ID code: '1KP7' 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' C A 3 alpha beta 73 93 79 76 109 C1' G A 4 alpha beta 104 127 110 107 143 C1' C A 5 alpha beta 138 158 144 141 174 C1' U A 6 alpha beta 169 189 175 172 204 C1' C A 7 alpha beta 199 219 205 202 235 C1' A A 8 alpha beta 230 252 236 233 268 C1' A A 9 alpha beta 263 285 269 266 301 C1' U A 10 alpha beta 296 316 302 299 331 C1' G A 11 alpha beta 326 349 332 329 365 C1' C A 12 alpha beta 360 380 366 363 396 C1' U A 13 alpha beta 391 411 397 394 426 C1' C A 14 alpha beta 421 441 427 424 457 C1' U A 15 alpha beta 452 472 458 455 487 C1' U A 16 alpha beta 482 502 488 485 517 C1' C A 17 alpha beta 512 532 518 515 548 C1' G A 18 alpha beta 543 566 549 546 582 C1' G A 19 alpha beta 577 600 583 580 616 C1' A A 20 alpha beta 611 633 617 614 649 C1' G A 21 alpha beta 644 667 650 647 683 C1' A A 22 alpha beta 678 700 684 681 716 C1' C A 23 alpha beta 711 731 717 714 747 C1' G A 24 alpha beta 742 765 748 745 781 C1' A A 25 alpha beta 776 798 782 779 814 C1' C A 26 alpha beta 809 829 815 812 845 C1' C A 27 alpha beta 840 860 846 843 876 C1' G A 28 alpha beta 871 894 877 874 910 C1' C A 29 alpha beta 905 925 911 908 941 C1' C A 30 alpha beta 936 957 942 939 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' C A 3 OK OK 78 74 91 77 107 C2' G A 4 OK OK 109 105 125 108 141 C2' C A 5 OK OK 143 139 156 142 172 C2' U A 6 OK OK 174 170 187 173 202 C2' C A 7 OK OK 204 200 217 203 233 C2' A A 8 OK OK 235 231 250 234 266 C2' A A 9 OK OK 268 264 283 267 299 C2' U A 10 OK OK 301 297 314 300 329 C2' G A 11 OK OK 331 327 347 330 363 C2' C A 12 OK OK 365 361 378 364 394 C2' U A 13 OK OK 396 392 409 395 424 C2' C A 14 OK OK 426 422 439 425 455 C2' U A 15 OK OK 457 453 470 456 485 C2' U A 16 OK OK 487 483 500 486 515 C2' C A 17 OK OK 517 513 530 516 546 C2' G A 18 OK OK 548 544 564 547 580 C2' G A 19 OK OK 582 578 598 581 614 C2' A A 20 OK OK 616 612 631 615 647 C2' G A 21 OK OK 649 645 665 648 681 C2' A A 22 OK OK 683 679 698 682 714 C2' C A 23 OK OK 716 712 729 715 745 C2' G A 24 OK OK 747 743 763 746 779 C2' A A 25 OK OK 781 777 796 780 812 C2' C A 26 OK OK 814 810 827 813 843 C2' C A 27 OK OK 845 841 858 844 874 C2' G A 28 OK OK 876 872 892 875 908 C2' C A 29 OK OK 910 906 923 909 939 C2' C A 30 OK OK 941 937 955 940 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' C A 3 OK OK 72 90 75 76 105 C3' G A 4 OK OK 103 124 106 107 139 C3' C A 5 OK OK 137 155 140 141 170 C3' U A 6 OK OK 168 186 171 172 200 C3' C A 7 OK OK 198 216 201 202 231 C3' A A 8 OK OK 229 249 232 233 264 C3' A A 9 OK OK 262 282 265 266 297 C3' U A 10 OK OK 295 313 298 299 327 C3' G A 11 OK OK 325 346 328 329 361 C3' C A 12 OK OK 359 377 362 363 392 C3' U A 13 OK OK 390 408 393 394 422 C3' C A 14 OK OK 420 438 423 424 453 C3' U A 15 OK OK 451 469 454 455 483 C3' U A 16 OK OK 481 499 484 485 513 C3' C A 17 OK OK 511 529 514 515 544 C3' G A 18 OK OK 542 563 545 546 578 C3' G A 19 OK OK 576 597 579 580 612 C3' A A 20 OK OK 610 630 613 614 645 C3' G A 21 OK OK 643 664 646 647 679 C3' A A 22 OK OK 677 697 680 681 712 C3' C A 23 OK OK 710 728 713 714 743 C3' G A 24 OK OK 741 762 744 745 777 C3' A A 25 OK OK 775 795 778 779 810 C3' C A 26 OK OK 808 826 811 812 841 C3' C A 27 OK OK 839 857 842 843 872 C3' G A 28 OK OK 870 891 873 874 906 C3' C A 29 OK OK 904 922 907 908 937 C3' C A 30 OK OK 935 953 938 939 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' C A 3 OK OK 74 89 71 73 103 C4' G A 4 OK OK 105 123 102 104 137 C4' C A 5 OK OK 139 154 136 