ID code: '1XSG' 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 alpha beta 4 27 10 7 44 C1' G A 2 alpha beta 39 62 45 42 78 C1' A A 3 alpha beta 73 95 79 76 111 C1' A A 4 alpha beta 106 128 112 109 144 C1' G A 5 alpha beta 139 162 145 142 178 C1' A A 6 alpha beta 173 195 179 176 211 C1' C A 7 alpha beta 206 226 212 209 242 C1' C A 8 alpha beta 237 257 243 240 273 C1' G A 9 alpha beta 268 291 274 271 307 C1' G A 10 alpha beta 302 325 308 305 341 C1' U A 11 alpha beta 336 356 342 339 371 C1' C A 12 alpha beta 366 386 372 369 402 C1' U A 13 alpha beta 397 417 403 400 432 C1' U A 14 alpha beta 427 447 433 430 462 C1' C A 15 alpha beta 457 477 463 460 493 C1' G A 16 alpha beta 488 511 494 491 527 C1' G A 17 alpha beta 522 545 528 525 561 C1' A A 18 alpha beta 556 578 562 559 594 C1' C A 19 alpha beta 589 609 595 592 625 C1' C A 20 alpha beta 620 640 626 623 656 C1' G A 21 alpha beta 651 674 657 654 690 C1' G A 22 alpha beta 685 708 691 688 724 C1' C A 23 alpha beta 719 739 725 722 755 C1' U A 24 alpha beta 750 770 756 753 785 C1' U A 25 alpha beta 780 800 786 783 815 C1' C A 26 alpha beta 810 830 816 813 846 C1' C A 27 alpha beta 841 862 847 844 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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 OK 9 5 25 8 42 C2' G A 2 OK OK 44 40 60 43 76 C2' A A 3 OK OK 78 74 93 77 109 C2' A A 4 OK OK 111 107 126 110 142 C2' G A 5 OK OK 144 140 160 143 176 C2' A A 6 OK OK 178 174 193 177 209 C2' C A 7 OK OK 211 207 224 210 240 C2' C A 8 OK OK 242 238 255 241 271 C2' G A 9 OK OK 273 269 289 272 305 C2' G A 10 OK OK 307 303 323 306 339 C2' U A 11 OK OK 341 337 354 340 369 C2' C A 12 OK OK 371 367 384 370 400 C2' U A 13 OK OK 402 398 415 401 430 C2' U A 14 OK OK 432 428 445 431 460 C2' C A 15 OK OK 462 458 475 461 491 C2' G A 16 OK OK 493 489 509 492 525 C2' G A 17 OK OK 527 523 543 526 559 C2' A A 18 OK OK 561 557 576 560 592 C2' C A 19 OK OK 594 590 607 593 623 C2' C A 20 OK OK 625 621 638 624 654 C2' G A 21 OK OK 656 652 672 655 688 C2' G A 22 OK OK 690 686 706 689 722 C2' C A 23 OK OK 724 720 737 723 753 C2' U A 24 OK OK 755 751 768 754 783 C2' U A 25 OK OK 785 781 798 784 813 C2' C A 26 OK OK 815 811 828 814 844 C2' C A 27 OK OK 846 842 860 845 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK OK 3 24 6 7 40 C3' G A 2 OK OK 38 59 41 42 74 C3' A A 3 OK OK 72 92 75 76 107 C3' A A 4 OK OK 105 125 108 109 140 C3' G A 5 OK OK 138 159 141 142 174 C3' A A 6 OK OK 172 192 175 176 207 C3' C A 7 OK OK 205 223 208 209 238 C3' C A 8 OK OK 236 254 239 240 269 C3' G A 9 OK OK 267 288 270 271 303 C3' G A 10 OK OK 301 322 304 305 337 C3' U A 11 OK OK 335 353 338 339 367 C3' C A 12 OK OK 365 383 368 369 398 C3' U A 13 OK OK 396 414 399 400 428 C3' U A 14 OK OK 426 444 429 430 458 C3' C A 15 OK OK 456 474 459 460 489 C3' G A 16 OK OK 487 508 490 491 523 C3' G A 17 OK OK 521 542 524 525 557 C3' A A 18 OK OK 555 575 558 559 590 C3' C A 19 OK OK 588 606 591 592 621 C3' C A 20 OK OK 619 637 622 623 652 C3' G A 21 OK OK 650 671 653 654 686 C3' G A 22 OK OK 684 705 687 688 720 C3' C A 23 OK OK 718 736 721 722 751 C3' U A 24 OK OK 749 767 752 753 781 C3' U A 25 OK OK 779 797 782 783 811 C3' C A 26 OK OK 809 827 812 813 842 C3' C A 27 OK OK 840 858 843 844 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK OK 5 23 2 4 38 C4' G A 2 OK