ID code: '1F4S' 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' C A 1 beta 7 12 10 41 C1' G A 2 beta 37 42 40 74 C1' T A 3 beta 70 75 73 106 C1' G A 4 beta 102 107 105 139 C1' C A 5 beta 135 140 138 169 C1' G A 6 beta 165 170 168 202 C1' G A 7 beta 198 203 201 235 C1' A A 8 beta 231 236 234 267 C1' T A 9 beta 263 268 266 299 C1' C A 10 beta 295 300 298 330 C1' G B 1 beta 326 331 329 363 C1' A B 2 beta 359 364 362 395 C1' T B 3 beta 391 396 394 427 C1' C B 4 beta 423 428 426 457 C1' C B 5 beta 453 458 456 487 C1' G B 6 beta 483 488 486 520 C1' C B 7 beta 516 521 519 550 C1' A B 8 beta 546 551 549 582 C1' C B 9 beta 578 583 581 612 C1' G B 10 beta 608 613 611 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' C A 1 11 8 40 C2' G A 2 41 38 73 C2' T A 3 74 71 105 C2' G A 4 106 103 138 C2' C A 5 139 136 168 C2' G A 6 169 166 201 C2' G A 7 202 199 234 C2' A A 8 235 232 266 C2' T A 9 267 264 298 C2' C A 10 299 296 329 C2' G B 1 330 327 362 C2' A B 2 363 360 394 C2' T B 3 395 392 426 C2' C B 4 427 424 456 C2' C B 5 457 454 486 C2' G B 6 487 484 519 C2' C B 7 520 517 549 C2' A B 8 550 547 581 C2' C B 9 582 579 611 C2' G B 10 612 609 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' C A 1 OK 6 9 10 38 C3' G A 2 OK 36 39 40 71 C3' T A 3 OK 69 72 73 103 C3' G A 4 OK 101 104 105 136 C3' C A 5 OK 134 137 138 166 C3' G A 6 OK 164 167 168 199 C3' G A 7 OK 197 200 201 232 C3' A A 8 OK 230 233 234 264 C3' T A 9 OK 262 265 266 296 C3' C A 10 OK 294 297 298 327 C3' G B 1 OK 325 328 329 360 C3' A B 2 OK 358 361 362 392 C3' T B 3 OK 390 393 394 424 C3' C B 4 OK 422 425 426 454 C3' C B 5 OK 452 455 456 484 C3' G B 6 OK 482 485 486 517 C3' C B 7 OK 515 518 519 547 C3' A B 8 OK 545 548 549 579 C3' C B 9 OK 577 580 581 609 C3' G B 10 OK 607 610 611 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' C A 1 OK 8 5 7 36 C4' G A 2 OK 38 35 37 69 C4' T A 3 OK 71 68 70 101 C4' G A 4 OK 103 100 102 134 C4' C A 5 OK 136 133 135 164 C4' G A 6 OK 166 163 165 197 C4' G A 7 OK 199 196 198 230 C4' A A 8 OK 232 229 231 262 C4' T A 9 OK 264 261 263 294 C4' C A 10 OK 296 293 295 325 C4' G B 1 OK 327 324 326 358 C4' A B 2 OK 360 357 359 390 C4' T B 3 OK 392 389 391 422 C4' C B 4 OK 424 421 423 452 C4' C B 5 OK 454 451 453 482 C4' G B 6 OK 484 481 483 515 C4' C B 7 OK 517 514 516 545 C4' A B 8 OK 547 544 546 577 C4' C B 9 OK 579 576 578 607 C4' G B 10 OK 609 606 608 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' C A 1 4 6 35 C5' G A 2 34 36 68 C5' T A 3 67 69 100 C5' G A 4 99 101 133 C5' C A 5 132 134 163 C5' G A 6 162 164 196 C5' G A 7 195 197 229 C5' A A 8 228 230 261 C5' T A 9 260 262 293 C5' C A 10 292 294 324 C5' G B 1 323 325 357 C5' A B 2 356 358 389 C5' T B 3 388 390 421 C5' C B 4 420 422 451 C5' C B 5 450 452 481 C5' G B 6 480 482 514 C5' C B 7 513 515 544 C5' A B 8 543 545 576 C5' C B 9 575 577 606 C5' G B 10 605 607 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P C A 1 distorted distorted 2 3 4 31 P G A 2 distorted distorted 9 32 33 34 64 P T A 3 distorted distorted 39 65 66 67 96 P G A 4 distorted distorted 72 97 98 99 129 P C A 5 distorted distorted 104 130 131 132 159 P G A 6 distorted distorted 137 160 161 162 192 P G A 7 distorted distorted 167 193 194 195 225 P A A 8 distorted distorted 200 226 227 228 257 P T A 9 distorted distorted 233 258 259 260 289 P C A 10 distorted distorted 265 290 291 292 320 P G B 1 distorted distorted 321 322 323 353 P A B 2 distorted distorted 328 354 355 356 385 P T B 3 distorted distorted 361 386 387 388 417 P C B 4 distorted distorted 393 418 419 420 447 P C B 5 distorted distorted 425 448 449 450 477 P G B 6 distorted distorted 455 478 479 480 510 P C B 7 distorted distorted 485 511 512 513 540 P A B 8 distorted distorted 518 541 542 543 572 P C B 9 distorted distorted 548 573 574 575 602 P G B 10 distorted distorted 580 603 604 605 ---------------------------------------------------------------------------------