ID code: '3MJA' 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' G B6174 beta 8 14 11 36 C1' G B6175 beta 31 37 34 59 C1' U B6176 beta 54 60 57 79 C1' U B6177 beta 74 80 77 99 C1' A B6178 beta 94 100 97 121 C1' U B6179 beta 116 122 119 141 C1' U B6180 beta 136 142 139 161 C1' C B6181 beta 156 162 159 181 C1' A B6182 beta 176 182 179 203 C1' G B6183 beta 198 204 201 226 C1' A B6184 beta 221 227 224 248 C1' U B6185 beta 243 249 246 268 C1' U B6186 beta 263 269 266 288 C1' A B6187 beta 283 289 286 310 C1' G B6188 beta 305 311 308 333 C1' G B6189 beta 328 334 331 356 C1' U B6190 beta 351 357 354 376 C1' A B6191 beta 371 377 374 398 C1' G B6192 beta 393 399 396 421 C1' U B6193 beta 416 422 419 441 C1' C B6194 beta 436 442 439 461 C1' G B6195 beta 456 462 459 484 C1' A B6196 beta 479 485 482 506 C1' A B6197 beta 501 507 504 528 C1' U B6198 beta 523 529 526 548 C1' G B6199 beta 543 549 546 571 C1' A B6200 beta 566 572 569 593 C1' C B6201 beta 588 594 591 613 C1' C B6202 beta 608 614 611 635 C1' U C6203 beta 630 636 633 655 C1' A C6204 beta 650 656 653 677 C1' A C6205 beta 672 678 675 699 C1' G C6206 beta 694 700 697 722 C1' A C6207 beta 717 723 720 744 C1' A C6208 beta 739 745 742 766 C1' A C6209 beta 761 767 764 788 C1' U C6210 beta 783 789 786 808 C1' U C6211 beta 803 809 806 828 C1' U C6212 beta 823 829 826 848 C1' A C6213 beta 843 849 846 870 C1' C C6214 beta 865 871 868 890 C1' C C6215 beta 885 891 888 910 C1' U C6216 beta 905 911 908 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 11 C2' G B6174 OK 13 9 12 34 C2' G B6175 OK 36 32 35 57 C2' U B6176 OK 59 55 58 77 C2' U B6177 OK 79 75 78 97 C2' A B6178 OK 99 95 98 119 C2' U B6179 OK 121 117 120 139 C2' U B6180 OK 141 137 140 159 C2' C B6181 OK 161 157 160 179 C2' A B6182 OK 181 177 180 201 C2' G B6183 OK 203 199 202 224 C2' A B6184 OK 226 222 225 246 C2' U B6185 OK 248 244 247 266 C2' U B6186 OK 268 264 267 286 C2' A B6187 OK 288 284 287 308 C2' G B6188 OK 310 306 309 331 C2' G B6189 OK 333 329 332 354 C2' U B6190 OK 356 352 355 374 C2' A B6191 OK 376 372 375 396 C2' G B6192 OK 398 394 397 419 C2' U B6193 OK 421 417 420 439 C2' C B6194 OK 441 437 440 459 C2' G B6195 OK 461 457 460 482 C2' A B6196 OK 484 480 483 504 C2' A B6197 OK 506 502 505 526 C2' U B6198 OK 528 524 527 546 C2' G B6199 OK 548 544 547 569 C2' A B6200 OK 571 567 570 591 C2' C B6201 OK 593 589 592 611 C2' C B6202 OK 613 609 612 633 C2' U C6203 OK 635 631 634 653 C2' A C6204 OK 655 651 654 675 C2' A C6205 OK 677 673 676 697 C2' G C6206 OK 699 695 698 720 C2' A C6207 OK 722 718 721 742 C2' A C6208 OK 744 740 743 764 C2' A C6209 OK 766 762 765 786 C2' U C6210 OK 788 784 787 806 C2' U C6211 OK 808 804 807 826 C2' U C6212 OK 828 824 827 846 C2' A C6213 OK 848 844 847 868 C2' C C6214 OK 870 866 869 888 C2' C C6215 OK 890 886 889 908 C2' U C6216 OK 910 906 909 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 9 C3' G B6174 OK 7 10 11 32 C3' G B6175 OK 30 33 34 55 C3' U B6176 