ID code: '2MIS' 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' A A 2 alpha beta 39 61 45 42 77 C1' G A 3 alpha beta 72 95 78 75 111 C1' C A 4 alpha beta 106 126 112 109 142 C1' U A 5 alpha beta 137 157 143 140 172 C1' G A 6 alpha beta 167 190 173 170 206 C1' C A 7 alpha beta 201 221 207 204 237 C1' A A 8 alpha beta 232 254 238 235 270 C1' G A 9 alpha beta 265 288 271 268 304 C1' C A 10 alpha beta 299 319 305 302 335 C1' A A 11 alpha beta 330 352 336 333 368 C1' C A 12 alpha beta 363 383 369 366 399 C1' G A 13 alpha beta 394 417 400 397 433 C1' A A 14 alpha beta 428 450 434 431 466 C1' A A 15 alpha beta 461 483 467 464 499 C1' A A 16 alpha beta 494 516 500 497 532 C1' G A 17 alpha beta 527 550 533 530 566 C1' U A 18 alpha beta 561 581 567 564 596 C1' G A 19 alpha beta 591 614 597 594 630 C1' A A 20 alpha beta 625 647 631 628 663 C1' C A 21 alpha beta 658 678 664 661 694 C1' G A 22 alpha beta 689 712 695 692 728 C1' G A 23 alpha beta 723 746 729 726 762 C1' C A 24 alpha beta 757 777 763 760 793 C1' U A 25 alpha beta 788 808 794 791 823 C1' C A 26 alpha beta 818 839 824 821 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' A A 2 OK OK 44 40 59 43 75 C2' G A 3 OK OK 77 73 93 76 109 C2' C A 4 OK OK 111 107 124 110 140 C2' U A 5 OK OK 142 138 155 141 170 C2' G A 6 OK OK 172 168 188 171 204 C2' C A 7 OK OK 206 202 219 205 235 C2' A A 8 OK OK 237 233 252 236 268 C2' G A 9 OK OK 270 266 286 269 302 C2' C A 10 OK OK 304 300 317 303 333 C2' A A 11 OK OK 335 331 350 334 366 C2' C A 12 OK OK 368 364 381 367 397 C2' G A 13 OK OK 399 395 415 398 431 C2' A A 14 OK OK 433 429 448 432 464 C2' A A 15 OK OK 466 462 481 465 497 C2' A A 16 OK OK 499 495 514 498 530 C2' G A 17 OK OK 532 528 548 531 564 C2' U A 18 OK OK 566 562 579 565 594 C2' G A 19 OK OK 596 592 612 595 628 C2' A A 20 OK OK 630 626 645 629 661 C2' C A 21 OK OK 663 659 676 662 692 C2' G A 22 OK OK 694 690 710 693 726 C2' G A 23 OK OK 728 724 744 727 760 C2' C A 24 OK OK 762 758 775 761 791 C2' U A 25 OK OK 793 789 806 792 821 C2' C A 26 OK OK 823 819 837 822 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK OK 3 24 6 7 40 C3' A A 2 OK OK 38 58 41 42 73 C3' G A 3 OK OK 71 92 74 75 107 C3' C A 4 OK OK 105 123 108 109 138 C3' U A 5 OK OK 136 154 139 140 168 C3' G A 6 OK OK 166 187 169 170 202 C3' C A 7 OK OK 200 218 203 204 233 C3' A A 8 OK OK 231 251 234 235 266 C3' G A 9 OK OK 264 285 267 268 300 C3' C A 10 OK OK 298 316 301 302 331 C3' A A 11 OK OK 329 349 332 333 364 C3' C A 12 OK OK 362 380 365 366 395 C3' G A 13 OK OK 393 414 396 397 429 C3' A A 14 OK OK 427 447 430 431 462 C3' A A 15 OK OK 460 480 463 464 495 C3' A A 16 OK OK 493 513 496 497 528 C3' G A 17 OK OK 526 547 529 530 562 C3' U A 18 OK OK 560 578 563 564 592 C3' G A 19 OK OK 590 611 593 594 626 C3' A A 20 OK OK 624 644 627 628 659 C3' C A 21 OK OK 657 675 660 661 690 C3' G A 22 OK OK 688 709 691 692 724 C3' G A 23 OK OK 722 743 725 726 758 C3' C A 24 OK OK 756 774 759 760 789 C3' U A 25 OK OK 787 805 790 791 819 C3' C A 26 OK OK 817 835 820 821 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK OK 5 23 2 4 38 C4' A A 2 OK OK 40 57 37 39 71 C4' G A 3 OK OK 73 