ID code: '1EON' 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' A C 2 beta 7 12 10 32 C1' A C 3 beta 28 33 31 53 C1' G C 4 beta 49 54 52 75 C1' A C 5 beta 71 76 74 96 C1' TSP C 6 beta 92 97 95 116 C1' A C 7 beta 112 117 115 137 C1' T C 8 beta 133 138 136 157 C1' C C 9 beta 153 158 156 176 C1' T C 10 beta 172 177 175 196 C1' T C 11 beta 192 197 195 217 C1' A D 2 beta 213 218 216 238 C1' A D 3 beta 234 239 237 259 C1' G D 4 beta 255 260 258 281 C1' A D 5 beta 277 282 280 302 C1' TSP D 6 beta 298 303 301 322 C1' A D 7 beta 318 323 321 343 C1' T D 8 beta 339 344 342 363 C1' C D 9 beta 359 364 362 382 C1' T D 10 beta 378 383 381 402 C1' T D 11 beta 398 403 401 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' A C 2 11 8 31 C2' A C 3 32 29 52 C2' G C 4 53 50 74 C2' A C 5 75 72 95 C2' TSP C 6 96 93 115 C2' A C 7 116 113 136 C2' T C 8 137 134 156 C2' C C 9 157 154 175 C2' T C 10 176 173 195 C2' T C 11 196 193 216 C2' A D 2 217 214 237 C2' A D 3 238 235 258 C2' G D 4 259 256 280 C2' A D 5 281 278 301 C2' TSP D 6 302 299 321 C2' A D 7 322 319 342 C2' T D 8 343 340 362 C2' C D 9 363 360 381 C2' T D 10 382 379 401 C2' T D 11 402 399 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' A C 2 OK 6 9 10 29 C3' A C 3 OK 27 30 31 50 C3' G C 4 OK 48 51 52 72 C3' A C 5 OK 70 73 74 93 C3' TSP C 6 91 95 113 C3' A C 7 OK 111 114 115 134 C3' T C 8 OK 132 135 136 154 C3' C C 9 OK 152 155 156 173 C3' T C 10 OK 171 174 175 193 C3' T C 11 OK 191 194 195 214 C3' A D 2 OK 212 215 216 235 C3' A D 3 OK 233 236 237 256 C3' G D 4 OK 254 257 258 278 C3' A D 5 OK 276 279 280 299 C3' TSP D 6 297 301 319 C3' A D 7 OK 317 320 321 340 C3' T D 8 OK 338 341 342 360 C3' C D 9 OK 358 361 362 379 C3' T D 10 OK 377 380 381 399 C3' T D 11 OK 397 400 401 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' A C 2 OK 8 5 7 27 C4' A C 3 OK 29 26 28 48 C4' G C 4 OK 50 47 49 70 C4' A C 5 OK 72 69 71 91 C4' TSP C 6 OK 93 90 92 111 C4' A C 7 OK 113 110 112 132 C4' T C 8 OK 134 131 133 152 C4' C C 9 OK 154 151 153 171 C4' T C 10 OK 173 170 172 191 C4' T C 11 OK 193 190 192 212 C4' A D 2 OK 214 211 213 233 C4' A D 3 OK 235 232 234 254 C4' G D 4 OK 256 253 255 276 C4' A D 5 OK 278 275 277 297 C4' TSP D 6 OK 299 296 298 317 C4' A D 7 OK 319 316 318 338 C4' T D 8 OK 340 337 339 358 C4' C D 9 OK 360 357 359 377 C4' T D 10 OK 379 376 378 397 C4' T D 11 OK 399 396 398 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' A C 2 4 6 26 C5' A C 3 25 27 47 C5' G C 4 46 48 69 C5' A C 5 68 70 90 C5' TSP C 6 89 91 110 C5' A C 7 109 111 131 C5' T C 8 130 132 151 C5' C C 9 150 152 170 C5' T C 10 169 171 190 C5' T C 11 189 191 211 C5' A D 2 210 212 232 C5' A D 3 231 233 253 C5' G D 4 252 254 275 C5' A D 5 274 276 296 C5' TSP D 6 295 297 316 C5' A D 7 315 317 337 C5' T D 8 336 338 357 C5' C D 9 356 358 376 C5' T D 10 375 377 396 C5' T D 11 395 397 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P A C 2 distorted distorted 2 3 4 22 P A C 3 distorted distorted 9 23 24 25 43 P G C 4 distorted distorted 30 44 45 46 65 P A C 5 distorted distorted 51 66 67 68 86 P TSP C 6 OK OK 73 87 88 89 106 P A C 7 OK OK 107 108 109 127 P T C 8 distorted distorted 114 128 129 130 147 P C C 9 distorted distorted 135 148 149 150 166 P T C 10 distorted distorted 155 167 168 169 186 P T C 11 distorted distorted 174 187 188 189 207 P A D 2 distorted distorted 208 209 210 228 P A D 3 distorted distorted 215 229 230 231 249 P G D 4 distorted distorted 236 250 251 252 271 P A D 5 distorted distorted 257 272 273 274 292 P TSP D 6 OK OK 279 293 294 295 312 P A D 7 OK OK 313 314 315 333 P T D 8 distorted distorted 320 334 335 336 353 P C D 9 distorted distorted 341 354 355 356 372 P T D 10 distorted distorted 361 373 374 375 392 P T D 11 distorted distorted 380 393 394 395 ---------------------------------------------------------------------------------