ID code: '1F4K' 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' --------------------------------------------------------------------------------- 8 C1' C D 1 beta 4 9 7 27 C1' T D 2 beta 23 28 26 47 C1' A D 3 beta 43 48 46 68 C1' T D 4 beta 64 69 67 88 C1' G D 5 beta 84 89 87 110 C1' A D 6 beta 106 111 109 131 C1' A D 7 beta 127 132 130 152 C1' C D 8 beta 148 153 151 171 C1' A D 9 beta 167 172 170 192 C1' T D 10 beta 188 193 191 212 C1' A D 11 beta 208 213 211 233 C1' A D 12 beta 229 234 232 254 C1' T D 13 beta 250 255 253 274 C1' G D 14 beta 270 275 273 296 C1' T D 15 beta 292 297 295 316 C1' T D 16 beta 312 317 315 336 C1' C D 17 beta 332 337 335 355 C1' A D 18 beta 351 356 354 376 C1' T D 19 beta 372 377 375 396 C1' A D 20 beta 392 397 395 417 C1' G D 21 beta 413 418 416 437 C1' C E 1 beta 433 438 436 456 C1' T E 2 beta 452 457 455 476 C1' A E 3 beta 472 477 475 497 C1' T E 4 beta 493 498 496 517 C1' G E 5 beta 513 518 516 539 C1' A E 6 beta 535 540 538 560 C1' A E 7 beta 556 561 559 581 C1' C E 8 beta 577 582 580 600 C1' A E 9 beta 596 601 599 621 C1' T E 10 beta 617 622 620 641 C1' T E 11 beta 637 642 640 661 C1' A E 12 beta 657 662 660 682 C1' T E 13 beta 678 683 681 702 C1' G E 14 beta 698 703 701 724 C1' T E 15 beta 720 725 723 744 C1' T E 16 beta 740 745 743 764 C1' C E 17 beta 760 765 763 783 C1' A E 18 beta 779 784 782 804 C1' T E 19 beta 800 805 803 824 C1' A E 20 beta 820 825 823 845 C1' G E 21 beta 841 846 844 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' C D 1 8 5 26 C2' T D 2 27 24 46 C2' A D 3 47 44 67 C2' T D 4 68 65 87 C2' G D 5 88 85 109 C2' A D 6 110 107 130 C2' A D 7 131 128 151 C2' C D 8 152 149 170 C2' A D 9 171 168 191 C2' T D 10 192 189 211 C2' A D 11 212 209 232 C2' A D 12 233 230 253 C2' T D 13 254 251 273 C2' G D 14 274 271 295 C2' T D 15 296 293 315 C2' T D 16 316 313 335 C2' C D 17 336 333 354 C2' A D 18 355 352 375 C2' T D 19 376 373 395 C2' A D 20 396 393 416 C2' G D 21 417 414 436 C2' C E 1 437 434 455 C2' T E 2 456 453 475 C2' A E 3 476 473 496 C2' T E 4 497 494 516 C2' G E 5 517 514 538 C2' A E 6 539 536 559 C2' A E 7 560 557 580 C2' C E 8 581 578 599 C2' A E 9 600 597 620 C2' T E 10 621 618 640 C2' T E 11 641 638 660 C2' A E 12 661 658 681 C2' T E 13 682 679 701 C2' G E 14 702 699 723 C2' T E 15 724 721 743 C2' T E 16 744 741 763 C2' C E 17 764 761 782 C2' A E 18 783 780 803 C2' T E 19 804 801 823 C2' A E 20 824 821 844 C2' G E 21 845 842 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' C D 1 OK 3 6 7 24 C3' T D 2 OK 22 25 26 44 C3' A D 3 OK 42 45 46 65 C3' T D 4 OK 63 66 67 85 C3' G D 5 OK 83 86 87 107 C3' A D 6 OK 105 108 109 128 C3' A D 7 OK 126 129 130 149 C3' C D 8 OK 147 150 151 168 C3' A D 9 OK 166 169 170 189 C3' T D 10 OK 187 190 191 209 C3' A D 11 OK 207 210 211 230 C3' A D 12 OK 228 231 232 251 C3' T D 13 OK 249 252 253 271 C3' G D 14 OK 269 272 273 293 C3' T D 15 OK 291 294 295 313 C3' T D 16 OK 311 314 315 333 C3' C D 17 OK 331 334 335 352 C3' A D 18 OK 350 353 354 373 C3' T D 19 OK 371 374 375 393 C3' A D 20 OK 391 394 395 414 C3' G D 21 OK 412 415 416 434 C3' C E 1 OK 432 435 436 453 C3' T E 2 OK 451 454 455 473 C3' A E 3 OK 471 474 475 494 C3' T E 4 OK 492 495 496 514 C3' G E 5 OK 512 515 516 536 C3' A E 6 OK 534 537 538 557 C3' A E 7 OK 555 558 559 578 C3' C E 8 OK 576 579 580 597 C3' A E 9 OK 595 598 599 618 C3' T E 10 OK 616 619 620 638 C3' T E 11 OK 636 639 640 658 C3' A E 12 OK 656 659 660 679 C3' T E 13 OK 677 680 681 699 C3' G E 14 OK 697 700 701 721 C3' T E 15 OK 719 722 723 741 C3' T E 16 OK 739 742 743 761 C3' C E 17 OK 759 762 763 780 C3' A E 18 OK 778 781 782 801 C3' T E 19 OK 799 802 803 821 C3' A E 20 OK 819 822 823 842 C3' G E 21 OK 840 843 844 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' C D 1 OK 5 2 4 22 C4' T D 2 OK 24 21 23 42 C4' A D 3 OK 44 41 43 63 C4' T D 4 OK 65 62 64 83 C4' G D 5 OK 85 82 84 105 C4' A D 6 OK 107 104 106 126 C4' A D 7 OK 128 125 127 147 C4' C D 8 OK 149 146 148 166 C4' A D 9 OK 168 165 167 187 C4' T D 10 