ID code: '3FAR' 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 1 beta 4 10 7 29 C1' U A 2 beta 24 30 27 49 C1' U A 3 beta 44 50 47 69 C1' G A 4 beta 64 70 67 92 C1' C A 5 beta 87 93 90 112 C1' U A 6 beta 107 113 110 132 C1' G A 7 beta 127 133 130 155 C1' A A 8 beta 150 156 153 177 C1' A A 9 beta 172 178 175 199 C1' G A 10 beta 194 200 197 222 C1' C A 11 beta 217 223 220 242 C1' G A 12 beta 237 243 240 265 C1' C A 13 beta 260 266 263 285 C1' G A 14 beta 280 286 283 308 C1' C A 15 beta 303 309 306 328 C1' A A 16 beta 323 329 326 350 C1' C A 17 beta 345 351 348 370 C1' G A 18 beta 365 371 368 393 C1' G A 19 beta 388 394 391 416 C1' C A 20 beta 411 417 414 436 C1' A A 21 beta 431 437 434 458 C1' A A 22 beta 453 459 456 480 C1' G A 23 beta 475 481 478 501 C1' C B 1 beta 496 502 499 521 C1' U B 2 beta 516 522 519 541 C1' U B 3 beta 536 542 539 561 C1' G B 4 beta 556 562 559 584 C1' C B 5 beta 579 585 582 604 C1' U B 6 beta 599 605 602 624 C1' G B 7 beta 619 625 622 647 C1' A B 8 beta 642 648 645 669 C1' A B 9 beta 664 670 667 691 C1' G B 10 beta 686 692 689 714 C1' C B 11 beta 709 715 712 734 C1' G B 12 beta 729 735 732 757 C1' C B 13 beta 752 758 755 777 C1' G B 14 beta 772 778 775 800 C1' C B 15 beta 795 801 798 820 C1' A B 16 beta 815 821 818 842 C1' C B 17 beta 837 843 840 862 C1' G B 18 beta 857 863 860 885 C1' G B 19 beta 880 886 883 908 C1' C B 20 beta 903 909 906 928 C1' A B 21 beta 923 929 926 950 C1' A B 22 beta 945 951 948 972 C1' G B 23 beta 967 973 970 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' C A 1 OK 9 5 8 27 C2' U A 2 OK 29 25 28 47 C2' U A 3 OK 49 45 48 67 C2' G A 4 OK 69 65 68 90 C2' C A 5 OK 92 88 91 110 C2' U A 6 OK 112 108 111 130 C2' G A 7 OK 132 128 131 153 C2' A A 8 OK 155 151 154 175 C2' A A 9 OK 177 173 176 197 C2' G A 10 OK 199 195 198 220 C2' C A 11 OK 222 218 221 240 C2' G A 12 OK 242 238 241 263 C2' C A 13 OK 265 261 264 283 C2' G A 14 OK 285 281 284 306 C2' C A 15 OK 308 304 307 326 C2' A A 16 OK 328 324 327 348 C2' C A 17 OK 350 346 349 368 C2' G A 18 OK 370 366 369 391 C2' G A 19 OK 393 389 392 414 C2' C A 20 OK 416 412 415 434 C2' A A 21 OK 436 432 435 456 C2' A A 22 OK 458 454 457 478 C2' G A 23 OK 480 476 479 499 C2' C B 1 OK 501 497 500 519 C2' U B 2 OK 521 517 520 539 C2' U B 3 OK 541 537 540 559 C2' G B 4 OK 561 557 560 582 C2' C B 5 OK 584 580 583 602 C2' U B 6 OK 604 600 603 622 C2' G B 7 OK 624 620 623 645 C2' A B 8 OK 647 643 646 667 C2' A B 9 OK 669 665 668 689 C2' G B 10 OK 691 687 690 712 C2' C B 11 OK 714 710 713 732 C2' G B 12 OK 734 730 733 755 C2' C B 13 OK 757 753 756 775 C2' G B 14 OK 777 773 776 798 C2' C B 15 OK 800 796 799 818 C2' A B 16 OK 820 816 819 840 C2' C B 17 OK 842 838 841 860 C2' G B 18 OK 862 858 861 883 C2' G B 19 OK 885 881 884 906 C2' C B 20 OK 908 904 907 926 C2' A B 21 OK 928 924 927 948 C2' A B 22 OK 950 946 949 970 C2' G B 23 OK 972 968 971 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' C A 1 OK 3 6 7 25 C3' U A 2 OK 23 26 27 45 C3' U A 3 OK 43 