ID code: '1EWQ' 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' --------------------------------------------------------------------------------- 11 C1' C C1902 beta 7 12 10 30 C1' G C1903 beta 26 31 29 52 C1' A C1904 beta 48 53 51 73 C1' C C1905 beta 69 74 72 92 C1' G C1906 beta 88 93 91 114 C1' C C1907 beta 110 115 113 133 C1' T C1908 beta 129 134 132 153 C1' A C1909 beta 149 154 152 174 C1' G C1910 beta 170 175 173 196 C1' C C1911 beta 192 197 195 215 C1' G C1912 beta 211 216 214 257 C1' G C1914 beta 253 258 256 279 C1' C C1915 beta 275 280 278 298 C1' G C1916 beta 294 299 297 320 C1' G C1917 beta 316 321 319 342 C1' C C1918 beta 338 343 341 361 C1' T C1919 beta 357 362 360 381 C1' C C1920 beta 377 382 380 400 C1' G C1921 beta 396 401 399 422 C1' T C1922 beta 418 423 421 442 C1' C C1923 beta 438 443 441 462 C1' G D1952 beta 458 463 461 484 C1' A D1953 beta 480 485 483 505 C1' C D1954 beta 501 506 504 524 C1' G D1955 beta 520 525 523 546 C1' A D1956 beta 542 547 545 567 C1' G D1957 beta 563 568 566 589 C1' C D1958 beta 585 590 588 608 C1' C D1959 beta 604 609 607 627 C1' G D1960 beta 623 628 626 649 C1' C D1961 beta 645 650 648 668 C1' C D1962 beta 664 669 667 687 C1' G D1963 beta 683 688 686 709 C1' C D1964 beta 705 710 708 728 C1' T D1965 beta 724 729 727 748 C1' A D1966 beta 744 749 747 769 C1' G D1967 beta 765 770 768 791 C1' C D1968 beta 787 792 790 810 C1' G D1969 beta 806 811 809 832 C1' T D1970 beta 828 833 831 852 C1' C D1971 beta 848 853 851 871 C1' G D1972 beta 867 872 870 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' C C1902 11 8 29 C2' G C1903 30 27 51 C2' A C1904 52 49 72 C2' C C1905 73 70 91 C2' G C1906 92 89 113 C2' C C1907 114 111 132 C2' T C1908 133 130 152 C2' A C1909 153 150 173 C2' G C1910 174 171 195 C2' C C1911 196 193 214 C2' G C1912 215 212 256 C2' G C1914 257 254 278 C2' C C1915 279 276 297 C2' G C1916 298 295 319 C2' G C1917 320 317 341 C2' C C1918 342 339 360 C2' T C1919 361 358 380 C2' C C1920 381 378 399 C2' G C1921 400 397 421 C2' T C1922 422 419 441 C2' C C1923 442 439 461 C2' G D1952 462 459 483 C2' A D1953 484 481 504 C2' C D1954 505 502 523 C2' G D1955 524 521 545 C2' A D1956 546 543 566 C2' G D1957 567 564 588 C2' C D1958 589 586 607 C2' C D1959 608 605 626 C2' G D1960 627 624 648 C2' C D1961 649 646 667 C2' C D1962 668 665 686 C2' G D1963 687 684 708 C2' C D1964 709 706 727 C2' T D1965 728 725 747 C2' A D1966 748 745 768 C2' G D1967 769 766 790 C2' C D1968 791 788 809 C2' G D1969 810 807 831 C2' T D1970 832 829 851 C2' C D1971 852 849 870 C2' G D1972 871 868 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' C C1902 OK 6 9 10 27 C3' G C1903 OK 25 28 29 49 C3' A C1904 OK 47 50 51 70 C3' C C1905 OK 68 71 72 89 C3' G C1906 OK 87 90 91 111 C3' C C1907 OK 109 112 113 130 C3' T C1908 OK 128 131 132 150 C3' A C1909 OK 148 151 152 171 C3' G C1910 OK 169 172 173 193 C3' C C1911 OK 191 194 195 212 C3' G C1912 OK 210 213 214 254 C3' G C1914 OK 252 255 256 276 C3' C C1915 OK 274 277 278 295 C3' G C1916 OK 293 296 297 317 C3' G C1917 OK 315 318 319 339 C3' C C1918 OK 337 340 341 358 C3' T C1919 OK 356 359 360 378 C3' C C1920 OK 376 379 380 397 C3' G C1921 OK 395 398 399 419 C3' T C1922 OK 417 420 421 439 C3' C C1923 OK 437 440 441 459 C3' G D1952 OK 457 460 461 481 C3' A D1953 OK 479 482 483 502 C3' C D1954 OK 500 503 504 521 C3' G D1955 OK 519 522 523 543 C3' A D1956 OK 541 544 545 564 C3' G D1957 OK 562 565 566 586 C3' C D1958 OK 584 587 588 605 C3' C D1959 OK 603 606 607 624 C3' G D1960 OK 622 625 626 646 C3' C D1961 OK 644 647 648 665 C3' C D1962 OK 663 666 667 684 C3' G D1963 OK 682 685 686 706 C3' C D1964 OK 704 707 708 725 C3' T D1965 OK 723 726 727 745 C3' A D1966 OK 743 746 747 766 C3' G D1967 OK 764 767 768 788 C3' C D1968 OK 786 789 790 807 C3' G D1969 OK 805 808 809 829 C3' T D1970 OK 827 830 831 849 C3' C D1971 OK 847 850 851 868 C3' G D1972 OK 866 869 870 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' C C1902 OK 8 5 7 25 C4' G C1903 OK 27 24 26 47 C4' A C1904 OK 49 46 48 68 C4' C C1905 OK 70 67 69 87 C4' G C1906 OK 89 86 88 109 C4' C C1907 OK 111 108 110 128 C4' T C1908 OK 130 127 129 148 C4' A C1909 OK 150 147 149 169 C4' G C1910 OK 171 168 170 191 C4' C C1911 