ID code: '1KB4' 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 401 beta 4 9 7 27 C1' A C 402 beta 23 28 26 48 C1' C C 403 beta 44 49 47 67 C1' A C 404 beta 63 68 66 88 C1' G C 405 beta 84 89 87 110 C1' G C 406 beta 106 111 109 132 C1' T C 407 beta 128 133 131 152 C1' C C 408 beta 148 153 151 171 C1' A C 409 beta 167 172 170 192 C1' C C 410 beta 188 193 191 211 C1' G C 411 beta 207 212 210 233 C1' A C 412 beta 229 234 232 254 C1' A C 413 beta 250 255 253 275 C1' G C 414 beta 271 276 274 297 C1' G C 415 beta 293 298 296 319 C1' T C 416 beta 315 320 318 339 C1' C C 417 beta 335 340 338 358 C1' A C 418 beta 354 359 357 377 C1' T D 419 beta 373 378 376 397 C1' G D 420 beta 393 398 396 419 C1' A D 421 beta 415 420 418 440 C1' C D 422 beta 436 441 439 459 C1' C D 423 beta 455 460 458 478 C1' T D 424 beta 474 479 477 498 C1' T D 425 beta 494 499 497 518 C1' C D 426 beta 514 519 517 537 C1' G D 427 beta 533 538 536 559 C1' T D 428 beta 555 560 558 579 C1' G D 429 beta 575 580 578 601 C1' A D 430 beta 597 602 600 622 C1' C D 431 beta 618 623 621 641 C1' C D 432 beta 637 642 640 660 C1' T D 433 beta 656 661 659 680 C1' G D 434 beta 676 681 679 702 C1' T D 435 beta 698 703 701 722 C1' G D 436 beta 718 723 721 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' C C 401 8 5 26 C2' A C 402 27 24 47 C2' C C 403 48 45 66 C2' A C 404 67 64 87 C2' G C 405 88 85 109 C2' G C 406 110 107 131 C2' T C 407 132 129 151 C2' C C 408 152 149 170 C2' A C 409 171 168 191 C2' C C 410 192 189 210 C2' G C 411 211 208 232 C2' A C 412 233 230 253 C2' A C 413 254 251 274 C2' G C 414 275 272 296 C2' G C 415 297 294 318 C2' T C 416 319 316 338 C2' C C 417 339 336 357 C2' A C 418 358 355 376 C2' T D 419 377 374 396 C2' G D 420 397 394 418 C2' A D 421 419 416 439 C2' C D 422 440 437 458 C2' C D 423 459 456 477 C2' T D 424 478 475 497 C2' T D 425 498 495 517 C2' C D 426 518 515 536 C2' G D 427 537 534 558 C2' T D 428 559 556 578 C2' G D 429 579 576 600 C2' A D 430 601 598 621 C2' C D 431 622 619 640 C2' C D 432 641 638 659 C2' T D 433 660 657 679 C2' G D 434 680 677 701 C2' T D 435 702 699 721 C2' G D 436 722 719 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' C C 401 OK 3 6 7 24 C3' A C 402 OK 22 25 26 45 C3' C C 403 OK 43 46 47 64 C3' A C 404 OK 62 65 66 85 C3' G C 405 OK 83 86 87 107 C3' G C 406 OK 105 108 109 129 C3' T C 407 OK 127 130 131 149 C3' C C 408 OK 147 150 151 168 C3' A C 409 OK 166 169 170 189 C3' C C 410 OK 187 190 191 208 C3' G C 411 OK 206 209 210 230 C3' A C 412 OK 228 231 232 251 C3' A C 413 OK 249 252 253 272 C3' G C 414 OK 270 273 274 294 C3' G C 415 OK 292 295 296 316 C3' T C 416 OK 314 317 318 336 C3' C C 417 OK 334 337 338 355 C3' A C 418 OK 353 356 357 374 C3' T D 419 OK 372 375 376 394 C3' G D 420 OK 392 395 396 416 C3' A D 421 OK 414 417 418 437 C3' C D 422 OK 435 438 439 456 C3' C D 423 OK 454 457 458 475 C3' T D 424 OK 473 476 477 495 C3' T D 425 OK 493 496 497 515 C3' C D 426 OK 513 516 517 534 C3' G D 427 OK 532 535 536 556 C3' T D 428 OK 554 557 558 576 C3' G D 429 OK 574 577 578 598 C3' A D 430 OK 596 599 600 619 C3' C D 431 OK 617 620 621 638 C3' C D 432 OK 636 639 640 657 C3' T D 433 OK 655 658 659 677 C3' G D 434 OK 675 678 679 699 C3' T D 435 OK 697 700 701 719 C3' G D 436 OK 717 720 721 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' C C 401 OK 5 2 4 22 C4' A C 402 OK 24 21 23 43 C4' C C 403 OK 45 42 44 62 C4' A C 404 OK 64 61 63 83 C4' G C 405 OK 85 82 84 105 C4' G C 406 OK 107 104 106 127 C4' T C 407 OK 129 126 128 147 C4' C C 408 OK 149 146 148 166 C4' A C 409 OK 168 