ID code: '3P4C' 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' --------------------------------------------------------------------------------- 9 C1' CFZ A 101 beta 15 1 10 29 C1' G A 102 beta 24 30 27 53 C1' AF2 A 103 beta 60 52 55 74 C1' A A 104 beta 69 75 72 102 C1' UFT A 105 beta 101 89 98 116 C1' U A 106 beta 111 117 114 134 C1' CFZ A 107 beta 142 126 136 199 C1' CFZ B 209 beta 205 191 200 219 C1' G B 210 beta 214 220 217 243 C1' AF2 B 211 beta 250 242 245 264 C1' A B 212 beta 259 265 262 292 C1' UFT B 213 beta 291 279 288 306 C1' U B 214 beta 301 307 304 324 C1' CFZ B 215 beta 332 316 326 346 C1' G B 216 beta 341 347 344 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' CFZ A 101 9 12 27 C2' G A 102 OK 29 25 28 55 C2' AF2 A 103 53 57 72 C2' A A 104 OK 74 70 73 98 C2' UFT A 105 102 103 114 C2' U A 106 OK 116 112 115 136 C2' CFZ A 107 134 139 200 C2' CFZ B 209 199 202 217 C2' G B 210 OK 219 215 218 245 C2' AF2 B 211 243 247 262 C2' A B 212 OK 264 260 263 288 C2' UFT B 213 292 293 304 C2' U B 214 OK 306 302 305 326 C2' CFZ B 215 324 329 344 C2' G B 216 OK 346 342 345 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 12 C3' CFZ A 101 OK 14 13 10 25 C3' G A 102 OK 23 26 27 57 C3' AF2 A 103 OK 59 58 55 70 C3' A A 104 OK 68 71 72 103 C3' UFT A 105 OK 100 104 98 112 C3' U A 106 OK 110 113 114 139 C3' CFZ A 107 OK 141 140 136 202 C3' CFZ B 209 OK 204 203 200 215 C3' G B 210 OK 213 216 217 247 C3' AF2 B 211 OK 249 248 245 260 C3' A B 212 OK 258 261 262 293 C3' UFT B 213 OK 290 294 288 302 C3' U B 214 OK 300 303 304 329 C3' CFZ B 215 OK 331 330 326 342 C3' G B 216 OK 340 343 344 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 14 C4' CFZ A 101 OK 12 16 15 23 C4' G A 102 OK 25 22 24 59 C4' AF2 A 103 OK 57 61 60 68 C4' A A 104 OK 70 67 69 100 C4' UFT A 105 OK 103 99 101 110 C4' U A 106 OK 112 109 111 141 C4' CFZ A 107 OK 139 143 142 204 C4' CFZ B 209 OK 202 206 205 213 C4' G B 210 OK 215 212 214 249 C4' AF2 B 211 OK 247 251 250 258 C4' A B 212 OK 260 257 259 290 C4' UFT B 213 OK 293 289 291 300 C4' U B 214 OK 302 299 301 331 C4' CFZ B 215 OK 329 333 332 340 C4' G B 216 OK 342 339 341 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 16 C5' CFZ A 101 17 14 22 C5' G A 102 21 23 61 C5' AF2 A 103 62 59 67 C5' A A 104 66 68 99 C5' UFT A 105 88 100 109 C5' U A 106 108 110 143 C5' CFZ A 107 144 141 206 C5' CFZ B 209 207 204 212 C5' G B 210 211 213 251 C5' AF2 B 211 252 249 257 C5' A B 212 256 258 289 C5' UFT B 213 278 290 299 C5' U B 214 298 300 333 C5' CFZ B 215 334 331 339 C5' G B 216 338 340 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 18 P G A 102 distorted distorted 13 19 20 21 42 P AF2 A 103 distorted distorted 26 56 54 62 63 P A A 104 distorted distorted 58 64 65 66 85 P UFT A 105 distorted distorted 71 86 87 88 105 P U A 106 distorted distorted 104 106 107 108 125 P CFZ A 107 distorted distorted 113 135 138 144 145 P G A 108 140 208 P G B 210 distorted distorted 203 209 210 211 232 P AF2 B 211 distorted distorted 216 246 244 252 253 P A B 212 distorted distorted 248 254 255 256 275 P UFT B 213 distorted distorted 261 276 277 278 295 P U B 214 distorted distorted 294 296 297 298 315 P CFZ B 215 distorted distorted 303 325 328 334 335 P G B 216 distorted distorted 330 336 337 338 ---------------------------------------------------------------------------------