ID code: '5M0H' 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' G A 1 beta 4 10 7 32 C1' A A 2 beta 27 33 30 54 C1' U A 3 beta 49 55 52 74 C1' A A 4 beta 69 75 72 96 C1' A A 5 beta 91 97 94 118 C1' C A 6 beta 113 119 116 138 C1' U A 7 beta 133 139 136 158 C1' G A 8 beta 153 159 156 181 C1' A A 9 beta 176 182 179 203 C1' A A 10 beta 198 204 201 225 C1' U A 11 beta 220 226 223 245 C1' C A 12 beta 240 246 243 265 C1' G A 13 beta 260 266 263 288 C1' C A 14 beta 283 289 286 308 C1' U A 15 beta 303 309 306 328 C1' A A 16 beta 323 329 326 350 C1' A A 17 beta 345 351 348 372 C1' G A 18 beta 367 373 370 395 C1' G A 19 beta 390 396 393 418 C1' A A 20 beta 413 419 416 440 C1' U A 21 beta 435 441 438 460 C1' G A 22 beta 455 461 458 483 C1' A A 23 beta 478 484 481 505 C1' A A 24 beta 500 506 503 527 C1' A A 25 beta 522 528 525 549 C1' G A 26 beta 544 550 547 572 C1' U A 27 beta 567 573 570 592 C1' C A 28 beta 587 593 590 612 C1' U A 29 beta 607 613 610 632 C1' A A 30 beta 627 633 630 654 C1' U A 31 beta 649 655 652 674 C1' G A 32 beta 669 675 672 697 C1' C A 33 beta 692 698 695 717 C1' G A 34 beta 712 718 715 740 C1' A A 35 beta 735 741 738 762 C1' C A 36 beta 757 763 760 782 C1' A A 37 beta 777 783 780 804 C1' U A 38 beta 799 805 802 824 C1' U A 39 beta 819 825 822 844 C1' A A 40 beta 839 845 842 866 C1' U A 41 beta 861 867 864 886 C1' C A 42 beta 881 887 884 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G A 1 OK 9 5 8 30 C2' A A 2 OK 32 28 31 52 C2' U A 3 OK 54 50 53 72 C2' A A 4 OK 74 70 73 94 C2' A A 5 OK 96 92 95 116 C2' C A 6 OK 118 114 117 136 C2' U A 7 OK 138 134 137 156 C2' G A 8 OK 158 154 157 179 C2' A A 9 OK 181 177 180 201 C2' A A 10 OK 203 199 202 223 C2' U A 11 OK 225 221 224 243 C2' C A 12 OK 245 241 244 263 C2' G A 13 OK 265 261 264 286 C2' C A 14 OK 288 284 287 306 C2' U A 15 OK 308 304 307 326 C2' A A 16 OK 328 324 327 348 C2' A A 17 OK 350 346 349 370 C2' G A 18 OK 372 368 371 393 C2' G A 19 OK 395 391 394 416 C2' A A 20 OK 418 414 417 438 C2' U A 21 OK 440 436 439 458 C2' G A 22 OK 460 456 459 481 C2' A A 23 OK 483 479 482 503 C2' A A 24 OK 505 501 504 525 C2' A A 25 OK 527 523 526 547 C2' G A 26 OK 549 545 548 570 C2' U A 27 OK 572 568 571 590 C2' C A 28 OK 592 588 591 610 C2' U A 29 OK 612 608 611 630 C2' A A 30 OK 632 628 631 652 C2' U A 31 OK 654 650 653 672 C2' G A 32 OK 674 670 673 695 C2' C A 33 OK 697 693 696 715 C2' G A 34 OK 717 713 716 738 C2' A A 35 OK 740 736 739 760 C2' C A 36 OK 762 758 761 780 C2' A A 37 OK 782 778 781 802 C2' U A 38 OK 804 800 803 822 C2' U A 39 OK 824 820 823 842 C2' A A 40 OK 844 840 843 864 C2' U A 41 OK 866 862 865 884 C2' C A 42 OK 886 882 885 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK 3 6 7 28 C3' A A 2 OK 26 29 30 50 C3' U A 3 