ID code: '1YG4' 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' --------------------------------------------------------------------------------- 12 C1' A A 3 alpha beta 7 29 13 10 45 C1' G A 4 alpha beta 40 63 46 43 79 C1' U A 5 alpha beta 74 94 80 77 109 C1' G A 6 alpha beta 104 127 110 107 143 C1' G A 7 alpha beta 138 161 144 141 177 C1' CH A 8 alpha beta 172 192 178 175 209 C1' G A 9 alpha beta 204 227 210 207 243 C1' C A 10 alpha beta 238 258 244 241 274 C1' C A 11 alpha beta 269 289 275 272 305 C1' G A 12 alpha beta 300 323 306 303 339 C1' A A 13 alpha beta 334 356 340 337 372 C1' C A 14 alpha beta 367 387 373 370 403 C1' C A 15 alpha beta 398 418 404 401 434 C1' A A 16 alpha beta 429 451 435 432 467 C1' C A 17 alpha beta 462 482 468 465 498 C1' U A 18 alpha beta 493 513 499 496 528 C1' U A 19 alpha beta 523 543 529 526 558 C1' A A 20 alpha beta 553 575 559 556 591 C1' A A 21 alpha beta 586 608 592 589 624 C1' A A 22 alpha beta 619 641 625 622 657 C1' A A 23 alpha beta 652 674 658 655 690 C1' A A 24 alpha beta 685 707 691 688 723 C1' C A 25 alpha beta 718 738 724 721 754 C1' A A 26 alpha beta 749 771 755 752 787 C1' C A 27 alpha beta 782 802 788 785 818 C1' C A 28 alpha beta 813 833 819 816 849 C1' G A 29 alpha beta 844 867 850 847 883 C1' G A 30 alpha beta 878 901 884 881 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' A A 3 OK OK 12 8 27 11 43 C2' G A 4 OK OK 45 41 61 44 77 C2' U A 5 OK OK 79 75 92 78 107 C2' G A 6 OK OK 109 105 125 108 141 C2' G A 7 OK OK 143 139 159 142 175 C2' CH A 8 OK OK 177 173 190 176 207 C2' G A 9 OK OK 209 205 225 208 241 C2' C A 10 OK OK 243 239 256 242 272 C2' C A 11 OK OK 274 270 287 273 303 C2' G A 12 OK OK 305 301 321 304 337 C2' A A 13 OK OK 339 335 354 338 370 C2' C A 14 OK OK 372 368 385 371 401 C2' C A 15 OK OK 403 399 416 402 432 C2' A A 16 OK OK 434 430 449 433 465 C2' C A 17 OK OK 467 463 480 466 496 C2' U A 18 OK OK 498 494 511 497 526 C2' U A 19 OK OK 528 524 541 527 556 C2' A A 20 OK OK 558 554 573 557 589 C2' A A 21 OK OK 591 587 606 590 622 C2' A A 22 OK OK 624 620 639 623 655 C2' A A 23 OK OK 657 653 672 656 688 C2' A A 24 OK OK 690 686 705 689 721 C2' C A 25 OK OK 723 719 736 722 752 C2' A A 26 OK OK 754 750 769 753 785 C2' C A 27 OK OK 787 783 800 786 816 C2' C A 28 OK OK 818 814 831 817 847 C2' G A 29 OK OK 849 845 865 848 881 C2' G A 30 OK OK 883 879 899 882 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' A A 3 OK OK 6 26 9 10 41 C3' G A 4 OK OK 39 60 42 43 75 C3' U A 5 OK OK 73 91 76 77 105 C3' G A 6 OK OK 103 124 106 107 139 C3' G A 7 OK OK 137 158 140 141 173 C3' CH A 8 OK OK 171 189 174 175 205 C3' G A 9 OK OK 203 224 206 207 239 C3' C A 10 OK OK 237 255 240 241 270 C3' C A 11 OK OK 268 286 271 272 301 C3' G A 12 OK OK 299 320 302 303 335 C3' A A 13 OK OK 333 353 336 337 368 C3' C A 14 OK OK 366 384 369 370 399 C3' C A 15 OK OK 397 415 400 401 430 C3' A A 16 OK OK 428 448 431 432 463 C3' C A 17 OK OK 461 479 464 465 494 C3' U A 18 OK OK 492 510 495 496 524 C3' U A 19 OK OK 522 540 525 526 554 C3' A A 20 OK OK 552 572 555 556 587 C3' A A 21 OK OK 585 605 588 589 620 C3' A A 22 OK OK 618 638 621 622 653 C3' A A 23 OK OK 651 671 654 655 686 C3' A A 24 OK OK 684 704 687 688 719 C3' C A 25 OK OK 717 735 720 721 750 C3' A A 26 OK OK 748 768 751 752 783 C3' C A 27 OK OK 781 799 784 785 814 C3' C A 28 OK OK 812 830 815 816 845 C3' G A 29 OK OK 843 864 846 847 879 C3' G A 30 OK OK 877 898 880 881 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' A A 3 OK OK 8 25 5 7 39 