ID code: '1K4S' 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' A B 1 beta 4 9 7 29 C1' A B 2 beta 25 30 28 50 C1' A B 3 beta 46 51 49 71 C1' A B 4 beta 67 72 70 92 C1' A B 5 beta 88 93 91 113 C1' G B 6 beta 109 114 112 135 C1' A B 7 beta 131 136 134 156 C1' C B 8 beta 152 157 155 175 C1' +U B 9 beta 171 176 174 193 C1' +U B 10 beta 190 194 192 213 C1' A D 113 beta 209 214 212 234 C1' A D 114 beta 230 235 233 255 C1' G D 115 beta 251 256 254 277 C1' +U D 116 beta 273 278 276 296 C1' C D 117 beta 292 297 295 315 C1' +U D 118 beta 311 316 314 334 C1' +U D 119 beta 330 335 333 353 C1' +U D 120 beta 349 354 352 372 C1' +U D 121 beta 368 373 371 391 C1' T D 122 beta 387 392 390 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' A B 1 8 5 28 C2' A B 2 29 26 49 C2' A B 3 50 47 70 C2' A B 4 71 68 91 C2' A B 5 92 89 112 C2' G B 6 113 110 134 C2' A B 7 135 132 155 C2' C B 8 156 153 174 C2' +U B 9 175 172 192 C2' +U B 10 193 191 212 C2' A D 113 213 210 233 C2' A D 114 234 231 254 C2' G D 115 255 252 276 C2' +U D 116 277 274 295 C2' C D 117 296 293 314 C2' +U D 118 315 312 333 C2' +U D 119 334 331 352 C2' +U D 120 353 350 371 C2' +U D 121 372 369 390 C2' T D 122 391 388 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' A B 1 OK 3 6 7 26 C3' A B 2 OK 24 27 28 47 C3' A B 3 OK 45 48 49 68 C3' A B 4 OK 66 69 70 89 C3' A B 5 OK 87 90 91 110 C3' G B 6 OK 108 111 112 132 C3' A B 7 OK 130 133 134 153 C3' C B 8 OK 151 154 155 172 C3' +U B 9 OK 170 173 174 191 C3' +U B 10 189 192 210 C3' A D 113 OK 208 211 212 231 C3' A D 114 OK 229 232 233 252 C3' G D 115 OK 250 253 254 274 C3' +U D 116 OK 272 275 276 293 C3' C D 117 OK 291 294 295 312 C3' +U D 118 OK 310 313 314 331 C3' +U D 119 OK 329 332 333 350 C3' +U D 120 OK 348 351 352 369 C3' +U D 121 OK 367 370 371 388 C3' T D 122 OK 386 389 390 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' A B 1 OK 5 2 4 24 C4' A B 2 OK 26 23 25 45 C4' A B 3 OK 47 44 46 66 C4' A B 4 OK 68 65 67 87 C4' A B 5 OK 89 86 88 108 C4' G B 6 OK 110 107 109 130 C4' A B 7 OK 132 129 131 151 C4' C B 8 OK 153 150 152 170 C4' +U B 9 OK 172 169 171 189 C4' +U B 10 OK 191 188 190 208 C4' A D 113 OK 210 207 209 229 C4' A D 114 OK 231 228 230 250 C4' G D 115 OK 252 249 251 272 C4' +U D 116 OK 274 271 273 291 C4' C D 117 OK 293 290 292 310 C4' +U D 118 OK 312 309 311 329 C4' +U D 119 OK 331 328 330 348 C4' +U D 120 OK 350 347 349 367 C4' +U D 121 OK 369 366 368 386 C4' T D 122 OK 388 385 387 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' A B 1 1 3 23 C5' A B 2 22 24 44 C5' A B 3 43 45 65 C5' A B 4 64 66 86 C5' A B 5 85 87 107 C5' G B 6 106 108 129 C5' A B 7 128 130 150 C5' C B 8 149 151 169 C5' +U B 9 168 170 188 C5' +U B 10 187 189 207 C5' A D 113 206 208 228 C5' A D 114 227 229 249 C5' G D 115 248 250 271 C5' +U D 116 270 272 290 C5' C D 117 289 291 309 C5' +U D 118 308 310 328 C5' +U D 119 327 329 347 C5' +U D 120 346 348 366 C5' +U D 121 365 367 385 C5' T D 122 384 386 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 19 P A B 2 distorted distorted 6 20 21 22 40 P A B 3 distorted distorted 27 41 42 43 61 P A B 4 distorted distorted 48 62 63 64 82 P A B 5 distorted distorted 69 83 84 85 103 P G B 6 distorted distorted 90 104 105 106 125 P A B 7 distorted distorted 111 126 127 128 146 P C B 8 distorted distorted 133 147 148 149 165 P +U B 9 distorted distorted 154 166 167 168 184 P +U B 10 distorted distorted 173 185 186 187 203 P A D 113 distorted distorted 204 205 206 224 P A D 114 distorted distorted 211 225 226 227 245 P G D 115 distorted distorted 232 246 247 248 267 P +U D 116 distorted distorted 253 268 269 270 286 P C D 117 distorted distorted 275 287 288 289 305 P +U D 118 distorted distorted 294 306 307 308 324 P +U D 119 distorted distorted 313 325 326 327 343 P +U D 120 distorted distorted 332 344 345 346 362 P +U D 121 distorted distorted 351 363 364 365 381 P T D 122 distorted distorted 370 382 383 384 ---------------------------------------------------------------------------------