ID code: '2Q1O' 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' C A 101 beta 4 10 7 29 C1' G A 102 beta 24 30 27 52 C1' C A 103 beta 47 53 50 70 C1' NF2 A 104 71 72 93 C1' A A 105 beta 88 94 91 115 C1' A A 106 beta 110 116 113 137 C1' U A 107 beta 132 138 135 157 C1' U A 108 beta 152 158 155 177 C1' G A 109 beta 172 178 175 200 C1' G A 110 beta 195 201 198 223 C1' C A 111 beta 218 224 221 243 C1' G A 112 beta 238 244 241 264 C1' C B 101 beta 259 265 262 284 C1' G B 102 beta 279 285 282 307 C1' C B 103 beta 302 308 305 325 C1' NF2 B 104 326 327 348 C1' A B 105 beta 343 349 346 370 C1' A B 106 beta 365 371 368 392 C1' U B 107 beta 387 393 390 412 C1' U B 108 beta 407 413 410 432 C1' G B 109 beta 427 433 430 455 C1' G B 110 beta 450 456 453 478 C1' C B 111 beta 473 479 476 498 C1' G B 112 beta 493 499 496 519 C1' C C 101 beta 514 520 517 539 C1' G C 102 beta 534 540 537 562 C1' C C 103 beta 557 563 560 580 C1' NF2 C 104 581 582 603 C1' A C 105 beta 598 604 601 625 C1' A C 106 beta 620 626 623 647 C1' U C 107 beta 642 648 645 667 C1' U C 108 beta 662 668 665 687 C1' G C 109 beta 682 688 685 710 C1' G C 110 beta 705 711 708 733 C1' C C 111 beta 728 734 731 753 C1' G C 112 beta 748 754 751 774 C1' C D 101 beta 769 775 772 794 C1' G D 102 beta 789 795 792 817 C1' C D 103 beta 812 818 815 835 C1' NF2 D 104 836 837 858 C1' A D 105 beta 853 859 856 880 C1' A D 106 beta 875 881 878 902 C1' U D 107 beta 897 903 900 922 C1' U D 108 beta 917 923 920 942 C1' G D 109 beta 937 943 940 965 C1' G D 110 beta 960 966 963 988 C1' C D 111 beta 983 989 986 1008 C1' G D 112 beta 1003 1009 1006 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' C A 101 OK 9 5 8 27 C2' G A 102 OK 29 25 28 50 C2' C A 103 OK 52 48 51 72 C2' NF2 A 104 OK 70 74 73 91 C2' A A 105 OK 93 89 92 113 C2' A A 106 OK 115 111 114 135 C2' U A 107 OK 137 133 136 155 C2' U A 108 OK 157 153 156 175 C2' G A 109 OK 177 173 176 198 C2' G A 110 OK 200 196 199 221 C2' C A 111 OK 223 219 222 241 C2' G A 112 OK 243 239 242 262 C2' C B 101 OK 264 260 263 282 C2' G B 102 OK 284 280 283 305 C2' C B 103 OK 307 303 306 327 C2' NF2 B 104 OK 325 329 328 346 C2' A B 105 OK 348 344 347 368 C2' A B 106 OK 370 366 369 390 C2' U B 107 OK 392 388 391 410 C2' U B 108 OK 412 408 411 430 C2' G B 109 OK 432 428 431 453 C2' G B 110 OK 455 451 454 476 C2' C B 111 OK 478 474 477 496 C2' G B 112 OK 498 494 497 517 C2' C C 101 OK 519 515 518 537 C2' G C 102 OK 539 535 538 560 C2' C C 103 OK 562 558 561 582 C2' NF2 C 104 OK 580 584 583 601 C2' A C 105 OK 603 599 602 623 C2' A C 106 OK 625 621 624 645 C2' U C 107 OK 647 643 646 665 C2' U C 108 OK 667 663 666 685 C2' G C 109 OK 687 683 686 708 C2' G C 110 OK 710 706 709 731 C2' C C 111 OK 733 729 732 751 C2' G C 112 OK 753 749 752 772 C2' C D 101 OK 774 770 773 792 C2' G D 102 OK 794 790 793 815 C2' C D 103 OK 817 813 816 837 C2' NF2 D 104 OK 835 839 838 856 C2' A D 105 OK 858 854 857 878 C2' A D 106 OK 880 876 879 900 C2' U D 107 OK 902 898 901 920 C2' U D 108 OK 922 918 921 940 C2' G D 109 OK 942 938 941 963 C2' G D 110 OK 965 961 964 986 C2' C D 111 OK 988 984 987 1006 C2' G D 112 OK 1008 1004 1007 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' C A 101 OK 3 6 7 25 C3' G A 102 OK 23 26 27 48 