ID code: '1TAU' 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' G T 901 beta 4 9 7 34 C1' C T 902 beta 30 35 33 55 C1' G T 903 beta 51 56 54 80 C1' A T 904 beta 76 81 79 103 C1' T T 905 beta 99 104 102 124 C1' C T 906 beta 120 125 123 145 C1' C T 907 beta 141 146 144 166 C1' G T 908 beta 162 167 165 190 C1' C P 958 beta 186 191 189 212 C1' G P 957 beta 208 213 211 237 C1' G P 956 beta 233 238 236 262 C1' A P 955 beta 258 263 261 285 C1' T P 954 beta 281 286 284 306 C1' C P 953 beta 302 307 305 327 C1' G P 952 beta 323 328 326 352 C1' C P 951 beta 348 353 351 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G T 901 8 5 33 C2' C T 902 34 31 54 C2' G T 903 55 52 79 C2' A T 904 80 77 102 C2' T T 905 103 100 123 C2' C T 906 124 121 144 C2' C T 907 145 142 165 C2' G T 908 166 163 189 C2' C P 958 190 187 211 C2' G P 957 212 209 236 C2' G P 956 237 234 261 C2' A P 955 262 259 284 C2' T P 954 285 282 305 C2' C P 953 306 303 326 C2' G P 952 327 324 351 C2' C P 951 352 349 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G T 901 OK 3 6 7 31 C3' C T 902 OK 29 32 33 52 C3' G T 903 OK 50 53 54 77 C3' A T 904 OK 75 78 79 100 C3' T T 905 OK 98 101 102 121 C3' C T 906 OK 119 122 123 142 C3' C T 907 OK 140 143 144 163 C3' G T 908 OK 161 164 165 187 C3' C P 958 OK 185 188 189 209 C3' G P 957 OK 207 210 211 234 C3' G P 956 OK 232 235 236 259 C3' A P 955 OK 257 260 261 282 C3' T P 954 OK 280 283 284 303 C3' C P 953 OK 301 304 305 324 C3' G P 952 OK 322 325 326 349 C3' C P 951 OK 347 350 351 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G T 901 OK 5 2 4 29 C4' C T 902 OK 31 28 30 50 C4' G T 903 OK 52 49 51 75 C4' A T 904 OK 77 74 76 98 C4' T T 905 OK 100 97 99 119 C4' C T 906 OK 121 118 120 140 C4' C T 907 OK 142 139 141 161 C4' G T 908 OK 163 160 162 185 C4' C P 958 OK 187 184 186 207 C4' G P 957 OK 209 206 208 232 C4' G P 956 OK 234 231 233 257 C4' A P 955 OK 259 256 258 280 C4' T P 954 OK 282 279 281 301 C4' C P 953 OK 303 300 302 322 C4' G P 952 OK 324 321 323 347 C4' C P 951 OK 349 346 348 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G T 901 1 3 28 C5' C T 902 27 29 49 C5' G T 903 48 50 74 C5' A T 904 73 75 97 C5' T T 905 96 98 118 C5' C T 906 117 119 139 C5' C T 907 138 140 160 C5' G T 908 159 161 184 C5' C P 958 183 185 206 C5' G P 957 205 207 231 C5' G P 956 230 232 256 C5' A P 955 255 257 279 C5' T P 954 278 280 300 C5' C P 953 299 301 321 C5' G P 952 320 322 346 C5' C P 951 345 347 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 24 P C T 902 distorted distorted 6 25 26 27 45 P G T 903 distorted distorted 32 46 47 48 70 P A T 904 distorted distorted 53 71 72 73 93 P T T 905 distorted distorted 78 94 95 96 114 P C T 906 distorted distorted 101 115 116 117 135 P C T 907 distorted distorted 122 136 137 138 156 P G T 908 distorted distorted 143 157 158 159 202 P G P 957 distorted distorted 188 203 204 205 227 P G P 956 distorted distorted 210 228 229 230 252 P A P 955 distorted distorted 235 253 254 255 275 P T P 954 distorted distorted 260 276 277 278 296 P C P 953 distorted distorted 283 297 298 299 317 P G P 952 distorted distorted 304 318 319 320 342 P C P 951 OK OK 325 343 344 345 ---------------------------------------------------------------------------------