ID code: '1MT4' 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' G A 1 alpha beta 7 30 13 10 46 C1' G A 2 alpha beta 41 64 47 44 80 C1' C A 3 alpha beta 75 95 81 78 111 C1' G A 4 alpha beta 106 129 112 109 145 C1' U A 5 alpha beta 140 160 146 143 175 C1' A A 6 alpha beta 170 192 176 173 208 C1' A A 7 alpha beta 203 225 209 206 241 C1' C A 8 alpha beta 236 256 242 239 272 C1' G A 9 alpha beta 267 290 273 270 306 C1' U A 10 alpha beta 301 321 307 304 336 C1' U A 11 alpha beta 331 351 337 334 366 C1' G A 12 alpha beta 361 384 367 364 400 C1' A A 13 alpha beta 395 417 401 398 433 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' U A 19 alpha beta 591 611 597 594 626 C1' A A 20 alpha beta 621 643 627 624 659 C1' C A 21 alpha beta 654 674 660 657 690 C1' G A 22 alpha beta 685 708 691 688 724 C1' C A 23 alpha beta 719 739 725 722 755 C1' C A 24 alpha beta 750 770 756 753 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' G A 1 OK OK 12 8 28 11 44 C2' G A 2 OK OK 46 42 62 45 78 C2' C A 3 OK OK 80 76 93 79 109 C2' G A 4 OK OK 111 107 127 110 143 C2' U A 5 OK OK 145 141 158 144 173 C2' A A 6 OK OK 175 171 190 174 206 C2' A A 7 OK OK 208 204 223 207 239 C2' C A 8 OK OK 241 237 254 240 270 C2' G A 9 OK OK 272 268 288 271 304 C2' U A 10 OK OK 306 302 319 305 334 C2' U A 11 OK OK 336 332 349 335 364 C2' G A 12 OK OK 366 362 382 365 398 C2' A A 13 OK OK 400 396 415 399 431 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' U A 19 OK OK 596 592 609 595 624 C2' A A 20 OK OK 626 622 641 625 657 C2' C A 21 OK OK 659 655 672 658 688 C2' G A 22 OK OK 690 686 706 689 722 C2' C A 23 OK OK 724 720 737 723 753 C2' C A 24 OK OK 755 751 768 754 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' G A 1 OK OK 6 27 9 10 42 C3' G A 2 OK OK 40 61 43 44 76 C3' C A 3 OK OK 74 92 77 78 107 C3' G A 4 OK OK 105 126 108 109 141 C3' U A 5 OK OK 139 157 142 143 171 C3' A A 6 OK OK 169 189 172 173 204 C3' A A 7 OK OK 202 222 205 206 237 C3' C A 8 OK OK 235 253 238 239 268 C3' G A 9 OK OK 266 287 269 270 302 C3' U A 10 OK OK 300 318 303 304 332 C3' U A 11 OK OK 330 348 333 334 362 C3' G A 12 OK OK 360 381 363 364 396 C3' A A 13 OK OK 394 414 397 398 429 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' U A 19 OK OK 590 608 593 594 622 C3' A A 20 OK OK 620 640 623 624 655 C3' C A 21 OK OK 653 671 656 657 686 C3' G A 22 OK OK 684 705 687 688 720 C3' C A 23 OK OK 718 736 721 722 751 C3' C A 24 OK OK 749 767 752 753 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' G A 1 OK OK 8 26 5 7 40 C4' G A 2 OK OK 42 60 39 41 74 C4' C A 3 OK OK 76 91 73 75 105 C4' G A 4 OK OK 107 125 104 106 139 C4' U A 5 OK OK 141 156 138 140 169 C4' A A 6 OK OK 171 188 168 170 202 C4' A A 7 OK OK 204 221 201 203 235 C4' C A 8 OK OK 237 252 234 236 266 C4' G A 9 OK OK 268 286 265 267 300 C4' U A 10 OK OK 302 317 299 301 330 C4' U A 11 OK OK 332 347 329 331 360 C4' G A 12 OK OK 362 380 359 361 394 C4' A A 13 OK OK 396 413 393 395 427 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' U A 19 OK OK 592 607 589 591 620 C4' A A 20 OK OK 622 639 619 621 653 C4' C A 21 OK OK 655 670 652 654 684 C4' G A 22 OK OK 686 704 683 685 718 C4' C A 23 OK OK 720 735 717 719 749 C4' C A 24 OK OK 751 766 748 750 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' G A 1 OK OK 4 24 25 6 39 C5' G A 2 OK OK 38 58 59 40 73 C5' C A 3 OK OK 72 89 90 74 104 C5' G A 4 OK OK 103 123 124 105 138 C5' U A 5 OK OK 137 154 155 139 168 C5' A A 6 OK OK 167 186 187 169 201 C5' A A 7 OK OK 200 219 220 202 234 C5' C A 8 OK OK 233 250 251 235 265 C5' G A 9 OK OK 264 284 285 266 299 C5' U A 10 OK OK 298 315 316 300 329 C5' U A 11 OK OK 328 345 346 330 359 C5' G A 12 OK OK 358 378 379 360 393 C5' A A 13 OK OK 392 411 412 394 426 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' U A 19 OK OK 588 605 606 590 619 C5' A A 20 OK OK 618 637 638 620 652 C5' C A 21 OK OK 651 668 669 653 683 C5' G A 22 OK OK 682 702 703 684 717 C5' C A 23 OK OK 716 733 734 718 748 C5' C A 24 OK OK 747 764 765 749 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P G A 1 OK OK 2 3 4 35 P G A 2 distorted distorted 9 36 37 38 69 P C A 3 distorted distorted 43 70 71 72 100 P G A 4 distorted distorted 77 101 102 103 134 P U A 5 distorted distorted 108 135 136 137 164 P A A 6 distorted distorted 142 165 166 167 197 P A A 7 distorted distorted 172 198 199 200 230 P C A 8 distorted distorted 205 231 232 233 261 P G A 9 distorted distorted 238 262 263 264 295 P U A 10 distorted distorted 269 296 297 298 325 P U A 11 distorted distorted 303 326 327 328 355 P G A 12 distorted distorted 333 356 357 358 389 P A A 13 distorted distorted 363 390 391 392 422 P A A 14 distorted distorted 397 423 424 425 455 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 U A 19 distorted distorted 563 586 587 588 615 P A A 20 distorted distorted 593 616 617 618 648 P C A 21 distorted distorted 623 649 650 651 679 P G A 22 distorted distorted 656 680 681 682 713 P C A 23 distorted distorted 687 714 715 716 744 P C A 24 distorted distorted 721 745 746 747 ---------------------------------------------------------------------------------