ID code: '1APL' 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' --------------------------------------------------------------------------------- 29 C1' C A 2 beta 25 30 28 48 C1' A A 3 beta 44 49 47 69 C1' T A 4 beta 65 70 68 89 C1' G A 5 beta 85 90 88 111 C1' T A 6 beta 107 112 110 131 C1' A A 7 beta 127 132 130 152 C1' A A 8 beta 148 153 151 173 C1' T A 9 beta 169 174 172 193 C1' T A 10 beta 189 194 192 213 C1' C A 11 beta 209 214 212 232 C1' A A 12 beta 228 233 231 253 C1' T A 13 beta 249 254 252 273 C1' T A 14 beta 269 274 272 293 C1' T A 15 beta 289 294 292 313 C1' A A 16 beta 309 314 312 334 C1' C A 17 beta 330 335 333 353 C1' A A 18 beta 349 354 352 374 C1' C A 19 beta 370 375 373 393 C1' G A 20 beta 389 394 392 415 C1' C A 21 beta 411 416 414 452 C1' G B 23 beta 448 453 451 474 C1' C B 24 beta 470 475 473 493 C1' G B 25 beta 489 494 492 515 C1' T B 26 beta 511 516 514 535 C1' G B 27 beta 531 536 534 557 C1' T B 28 beta 553 558 556 577 C1' A B 29 beta 573 578 576 598 C1' A B 30 beta 594 599 597 619 C1' A B 31 beta 615 620 618 640 C1' T B 32 beta 636 641 639 660 C1' G B 33 beta 656 661 659 682 C1' A B 34 beta 678 683 681 703 C1' A B 35 beta 699 704 702 724 C1' T B 36 beta 720 725 723 744 C1' T B 37 beta 740 745 743 764 C1' A B 38 beta 760 765 763 785 C1' C B 39 beta 781 786 784 804 C1' A B 40 beta 800 805 803 825 C1' T B 41 beta 821 826 824 845 C1' G B 42 beta 841 846 844 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 28 C2' C A 2 29 26 47 C2' A A 3 48 45 68 C2' T A 4 69 66 88 C2' G A 5 89 86 110 C2' T A 6 111 108 130 C2' A A 7 131 128 151 C2' A A 8 152 149 172 C2' T A 9 173 170 192 C2' T A 10 193 190 212 C2' C A 11 213 210 231 C2' A A 12 232 229 252 C2' T A 13 253 250 272 C2' T A 14 273 270 292 C2' T A 15 293 290 312 C2' A A 16 313 310 333 C2' C A 17 334 331 352 C2' A A 18 353 350 373 C2' C A 19 374 371 392 C2' G A 20 393 390 414 C2' C A 21 415 412 451 C2' G B 23 452 449 473 C2' C B 24 474 471 492 C2' G B 25 493 490 514 C2' T B 26 515 512 534 C2' G B 27 535 532 556 C2' T B 28 557 554 576 C2' A B 29 577 574 597 C2' A B 30 598 595 618 C2' A B 31 619 616 639 C2' T B 32 640 637 659 C2' G B 33 660 657 681 C2' A B 34 682 679 702 C2' A B 35 703 700 723 C2' T B 36 724 721 743 C2' T B 37 744 741 763 C2' A B 38 764 761 784 C2' C B 39 785 782 803 C2' A B 40 804 801 824 C2' T B 41 825 822 844 C2' G B 42 845 842 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 26 C3' C A 2 OK 24 27 28 45 C3' A A 3 OK 43 46 47 66 C3' T A 4 OK 64 67 68 86 C3' G A 5 OK 84 87 88 108 C3' T A 6 OK 106 109 110 128 C3' A A 7 OK 126 129 130 149 C3' A A 8 OK 147 150 151 170 C3' T A 9 OK 168 171 172 190 C3' T A 10 OK 188 191 192 210 C3' C A 11 OK 208 211 212 229 C3' A A 12 OK 227 230 231 250 C3' T A 13 OK 248 251 252 270 C3' T A 14 OK 268 271 272 290 C3' T A 15 OK 288 291 292 310 C3' A A 16 OK 308 311 312 331 C3' C A 17 OK 329 332 333 350 C3' A A 18 OK 348 351 352 371 C3' C A 19 OK 369 372 373 390 C3' G A 20 OK 388 391 392 412 C3' C A 21 OK 410 413 414 449 C3' G B 23 OK 447 450 451 471 C3' C B 24 OK 469 472 473 490 C3' G B 25 OK 488 491 492 512 C3' T B 26 OK 510 513 514 532 C3' G B 27 OK 530 533 534 554 C3' T B 28 OK 552 555 556 574 C3' A B 29 OK 572 575 576 595 C3' A B 30 OK 593 596 597 616 C3' A B 31 OK 614 617 618 637 C3' T B 32 OK 635 638 639 657 C3' G B 33 OK 655 658 659 679 C3' A B 34 OK 677 680 681 700 C3' A B 35 OK 698 701 702 721 C3' T B 36 OK 719 722 723 741 C3' T B 37 OK 739 742 743 761 C3' A B 38 OK 759 762 763 782 C3' C B 39 OK 780 783 784 801 C3' A B 40 OK 799 802 803 822 C3' T B 41 OK 820 823 824 842 C3' G B 42 OK 840 843 844 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 24 