ID code: '2KGP' 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' C A 3 alpha beta 73 93 79 76 109 C1' A A 4 alpha beta 104 126 110 107 142 C1' G A 5 alpha beta 137 160 143 140 176 C1' U A 6 alpha beta 171 191 177 174 206 C1' G A 7 alpha beta 201 224 207 204 240 C1' U A 8 alpha beta 235 255 241 238 270 C1' G A 9 alpha beta 265 288 271 268 304 C1' A A 10 alpha beta 299 321 305 302 337 C1' G A 11 alpha beta 332 355 338 335 371 C1' U A 12 alpha beta 366 386 372 369 401 C1' A A 13 alpha beta 396 418 402 399 434 C1' C A 14 alpha beta 429 449 435 432 465 C1' C A 15 alpha beta 460 480 466 463 496 C1' U A 16 alpha beta 491 511 497 494 526 C1' U A 17 alpha beta 521 541 527 524 556 C1' C A 18 alpha beta 551 571 557 554 587 C1' A A 19 alpha beta 582 604 588 585 620 C1' C A 20 alpha beta 615 635 621 618 651 C1' A A 21 alpha beta 646 668 652 649 684 C1' C A 22 alpha beta 679 699 685 682 715 C1' G A 23 alpha beta 710 733 716 713 749 C1' U A 24 alpha beta 744 764 750 747 779 C1' C A 25 alpha beta 774 795 780 777 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' C A 3 OK OK 78 74 91 77 107 C2' A A 4 OK OK 109 105 124 108 140 C2' G A 5 OK OK 142 138 158 141 174 C2' U A 6 OK OK 176 172 189 175 204 C2' G A 7 OK OK 206 202 222 205 238 C2' U A 8 OK OK 240 236 253 239 268 C2' G A 9 OK OK 270 266 286 269 302 C2' A A 10 OK OK 304 300 319 303 335 C2' G A 11 OK OK 337 333 353 336 369 C2' U A 12 OK OK 371 367 384 370 399 C2' A A 13 OK OK 401 397 416 400 432 C2' C A 14 OK OK 434 430 447 433 463 C2' C A 15 OK OK 465 461 478 464 494 C2' U A 16 OK OK 496 492 509 495 524 C2' U A 17 OK OK 526 522 539 525 554 C2' C A 18 OK OK 556 552 569 555 585 C2' A A 19 OK OK 587 583 602 586 618 C2' C A 20 OK OK 620 616 633 619 649 C2' A A 21 OK OK 651 647 666 650 682 C2' C A 22 OK OK 684 680 697 683 713 C2' G A 23 OK OK 715 711 731 714 747 C2' U A 24 OK OK 749 745 762 748 777 C2' C A 25 OK OK 779 775 793 778 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' C A 3 OK OK 72 90 75 76 105 C3' A A 4 OK OK 103 123 106 107 138 C3' G A 5 OK OK 136 157 139 140 172 C3' U A 6 OK OK 170 188 173 174 202 C3' G A 7 OK OK 200 221 203 204 236 C3' U A 8 OK OK 234 252 237 238 266 C3' G A 9 OK OK 264 285 267 268 300 C3' A A 10 OK OK 298 318 301 302 333 C3' G A 11 OK OK 331 352 334 335 367 C3' U A 12 OK OK 365 383 368 369 397 C3' A A 13 OK OK 395 415 398 399 430 C3' C A 14 OK OK 428 446 431 432 461 C3' C A 15 OK OK 459 477 462 463 492 C3' U A 16 OK OK 490 508 493 494 522 C3' U A 17 OK OK 520 538 523 524 552 C3' C A 18 OK OK 550 568 553 554 583 C3' A A 19 OK OK 581 601 584 585 616 C3' C A 20 OK OK 614 632 617 618 647 C3' A A 21 OK OK 645 665 648 649 680 C3' C A 22 OK OK 678 696 681 682 711 C3' G A 23 OK OK 709 730 712 713 745 C3' U A 24 OK OK 743 761 746 747 775 C3' C A 25 OK OK 773 791 776 777 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' C A 3 OK OK 74 89 71 73 103 C4' A A 4 OK OK 105 122 102 104 136 C4' G A 5 OK