ID code: '1HWT' 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 A 1 beta 4 9 7 30 C1' C A 2 beta 26 31 29 49 C1' G A 3 beta 45 50 48 71 C1' C A 4 beta 67 72 70 90 C1' T A 5 beta 86 91 89 110 C1' A A 6 beta 106 111 109 131 C1' T A 7 beta 127 132 130 151 C1' T A 8 beta 147 152 150 171 C1' A A 9 beta 167 172 170 192 C1' T A 10 beta 188 193 191 212 C1' C A 11 beta 208 213 211 231 C1' G A 12 beta 227 232 230 253 C1' C A 13 beta 249 254 252 272 C1' T A 14 beta 268 273 271 292 C1' A A 15 beta 288 293 291 313 C1' T A 16 beta 309 314 312 333 C1' T A 17 beta 329 334 332 353 C1' A A 18 beta 349 354 352 374 C1' G A 19 beta 370 375 373 396 C1' C A 20 beta 392 397 395 413 C1' G B 1 beta 409 414 412 435 C1' C B 2 beta 431 436 434 454 C1' T B 3 beta 450 455 453 474 C1' A B 4 beta 470 475 473 495 C1' A B 5 beta 491 496 494 516 C1' T B 6 beta 512 517 515 536 C1' A B 7 beta 532 537 535 557 C1' G B 8 beta 553 558 556 579 C1' C B 9 beta 575 580 578 598 C1' G B 10 beta 594 599 597 620 C1' A B 11 beta 616 621 619 641 C1' T B 12 beta 637 642 640 661 C1' A B 13 beta 657 662 660 682 C1' A B 14 beta 678 683 681 703 C1' T B 15 beta 699 704 702 723 C1' A B 16 beta 719 724 722 744 C1' G B 17 beta 740 745 743 766 C1' C B 18 beta 762 767 765 785 C1' G B 19 beta 781 786 784 807 C1' C B 20 beta 803 808 806 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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 8 5 29 C2' C A 2 30 27 48 C2' G A 3 49 46 70 C2' C A 4 71 68 89 C2' T A 5 90 87 109 C2' A A 6 110 107 130 C2' T A 7 131 128 150 C2' T A 8 151 148 170 C2' A A 9 171 168 191 C2' T A 10 192 189 211 C2' C A 11 212 209 230 C2' G A 12 231 228 252 C2' C A 13 253 250 271 C2' T A 14 272 269 291 C2' A A 15 292 289 312 C2' T A 16 313 310 332 C2' T A 17 333 330 352 C2' A A 18 353 350 373 C2' G A 19 374 371 395 C2' C A 20 396 393 412 C2' G B 1 413 410 434 C2' C B 2 435 432 453 C2' T B 3 454 451 473 C2' A B 4 474 471 494 C2' A B 5 495 492 515 C2' T B 6 516 513 535 C2' A B 7 536 533 556 C2' G B 8 557 554 578 C2' C B 9 579 576 597 C2' G B 10 598 595 619 C2' A B 11 620 617 640 C2' T B 12 641 638 660 C2' A B 13 661 658 681 C2' A B 14 682 679 702 C2' T B 15 703 700 722 C2' A B 16 723 720 743 C2' G B 17 744 741 765 C2' C B 18 766 763 784 C2' G B 19 785 782 806 C2' C B 20 807 804 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK 3 6 7 27 C3' C A 2 OK 25 28 29 46 C3' G A 3 OK 44 47 48 68 C3' C A 4 OK 66 69 70 87 C3' T A 5 OK 85 88 89 107 C3' A A 6 OK 105 108 109 128 C3' T A 7 OK 126 129 130 148 C3' T A 8 OK 146 149 150 168 C3' A A 9 OK 166 169 170 189 C3' T A 10 OK 187 190 191 209 C3' C A 11 OK 207 210 211 228 C3' G A 12 OK 226 229 230 250 C3' C A 13 OK 248 251 252 269 C3' T A 14 OK 267 270 271 289 C3' A A 15 OK 287 290 291 310 C3' T A 16 OK 308 311 312 330 C3' T A 17 OK 328 331 332 350 C3' A A 18 OK 348 351 352 371 C3' G A 19 OK 369 372 373 393 C3' C A 20 OK 391 394 395 410 C3' G B 1 OK 408 411 412 432 C3' C B 2 OK 430 433 434 451 C3' T B 3 OK 449 452 453 471 C3' A B 4 OK 469 472 473 492 C3' A B 5 OK 490 493 494 513 C3' T B 6 OK 511 514 515 533 C3' A B 7 OK 531 534 535 554 C3' G B 8 OK 552 555 556 576 C3' C B 9 OK 574 577 578 595 C3' G B 10 OK 593 596 597 617 C3' A B 11 OK 615 618 619 638 C3' T B 12 OK 636 639 640 658 C3' A B 13 OK 656 659 660 679 C3' A B 14 OK 677 680 681 700 C3' T B 15 OK 698 701 702 720 C3' A B 16 OK 718 721 722 741 C3' G B 17 OK 739 742 743 763 C3' C B 18 OK 761 764 765 782 C3' G B 19 OK 780 783 784 804 C3' C B 20 OK 802 805 806 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK 5 2 4 25 C4' C A 2 OK 27 24 26 44 C4' G A 3 OK 46 43 45 66 C4' C A 4 OK 68 65 67 85 C4' T A 5 OK 87 84 86 105 C4' A A 6 OK 107 104 106 126 C4' T A 7 OK 128 125 127 146 C4' T A 8 OK 148 145 147 166 C4' A A 9 OK 168 165 167 187 C4' T A 10 OK 189 186 188 207 C4' C A 11 OK 209 206 208 226 C4' G A 12 OK 228 225 227 248 C4' C A 13 OK 250 247 249 267 C4' T A 14 OK 269 266 268 287 C4' A A 15 OK 289 286 288 308 C4' T A 16 OK 310 307 309 328 C4' T A 17 OK 330 327 329 348 C4' A A 18 OK 350 347 349 369 C4' G A 19 OK 371 368 370 391 C4' C A 20 OK 393 390 392 408 C4' G B 1 OK 410 407 409 430 C4' C B 2 OK 432 429 431 449 C4' T B 3 OK 451 448 450 469 C4' A B 4 OK 471 468 470 490 C4' A B 5 OK 492 489 491 511 C4' T B 6 OK 513 510 512 531 C4' A B 7 OK 533 530 532 552 C4' G B 8 OK 554 551 553 574 C4' C B 9 OK 576 573 575 593 C4' G B 10 OK 595 592 594 615 C4' A B 11 OK 617 614 616 636 C4' T B 12 OK 638 635 637 656 C4' A B 13 OK 658 655 657 677 C4' A B 14 OK 679 676 678 698 C4' T B 15 OK 700 697 699 718 C4' A B 16 OK 720 717 719 739 C4' G B 17 OK 741 738 740 761 C4' C B 18 OK 763 760 762 780 C4' G B 19 OK 782 779 781 802 C4' C B 20 OK 804 801 803 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 1 1 3 24 C5' C A 2 23 25 43 C5' G A 3 42 44 65 C5' C A 4 64 66 84 C5' T A 5 83 85 104 C5' A A 6 103 105 125 C5' T A 7 124 126 145 C5' T A 8 144 146 165 C5' A A 9 164 166 186 C5' T A 10 185 187 206 C5' C A 11 205 207 225 C5' G A 12 224 226 247 C5' C A 13 246 248 266 C5' T A 14 265 267 286 C5' A A 15 285 287 307 C5' T A 16 306 308 327 C5' T A 17 326 328 347 C5' A A 18 346 348 368 C5' G A 19 367 369 390 C5' C A 20 389 391 407 C5' G B 1 406 408 429 C5' C B 2 428 430 448 C5' T B 3 447 449 468 C5' A B 4 467 469 489 C5' A B 5 488 490 510 C5' T B 6 509 511 530 C5' A B 7 529 531 551 C5' G B 8 550 552 573 C5' C B 9 572 574 592 C5' G B 10 591 593 614 C5' A B 11 613 615 635 C5' T B 12 634 636 655 C5' A B 13 654 656 676 C5' A B 14 675 677 697 C5' T B 15 696 698 717 C5' A B 16 716 718 738 C5' G B 17 737 739 760 C5' C B 18 759 761 779 C5' G B 19 778 780 801 C5' C B 20 800 802 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 20 P C A 2 OK OK 6 21 22 23 39 P G A 3 OK OK 28 40 41 42 61 P C A 4 OK OK 47 62 63 64 80 P T A 5 OK OK 69 81 82 83 100 P A A 6 OK OK 88 101 102 103 121 P T A 7 OK OK 108 122 123 124 141 P T A 8 OK OK 129 142 143 144 161 P A A 9 OK OK 149 162 163 164 182 P T A 10 OK OK 169 183 184 185 202 P C A 11 OK OK 190 203 204 205 221 P G A 12 OK OK 210 222 223 224 243 P C A 13 OK OK 229 244 245 246 262 P T A 14 OK OK 251 263 264 265 282 P A A 15 OK OK 270 283 284 285 303 P T A 16 OK OK 290 304 305 306 323 P T A 17 OK OK 311 324 325 326 343 P A A 18 OK OK 331 344 345 346 364 P G A 19 OK OK 351 365 366 367 386 P C A 20 OK OK 372 387 388 389 425 P C B 2 OK OK 411 426 427 428 444 P T B 3 OK OK 433 445 446 447 464 P A B 4 OK OK 452 465 466 467 485 P A B 5 OK OK 472 486 487 488 506 P T B 6 OK OK 493 507 508 509 526 P A B 7 OK OK 514 527 528 529 547 P G B 8 OK OK 534 548 549 550 569 P C B 9 OK OK 555 570 571 572 588 P G B 10 OK OK 577 589 590 591 610 P A B 11 OK OK 596 611 612 613 631 P T B 12 OK OK 618 632 633 634 651 P A B 13 OK OK 639 652 653 654 672 P A B 14 OK OK 659 673 674 675 693 P T B 15 OK OK 680 694 695 696 713 P A B 16 OK OK 701 714 715 716 734 P G B 17 OK OK 721 735 736 737 756 P C B 18 OK OK 742 757 758 759 775 P G B 19 OK OK 764 776 777 778 797 P C B 20 OK OK 783 798 799 800 ---------------------------------------------------------------------------------