C4' C A 2 OK 26 23 25 43 C4' A A 3 OK 45 42 44 64 C4' T A 4 OK 66 63 65 84 C4' G A 5 OK 86 83 85 106 C4' T A 6 OK 108 105 107 126 C4' A A 7 OK 128 125 127 147 C4' A A 8 OK 149 146 148 168 C4' T A 9 OK 170 167 169 188 C4' T A 10 OK 190 187 189 208 C4' C A 11 OK 210 207 209 227 C4' A A 12 OK 229 226 228 248 C4' T A 13 OK 250 247 249 268 C4' T A 14 OK 270 267 269 288 C4' T A 15 OK 290 287 289 308 C4' A A 16 OK 310 307 309 329 C4' C A 17 OK 331 328 330 348 C4' A A 18 OK 350 347 349 369 C4' C A 19 OK 371 368 370 388 C4' G A 20 OK 390 387 389 410 C4' C A 21 OK 412 409 411 447 C4' G B 23 OK 449 446 448 469 C4' C B 24 OK 471 468 470 488 C4' G B 25 OK 490 487 489 510 C4' T B 26 OK 512 509 511 530 C4' G B 27 OK 532 529 531 552 C4' T B 28 OK 554 551 553 572 C4' A B 29 OK 574 571 573 593 C4' A B 30 OK 595 592 594 614 C4' A B 31 OK 616 613 615 635 C4' T B 32 OK 637 634 636 655 C4' G B 33 OK 657 654 656 677 C4' A B 34 OK 679 676 678 698 C4' A B 35 OK 700 697 699 719 C4' T B 36 OK 721 718 720 739 C4' T B 37 OK 741 738 740 759 C4' A B 38 OK 761 758 760 780 C4' C B 39 OK 782 779 781 799 C4' A B 40 OK 801 798 800 820 C4' T B 41 OK 822 819 821 840 C4' G B 42 OK 842 839 841 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 23 C5' C A 2 22 24 42 C5' A A 3 41 43 63 C5' T A 4 62 64 83 C5' G A 5 82 84 105 C5' T A 6 104 106 125 C5' A A 7 124 126 146 C5' A A 8 145 147 167 C5' T A 9 166 168 187 C5' T A 10 186 188 207 C5' C A 11 206 208 226 C5' A A 12 225 227 247 C5' T A 13 246 248 267 C5' T A 14 266 268 287 C5' T A 15 286 288 307 C5' A A 16 306 308 328 C5' C A 17 327 329 347 C5' A A 18 346 348 368 C5' C A 19 367 369 387 C5' G A 20 386 388 409 C5' C A 21 408 410 446 C5' G B 23 445 447 468 C5' C B 24 467 469 487 C5' G B 25 486 488 509 C5' T B 26 508 510 529 C5' G B 27 528 530 551 C5' T B 28 550 552 571 C5' A B 29 570 572 592 C5' A B 30 591 593 613 C5' A B 31 612 614 634 C5' T B 32 633 635 654 C5' G B 33 653 655 676 C5' A B 34 675 677 697 C5' A B 35 696 698 718 C5' T B 36 717 719 738 C5' T B 37 737 739 758 C5' A B 38 757 759 779 C5' C B 39 778 780 798 C5' A B 40 797 799 819 C5' T B 41 818 820 839 C5' G B 42 838 840 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 38 P A A 3 distorted distorted 27 39 40 41 59 P T A 4 OK OK 46 60 61 62 79 P G A 5 OK OK 67 80 81 82 101 P T A 6 OK OK 87 102 103 104 121 P A A 7 OK OK 109 122 123 124 142 P A A 8 OK OK 129 143 144 145 163 P T A 9 OK OK 150 164 165 166 183 P T A 10 OK OK 171 184 185 186 203 P C A 11 distorted distorted 191 204 205 206 222 P A A 12 OK OK 211 223 224 225 243 P T A 13 OK OK 230 244 245 246 263 P T A 14 OK OK 251 264 265 266 283 P T A 15 OK OK 271 284 285 286 303 P A A 16 distorted distorted 291 304 305 306 324 P C A 17 distorted distorted 311 325 326 327 343 P A A 18 OK OK 332 344 345 346 364 P C A 19 OK OK 351 365 366 367 383 P G A 20 OK OK 372 384 385 386 405 P C A 21 OK OK 391 406 407 408 464 P C B 24 OK OK 450 465 466 467 483 P G B 25 OK OK 472 484 485 486 505 P T B 26 OK OK 491 506 507 508 525 P G B 27 OK OK 513 526 527 528 547 P T B 28 OK OK 533 548 549 550 567 P A B 29 distorted distorted 555 568 569 570 588 P A B 30 OK OK 575 589 590 591 609 P A B 31 OK OK 596 610 611 612 630 P T B 32 distorted distorted 617 631 632 633 650 P G B 33 OK OK 638 651 652 653 672 P A B 34 OK OK 658 673 674 675 693 P A B 35 OK OK 680 694 695 696 714 P T B 36 OK OK 701 715 716 717 734 P T B 37 OK OK 722 735 736 737 754 P A B 38 OK OK 742 755 756 757 775 P C B 39 OK OK 762 776 777 778 794 P A B 40 OK OK 783 795 796 797 815 P T B 41 OK OK 802 816 817 818 835 P G B 42 OK OK 823 836 837 838 ---------------------------------------------------------------------------------