OK 40 58 37 39 72 C4' A A 3 OK OK 74 91 71 73 105 C4' A A 4 OK OK 107 124 104 106 138 C4' G A 5 OK OK 140 158 137 139 172 C4' A A 6 OK OK 174 191 171 173 205 C4' C A 7 OK OK 207 222 204 206 236 C4' C A 8 OK OK 238 253 235 237 267 C4' G A 9 OK OK 269 287 266 268 301 C4' G A 10 OK OK 303 321 300 302 335 C4' U A 11 OK OK 337 352 334 336 365 C4' C A 12 OK OK 367 382 364 366 396 C4' U A 13 OK OK 398 413 395 397 426 C4' U A 14 OK OK 428 443 425 427 456 C4' C A 15 OK OK 458 473 455 457 487 C4' G A 16 OK OK 489 507 486 488 521 C4' G A 17 OK OK 523 541 520 522 555 C4' A A 18 OK OK 557 574 554 556 588 C4' C A 19 OK OK 590 605 587 589 619 C4' C A 20 OK OK 621 636 618 620 650 C4' G A 21 OK OK 652 670 649 651 684 C4' G A 22 OK OK 686 704 683 685 718 C4' C A 23 OK OK 720 735 717 719 749 C4' U A 24 OK OK 751 766 748 750 779 C4' U A 25 OK OK 781 796 778 780 809 C4' C A 26 OK OK 811 826 808 810 840 C4' C A 27 OK OK 842 857 839 841 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 1 OK OK 1 21 22 3 37 C5' G A 2 OK OK 36 56 57 38 71 C5' A A 3 OK OK 70 89 90 72 104 C5' A A 4 OK OK 103 122 123 105 137 C5' G A 5 OK OK 136 156 157 138 171 C5' A A 6 OK OK 170 189 190 172 204 C5' C A 7 OK OK 203 220 221 205 235 C5' C A 8 OK OK 234 251 252 236 266 C5' G A 9 OK OK 265 285 286 267 300 C5' G A 10 OK OK 299 319 320 301 334 C5' U A 11 OK OK 333 350 351 335 364 C5' C A 12 OK OK 363 380 381 365 395 C5' U A 13 OK OK 394 411 412 396 425 C5' U A 14 OK OK 424 441 442 426 455 C5' C A 15 OK OK 454 471 472 456 486 C5' G A 16 OK OK 485 505 506 487 520 C5' G A 17 OK OK 519 539 540 521 554 C5' A A 18 OK OK 553 572 573 555 587 C5' C A 19 OK OK 586 603 604 588 618 C5' C A 20 OK OK 617 634 635 619 649 C5' G A 21 OK OK 648 668 669 650 683 C5' G A 22 OK OK 682 702 703 684 717 C5' C A 23 OK OK 716 733 734 718 748 C5' U A 24 OK OK 747 764 765 749 778 C5' U A 25 OK OK 777 794 795 779 808 C5' C A 26 OK OK 807 824 825 809 839 C5' C A 27 OK OK 838 855 856 840 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 2 distorted distorted 6 34 35 36 67 P A A 3 distorted distorted 41 68 69 70 100 P A A 4 distorted distorted 75 101 102 103 133 P G A 5 distorted distorted 108 134 135 136 167 P A A 6 distorted distorted 141 168 169 170 200 P C A 7 distorted distorted 175 201 202 203 231 P C A 8 distorted distorted 208 232 233 234 262 P G A 9 distorted distorted 239 263 264 265 296 P G A 10 distorted distorted 270 297 298 299 330 P U A 11 distorted distorted 304 331 332 333 360 P C A 12 distorted distorted 338 361 362 363 391 P U A 13 distorted distorted 368 392 393 394 421 P U A 14 distorted distorted 399 422 423 424 451 P C A 15 distorted distorted 429 452 453 454 482 P G A 16 distorted distorted 459 483 484 485 516 P G A 17 distorted distorted 490 517 518 519 550 P A A 18 distorted distorted 524 551 552 553 583 P C A 19 distorted distorted 558 584 585 586 614 P C A 20 distorted distorted 591 615 616 617 645 P G A 21 distorted distorted 622 646 647 648 679 P G A 22 distorted distorted 653 680 681 682 713 P C A 23 distorted distorted 687 714 715 716 744 P U A 24 distorted distorted 721 745 746 747 774 P U A 25 distorted distorted 752 775 776 777 804 P C A 26 distorted distorted 782 805 806 807 835 P C A 27 distorted distorted 812 836 837 838 ---------------------------------------------------------------------------------