ID code: '1HF0' 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' C M 1 beta 4 9 7 27 C1' A M 2 beta 23 28 26 48 C1' C M 3 beta 44 49 47 67 C1' A M 4 beta 63 68 66 88 C1' T M 5 beta 84 89 87 108 C1' T M 6 beta 104 109 107 128 C1' T M 7 beta 124 129 127 148 C1' G M 8 beta 144 149 147 170 C1' A M 9 beta 166 171 169 191 C1' A M 10 beta 187 192 190 212 C1' A M 11 beta 208 213 211 233 C1' G M 12 beta 229 234 232 255 C1' G M 13 beta 251 256 254 277 C1' C M 14 beta 273 278 276 296 C1' A M 15 beta 292 297 295 317 C1' A M 16 beta 313 318 316 338 C1' A M 17 beta 334 339 337 359 C1' T M 18 beta 355 360 358 379 C1' G M 19 beta 375 380 378 401 C1' G M 20 beta 397 402 400 423 C1' A M 21 beta 419 424 422 444 C1' G M 22 beta 440 445 443 464 C1' C N 1 beta 460 465 463 483 C1' T N 2 beta 479 484 482 503 C1' C N 3 beta 499 504 502 522 C1' C N 4 beta 518 523 521 541 C1' A N 5 beta 537 542 540 562 C1' T N 6 beta 558 563 561 582 C1' T N 7 beta 578 583 581 602 C1' T N 8 beta 598 603 601 622 C1' G N 9 beta 618 623 621 644 C1' C N 10 beta 640 645 643 663 C1' C N 11 beta 659 664 662 682 C1' T N 12 beta 678 683 681 702 C1' T N 13 beta 698 703 701 722 C1' T N 14 beta 718 723 721 742 C1' C N 15 beta 738 743 741 761 C1' A N 16 beta 757 762 760 782 C1' A N 17 beta 778 783 781 803 C1' A N 18 beta 799 804 802 824 C1' T N 19 beta 820 825 823 844 C1' G N 20 beta 840 845 843 866 C1' T N 21 beta 862 867 865 886 C1' G N 22 beta 882 887 885 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' C M 1 8 5 26 C2' A M 2 27 24 47 C2' C M 3 48 45 66 C2' A M 4 67 64 87 C2' T M 5 88 85 107 C2' T M 6 108 105 127 C2' T M 7 128 125 147 C2' G M 8 148 145 169 C2' A M 9 170 167 190 C2' A M 10 191 188 211 C2' A M 11 212 209 232 C2' G M 12 233 230 254 C2' G M 13 255 252 276 C2' C M 14 277 274 295 C2' A M 15 296 293 316 C2' A M 16 317 314 337 C2' A M 17 338 335 358 C2' T M 18 359 356 378 C2' G M 19 379 376 400 C2' G M 20 401 398 422 C2' A M 21 423 420 443 C2' G M 22 444 441 463 C2' C N 1 464 461 482 C2' T N 2 483 480 502 C2' C N 3 503 500 521 C2' C N 4 522 519 540 C2' A N 5 541 538 561 C2' T N 6 562 559 581 C2' T N 7 582 579 601 C2' T N 8 602 599 621 C2' G N 9 622 619 643 C2' C N 10 644 641 662 C2' C N 11 663 660 681 C2' T N 12 682 679 701 C2' T N 13 702 699 721 C2' T N 14 722 719 741 C2' C N 15 742 739 760 C2' A N 16 761 758 781 C2' A N 17 782 779 802 C2' A N 18 803 800 823 C2' T N 19 824 821 843 C2' G N 20 844 841 865 C2' T N 21 866 863 885 C2' G N 22 886 883 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' C M 1 OK 3 6 7 24 C3' A M 2 OK 22 25 26 45 C3' C M 3 OK 43 46 47 64 C3' A M 4 OK 62 65 66 85 C3' T M 5 OK 83 86 87 105 C3' T M 6 OK 103 106 107 125 C3' T M 7 OK 123 126 127 145 C3' G M 8 OK 143 146 147 167 C3' A M 9 OK 165 168 169 188 C3' A M 10 OK 186 