ID code: '2KXM' 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 43 C1' G A 2 alpha beta 38 61 44 41 77 C1' C A 3 alpha beta 72 92 78 75 108 C1' U A 4 alpha beta 103 123 109 106 138 C1' G A 5 alpha beta 133 156 139 136 172 C1' C A 6 alpha beta 167 187 173 170 203 C1' U A 7 alpha beta 198 218 204 201 233 C1' U A 8 alpha beta 228 248 234 231 263 C1' G A 9 alpha beta 258 281 264 261 297 C1' U A 10 alpha beta 292 312 298 295 327 C1' C A 11 alpha beta 322 342 328 325 358 C1' C A 12 alpha beta 353 373 359 356 389 C1' U A 13 alpha beta 384 404 390 387 419 C1' U A 14 alpha beta 414 434 420 417 449 C1' U A 15 alpha beta 444 464 450 447 479 C1' A A 16 alpha beta 474 496 480 477 512 C1' A A 17 alpha beta 507 529 513 510 545 C1' U A 18 alpha beta 540 560 546 543 575 C1' G A 19 alpha beta 570 593 576 573 609 C1' G A 20 alpha beta 604 627 610 607 643 C1' U A 21 alpha beta 638 658 644 641 673 C1' C A 22 alpha beta 668 688 674 671 704 C1' C A 23 alpha beta 699 719 705 702 735 C1' A A 24 alpha beta 730 752 736 733 768 C1' G A 25 alpha beta 763 786 769 766 802 C1' U A 26 alpha beta 797 817 803 800 832 C1' C A 27 alpha beta 827 847 833 830 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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 41 C2' G A 2 OK OK 43 39 59 42 75 C2' C A 3 OK OK 77 73 90 76 106 C2' U A 4 OK OK 108 104 121 107 136 C2' G A 5 OK OK 138 134 154 137 170 C2' C A 6 OK OK 172 168 185 171 201 C2' U A 7 OK OK 203 199 216 202 231 C2' U A 8 OK OK 233 229 246 232 261 C2' G A 9 OK OK 263 259 279 262 295 C2' U A 10 OK OK 297 293 310 296 325 C2' C A 11 OK OK 327 323 340 326 356 C2' C A 12 OK OK 358 354 371 357 387 C2' U A 13 OK OK 389 385 402 388 417 C2' U A 14 OK OK 419 415 432 418 447 C2' U A 15 OK OK 449 445 462 448 477 C2' A A 16 OK OK 479 475 494 478 510 C2' A A 17 OK OK 512 508 527 511 543 C2' U A 18 OK OK 545 541 558 544 573 C2' G A 19 OK OK 575 571 591 574 607 C2' G A 20 OK OK 609 605 625 608 641 C2' U A 21 OK OK 643 639 656 642 671 C2' C A 22 OK OK 673 669 686 672 702 C2' C A 23 OK OK 704 700 717 703 733 C2' A A 24 OK OK 735 731 750 734 766 C2' G A 25 OK OK 768 764 784 767 800 C2' U A 26 OK OK 802 798 815 801 830 C2' C A 27 OK OK 832 828 845 831 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK OK 3 24 6 7 39 C3' G A 2 OK OK 37 58 40 41 73 C3' C A 3 OK OK 71 89 74 75 104 C3' U A 4 OK OK 102 120 105 106 134 C3' G A 5 OK OK 132 153 135 136 168 C3' C A 6 OK OK 166 184 169 170 199 C3' U A 7 OK OK 197 215 200 201 229 C3' U A 8 OK OK 227 245 230 231 259 C3' G A 9 OK OK 257 278 260 261 293 C3' U A 10 OK OK 291 309 294 295 323 C3' C A 11 OK OK 321 339 324 325 354 C3' C A 12 OK OK 352 370 355 356 385 C3' U A 13 OK OK 383 401 386 387 415 C3' U A 14 OK OK 413 431 416 417 445 C3' U A 15 OK OK 443 461 446 447 475 C3' A A 16 OK OK 473 493 476 477 508 C3' A A 17 OK OK 506 526 509 510 541 C3' U A 18 OK OK 539 557 542 543 571 C3' G A 19 OK OK 569 590 572 573 605 C3' G A 20 OK OK 603 624 606 607 639 C3' U A 21 OK OK 637 655 640 641 669 C3' C A 22 OK OK 667 685 670 671 700 C3' C A 23 OK OK 698 716 701 702 731 C3' A A 24 OK OK 729 749 732 733 764 C3' G A 25 OK OK 762 783 765 766 798 C3' U A 26 OK OK 796 814 799 800 828 C3' C A 27 OK OK 826 844 829 830 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK OK 5 23 2 4 37 C4' G A 2 OK OK 39 57 36 