ID code: '1JFS' 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' --------------------------------------------------------------------------------- 11 C1' A B 700 beta 7 12 10 32 C1' C B 701 beta 28 33 31 51 C1' G B 702 beta 47 52 50 73 C1' C B 703 beta 69 74 72 92 C1' A B 704 beta 88 93 91 113 C1' A B 705 beta 109 114 112 134 C1' A B 706 beta 130 135 133 155 C1' C B 707 beta 151 156 154 174 C1' G B 708 beta 170 175 173 196 C1' T B 709 beta 192 197 195 216 C1' T B 710 beta 212 217 215 236 C1' T B 711 beta 232 237 235 256 C1' G B 712 beta 252 257 255 278 C1' C B 713 beta 274 279 277 297 C1' G B 714 beta 293 298 296 319 C1' T B 715 beta 315 320 318 339 C1' A B 700 beta 335 340 338 360 C1' C B 701 beta 356 361 359 379 C1' G B 702 beta 375 380 378 401 C1' C B 703 beta 397 402 400 420 C1' A B 704 beta 416 421 419 441 C1' A B 705 beta 437 442 440 462 C1' A B 706 beta 458 463 461 483 C1' C B 707 beta 479 484 482 502 C1' G B 708 beta 498 503 501 524 C1' T B 709 beta 520 525 523 544 C1' T B 710 beta 540 545 543 564 C1' T B 711 beta 560 565 563 584 C1' G B 712 beta 580 585 583 606 C1' C B 713 beta 602 607 605 625 C1' G B 714 beta 621 626 624 647 C1' T B 715 beta 643 648 646 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' A B 700 11 8 31 C2' C B 701 32 29 50 C2' G B 702 51 48 72 C2' C B 703 73 70 91 C2' A B 704 92 89 112 C2' A B 705 113 110 133 C2' A B 706 134 131 154 C2' C B 707 155 152 173 C2' G B 708 174 171 195 C2' T B 709 196 193 215 C2' T B 710 216 213 235 C2' T B 711 236 233 255 C2' G B 712 256 253 277 C2' C B 713 278 275 296 C2' G B 714 297 294 318 C2' T B 715 319 316 338 C2' A B 700 339 336 359 C2' C B 701 360 357 378 C2' G B 702 379 376 400 C2' C B 703 401 398 419 C2' A B 704 420 417 440 C2' A B 705 441 438 461 C2' A B 706 462 459 482 C2' C B 707 483 480 501 C2' G B 708 502 499 523 C2' T B 709 524 521 543 C2' T B 710 544 541 563 C2' T B 711 564 561 583 C2' G B 712 584 581 605 C2' C B 713 606 603 624 C2' G B 714 625 622 646 C2' T B 715 647 644 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' A B 700 OK 6 9 10 29 C3' C B 701 OK 27 30 31 48 C3' G B 702 OK 46 49 50 70 C3' C B 703 OK 68 71 72 89 C3' A B 704 OK 87 90 91 110 C3' A B 705 OK 108 111 112 131 C3' A B 706 OK 129 132 133 152 C3' C B 707 OK 150 153 154 171 C3' G B 708 OK 169 172 173 193 C3' T B 709 OK 191 194 195 213 C3' T B 710 OK 211 214 215 233 C3' T B 711 OK 231 234 235 253 C3' G B 712 OK 251 254 255 275 C3' C B 713 OK 273 276 277 294 C3' G B 714 OK 292 295 296 316 C3' T B 715 OK 314 317 318 336 C3' A B 700 OK 334 337 338 357 C3' C B 701 OK 355 358 359 376 C3' G B 702 OK 374 377 378 398 C3' C B 703 OK 396 399 400 417 C3' A B 704 OK 415 418 419 438 C3' A B 705 OK 436 439 440 459 C3' A B 706 OK 457 460 461 480 C3' C B 707 OK 478 481 482 499 C3' G B 708 OK 497 500 501 521 C3' T B 709 OK 519 522 523 541 C3' T B 710 OK 539 542 543 561 C3' T B 711 OK 559 562 563 581 C3' G B 712 OK 579 582 583 603 C3' C B 713 OK 601 604 605 622 C3' G B 714 OK 620 623 624 644 C3' T B 715 OK 642 645 646 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' A B 700 OK 8 5 7 27 C4' C B 701 OK 29 26 28 46 C4' G B 702 OK 48 45 47 68 C4' C B 703 OK 70 67 69 87 C4' A B 704 OK 89 86 88 108 C4' A B 705 OK 110 107 109 129 C4' A B 706 OK 131 128 130 150 C4' C