ID code: '3KNC' 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' --------------------------------------------------------------------------------- 12 C1' XGR A 1 11 13 30 C1' XCR A 2 22 31 53 C1' XGR A 3 52 54 67 C1' XTR A 4 76 77 94 C1' XAR A 5 97 93 119 C1' XGR A 6 118 120 139 C1' XCR A 7 131 140 162 C1' XGR A 8 161 163 186 C1' C B 1 beta 181 187 184 206 C1' G B 2 beta 201 207 204 229 C1' C B 3 beta 224 230 227 249 C1' U B 4 beta 244 250 247 269 C1' A B 5 beta 264 270 267 291 C1' C B 6 beta 286 292 289 311 C1' G B 7 beta 306 312 309 334 C1' C B 8 beta 329 335 332 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 13 C2' XGR A 1 12 14 31 C2' XCR A 2 30 32 54 C2' XGR A 3 53 55 77 C2' XTR A 4 67 78 93 C2' XAR A 5 94 91 120 C2' XGR A 6 119 121 140 C2' XCR A 7 139 141 163 C2' XGR A 8 162 164 184 C2' C B 1 OK 186 182 185 204 C2' G B 2 OK 206 202 205 227 C2' C B 3 OK 229 225 228 247 C2' U B 4 OK 249 245 248 267 C2' A B 5 OK 269 265 268 289 C2' C B 6 OK 291 287 290 309 C2' G B 7 OK 311 307 310 332 C2' C B 8 OK 334 330 333 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 14 C3' XGR A 1 OK 16 15 13 32 C3' XCR A 2 OK 34 33 31 55 C3' XGR A 3 OK 57 56 54 78 C3' XTR A 4 OK 64 84 77 91 C3' XAR A 5 OK 90 92 93 121 C3' XGR A 6 OK 123 122 120 141 C3' XCR A 7 OK 143 142 140 164 C3' XGR A 8 OK 166 165 163 182 C3' C B 1 OK 180 183 184 202 C3' G B 2 OK 200 203 204 225 C3' C B 3 OK 223 226 227 245 C3' U B 4 OK 243 246 247 265 C3' A B 5 OK 263 266 267 287 C3' C B 6 OK 285 288 289 307 C3' G B 7 OK 305 308 309 330 C3' C B 8 OK 328 331 332 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 16 C4' XGR A 1 14 17 34 C4' XCR A 2 32 35 57 C4' XGR A 3 55 58 64 C4' XTR A 4 78 83 90 C4' XAR A 5 91 89 123 C4' XGR A 6 121 124 143 C4' XCR A 7 141 144 166 C4' XGR A 8 164 167 180 C4' C B 1 OK 182 179 181 200 C4' G B 2 OK 202 199 201 223 C4' C B 3 OK 225 222 224 243 C4' U B 4 OK 245 242 244 263 C4' A B 5 OK 265 262 264 285 C4' C B 6 OK 287 284 286 305 C4' G B 7 OK 307 304 306 328 C4' C B 8 OK 330 327 329 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 17 C5' XGR A 1 18 16 35 C5' XCR A 2 36 34 58 C5' XGR A 3 59 57 83 C5' XTR A 4 82 64 89 C5' XAR A 5 88 90 124 C5' XGR A 6 125 123 144 C5' XCR A 7 145 143 167 C5' XGR A 8 168 166 179 C5' C B 1 178 180 199 C5' G B 2 198 200 222 C5' C B 3 221 223 242 C5' U B 4 241 243 262 C5' A B 5 261 263 284 C5' C B 6 283 285 304 C5' G B 7 303 305 327 C5' C B 8 326 328 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 21 P XCR A 2 distorted distorted 15 39 40 36 41 P XGR A 3 distorted distorted 33 62 63 59 79 P XTR A 4 distorted distorted 56 80 81 82 86 P XAR A 5 OK OK 84 85 87 88 107 P XGR A 6 distorted distorted 92 128 129 125 130 P XCR A 7 distorted distorted 122 148 149 145 150 P XGR A 8 distorted distorted 142 171 172 168 173 P XGR A 9 distorted distorted 165 175 176 174 195 P G B 2 distorted distorted 183 196 197 198 218 P C B 3 distorted distorted 203 219 220 221 238 P U B 4 distorted distorted 226 239 240 241 258 P A B 5 distorted distorted 246 259 260 261 280 P C B 6 distorted distorted 266 281 282 283 300 P G B 7 distorted distorted 288 301 302 303 323 P C B 8 distorted distorted 308 324 325 326 ---------------------------------------------------------------------------------