ID code: '4C40' 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' G A 1 beta 7 13 10 35 C1' G A 2 beta 30 36 33 58 C1' C A 3 beta 53 59 56 78 C1' G A 4 beta 73 79 76 101 C1' A A 5 beta 96 102 99 123 C1' A A 6 beta 118 124 121 145 C1' G A 7 beta 140 146 143 168 C1' A A 8 beta 163 169 166 190 C1' A A 9 beta 185 191 188 212 C1' C A 10 beta 207 213 210 232 C1' C A 11 beta 227 233 230 252 C1' G A 12 beta 247 253 250 275 C1' G A 13 beta 270 276 273 298 C1' G A 14 beta 293 299 296 321 C1' G A 15 beta 316 322 319 344 C1' A A 16 beta 339 345 342 366 C1' G A 17 beta 361 367 364 389 C1' C A 18 beta 384 390 387 409 C1' C A 19 beta 404 410 407 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' G A 1 OK 12 8 11 33 C2' G A 2 OK 35 31 34 56 C2' C A 3 OK 58 54 57 76 C2' G A 4 OK 78 74 77 99 C2' A A 5 OK 101 97 100 121 C2' A A 6 OK 123 119 122 143 C2' G A 7 OK 145 141 144 166 C2' A A 8 OK 168 164 167 188 C2' A A 9 OK 190 186 189 210 C2' C A 10 OK 212 208 211 230 C2' C A 11 OK 232 228 231 250 C2' G A 12 OK 252 248 251 273 C2' G A 13 OK 275 271 274 296 C2' G A 14 OK 298 294 297 319 C2' G A 15 OK 321 317 320 342 C2' A A 16 OK 344 340 343 364 C2' G A 17 OK 366 362 365 387 C2' C A 18 OK 389 385 388 407 C2' C A 19 OK 409 405 408 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' G A 1 OK 6 9 10 31 C3' G A 2 OK 29 32 33 54 C3' C A 3 OK 52 55 56 74 C3' G A 4 OK 72 75 76 97 C3' A A 5 OK 95 98 99 119 C3' A A 6 OK 117 120 121 141 C3' G A 7 OK 139 142 143 164 C3' A A 8 OK 162 165 166 186 C3' A A 9 OK 184 187 188 208 C3' C A 10 OK 206 209 210 228 C3' C A 11 OK 226 229 230 248 C3' G A 12 OK 246 249 250 271 C3' G A 13 OK 269 272 273 294 C3' G A 14 OK 292 295 296 317 C3' G A 15 OK 315 318 319 340 C3' A A 16 OK 338 341 342 362 C3' G A 17 OK 360 363 364 385 C3' C A 18 OK 383 386 387 405 C3' C A 19 OK 403 406 407 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' G A 1 OK 8 5 7 29 C4' G A 2 OK 31 28 30 52 C4' C A 3 OK 54 51 53 72 C4' G A 4 OK 74 71 73 95 C4' A A 5 OK 97 94 96 117 C4' A A 6 OK 119 116 118 139 C4' G A 7 OK 141 138 140 162 C4' A A 8 OK 164 161 163 184 C4' A A 9 OK 186 183 185 206 C4' C A 10 OK 208 205 207 226 C4' C A 11 OK 228 225 227 246 C4' G A 12 OK 248 245 247 269 C4' G A 13 OK 271 268 270 292 C4' G A 14 OK 294 291 293 315 C4' G A 15 OK 317 314 316 338 C4' A A 16 OK 340 337 339 360 C4' G A 17 OK 362 359 361 383 C4' C A 18 OK 385 382 384 403 C4' C A 19 OK 405 402 404 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' G A 1 4 6 28 C5' G A 2 27 29 51 C5' C A 3 50 52 71 C5' G A 4 70 72 94 C5' A A 5 93 95 116 C5' A A 6 115 117 138 C5' G A 7 137 139 161 C5' A A 8 160 162 183 C5' A A 9 182 184 205 C5' C A 10 204 206 225 C5' C A 11 224 226 245 C5' G A 12 244 246 268 C5' G A 13 267 269 291 C5' G A 14 290 292 314 C5' G A 15 313 315 337 C5' A A 16 336 338 359 C5' G A 17 358 360 382 C5' C A 18 381 383 402 C5' C A 19 401 403 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P G A 1 distorted distorted 2 3 4 24 P G A 2 distorted distorted 9 25 26 27 47 P C A 3 distorted distorted 32 48 49 50 67 P G A 4 distorted distorted 55 68 69 70 90 P A A 5 distorted distorted 75 91 92 93 112 P A A 6 OK OK 98 113 114 115 134 P G A 7 OK OK 120 135 136 137 157 P A A 8 distorted distorted 142 158 159 160 179 P A A 9 distorted distorted 165 180 181 182 201 P C A 10 distorted distorted 187 202 203 204 221 P C A 11 distorted distorted 209 222 223 224 241 P G A 12 distorted distorted 229 242 243 244 264 P G A 13 distorted distorted 249 265 266 267 287 P G A 14 OK OK 272 288 289 290 310 P G A 15 OK OK 295 311 312 313 333 P A A 16 distorted distorted 318 334 335 336 355 P G A 17 OK OK 341 356 357 358 378 P C A 18 distorted distorted 363 379 380 381 398 P C A 19 distorted distorted 386 399 400 401 ---------------------------------------------------------------------------------