ID code: '2KKK' 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' MCY A 1 alpha beta 13 21 1 10 42 C1' DC A 2 alpha beta 38 57 43 41 72 C1' DT A 3 alpha beta 68 88 73 71 104 C1' DC A 4 alpha beta 100 119 105 103 134 C1' DT A 5 alpha beta 130 150 135 133 166 C1' DC A 6 alpha beta 162 181 167 165 196 C1' DT A 7 alpha beta 192 212 197 195 228 C1' DC A 8 alpha beta 224 243 229 227 258 C1' DC A 9 alpha beta 254 274 259 257 288 C1' MCY B 1 alpha beta 292 300 280 289 321 C1' DC B 2 alpha beta 317 336 322 320 351 C1' DT B 3 alpha beta 347 367 352 350 383 C1' DC B 4 alpha beta 379 398 384 382 413 C1' DT B 5 alpha beta 409 429 414 412 445 C1' DC B 6 alpha beta 441 460 446 444 475 C1' DT B 7 alpha beta 471 491 476 474 507 C1' DC B 8 alpha beta 503 522 508 506 537 C1' DC B 9 alpha beta 533 553 538 536 567 C1' MCY C 1 alpha beta 571 579 559 568 600 C1' DC C 2 alpha beta 596 615 601 599 630 C1' DT C 3 alpha beta 626 646 631 629 662 C1' DC C 4 alpha beta 658 677 663 661 692 C1' DT C 5 alpha beta 688 708 693 691 724 C1' DC C 6 alpha beta 720 739 725 723 754 C1' DT C 7 alpha beta 750 770 755 753 786 C1' DC C 8 alpha beta 782 801 787 785 816 C1' DC C 9 alpha beta 812 832 817 815 846 C1' MCY D 1 alpha beta 850 858 838 847 879 C1' DC D 2 alpha beta 875 894 880 878 909 C1' DT D 3 alpha beta 905 925 910 908 941 C1' DC D 4 alpha beta 937 956 942 940 971 C1' DT D 5 alpha beta 967 987 972 970 1003 C1' DC D 6 alpha beta 999 1018 1004 1002 1033 C1' DT D 7 alpha beta 1029 1049 1034 1032 1065 C1' DC D 8 alpha beta 1061 1080 1066 1064 1095 C1' DC D 9 alpha beta 1091 1111 1096 1094 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' MCY A 1 OK OK 9 11 22 23 41 C2' DC A 2 OK OK 42 39 55 56 71 C2' DT A 3 OK OK 72 69 86 87 103 C2' DC A 4 OK OK 104 101 117 118 133 C2' DT A 5 OK OK 134 131 148 149 165 C2' DC A 6 OK OK 166 163 179 180 195 C2' DT A 7 OK OK 196 193 210 211 227 C2' DC A 8 OK OK 228 225 241 242 257 C2' DC A 9 OK OK 258 255 272 273 289 C2' MCY B 1 OK OK 288 290 301 302 320 C2' DC B 2 OK OK 321 318 334 335 350 C2' DT B 3 OK OK 351 348 365 366 382 C2' DC B 4 OK OK 383 380 396 397 412 C2' DT B 5 OK OK 413 410 427 428 444 C2' DC B 6 OK OK 445 442 458 459 474 C2' DT B 7 OK OK 475 472 489 490 506 C2' DC B 8 OK OK 507 504 520 521 536 C2' DC B 9 OK OK 537 534 551 552 568 C2' MCY C 1 OK OK 567 569 580 581 599 C2' DC C 2 OK OK 600 597 613 614 629 C2' DT C 3 OK OK 630 627 644 645 661 C2' DC C 4 OK OK 662 659 675 676 691 C2' DT C 5 OK OK 692 689 706 707 723 C2' DC C 6 OK OK 724 721 737 738 753 C2' DT C 7 OK OK 754 751 768 769 785 C2' DC C 8 OK OK 786 783 799 800 815 C2' DC C 9 OK OK 816 813 830 831 847 C2' MCY D 1 OK OK 846 848 859 860 878 C2' DC D 2 OK OK 879 876 892 893 908 C2' DT D 3 OK OK 909 906 923 924 940 C2' DC D 4 OK OK 941 938 954 955 970 C2' DT D 5 OK OK 971 968 985 986 1002 C2' DC D 6 OK OK 1003 1000 1016 1017 1032 C2' DT D 7 OK OK 1033 1030 1047 1048 1064 C2' DC D 8 OK OK 1065 1062 1078 1079 1094 C2' DC D 9 OK