Contacts of the helix formed by residues 164 - 197 (chain C) in PDB entry 1O9I
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 164 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C ASP* 2.8 25.3 + - - +
16C ARG* 3.0 53.0 + - + +
18C ASP* 6.1 0.6 - - + +
80C LEU* 5.2 0.4 - - + +
162C THR* 2.9 16.0 + - - +
163C GLU* 1.3 74.9 - - - +
165C GLU* 1.3 59.1 + - - +
166C GLY 2.8 21.5 + - - -
167C VAL* 3.0 22.1 + - + +
168C ARG* 2.8 31.1 + - - +
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Residues in contact with GLU 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C ASP* 3.7 14.0 + - - +
16C ARG* 5.0 0.6 - - - +
159C TYR* 5.2 0.9 + - - -
163C GLU* 3.2 11.7 + - - +
164C ASP* 1.3 74.9 + - - +
166C GLY* 1.3 57.9 + - - +
168C ARG* 3.4 42.7 + - - +
169C ASP* 2.8 29.1 + - - +
172C LYS* 4.8 10.7 + - - -
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Residues in contact with GLY 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C ASN* 5.5 1.9 - - - +
13C LYS 3.5 24.9 + - - +
15C ASP* 3.4 17.3 + - - -
76C MET* 4.1 0.9 - - - +
164C ASP* 2.8 9.0 + - - -
165C GLU* 1.3 72.9 - - - +
167C VAL* 1.3 67.6 + - - +
169C ASP* 3.3 13.6 + - - +
170C MET* 3.3 12.3 + - - +
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Residues in contact with VAL 167 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C PRO* 3.7 18.4 - - + +
21C MET* 4.0 18.2 - - + -
25C LEU* 4.6 11.7 - - + -
76C MET* 3.9 16.6 - - + -
80C LEU* 4.2 11.9 - - + -
162C THR* 3.9 20.9 - - + +
164C ASP* 3.0 34.2 + - + +
166C GLY* 1.3 75.5 - - - +
168C ARG* 1.3 63.4 + - - +
170C MET* 3.2 6.2 + - + +
171C LEU* 3.0 35.2 + - + +
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Residues in contact with ARG 168 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159C TYR* 2.9 70.3 + - + +
160C SER* 4.5 5.3 + - - +
162C THR* 3.1 27.2 + - + -
163C GLU* 4.2 16.6 + - - +
164C ASP 2.8 18.4 + - - +
165C GLU* 3.4 37.8 + - - +
167C VAL* 1.3 78.4 - - - +
169C ASP* 1.3 56.2 + - - +
171C LEU* 3.2 7.8 + - + +
172C LYS* 2.8 38.2 + - - +
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Residues in contact with ASP 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B HIS* 2.8 26.9 + - - -
10C TYR* 2.6 29.3 + - - -
11C ASN* 3.1 33.1 + - - +
165C GLU* 2.8 19.1 + - - +
166C GLY* 3.5 9.2 - - - +
167C VAL 3.2 0.4 - - - -
168C ARG* 1.3 75.9 - - - +
170C MET* 1.3 61.9 + - - +
172C LYS* 3.3 4.6 + - - -
173C PHE 3.2 17.0 + - - -
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Residues in contact with MET 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C TYR* 4.4 4.7 - - - -
11C ASN* 3.4 23.5 + - - +
12C ALA* 3.8 17.9 - - - -
25C LEU* 4.6 6.1 - - + -
72C MET* 3.7 22.2 - - + +
73C ILE* 3.6 28.9 - - + -
76C MET* 3.7 41.3 - - + -
166C GLY 3.3 3.3 + - - +
167C VAL* 3.2 8.6 + - + +
169C ASP* 1.3 79.5 + - - +
171C LEU* 1.3 76.9 + - + +
173C PHE* 3.1 5.4 + - - +
174C LEU* 3.0 30.2 + - + +
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Residues in contact with LEU 171 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C MET* 4.7 0.9 - - + -
25C LEU* 4.5 11.4 - - + -
73C ILE* 5.9 0.2 - - + -
155C VAL* 3.6 22.0 - - + +
158C LEU* 3.9 20.4 - - + +
159C TYR* 3.7 41.1 - - + +
162C THR* 4.7 1.8 - - + -
167C VAL* 3.0 34.0 + - + +
168C ARG* 3.7 10.8 - - - +
170C MET* 1.3 93.9 - - + +
172C LYS* 1.3 56.9 + - - +
174C LEU* 3.2 9.5 + - + +
175C LEU* 2.8 35.0 + - + +
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Residues in contact with LYS 172 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207B ILE* 3.2 32.9 + - + +
208B GLU* 3.7 1.7 - - - -
209B HIS* 3.1 53.3 + - + +
159C TYR* 3.7 35.0 + - + -
