ID code: '1GA5' 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 C 600 beta 4 9 7 27 C1' A C 601 beta 23 28 26 48 C1' A C 602 beta 44 49 47 69 C1' C C 603 beta 65 70 68 88 C1' T C 604 beta 84 89 87 108 C1' A C 605 beta 104 109 107 129 C1' G C 606 beta 125 130 128 151 C1' G C 607 beta 147 152 150 173 C1' T C 608 beta 169 174 172 193 C1' C C 609 beta 189 194 192 212 C1' A C 610 beta 208 213 211 233 C1' C C 611 beta 229 234 232 252 C1' T C 612 beta 248 253 251 272 C1' A C 613 beta 268 273 271 293 C1' G C 614 beta 289 294 292 315 C1' G C 615 beta 311 316 314 337 C1' T C 616 beta 333 338 336 357 C1' C C 617 beta 353 358 356 376 C1' A C 618 beta 372 377 375 397 C1' G C 619 beta 393 398 396 417 C1' C D 621 beta 413 418 416 436 C1' T D 622 beta 432 437 435 456 C1' G D 623 beta 452 457 455 478 C1' A D 624 beta 474 479 477 499 C1' C D 625 beta 495 500 498 518 C1' C D 626 beta 514 519 517 537 C1' T D 627 beta 533 538 536 557 C1' A D 628 beta 553 558 556 578 C1' G D 629 beta 574 579 577 600 C1' T D 630 beta 596 601 599 620 C1' G D 631 beta 616 621 619 642 C1' A D 632 beta 638 643 641 663 C1' C D 633 beta 659 664 662 682 C1' C D 634 beta 678 683 681 701 C1' T D 635 beta 697 702 700 721 C1' A D 636 beta 717 722 720 742 C1' G D 637 beta 738 743 741 764 C1' T D 638 beta 760 765 763 784 C1' 5IT D 639 beta 780 785 783 804 C1' G D 640 beta 800 805 803 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' C C 600 8 5 26 C2' A C 601 27 24 47 C2' A C 602 48 45 68 C2' C C 603 69 66 87 C2' T C 604 88 85 107 C2' A C 605 108 105 128 C2' G C 606 129 126 150 C2' G C 607 151 148 172 C2' T C 608 173 170 192 C2' C C 609 193 190 211 C2' A C 610 212 209 232 C2' C C 611 233 230 251 C2' T C 612 252 249 271 C2' A C 613 272 269 292 C2' G C 614 293 290 314 C2' G C 615 315 312 336 C2' T C 616 337 334 356 C2' C C 617 357 354 375 C2' A C 618 376 373 396 C2' G C 619 397 394 416 C2' C D 621 417 414 435 C2' T D 622 436 433 455 C2' G D 623 456 453 477 C2' A D 624 478 475 498 C2' C D 625 499 496 517 C2' C D 626 518 515 536 C2' T D 627 537 534 556 C2' A D 628 557 554 577 C2' G D 629 578 575 599 C2' T D 630 600 597 619 C2' G D 631 620 617 641 C2' A D 632 642 639 662 C2' C D 633 663 660 681 C2' C D 634 682 679 700 C2' T D 635 701 698 720 C2' A D 636 721 718 741 C2' G D 637 742 739 763 C2' T D 638 764 761 783 C2' 5IT D 639 784 781 803 C2' G D 640 804 801 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' C C 600 OK 3 6 7 24 C3' A C 601 OK 22 25 26 45 C3' A C 602 OK 43 46 47 66 C3' C C 603 OK 64 67 68 85 C3' T C 604 OK 83 86 87 105 C3' A C 605 OK 103 106 107 126 C3' G C 606 OK 124 127 128 148 C3' G C 607 OK 146 149 150 170 C3' T C 608 OK 168 171 172 190 C3' C C 609 OK 188 191 192 209 C3' A C 610 OK 207 210 211 230 C3' C C 611 OK 228 231 232 249 C3' T C 612 OK 247 250 251 269 C3' A C 613 OK 267 270 271 290 C3' G C 614 OK 288 291 292 312 C3' G C 615 OK 310 313 314 334 C3' T C 616 OK 332 335 336 354 C3' C C 617 OK 352 355 356 373 C3' A C 618 OK 371 374 375 394 C3' G C 619 OK 392 395 396 414 C3' C D 621 OK 412 415 416 433 C3' T D 622 OK 431 434 435 453 C3' G D 623 OK 451 454 455 475 C3' A D 624 OK 473 476 477 496 C3' C D 625 OK 494 497 498 515 C3' C D 626 OK 513 516 517 534 C3' T D 627 OK 532 535 536 554 C3' A D 628 OK 552 555 556 575 C3' G D 629 OK 573 576 577 597 C3' T D 630 OK 595 598 599 617 C3' G D 631 OK 615 618 619 639 C3' A D 632 OK 637 640 641 660 C3' C D 633 OK 658 661 662 679 C3' C D 634 OK 677 680 681 698 C3' T D 635 OK 696 699 700 718 C3' A D 636 OK 716 719 720 739 C3' G D 637 OK 737 740 741 761 C3' T D 638 OK 759 762 763 781 C3' 5IT D 639 OK 779 782 783 801 C3' G D 640 OK 799 802 803 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' C C 600 OK 5 2 4 22 C4' A C 601 OK 24 21 23 43 C4' A C 602 OK 45 42 44 64 C4' C C 603 OK 66 63 65 83 C4' T C 604 OK 85 82 84 103 C4' A C 605 OK 105 102 104 124 C4' G C 606 OK 126 123 125 146 C4' G C 607 OK 148 145 147 168 C4' T C 608 OK 170 167 169 188 C4' C C 