OK 1095 1092 1109 1110 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 11 C3' MCY A 1 OK OK 12 24 14 10 39 C3' DC A 2 OK OK 37 54 40 41 69 C3' DT A 3 OK OK 67 85 70 71 101 C3' DC A 4 OK OK 99 116 102 103 131 C3' DT A 5 OK OK 129 147 132 133 163 C3' DC A 6 OK OK 161 178 164 165 193 C3' DT A 7 OK OK 191 209 194 195 225 C3' DC A 8 OK OK 223 240 226 227 255 C3' DC A 9 OK OK 253 270 256 257 290 C3' MCY B 1 OK OK 291 303 293 289 318 C3' DC B 2 OK OK 316 333 319 320 348 C3' DT B 3 OK OK 346 364 349 350 380 C3' DC B 4 OK OK 378 395 381 382 410 C3' DT B 5 OK OK 408 426 411 412 442 C3' DC B 6 OK OK 440 457 443 444 472 C3' DT B 7 OK OK 470 488 473 474 504 C3' DC B 8 OK OK 502 519 505 506 534 C3' DC B 9 OK OK 532 549 535 536 569 C3' MCY C 1 OK OK 570 582 572 568 597 C3' DC C 2 OK OK 595 612 598 599 627 C3' DT C 3 OK OK 625 643 628 629 659 C3' DC C 4 OK OK 657 674 660 661 689 C3' DT C 5 OK OK 687 705 690 691 721 C3' DC C 6 OK OK 719 736 722 723 751 C3' DT C 7 OK OK 749 767 752 753 783 C3' DC C 8 OK OK 781 798 784 785 813 C3' DC C 9 OK OK 811 828 814 815 848 C3' MCY D 1 OK OK 849 861 851 847 876 C3' DC D 2 OK OK 874 891 877 878 906 C3' DT D 3 OK OK 904 922 907 908 938 C3' DC D 4 OK OK 936 953 939 940 968 C3' DT D 5 OK OK 966 984 969 970 1000 C3' DC D 6 OK OK 998 1015 1001 1002 1030 C3' DT D 7 OK OK 1028 1046 1031 1032 1062 C3' DC D 8 OK OK 1060 1077 1063 1064 1092 C3' DC D 9 OK OK 1090 1107 1093 1094 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 12 C4' MCY A 1 OK OK 11 25 15 13 37 C4' DC A 2 OK OK 39 53 36 38 67 C4' DT A 3 OK OK 69 84 66 68 99 C4' DC A 4 OK OK 101 115 98 100 129 C4' DT A 5 OK OK 131 146 128 130 161 C4' DC A 6 OK OK 163 177 160 162 191 C4' DT A 7 OK OK 193 208 190 192 223 C4' DC A 8 OK OK 225 239 222 224 253 C4' DC A 9 OK OK 255 269 252 254 291 C4' MCY B 1 OK OK 290 304 294 292 316 C4' DC B 2 OK OK 318 332 315 317 346 C4' DT B 3 OK OK 348 363 345 347 378 C4' DC B 4 OK OK 380 394 377 379 408 C4' DT B 5 OK OK 410 425 407 409 440 C4' DC B 6 OK OK 442 456 439 441 470 C4' DT B 7 OK OK 472 487 469 471 502 C4' DC B 8 OK OK 504 518 501 503 532 C4' DC B 9 OK OK 534 548 531 533 570 C4' MCY C 1 OK OK 569 583 573 571 595 C4' DC C 2 OK OK 597 611 594 596 625 C4' DT C 3 OK OK 627 642 624 626 657 C4' DC C 4 OK OK 659 673 656 658 687 C4' DT C 5 OK OK 689 704 686 688 719 C4' DC C 6 OK OK 721 735 718 720 749 C4' DT C 7 OK OK 751 766 748 750 781 C4' DC C 8 OK OK 783 797 780 782 811 C4' DC C 9 OK OK 813 827 810 812 849 C4' MCY D 1 OK OK 848 862 852 850 874 C4' DC D 2 OK OK 876 890 873 875 904 C4' DT D 3 OK OK 906 921 903 905 936 C4' DC D 4 OK OK 938 952 935 937 966 C4' DT D 5 OK OK 968 983 965 967 998 C4' DC D 6 OK OK 1000 1014 997 999 1028 C4' DT D 7 OK OK 1030 1045 1027 1029 1060 C4' DC D 8 OK OK 1062 1076 1059 1061 1090 C4' DC D 9 OK OK 1092 1106 1089 1091 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 15 C5' MCY A 1 OK OK 16 26 27 12 36 C5' DC A 2 OK OK 35 51 52 37 66 C5' DT A 3 OK OK 65 