ID code: '4RVE' 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' --------------------------------------------------------------------------------- 5972 C1' G D 1 beta 5968 5973 5971 5994 C1' G D 2 beta 5990 5995 5993 6016 C1' G D 3 beta 6012 6017 6015 6038 C1' A D 4 beta 6034 6039 6037 6059 C1' T D 5 beta 6055 6060 6058 6079 C1' A D 6 beta 6075 6080 6078 6100 C1' T D 7 beta 6096 6101 6099 6120 C1' C D 8 beta 6116 6121 6119 6139 C1' C D 9 beta 6135 6140 6138 6158 C1' C D 10 beta 6154 6159 6157 6175 C1' G E 1 beta 6171 6176 6174 6197 C1' G E 2 beta 6193 6198 6196 6219 C1' G E 3 beta 6215 6220 6218 6241 C1' A E 4 beta 6237 6242 6240 6262 C1' T E 5 beta 6258 6263 6261 6282 C1' A E 6 beta 6278 6283 6281 6303 C1' T E 7 beta 6299 6304 6302 6323 C1' C E 8 beta 6319 6324 6322 6342 C1' C E 9 beta 6338 6343 6341 6361 C1' C E 10 beta 6357 6362 6360 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 5971 C2' G D 1 5972 5969 5993 C2' G D 2 5994 5991 6015 C2' G D 3 6016 6013 6037 C2' A D 4 6038 6035 6058 C2' T D 5 6059 6056 6078 C2' A D 6 6079 6076 6099 C2' T D 7 6100 6097 6119 C2' C D 8 6120 6117 6138 C2' C D 9 6139 6136 6157 C2' C D 10 6158 6155 6174 C2' G E 1 6175 6172 6196 C2' G E 2 6197 6194 6218 C2' G E 3 6219 6216 6240 C2' A E 4 6241 6238 6261 C2' T E 5 6262 6259 6281 C2' A E 6 6282 6279 6302 C2' T E 7 6303 6300 6322 C2' C E 8 6323 6320 6341 C2' C E 9 6342 6339 6360 C2' C E 10 6361 6358 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5969 C3' G D 1 OK 5967 5970 5971 5991 C3' G D 2 OK 5989 5992 5993 6013 C3' G D 3 OK 6011 6014 6015 6035 C3' A D 4 OK 6033 6036 6037 6056 C3' T D 5 OK 6054 6057 6058 6076 C3' A D 6 OK 6074 6077 6078 6097 C3' T D 7 OK 6095 6098 6099 6117 C3' C D 8 OK 6115 6118 6119 6136 C3' C D 9 OK 6134 6137 6138 6155 C3' C D 10 OK 6153 6156 6157 6172 C3' G E 1 OK 6170 6173 6174 6194 C3' G E 2 OK 6192 6195 6196 6216 C3' G E 3 OK 6214 6217 6218 6238 C3' A E 4 OK 6236 6239 6240 6259 C3' T E 5 OK 6257 6260 6261 6279 C3' A E 6 OK 6277 6280 6281 6300 C3' T E 7 OK 6298 6301 6302 6320 C3' C E 8 OK 6318 6321 6322 6339 C3' C E 9 OK 6337 6340 6341 6358 C3' C E 10 OK 6356 6359 6360 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 5967 C4' G D 1 OK 5969 5966 5968 5989 C4' G D 2 OK 5991 5988 5990 6011 C4' G D 3 OK 6013 6010 6012 6033 C4' A D 4 OK 6035 6032 6034 6054 C4' T D 5 OK 6056 6053 6055 6074 C4' A D 6 OK 6076 6073 6075 6095 C4' T D 7 OK 6097 6094 6096 6115 C4' C D 8 OK 6117 6114 6116 6134 C4' C D 9 OK 6136 6133 6135 6153 C4' C D 10 OK 6155 6152 6154 6170 C4' G E 1 OK 6172 6169 6171 6192 C4' G E 2 OK 6194 6191 6193 6214 C4' G E 3 OK 6216 6213 6215 6236 C4' A E 4 OK 6238 6235 6237 6257 C4' T E 5 OK 6259 6256 6258 6277 C4' A E 6 OK 6279 6276 6278 6298 C4' T E 7 OK 6300 6297 6299 6318 C4' C E 8 OK 6320 6317 6319 6337 C4' C E 9 OK 6339 6336 6338 6356 C4' C E 10 OK 6358 6355 6357 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5966 C5' G D 1 5965 5967 5988 C5' G D 2 5987 5989 6010 C5' G D 3 6009 6011 6032 C5' A D 4 6031 6033 6053 C5' T D 5 6052 6054 6073 C5' A D 6 6072 6074 6094 C5' T D 7 6093 6095 6114 C5' C D 8 6113 6115 6133 C5' C D 9 6132 6134 6152 C5' C D 10 6151 6153 6169 C5' G E 1 6168 6170 6191 C5' G E 2 6190 6192 6213 C5' G E 3 6212 6214 6235 C5' A E 4 6234 6236 6256 C5' T E 5 6255 6257 6276 C5' A E 6 6275 6277 6297 C5' T E 7 6296 6298 6317 C5' C E 8 6316 6318 6336 C5' C E 9 6335 6337 6355 C5' C E 10 6354 6356 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 5984 P G D 2 distorted distorted 5970 5985 5986 5987 6006 P G D 3 distorted distorted 5992 6007 6008 6009 6028 P A D 4 distorted distorted 6014 6029 6030 6031 6049 P T D 5 distorted distorted 6036 6050 6051 6052 6069 P A D 6 distorted distorted 6057 6070 6071 6072 6090 P T D 7 distorted distorted 6077 6091 6092 6093 6110 P C D 8 distorted distorted 6098 6111 6112 6113 6129 P C D 9 distorted distorted 6118 6130 6131 6132 6148 P C D 10 distorted distorted 6137 6149 6150 6151 6187 P G E 2 distorted distorted 6173 6188 6189 6190 6209 P G E 3 distorted distorted 6195 6210 6211 6212 6231 P A E 4 distorted distorted 6217 6232 6233 6234 6252 P T E 5 distorted distorted 6239 6253 6254 6255 6272 P A E 6 distorted distorted 6260 6273 6274 6275 6293 P T E 7 distorted distorted 6280 6294 6295 6296 6313 P C E 8 distorted distorted 6301 6314 6315 6316 6332 P C E 9 distorted distorted 6321 6333 6334 6335 6351 P C E 10 distorted distorted 6340 6352 6353 6354 ---------------------------------------------------------------------------------