ID code: '1JJ4' 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 602 beta 4 9 7 27 C1' A C 603 beta 23 28 26 48 C1' A C 604 beta 44 49 47 69 C1' C C 605 beta 65 70 68 88 C1' C C 606 beta 84 89 87 107 C1' G C 607 beta 103 108 106 129 C1' A C 608 beta 125 130 128 150 C1' A C 609 beta 146 151 149 171 C1' T C 610 beta 167 172 170 191 C1' T C 611 beta 187 192 190 211 C1' C C 612 beta 207 212 210 230 C1' G C 613 beta 226 231 229 252 C1' G C 614 beta 248 253 251 274 C1' T C 615 beta 270 275 273 294 C1' T C 616 beta 290 295 293 314 C1' G C 617 beta 310 315 313 334 C1' C D 902 beta 330 335 333 353 C1' A D 903 beta 349 354 352 374 C1' A D 904 beta 370 375 373 395 C1' C D 905 beta 391 396 394 414 C1' C D 906 beta 410 415 413 433 C1' G D 907 beta 429 434 432 455 C1' A D 908 beta 451 456 454 476 C1' A D 909 beta 472 477 475 497 C1' T D 910 beta 493 498 496 517 C1' T D 911 beta 513 518 516 537 C1' C D 912 beta 533 538 536 556 C1' G D 913 beta 552 557 555 578 C1' G D 914 beta 574 579 577 600 C1' T D 915 beta 596 601 599 620 C1' T D 916 beta 616 621 619 640 C1' G D 917 beta 636 641 639 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' C C 602 8 5 26 C2' A C 603 27 24 47 C2' A C 604 48 45 68 C2' C C 605 69 66 87 C2' C C 606 88 85 106 C2' G C 607 107 104 128 C2' A C 608 129 126 149 C2' A C 609 150 147 170 C2' T C 610 171 168 190 C2' T C 611 191 188 210 C2' C C 612 211 208 229 C2' G C 613 230 227 251 C2' G C 614 252 249 273 C2' T C 615 274 271 293 C2' T C 616 294 291 313 C2' G C 617 314 311 333 C2' C D 902 334 331 352 C2' A D 903 353 350 373 C2' A D 904 374 371 394 C2' C D 905 395 392 413 C2' C D 906 414 411 432 C2' G D 907 433 430 454 C2' A D 908 455 452 475 C2' A D 909 476 473 496 C2' T D 910 497 494 516 C2' T D 911 517 514 536 C2' C D 912 537 534 555 C2' G D 913 556 553 577 C2' G D 914 578 575 599 C2' T D 915 600 597 619 C2' T D 916 620 617 639 C2' G D 917 640 637 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' C C 602 OK 3 6 7 24 C3' A C 603 OK 22 25 26 45 C3' A C 604 OK 43 46 47 66 C3' C C 605 OK 64 67 68 85 C3' C C 606 OK 83 86 87 104 C3' G C 607 OK 102 105 106 126 C3' A C 608 OK 124 127 128 147 C3' A C 609 OK 145 148 149 168 C3' T C 610 OK 166 169 170 188 C3' T C 611 OK 186 189 190 208 C3' C C 612 OK 206 209 210 227 C3' G C 613 OK 225 228 229 249 C3' G C 614 OK 247 250 251 271 C3' T C 615 OK 269 272 273 291 C3' T C 616 OK 289 292 293 311 C3' G C 617 OK 309 312 313 331 C3' C D 902 OK 329 332 333 350 C3' A D 903 OK 348 351 352 371 C3' A D 904 OK 369 372 373 392 C3' C D 905 OK 390 393 394 411 C3' C D 906 OK 409 412 413 430 C3' G D 907 OK 428 431 432 452 C3' A D 908 OK 450 453 454 473 C3' A D 909 OK 471 474 475 494 C3' T D 910 OK 492 495 496 514 C3' T D 911 OK 512 515 516 534 C3' C D 912 OK 532 535 536 553 C3' G D 913 OK 551 554 555 575 C3' G D 914 OK 573 576 577 597 C3' T D 915 OK 595 598 599 617 C3' T D 916 OK 615 618 619 637 C3' G D 917 OK 635 638 639 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' C C 602 OK 5 2 4 22 C4' A C 603 OK 24 21 23 43 C4' A C 604 OK 45 42 44 64 C4' C C 605 OK 66 63 65 83 C4' C C 606 OK 85 82 84 102 C4' G C 607 OK 104 101 103 124 C4' A C 608 OK 126 123 125 145 