138 168 C4' U A 6 OK OK 170 185 167 169 198 C4' C A 7 OK OK 200 215 197 199 229 C4' A A 8 OK OK 231 248 228 230 262 C4' A A 9 OK OK 264 281 261 263 295 C4' U A 10 OK OK 297 312 294 296 325 C4' G A 11 OK OK 327 345 324 326 359 C4' C A 12 OK OK 361 376 358 360 390 C4' U A 13 OK OK 392 407 389 391 420 C4' C A 14 OK OK 422 437 419 421 451 C4' U A 15 OK OK 453 468 450 452 481 C4' U A 16 OK OK 483 498 480 482 511 C4' C A 17 OK OK 513 528 510 512 542 C4' G A 18 OK OK 544 562 541 543 576 C4' G A 19 OK OK 578 596 575 577 610 C4' A A 20 OK OK 612 629 609 611 643 C4' G A 21 OK OK 645 663 642 644 677 C4' A A 22 OK OK 679 696 676 678 710 C4' C A 23 OK OK 712 727 709 711 741 C4' G A 24 OK OK 743 761 740 742 775 C4' A A 25 OK OK 777 794 774 776 808 C4' C A 26 OK OK 810 825 807 809 839 C4' C A 27 OK OK 841 856 838 840 870 C4' G A 28 OK OK 872 890 869 871 904 C4' C A 29 OK OK 906 921 903 905 935 C4' C A 30 OK OK 937 952 934 936 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' C A 3 OK OK 70 87 88 72 102 C5' G A 4 OK OK 101 121 122 103 136 C5' C A 5 OK OK 135 152 153 137 167 C5' U A 6 OK OK 166 183 184 168 197 C5' C A 7 OK OK 196 213 214 198 228 C5' A A 8 OK OK 227 246 247 229 261 C5' A A 9 OK OK 260 279 280 262 294 C5' U A 10 OK OK 293 310 311 295 324 C5' G A 11 OK OK 323 343 344 325 358 C5' C A 12 OK OK 357 374 375 359 389 C5' U A 13 OK OK 388 405 406 390 419 C5' C A 14 OK OK 418 435 436 420 450 C5' U A 15 OK OK 449 466 467 451 480 C5' U A 16 OK OK 479 496 497 481 510 C5' C A 17 OK OK 509 526 527 511 541 C5' G A 18 OK OK 540 560 561 542 575 C5' G A 19 OK OK 574 594 595 576 609 C5' A A 20 OK OK 608 627 628 610 642 C5' G A 21 OK OK 641 661 662 643 676 C5' A A 22 OK OK 675 694 695 677 709 C5' C A 23 OK OK 708 725 726 710 740 C5' G A 24 OK OK 739 759 760 741 774 C5' A A 25 OK OK 773 792 793 775 807 C5' C A 26 OK OK 806 823 824 808 838 C5' C A 27 OK OK 837 854 855 839 869 C5' G A 28 OK OK 868 888 889 870 903 C5' C A 29 OK OK 902 919 920 904 934 C5' C A 30 OK OK 933 950 951 935 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 2 distorted distorted 6 34 35 36 67 P C A 3 distorted distorted 41 68 69 70 98 P G A 4 distorted distorted 75 99 100 101 132 P C A 5 distorted distorted 106 133 134 135 163 P U A 6 distorted distorted 140 164 165 166 193 P C A 7 distorted distorted 171 194 195 196 224 P A A 8 distorted distorted 201 225 226 227 257 P A A 9 distorted distorted 232 258 259 260 290 P U A 10 distorted distorted 265 291 292 293 320 P G A 11 distorted distorted 298 321 322 323 354 P C A 12 distorted distorted 328 355 356 357 385 P U A 13 distorted distorted 362 386 387 388 415 P C A 14 distorted distorted 393 416 417 418 446 P U A 15 distorted distorted 423 447 448 449 476 P U A 16 distorted distorted 454 477 478 479 506 P C A 17 distorted distorted 484 507 508 509 537 P G A 18 distorted distorted 514 538 539 540 571 P G A 19 distorted distorted 545 572 573 574 605 P A A 20 distorted distorted 579 606 607 608 638 P G A 21 distorted distorted 613 639 640 641 672 P A A 22 distorted distorted 646 673 674 675 705 P C A 23 distorted distorted 680 706 707 708 736 P G A 24 distorted distorted 713 737 738 739 770 P A A 25 distorted distorted 744 771 772 773 803 P C A 26 distorted distorted 778 804 805 806 834 P C A 27 distorted distorted 811 835 836 837 865 P G A 28 distorted distorted 842 866 867 868 899 P C A 29 distorted distorted 873 900 901 902 930 P C A 30 distorted distorted 907 931 932 933 ---------------------------------------------------------------------------------