46 47 65 C3' G A 4 OK 63 66 67 88 C3' C A 5 OK 86 89 90 108 C3' U A 6 OK 106 109 110 128 C3' G A 7 OK 126 129 130 151 C3' A A 8 OK 149 152 153 173 C3' A A 9 OK 171 174 175 195 C3' G A 10 OK 193 196 197 218 C3' C A 11 OK 216 219 220 238 C3' G A 12 OK 236 239 240 261 C3' C A 13 OK 259 262 263 281 C3' G A 14 OK 279 282 283 304 C3' C A 15 OK 302 305 306 324 C3' A A 16 OK 322 325 326 346 C3' C A 17 OK 344 347 348 366 C3' G A 18 OK 364 367 368 389 C3' G A 19 OK 387 390 391 412 C3' C A 20 OK 410 413 414 432 C3' A A 21 OK 430 433 434 454 C3' A A 22 OK 452 455 456 476 C3' G A 23 OK 474 477 478 497 C3' C B 1 OK 495 498 499 517 C3' U B 2 OK 515 518 519 537 C3' U B 3 OK 535 538 539 557 C3' G B 4 OK 555 558 559 580 C3' C B 5 OK 578 581 582 600 C3' U B 6 OK 598 601 602 620 C3' G B 7 OK 618 621 622 643 C3' A B 8 OK 641 644 645 665 C3' A B 9 OK 663 666 667 687 C3' G B 10 OK 685 688 689 710 C3' C B 11 OK 708 711 712 730 C3' G B 12 OK 728 731 732 753 C3' C B 13 OK 751 754 755 773 C3' G B 14 OK 771 774 775 796 C3' C B 15 OK 794 797 798 816 C3' A B 16 OK 814 817 818 838 C3' C B 17 OK 836 839 840 858 C3' G B 18 OK 856 859 860 881 C3' G B 19 OK 879 882 883 904 C3' C B 20 OK 902 905 906 924 C3' A B 21 OK 922 925 926 946 C3' A B 22 OK 944 947 948 968 C3' G B 23 OK 966 969 970 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' C A 1 OK 5 2 4 23 C4' U A 2 OK 25 22 24 43 C4' U A 3 OK 45 42 44 63 C4' G A 4 OK 65 62 64 86 C4' C A 5 OK 88 85 87 106 C4' U A 6 OK 108 105 107 126 C4' G A 7 OK 128 125 127 149 C4' A A 8 OK 151 148 150 171 C4' A A 9 OK 173 170 172 193 C4' G A 10 OK 195 192 194 216 C4' C A 11 OK 218 215 217 236 C4' G A 12 OK 238 235 237 259 C4' C A 13 OK 261 258 260 279 C4' G A 14 OK 281 278 280 302 C4' C A 15 OK 304 301 303 322 C4' A A 16 OK 324 321 323 344 C4' C A 17 OK 346 343 345 364 C4' G A 18 OK 366 363 365 387 C4' G A 19 OK 389 386 388 410 C4' C A 20 OK 412 409 411 430 C4' A A 21 OK 432 429 431 452 C4' A A 22 OK 454 451 453 474 C4' G A 23 OK 476 473 475 495 C4' C B 1 OK 497 494 496 515 C4' U B 2 OK 517 514 516 535 C4' U B 3 OK 537 534 536 555 C4' G B 4 OK 557 554 556 578 C4' C B 5 OK 580 577 579 598 C4' U B 6 OK 600 597 599 618 C4' G B 7 OK 620 617 619 641 C4' A B 8 OK 643 640 642 663 C4' A B 9 OK 665 662 664 685 C4' G B 10 OK 687 684 686 708 C4' C B 11 OK 710 707 709 728 C4' G B 12 OK 730 727 729 751 C4' C B 13 OK 753 750 752 771 C4' G B 14 OK 773 770 772 794 C4' C B 15 OK 796 793 795 814 C4' A B 16 OK 816 813 815 836 C4' C B 17 OK 838 835 837 856 C4' G B 18 OK 858 855 857 879 C4' G B 19 OK 881 878 880 902 C4' C B 20 OK 904 901 903 922 C4' A B 21 OK 924 921 923 944 C4' A B 22 OK 946 943 945 966 C4' G B 23 OK 968 965 967 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' C A 1 1 3 22 C5' U A 2 21 23 42 C5' U A 3 41 43 62 C5' G A 4 61 63 85 C5' C A 5 84 86 105 C5' U A 6 104 106 125 C5' G A 7 124 126 148 C5' A A 8 147 149 170 C5' A A 9 169 171 192 C5' G A 10 191 193 215 C5' C A 11 214 216 235 C5' G A 12 234 236 258 C5' C A 13 257 259 278 C5' G