OK 48 51 52 70 C3' A A 4 OK 68 71 72 92 C3' A A 5 OK 90 93 94 114 C3' C A 6 OK 112 115 116 134 C3' U A 7 OK 132 135 136 154 C3' G A 8 OK 152 155 156 177 C3' A A 9 OK 175 178 179 199 C3' A A 10 OK 197 200 201 221 C3' U A 11 OK 219 222 223 241 C3' C A 12 OK 239 242 243 261 C3' G A 13 OK 259 262 263 284 C3' C A 14 OK 282 285 286 304 C3' U A 15 OK 302 305 306 324 C3' A A 16 OK 322 325 326 346 C3' A A 17 OK 344 347 348 368 C3' G A 18 OK 366 369 370 391 C3' G A 19 OK 389 392 393 414 C3' A A 20 OK 412 415 416 436 C3' U A 21 OK 434 437 438 456 C3' G A 22 OK 454 457 458 479 C3' A A 23 OK 477 480 481 501 C3' A A 24 OK 499 502 503 523 C3' A A 25 OK 521 524 525 545 C3' G A 26 OK 543 546 547 568 C3' U A 27 OK 566 569 570 588 C3' C A 28 OK 586 589 590 608 C3' U A 29 OK 606 609 610 628 C3' A A 30 OK 626 629 630 650 C3' U A 31 OK 648 651 652 670 C3' G A 32 OK 668 671 672 693 C3' C A 33 OK 691 694 695 713 C3' G A 34 OK 711 714 715 736 C3' A A 35 OK 734 737 738 758 C3' C A 36 OK 756 759 760 778 C3' A A 37 OK 776 779 780 800 C3' U A 38 OK 798 801 802 820 C3' U A 39 OK 818 821 822 840 C3' A A 40 OK 838 841 842 862 C3' U A 41 OK 860 863 864 882 C3' C A 42 OK 880 883 884 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK 5 2 4 26 C4' A A 2 OK 28 25 27 48 C4' U A 3 OK 50 47 49 68 C4' A A 4 OK 70 67 69 90 C4' A A 5 OK 92 89 91 112 C4' C A 6 OK 114 111 113 132 C4' U A 7 OK 134 131 133 152 C4' G A 8 OK 154 151 153 175 C4' A A 9 OK 177 174 176 197 C4' A A 10 OK 199 196 198 219 C4' U A 11 OK 221 218 220 239 C4' C A 12 OK 241 238 240 259 C4' G A 13 OK 261 258 260 282 C4' C A 14 OK 284 281 283 302 C4' U A 15 OK 304 301 303 322 C4' A A 16 OK 324 321 323 344 C4' A A 17 OK 346 343 345 366 C4' G A 18 OK 368 365 367 389 C4' G A 19 OK 391 388 390 412 C4' A A 20 OK 414 411 413 434 C4' U A 21 OK 436 433 435 454 C4' G A 22 OK 456 453 455 477 C4' A A 23 OK 479 476 478 499 C4' A A 24 OK 501 498 500 521 C4' A A 25 OK 523 520 522 543 C4' G A 26 OK 545 542 544 566 C4' U A 27 OK 568 565 567 586 C4' C A 28 OK 588 585 587 606 C4' U A 29 OK 608 605 607 626 C4' A A 30 OK 628 625 627 648 C4' U A 31 OK 650 647 649 668 C4' G A 32 OK 670 667 669 691 C4' C A 33 OK 693 690 692 711 C4' G A 34 OK 713 710 712 734 C4' A A 35 OK 736 733 735 756 C4' C A 36 OK 758 755 757 776 C4' A A 37 OK 778 775 777 798 C4' U A 38 OK 800 797 799 818 C4' U A 39 OK 820 817 819 838 C4' A A 40 OK 840 837 839 860 C4' U A 41 OK 862 859 861 880 C4' C A 42 OK 882 879 881 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 1 1 3 25 C5' A A 2 24 26 47 C5' U A 3 46 48 67 C5' A A 4 66 68 89 C5' A A 5 88 90 111 C5' C A 6 110 112 131 C5' U A 7 130 132 151 C5' G A 8 150 152 174 C5' A A 9 173 175 196 C5' A A 10 195 197 218 C5' U A 11 217 219 238 C5' C A 12 237 239 258 C5' G A 13 257 259 