189 190 209 C3' A M 11 OK 207 210 211 230 C3' G M 12 OK 228 231 232 252 C3' G M 13 OK 250 253 254 274 C3' C M 14 OK 272 275 276 293 C3' A M 15 OK 291 294 295 314 C3' A M 16 OK 312 315 316 335 C3' A M 17 OK 333 336 337 356 C3' T M 18 OK 354 357 358 376 C3' G M 19 OK 374 377 378 398 C3' G M 20 OK 396 399 400 420 C3' A M 21 OK 418 421 422 441 C3' G M 22 OK 439 442 443 461 C3' C N 1 OK 459 462 463 480 C3' T N 2 OK 478 481 482 500 C3' C N 3 OK 498 501 502 519 C3' C N 4 OK 517 520 521 538 C3' A N 5 OK 536 539 540 559 C3' T N 6 OK 557 560 561 579 C3' T N 7 OK 577 580 581 599 C3' T N 8 OK 597 600 601 619 C3' G N 9 OK 617 620 621 641 C3' C N 10 OK 639 642 643 660 C3' C N 11 OK 658 661 662 679 C3' T N 12 OK 677 680 681 699 C3' T N 13 OK 697 700 701 719 C3' T N 14 OK 717 720 721 739 C3' C N 15 OK 737 740 741 758 C3' A N 16 OK 756 759 760 779 C3' A N 17 OK 777 780 781 800 C3' A N 18 OK 798 801 802 821 C3' T N 19 OK 819 822 823 841 C3' G N 20 OK 839 842 843 863 C3' T N 21 OK 861 864 865 883 C3' G N 22 OK 881 884 885 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' C M 1 OK 5 2 4 22 C4' A M 2 OK 24 21 23 43 C4' C M 3 OK 45 42 44 62 C4' A M 4 OK 64 61 63 83 C4' T M 5 OK 85 82 84 103 C4' T M 6 OK 105 102 104 123 C4' T M 7 OK 125 122 124 143 C4' G M 8 OK 145 142 144 165 C4' A M 9 OK 167 164 166 186 C4' A M 10 OK 188 185 187 207 C4' A M 11 OK 209 206 208 228 C4' G M 12 OK 230 227 229 250 C4' G M 13 OK 252 249 251 272 C4' C M 14 OK 274 271 273 291 C4' A M 15 OK 293 290 292 312 C4' A M 16 OK 314 311 313 333 C4' A M 17 OK 335 332 334 354 C4' T M 18 OK 356 353 355 374 C4' G M 19 OK 376 373 375 396 C4' G M 20 OK 398 395 397 418 C4' A M 21 OK 420 417 419 439 C4' G M 22 OK 441 438 440 459 C4' C N 1 OK 461 458 460 478 C4' T N 2 OK 480 477 479 498 C4' C N 3 OK 500 497 499 517 C4' C N 4 OK 519 516 518 536 C4' A N 5 OK 538 535 537 557 C4' T N 6 OK 559 556 558 577 C4' T N 7 OK 579 576 578 597 C4' T N 8 OK 599 596 598 617 C4' G N 9 OK 619 616 618 639 C4' C N 10 OK 641 638 640 658 C4' C N 11 OK 660 657 659 677 C4' T N 12 OK 679 676 678 697 C4' T N 13 OK 699 696 698 717 C4' T N 14 OK 719 716 718 737 C4' C N 15 OK 739 736 738 756 C4' A N 16 OK 758 755 757 777 C4' A N 17 OK 779 776 778 798 C4' A N 18 OK 800 797 799 819 C4' T N 19 OK 821 818 820 839 C4' G N 20 OK 841 838 840 861 C4' T N 21 OK 863 860 862 881 C4' G N 22 OK 883 880 882 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' C M 1 1 3 21 C5' A M 2 20 22 42 C5' C M 3 41 43 61 C5' A M 4 60 62 82 C5' T M 5 81 83 102 C5' T M 6 101 103 122 C5' T M 7 121 123 142 C5' G M 8 141 143 164 C5' A M 9 163 165 185 C5' A M 10 184 186 206 C5' A M 11 205 207 227 C5' G M 12 226 228 249 C5' G M 13 248 250 271 C5' C M 14 270 272 290 C5' A M 15 289 291 311 C5' A M 16 310 312 332 C5' A M 17 331 333 353 