ID code: '3BNL' 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' --------------------------------------------------------------------------------- 13 C1' U A 1 beta 8 14 11 33 C1' G A 2 beta 28 34 31 56 C1' C A 3 beta 51 57 54 76 C1' G A 4 beta 71 77 74 99 C1' U A 5 beta 94 100 97 119 C1' C A 6 beta 114 120 117 139 C1' A A 7 beta 134 140 137 161 C1' C A 8 beta 156 162 159 181 C1' A A 9 beta 176 182 179 203 C1' C A 10 beta 198 204 201 223 C1' C A 11 beta 218 224 221 243 C1' G A 12 beta 238 244 241 266 C1' G A 13 beta 261 267 264 289 C1' U A 14 beta 284 290 287 309 C1' G A 15 beta 304 310 307 332 C1' A A 16 beta 327 333 330 354 C1' A A 17 beta 349 355 352 376 C1' G A 18 beta 371 377 374 399 C1' U A 19 beta 394 400 397 419 C1' C A 20 beta 414 420 417 439 C1' G A 21 beta 434 440 437 462 C1' C A 22 beta 457 463 460 484 C1' U B 1 beta 479 485 482 504 C1' G B 2 beta 499 505 502 527 C1' C B 3 beta 522 528 525 547 C1' G B 4 beta 542 548 545 570 C1' U B 5 beta 565 571 568 590 C1' C B 6 beta 585 591 588 610 C1' A B 7 beta 605 611 608 632 C1' C B 8 beta 627 633 630 652 C1' A B 9 beta 647 653 650 674 C1' C B 10 beta 669 675 672 694 C1' C B 11 beta 689 695 692 714 C1' G B 12 beta 709 715 712 737 C1' G B 13 beta 732 738 735 760 C1' U B 14 beta 755 761 758 780 C1' G B 15 beta 775 781 778 803 C1' A B 16 beta 798 804 801 825 C1' A B 17 beta 820 826 823 847 C1' G B 18 beta 842 848 845 870 C1' U B 19 beta 865 871 868 890 C1' C B 20 beta 885 891 888 910 C1' G B 21 beta 905 911 908 933 C1' C B 22 beta 928 934 931 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 11 C2' U A 1 OK 13 9 12 31 C2' G A 2 OK 33 29 32 54 C2' C A 3 OK 56 52 55 74 C2' G A 4 OK 76 72 75 97 C2' U A 5 OK 99 95 98 117 C2' C A 6 OK 119 115 118 137 C2' A A 7 OK 139 135 138 159 C2' C A 8 OK 161 157 160 179 C2' A A 9 OK 181 177 180 201 C2' C A 10 OK 203 199 202 221 C2' C A 11 OK 223 219 222 241 C2' G A 12 OK 243 239 242 264 C2' G A 13 OK 266 262 265 287 C2' U A 14 OK 289 285 288 307 C2' G A 15 OK 309 305 308 330 C2' A A 16 OK 332 328 331 352 C2' A A 17 OK 354 350 353 374 C2' G A 18 OK 376 372 375 397 C2' U A 19 OK 399 395 398 417 C2' C A 20 OK 419 415 418 437 C2' G A 21 OK 439 435 438 460 C2' C A 22 OK 462 458 461 482 C2' U B 1 OK 484 480 483 502 C2' G B 2 OK 504 500 503 525 C2' C B 3 OK 527 523 526 545 C2' G B 4 OK 547 543 546 568 C2' U B 5 OK 570 566 569 588 C2' C B 6 OK 590 586 589 608 C2' A B 7 OK 610 606 609 630 C2' C B 8 OK 632 628 631 650 C2' A B 9 OK 652 648 651 672 C2' C B 10 OK 674 670 673 692 C2' C B 11 OK 694 690 693 712 C2' G B 12 OK 714 710 713 735 C2' G B 13 OK 737 733 736 758 C2' U B 14 OK 760 756 759 778 C2' G B 15 OK 780 776 779 801 C2' A B 16 OK 803 799 802 823 C2' A B 17 OK 825 821 824 845 C2' G B 18 OK 847 843 846 868 C2' U B 19 OK 870 866 869 888 C2' C B 20 OK 890 886 889 908 C2' G B 21 OK 910 906 909 931 C2' C B 22 OK 933 929 932 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 9 C3' U