ID code: '5D0B' 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' --------------------------------------------------------------------------------- 5929 C1' G F 27 beta 5924 5930 5927 5952 C1' C F 28 beta 5947 5953 5950 5972 C1' A F 29 beta 5967 5973 5970 5994 C1' G F 30 beta 5989 5995 5992 6017 C1' A F 31 beta 6012 6018 6015 6039 C1' C F 32 beta 6034 6040 6037 6059 C1' U F 33 beta 6054 6060 6057 6072 C1' 56B F 34 beta 6083 6068 6069 6111 C1' U F 35 beta 6106 6112 6109 6131 C1' A F 36 beta 6126 6132 6129 6153 C1' A F 37 beta 6148 6154 6151 6175 C1' A F 38 beta 6170 6176 6173 6197 C1' U F 39 beta 6192 6198 6195 6217 C1' C F 40 beta 6212 6218 6215 6237 C1' U F 41 beta 6232 6238 6235 6257 C1' G F 42 beta 6252 6258 6255 6280 C1' C F 43 beta 6275 6281 6278 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 5927 C2' G F 27 OK 5929 5925 5928 5950 C2' C F 28 OK 5952 5948 5951 5970 C2' A F 29 OK 5972 5968 5971 5992 C2' G F 30 OK 5994 5990 5993 6015 C2' A F 31 OK 6017 6013 6016 6037 C2' C F 32 OK 6039 6035 6038 6057 C2' U F 33 OK 6059 6055 6058 6069 C2' 56B F 34 OK 6072 6099 6070 6109 C2' U F 35 OK 6111 6107 6110 6129 C2' A F 36 OK 6131 6127 6130 6151 C2' A F 37 OK 6153 6149 6152 6173 C2' A F 38 OK 6175 6171 6174 6195 C2' U F 39 OK 6197 6193 6196 6215 C2' C F 40 OK 6217 6213 6216 6235 C2' U F 41 OK 6237 6233 6236 6255 C2' G F 42 OK 6257 6253 6256 6278 C2' C F 43 OK 6280 6276 6279 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5925 C3' G F 27 OK 5923 5926 5927 5948 C3' C F 28 OK 5946 5949 5950 5968 C3' A F 29 OK 5966 5969 5970 5990 C3' G F 30 OK 5988 5991 5992 6013 C3' A F 31 OK 6011 6014 6015 6035 C3' C F 32 OK 6033 6036 6037 6055 C3' U F 33 OK 6053 6056 6057 6099 C3' 56B F 34 OK 6097 6092 6069 6107 C3' U F 35 OK 6105 6108 6109 6127 C3' A F 36 OK 6125 6128 6129 6149 C3' A F 37 OK 6147 6150 6151 6171 C3' A F 38 OK 6169 6172 6173 6193 C3' U F 39 OK 6191 6194 6195 6213 C3' C F 40 OK 6211 6214 6215 6233 C3' U F 41 OK 6231 6234 6235 6253 C3' G F 42 OK 6251 6254 6255 6276 C3' C F 43 OK 6274 6277 6278 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 5923 C4' G F 27 OK 5925 5922 5924 5946 C4' C F 28 OK 5948 5945 5947 5966 C4' A F 29 OK 5968 5965 5967 5988 C4' G F 30 OK 5990 5987 5989 6011 C4' A F 31 OK 6013 6010 6012 6033 C4' C F 32 OK 6035 6032 6034 6053 C4' U F 33 OK 6055 6052 6054 6097 C4' 56B F 34 OK 6099 6098 6083 6105 C4' U F 35 OK 6107 6104 6106 6125 C4' A F 36 OK 6127 6124 6126 6147 C4' A F 37 OK 6149 6146 6148 6169 C4' A F 38 OK 6171 6168 6170 6191 C4' U F 39 OK 6193 6190 6192 6211 C4' C F 40 OK 6213 6210 6212 6231 C4' U F 41 OK 6233 6230 6232 6251 C4' G F 42 OK 6253 6250 6252 6274 C4' C F 43 OK 6276 6273 6275 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5922 C5' G F 27 5921 5923 5945 C5' C F 28 5944 5946 5965 C5' A F 29 5964 5966 5987 C5' G F 30 5986 5988 6010 C5' A F 31 6009 6011 6032 C5' C F 32 6031 6033 6052 C5' U F 33 6051 6053 6098 C5' 56B F 34 6085 6097 6104 C5' U F 35 6103 6105 6124 C5' A F 36 6123 6125 6146 C5' A F 37 6145 6147 6168 C5' A F 38 6167 6169 6190 C5' U F 39 6189 6191 6210 C5' C F 40 6209 6211 6230 C5' U F 41 6229 6231 6250 C5' G F 42 6249 6251 6273 C5' C F 43 6272 6274 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 5941 P C F 28 distorted distorted 5926 5942 5943 5944 5961 P A F 29 distorted distorted 5949 5962 5963 5964 5983 P G F 30 distorted distorted 5969 5984 5985 5986 6006 P A F 31 distorted distorted 5991 6007 6008 6009 6028 P C F 32 distorted distorted 6014 6029 6030 6031 6048 P U F 33 distorted distorted 6036 6049 6050 6051 6071 P 56B F 34 distorted distorted 6056 6090 6087 6085 6100 P U F 35 distorted distorted 6092 6101 6102 6103 6120 P A F 36 distorted distorted 6108 6121 6122 6123 6142 P A F 37 distorted distorted 6128 6143 6144 6145 6164 P A F 38 distorted distorted 6150 6165 6166 6167 6186 P U F 39 distorted distorted 6172 6187 6188 6189 6206 P C F 40 distorted distorted 6194 6207 6208 6209 6226 P U F 41 distorted distorted 6214 6227 6228 6229 6246 P G F 42 distorted distorted 6234 6247 6248 6249 6269 P C F 43 distorted distorted 6254 6270 6271 6272 6376 P B12 A 503 6397 P PO4 A 504 6494 P B12 B 503 6515 P PO4 B 504 ---------------------------------------------------------------------------------