165 167 187 C4' C C 410 OK 189 186 188 206 C4' G C 411 OK 208 205 207 228 C4' A C 412 OK 230 227 229 249 C4' A C 413 OK 251 248 250 270 C4' G C 414 OK 272 269 271 292 C4' G C 415 OK 294 291 293 314 C4' T C 416 OK 316 313 315 334 C4' C C 417 OK 336 333 335 353 C4' A C 418 OK 355 352 354 372 C4' T D 419 OK 374 371 373 392 C4' G D 420 OK 394 391 393 414 C4' A D 421 OK 416 413 415 435 C4' C D 422 OK 437 434 436 454 C4' C D 423 OK 456 453 455 473 C4' T D 424 OK 475 472 474 493 C4' T D 425 OK 495 492 494 513 C4' C D 426 OK 515 512 514 532 C4' G D 427 OK 534 531 533 554 C4' T D 428 OK 556 553 555 574 C4' G D 429 OK 576 573 575 596 C4' A D 430 OK 598 595 597 617 C4' C D 431 OK 619 616 618 636 C4' C D 432 OK 638 635 637 655 C4' T D 433 OK 657 654 656 675 C4' G D 434 OK 677 674 676 697 C4' T D 435 OK 699 696 698 717 C4' G D 436 OK 719 716 718 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' C C 401 1 3 21 C5' A C 402 20 22 42 C5' C C 403 41 43 61 C5' A C 404 60 62 82 C5' G C 405 81 83 104 C5' G C 406 103 105 126 C5' T C 407 125 127 146 C5' C C 408 145 147 165 C5' A C 409 164 166 186 C5' C C 410 185 187 205 C5' G C 411 204 206 227 C5' A C 412 226 228 248 C5' A C 413 247 249 269 C5' G C 414 268 270 291 C5' G C 415 290 292 313 C5' T C 416 312 314 333 C5' C C 417 332 334 352 C5' A C 418 351 353 371 C5' T D 419 370 372 391 C5' G D 420 390 392 413 C5' A D 421 412 414 434 C5' C D 422 433 435 453 C5' C D 423 452 454 472 C5' T D 424 471 473 492 C5' T D 425 491 493 512 C5' C D 426 511 513 531 C5' G D 427 530 532 553 C5' T D 428 552 554 573 C5' G D 429 572 574 595 C5' A D 430 594 596 616 C5' C D 431 615 617 635 C5' C D 432 634 636 654 C5' T D 433 653 655 674 C5' G D 434 673 675 696 C5' T D 435 695 697 716 C5' G D 436 715 717 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 17 P A C 402 distorted distorted 6 18 19 20 38 P C C 403 distorted distorted 25 39 40 41 57 P A C 404 distorted distorted 46 58 59 60 78 P G C 405 distorted distorted 65 79 80 81 100 P G C 406 distorted distorted 86 101 102 103 122 P T C 407 distorted distorted 108 123 124 125 142 P C C 408 distorted distorted 130 143 144 145 161 P A C 409 distorted distorted 150 162 163 164 182 P C C 410 distorted distorted 169 183 184 185 201 P G C 411 distorted distorted 190 202 203 204 223 P A C 412 distorted distorted 209 224 225 226 244 P A C 413 distorted distorted 231 245 246 247 265 P G C 414 distorted distorted 252 266 267 268 287 P G C 415 distorted distorted 273 288 289 290 309 P T C 416 distorted distorted 295 310 311 312 329 P C C 417 distorted distorted 317 330 331 332 348 P A C 418 distorted distorted 337 349 350 351 387 P G D 420 distorted distorted 375 388 389 390 409 P A D 421 distorted distorted 395 410 411 412 430 P C D 422 distorted distorted 417 431 432 433 449 P C D 423 distorted distorted 438 450 451 452 468 P T D 424 distorted distorted 457 469 470 471 488 P T D 425 distorted distorted 476 489 490 491 508 P C D 426 distorted distorted 496 509 510 511 527 P G D 427 distorted distorted 516 528 529 530 549 P T D 428 distorted distorted 535 550 551 552 569 P G D 429 distorted distorted 557 570 571 572 591 P A D 430 distorted distorted 577 592 593 594 612 P C D 431 distorted distorted 599 613 614 615 631 P C D 432 distorted distorted 620 632 633 634 650 P T D 433 distorted distorted 639 651 652 653 670 P G D 434 distorted distorted 658 671 672 673 692 P T D 435 distorted distorted 678 693 694 695 712 P G D 436 distorted distorted 700 713 714 715 ---------------------------------------------------------------------------------