C3' C A 103 OK 46 49 50 74 C3' NF2 A 104 OK 76 75 72 89 C3' A A 105 OK 87 90 91 111 C3' A A 106 OK 109 112 113 133 C3' U A 107 OK 131 134 135 153 C3' U A 108 OK 151 154 155 173 C3' G A 109 OK 171 174 175 196 C3' G A 110 OK 194 197 198 219 C3' C A 111 OK 217 220 221 239 C3' G A 112 OK 237 240 241 260 C3' C B 101 OK 258 261 262 280 C3' G B 102 OK 278 281 282 303 C3' C B 103 OK 301 304 305 329 C3' NF2 B 104 OK 331 330 327 344 C3' A B 105 OK 342 345 346 366 C3' A B 106 OK 364 367 368 388 C3' U B 107 OK 386 389 390 408 C3' U B 108 OK 406 409 410 428 C3' G B 109 OK 426 429 430 451 C3' G B 110 OK 449 452 453 474 C3' C B 111 OK 472 475 476 494 C3' G B 112 OK 492 495 496 515 C3' C C 101 OK 513 516 517 535 C3' G C 102 OK 533 536 537 558 C3' C C 103 OK 556 559 560 584 C3' NF2 C 104 OK 586 585 582 599 C3' A C 105 OK 597 600 601 621 C3' A C 106 OK 619 622 623 643 C3' U C 107 OK 641 644 645 663 C3' U C 108 OK 661 664 665 683 C3' G C 109 OK 681 684 685 706 C3' G C 110 OK 704 707 708 729 C3' C C 111 OK 727 730 731 749 C3' G C 112 OK 747 750 751 770 C3' C D 101 OK 768 771 772 790 C3' G D 102 OK 788 791 792 813 C3' C D 103 OK 811 814 815 839 C3' NF2 D 104 OK 841 840 837 854 C3' A D 105 OK 852 855 856 876 C3' A D 106 OK 874 877 878 898 C3' U D 107 OK 896 899 900 918 C3' U D 108 OK 916 919 920 938 C3' G D 109 OK 936 939 940 961 C3' G D 110 OK 959 962 963 984 C3' C D 111 OK 982 985 986 1004 C3' G D 112 OK 1002 1005 1006 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' C A 101 OK 5 2 4 23 C4' G A 102 OK 25 22 24 46 C4' C A 103 OK 48 45 47 76 C4' NF2 A 104 OK 74 77 71 87 C4' A A 105 OK 89 86 88 109 C4' A A 106 OK 111 108 110 131 C4' U A 107 OK 133 130 132 151 C4' U A 108 OK 153 150 152 171 C4' G A 109 OK 173 170 172 194 C4' G A 110 OK 196 193 195 217 C4' C A 111 OK 219 216 218 237 C4' G A 112 OK 239 236 238 258 C4' C B 101 OK 260 257 259 278 C4' G B 102 OK 280 277 279 301 C4' C B 103 OK 303 300 302 331 C4' NF2 B 104 OK 329 332 326 342 C4' A B 105 OK 344 341 343 364 C4' A B 106 OK 366 363 365 386 C4' U B 107 OK 388 385 387 406 C4' U B 108 OK 408 405 407 426 C4' G B 109 OK 428 425 427 449 C4' G B 110 OK 451 448 450 472 C4' C B 111 OK 474 471 473 492 C4' G B 112 OK 494 491 493 513 C4' C C 101 OK 515 512 514 533 C4' G C 102 OK 535 532 534 556 C4' C C 103 OK 558 555 557 586 C4' NF2 C 104 OK 584 587 581 597 C4' A C 105 OK 599 596 598 619 C4' A C 106 OK 621 618 620 641 C4' U C 107 OK 643 640 642 661 C4' U C 108 OK 663 660 662 681 C4' G C 109 OK 683 680 682 704 C4' G C 110 OK 706 703 705 727 C4' C C 111 OK 729 726 728 747 C4' G C 112 OK 749 746 748 768 C4' C D 101 OK 770 767 769 788 C4' G D 102 OK 790 787 789 811 C4' C D 103 OK 813 810 812 841 C4' NF2 D 104 OK 839 842 836 852 C4' A D 105 OK 854 851 853 874 C4' A D 106 OK 876 873 875 896 C4' U D 107 OK 898 895 897 916 C4' U D 108 OK 918 915 917 936 C4' G D 109 OK 938 935 937 959 C4' G D 110 OK 961 958 960 982 C4' C D 111 OK 984 981 983 1002 C4' G D 112 OK 1004 1001 1003 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' C A 101 1 3 22 C5' G A 102 21 23 45 C5' C A 103 44 46 77 C5' NF2 A 104 78 76 86 C5' A A 105 85 87 108 C5' A A 106 107 109 130 C5' U A 107 129 131 150 C5' U A 108 149 151 170 C5' G A 109 169 171 193 C5' G A 110 192 194 216 C5' C A 