ID code: '1HLV' 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' G B 1 beta 4 9 7 30 C1' C B 2 beta 26 31 29 49 C1' C B 3 beta 45 50 48 68 C1' T B 4 beta 64 69 67 88 C1' T B 5 beta 84 89 87 108 C1' C B 6 beta 104 109 107 127 C1' G B 7 beta 123 128 126 149 C1' T B 8 beta 145 150 148 169 C1' T B 9 beta 165 170 168 189 C1' G B 10 beta 185 190 188 211 C1' G B 11 beta 207 212 210 233 C1' A B 12 beta 229 234 232 254 C1' A B 13 beta 250 255 253 275 C1' A B 14 beta 271 276 274 296 C1' C B 15 beta 292 297 295 315 C1' G B 16 beta 311 316 314 337 C1' G B 17 beta 333 338 336 359 C1' G B 18 beta 355 360 358 381 C1' A B 19 beta 377 382 380 402 C1' T B 20 beta 398 403 401 422 C1' T B 21 beta 418 423 421 440 C1' A C 1 beta 436 441 439 461 C1' A C 2 beta 457 462 460 482 C1' T C 3 beta 478 483 481 502 C1' C C 4 beta 498 503 501 521 C1' C C 5 beta 517 522 520 540 C1' C C 6 beta 536 541 539 559 C1' G C 7 beta 555 560 558 581 C1' T C 8 beta 577 582 580 601 C1' T C 9 beta 597 602 600 621 C1' T C 10 beta 617 622 620 641 C1' C C 11 beta 637 642 640 660 C1' C C 12 beta 656 661 659 679 C1' A C 13 beta 675 680 678 700 C1' A C 14 beta 696 701 699 721 C1' C C 15 beta 717 722 720 740 C1' G C 16 beta 736 741 739 762 C1' A C 17 beta 758 763 761 783 C1' A C 18 beta 779 784 782 804 C1' G C 19 beta 800 805 803 826 C1' G C 20 beta 822 827 825 848 C1' C C 21 beta 844 849 847 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G B 1 8 5 29 C2' C B 2 30 27 48 C2' C B 3 49 46 67 C2' T B 4 68 65 87 C2' T B 5 88 85 107 C2' C B 6 108 105 126 C2' G B 7 127 124 148 C2' T B 8 149 146 168 C2' T B 9 169 166 188 C2' G B 10 189 186 210 C2' G B 11 211 208 232 C2' A B 12 233 230 253 C2' A B 13 254 251 274 C2' A B 14 275 272 295 C2' C B 15 296 293 314 C2' G B 16 315 312 336 C2' G B 17 337 334 358 C2' G B 18 359 356 380 C2' A B 19 381 378 401 C2' T B 20 402 399 421 C2' T B 21 422 419 439 C2' A C 1 440 437 460 C2' A C 2 461 458 481 C2' T C 3 482 479 501 C2' C C 4 502 499 520 C2' C C 5 521 518 539 C2' C C 6 540 537 558 C2' G C 7 559 556 580 C2' T C 8 581 578 600 C2' T C 9 601 598 620 C2' T C 10 621 618 640 C2' C C 11 641 638 659 C2' C C 12 660 657 678 C2' A C 13 679 676 699 C2' A C 14 700 697 720 C2' C C 15 721 718 739 C2' G C 16 740 737 761 C2' A C 17 762 759 782 C2' A C 18 783 780 803 C2' G C 19 804 801 825 C2' G C 20 826 823 847 C2' C C 21 848 845 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G B 1 OK 3 6 7 27 C3' C B 2 OK 25 28 29 46 C3' C B 3 OK 44 47 48 65 C3' T B 4 OK 63 66 67 85 C3' T B 5 OK 83 86 87 105 C3' C B 6 OK 103 106 107 124 C3' G B 7 OK 122 125 126 146 C3' T B 8 OK 144 147 148 166 C3' T B 9 OK 164 167 168 186 C3' G B 10 OK 184 187 188 208 C3' G B 11 OK 206 209 210 230 C3' A B 12 OK 228 231 232 251 C3' A B 13 OK 249 252 253 272 C3' A B 14 OK 270 273 274 293 C3' C B 15 OK 291 294 295 312 C3' G B 16 OK 310 313 314 334 C3' G B 17 OK 332 335 336 356 C3' G B 18 OK 354 357 358 378 C3' A B 19 OK 376 379 380 399 C3' T B 20 OK 397 400 401 419 C3' T B 21 OK 417 420 421 437 C3' A C 1 OK 435 438 439 458 C3' A C 2 OK 456 459 460 479 C3' T C 3 OK 477 480 481 499 C3' C C 4 OK 497 500 501 518 C3' C C 5 OK 516 519 520 537 C3' C C 6 OK 535 538 539 556 C3' G C 7 OK 554 557 558 578 C3' T C 8 OK 576 579 580 598 C3' T C 9 OK 596 599 600 618 C3' T C 10 OK 616 619 620 638 C3' C C 11 OK 636 639 640 657 C3' C C 12 OK 655 658 659 676 C3' A C 13 OK 674 677 678 697 C3' A C 14 OK 695 698 699 718 C3' C C 15 OK 716 719 720 737 C3' G C 16 OK 735 738 739 759 C3' A C 17 OK 757 760 761 780 C3' A C 18 OK 778 781 782 801 C3' G C 19 OK 799 802 803 823 C3' G C 20 OK 821 824 825 845 C3' C C 21 OK 843 846 847 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G B 1 OK 5 2 4 25 C4' C B 2 OK 27 24 26 44 C4' C B 3 OK 46 43 45 63 C4' T B 4 OK 65 62 64 83 C4' T B 5 OK 85 82 84 103 C4' C B 6 OK 105 102 104 122 C4' G B 7 OK 124 121 123 144 C4' T B 8 OK 146 143 145 164 C4' T B 9 OK 166 163 165 184 C4' G B 10 OK 186 183 185 206 C4' G B 11 OK 208 205 207 