ID code: '1KKS' 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' --------------------------------------------------------------------------------- 9 C1' G A 1 alpha beta 4 27 10 7 44 C1' G A 2 alpha beta 39 62 45 42 78 C1' A A 3 alpha beta 73 95 79 76 111 C1' A A 4 alpha beta 106 128 112 109 144 C1' G A 5 alpha beta 139 162 145 142 178 C1' G A 6 alpha beta 173 196 179 176 212 C1' C A 7 alpha beta 207 227 213 210 243 C1' C A 8 alpha beta 238 258 244 241 274 C1' C A 9 alpha beta 269 289 275 272 305 C1' U A 10 alpha beta 300 320 306 303 335 C1' U A 11 alpha beta 330 350 336 333 365 C1' U A 12 alpha beta 360 380 366 363 395 C1' U A 13 alpha beta 390 410 396 393 425 C1' C A 14 alpha beta 420 440 426 423 456 C1' A A 15 alpha beta 451 473 457 454 489 C1' G A 16 alpha beta 484 507 490 487 523 C1' G A 17 alpha beta 518 541 524 521 557 C1' G A 18 alpha beta 552 575 558 555 591 C1' C A 19 alpha beta 586 606 592 589 622 C1' C A 20 alpha beta 617 637 623 620 653 C1' A A 21 alpha beta 648 670 654 651 686 C1' C A 22 alpha beta 681 701 687 684 717 C1' C A 23 alpha beta 712 732 718 715 748 C1' C A 24 alpha beta 743 764 749 746 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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 OK OK 9 5 25 8 42 C2' G A 2 OK OK 44 40 60 43 76 C2' A A 3 OK OK 78 74 93 77 109 C2' A A 4 OK OK 111 107 126 110 142 C2' G A 5 OK OK 144 140 160 143 176 C2' G A 6 OK OK 178 174 194 177 210 C2' C A 7 OK OK 212 208 225 211 241 C2' C A 8 OK OK 243 239 256 242 272 C2' C A 9 OK OK 274 270 287 273 303 C2' U A 10 OK OK 305 301 318 304 333 C2' U A 11 OK OK 335 331 348 334 363 C2' U A 12 OK OK 365 361 378 364 393 C2' U A 13 OK OK 395 391 408 394 423 C2' C A 14 OK OK 425 421 438 424 454 C2' A A 15 OK OK 456 452 471 455 487 C2' G A 16 OK OK 489 485 505 488 521 C2' G A 17 OK OK 523 519 539 522 555 C2' G A 18 OK OK 557 553 573 556 589 C2' C A 19 OK OK 591 587 604 590 620 C2' C A 20 OK OK 622 618 635 621 651 C2' A A 21 OK OK 653 649 668 652 684 C2' C A 22 OK OK 686 682 699 685 715 C2' C A 23 OK OK 717 713 730 716 746 C2' C A 24 OK OK 748 744 762 747 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK OK 3 24 6 7 40 C3' G A 2 OK OK 38 59 41 42 74 C3' A A 3 OK OK 72 92 75 76 107 C3' A A 4 OK OK 105 125 108 109 140 C3' G A 5 OK OK 138 159 141 142 174 C3' G A 6 OK OK 172 193 175 176 208 C3' C A 7 OK OK 206 224 209 210 239 C3' C A 8 OK OK 237 255 240 241 270 C3' C A 9 OK OK 268 286 271 272 301 C3' U A 10 OK OK 299 317 302 303 331 C3' U A 11 OK OK 329 347 332 333 361 C3' U A 12 OK OK 359 377 362 363 391 C3' U A 13 OK OK 389 407 392 393 421 C3' C A 14 OK OK 419 437 422 423 452 C3' A A 15 OK OK 450 470 453 454 485 C3' G A 16 OK OK 483 504 486 487 519 C3' G A 17 OK OK 517 538 520 521 553 C3' G A 18 OK OK 551 572 554 555 587 C3' C A 19 OK OK 585 603 588 589 618 C3' C A 20 OK OK 616 634 619 620 649 C3' A A 21 OK OK 647 667 650 651 682 C3' C A 22 OK OK 680 698 683 684 713 C3' C A 23 OK OK 711 729 714 715 744 C3' C A 24 OK OK 742 760 745 746 