ID code: '2K5Z' 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' --------------------------------------------------------------------------------- 12 C1' G A 1 alpha beta 7 30 13 10 46 C1' G A 2 alpha beta 41 64 47 44 80 C1' U A 3 alpha beta 75 95 81 78 110 C1' C A 4 alpha beta 105 125 111 108 141 C1' U A 5 alpha beta 136 156 142 139 171 C1' A A 6 alpha beta 166 188 172 169 204 C1' C A 7 alpha beta 199 219 205 202 235 C1' A A 8 alpha beta 230 252 236 233 268 C1' U A 9 alpha beta 263 283 269 266 298 C1' U A 10 alpha beta 293 313 299 296 328 C1' G A 11 alpha beta 323 346 329 326 362 C1' C A 12 alpha beta 357 377 363 360 393 C1' U A 13 alpha beta 388 408 394 391 423 C1' G A 14 alpha beta 418 441 424 421 457 C1' U A 15 alpha beta 452 472 458 455 487 C1' U A 16 alpha beta 482 502 488 485 517 C1' G A 17 alpha beta 512 535 518 515 551 C1' U A 18 alpha beta 546 566 552 549 581 C1' C A 19 alpha beta 576 596 582 579 612 C1' G A 20 alpha beta 607 630 613 610 646 C1' U A 21 alpha beta 641 661 647 644 676 C1' G A 22 alpha beta 671 694 677 674 710 C1' U A 23 alpha beta 705 725 711 708 740 C1' G A 24 alpha beta 735 758 741 738 774 C1' U A 25 alpha beta 769 789 775 772 804 C1' G A 26 alpha beta 799 822 805 802 838 C1' A A 27 alpha beta 833 855 839 836 871 C1' C A 28 alpha beta 866 886 872 869 902 C1' C A 29 alpha beta 897 917 903 900 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' G A 1 OK OK 12 8 28 11 44 C2' G A 2 OK OK 46 42 62 45 78 C2' U A 3 OK OK 80 76 93 79 108 C2' C A 4 OK OK 110 106 123 109 139 C2' U A 5 OK OK 141 137 154 140 169 C2' A A 6 OK OK 171 167 186 170 202 C2' C A 7 OK OK 204 200 217 203 233 C2' A A 8 OK OK 235 231 250 234 266 C2' U A 9 OK OK 268 264 281 267 296 C2' U A 10 OK OK 298 294 311 297 326 C2' G A 11 OK OK 328 324 344 327 360 C2' C A 12 OK OK 362 358 375 361 391 C2' U A 13 OK OK 393 389 406 392 421 C2' G A 14 OK OK 423 419 439 422 455 C2' U A 15 OK OK 457 453 470 456 485 C2' U A 16 OK OK 487 483 500 486 515 C2' G A 17 OK OK 517 513 533 516 549 C2' U A 18 OK OK 551 547 564 550 579 C2' C A 19 OK OK 581 577 594 580 610 C2' G A 20 OK OK 612 608 628 611 644 C2' U A 21 OK OK 646 642 659 645 674 C2' G A 22 OK OK 676 672 692 675 708 C2' U A 23 OK OK 710 706 723 709 738 C2' G A 24 OK OK 740 736 756 739 772 C2' U A 25 OK OK 774 770 787 773 802 C2' G A 26 OK OK 804 800 820 803 836 C2' A A 27 OK OK 838 834 853 837 869 C2' C A 28 OK OK 871 867 884 870 900 C2' C A 29 OK OK 902 898 915 901 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' G A 1 OK OK 6 27 9 10 42 C3' G A 2 OK OK 40 61 43 44 76 C3' U A 3 OK OK 74 92 77 78 106 C3' C A 4 OK OK 104 122 107 108 137 C3' U A 5 OK OK 135 153 138 139 167 C3' A A 6 OK OK 165 185 168 169 200 C3' C A 7 OK OK 198 216 201 202 231 C3' A A 8 OK OK 229 249 232 233 264 C3' U A 9 OK OK 262 280 265 266 294 C3' U A 10 OK OK 292 310 295 296 324 C3' G A 11 OK OK 322 343 325 326 358 C3' C A 12 OK OK 356 374 359 360 389 C3' U A 13 OK OK 387 405 390 391 419 C3' G A 14 OK OK 417 438 420 421 453 C3' U A 15 OK OK 451 469 454 455 483 C3' U A 16 OK OK 481 499 484 485 513 C3' G A 17 OK OK 511 532 514 515 547 C3' U A 18 OK OK 545 563 548 549 577 C3' C A 19 OK OK 575 593 578 579 608 C3' G A 20 OK OK 606 627 609 610 642 C3' U A 21 OK OK 640 658 643 644 672 C3' G A 22 OK OK 670 691 673 674 706 C3' U A 23 OK OK 704 722 707 708 736 C3' G A 24 OK OK 734 755 737 738 770 C3' U A 25 OK OK 768 786 771 772 800 C3' G A 26 OK OK 798 819 801 802 834 C3' A A 27 OK OK 832 852 835 836 867 C3' C A 28 OK OK 865 883 868 869 898 C3' C A 29 OK OK 896 914 899 900 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' G A 1 OK OK 8 26 