ID code: '1C8C' 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 101 beta 4 9 7 34 C1' T B 102 beta 30 35 33 55 C1' G B 103 beta 51 56 54 80 C1' A B 104 beta 76 81 79 103 C1' T B 105 beta 99 104 102 124 C1' C B 106 beta 120 125 123 145 C1' G B 107 beta 141 146 144 170 C1' C B 108 beta 166 171 169 190 C1' G C 109 beta 186 191 189 216 C1' T C 110 beta 212 217 215 237 C1' G C 111 beta 233 238 236 262 C1' A C 112 beta 258 263 261 285 C1' T C 113 beta 281 286 284 306 C1' C C 114 beta 302 307 305 327 C1' G C 115 beta 323 328 326 352 C1' C C 116 beta 348 353 351 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G B 101 8 5 33 C2' T B 102 34 31 54 C2' G B 103 55 52 79 C2' A B 104 80 77 102 C2' T B 105 103 100 123 C2' C B 106 124 121 144 C2' G B 107 145 142 169 C2' C B 108 170 167 189 C2' G C 109 190 187 215 C2' T C 110 216 213 236 C2' G C 111 237 234 261 C2' A C 112 262 259 284 C2' T C 113 285 282 305 C2' C C 114 306 303 326 C2' G C 115 327 324 351 C2' C C 116 352 349 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G B 101 OK 3 6 7 31 C3' T B 102 OK 29 32 33 52 C3' G B 103 OK 50 53 54 77 C3' A B 104 OK 75 78 79 100 C3' T B 105 OK 98 101 102 121 C3' C B 106 OK 119 122 123 142 C3' G B 107 OK 140 143 144 167 C3' C B 108 OK 165 168 169 187 C3' G C 109 OK 185 188 189 213 C3' T C 110 OK 211 214 215 234 C3' G C 111 OK 232 235 236 259 C3' A C 112 OK 257 260 261 282 C3' T C 113 OK 280 283 284 303 C3' C C 114 OK 301 304 305 324 C3' G C 115 OK 322 325 326 349 C3' C C 116 OK 347 350 351 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G B 101 OK 5 2 4 29 C4' T B 102 OK 31 28 30 50 C4' G B 103 OK 52 49 51 75 C4' A B 104 OK 77 74 76 98 C4' T B 105 OK 100 97 99 119 C4' C B 106 OK 121 118 120 140 C4' G B 107 OK 142 139 141 165 C4' C B 108 OK 167 164 166 185 C4' G C 109 OK 187 184 186 211 C4' T C 110 OK 213 210 212 232 C4' G C 111 OK 234 231 233 257 C4' A C 112 OK 259 256 258 280 C4' T C 113 OK 282 279 281 301 C4' C C 114 OK 303 300 302 322 C4' G C 115 OK 324 321 323 347 C4' C C 116 OK 349 346 348 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G B 101 1 3 28 C5' T B 102 27 29 49 C5' G B 103 48 50 74 C5' A B 104 73 75 97 C5' T B 105 96 98 118 C5' C B 106 117 119 139 C5' G B 107 138 140 164 C5' C B 108 163 165 184 C5' G C 109 183 185 210 C5' T C 110 209 211 231 C5' G C 111 230 232 256 C5' A C 112 255 257 279 C5' T C 113 278 280 300 C5' C C 114 299 301 321 C5' G C 115 320 322 346 C5' C C 116 345 347 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 24 P T B 102 distorted distorted 6 25 26 27 45 P G B 103 distorted distorted 32 46 47 48 70 P A B 104 distorted distorted 53 71 72 73 93 P T B 105 distorted distorted 78 94 95 96 114 P C B 106 distorted distorted 101 115 116 117 135 P G B 107 distorted distorted 122 136 137 138 160 P C B 108 distorted distorted 143 161 162 163 206 P T C 110 distorted distorted 188 207 208 209 227 P G C 111 distorted distorted 214 228 229 230 252 P A C 112 distorted distorted 235 253 254 255 275 P T C 113 distorted distorted 260 276 277 278 296 P C C 114 distorted distorted 283 297 298 299 317 P G C 115 distorted distorted 304 318 319 320 342 P C C 116 distorted distorted 325 343 344 345 ---------------------------------------------------------------------------------