609 OK 190 187 189 207 C4' A C 610 OK 209 206 208 228 C4' C C 611 OK 230 227 229 247 C4' T C 612 OK 249 246 248 267 C4' A C 613 OK 269 266 268 288 C4' G C 614 OK 290 287 289 310 C4' G C 615 OK 312 309 311 332 C4' T C 616 OK 334 331 333 352 C4' C C 617 OK 354 351 353 371 C4' A C 618 OK 373 370 372 392 C4' G C 619 OK 394 391 393 412 C4' C D 621 OK 414 411 413 431 C4' T D 622 OK 433 430 432 451 C4' G D 623 OK 453 450 452 473 C4' A D 624 OK 475 472 474 494 C4' C D 625 OK 496 493 495 513 C4' C D 626 OK 515 512 514 532 C4' T D 627 OK 534 531 533 552 C4' A D 628 OK 554 551 553 573 C4' G D 629 OK 575 572 574 595 C4' T D 630 OK 597 594 596 615 C4' G D 631 OK 617 614 616 637 C4' A D 632 OK 639 636 638 658 C4' C D 633 OK 660 657 659 677 C4' C D 634 OK 679 676 678 696 C4' T D 635 OK 698 695 697 716 C4' A D 636 OK 718 715 717 737 C4' G D 637 OK 739 736 738 759 C4' T D 638 OK 761 758 760 779 C4' 5IT D 639 OK 781 778 780 799 C4' G D 640 OK 801 798 800 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' C C 600 1 3 21 C5' A C 601 20 22 42 C5' A C 602 41 43 63 C5' C C 603 62 64 82 C5' T C 604 81 83 102 C5' A C 605 101 103 123 C5' G C 606 122 124 145 C5' G C 607 144 146 167 C5' T C 608 166 168 187 C5' C C 609 186 188 206 C5' A C 610 205 207 227 C5' C C 611 226 228 246 C5' T C 612 245 247 266 C5' A C 613 265 267 287 C5' G C 614 286 288 309 C5' G C 615 308 310 331 C5' T C 616 330 332 351 C5' C C 617 350 352 370 C5' A C 618 369 371 391 C5' G C 619 390 392 411 C5' C D 621 410 412 430 C5' T D 622 429 431 450 C5' G D 623 449 451 472 C5' A D 624 471 473 493 C5' C D 625 492 494 512 C5' C D 626 511 513 531 C5' T D 627 530 532 551 C5' A D 628 550 552 572 C5' G D 629 571 573 594 C5' T D 630 593 595 614 C5' G D 631 613 615 636 C5' A D 632 635 637 657 C5' C D 633 656 658 676 C5' C D 634 675 677 695 C5' T D 635 694 696 715 C5' A D 636 714 716 736 C5' G D 637 735 737 758 C5' T D 638 757 759 778 C5' 5IT D 639 777 779 798 C5' G D 640 797 799 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 17 P A C 601 distorted distorted 6 18 19 20 38 P A C 602 distorted distorted 25 39 40 41 59 P C C 603 distorted distorted 46 60 61 62 78 P T C 604 distorted distorted 67 79 80 81 98 P A C 605 distorted distorted 86 99 100 101 119 P G C 606 distorted distorted 106 120 121 122 141 P G C 607 distorted distorted 127 142 143 144 163 P T C 608 distorted distorted 149 164 165 166 183 P C C 609 distorted distorted 171 184 185 186 202 P A C 610 distorted distorted 191 203 204 205 223 P C C 611 distorted distorted 210 224 225 226 242 P T C 612 distorted distorted 231 243 244 245 262 P A C 613 distorted distorted 250 263 264 265 283 P G C 614 distorted distorted 270 284 285 286 305 P G C 615 distorted distorted 291 306 307 308 327 P T C 616 distorted distorted 313 328 329 330 347 P C C 617 distorted distorted 335 348 349 350 366 P A C 618 distorted distorted 355 367 368 369 387 P G C 619 distorted distorted 374 388 389 390 426 P T D 622 distorted distorted 415 427 428 429 446 P G D 623 distorted distorted 434 447 448 449 468 P A D 624 distorted distorted 454 469 470 471 489 P C D 625 distorted distorted 476 490 491 492 508 P C D 626 distorted distorted 497 509 510 511 527 P T D 627 distorted distorted 516 528 529 530 547 P A D 628 distorted distorted 535 548 549 550 568 P G D 629 distorted distorted 555 569 570 571 590 P T D 630 distorted distorted 576 591 592 593 610 P G D 631 distorted distorted 598 611 612 613 632 P A D 632 distorted distorted 618 633 634 635 653 P C D 633 distorted distorted 640 654 655 656 672 P C D 634 distorted distorted 661 673 674 675 691 P T D 635 distorted distorted 680 692 693 694 711 P A D 636 distorted distorted 699 712 713 714 732 P G D 637 distorted distorted 719 733 734 735 754 P T D 638 distorted distorted 740 755 756 757 774 P 5IT D 639 OK OK 762 775 776 777 794 P G D 640 distorted distorted 795 796 797 ---------------------------------------------------------------------------------