C4' G A 4 OK OK 41 59 38 40 73 C4' U A 5 OK OK 75 90 72 74 103 C4' G A 6 OK OK 105 123 102 104 137 C4' G A 7 OK OK 139 157 136 138 171 C4' CH A 8 OK OK 173 188 170 172 203 C4' G A 9 OK OK 205 223 202 204 237 C4' C A 10 OK OK 239 254 236 238 268 C4' C A 11 OK OK 270 285 267 269 299 C4' G A 12 OK OK 301 319 298 300 333 C4' A A 13 OK OK 335 352 332 334 366 C4' C A 14 OK OK 368 383 365 367 397 C4' C A 15 OK OK 399 414 396 398 428 C4' A A 16 OK OK 430 447 427 429 461 C4' C A 17 OK OK 463 478 460 462 492 C4' U A 18 OK OK 494 509 491 493 522 C4' U A 19 OK OK 524 539 521 523 552 C4' A A 20 OK OK 554 571 551 553 585 C4' A A 21 OK OK 587 604 584 586 618 C4' A A 22 OK OK 620 637 617 619 651 C4' A A 23 OK OK 653 670 650 652 684 C4' A A 24 OK OK 686 703 683 685 717 C4' C A 25 OK OK 719 734 716 718 748 C4' A A 26 OK OK 750 767 747 749 781 C4' C A 27 OK OK 783 798 780 782 812 C4' C A 28 OK OK 814 829 811 813 843 C4' G A 29 OK OK 845 863 842 844 877 C4' G A 30 OK OK 879 897 876 878 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' A A 3 OK OK 4 23 24 6 38 C5' G A 4 OK OK 37 57 58 39 72 C5' U A 5 OK OK 71 88 89 73 102 C5' G A 6 OK OK 101 121 122 103 136 C5' G A 7 OK OK 135 155 156 137 170 C5' CH A 8 OK OK 169 186 187 171 202 C5' G A 9 OK OK 201 221 222 203 236 C5' C A 10 OK OK 235 252 253 237 267 C5' C A 11 OK OK 266 283 284 268 298 C5' G A 12 OK OK 297 317 318 299 332 C5' A A 13 OK OK 331 350 351 333 365 C5' C A 14 OK OK 364 381 382 366 396 C5' C A 15 OK OK 395 412 413 397 427 C5' A A 16 OK OK 426 445 446 428 460 C5' C A 17 OK OK 459 476 477 461 491 C5' U A 18 OK OK 490 507 508 492 521 C5' U A 19 OK OK 520 537 538 522 551 C5' A A 20 OK OK 550 569 570 552 584 C5' A A 21 OK OK 583 602 603 585 617 C5' A A 22 OK OK 616 635 636 618 650 C5' A A 23 OK OK 649 668 669 651 683 C5' A A 24 OK OK 682 701 702 684 716 C5' C A 25 OK OK 715 732 733 717 747 C5' A A 26 OK OK 746 765 766 748 780 C5' C A 27 OK OK 779 796 797 781 811 C5' C A 28 OK OK 810 827 828 812 842 C5' G A 29 OK OK 841 861 862 843 876 C5' G A 30 OK OK 875 895 896 877 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P A A 3 distorted distorted 2 3 4 34 P G A 4 distorted distorted 9 35 36 37 68 P U A 5 distorted distorted 42 69 70 71 98 P G A 6 distorted distorted 76 99 100 101 132 P G A 7 distorted distorted 106 133 134 135 166 P CH A 8 distorted distorted 140 167 168 169 198 P G A 9 distorted distorted 174 199 200 201 232 P C A 10 distorted distorted 206 233 234 235 263 P C A 11 distorted distorted 240 264 265 266 294 P G A 12 distorted distorted 271 295 296 297 328 P A A 13 distorted distorted 302 329 330 331 361 P C A 14 distorted distorted 336 362 363 364 392 P C A 15 distorted distorted 369 393 394 395 423 P A A 16 distorted distorted 400 424 425 426 456 P C A 17 distorted distorted 431 457 458 459 487 P U A 18 distorted distorted 464 488 489 490 517 P U A 19 distorted distorted 495 518 519 520 547 P A A 20 distorted distorted 525 548 549 550 580 P A A 21 distorted distorted 555 581 582 583 613 P A A 22 distorted distorted 588 614 615 616 646 P A A 23 distorted distorted 621 647 648 649 679 P A A 24 distorted distorted 654 680 681 682 712 P C A 25 distorted distorted 687 713 714 715 743 P A A 26 distorted distorted 720 744 745 746 776 P C A 27 distorted distorted 751 777 778 779 807 P C A 28 distorted distorted 784 808 809 810 838 P G A 29 distorted distorted 815 839 840 841 872 P G A 30 distorted distorted 846 873 874 875 ---------------------------------------------------------------------------------