228 C4' A B 12 OK 230 227 229 249 C4' A B 13 OK 251 248 250 270 C4' A B 14 OK 272 269 271 291 C4' C B 15 OK 293 290 292 310 C4' G B 16 OK 312 309 311 332 C4' G B 17 OK 334 331 333 354 C4' G B 18 OK 356 353 355 376 C4' A B 19 OK 378 375 377 397 C4' T B 20 OK 399 396 398 417 C4' T B 21 OK 419 416 418 435 C4' A C 1 OK 437 434 436 456 C4' A C 2 OK 458 455 457 477 C4' T C 3 OK 479 476 478 497 C4' C C 4 OK 499 496 498 516 C4' C C 5 OK 518 515 517 535 C4' C C 6 OK 537 534 536 554 C4' G C 7 OK 556 553 555 576 C4' T C 8 OK 578 575 577 596 C4' T C 9 OK 598 595 597 616 C4' T C 10 OK 618 615 617 636 C4' C C 11 OK 638 635 637 655 C4' C C 12 OK 657 654 656 674 C4' A C 13 OK 676 673 675 695 C4' A C 14 OK 697 694 696 716 C4' C C 15 OK 718 715 717 735 C4' G C 16 OK 737 734 736 757 C4' A C 17 OK 759 756 758 778 C4' A C 18 OK 780 777 779 799 C4' G C 19 OK 801 798 800 821 C4' G C 20 OK 823 820 822 843 C4' C C 21 OK 845 842 844 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G B 1 1 3 24 C5' C B 2 23 25 43 C5' C B 3 42 44 62 C5' T B 4 61 63 82 C5' T B 5 81 83 102 C5' C B 6 101 103 121 C5' G B 7 120 122 143 C5' T B 8 142 144 163 C5' T B 9 162 164 183 C5' G B 10 182 184 205 C5' G B 11 204 206 227 C5' A B 12 226 228 248 C5' A B 13 247 249 269 C5' A B 14 268 270 290 C5' C B 15 289 291 309 C5' G B 16 308 310 331 C5' G B 17 330 332 353 C5' G B 18 352 354 375 C5' A B 19 374 376 396 C5' T B 20 395 397 416 C5' T B 21 415 417 434 C5' A C 1 433 435 455 C5' A C 2 454 456 476 C5' T C 3 475 477 496 C5' C C 4 495 497 515 C5' C C 5 514 516 534 C5' C C 6 533 535 553 C5' G C 7 552 554 575 C5' T C 8 574 576 595 C5' T C 9 594 596 615 C5' T C 10 614 616 635 C5' C C 11 634 636 654 C5' C C 12 653 655 673 C5' A C 13 672 674 694 C5' A C 14 693 695 715 C5' C C 15 714 716 734 C5' G C 16 733 735 756 C5' A C 17 755 757 777 C5' A C 18 776 778 798 C5' G C 19 797 799 820 C5' G C 20 819 821 842 C5' C C 21 841 843 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 20 P C B 2 distorted distorted 6 21 22 23 39 P C B 3 distorted distorted 28 40 41 42 58 P T B 4 distorted distorted 47 59 60 61 78 P T B 5 distorted distorted 66 79 80 81 98 P C B 6 distorted distorted 86 99 100 101 117 P G B 7 distorted distorted 106 118 119 120 139 P T B 8 distorted distorted 125 140 141 142 159 P T B 9 distorted distorted 147 160 161 162 179 P G B 10 distorted distorted 167 180 181 182 201 P G B 11 distorted distorted 187 202 203 204 223 P A B 12 distorted distorted 209 224 225 226 244 P A B 13 distorted distorted 231 245 246 247 265 P A B 14 distorted distorted 252 266 267 268 286 P C B 15 distorted distorted 273 287 288 289 305 P G B 16 distorted distorted 294 306 307 308 327 P G B 17 distorted distorted 313 328 329 330 349 P G B 18 distorted distorted 335 350 351 352 371 P A B 19 distorted distorted 357 372 373 374 392 P T B 20 distorted distorted 379 393 394 395 412 P T B 21 distorted distorted 400 413 414 415 451 P A C 2 distorted distorted 438 452 453 454 472 P T C 3 distorted distorted 459 473 474 475 492 P C C 4 distorted distorted 480 493 494 495 511 P C C 5 distorted distorted 500 512 513 514 530 P C C 6 distorted distorted 519 531 532 533 549 P G C 7 distorted distorted 538 550 551 552 571 P T C 8 distorted distorted 557 572 573 574 591 P T C 9 distorted distorted 579 592 593 594 611 P T C 10 distorted distorted 599 612 613 614 631 P C C 11 distorted distorted 619 632 633 634 650 P C C 12 distorted distorted 639 651 652 653 669 P A C 13 distorted distorted 658 670 671 672 690 P A C 14 distorted distorted 677 691 692 693 711 P C C 15 distorted distorted 698 712 713 714 730 P G C 16 distorted distorted 719 731 732 733 752 P A C 17 distorted distorted 738 753 754 755 773 P A C 18 distorted distorted 760 774 775 776 794 P G C 19 distorted distorted 781 795 796 797 816 P G C 20 distorted distorted 802 817 818 819 838 P C C 21 distorted distorted 824 839 840 841 ---------------------------------------------------------------------------------