ID code: '1NK4' 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 21 beta 4 9 7 30 C1' C B 22 beta 26 31 29 49 C1' G B 23 beta 45 50 48 71 C1' A B 24 beta 67 72 70 92 C1' T B 25 beta 88 93 91 112 C1' C B 26 beta 108 113 111 131 C1' A B 27 beta 127 132 130 152 C1' G B 28 beta 148 153 151 174 C1' G B 29 beta 170 175 173 197 C1' G C 4 beta 193 198 196 219 C1' C C 5 beta 215 220 218 238 C1' T C 6 beta 234 239 237 258 C1' G C 7 beta 254 259 257 280 C1' A C 8 beta 276 281 279 301 C1' T C 9 beta 297 302 300 321 C1' C C 10 beta 317 322 320 340 C1' G C 11 beta 336 341 339 362 C1' C C 12 beta 358 363 361 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G B 21 8 5 29 C2' C B 22 30 27 48 C2' G B 23 49 46 70 C2' A B 24 71 68 91 C2' T B 25 92 89 111 C2' C B 26 112 109 130 C2' A B 27 131 128 151 C2' G B 28 152 149 173 C2' G B 29 174 171 196 C2' G C 4 197 194 218 C2' C C 5 219 216 237 C2' T C 6 238 235 257 C2' G C 7 258 255 279 C2' A C 8 280 277 300 C2' T C 9 301 298 320 C2' C C 10 321 318 339 C2' G C 11 340 337 361 C2' C C 12 362 359 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G B 21 OK 3 6 7 27 C3' C B 22 OK 25 28 29 46 C3' G B 23 OK 44 47 48 68 C3' A B 24 OK 66 69 70 89 C3' T B 25 OK 87 90 91 109 C3' C B 26 OK 107 110 111 128 C3' A B 27 OK 126 129 130 149 C3' G B 28 OK 147 150 151 171 C3' G B 29 OK 169 172 173 194 C3' G C 4 OK 192 195 196 216 C3' C C 5 OK 214 217 218 235 C3' T C 6 OK 233 236 237 255 C3' G C 7 OK 253 256 257 277 C3' A C 8 OK 275 278 279 298 C3' T C 9 OK 296 299 300 318 C3' C C 10 OK 316 319 320 337 C3' G C 11 OK 335 338 339 359 C3' C C 12 OK 357 360 361 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G B 21 OK 5 2 4 25 C4' C B 22 OK 27 24 26 44 C4' G B 23 OK 46 43 45 66 C4' A B 24 OK 68 65 67 87 C4' T B 25 OK 89 86 88 107 C4' C B 26 OK 109 106 108 126 C4' A B 27 OK 128 125 127 147 C4' G B 28 OK 149 146 148 169 C4' G B 29 OK 171 168 170 192 C4' G C 4 OK 194 191 193 214 C4' C C 5 OK 216 213 215 233 C4' T C 6 OK 235 232 234 253 C4' G C 7 OK 255 252 254 275 C4' A C 8 OK 277 274 276 296 C4' T C 9 OK 298 295 297 316 C4' C C 10 OK 318 315 317 335 C4' G C 11 OK 337 334 336 357 C4' C C 12 OK 359 356 358 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G B 21 1 3 24 C5' C B 22 23 25 43 C5' G B 23 42 44 65 C5' A B 24 64 66 86 C5' T B 25 85 87 106 C5' C B 26 105 107 125 C5' A B 27 124 126 146 C5' G B 28 145 147 168 C5' G B 29 167 169 191 C5' G C 4 190 192 213 C5' C C 5 212 214 232 C5' T C 6 231 233 252 C5' G C 7 251 253 274 C5' A C 8 273 275 295 C5' T C 9 294 296 315 C5' C C 10 314 316 334 C5' G C 11 333 335 356 C5' C C 12 355 357 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 20 P C B 22 distorted distorted 6 21 22 23 39 P G B 23 distorted distorted 28 40 41 42 61 P A B 24 distorted distorted 47 62 63 64 82 P T B 25 distorted distorted 69 83 84 85 102 P C B 26 distorted distorted 90 103 104 105 121 P A B 27 distorted distorted 110 122 123 124 142 P G B 28 distorted distorted 129 143 144 145 164 P G B 29 distorted distorted 150 165 166 167 187 P G C 4 OK OK 188 189 190 209 P C C 5 distorted distorted 195 210 211 212 228 P T C 6 distorted distorted 217 229 230 231 248 P G C 7 distorted distorted 236 249 250 251 270 P A C 8 distorted distorted 256 271 272 273 291 P T C 9 distorted distorted 278 292 293 294 311 P C C 10 distorted distorted 299 312 313 314 330 P G C 11 distorted distorted 319 331 332 333 352 P C C 12 distorted distorted 338 353 354 355 ---------------------------------------------------------------------------------