ID code: '1NK9' 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' G B 18 beta 4 9 7 30 C1' C B 19 beta 26 31 29 49 C1' G B 20 beta 45 50 48 71 C1' A B 21 beta 67 72 70 92 C1' T B 22 beta 88 93 91 112 C1' C B 23 beta 108 113 111 131 C1' A B 24 beta 127 132 130 152 C1' G B 25 beta 148 153 151 174 C1' C B 26 beta 170 175 173 193 C1' G B 27 beta 189 194 192 215 C1' C B 28 beta 211 216 214 234 C1' G B 29 beta 230 235 233 254 C1' C C 4 beta 250 255 253 273 C1' G C 5 beta 269 274 272 295 C1' T C 6 beta 291 296 294 315 C1' G C 7 beta 311 316 314 337 C1' C C 8 beta 333 338 336 356 C1' T C 9 beta 352 357 355 376 C1' G C 10 beta 372 377 375 398 C1' A C 11 beta 394 399 397 419 C1' T C 12 beta 415 420 418 439 C1' C C 13 beta 435 440 438 458 C1' G C 14 beta 454 459 457 480 C1' C C 15 beta 476 481 479 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G B 18 8 5 29 C2' C B 19 30 27 48 C2' G B 20 49 46 70 C2' A B 21 71 68 91 C2' T B 22 92 89 111 C2' C B 23 112 109 130 C2' A B 24 131 128 151 C2' G B 25 152 149 173 C2' C B 26 174 171 192 C2' G B 27 193 190 214 C2' C B 28 215 212 233 C2' G B 29 234 231 253 C2' C C 4 254 251 272 C2' G C 5 273 270 294 C2' T C 6 295 292 314 C2' G C 7 315 312 336 C2' C C 8 337 334 355 C2' T C 9 356 353 375 C2' G C 10 376 373 397 C2' A C 11 398 395 418 C2' T C 12 419 416 438 C2' C C 13 439 436 457 C2' G C 14 458 455 479 C2' C C 15 480 477 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G B 18 OK 3 6 7 27 C3' C B 19 OK 25 28 29 46 C3' G B 20 OK 44 47 48 68 C3' A B 21 OK 66 69 70 89 C3' T B 22 OK 87 90 91 109 C3' C B 23 OK 107 110 111 128 C3' A B 24 OK 126 129 130 149 C3' G B 25 OK 147 150 151 171 C3' C B 26 OK 169 172 173 190 C3' G B 27 OK 188 191 192 212 C3' C B 28 OK 210 213 214 231 C3' G B 29 OK 229 232 233 251 C3' C C 4 OK 249 252 253 270 C3' G C 5 OK 268 271 272 292 C3' T C 6 OK 290 293 294 312 C3' G C 7 OK 310 313 314 334 C3' C C 8 OK 332 335 336 353 C3' T C 9 OK 351 354 355 373 C3' G C 10 OK 371 374 375 395 C3' A C 11 OK 393 396 397 416 C3' T C 12 OK 414 417 418 436 C3' C C 13 OK 434 437 438 455 C3' G C 14 OK 453 456 457 477 C3' C C 15 OK 475 478 479 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G B 18 OK 5 2 4 25 C4' C B 19 OK 27 24 26 44 C4' G B 20 OK 46 43 45 66 C4' A B 21 OK 68 65 67 87 C4' T B 22 OK 89 86 88 107 C4' C B 23 OK 109 106 108 126 C4' A B 24 OK 128 125 127 147 C4' G B 25 OK 149 146 148 169 C4' C B 26 OK 171 168 170 188 C4' G B 27 OK 190 187 189 210 C4' C B 28 OK 212 209 211 229 C4' G B 29 OK 231 228 230 249 C4' C C 4 OK 251 248 250 268 C4' G C 5 OK 270 267 269 290 C4' T C 6 OK 292 289 291 310 C4' G C 7 OK 312 309 311 332 C4' C C 8 OK 334 331 333 351 C4' T C 9 OK 353 350 352 371 C4' G C 10 OK 373 370 372 393 C4' A C 11 OK 395 392 394 414 C4' T C 12 OK 416 413 415 434 C4' C C 13 OK 436 433 435 453 C4' G C 14 OK 455 452 454 475 C4' C C 15 OK 477 474 476 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G B 18 1 3 24 C5' C B 19 23 25 43 C5' G B 20 42 44 65 C5' A B 21 64 66 86 C5' T B 22 85 87 106 C5' C B 23 105 107 125 C5' A B 24 124 126 146 C5' G B 25 145 147 168 C5' C B 26 167 169 187 C5' G B 27 186 188 209 C5' C B 28 208 210 228 C5' G B 29 227 229 248 C5' C C 4 247 249 267 C5' G C 5 266 268 289 C5' T C 6 288 290 309 C5' G C 7 308 310 331 C5' C C 8 330 332 350 C5' T C 9 349 351 370 C5' G C 10 369 371 392 C5' A C 11 391 393 413 C5' T C 12 412 414 433 C5' C C 13 432 434 452 C5' G C 14 451 453 474 C5' C C 15 473 475 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 20 P C B 19 distorted distorted 6 21 22 23 39 P G B 20 distorted distorted 28 40 41 42 61 P A B 21 distorted distorted 47 62 63 64 82 P T B 22 distorted distorted 69 83 84 85 102 P C B 23 distorted distorted 90 103 104 105 121 P A B 24 distorted distorted 110 122 123 124 142 P G B 25 distorted distorted 129 143 144 145 164 P C B 26 distorted distorted 150 165 166 167 183 P G B 27 distorted distorted 172 184 185 186 205 P C B 28 distorted distorted 191 206 207 208 224 P G B 29 distorted distorted 213 225 226 227 263 P G C 5 distorted distorted 252 264 265 266 285 P T C 6 distorted distorted 271 286 287 288 305 P G C 7 distorted distorted 293 306 307 308 327 P C C 8 distorted distorted 313 328 329 330 346 P T C 9 distorted distorted 335 347 348 349 366 P G C 10 distorted distorted 354 367 368 369 388 P A C 11 distorted distorted 374 389 390 391 409 P T C 12 distorted distorted 396 410 411 412 429 P C C 13 distorted distorted 417 430 431 432 448 P G C 14 distorted distorted 437 449 450 451 470 P C C 15 distorted distorted 456 471 472 473 ---------------------------------------------------------------------------------