82 83 67 98 C5' DC A 4 OK OK 97 113 114 99 128 C5' DT A 5 OK OK 127 144 145 129 160 C5' DC A 6 OK OK 159 175 176 161 190 C5' DT A 7 OK OK 189 206 207 191 222 C5' DC A 8 OK OK 221 237 238 223 252 C5' DC A 9 OK OK 251 267 268 253 294 C5' MCY B 1 OK OK 295 305 306 291 315 C5' DC B 2 OK OK 314 330 331 316 345 C5' DT B 3 OK OK 344 361 362 346 377 C5' DC B 4 OK OK 376 392 393 378 407 C5' DT B 5 OK OK 406 423 424 408 439 C5' DC B 6 OK OK 438 454 455 440 469 C5' DT B 7 OK OK 468 485 486 470 501 C5' DC B 8 OK OK 500 516 517 502 531 C5' DC B 9 OK OK 530 546 547 532 573 C5' MCY C 1 OK OK 574 584 585 570 594 C5' DC C 2 OK OK 593 609 610 595 624 C5' DT C 3 OK OK 623 640 641 625 656 C5' DC C 4 OK OK 655 671 672 657 686 C5' DT C 5 OK OK 685 702 703 687 718 C5' DC C 6 OK OK 717 733 734 719 748 C5' DT C 7 OK OK 747 764 765 749 780 C5' DC C 8 OK OK 779 795 796 781 810 C5' DC C 9 OK OK 809 825 826 811 852 C5' MCY D 1 OK OK 853 863 864 849 873 C5' DC D 2 OK OK 872 888 889 874 903 C5' DT D 3 OK OK 902 919 920 904 935 C5' DC D 4 OK OK 934 950 951 936 965 C5' DT D 5 OK OK 964 981 982 966 997 C5' DC D 6 OK OK 996 1012 1013 998 1027 C5' DT D 7 OK OK 1026 1043 1044 1028 1059 C5' DC D 8 OK OK 1058 1074 1075 1060 1089 C5' DC D 9 OK OK 1088 1104 1105 1090 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 32 P DC A 2 distorted distorted 14 33 34 35 62 P DT A 3 distorted distorted 40 63 64 65 94 P DC A 4 distorted distorted 70 95 96 97 124 P DT A 5 distorted distorted 102 125 126 127 156 P DC A 6 distorted distorted 132 157 158 159 186 P DT A 7 distorted distorted 164 187 188 189 218 P DC A 8 distorted distorted 194 219 220 221 248 P DC A 9 distorted distorted 226 249 250 251 311 P DC B 2 distorted distorted 293 312 313 314 341 P DT B 3 distorted distorted 319 342 343 344 373 P DC B 4 distorted distorted 349 374 375 376 403 P DT B 5 distorted distorted 381 404 405 406 435 P DC B 6 distorted distorted 411 436 437 438 465 P DT B 7 distorted distorted 443 466 467 468 497 P DC B 8 distorted distorted 473 498 499 500 527 P DC B 9 distorted distorted 505 528 529 530 590 P DC C 2 distorted distorted 572 591 592 593 620 P DT C 3 distorted distorted 598 621 622 623 652 P DC C 4 distorted distorted 628 653 654 655 682 P DT C 5 distorted distorted 660 683 684 685 714 P DC C 6 distorted distorted 690 715 716 717 744 P DT C 7 distorted distorted 722 745 746 747 776 P DC C 8 distorted distorted 752 777 778 779 806 P DC C 9 distorted distorted 784 807 808 809 869 P DC D 2 distorted distorted 851 870 871 872 899 P DT D 3 distorted distorted 877 900 901 902 931 P DC D 4 distorted distorted 907 932 933 934 961 P DT D 5 distorted distorted 939 962 963 964 993 P DC D 6 distorted distorted 969 994 995 996 1023 P DT D 7 distorted distorted 1001 1024 1025 1026 1055 P DC D 8 distorted distorted 1031 1056 1057 1058 1085 P DC D 9 distorted distorted 1063 1086 1087 1088 ---------------------------------------------------------------------------------