38 71 C4' C A 3 OK OK 73 88 70 72 102 C4' U A 4 OK OK 104 119 101 103 132 C4' G A 5 OK OK 134 152 131 133 166 C4' C A 6 OK OK 168 183 165 167 197 C4' U A 7 OK OK 199 214 196 198 227 C4' U A 8 OK OK 229 244 226 228 257 C4' G A 9 OK OK 259 277 256 258 291 C4' U A 10 OK OK 293 308 290 292 321 C4' C A 11 OK OK 323 338 320 322 352 C4' C A 12 OK OK 354 369 351 353 383 C4' U A 13 OK OK 385 400 382 384 413 C4' U A 14 OK OK 415 430 412 414 443 C4' U A 15 OK OK 445 460 442 444 473 C4' A A 16 OK OK 475 492 472 474 506 C4' A A 17 OK OK 508 525 505 507 539 C4' U A 18 OK OK 541 556 538 540 569 C4' G A 19 OK OK 571 589 568 570 603 C4' G A 20 OK OK 605 623 602 604 637 C4' U A 21 OK OK 639 654 636 638 667 C4' C A 22 OK OK 669 684 666 668 698 C4' C A 23 OK OK 700 715 697 699 729 C4' A A 24 OK OK 731 748 728 730 762 C4' G A 25 OK OK 764 782 761 763 796 C4' U A 26 OK OK 798 813 795 797 826 C4' C A 27 OK OK 828 843 825 827 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 36 C5' G A 2 OK OK 35 55 56 37 70 C5' C A 3 OK OK 69 86 87 71 101 C5' U A 4 OK OK 100 117 118 102 131 C5' G A 5 OK OK 130 150 151 132 165 C5' C A 6 OK OK 164 181 182 166 196 C5' U A 7 OK OK 195 212 213 197 226 C5' U A 8 OK OK 225 242 243 227 256 C5' G A 9 OK OK 255 275 276 257 290 C5' U A 10 OK OK 289 306 307 291 320 C5' C A 11 OK OK 319 336 337 321 351 C5' C A 12 OK OK 350 367 368 352 382 C5' U A 13 OK OK 381 398 399 383 412 C5' U A 14 OK OK 411 428 429 413 442 C5' U A 15 OK OK 441 458 459 443 472 C5' A A 16 OK OK 471 490 491 473 505 C5' A A 17 OK OK 504 523 524 506 538 C5' U A 18 OK OK 537 554 555 539 568 C5' G A 19 OK OK 567 587 588 569 602 C5' G A 20 OK OK 601 621 622 603 636 C5' U A 21 OK OK 635 652 653 637 666 C5' C A 22 OK OK 665 682 683 667 697 C5' C A 23 OK OK 696 713 714 698 728 C5' A A 24 OK OK 727 746 747 729 761 C5' G A 25 OK OK 760 780 781 762 795 C5' U A 26 OK OK 794 811 812 796 825 C5' C A 27 OK OK 824 841 842 826 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 32 P G A 2 distorted distorted 6 33 34 35 66 P C A 3 distorted distorted 40 67 68 69 97 P U A 4 distorted distorted 74 98 99 100 127 P G A 5 distorted distorted 105 128 129 130 161 P C A 6 distorted distorted 135 162 163 164 192 P U A 7 distorted distorted 169 193 194 195 222 P U A 8 distorted distorted 200 223 224 225 252 P G A 9 distorted distorted 230 253 254 255 286 P U A 10 distorted distorted 260 287 288 289 316 P C A 11 distorted distorted 294 317 318 319 347 P C A 12 distorted distorted 324 348 349 350 378 P U A 13 distorted distorted 355 379 380 381 408 P U A 14 distorted distorted 386 409 410 411 438 P U A 15 distorted distorted 416 439 440 441 468 P A A 16 distorted distorted 446 469 470 471 501 P A A 17 distorted distorted 476 502 503 504 534 P U A 18 distorted distorted 509 535 536 537 564 P G A 19 distorted distorted 542 565 566 567 598 P G A 20 distorted distorted 572 599 600 601 632 P U A 21 distorted distorted 606 633 634 635 662 P C A 22 distorted distorted 640 663 664 665 693 P C A 23 distorted distorted 670 694 695 696 724 P A A 24 distorted distorted 701 725 726 727 757 P G A 25 distorted distorted 732 758 759 760 791 P U A 26 distorted distorted 765 792 793 794 821 P C A 27 distorted distorted 799 822 823 824 ---------------------------------------------------------------------------------