OK 53 56 57 75 C3' U B6177 OK 73 76 77 95 C3' A B6178 OK 93 96 97 117 C3' U B6179 OK 115 118 119 137 C3' U B6180 OK 135 138 139 157 C3' C B6181 OK 155 158 159 177 C3' A B6182 OK 175 178 179 199 C3' G B6183 OK 197 200 201 222 C3' A B6184 OK 220 223 224 244 C3' U B6185 OK 242 245 246 264 C3' U B6186 OK 262 265 266 284 C3' A B6187 OK 282 285 286 306 C3' G B6188 OK 304 307 308 329 C3' G B6189 OK 327 330 331 352 C3' U B6190 OK 350 353 354 372 C3' A B6191 OK 370 373 374 394 C3' G B6192 OK 392 395 396 417 C3' U B6193 OK 415 418 419 437 C3' C B6194 OK 435 438 439 457 C3' G B6195 OK 455 458 459 480 C3' A B6196 OK 478 481 482 502 C3' A B6197 OK 500 503 504 524 C3' U B6198 OK 522 525 526 544 C3' G B6199 OK 542 545 546 567 C3' A B6200 OK 565 568 569 589 C3' C B6201 OK 587 590 591 609 C3' C B6202 OK 607 610 611 631 C3' U C6203 OK 629 632 633 651 C3' A C6204 OK 649 652 653 673 C3' A C6205 OK 671 674 675 695 C3' G C6206 OK 693 696 697 718 C3' A C6207 OK 716 719 720 740 C3' A C6208 OK 738 741 742 762 C3' A C6209 OK 760 763 764 784 C3' U C6210 OK 782 785 786 804 C3' U C6211 OK 802 805 806 824 C3' U C6212 OK 822 825 826 844 C3' A C6213 OK 842 845 846 866 C3' C C6214 OK 864 867 868 886 C3' C C6215 OK 884 887 888 906 C3' U C6216 OK 904 907 908 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 7 C4' G B6174 OK 9 6 8 30 C4' G B6175 OK 32 29 31 53 C4' U B6176 OK 55 52 54 73 C4' U B6177 OK 75 72 74 93 C4' A B6178 OK 95 92 94 115 C4' U B6179 OK 117 114 116 135 C4' U B6180 OK 137 134 136 155 C4' C B6181 OK 157 154 156 175 C4' A B6182 OK 177 174 176 197 C4' G B6183 OK 199 196 198 220 C4' A B6184 OK 222 219 221 242 C4' U B6185 OK 244 241 243 262 C4' U B6186 OK 264 261 263 282 C4' A B6187 OK 284 281 283 304 C4' G B6188 OK 306 303 305 327 C4' G B6189 OK 329 326 328 350 C4' U B6190 OK 352 349 351 370 C4' A B6191 OK 372 369 371 392 C4' G B6192 OK 394 391 393 415 C4' U B6193 OK 417 414 416 435 C4' C B6194 OK 437 434 436 455 C4' G B6195 OK 457 454 456 478 C4' A B6196 OK 480 477 479 500 C4' A B6197 OK 502 499 501 522 C4' U B6198 OK 524 521 523 542 C4' G B6199 OK 544 541 543 565 C4' A B6200 OK 567 564 566 587 C4' C B6201 OK 589 586 588 607 C4' C B6202 OK 609 606 608 629 C4' U C6203 OK 631 628 630 649 C4' A C6204 OK 651 648 650 671 C4' A C6205 OK 673 670 672 693 C4' G C6206 OK 695 692 694 716 C4' A C6207 OK 718 715 717 738 C4' A C6208 OK 740 737 739 760 C4' A C6209 OK 762 759 761 782 C4' U C6210 OK 784 781 783 802 C4' U C6211 OK 804 801 803 822 C4' U C6212 OK 824 821 823 842 C4' A C6213 OK 844 841 843 864 C4' C C6214 OK 866 863 865 884 C4' C C6215 OK 886 883 885 904 C4' U C6216 OK 906 903 905 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 6 C5' G B6174 5 7 29 C5' G B6175 28 30 52 C5' U B6176 51 53 72 C5' U B6177 71 73 92 C5' A B6178 91 93 114 C5' U B6179 113 115 134 C5' U B6180 133 135 154 C5' C B6181 153 155 174 C5' A B6182 173 175 196 C5' G B6183 195 197 219 C5' A B6184 218 220 241 C5' U B6185 240 242 261 C5' U B6186 