C4' A C 609 OK 147 144 146 166 C4' T C 610 OK 168 165 167 186 C4' T C 611 OK 188 185 187 206 C4' C C 612 OK 208 205 207 225 C4' G C 613 OK 227 224 226 247 C4' G C 614 OK 249 246 248 269 C4' T C 615 OK 271 268 270 289 C4' T C 616 OK 291 288 290 309 C4' G C 617 OK 311 308 310 329 C4' C D 902 OK 331 328 330 348 C4' A D 903 OK 350 347 349 369 C4' A D 904 OK 371 368 370 390 C4' C D 905 OK 392 389 391 409 C4' C D 906 OK 411 408 410 428 C4' G D 907 OK 430 427 429 450 C4' A D 908 OK 452 449 451 471 C4' A D 909 OK 473 470 472 492 C4' T D 910 OK 494 491 493 512 C4' T D 911 OK 514 511 513 532 C4' C D 912 OK 534 531 533 551 C4' G D 913 OK 553 550 552 573 C4' G D 914 OK 575 572 574 595 C4' T D 915 OK 597 594 596 615 C4' T D 916 OK 617 614 616 635 C4' G D 917 OK 637 634 636 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' C C 602 1 3 21 C5' A C 603 20 22 42 C5' A C 604 41 43 63 C5' C C 605 62 64 82 C5' C C 606 81 83 101 C5' G C 607 100 102 123 C5' A C 608 122 124 144 C5' A C 609 143 145 165 C5' T C 610 164 166 185 C5' T C 611 184 186 205 C5' C C 612 204 206 224 C5' G C 613 223 225 246 C5' G C 614 245 247 268 C5' T C 615 267 269 288 C5' T C 616 287 289 308 C5' G C 617 307 309 328 C5' C D 902 327 329 347 C5' A D 903 346 348 368 C5' A D 904 367 369 389 C5' C D 905 388 390 408 C5' C D 906 407 409 427 C5' G D 907 426 428 449 C5' A D 908 448 450 470 C5' A D 909 469 471 491 C5' T D 910 490 492 511 C5' T D 911 510 512 531 C5' C D 912 530 532 550 C5' G D 913 549 551 572 C5' G D 914 571 573 594 C5' T D 915 593 595 614 C5' T D 916 613 615 634 C5' G D 917 633 635 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 17 P A C 603 distorted distorted 6 18 19 20 38 P A C 604 distorted distorted 25 39 40 41 59 P C C 605 distorted distorted 46 60 61 62 78 P C C 606 distorted distorted 67 79 80 81 97 P G C 607 distorted distorted 86 98 99 100 119 P A C 608 distorted distorted 105 120 121 122 140 P A C 609 distorted distorted 127 141 142 143 161 P T C 610 distorted distorted 148 162 163 164 181 P T C 611 distorted distorted 169 182 183 184 201 P C C 612 distorted distorted 189 202 203 204 220 P G C 613 distorted distorted 209 221 222 223 242 P G C 614 distorted distorted 228 243 244 245 264 P T C 615 distorted distorted 250 265 266 267 284 P T C 616 distorted distorted 272 285 286 287 304 P G C 617 distorted distorted 292 305 306 307 343 P A D 903 distorted distorted 332 344 345 346 364 P A D 904 distorted distorted 351 365 366 367 385 P C D 905 distorted distorted 372 386 387 388 404 P C D 906 distorted distorted 393 405 406 407 423 P G D 907 distorted distorted 412 424 425 426 445 P A D 908 distorted distorted 431 446 447 448 466 P A D 909 distorted distorted 453 467 468 469 487 P T D 910 distorted distorted 474 488 489 490 507 P T D 911 distorted distorted 495 508 509 510 527 P C D 912 distorted distorted 515 528 529 530 546 P G D 913 distorted distorted 535 547 548 549 568 P G D 914 distorted distorted 554 569 570 571 590 P T D 915 distorted distorted 576 591 592 593 610 P T D 916 distorted distorted 598 611 612 613 630 P G D 917 distorted distorted 618 631 632 633 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