B 707 OK 152 149 151 169 C4' G B 708 OK 171 168 170 191 C4' T B 709 OK 193 190 192 211 C4' T B 710 OK 213 210 212 231 C4' T B 711 OK 233 230 232 251 C4' G B 712 OK 253 250 252 273 C4' C B 713 OK 275 272 274 292 C4' G B 714 OK 294 291 293 314 C4' T B 715 OK 316 313 315 334 C4' A B 700 OK 336 333 335 355 C4' C B 701 OK 357 354 356 374 C4' G B 702 OK 376 373 375 396 C4' C B 703 OK 398 395 397 415 C4' A B 704 OK 417 414 416 436 C4' A B 705 OK 438 435 437 457 C4' A B 706 OK 459 456 458 478 C4' C B 707 OK 480 477 479 497 C4' G B 708 OK 499 496 498 519 C4' T B 709 OK 521 518 520 539 C4' T B 710 OK 541 538 540 559 C4' T B 711 OK 561 558 560 579 C4' G B 712 OK 581 578 580 601 C4' C B 713 OK 603 600 602 620 C4' G B 714 OK 622 619 621 642 C4' T B 715 OK 644 641 643 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' A B 700 4 6 26 C5' C B 701 25 27 45 C5' G B 702 44 46 67 C5' C B 703 66 68 86 C5' A B 704 85 87 107 C5' A B 705 106 108 128 C5' A B 706 127 129 149 C5' C B 707 148 150 168 C5' G B 708 167 169 190 C5' T B 709 189 191 210 C5' T B 710 209 211 230 C5' T B 711 229 231 250 C5' G B 712 249 251 272 C5' C B 713 271 273 291 C5' G B 714 290 292 313 C5' T B 715 312 314 333 C5' A B 700 332 334 354 C5' C B 701 353 355 373 C5' G B 702 372 374 395 C5' C B 703 394 396 414 C5' A B 704 413 415 435 C5' A B 705 434 436 456 C5' A B 706 455 457 477 C5' C B 707 476 478 496 C5' G B 708 495 497 518 C5' T B 709 517 519 538 C5' T B 710 537 539 558 C5' T B 711 557 559 578 C5' G B 712 577 579 600 C5' C B 713 599 601 619 C5' G B 714 618 620 641 C5' T B 715 640 642 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P A B 700 distorted distorted 2 3 4 22 P C B 701 distorted distorted 9 23 24 25 41 P G B 702 distorted distorted 30 42 43 44 63 P C B 703 distorted distorted 49 64 65 66 82 P A B 704 distorted distorted 71 83 84 85 103 P A B 705 distorted distorted 90 104 105 106 124 P A B 706 distorted distorted 111 125 126 127 145 P C B 707 distorted distorted 132 146 147 148 164 P G B 708 distorted distorted 153 165 166 167 186 P T B 709 distorted distorted 172 187 188 189 206 P T B 710 distorted distorted 194 207 208 209 226 P T B 711 distorted distorted 214 227 228 229 246 P G B 712 distorted distorted 234 247 248 249 268 P C B 713 distorted distorted 254 269 270 271 287 P G B 714 distorted distorted 276 288 289 290 309 P T B 715 distorted distorted 295 310 311 312 329 P A B 700 distorted distorted 330 331 332 350 P C B 701 distorted distorted 337 351 352 353 369 P G B 702 distorted distorted 358 370 371 372 391 P C B 703 distorted distorted 377 392 393 394 410 P A B 704 distorted distorted 399 411 412 413 431 P A B 705 distorted distorted 418 432 433 434 452 P A B 706 distorted distorted 439 453 454 455 473 P C B 707 distorted distorted 460 474 475 476 492 P G B 708 distorted distorted 481 493 494 495 514 P T B 709 distorted distorted 500 515 516 517 534 P T B 710 distorted distorted 522 535 536 537 554 P T B 711 distorted distorted 542 555 556 557 574 P G B 712 distorted distorted 562 575 576 577 596 P C B 713 distorted distorted 582 597 598 599 615 P G B 714 distorted distorted 604 616 617 618 637 P T B 715 distorted distorted 623 638 639 640 ---------------------------------------------------------------------------------