OK 189 186 188 207 C4' A D 11 OK 209 206 208 228 C4' A D 12 OK 230 227 229 249 C4' T D 13 OK 251 248 250 269 C4' G D 14 OK 271 268 270 291 C4' T D 15 OK 293 290 292 311 C4' T D 16 OK 313 310 312 331 C4' C D 17 OK 333 330 332 350 C4' A D 18 OK 352 349 351 371 C4' T D 19 OK 373 370 372 391 C4' A D 20 OK 393 390 392 412 C4' G D 21 OK 414 411 413 432 C4' C E 1 OK 434 431 433 451 C4' T E 2 OK 453 450 452 471 C4' A E 3 OK 473 470 472 492 C4' T E 4 OK 494 491 493 512 C4' G E 5 OK 514 511 513 534 C4' A E 6 OK 536 533 535 555 C4' A E 7 OK 557 554 556 576 C4' C E 8 OK 578 575 577 595 C4' A E 9 OK 597 594 596 616 C4' T E 10 OK 618 615 617 636 C4' T E 11 OK 638 635 637 656 C4' A E 12 OK 658 655 657 677 C4' T E 13 OK 679 676 678 697 C4' G E 14 OK 699 696 698 719 C4' T E 15 OK 721 718 720 739 C4' T E 16 OK 741 738 740 759 C4' C E 17 OK 761 758 760 778 C4' A E 18 OK 780 777 779 799 C4' T E 19 OK 801 798 800 819 C4' A E 20 OK 821 818 820 840 C4' G E 21 OK 842 839 841 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' C D 1 1 3 21 C5' T D 2 20 22 41 C5' A D 3 40 42 62 C5' T D 4 61 63 82 C5' G D 5 81 83 104 C5' A D 6 103 105 125 C5' A D 7 124 126 146 C5' C D 8 145 147 165 C5' A D 9 164 166 186 C5' T D 10 185 187 206 C5' A D 11 205 207 227 C5' A D 12 226 228 248 C5' T D 13 247 249 268 C5' G D 14 267 269 290 C5' T D 15 289 291 310 C5' T D 16 309 311 330 C5' C D 17 329 331 349 C5' A D 18 348 350 370 C5' T D 19 369 371 390 C5' A D 20 389 391 411 C5' G D 21 410 412 431 C5' C E 1 430 432 450 C5' T E 2 449 451 470 C5' A E 3 469 471 491 C5' T E 4 490 492 511 C5' G E 5 510 512 533 C5' A E 6 532 534 554 C5' A E 7 553 555 575 C5' C E 8 574 576 594 C5' A E 9 593 595 615 C5' T E 10 614 616 635 C5' T E 11 634 636 655 C5' A E 12 654 656 676 C5' T E 13 675 677 696 C5' G E 14 695 697 718 C5' T E 15 717 719 738 C5' T E 16 737 739 758 C5' C E 17 757 759 777 C5' A E 18 776 778 798 C5' T E 19 797 799 818 C5' A E 20 817 819 839 C5' G E 21 838 840 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 17 P T D 2 distorted distorted 6 18 19 20 37 P A D 3 distorted distorted 25 38 39 40 58 P T D 4 distorted distorted 45 59 60 61 78 P G D 5 distorted distorted 66 79 80 81 100 P A D 6 distorted distorted 86 101 102 103 121 P A D 7 distorted distorted 108 122 123 124 142 P C D 8 distorted distorted 129 143 144 145 161 P A D 9 distorted distorted 150 162 163 164 182 P T D 10 distorted distorted 169 183 184 185 202 P A D 11 distorted distorted 190 203 204 205 223 P A D 12 distorted distorted 210 224 225 226 244 P T D 13 distorted distorted 231 245 246 247 264 P G D 14 distorted distorted 252 265 266 267 286 P T D 15 distorted distorted 272 287 288 289 306 P T D 16 distorted distorted 294 307 308 309 326 P C D 17 distorted distorted 314 327 328 329 345 P A D 18 distorted distorted 334 346 347 348 366 P T D 19 distorted distorted 353 367 368 369 386 P A D 20 distorted distorted 374 387 388 389 407 P G D 21 distorted distorted 394 408 409 410 446 P T E 2 distorted distorted 435 447 448 449 466 P A E 3 distorted distorted 454 467 468 469 487 P T E 4 distorted distorted 474 488 489 490 507 P G E 5 distorted distorted 495 508 509 510 529 P A E 6 distorted distorted 515 530 531 532 550 P A E 7 distorted distorted 537 551 552 553 571 P C E 8 distorted distorted 558 572 573 574 590 P A E 9 distorted distorted 579 591 592 593 611 P T E 10 distorted distorted 598 612 613 614 631 P T E 11 distorted distorted 619 632 633 634 651 P A E 12 distorted distorted 639 652 653 654 672 P T E 13 distorted distorted 659 673 674 675 692 P G E 14 distorted distorted 680 693 694 695 714 P T E 15 distorted distorted 700 715 716 717 734 P T E 16 distorted distorted 722 735 736 737 754 P C E 17 distorted distorted 742 755 756 757 773 P A E 18 distorted distorted 762 774 775 776 794 P T E 19 distorted distorted 781 795 796 797 814 P A E 20 distorted distorted 802 815 816 817 835 P G E 21 distorted distorted 822 836 837 838 ---------------------------------------------------------------------------------