281 C5' C A 14 280 282 301 C5' U A 15 300 302 321 C5' A A 16 320 322 343 C5' A A 17 342 344 365 C5' G A 18 364 366 388 C5' G A 19 387 389 411 C5' A A 20 410 412 433 C5' U A 21 432 434 453 C5' G A 22 452 454 476 C5' A A 23 475 477 498 C5' A A 24 497 499 520 C5' A A 25 519 521 542 C5' G A 26 541 543 565 C5' U A 27 564 566 585 C5' C A 28 584 586 605 C5' U A 29 604 606 625 C5' A A 30 624 626 647 C5' U A 31 646 648 667 C5' G A 32 666 668 690 C5' C A 33 689 691 710 C5' G A 34 709 711 733 C5' A A 35 732 734 755 C5' C A 36 754 756 775 C5' A A 37 774 776 797 C5' U A 38 796 798 817 C5' U A 39 816 818 837 C5' A A 40 836 838 859 C5' U A 41 858 860 879 C5' C A 42 878 880 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 21 P A A 2 distorted distorted 6 22 23 24 43 P U A 3 distorted distorted 29 44 45 46 63 P A A 4 distorted distorted 51 64 65 66 85 P A A 5 distorted distorted 71 86 87 88 107 P C A 6 distorted distorted 93 108 109 110 127 P U A 7 distorted distorted 115 128 129 130 147 P G A 8 distorted distorted 135 148 149 150 170 P A A 9 distorted distorted 155 171 172 173 192 P A A 10 distorted distorted 178 193 194 195 214 P U A 11 distorted distorted 200 215 216 217 234 P C A 12 distorted distorted 222 235 236 237 254 P G A 13 distorted distorted 242 255 256 257 277 P C A 14 distorted distorted 262 278 279 280 297 P U A 15 distorted distorted 285 298 299 300 317 P A A 16 distorted distorted 305 318 319 320 339 P A A 17 distorted distorted 325 340 341 342 361 P G A 18 distorted distorted 347 362 363 364 384 P G A 19 distorted distorted 369 385 386 387 407 P A A 20 distorted distorted 392 408 409 410 429 P U A 21 distorted distorted 415 430 431 432 449 P G A 22 distorted distorted 437 450 451 452 472 P A A 23 distorted distorted 457 473 474 475 494 P A A 24 distorted distorted 480 495 496 497 516 P A A 25 distorted distorted 502 517 518 519 538 P G A 26 distorted distorted 524 539 540 541 561 P U A 27 distorted distorted 546 562 563 564 581 P C A 28 distorted distorted 569 582 583 584 601 P U A 29 distorted distorted 589 602 603 604 621 P A A 30 distorted distorted 609 622 623 624 643 P U A 31 distorted distorted 629 644 645 646 663 P G A 32 distorted distorted 651 664 665 666 686 P C A 33 distorted distorted 671 687 688 689 706 P G A 34 distorted distorted 694 707 708 709 729 P A A 35 distorted distorted 714 730 731 732 751 P C A 36 distorted distorted 737 752 753 754 771 P A A 37 distorted distorted 759 772 773 774 793 P U A 38 distorted distorted 779 794 795 796 813 P U A 39 distorted distorted 801 814 815 816 833 P A A 40 distorted distorted 821 834 835 836 855 P U A 41 distorted distorted 841 856 857 858 875 P C A 42 distorted distorted 863 876 877 878 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