ID code: '1H9T' 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 X 1 beta 4 9 7 27 C1' A X 2 beta 23 28 26 48 C1' T X 3 beta 44 49 47 68 C1' C X 4 beta 64 69 67 87 C1' T X 5 beta 83 88 86 107 C1' G X 6 beta 103 108 106 129 C1' G X 7 beta 125 130 128 151 C1' T X 8 beta 147 152 150 171 C1' A X 9 beta 167 172 170 192 C1' C X 10 beta 188 193 191 211 C1' G X 11 beta 207 212 210 233 C1' A X 12 beta 229 234 232 254 C1' C X 13 beta 250 255 253 273 C1' C X 14 beta 269 274 272 292 C1' A X 15 beta 288 293 291 313 C1' G X 16 beta 309 314 312 335 C1' A X 17 beta 331 336 334 356 C1' T X 18 beta 352 357 355 376 C1' C X 19 beta 372 377 375 393 C1' G Y 1 beta 389 394 392 415 C1' A Y 2 beta 411 416 414 436 C1' T Y 3 beta 432 437 435 456 C1' C Y 4 beta 452 457 455 475 C1' T Y 5 beta 471 476 474 495 C1' G Y 6 beta 491 496 494 517 C1' G Y 7 beta 513 518 516 539 C1' T Y 8 beta 535 540 538 559 C1' C Y 9 beta 555 560 558 578 C1' G Y 10 beta 574 579 577 600 C1' T Y 11 beta 596 601 599 620 C1' A Y 12 beta 616 621 619 641 C1' C Y 13 beta 637 642 640 660 C1' C Y 14 beta 656 661 659 679 C1' A Y 15 beta 675 680 678 700 C1' G Y 16 beta 696 701 699 722 C1' A Y 17 beta 718 723 721 743 C1' T Y 18 beta 739 744 742 763 C1' G Y 19 beta 759 764 762 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' C X 1 8 5 26 C2' A X 2 27 24 47 C2' T X 3 48 45 67 C2' C X 4 68 65 86 C2' T X 5 87 84 106 C2' G X 6 107 104 128 C2' G X 7 129 126 150 C2' T X 8 151 148 170 C2' A X 9 171 168 191 C2' C X 10 192 189 210 C2' G X 11 211 208 232 C2' A X 12 233 230 253 C2' C X 13 254 251 272 C2' C X 14 273 270 291 C2' A X 15 292 289 312 C2' G X 16 313 310 334 C2' A X 17 335 332 355 C2' T X 18 356 353 375 C2' C X 19 376 373 392 C2' G Y 1 393 390 414 C2' A Y 2 415 412 435 C2' T Y 3 436 433 455 C2' C Y 4 456 453 474 C2' T Y 5 475 472 494 C2' G Y 6 495 492 516 C2' G Y 7 517 514 538 C2' T Y 8 539 536 558 C2' C Y 9 559 556 577 C2' G Y 10 578 575 599 C2' T Y 11 600 597 619 C2' A Y 12 620 617 640 C2' C Y 13 641 638 659 C2' C Y 14 660 657 678 C2' A Y 15 679 676 699 C2' G Y 16 700 697 721 C2' A Y 17 722 719 742 C2' T Y 18 743 740 762 C2' G Y 19 763 760 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' C X 1 OK 3 6 7 24 C3' A X 2 OK 22 25 26 45 C3' T X 3 OK 43 46 47 65 C3' C X 4 OK 63 66 67 84 C3' T X 5 OK 82 85 86 104 C3' G X 6 OK 102 105 106 126 C3' G X 7 OK 124 127 128 148 C3' T X 8 OK 146 149 150 168 C3' A X 9 OK 166 169 170 189 C3' C X 10 OK 187 190 191 208 C3' G X 11 OK 206 209 210 230 C3' A X 12 OK 228 231 232 251 C3' C X 13 OK 249 252 253 270 C3' C X 14 OK 268 271 272 289 C3' A X 15 OK 287 290 291 310 C3' G X 16 OK 308 311 312 332 C3' A X 17 OK 330 333 334 353 C3' T X 18 OK 351 354 355 373 C3' C X 19 OK 371 374 375 390 C3' G Y 1 OK 388 391 392 412 C3' A Y 2 OK 410 413 414 433 C3' T Y 3 OK 431 434 435 453 C3' C Y 4 OK 451 454 455 472 C3' T Y 5 OK 470 473 474 492 C3' G Y 6 OK 490 493 494 514 C3' G Y 7 OK 512 515 516 536 C3' T Y 8 OK 534 537 538 556 C3' C Y 9 OK 554 557 558 575 C3' G Y 10 OK 573 576 577 597 C3' T Y 11 OK 595 598 599 617 C3' A Y 12 OK 615 618 619 638 C3' C Y 13 OK 636 639 640 657 C3' C Y 14 OK 655 658 659 676 C3' A Y 15 OK 674 677 678 697 C3' G Y 16 OK 695 698 699 719 C3' A Y 17 OK 717 720 721 740 C3' T Y 18 OK 738 741 742 760 C3' G Y 19 OK 758 761 762 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' C X 1 OK 5 2 4 22 C4' A X 2 OK 24 21 23 43 C4' T X 3 OK 45 42 44 63 C4' C X 4 OK 65 62 64 82 C4' T X 5 OK 84 81 83 102 C4' G X 6 OK 104 101 103 124 C4' G X 7 OK 126 123 125 146 C4' T X 8 OK 148 145 147 166 C4' A X 9 OK 168 165 167 187 C4' C