OK 138 156 135 137 170 C4' U A 6 OK OK 172 187 169 171 200 C4' G A 7 OK OK 202 220 199 201 234 C4' U A 8 OK OK 236 251 233 235 264 C4' G A 9 OK OK 266 284 263 265 298 C4' A A 10 OK OK 300 317 297 299 331 C4' G A 11 OK OK 333 351 330 332 365 C4' U A 12 OK OK 367 382 364 366 395 C4' A A 13 OK OK 397 414 394 396 428 C4' C A 14 OK OK 430 445 427 429 459 C4' C A 15 OK OK 461 476 458 460 490 C4' U A 16 OK OK 492 507 489 491 520 C4' U A 17 OK OK 522 537 519 521 550 C4' C A 18 OK OK 552 567 549 551 581 C4' A A 19 OK OK 583 600 580 582 614 C4' C A 20 OK OK 616 631 613 615 645 C4' A A 21 OK OK 647 664 644 646 678 C4' C A 22 OK OK 680 695 677 679 709 C4' G A 23 OK OK 711 729 708 710 743 C4' U A 24 OK OK 745 760 742 744 773 C4' C A 25 OK OK 775 790 772 774 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' C A 3 OK OK 70 87 88 72 102 C5' A A 4 OK OK 101 120 121 103 135 C5' G A 5 OK OK 134 154 155 136 169 C5' U A 6 OK OK 168 185 186 170 199 C5' G A 7 OK OK 198 218 219 200 233 C5' U A 8 OK OK 232 249 250 234 263 C5' G A 9 OK OK 262 282 283 264 297 C5' A A 10 OK OK 296 315 316 298 330 C5' G A 11 OK OK 329 349 350 331 364 C5' U A 12 OK OK 363 380 381 365 394 C5' A A 13 OK OK 393 412 413 395 427 C5' C A 14 OK OK 426 443 444 428 458 C5' C A 15 OK OK 457 474 475 459 489 C5' U A 16 OK OK 488 505 506 490 519 C5' U A 17 OK OK 518 535 536 520 549 C5' C A 18 OK OK 548 565 566 550 580 C5' A A 19 OK OK 579 598 599 581 613 C5' C A 20 OK OK 612 629 630 614 644 C5' A A 21 OK OK 643 662 663 645 677 C5' C A 22 OK OK 676 693 694 678 708 C5' G A 23 OK OK 707 727 728 709 742 C5' U A 24 OK OK 741 758 759 743 772 C5' C A 25 OK OK 771 788 789 773 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 2 distorted distorted 6 34 35 36 67 P C A 3 distorted distorted 41 68 69 70 98 P A A 4 distorted distorted 75 99 100 101 131 P G A 5 distorted distorted 106 132 133 134 165 P U A 6 distorted distorted 139 166 167 168 195 P G A 7 distorted distorted 173 196 197 198 229 P U A 8 distorted distorted 203 230 231 232 259 P G A 9 distorted distorted 237 260 261 262 293 P A A 10 distorted distorted 267 294 295 296 326 P G A 11 distorted distorted 301 327 328 329 360 P U A 12 distorted distorted 334 361 362 363 390 P A A 13 distorted distorted 368 391 392 393 423 P C A 14 distorted distorted 398 424 425 426 454 P C A 15 distorted distorted 431 455 456 457 485 P U A 16 distorted distorted 462 486 487 488 515 P U A 17 distorted distorted 493 516 517 518 545 P C A 18 distorted distorted 523 546 547 548 576 P A A 19 distorted distorted 553 577 578 579 609 P C A 20 distorted distorted 584 610 611 612 640 P A A 21 distorted distorted 617 641 642 643 673 P C A 22 distorted distorted 648 674 675 676 704 P G A 23 distorted distorted 681 705 706 707 738 P U A 24 distorted distorted 712 739 740 741 768 P C A 25 distorted distorted 746 769 770 771 ---------------------------------------------------------------------------------