C5' T M 18 352 354 373 C5' G M 19 372 374 395 C5' G M 20 394 396 417 C5' A M 21 416 418 438 C5' G M 22 437 439 458 C5' C N 1 457 459 477 C5' T N 2 476 478 497 C5' C N 3 496 498 516 C5' C N 4 515 517 535 C5' A N 5 534 536 556 C5' T N 6 555 557 576 C5' T N 7 575 577 596 C5' T N 8 595 597 616 C5' G N 9 615 617 638 C5' C N 10 637 639 657 C5' C N 11 656 658 676 C5' T N 12 675 677 696 C5' T N 13 695 697 716 C5' T N 14 715 717 736 C5' C N 15 735 737 755 C5' A N 16 754 756 776 C5' A N 17 775 777 797 C5' A N 18 796 798 818 C5' T N 19 817 819 838 C5' G N 20 837 839 860 C5' T N 21 859 861 880 C5' G N 22 879 881 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 17 P A M 2 distorted distorted 6 18 19 20 38 P C M 3 distorted distorted 25 39 40 41 57 P A M 4 distorted distorted 46 58 59 60 78 P T M 5 distorted distorted 65 79 80 81 98 P T M 6 distorted distorted 86 99 100 101 118 P T M 7 distorted distorted 106 119 120 121 138 P G M 8 distorted distorted 126 139 140 141 160 P A M 9 distorted distorted 146 161 162 163 181 P A M 10 distorted distorted 168 182 183 184 202 P A M 11 distorted distorted 189 203 204 205 223 P G M 12 distorted distorted 210 224 225 226 245 P G M 13 distorted distorted 231 246 247 248 267 P C M 14 distorted distorted 253 268 269 270 286 P A M 15 distorted distorted 275 287 288 289 307 P A M 16 distorted distorted 294 308 309 310 328 P A M 17 distorted distorted 315 329 330 331 349 P T M 18 distorted distorted 336 350 351 352 369 P G M 19 distorted distorted 357 370 371 372 391 P G M 20 distorted distorted 377 392 393 394 413 P A M 21 distorted distorted 399 414 415 416 434 P G M 22 distorted distorted 421 435 436 437 473 P T N 2 distorted distorted 462 474 475 476 493 P C N 3 distorted distorted 481 494 495 496 512 P C N 4 distorted distorted 501 513 514 515 531 P A N 5 distorted distorted 520 532 533 534 552 P T N 6 distorted distorted 539 553 554 555 572 P T N 7 distorted distorted 560 573 574 575 592 P T N 8 distorted distorted 580 593 594 595 612 P G N 9 distorted distorted 600 613 614 615 634 P C N 10 distorted distorted 620 635 636 637 653 P C N 11 distorted distorted 642 654 655 656 672 P T N 12 distorted distorted 661 673 674 675 692 P T N 13 distorted distorted 680 693 694 695 712 P T N 14 distorted distorted 700 713 714 715 732 P C N 15 distorted distorted 720 733 734 735 751 P A N 16 distorted distorted 740 752 753 754 772 P A N 17 distorted distorted 759 773 774 775 793 P A N 18 distorted distorted 780 794 795 796 814 P T N 19 distorted distorted 801 815 816 817 834 P G N 20 distorted distorted 822 835 836 837 856 P T N 21 distorted distorted 842 857 858 859 876 P G N 22 distorted distorted 864 877 878 879 ---------------------------------------------------------------------------------