ID code: '1CLQ' 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' G E 4 beta 7 12 10 33 C1' G E 5 beta 29 34 32 55 C1' A E 6 beta 51 56 54 76 C1' A E 7 beta 72 77 75 97 C1' C E 8 beta 93 98 96 116 C1' T E 9 beta 112 117 115 136 C1' A E 10 beta 132 137 135 157 C1' C E 11 beta 153 158 156 176 C1' T E 12 beta 172 177 175 194 C1' A D 12 beta 190 195 193 215 C1' G D 11 beta 211 216 214 237 C1' T D 10 beta 233 238 236 257 C1' A D 9 beta 253 258 256 278 C1' G D 8 beta 274 279 277 300 C1' T D 7 beta 296 301 299 320 C1' T D 6 beta 316 321 319 340 C1' C D 5 beta 336 341 339 359 C1' C D 4 beta 355 360 358 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' G E 4 11 8 32 C2' G E 5 33 30 54 C2' A E 6 55 52 75 C2' A E 7 76 73 96 C2' C E 8 97 94 115 C2' T E 9 116 113 135 C2' A E 10 136 133 156 C2' C E 11 157 154 175 C2' T E 12 176 173 193 C2' A D 12 194 191 214 C2' G D 11 215 212 236 C2' T D 10 237 234 256 C2' A D 9 257 254 277 C2' G D 8 278 275 299 C2' T D 7 300 297 319 C2' T D 6 320 317 339 C2' C D 5 340 337 358 C2' C D 4 359 356 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' G E 4 OK 6 9 10 30 C3' G E 5 OK 28 31 32 52 C3' A E 6 OK 50 53 54 73 C3' A E 7 OK 71 74 75 94 C3' C E 8 OK 92 95 96 113 C3' T E 9 OK 111 114 115 133 C3' A E 10 OK 131 134 135 154 C3' C E 11 OK 152 155 156 173 C3' T E 12 OK 171 174 175 191 C3' A D 12 OK 189 192 193 212 C3' G D 11 OK 210 213 214 234 C3' T D 10 OK 232 235 236 254 C3' A D 9 OK 252 255 256 275 C3' G D 8 OK 273 276 277 297 C3' T D 7 OK 295 298 299 317 C3' T D 6 OK 315 318 319 337 C3' C D 5 OK 335 338 339 356 C3' C D 4 OK 354 357 358 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' G E 4 OK 8 5 7 28 C4' G E 5 OK 30 27 29 50 C4' A E 6 OK 52 49 51 71 C4' A E 7 OK 73 70 72 92 C4' C E 8 OK 94 91 93 111 C4' T E 9 OK 113 110 112 131 C4' A E 10 OK 133 130 132 152 C4' C E 11 OK 154 151 153 171 C4' T E 12 OK 173 170 172 189 C4' A D 12 OK 191 188 190 210 C4' G D 11 OK 212 209 211 232 C4' T D 10 OK 234 231 233 252 C4' A D 9 OK 254 251 253 273 C4' G D 8 OK 275 272 274 295 C4' T D 7 OK 297 294 296 315 C4' T D 6 OK 317 314 316 335 C4' C D 5 OK 337 334 336 354 C4' C D 4 OK 356 353 355 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' G E 4 4 6 27 C5' G E 5 26 28 49 C5' A E 6 48 50 70 C5' A E 7 69 71 91 C5' C E 8 90 92 110 C5' T E 9 109 111 130 C5' A E 10 129 131 151 C5' C E 11 150 152 170 C5' T E 12 169 171 188 C5' A D 12 187 189 209 C5' G D 11 208 210 231 C5' T D 10 230 232 251 C5' A D 9 250 252 272 C5' G D 8 271 273 294 C5' T D 7 293 295 314 C5' T D 6 313 315 334 C5' C D 5 333 335 353 C5' C D 4 352 354 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P G E 4 distorted distorted 2 3 4 23 P G E 5 distorted distorted 9 24 25 26 45 P A E 6 distorted distorted 31 46 47 48 66 P A E 7 distorted distorted 53 67 68 69 87 P C E 8 distorted distorted 74 88 89 90 106 P T E 9 distorted distorted 95 107 108 109 126 P A E 10 distorted distorted 114 127 128 129 147 P C E 11 distorted distorted 134 148 149 150 166 P T E 12 distorted distorted 155 167 168 169 205 P G D 11 distorted distorted 192 206 207 208 227 P T D 10 distorted distorted 213 228 229 230 247 P A D 9 distorted distorted 235 248 249 250 268 P G D 8 distorted distorted 255 269 270 271 290 P T D 7 distorted distorted 276 291 292 293 310 P T D 6 distorted distorted 298 311 312 313 330 P C D 5 distorted distorted 318 331 332 333 349 P C D 4 distorted distorted 338 350 351 352 ---------------------------------------------------------------------------------