X 10 OK 189 186 188 206 C4' G X 11 OK 208 205 207 228 C4' A X 12 OK 230 227 229 249 C4' C X 13 OK 251 248 250 268 C4' C X 14 OK 270 267 269 287 C4' A X 15 OK 289 286 288 308 C4' G X 16 OK 310 307 309 330 C4' A X 17 OK 332 329 331 351 C4' T X 18 OK 353 350 352 371 C4' C X 19 OK 373 370 372 388 C4' G Y 1 OK 390 387 389 410 C4' A Y 2 OK 412 409 411 431 C4' T Y 3 OK 433 430 432 451 C4' C Y 4 OK 453 450 452 470 C4' T Y 5 OK 472 469 471 490 C4' G Y 6 OK 492 489 491 512 C4' G Y 7 OK 514 511 513 534 C4' T Y 8 OK 536 533 535 554 C4' C Y 9 OK 556 553 555 573 C4' G Y 10 OK 575 572 574 595 C4' T Y 11 OK 597 594 596 615 C4' A Y 12 OK 617 614 616 636 C4' C Y 13 OK 638 635 637 655 C4' C Y 14 OK 657 654 656 674 C4' A Y 15 OK 676 673 675 695 C4' G Y 16 OK 697 694 696 717 C4' A Y 17 OK 719 716 718 738 C4' T Y 18 OK 740 737 739 758 C4' G Y 19 OK 760 757 759 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' C X 1 1 3 21 C5' A X 2 20 22 42 C5' T X 3 41 43 62 C5' C X 4 61 63 81 C5' T X 5 80 82 101 C5' G X 6 100 102 123 C5' G X 7 122 124 145 C5' T X 8 144 146 165 C5' A X 9 164 166 186 C5' C X 10 185 187 205 C5' G X 11 204 206 227 C5' A X 12 226 228 248 C5' C X 13 247 249 267 C5' C X 14 266 268 286 C5' A X 15 285 287 307 C5' G X 16 306 308 329 C5' A X 17 328 330 350 C5' T X 18 349 351 370 C5' C X 19 369 371 387 C5' G Y 1 386 388 409 C5' A Y 2 408 410 430 C5' T Y 3 429 431 450 C5' C Y 4 449 451 469 C5' T Y 5 468 470 489 C5' G Y 6 488 490 511 C5' G Y 7 510 512 533 C5' T Y 8 532 534 553 C5' C Y 9 552 554 572 C5' G Y 10 571 573 594 C5' T Y 11 593 595 614 C5' A Y 12 613 615 635 C5' C Y 13 634 636 654 C5' C Y 14 653 655 673 C5' A Y 15 672 674 694 C5' G Y 16 693 695 716 C5' A Y 17 715 717 737 C5' T Y 18 736 738 757 C5' G Y 19 756 758 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 17 P A X 2 distorted distorted 6 18 19 20 38 P T X 3 distorted distorted 25 39 40 41 58 P C X 4 distorted distorted 46 59 60 61 77 P T X 5 OK OK 66 78 79 80 97 P G X 6 distorted distorted 85 98 99 100 119 P G X 7 distorted distorted 105 120 121 122 141 P T X 8 distorted distorted 127 142 143 144 161 P A X 9 distorted distorted 149 162 163 164 182 P C X 10 distorted distorted 169 183 184 185 201 P G X 11 distorted distorted 190 202 203 204 223 P A X 12 distorted distorted 209 224 225 226 244 P C X 13 distorted distorted 231 245 246 247 263 P C X 14 distorted distorted 252 264 265 266 282 P A X 15 distorted distorted 271 283 284 285 303 P G X 16 distorted distorted 290 304 305 306 325 P A X 17 distorted distorted 311 326 327 328 346 P T X 18 distorted distorted 333 347 348 349 366 P C X 19 distorted distorted 354 367 368 369 405 P A Y 2 distorted distorted 391 406 407 408 426 P T Y 3 distorted distorted 413 427 428 429 446 P C Y 4 distorted distorted 434 447 448 449 465 P T Y 5 OK OK 454 466 467 468 485 P G Y 6 distorted distorted 473 486 487 488 507 P G Y 7 distorted distorted 493 508 509 510 529 P T Y 8 distorted distorted 515 530 531 532 549 P C Y 9 distorted distorted 537 550 551 552 568 P G Y 10 distorted distorted 557 569 570 571 590 P T Y 11 distorted distorted 576 591 592 593 610 P A Y 12 distorted distorted 598 611 612 613 631 P C Y 13 distorted distorted 618 632 633 634 650 P C Y 14 distorted distorted 639 651 652 653 669 P A Y 15 distorted distorted 658 670 671 672 690 P G Y 16 distorted distorted 677 691 692 693 712 P A Y 17 distorted distorted 698 713 714 715 733 P T Y 18 distorted distorted 720 734 735 736 753 P G Y 19 distorted distorted 741 754 755 756 ---------------------------------------------------------------------------------