A 1 OK 7 10 11 29 C3' G A 2 OK 27 30 31 52 C3' C A 3 OK 50 53 54 72 C3' G A 4 OK 70 73 74 95 C3' U A 5 OK 93 96 97 115 C3' C A 6 OK 113 116 117 135 C3' A A 7 OK 133 136 137 157 C3' C A 8 OK 155 158 159 177 C3' A A 9 OK 175 178 179 199 C3' C A 10 OK 197 200 201 219 C3' C A 11 OK 217 220 221 239 C3' G A 12 OK 237 240 241 262 C3' G A 13 OK 260 263 264 285 C3' U A 14 OK 283 286 287 305 C3' G A 15 OK 303 306 307 328 C3' A A 16 OK 326 329 330 350 C3' A A 17 OK 348 351 352 372 C3' G A 18 OK 370 373 374 395 C3' U A 19 OK 393 396 397 415 C3' C A 20 OK 413 416 417 435 C3' G A 21 OK 433 436 437 458 C3' C A 22 OK 456 459 460 480 C3' U B 1 OK 478 481 482 500 C3' G B 2 OK 498 501 502 523 C3' C B 3 OK 521 524 525 543 C3' G B 4 OK 541 544 545 566 C3' U B 5 OK 564 567 568 586 C3' C B 6 OK 584 587 588 606 C3' A B 7 OK 604 607 608 628 C3' C B 8 OK 626 629 630 648 C3' A B 9 OK 646 649 650 670 C3' C B 10 OK 668 671 672 690 C3' C B 11 OK 688 691 692 710 C3' G B 12 OK 708 711 712 733 C3' G B 13 OK 731 734 735 756 C3' U B 14 OK 754 757 758 776 C3' G B 15 OK 774 777 778 799 C3' A B 16 OK 797 800 801 821 C3' A B 17 OK 819 822 823 843 C3' G B 18 OK 841 844 845 866 C3' U B 19 OK 864 867 868 886 C3' C B 20 OK 884 887 888 906 C3' G B 21 OK 904 907 908 929 C3' C B 22 OK 927 930 931 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 7 C4' U A 1 OK 9 6 8 27 C4' G A 2 OK 29 26 28 50 C4' C A 3 OK 52 49 51 70 C4' G A 4 OK 72 69 71 93 C4' U A 5 OK 95 92 94 113 C4' C A 6 OK 115 112 114 133 C4' A A 7 OK 135 132 134 155 C4' C A 8 OK 157 154 156 175 C4' A A 9 OK 177 174 176 197 C4' C A 10 OK 199 196 198 217 C4' C A 11 OK 219 216 218 237 C4' G A 12 OK 239 236 238 260 C4' G A 13 OK 262 259 261 283 C4' U A 14 OK 285 282 284 303 C4' G A 15 OK 305 302 304 326 C4' A A 16 OK 328 325 327 348 C4' A A 17 OK 350 347 349 370 C4' G A 18 OK 372 369 371 393 C4' U A 19 OK 395 392 394 413 C4' C A 20 OK 415 412 414 433 C4' G A 21 OK 435 432 434 456 C4' C A 22 OK 458 455 457 478 C4' U B 1 OK 480 477 479 498 C4' G B 2 OK 500 497 499 521 C4' C B 3 OK 523 520 522 541 C4' G B 4 OK 543 540 542 564 C4' U B 5 OK 566 563 565 584 C4' C B 6 OK 586 583 585 604 C4' A B 7 OK 606 603 605 626 C4' C B 8 OK 628 625 627 646 C4' A B 9 OK 648 645 647 668 C4' C B 10 OK 670 667 669 688 C4' C B 11 OK 690 687 689 708 C4' G B 12 OK 710 707 709 731 C4' G B 13 OK 733 730 732 754 C4' U B 14 OK 756 753 755 774 C4' G B 15 OK 776 773 775 797 C4' A B 16 OK 799 796 798 819 C4' A B 17 OK 821 818 820 841 C4' G B 18 OK 843 840 842 864 C4' U B 19 OK 866 863 865 884 C4' C B 20 OK 886 883 885 904 C4' G B 21 OK 906 903 905 927 C4' C B 22 OK 929 926 928 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 6 C5' U A 1 5 7 26 C5' G A 2 25 27 49 C5' C A 3 48 50 69 C5' G A 4 68 70 92 C5' U A 5 91 93 112 C5' C A 6 111 113 132 C5' A A 7 131 133 154 C5' C A 8 153 155 174 C5' A A 9 173 175 196 C5' C A 10 195 197 216 C5' C A 11 215 217 236 C5' G A 12 235 237 259 C5' G A 13 