ID code: '1J5N' 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' --------------------------------------------------------------------------------- 8 C1' G B 101 beta 4 9 7 42 C1' G B 102 beta 38 43 41 75 C1' G B 103 beta 71 76 74 108 C1' G B 104 beta 104 109 107 141 C1' T B 105 beta 137 142 140 173 C1' G B 106 beta 169 174 172 206 C1' A B 107 beta 202 207 205 238 C1' T B 108 beta 234 239 237 270 C1' T B 109 beta 266 271 269 302 C1' G B 110 beta 298 303 301 335 C1' T B 111 beta 331 336 334 367 C1' T B 112 beta 363 368 366 399 C1' C B 113 beta 395 400 398 429 C1' A B 114 beta 425 430 428 461 C1' G B 115 beta 457 462 460 493 C1' C C 116 beta 489 494 492 524 C1' T C 117 beta 520 525 523 556 C1' G C 118 beta 552 557 555 589 C1' A C 119 beta 585 590 588 621 C1' A C 120 beta 617 622 620 653 C1' C C 121 beta 649 654 652 683 C1' A C 122 beta 679 684 682 715 C1' A C 123 beta 711 716 714 747 C1' T C 124 beta 743 748 746 779 C1' C C 125 beta 775 780 778 809 C1' A C 126 beta 805 810 808 841 C1' C C 127 beta 837 842 840 871 C1' C C 128 beta 867 872 870 901 C1' C C 129 beta 897 902 900 931 C1' C C 130 beta 927 932 930 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G B 101 8 5 41 C2' G B 102 42 39 74 C2' G B 103 75 72 107 C2' G B 104 108 105 140 C2' T B 105 141 138 172 C2' G B 106 173 170 205 C2' A B 107 206 203 237 C2' T B 108 238 235 269 C2' T B 109 270 267 301 C2' G B 110 302 299 334 C2' T B 111 335 332 366 C2' T B 112 367 364 398 C2' C B 113 399 396 428 C2' A B 114 429 426 460 C2' G B 115 461 458 492 C2' C C 116 493 490 523 C2' T C 117 524 521 555 C2' G C 118 556 553 588 C2' A C 119 589 586 620 C2' A C 120 621 618 652 C2' C C 121 653 650 682 C2' A C 122 683 680 714 C2' A C 123 715 712 746 C2' T C 124 747 744 778 C2' C C 125 779 776 808 C2' A C 126 809 806 840 C2' C C 127 841 838 870 C2' C C 128 871 868 900 C2' C C 129 901 898 930 C2' C C 130 931 928 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G B 101 OK 3 6 7 39 C3' G B 102 OK 37 40 41 72 C3' G B 103 OK 70 73 74 105 C3' G B 104 OK 103 106 107 138 C3' T B 105 OK 136 139 140 170 C3' G B 106 OK 168 171 172 203 C3' A B 107 OK 201 204 205 235 C3' T B 108 OK 233 236 237 267 C3' T B 109 OK 265 268 269 299 C3' G B 110 OK 297 300 301 332 C3' T B 111 OK 330 333 334 364 C3' T B 112 OK 362 365 366 396 C3' C B 113 OK 394 397 398 426 C3' A B 114 OK 424 427 428 458 C3' G B 115 OK 456 459 460 490 C3' C C 116 OK 488 491 492 521 C3' T C 117 OK 519 522 523 553 C3' G C 118 OK 551 554 555 586 C3' A C 119 OK 584 587 588 618 C3' A C 120 OK 616 619 620 650 C3' C C 121 OK 648 651 652 680 C3' A C 122 OK 678 681 682 712 C3' A C 123 OK 710 713 714 744 C3' T C 124 OK 742 745 746 776 C3' C C 125 OK 774 777 778 806 C3' A C 126 OK 804 807 808 838 C3' C C 127 OK 836 839 840 868 C3' C C 128 OK 866 869 870 898 C3' C C 129 OK 896 899 900 928 C3' C C 130 OK 926 929 930 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G B 101 OK 5 2 4 37 C4' G B 102 OK 39 36 38 70 C4' G B 103 OK 72 69 71 103 C4' G B 104 OK 105 102 104 136 C4' T B 105 OK 138 135 137 168 C4' G