ID code: '1NKE' 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 19 beta 4 9 7 30 C1' C B 20 beta 26 31 29 49 C1' G B 21 beta 45 50 48 71 C1' A B 22 beta 67 72 70 92 C1' T B 23 beta 88 93 91 112 C1' C B 24 beta 108 113 111 131 C1' A B 25 beta 127 132 130 152 C1' G B 26 beta 148 153 151 174 C1' C B 27 beta 170 175 173 193 C1' C B 28 beta 189 194 192 212 C1' C B 29 beta 208 213 211 229 C1' G C 6 beta 225 230 228 251 C1' T C 7 beta 247 252 250 271 C1' G C 8 beta 267 272 270 293 C1' C C 9 beta 289 294 292 312 C1' T C 10 beta 308 313 311 332 C1' G C 11 beta 328 333 331 354 C1' A C 12 beta 350 355 353 375 C1' T C 13 beta 371 376 374 395 C1' C C 14 beta 391 396 394 414 C1' G C 15 beta 410 415 413 436 C1' C C 16 beta 432 437 435 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G B 19 8 5 29 C2' C B 20 30 27 48 C2' G B 21 49 46 70 C2' A B 22 71 68 91 C2' T B 23 92 89 111 C2' C B 24 112 109 130 C2' A B 25 131 128 151 C2' G B 26 152 149 173 C2' C B 27 174 171 192 C2' C B 28 193 190 211 C2' C B 29 212 209 228 C2' G C 6 229 226 250 C2' T C 7 251 248 270 C2' G C 8 271 268 292 C2' C C 9 293 290 311 C2' T C 10 312 309 331 C2' G C 11 332 329 353 C2' A C 12 354 351 374 C2' T C 13 375 372 394 C2' C C 14 395 392 413 C2' G C 15 414 411 435 C2' C C 16 436 433 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G B 19 OK 3 6 7 27 C3' C B 20 OK 25 28 29 46 C3' G B 21 OK 44 47 48 68 C3' A B 22 OK 66 69 70 89 C3' T B 23 OK 87 90 91 109 C3' C B 24 OK 107 110 111 128 C3' A B 25 OK 126 129 130 149 C3' G B 26 OK 147 150 151 171 C3' C B 27 OK 169 172 173 190 C3' C B 28 OK 188 191 192 209 C3' C B 29 OK 207 210 211 226 C3' G C 6 OK 224 227 228 248 C3' T C 7 OK 246 249 250 268 C3' G C 8 OK 266 269 270 290 C3' C C 9 OK 288 291 292 309 C3' T C 10 OK 307 310 311 329 C3' G C 11 OK 327 330 331 351 C3' A C 12 OK 349 352 353 372 C3' T C 13 OK 370 373 374 392 C3' C C 14 OK 390 393 394 411 C3' G C 15 OK 409 412 413 433 C3' C C 16 OK 431 434 435 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G B 19 OK 5 2 4 25 C4' C B 20 OK 27 24 26 44 C4' G B 21 OK 46 43 45 66 C4' A B 22 OK 68 65 67 87 C4' T B 23 OK 89 86 88 107 C4' C B 24 OK 109 106 108 126 C4' A B 25 OK 128 125 127 147 C4' G B 26 OK 149 146 148 169 C4' C B 27 OK 171 168 170 188 C4' C B 28 OK 190 187 189 207 C4' C B 29 OK 209 206 208 224 C4' G C 6 OK 226 223 225 246 C4' T C 7 OK 248 245 247 266 C4' G C 8 OK 268 265 267 288 C4' C C 9 OK 290 287 289 307 C4' T C 10 OK 309 306 308 327 C4' G C 11 OK 329 326 328 349 C4' A C 12 OK 351 348 350 370 C4' T C 13 OK 372 369 371 390 C4' C C 14 OK 392 389 391 409 C4' G C 15 OK 411 408 410 431 C4' C C 16 OK 433 430 432 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G B 19 1 3 24 C5' C B 20 23 25 43 C5' G B 21 42 44 65 C5' A B 22 64 66 86 C5' T B 23 85 87 106 C5' C B 24 105 107 125 C5' A B 25 124 126 146 C5' G B 26 145 147 168 C5' C B 27 167 169 187 C5' C B 28 186 188 206 C5' C B 29 205 207 223 C5' G C 6 222 224 245 C5' T C 7 244 246 265 C5' G C 8 264 266 287 C5' C C 9 286 288 306 C5' T C 10 305 307 326 C5' G C 11 325 327 348 C5' A C 12 347 349 369 C5' T C 13 368 370 389 C5' C C 14 388 390 408 C5' G C 15 407 409 430 C5' C C 16 429 431 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 20 P C B 20 distorted distorted 6 21 22 23 39 P G B 21 distorted distorted 28 40 41 42 61 P A B 22 distorted distorted 47 62 63 64 82 P T B 23 distorted distorted 69 83 84 85 102 P C B 24 distorted distorted 90 103 104 105 121 P A B 25 distorted distorted 110 122 123 124 142 P G B 26 distorted distorted 129 143 144 145 164 P C B 27 distorted distorted 150 165 166 167 183 P C B 28 distorted distorted 172 184 185 186 202 P C B 29 distorted distorted 191 203 204 205 241 P T C 7 distorted distorted 227 242 243 244 261 P G C 8 distorted distorted 249 262 263 264 283 P C C 9 distorted distorted 269 284 285 286 302 P T C 10 distorted distorted 291 303 304 305 322 P G C 11 distorted distorted 310 323 324 325 344 P A C 12 distorted distorted 330 345 346 347 365 P T C 13 distorted distorted 352 366 367 368 385 P C C 14 distorted distorted 373 386 387 388 404 P G C 15 distorted distorted 393 405 406 407 426 P C C 16 distorted distorted 412 427 428 429 ---------------------------------------------------------------------------------