ID code: '2D17' 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 alpha beta 4 24 10 7 41 C1' G A 2 alpha beta 36 59 42 39 75 C1' G A 3 alpha beta 70 93 76 73 109 C1' C A 4 alpha beta 104 124 110 107 140 C1' A A 5 alpha beta 135 157 141 138 173 C1' A A 6 alpha beta 168 190 174 171 206 C1' G A 7 alpha beta 201 224 207 204 240 C1' A A 8 alpha beta 235 257 241 238 273 C1' G A 9 alpha beta 268 291 274 271 307 C1' G A 10 alpha beta 302 325 308 305 341 C1' C A 11 alpha beta 336 356 342 339 372 C1' G A 12 alpha beta 367 390 373 370 406 C1' A A 13 alpha beta 401 423 407 404 439 C1' C A 14 alpha beta 434 454 440 437 470 C1' C A 15 alpha beta 465 485 471 468 501 C1' C A 16 alpha beta 496 516 502 499 530 C1' G B 1 alpha beta 525 548 531 528 565 C1' G B 2 alpha beta 560 583 566 563 599 C1' G B 3 alpha beta 594 617 600 597 633 C1' U B 4 alpha beta 628 648 634 631 663 C1' C B 5 alpha beta 658 678 664 661 694 C1' G B 6 alpha beta 689 712 695 692 728 C1' G B 7 alpha beta 723 746 729 726 762 C1' C B 8 alpha beta 757 777 763 760 793 C1' U B 9 alpha beta 788 808 794 791 823 C1' U B 10 alpha beta 818 838 824 821 853 C1' G B 11 alpha beta 848 871 854 851 887 C1' C B 12 alpha beta 882 902 888 885 918 C1' U B 13 alpha beta 913 933 919 916 948 C1' G B 14 alpha beta 943 966 949 946 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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 OK 9 5 22 8 39 C2' G A 2 OK OK 41 37 57 40 73 C2' G A 3 OK OK 75 71 91 74 107 C2' C A 4 OK OK 109 105 122 108 138 C2' A A 5 OK OK 140 136 155 139 171 C2' A A 6 OK OK 173 169 188 172 204 C2' G A 7 OK OK 206 202 222 205 238 C2' A A 8 OK OK 240 236 255 239 271 C2' G A 9 OK OK 273 269 289 272 305 C2' G A 10 OK OK 307 303 323 306 339 C2' C A 11 OK OK 341 337 354 340 370 C2' G A 12 OK OK 372 368 388 371 404 C2' A A 13 OK OK 406 402 421 405 437 C2' C A 14 OK OK 439 435 452 438 468 C2' C A 15 OK OK 470 466 483 469 499 C2' C A 16 OK OK 501 497 514 500 528 C2' G B 1 OK OK 530 526 546 529 563 C2' G B 2 OK OK 565 561 581 564 597 C2' G B 3 OK OK 599 595 615 598 631 C2' U B 4 OK OK 633 629 646 632 661 C2' C B 5 OK OK 663 659 676 662 692 C2' G B 6 OK OK 694 690 710 693 726 C2' G B 7 OK OK 728 724 744 727 760 C2' C B 8 OK OK 762 758 775 761 791 C2' U B 9 OK OK 793 789 806 792 821 C2' U B 10 OK OK 823 819 836 822 851 C2' G B 11 OK OK 853 849 869 852 885 C2' C B 12 OK OK 887 883 900 886 916 C2' U B 13 OK OK 918 914 931 917 946 C2' G B 14 OK OK 948 944 964 947 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' C A 1 OK OK 3 21 6 7 37 C3' G A 2 OK OK 35 56 38 39 71 C3' G A 3 OK OK 69 90 72 73 105 C3' C A 4 OK OK 103 121 106 107 136 C3' A A 5 OK OK 134 154 137 138 169 C3' A A 6 OK OK 167 187 170 171 202 C3' G A 7 OK OK 200 221 203 204 236 C3' A A 8 OK OK 234 254 237 238 269 C3' G A 9 OK OK 267 288 270 271 303 C3' G A 10 OK OK 301 322 304 305 337 C3' C A 11 OK OK 335 353 338 339 368 C3' G A 12 OK OK 366 387 369 370 402 C3' A A 13 OK OK 400 420 403 404 435 C3' C A 14 OK OK 433 451 436 437 466 C3' C A 15 OK OK 464 482 467 468 497 C3' C A 16 OK OK 495 513 498 499 526 C3' G B 1 OK OK 524 545 527 528 561 C3' G B 2 OK OK 559 580 562 563 595 C3' G B 3 OK OK 593 614 596 597 629 C3' U B 4 OK OK 627 645 630 631 659 C3' C B 5 OK OK 657 675 660 661 690 C3' G B 6 OK OK 688 709 691 692 724 C3' G B 7 OK OK 722 743 725 726 758 C3' C B 8 OK OK 756 774 759 760 789 C3' U B 9 OK OK 787 805 790 791 819 C3' U B 10 OK OK 817 835 820 821 849 C3' G B 11 OK OK 847 868 850 851 883 C3' C B 12 OK OK 881 899 884 885 914 C3' U B 13 OK OK 912 930 915 916 944 C3' G B 14 OK OK 942 963 945 946 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' C A 1 OK OK 5 20 2 4 