A 14 277 279 301 C5' C A 15 300 302 321 C5' A A 16 320 322 343 C5' C A 17 342 344 363 C5' G A 18 362 364 386 C5' G A 19 385 387 409 C5' C A 20 408 410 429 C5' A A 21 428 430 451 C5' A A 22 450 452 473 C5' G A 23 472 474 494 C5' C B 1 493 495 514 C5' U B 2 513 515 534 C5' U B 3 533 535 554 C5' G B 4 553 555 577 C5' C B 5 576 578 597 C5' U B 6 596 598 617 C5' G B 7 616 618 640 C5' A B 8 639 641 662 C5' A B 9 661 663 684 C5' G B 10 683 685 707 C5' C B 11 706 708 727 C5' G B 12 726 728 750 C5' C B 13 749 751 770 C5' G B 14 769 771 793 C5' C B 15 792 794 813 C5' A B 16 812 814 835 C5' C B 17 834 836 855 C5' G B 18 854 856 878 C5' G B 19 877 879 901 C5' C B 20 900 902 921 C5' A B 21 920 922 943 C5' A B 22 942 944 965 C5' G B 23 964 966 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 18 P U A 2 distorted distorted 6 19 20 21 38 P U A 3 distorted distorted 26 39 40 41 58 P G A 4 distorted distorted 46 59 60 61 81 P C A 5 distorted distorted 66 82 83 84 101 P U A 6 distorted distorted 89 102 103 104 121 P G A 7 distorted distorted 109 122 123 124 144 P A A 8 distorted distorted 129 145 146 147 166 P A A 9 distorted distorted 152 167 168 169 188 P G A 10 distorted distorted 174 189 190 191 211 P C A 11 distorted distorted 196 212 213 214 231 P G A 12 distorted distorted 219 232 233 234 254 P C A 13 distorted distorted 239 255 256 257 274 P G A 14 distorted distorted 262 275 276 277 297 P C A 15 distorted distorted 282 298 299 300 317 P A A 16 distorted distorted 305 318 319 320 339 P C A 17 distorted distorted 325 340 341 342 359 P G A 18 distorted distorted 347 360 361 362 382 P G A 19 distorted distorted 367 383 384 385 405 P C A 20 distorted distorted 390 406 407 408 425 P A A 21 distorted distorted 413 426 427 428 447 P A A 22 distorted distorted 433 448 449 450 469 P G A 23 distorted distorted 455 470 471 472 510 P U B 2 distorted distorted 498 511 512 513 530 P U B 3 distorted distorted 518 531 532 533 550 P G B 4 distorted distorted 538 551 552 553 573 P C B 5 distorted distorted 558 574 575 576 593 P U B 6 distorted distorted 581 594 595 596 613 P G B 7 distorted distorted 601 614 615 616 636 P A B 8 distorted distorted 621 637 638 639 658 P A B 9 distorted distorted 644 659 660 661 680 P G B 10 distorted distorted 666 681 682 683 703 P C B 11 distorted distorted 688 704 705 706 723 P G B 12 distorted distorted 711 724 725 726 746 P C B 13 distorted distorted 731 747 748 749 766 P G B 14 distorted distorted 754 767 768 769 789 P C B 15 distorted distorted 774 790 791 792 809 P A B 16 distorted distorted 797 810 811 812 831 P C B 17 distorted distorted 817 832 833 834 851 P G B 18 distorted distorted 839 852 853 854 874 P G B 19 distorted distorted 859 875 876 877 897 P C B 20 distorted distorted 882 898 899 900 917 P A B 21 distorted distorted 905 918 919 920 939 P A B 22 distorted distorted 925 940 941 942 961 P G B 23 distorted distorted 947 962 963 964 ---------------------------------------------------------------------------------