B 106 OK 170 167 169 201 C4' A B 107 OK 203 200 202 233 C4' T B 108 OK 235 232 234 265 C4' T B 109 OK 267 264 266 297 C4' G B 110 OK 299 296 298 330 C4' T B 111 OK 332 329 331 362 C4' T B 112 OK 364 361 363 394 C4' C B 113 OK 396 393 395 424 C4' A B 114 OK 426 423 425 456 C4' G B 115 OK 458 455 457 488 C4' C C 116 OK 490 487 489 519 C4' T C 117 OK 521 518 520 551 C4' G C 118 OK 553 550 552 584 C4' A C 119 OK 586 583 585 616 C4' A C 120 OK 618 615 617 648 C4' C C 121 OK 650 647 649 678 C4' A C 122 OK 680 677 679 710 C4' A C 123 OK 712 709 711 742 C4' T C 124 OK 744 741 743 774 C4' C C 125 OK 776 773 775 804 C4' A C 126 OK 806 803 805 836 C4' C C 127 OK 838 835 837 866 C4' C C 128 OK 868 865 867 896 C4' C C 129 OK 898 895 897 926 C4' C C 130 OK 928 925 927 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G B 101 1 3 36 C5' G B 102 35 37 69 C5' G B 103 68 70 102 C5' G B 104 101 103 135 C5' T B 105 134 136 167 C5' G B 106 166 168 200 C5' A B 107 199 201 232 C5' T B 108 231 233 264 C5' T B 109 263 265 296 C5' G B 110 295 297 329 C5' T B 111 328 330 361 C5' T B 112 360 362 393 C5' C B 113 392 394 423 C5' A B 114 422 424 455 C5' G B 115 454 456 487 C5' C C 116 486 488 518 C5' T C 117 517 519 550 C5' G C 118 549 551 583 C5' A C 119 582 584 615 C5' A C 120 614 616 647 C5' C C 121 646 648 677 C5' A C 122 676 678 709 C5' A C 123 708 710 741 C5' T C 124 740 742 773 C5' C C 125 772 774 803 C5' A C 126 802 804 835 C5' C C 127 834 836 865 C5' C C 128 864 866 895 C5' C C 129 894 896 925 C5' C C 130 924 926 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 32 P G B 102 distorted distorted 6 33 34 35 65 P G B 103 distorted distorted 40 66 67 68 98 P G B 104 distorted distorted 73 99 100 101 131 P T B 105 distorted distorted 106 132 133 134 163 P G B 106 distorted distorted 139 164 165 166 196 P A B 107 distorted distorted 171 197 198 199 228 P T B 108 distorted distorted 204 229 230 231 260 P T B 109 distorted distorted 236 261 262 263 292 P G B 110 distorted distorted 268 293 294 295 325 P T B 111 distorted distorted 300 326 327 328 357 P T B 112 distorted distorted 333 358 359 360 389 P C B 113 distorted distorted 365 390 391 392 419 P A B 114 distorted distorted 397 420 421 422 451 P G B 115 distorted distorted 427 452 453 454 514 P T C 117 distorted distorted 491 515 516 517 546 P G C 118 distorted distorted 522 547 548 549 579 P A C 119 distorted distorted 554 580 581 582 611 P A C 120 distorted distorted 587 612 613 614 643 P C C 121 distorted distorted 619 644 645 646 673 P A C 122 distorted distorted 651 674 675 676 705 P A C 123 distorted distorted 681 706 707 708 737 P T C 124 distorted distorted 713 738 739 740 769 P C C 125 distorted distorted 745 770 771 772 799 P A C 126 distorted distorted 777 800 801 802 831 P C C 127 distorted distorted 807 832 833 834 861 P C C 128 distorted distorted 839 862 863 864 891 P C C 129 distorted distorted 869 892 893 894 921 P C C 130 distorted distorted 899 922 923 924 ---------------------------------------------------------------------------------