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK OK 5 23 2 4 38 C4' G A 2 OK OK 40 58 37 39 72 C4' A A 3 OK OK 74 91 71 73 105 C4' A A 4 OK OK 107 124 104 106 138 C4' G A 5 OK OK 140 158 137 139 172 C4' G A 6 OK OK 174 192 171 173 206 C4' C A 7 OK OK 208 223 205 207 237 C4' C A 8 OK OK 239 254 236 238 268 C4' C A 9 OK OK 270 285 267 269 299 C4' U A 10 OK OK 301 316 298 300 329 C4' U A 11 OK OK 331 346 328 330 359 C4' U A 12 OK OK 361 376 358 360 389 C4' U A 13 OK OK 391 406 388 390 419 C4' C A 14 OK OK 421 436 418 420 450 C4' A A 15 OK OK 452 469 449 451 483 C4' G A 16 OK OK 485 503 482 484 517 C4' G A 17 OK OK 519 537 516 518 551 C4' G A 18 OK OK 553 571 550 552 585 C4' C A 19 OK OK 587 602 584 586 616 C4' C A 20 OK OK 618 633 615 617 647 C4' A A 21 OK OK 649 666 646 648 680 C4' C A 22 OK OK 682 697 679 681 711 C4' C A 23 OK OK 713 728 710 712 742 C4' C A 24 OK OK 744 759 741 743 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 1 OK OK 1 21 22 3 37 C5' G A 2 OK OK 36 56 57 38 71 C5' A A 3 OK OK 70 89 90 72 104 C5' A A 4 OK OK 103 122 123 105 137 C5' G A 5 OK OK 136 156 157 138 171 C5' G A 6 OK OK 170 190 191 172 205 C5' C A 7 OK OK 204 221 222 206 236 C5' C A 8 OK OK 235 252 253 237 267 C5' C A 9 OK OK 266 283 284 268 298 C5' U A 10 OK OK 297 314 315 299 328 C5' U A 11 OK OK 327 344 345 329 358 C5' U A 12 OK OK 357 374 375 359 388 C5' U A 13 OK OK 387 404 405 389 418 C5' C A 14 OK OK 417 434 435 419 449 C5' A A 15 OK OK 448 467 468 450 482 C5' G A 16 OK OK 481 501 502 483 516 C5' G A 17 OK OK 515 535 536 517 550 C5' G A 18 OK OK 549 569 570 551 584 C5' C A 19 OK OK 583 600 601 585 615 C5' C A 20 OK OK 614 631 632 616 646 C5' A A 21 OK OK 645 664 665 647 679 C5' C A 22 OK OK 678 695 696 680 710 C5' C A 23 OK OK 709 726 727 711 741 C5' C A 24 OK OK 740 757 758 742 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 2 distorted distorted 6 34 35 36 67 P A A 3 distorted distorted 41 68 69 70 100 P A A 4 distorted distorted 75 101 102 103 133 P G A 5 distorted distorted 108 134 135 136 167 P G A 6 distorted distorted 141 168 169 170 201 P C A 7 distorted distorted 175 202 203 204 232 P C A 8 distorted distorted 209 233 234 235 263 P C A 9 distorted distorted 240 264 265 266 294 P U A 10 distorted distorted 271 295 296 297 324 P U A 11 distorted distorted 302 325 326 327 354 P U A 12 distorted distorted 332 355 356 357 384 P U A 13 distorted distorted 362 385 386 387 414 P C A 14 distorted distorted 392 415 416 417 445 P A A 15 distorted distorted 422 446 447 448 478 P G A 16 distorted distorted 453 479 480 481 512 P G A 17 distorted distorted 486 513 514 515 546 P G A 18 distorted distorted 520 547 548 549 580 P C A 19 distorted distorted 554 581 582 583 611 P C A 20 distorted distorted 588 612 613 614 642 P A A 21 distorted distorted 619 643 644 645 675 P C A 22 distorted distorted 650 676 677 678 706 P C A 23 distorted distorted 683 707 708 709 737 P C A 24 distorted distorted 714 738 739 740 ---------------------------------------------------------------------------------