111 215 217 236 C5' G A 112 235 237 257 C5' C B 101 256 258 277 C5' G B 102 276 278 300 C5' C B 103 299 301 332 C5' NF2 B 104 333 331 341 C5' A B 105 340 342 363 C5' A B 106 362 364 385 C5' U B 107 384 386 405 C5' U B 108 404 406 425 C5' G B 109 424 426 448 C5' G B 110 447 449 471 C5' C B 111 470 472 491 C5' G B 112 490 492 512 C5' C C 101 511 513 532 C5' G C 102 531 533 555 C5' C C 103 554 556 587 C5' NF2 C 104 588 586 596 C5' A C 105 595 597 618 C5' A C 106 617 619 640 C5' U C 107 639 641 660 C5' U C 108 659 661 680 C5' G C 109 679 681 703 C5' G C 110 702 704 726 C5' C C 111 725 727 746 C5' G C 112 745 747 767 C5' C D 101 766 768 787 C5' G D 102 786 788 810 C5' C D 103 809 811 842 C5' NF2 D 104 843 841 851 C5' A D 105 850 852 873 C5' A D 106 872 874 895 C5' U D 107 894 896 915 C5' U D 108 914 916 935 C5' G D 109 934 936 958 C5' G D 110 957 959 981 C5' C D 111 980 982 1001 C5' G D 112 1000 1002 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 18 P G A 102 distorted distorted 6 19 20 21 41 P C A 103 distorted distorted 26 42 43 44 79 P NF2 A 104 distorted distorted 49 80 81 78 82 P A A 105 distorted distorted 75 83 84 85 104 P A A 106 distorted distorted 90 105 106 107 126 P U A 107 distorted distorted 112 127 128 129 146 P U A 108 distorted distorted 134 147 148 149 166 P G A 109 distorted distorted 154 167 168 169 189 P G A 110 distorted distorted 174 190 191 192 212 P C A 111 distorted distorted 197 213 214 215 232 P G A 112 distorted distorted 220 233 234 235 273 P G B 102 distorted distorted 261 274 275 276 296 P C B 103 distorted distorted 281 297 298 299 334 P NF2 B 104 distorted distorted 304 335 336 333 337 P A B 105 distorted distorted 330 338 339 340 359 P A B 106 distorted distorted 345 360 361 362 381 P U B 107 distorted distorted 367 382 383 384 401 P U B 108 distorted distorted 389 402 403 404 421 P G B 109 distorted distorted 409 422 423 424 444 P G B 110 distorted distorted 429 445 446 447 467 P C B 111 distorted distorted 452 468 469 470 487 P G B 112 distorted distorted 475 488 489 490 528 P G C 102 distorted distorted 516 529 530 531 551 P C C 103 distorted distorted 536 552 553 554 589 P NF2 C 104 distorted distorted 559 590 591 588 592 P A C 105 distorted distorted 585 593 594 595 614 P A C 106 distorted distorted 600 615 616 617 636 P U C 107 distorted distorted 622 637 638 639 656 P U C 108 distorted distorted 644 657 658 659 676 P G C 109 distorted distorted 664 677 678 679 699 P G C 110 distorted distorted 684 700 701 702 722 P C C 111 distorted distorted 707 723 724 725 742 P G C 112 distorted distorted 730 743 744 745 783 P G D 102 distorted distorted 771 784 785 786 806 P C D 103 distorted distorted 791 807 808 809 844 P NF2 D 104 distorted distorted 814 845 846 843 847 P A D 105 distorted distorted 840 848 849 850 869 P A D 106 distorted distorted 855 870 871 872 891 P U D 107 distorted distorted 877 892 893 894 911 P U D 108 distorted distorted 899 912 913 914 931 P G D 109 distorted distorted 919 932 933 934 954 P G D 110 distorted distorted 939 955 956 957 977 P C D 111 distorted distorted 962 978 979 980 997 P G D 112 distorted distorted 985 998 999 1000 ---------------------------------------------------------------------------------