ID code: '1NK5' 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 B 17 beta 4 9 7 27 C1' A B 18 beta 23 28 26 48 C1' T B 19 beta 44 49 47 68 C1' G B 20 beta 64 69 67 90 C1' G B 21 beta 86 91 89 112 C1' C B 22 beta 108 113 111 131 C1' A B 23 beta 127 132 130 152 C1' T B 24 beta 148 153 151 172 C1' T B 25 beta 168 173 171 192 C1' G B 26 beta 188 193 191 214 C1' A B 27 beta 210 215 213 235 C1' T B 28 beta 231 236 234 255 C1' A B 29 beta 251 256 254 277 C1' T C 4 beta 273 278 276 297 C1' A C 5 beta 293 298 296 318 C1' T C 6 beta 314 319 317 338 C1' C C 7 beta 334 339 337 357 C1' A C 8 beta 353 358 356 378 C1' A C 9 beta 374 379 377 399 C1' T C 10 beta 395 400 398 419 C1' G C 11 beta 415 420 418 441 C1' C C 12 beta 437 442 440 460 C1' C C 13 beta 456 461 459 479 C1' A C 14 beta 475 480 478 500 C1' T C 15 beta 496 501 499 520 C1' G C 16 beta 516 521 519 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' C B 17 8 5 26 C2' A B 18 27 24 47 C2' T B 19 48 45 67 C2' G B 20 68 65 89 C2' G B 21 90 87 111 C2' C B 22 112 109 130 C2' A B 23 131 128 151 C2' T B 24 152 149 171 C2' T B 25 172 169 191 C2' G B 26 192 189 213 C2' A B 27 214 211 234 C2' T B 28 235 232 254 C2' A B 29 255 252 276 C2' T C 4 277 274 296 C2' A C 5 297 294 317 C2' T C 6 318 315 337 C2' C C 7 338 335 356 C2' A C 8 357 354 377 C2' A C 9 378 375 398 C2' T C 10 399 396 418 C2' G C 11 419 416 440 C2' C C 12 441 438 459 C2' C C 13 460 457 478 C2' A C 14 479 476 499 C2' T C 15 500 497 519 C2' G C 16 520 517 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' C B 17 OK 3 6 7 24 C3' A B 18 OK 22 25 26 45 C3' T B 19 OK 43 46 47 65 C3' G B 20 OK 63 66 67 87 C3' G B 21 OK 85 88 89 109 C3' C B 22 OK 107 110 111 128 C3' A B 23 OK 126 129 130 149 C3' T B 24 OK 147 150 151 169 C3' T B 25 OK 167 170 171 189 C3' G B 26 OK 187 190 191 211 C3' A B 27 OK 209 212 213 232 C3' T B 28 OK 230 233 234 252 C3' A B 29 OK 250 253 254 274 C3' T C 4 OK 272 275 276 294 C3' A C 5 OK 292 295 296 315 C3' T C 6 OK 313 316 317 335 C3' C C 7 OK 333 336 337 354 C3' A C 8 OK 352 355 356 375 C3' A C 9 OK 373 376 377 396 C3' T C 10 OK 394 397 398 416 C3' G C 11 OK 414 417 418 438 C3' C C 12 OK 436 439 440 457 C3' C C 13 OK 455 458 459 476 C3' A C 14 OK 474 477 478 497 C3' T C 15 OK 495 498 499 517 C3' G C 16 OK 515 518 519 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' C B 17 OK 5 2 4 22 C4' A B 18 OK 24 21 23 43 C4' T B 19 OK 45 42 44 63 C4' G B 20 OK 65 62 64 85 C4' G B 21 OK 87 84 86 107 C4' C B 22 OK 109 106 108 126 C4' A B 23 OK 128 125 127 147 C4' T B 24 OK 149 146 148 167 C4' T B 25 OK 169 166 168 187 C4' G B 26 OK 189 186 188 209 C4' A B 27 OK 211 208 210 230 C4' T B 28 OK 232 229 231 250 C4' A B 29 OK 252 249 251 272 C4' T C 4 OK 274 271 273 292 C4' A C 5 OK 294 291 293 313 C4' T C 6 OK 315 312 314 333 C4' C C 7 OK 335 332 334 352 C4' A C 8 OK 354 351 353 373 C4' A C 9 OK 375 372 374 394 C4' T C 10 OK 396 393 395 414 C4' G C 11 OK 416 413 415 436 C4' C C 12 OK 438 435 437 455 C4' C C 13 OK 457 454 456 474 C4' A C 14 OK 476 473 475 495 C4' T C 15 OK 497 494 496 515 C4' G C 16 OK 517 514 516 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' C B 17 1 3 21 C5' A B 18 20 22 42 C5' T B 19 41 43 62 C5' G B 20 61 63 84 C5' G B 21 83 85 106 C5' C B 22 105 107 125 C5' A B 23 124 126 146 C5' T B 24 145 147 166 C5' T B 25 165 167 186 C5' G B 26 185 187 208 C5' A B 27 207 209 229 C5' T B 28 228 230 249 C5' A B 29 248 250 271 C5' T C 4 270 272 291 C5' A C 5 290 292 312 C5' T C 6 311 313 332 C5' C C 7 331 333 351 C5' A C 8 350 352 372 C5' A C 9 371 373 393 C5' T C 10 392 394 413 C5' G C 11 412 414 435 C5' C C 12 434 436 454 C5' C C 13 453 455 473 C5' A C 14 472 474 494 C5' T C 15 493 495 514 C5' G C 16 513 515 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 17 P A B 18 distorted distorted 6 18 19 20 38 P T B 19 distorted distorted 25 39 40 41 58 P G B 20 distorted distorted 46 59 60 61 80 P G B 21 distorted distorted 66 81 82 83 102 P C B 22 distorted distorted 88 103 104 105 121 P A B 23 distorted distorted 110 122 123 124 142 P T B 24 distorted distorted 129 143 144 145 162 P T B 25 distorted distorted 150 163 164 165 182 P G B 26 distorted distorted 170 183 184 185 204 P A B 27 distorted distorted 190 205 206 207 225 P T B 28 distorted distorted 212 226 227 228 245 P A B 29 distorted distorted 233 246 247 248 267 P T C 4 distorted distorted 268 269 270 287 P A C 5 distorted distorted 275 288 289 290 308 P T C 6 distorted distorted 295 309 310 311 328 P C C 7 distorted distorted 316 329 330 331 347 P A C 8 distorted distorted 336 348 349 350 368 P A C 9 distorted distorted 355 369 370 371 389 P T C 10 distorted distorted 376 390 391 392 409 P G C 11 distorted distorted 397 410 411 412 431 P C C 12 distorted distorted 417 432 433 434 450 P C C 13 distorted distorted 439 451 452 453 469 P A C 14 distorted distorted 458 470 471 472 490 P T C 15 distorted distorted 477 491 492 493 510 P G C 16 distorted distorted 498 511 512 513 ---------------------------------------------------------------------------------