OK 193 190 192 210 C4' G C1912 OK 212 209 211 252 C4' G C1914 OK 254 251 253 274 C4' C C1915 OK 276 273 275 293 C4' G C1916 OK 295 292 294 315 C4' G C1917 OK 317 314 316 337 C4' C C1918 OK 339 336 338 356 C4' T C1919 OK 358 355 357 376 C4' C C1920 OK 378 375 377 395 C4' G C1921 OK 397 394 396 417 C4' T C1922 OK 419 416 418 437 C4' C C1923 OK 439 436 438 457 C4' G D1952 OK 459 456 458 479 C4' A D1953 OK 481 478 480 500 C4' C D1954 OK 502 499 501 519 C4' G D1955 OK 521 518 520 541 C4' A D1956 OK 543 540 542 562 C4' G D1957 OK 564 561 563 584 C4' C D1958 OK 586 583 585 603 C4' C D1959 OK 605 602 604 622 C4' G D1960 OK 624 621 623 644 C4' C D1961 OK 646 643 645 663 C4' C D1962 OK 665 662 664 682 C4' G D1963 OK 684 681 683 704 C4' C D1964 OK 706 703 705 723 C4' T D1965 OK 725 722 724 743 C4' A D1966 OK 745 742 744 764 C4' G D1967 OK 766 763 765 786 C4' C D1968 OK 788 785 787 805 C4' G D1969 OK 807 804 806 827 C4' T D1970 OK 829 826 828 847 C4' C D1971 OK 849 846 848 866 C4' G D1972 OK 868 865 867 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' C C1902 4 6 24 C5' G C1903 23 25 46 C5' A C1904 45 47 67 C5' C C1905 66 68 86 C5' G C1906 85 87 108 C5' C C1907 107 109 127 C5' T C1908 126 128 147 C5' A C1909 146 148 168 C5' G C1910 167 169 190 C5' C C1911 189 191 209 C5' G C1912 208 210 251 C5' G C1914 250 252 273 C5' C C1915 272 274 292 C5' G C1916 291 293 314 C5' G C1917 313 315 336 C5' C C1918 335 337 355 C5' T C1919 354 356 375 C5' C C1920 374 376 394 C5' G C1921 393 395 416 C5' T C1922 415 417 436 C5' C C1923 435 437 456 C5' G D1952 455 457 478 C5' A D1953 477 479 499 C5' C D1954 498 500 518 C5' G D1955 517 519 540 C5' A D1956 539 541 561 C5' G D1957 560 562 583 C5' C D1958 582 584 602 C5' C D1959 601 603 621 C5' G D1960 620 622 643 C5' C D1961 642 644 662 C5' C D1962 661 663 681 C5' G D1963 680 682 703 C5' C D1964 702 704 722 C5' T D1965 721 723 742 C5' A D1966 741 743 763 C5' G D1967 762 764 785 C5' C D1968 784 786 804 C5' G D1969 803 805 826 C5' T D1970 825 827 846 C5' C D1971 845 847 865 C5' G D1972 864 866 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P C C1902 distorted distorted 2 3 4 20 P G C1903 distorted distorted 9 21 22 23 42 P A C1904 distorted distorted 28 43 44 45 63 P C C1905 distorted distorted 50 64 65 66 82 P G C1906 distorted distorted 71 83 84 85 104 P C C1907 distorted distorted 90 105 106 107 123 P T C1908 distorted distorted 112 124 125 126 143 P A C1909 distorted distorted 131 144 145 146 164 P G C1910 distorted distorted 151 165 166 167 186 P C C1911 distorted distorted 172 187 188 189 205 P G C1912 distorted distorted 194 206 207 208 247 P G C1914 distorted distorted 248 249 250 269 P C C1915 distorted distorted 255 270 271 272 288 P G C1916 distorted distorted 277 289 290 291 310 P G C1917 distorted distorted 296 311 312 313 332 P C C1918 distorted distorted 318 333 334 335 351 P T C1919 distorted distorted 340 352 353 354 371 P C C1920 distorted distorted 359 372 373 374 390 P G C1921 distorted distorted 379 391 392 393 412 P T C1922 distorted distorted 398 413 414 415 432 P C C1923 distorted distorted 420 433 434 435 452 P G D1952 distorted distorted 453 454 455 474 P A D1953 distorted distorted 460 475 476 477 495 P C D1954 distorted distorted 482 496 497 498 514 P G D1955 distorted distorted 503 515 516 517 536 P A D1956 distorted distorted 522 537 538 539 557 P G D1957 distorted distorted 544 558 559 560 579 P C D1958 distorted distorted 565 580 581 582 598 P C D1959 distorted distorted 587 599 600 601 617 P G D1960 distorted distorted 606 618 619 620 639 P C D1961 distorted distorted 625 640 641 642 658 P C D1962 distorted distorted 647 659 660 661 677 P G D1963 distorted distorted 666 678 679 680 699 P C D1964 distorted distorted 685 700 701 702 718 P T D1965 distorted distorted 707 719 720 721 738 P A D1966 distorted distorted 726 739 740 741 759 P G D1967 distorted distorted 746 760 761 762 781 P C D1968 distorted distorted 767 782 783 784 800 P G D1969 distorted distorted 789 801 802 803 822 P T D1970 distorted distorted 808 823 824 825 842 P C D1971 distorted distorted 830 843 844 845 861 P G D1972 distorted distorted 850 862 863 864 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