35 C4' G A 2 OK OK 37 55 34 36 69 C4' G A 3 OK OK 71 89 68 70 103 C4' C A 4 OK OK 105 120 102 104 134 C4' A A 5 OK OK 136 153 133 135 167 C4' A A 6 OK OK 169 186 166 168 200 C4' G A 7 OK OK 202 220 199 201 234 C4' A A 8 OK OK 236 253 233 235 267 C4' G A 9 OK OK 269 287 266 268 301 C4' G A 10 OK OK 303 321 300 302 335 C4' C A 11 OK OK 337 352 334 336 366 C4' G A 12 OK OK 368 386 365 367 400 C4' A A 13 OK OK 402 419 399 401 433 C4' C A 14 OK OK 435 450 432 434 464 C4' C A 15 OK OK 466 481 463 465 495 C4' C A 16 OK OK 497 512 494 496 524 C4' G B 1 OK OK 526 544 523 525 559 C4' G B 2 OK OK 561 579 558 560 593 C4' G B 3 OK OK 595 613 592 594 627 C4' U B 4 OK OK 629 644 626 628 657 C4' C B 5 OK OK 659 674 656 658 688 C4' G B 6 OK OK 690 708 687 689 722 C4' G B 7 OK OK 724 742 721 723 756 C4' C B 8 OK OK 758 773 755 757 787 C4' U B 9 OK OK 789 804 786 788 817 C4' U B 10 OK OK 819 834 816 818 847 C4' G B 11 OK OK 849 867 846 848 881 C4' C B 12 OK OK 883 898 880 882 912 C4' U B 13 OK OK 914 929 911 913 942 C4' G B 14 OK OK 944 962 941 943 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' C A 1 OK OK 1 18 19 3 34 C5' G A 2 OK OK 33 53 54 35 68 C5' G A 3 OK OK 67 87 88 69 102 C5' C A 4 OK OK 101 118 119 103 133 C5' A A 5 OK OK 132 151 152 134 166 C5' A A 6 OK OK 165 184 185 167 199 C5' G A 7 OK OK 198 218 219 200 233 C5' A A 8 OK OK 232 251 252 234 266 C5' G A 9 OK OK 265 285 286 267 300 C5' G A 10 OK OK 299 319 320 301 334 C5' C A 11 OK OK 333 350 351 335 365 C5' G A 12 OK OK 364 384 385 366 399 C5' A A 13 OK OK 398 417 418 400 432 C5' C A 14 OK OK 431 448 449 433 463 C5' C A 15 OK OK 462 479 480 464 494 C5' C A 16 OK OK 493 510 511 495 523 C5' G B 1 OK OK 522 542 543 524 558 C5' G B 2 OK OK 557 577 578 559 592 C5' G B 3 OK OK 591 611 612 593 626 C5' U B 4 OK OK 625 642 643 627 656 C5' C B 5 OK OK 655 672 673 657 687 C5' G B 6 OK OK 686 706 707 688 721 C5' G B 7 OK OK 720 740 741 722 755 C5' C B 8 OK OK 754 771 772 756 786 C5' U B 9 OK OK 785 802 803 787 816 C5' U B 10 OK OK 815 832 833 817 846 C5' G B 11 OK OK 845 865 866 847 880 C5' C B 12 OK OK 879 896 897 881 911 C5' U B 13 OK OK 910 927 928 912 941 C5' G B 14 OK OK 940 960 961 942 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 30 P G A 2 distorted distorted 6 31 32 33 64 P G A 3 distorted distorted 38 65 66 67 98 P C A 4 distorted distorted 72 99 100 101 129 P A A 5 distorted distorted 106 130 131 132 162 P A A 6 distorted distorted 137 163 164 165 195 P G A 7 distorted distorted 170 196 197 198 229 P A A 8 distorted distorted 203 230 231 232 262 P G A 9 distorted distorted 237 263 264 265 296 P G A 10 distorted distorted 270 297 298 299 330 P C A 11 distorted distorted 304 331 332 333 361 P G A 12 distorted distorted 338 362 363 364 395 P A A 13 distorted distorted 369 396 397 398 428 P C A 14 distorted distorted 403 429 430 431 459 P C A 15 distorted distorted 436 460 461 462 490 P C A 16 distorted distorted 467 491 492 493 554 P G B 2 distorted distorted 527 555 556 557 588 P G B 3 distorted distorted 562 589 590 591 622 P U B 4 distorted distorted 596 623 624 625 652 P C B 5 distorted distorted 630 653 654 655 683 P G B 6 distorted distorted 660 684 685 686 717 P G B 7 distorted distorted 691 718 719 720 751 P C B 8 distorted distorted 725 752 753 754 782 P U B 9 distorted distorted 759 783 784 785 812 P U B 10 distorted distorted 790 813 814 815 842 P G B 11 distorted distorted 820 843 844 845 876 P C B 12 distorted distorted 850 877 878 879 907 P U B 13 distorted distorted 884 908 909 910 937 P G B 14 distorted distorted 915 938 939 940 ---------------------------------------------------------------------------------