ID code: '5HAB' 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' --------------------------------------------------------------------------------- 7157 C1' A C 1 beta 7152 7158 7155 7179 C1' A C 2 beta 7174 7180 7177 7201 C1' A C 3 beta 7196 7202 7199 7223 C1' A C 4 beta 7218 7224 7221 7245 C1' A C 5 beta 7240 7246 7243 7269 C1' A D 1 beta 7264 7270 7267 7291 C1' A D 2 beta 7286 7292 7289 7313 C1' A D 3 beta 7308 7314 7311 7335 C1' A D 4 beta 7330 7336 7333 7357 C1' A D 5 beta 7352 7358 7355 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7155 C2' A C 1 OK 7157 7153 7156 7177 C2' A C 2 OK 7179 7175 7178 7199 C2' A C 3 OK 7201 7197 7200 7221 C2' A C 4 OK 7223 7219 7222 7243 C2' A C 5 OK 7245 7241 7244 7267 C2' A D 1 OK 7269 7265 7268 7289 C2' A D 2 OK 7291 7287 7290 7311 C2' A D 3 OK 7313 7309 7312 7333 C2' A D 4 OK 7335 7331 7334 7355 C2' A D 5 OK 7357 7353 7356 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 7153 C3' A C 1 OK 7151 7154 7155 7175 C3' A C 2 OK 7173 7176 7177 7197 C3' A C 3 OK 7195 7198 7199 7219 C3' A C 4 OK 7217 7220 7221 7241 C3' A C 5 OK 7239 7242 7243 7265 C3' A D 1 OK 7263 7266 7267 7287 C3' A D 2 OK 7285 7288 7289 7309 C3' A D 3 OK 7307 7310 7311 7331 C3' A D 4 OK 7329 7332 7333 7353 C3' A D 5 OK 7351 7354 7355 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 7151 C4' A C 1 OK 7153 7150 7152 7173 C4' A C 2 OK 7175 7172 7174 7195 C4' A C 3 OK 7197 7194 7196 7217 C4' A C 4 OK 7219 7216 7218 7239 C4' A C 5 OK 7241 7238 7240 7263 C4' A D 1 OK 7265 7262 7264 7285 C4' A D 2 OK 7287 7284 7286 7307 C4' A D 3 OK 7309 7306 7308 7329 C4' A D 4 OK 7331 7328 7330 7351 C4' A D 5 OK 7353 7350 7352 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 7150 C5' A C 1 7149 7151 7172 C5' A C 2 7171 7173 7194 C5' A C 3 7193 7195 7216 C5' A C 4 7215 7217 7238 C5' A C 5 7237 7239 7262 C5' A D 1 7261 7263 7284 C5' A D 2 7283 7285 7306 C5' A D 3 7305 7307 7328 C5' A D 4 7327 7329 7350 C5' A D 5 7349 7351 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 7146 P A C 1 OK OK 7147 7148 7149 7168 P A C 2 distorted distorted 7154 7169 7170 7171 7190 P A C 3 distorted distorted 7176 7191 7192 7193 7212 P A C 4 distorted distorted 7198 7213 7214 7215 7234 P A C 5 distorted distorted 7220 7235 7236 7237 7258 P A D 1 distorted distorted 7259 7260 7261 7280 P A D 2 distorted distorted 7266 7281 7282 7283 7302 P A D 3 distorted distorted 7288 7303 7304 7305 7324 P A D 4 distorted distorted 7310 7325 7326 7327 7346 P A D 5 distorted distorted 7332 7347 7348 7349 ---------------------------------------------------------------------------------