 14 OK OK 1014 1029 1011 1013 1043 C4' C B 15 OK OK 1045 1060 1042 1044 1074 C4' A B 16 OK OK 1076 1093 1073 1075 1107 C4' C B 17 OK OK 1109 1124 1106 1108 1138 C4' C B 18 OK OK 1140 1155 1137 1139 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 1 OK OK 1 21 22 3 37 C5' G A 2 OK OK 36 56 57 38 71 C5' U A 3 OK OK 70 87 88 72 101 C5' G A 4 OK OK 100 120 121 102 135 C5' G A 5 OK OK 134 154 155 136 169 C5' G A 6 OK OK 168 188 189 170 203 C5' A A 7 OK OK 202 221 222 204 236 C5' G A 8 OK OK 235 255 256 237 270 C5' A A 9 OK OK 269 288 289 271 303 C5' C A 10 OK OK 302 319 320 304 334 C5' G A 11 OK OK 333 353 354 335 368 C5' U A 12 OK OK 367 384 385 369 398 C5' C A 13 OK OK 397 414 415 399 429 C5' C A 14 OK OK 428 445 446 430 460 C5' C A 15 OK OK 459 476 477 461 491 C5' A A 16 OK OK 490 509 510 492 524 C5' C A 17 OK OK 523 540 541 525 555 C5' C A 18 OK OK 554 571 572 556 584 C5' G B 1 OK OK 583 603 604 585 619 C5' G B 2 OK OK 618 638 639 620 653 C5' U B 3 OK OK 652 669 670 654 683 C5' G B 4 OK OK 682 702 703 684 717 C5' G B 5 OK OK 716 736 737 718 751 C5' G B 6 OK OK 750 770 771 752 785 C5' A B 7 OK OK 784 803 804 786 818 C5' G B 8 OK OK 817 837 838 819 852 C5' A B 9 OK OK 851 870 871 853 885 C5' C B 10 OK OK 884 901 902 886 916 C5' G B 11 OK OK 915 935 936 917 950 C5' U B 12 OK OK 949 966 967 951 980 C5' C B 13 OK OK 979 996 997 981 1011 C5' C B 14 OK OK 1010 1027 1028 1012 1042 C5' C B 15 OK OK 1041 1058 1059 1043 1073 C5' A B 16 OK OK 1072 1091 1092 1074 1106 C5' C B 17 OK OK 1105 1122 1123 1107 1137 C5' C B 18 OK OK 1136 1153 1154 1138 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 2 distorted distorted 6 34 35 36 67 P U A 3 distorted distorted 41 68 69 70 97 P G A 4 distorted distorted 75 98 99 100 131 P G A 5 distorted distorted 105 132 133 134 165 P G A 6 distorted distorted 139 166 167 168 199 P A A 7 distorted distorted 173 200 201 202 232 P G A 8 distorted distorted 207 233 234 235 266 P A A 9 distorted distorted 240 267 268 269 299 P C A 10 distorted distorted 274 300 301 302 330 P G A 11 distorted distorted 307 331 332 333 364 P U A 12 distorted distorted 338 365 366 367 394 P C A 13 distorted distorted 372 395 396 397 425 P C A 14 distorted distorted 402 426 427 428 456 P C A 15 distorted distorted 433 457 458 459 487 P A A 16 distorted distorted 464 488 489 490 520 P C A 17 distorted distorted 495 521 522 523 551 P C A 18 distorted distorted 528 552 553 554 615 P G B 2 distorted distorted 588 616 617 618 649 P U B 3 distorted distorted 623 650 651 652 679 P G B 4 distorted distorted 657 680 681 682 713 P G B 5 distorted distorted 687 714 715 716 747 P G B 6 distorted distorted 721 748 749 750 781 P A B 7 distorted distorted 755 782 783 784 814 P G B 8 distorted distorted 789 815 816 817 848 P A B 9 distorted distorted 822 849 850 851 881 P C B 10 distorted distorted 856 882 883 884 912 P G B 11 distorted distorted 889 913 914 915 946 P U B 12 distorted distorted 920 947 948 949 976 P C B 13 distorted distorted 954 977 978 979 1007 P C B 14 distorted distorted 984 1008 1009 1010 1038 P C B 15 distorted distorted 1015 1039 1040 1041 1069 P A B 16 distorted distorted 1046 1070 1071 1072 1102 P C B 17 distorted distorted 1077 1103 1104 1105 1133 P C B 18 distorted distorted 1110 1134 1135 1136 ---------------------------------------------------------------------------------