258 260 282 C5' U A 14 281 283 302 C5' G A 15 301 303 325 C5' A A 16 324 326 347 C5' A A 17 346 348 369 C5' G A 18 368 370 392 C5' U A 19 391 393 412 C5' C A 20 411 413 432 C5' G A 21 431 433 455 C5' C A 22 454 456 477 C5' U B 1 476 478 497 C5' G B 2 496 498 520 C5' C B 3 519 521 540 C5' G B 4 539 541 563 C5' U B 5 562 564 583 C5' C B 6 582 584 603 C5' A B 7 602 604 625 C5' C B 8 624 626 645 C5' A B 9 644 646 667 C5' C B 10 666 668 687 C5' C B 11 686 688 707 C5' G B 12 706 708 730 C5' G B 13 729 731 753 C5' U B 14 752 754 773 C5' G B 15 772 774 796 C5' A B 16 795 797 818 C5' A B 17 817 819 840 C5' G B 18 839 841 863 C5' U B 19 862 864 883 C5' C B 20 882 884 903 C5' G B 21 902 904 926 C5' C B 22 925 927 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2 P U A 1 OK OK 3 4 5 22 P G A 2 distorted distorted 10 23 24 25 45 P C A 3 distorted distorted 30 46 47 48 65 P G A 4 distorted distorted 53 66 67 68 88 P U A 5 distorted distorted 73 89 90 91 108 P C A 6 distorted distorted 96 109 110 111 128 P A A 7 distorted distorted 116 129 130 131 150 P C A 8 distorted distorted 136 151 152 153 170 P A A 9 distorted distorted 158 171 172 173 192 P C A 10 distorted distorted 178 193 194 195 212 P C A 11 distorted distorted 200 213 214 215 232 P G A 12 distorted distorted 220 233 234 235 255 P G A 13 distorted distorted 240 256 257 258 278 P U A 14 distorted distorted 263 279 280 281 298 P G A 15 distorted distorted 286 299 300 301 321 P A A 16 distorted distorted 306 322 323 324 343 P A A 17 distorted distorted 329 344 345 346 365 P G A 18 distorted distorted 351 366 367 368 388 P U A 19 distorted distorted 373 389 390 391 408 P C A 20 distorted distorted 396 409 410 411 428 P G A 21 distorted distorted 416 429 430 431 451 P C A 22 distorted distorted 436 452 453 454 473 P U B 1 OK OK 474 475 476 493 P G B 2 distorted distorted 481 494 495 496 516 P C B 3 distorted distorted 501 517 518 519 536 P G B 4 distorted distorted 524 537 538 539 559 P U B 5 distorted distorted 544 560 561 562 579 P C B 6 distorted distorted 567 580 581 582 599 P A B 7 distorted distorted 587 600 601 602 621 P C B 8 distorted distorted 607 622 623 624 641 P A B 9 distorted distorted 629 642 643 644 663 P C B 10 distorted distorted 649 664 665 666 683 P C B 11 distorted distorted 671 684 685 686 703 P G B 12 distorted distorted 691 704 705 706 726 P G B 13 distorted distorted 711 727 728 729 749 P U B 14 distorted distorted 734 750 751 752 769 P G B 15 distorted distorted 757 770 771 772 792 P A B 16 distorted distorted 777 793 794 795 814 P A B 17 distorted distorted 800 815 816 817 836 P G B 18 distorted distorted 822 837 838 839 859 P U B 19 distorted distorted 844 860 861 862 879 P C B 20 distorted distorted 867 880 881 882 899 P G B 21 distorted distorted 887 900 901 902 922 P C B 22 distorted distorted 907 923 924 925 ---------------------------------------------------------------------------------