260 262 281 C5' A B6187 280 282 303 C5' G B6188 302 304 326 C5' G B6189 325 327 349 C5' U B6190 348 350 369 C5' A B6191 368 370 391 C5' G B6192 390 392 414 C5' U B6193 413 415 434 C5' C B6194 433 435 454 C5' G B6195 453 455 477 C5' A B6196 476 478 499 C5' A B6197 498 500 521 C5' U B6198 520 522 541 C5' G B6199 540 542 564 C5' A B6200 563 565 586 C5' C B6201 585 587 606 C5' C B6202 605 607 628 C5' U C6203 627 629 648 C5' A C6204 647 649 670 C5' A C6205 669 671 692 C5' G C6206 691 693 715 C5' A C6207 714 716 737 C5' A C6208 736 738 759 C5' A C6209 758 760 781 C5' U C6210 780 782 801 C5' U C6211 800 802 821 C5' U C6212 820 822 841 C5' A C6213 840 842 863 C5' C C6214 862 864 883 C5' C C6215 882 884 903 C5' U C6216 902 904 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2 P G B6174 OK OK 3 4 5 25 P G B6175 distorted distorted 10 26 27 28 48 P U B6176 distorted distorted 33 49 50 51 68 P U B6177 distorted distorted 56 69 70 71 88 P A B6178 distorted distorted 76 89 90 91 110 P U B6179 distorted distorted 96 111 112 113 130 P U B6180 distorted distorted 118 131 132 133 150 P C B6181 distorted distorted 138 151 152 153 170 P A B6182 distorted distorted 158 171 172 173 192 P G B6183 distorted distorted 178 193 194 195 215 P A B6184 distorted distorted 200 216 217 218 237 P U B6185 distorted distorted 223 238 239 240 257 P U B6186 distorted distorted 245 258 259 260 277 P A B6187 distorted distorted 265 278 279 280 299 P G B6188 distorted distorted 285 300 301 302 322 P G B6189 distorted distorted 307 323 324 325 345 P U B6190 distorted distorted 330 346 347 348 365 P A B6191 distorted distorted 353 366 367 368 387 P G B6192 distorted distorted 373 388 389 390 410 P U B6193 distorted distorted 395 411 412 413 430 P C B6194 distorted distorted 418 431 432 433 450 P G B6195 distorted distorted 438 451 452 453 473 P A B6196 distorted distorted 458 474 475 476 495 P A B6197 distorted distorted 481 496 497 498 517 P U B6198 distorted distorted 503 518 519 520 537 P G B6199 distorted distorted 525 538 539 540 560 P A B6200 distorted distorted 545 561 562 563 582 P C B6201 distorted distorted 568 583 584 585 602 P C B6202 distorted distorted 590 603 604 605 624 P U C6203 OK OK 625 626 627 644 P A C6204 distorted distorted 632 645 646 647 666 P A C6205 distorted distorted 652 667 668 669 688 P G C6206 distorted distorted 674 689 690 691 711 P A C6207 distorted distorted 696 712 713 714 733 P A C6208 distorted distorted 719 734 735 736 755 P A C6209 distorted distorted 741 756 757 758 777 P U C6210 distorted distorted 763 778 779 780 797 P U C6211 distorted distorted 785 798 799 800 817 P U C6212 distorted distorted 805 818 819 820 837 P A C6213 distorted distorted 825 838 839 840 859 P C C6214 distorted distorted 845 860 861 862 879 P C C6215 distorted distorted 867 880 881 882 899 P U C6216 distorted distorted 887 900 901 902 ---------------------------------------------------------------------------------