91 70 72 105 C4' C A 4 OK OK 107 122 104 106 136 C4' U A 5 OK OK 138 153 135 137 166 C4' G A 6 OK OK 168 186 165 167 200 C4' C A 7 OK OK 202 217 199 201 231 C4' A A 8 OK OK 233 250 230 232 264 C4' G A 9 OK OK 266 284 263 265 298 C4' C A 10 OK OK 300 315 297 299 329 C4' A A 11 OK OK 331 348 328 330 362 C4' C A 12 OK OK 364 379 361 363 393 C4' G A 13 OK OK 395 413 392 394 427 C4' A A 14 OK OK 429 446 426 428 460 C4' A A 15 OK OK 462 479 459 461 493 C4' A A 16 OK OK 495 512 492 494 526 C4' G A 17 OK OK 528 546 525 527 560 C4' U A 18 OK OK 562 577 559 561 590 C4' G A 19 OK OK 592 610 589 591 624 C4' A A 20 OK OK 626 643 623 625 657 C4' C A 21 OK OK 659 674 656 658 688 C4' G A 22 OK OK 690 708 687 689 722 C4' G A 23 OK OK 724 742 721 723 756 C4' C A 24 OK OK 758 773 755 757 787 C4' U A 25 OK OK 789 804 786 788 817 C4' C A 26 OK OK 819 834 816 818 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' A A 2 OK OK 36 55 56 38 70 C5' G A 3 OK OK 69 89 90 71 104 C5' C A 4 OK OK 103 120 121 105 135 C5' U A 5 OK OK 134 151 152 136 165 C5' G A 6 OK OK 164 184 185 166 199 C5' C A 7 OK OK 198 215 216 200 230 C5' A A 8 OK OK 229 248 249 231 263 C5' G A 9 OK OK 262 282 283 264 297 C5' C A 10 OK OK 296 313 314 298 328 C5' A A 11 OK OK 327 346 347 329 361 C5' C A 12 OK OK 360 377 378 362 392 C5' G A 13 OK OK 391 411 412 393 426 C5' A A 14 OK OK 425 444 445 427 459 C5' A A 15 OK OK 458 477 478 460 492 C5' A A 16 OK OK 491 510 511 493 525 C5' G A 17 OK OK 524 544 545 526 559 C5' U A 18 OK OK 558 575 576 560 589 C5' G A 19 OK OK 588 608 609 590 623 C5' A A 20 OK OK 622 641 642 624 656 C5' C A 21 OK OK 655 672 673 657 687 C5' G A 22 OK OK 686 706 707 688 721 C5' G A 23 OK OK 720 740 741 722 755 C5' C A 24 OK OK 754 771 772 756 786 C5' U A 25 OK OK 785 802 803 787 816 C5' C A 26 OK OK 815 832 833 817 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P A A 2 distorted distorted 6 34 35 36 66 P G A 3 distorted distorted 41 67 68 69 100 P C A 4 distorted distorted 74 101 102 103 131 P U A 5 distorted distorted 108 132 133 134 161 P G A 6 distorted distorted 139 162 163 164 195 P C A 7 distorted distorted 169 196 197 198 226 P A A 8 distorted distorted 203 227 228 229 259 P G A 9 distorted distorted 234 260 261 262 293 P C A 10 distorted distorted 267 294 295 296 324 P A A 11 distorted distorted 301 325 326 327 357 P C A 12 distorted distorted 332 358 359 360 388 P G A 13 distorted distorted 365 389 390 391 422 P A A 14 distorted distorted 396 423 424 425 455 P A A 15 distorted distorted 430 456 457 458 488 P A A 16 distorted distorted 463 489 490 491 521 P G A 17 distorted distorted 496 522 523 524 555 P U A 18 distorted distorted 529 556 557 558 585 P G A 19 distorted distorted 563 586 587 588 619 P A A 20 distorted distorted 593 620 621 622 652 P C A 21 distorted distorted 627 653 654 655 683 P G A 22 distorted distorted 660 684 685 686 717 P G A 23 distorted distorted 691 718 719 720 751 P C A 24 distorted distorted 725 752 753 754 782 P U A 25 distorted distorted 759 783 784 785 812 P C A 26 distorted distorted 790 813 814 815 ---------------------------------------------------------------------------------