ID code: '1EO3' 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 3 beta 7 12 10 32 C1' G C 4 beta 28 33 31 54 C1' A C 5 beta 50 55 53 75 C1' TSP C 6 beta 71 76 74 95 C1' A C 7 beta 91 96 94 116 C1' T C 8 beta 112 117 115 136 C1' C C 9 beta 132 137 135 155 C1' T C 10 beta 151 156 154 175 C1' T C 11 beta 171 176 174 196 C1' A D 2 beta 192 197 195 217 C1' A D 3 beta 213 218 216 238 C1' G D 4 beta 234 239 237 260 C1' A D 5 beta 256 261 259 281 C1' TSP D 6 beta 277 282 280 301 C1' A D 7 beta 297 302 300 322 C1' T D 8 beta 318 323 321 342 C1' C D 9 beta 338 343 341 361 C1' T D 10 beta 357 362 360 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' A C 3 11 8 31 C2' G C 4 32 29 53 C2' A C 5 54 51 74 C2' TSP C 6 75 72 94 C2' A C 7 95 92 115 C2' T C 8 116 113 135 C2' C C 9 136 133 154 C2' T C 10 155 152 174 C2' T C 11 175 172 195 C2' A D 2 196 193 216 C2' A D 3 217 214 237 C2' G D 4 238 235 259 C2' A D 5 260 257 280 C2' TSP D 6 281 278 300 C2' A D 7 301 298 321 C2' T D 8 322 319 341 C2' C D 9 342 339 360 C2' T D 10 361 358 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' A C 3 OK 6 9 10 29 C3' G C 4 OK 27 30 31 51 C3' A C 5 OK 49 52 53 72 C3' TSP C 6 70 74 92 C3' A C 7 OK 90 93 94 113 C3' T C 8 OK 111 114 115 133 C3' C C 9 OK 131 134 135 152 C3' T C 10 OK 150 153 154 172 C3' T C 11 OK 170 173 174 193 C3' A D 2 OK 191 194 195 214 C3' A D 3 OK 212 215 216 235 C3' G D 4 OK 233 236 237 257 C3' A D 5 OK 255 258 259 278 C3' TSP D 6 276 280 298 C3' A D 7 OK 296 299 300 319 C3' T D 8 OK 317 320 321 339 C3' C D 9 OK 337 340 341 358 C3' T D 10 OK 356 359 360 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' A C 3 OK 8 5 7 27 C4' G C 4 OK 29 26 28 49 C4' A C 5 OK 51 48 50 70 C4' TSP C 6 OK 72 69 71 90 C4' A C 7 OK 92 89 91 111 C4' T C 8 OK 113 110 112 131 C4' C C 9 OK 133 130 132 150 C4' T C 10 OK 152 149 151 170 C4' T C 11 OK 172 169 171 191 C4' A D 2 OK 193 190 192 212 C4' A D 3 OK 214 211 213 233 C4' G D 4 OK 235 232 234 255 C4' A D 5 OK 257 254 256 276 C4' TSP D 6 OK 278 275 277 296 C4' A D 7 OK 298 295 297 317 C4' T D 8 OK 319 316 318 337 C4' C D 9 OK 339 336 338 356 C4' T D 10 OK 358 355 357 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' A C 3 4 6 26 C5' G C 4 25 27 48 C5' A C 5 47 49 69 C5' TSP C 6 68 70 89 C5' A C 7 88 90 110 C5' T C 8 109 111 130 C5' C C 9 129 131 149 C5' T C 10 148 150 169 C5' T C 11 168 170 190 C5' A D 2 189 191 211 C5' A D 3 210 212 232 C5' G D 4 231 233 254 C5' A D 5 253 255 275 C5' TSP D 6 274 276 295 C5' A D 7 294 296 316 C5' T D 8 315 317 336 C5' C D 9 335 337 355 C5' T D 10 354 356 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P A C 3 distorted distorted 2 3 4 22 P G C 4 distorted distorted 9 23 24 25 44 P A C 5 distorted distorted 30 45 46 47 65 P TSP C 6 OK OK 52 66 67 68 85 P A C 7 OK OK 86 87 88 106 P T C 8 distorted distorted 93 107 108 109 126 P C C 9 distorted distorted 114 127 128 129 145 P T C 10 distorted distorted 134 146 147 148 165 P T C 11 distorted distorted 153 166 167 168 186 P A D 2 distorted distorted 187 188 189 207 P A D 3 distorted distorted 194 208 209 210 228 P G D 4 distorted distorted 215 229 230 231 250 P A D 5 distorted distorted 236 251 252 253 271 P TSP D 6 OK OK 258 272 273 274 291 P A D 7 OK OK 292 293 294 312 P T D 8 distorted distorted 299 313 314 315 332 P C D 9 distorted distorted 320 333 334 335 351 P T D 10 distorted distorted 340 352 353 354 ---------------------------------------------------------------------------------