5 7 40 C4' G A 2 OK OK 42 60 39 41 74 C4' U A 3 OK OK 76 91 73 75 104 C4' C A 4 OK OK 106 121 103 105 135 C4' U A 5 OK OK 137 152 134 136 165 C4' A A 6 OK OK 167 184 164 166 198 C4' C A 7 OK OK 200 215 197 199 229 C4' A A 8 OK OK 231 248 228 230 262 C4' U A 9 OK OK 264 279 261 263 292 C4' U A 10 OK OK 294 309 291 293 322 C4' G A 11 OK OK 324 342 321 323 356 C4' C A 12 OK OK 358 373 355 357 387 C4' U A 13 OK OK 389 404 386 388 417 C4' G A 14 OK OK 419 437 416 418 451 C4' U A 15 OK OK 453 468 450 452 481 C4' U A 16 OK OK 483 498 480 482 511 C4' G A 17 OK OK 513 531 510 512 545 C4' U A 18 OK OK 547 562 544 546 575 C4' C A 19 OK OK 577 592 574 576 606 C4' G A 20 OK OK 608 626 605 607 640 C4' U A 21 OK OK 642 657 639 641 670 C4' G A 22 OK OK 672 690 669 671 704 C4' U A 23 OK OK 706 721 703 705 734 C4' G A 24 OK OK 736 754 733 735 768 C4' U A 25 OK OK 770 785 767 769 798 C4' G A 26 OK OK 800 818 797 799 832 C4' A A 27 OK OK 834 851 831 833 865 C4' C A 28 OK OK 867 882 864 866 896 C4' C A 29 OK OK 898 913 895 897 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' G A 1 OK OK 4 24 25 6 39 C5' G A 2 OK OK 38 58 59 40 73 C5' U A 3 OK OK 72 89 90 74 103 C5' C A 4 OK OK 102 119 120 104 134 C5' U A 5 OK OK 133 150 151 135 164 C5' A A 6 OK OK 163 182 183 165 197 C5' C A 7 OK OK 196 213 214 198 228 C5' A A 8 OK OK 227 246 247 229 261 C5' U A 9 OK OK 260 277 278 262 291 C5' U A 10 OK OK 290 307 308 292 321 C5' G A 11 OK OK 320 340 341 322 355 C5' C A 12 OK OK 354 371 372 356 386 C5' U A 13 OK OK 385 402 403 387 416 C5' G A 14 OK OK 415 435 436 417 450 C5' U A 15 OK OK 449 466 467 451 480 C5' U A 16 OK OK 479 496 497 481 510 C5' G A 17 OK OK 509 529 530 511 544 C5' U A 18 OK OK 543 560 561 545 574 C5' C A 19 OK OK 573 590 591 575 605 C5' G A 20 OK OK 604 624 625 606 639 C5' U A 21 OK OK 638 655 656 640 669 C5' G A 22 OK OK 668 688 689 670 703 C5' U A 23 OK OK 702 719 720 704 733 C5' G A 24 OK OK 732 752 753 734 767 C5' U A 25 OK OK 766 783 784 768 797 C5' G A 26 OK OK 796 816 817 798 831 C5' A A 27 OK OK 830 849 850 832 864 C5' C A 28 OK OK 863 880 881 865 895 C5' C A 29 OK OK 894 911 912 896 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P G A 1 distorted distorted 2 3 4 35 P G A 2 distorted distorted 9 36 37 38 69 P U A 3 distorted distorted 43 70 71 72 99 P C A 4 distorted distorted 77 100 101 102 130 P U A 5 distorted distorted 107 131 132 133 160 P A A 6 distorted distorted 138 161 162 163 193 P C A 7 distorted distorted 168 194 195 196 224 P A A 8 distorted distorted 201 225 226 227 257 P U A 9 distorted distorted 232 258 259 260 287 P U A 10 distorted distorted 265 288 289 290 317 P G A 11 distorted distorted 295 318 319 320 351 P C A 12 distorted distorted 325 352 353 354 382 P U A 13 distorted distorted 359 383 384 385 412 P G A 14 distorted distorted 390 413 414 415 446 P U A 15 distorted distorted 420 447 448 449 476 P U A 16 distorted distorted 454 477 478 479 506 P G A 17 distorted distorted 484 507 508 509 540 P U A 18 distorted distorted 514 541 542 543 570 P C A 19 distorted distorted 548 571 572 573 601 P G A 20 distorted distorted 578 602 603 604 635 P U A 21 distorted distorted 609 636 637 638 665 P G A 22 distorted distorted 643 666 667 668 699 P U A 23 distorted distorted 673 700 701 702 729 P G A 24 distorted distorted 707 730 731 732 763 P U A 25 distorted distorted 737 764 765 766 793 P G A 26 distorted distorted 771 794 795 796 827 P A A 27 distorted distorted 801 828 829 830 860 P C A 28 distorted distorted 835 861 862 863 891 P C A 29 distorted distorted 868 892 893 894 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