165C GLU* 4.8 8.7 + - - -
168C ARG* 2.8 28.6 + - - +
169C ASP* 4.7 1.8 - - - -
170C MET 3.2 0.2 - - - -
171C LEU* 1.3 72.5 - - - +
173C PHE* 1.3 60.7 + - - +
175C LEU* 3.6 7.8 + - - -
176C ALA* 3.3 12.3 + - - +
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Residues in contact with PHE 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209B HIS* 3.5 8.9 - - + -
212B PHE* 3.6 36.6 - + - -
217B MET* 5.1 1.1 - - + -
248B MET* 4.1 9.2 - - + -
9C GLN* 3.6 37.9 - - + -
10C TYR* 3.5 57.0 - + + -
69C HIS* 4.2 4.7 - - - -
72C MET* 4.1 12.8 - - + -
169C ASP 3.2 4.4 + - - -
170C MET 3.1 8.1 + - - +
172C LYS* 1.3 73.9 - - - +
174C LEU* 1.3 64.7 + - + +
176C ALA* 3.1 4.9 + - - +
177C ARG* 2.9 50.0 + - + +
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Residues in contact with LEU 174 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C SER* 6.2 0.4 - - - -
35C GLU* 4.4 7.6 - - - +
69C HIS* 3.8 44.4 - - + +
72C MET* 4.4 5.6 - - + -
73C ILE* 3.9 28.5 - - + -
155C VAL* 4.4 11.9 - - + -
170C MET* 3.0 32.7 + - + +
171C LEU* 3.6 15.5 - - + +
173C PHE* 1.3 84.0 - - + +
175C LEU* 1.3 62.8 + - - +
177C ARG* 3.3 2.5 + - - +
178C GLU* 2.9 42.2 + - + +
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Residues in contact with LEU 175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204B MET* 3.8 25.8 - - + -
207B ILE* 3.9 17.5 - - + -
208B GLU* 3.6 20.0 - - + +
152C ARG* 2.9 41.1 + - + +
155C VAL* 3.6 21.0 - - + +
156C SER* 3.3 27.4 - - - +
159C TYR* 5.0 4.3 - - + -
171C LEU 2.8 24.2 + - - +
172C LYS* 3.7 8.3 - - + +
173C PHE 3.2 0.2 - - - -
174C LEU* 1.3 73.0 - - - +
176C ALA* 1.3 58.4 + - - +
178C GLU* 3.4 4.4 + - - -
179C THR* 3.0 16.1 + - - -
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Residues in contact with ALA 176 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208B GLU* 3.6 11.6 + - + -
209B HIS* 3.0 32.8 - - + +
212B PHE* 4.0 9.2 - - + -
213B SER* 3.4 21.8 - - - +
172C LYS 3.3 8.4 + - - +
173C PHE 3.1 9.4 + - - +
175C LEU* 1.3 78.3 - - - +
177C ARG* 1.3 66.3 + - - +
179C THR* 3.2 4.7 + - - -
180C GLN 3.1 17.5 + - - -
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Residues in contact with ARG 177 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212B PHE* 2.8 39.4 + - - -
215B VAL* 2.7 29.7 + - - +
217B MET* 3.5 30.5 - - - +
65C GLU* 2.8 42.1 + - - +
69C HIS* 4.1 14.1 - - + -
173C PHE* 2.9 50.2 + - + +
174C LEU* 3.9 4.0 - - - +
176C ALA* 1.3 77.3 - - - +
178C GLU* 1.3 58.0 + - + +
180C GLN* 3.3 13.0 + - - +
181C HIS* 2.8 47.4 + - + -
184C GLN* 5.4 0.4 + - - -
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Residues in contact with GLU 178 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C GLU* 4.1 15.4 - - - +
69C HIS* 6.2 2.2 - - + +
147C ARG* 5.6 1.3 - - - +
148C GLU* 3.4 27.4 - - - +
151C ALA* 3.9 11.9 - - + +
152C ARG* 3.1 50.6 - - + +
155C VAL* 3.6 26.3 - - - +
174C LEU* 2.9 29.6 + - + +
175C LEU* 3.9 0.2 - - - -
177C ARG* 1.3 74.7 - - + +
179C THR* 1.3 61.0 + - - +
181C HIS* 4.0 1.0 - - - +
182C GLN* 2.9 33.1 + - - +
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Residues in contact with THR 179 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199B ILE* 3.7 21.4 - - + +
205B LYS* 6.3 0.4 - - - +
208B GLU* 2.8 28.0 + - - +
213B SER* 3.6 20.9 - - - +
214B HIS* 4.4 6.1 - - + -
152C ARG* 3.1 18.5 + - - +
175C LEU 3.0 7.2 + - - -
176C ALA 3.3 9.0 - - - -
178C GLU* 1.3 77.4 - - - +
180C GLN* 1.3 64.1 + - - +
182C GLN* 3.2 3.0 + - - +
183C LEU* 2.9 38.7 + - + +
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Residues in contact with GLN 180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213B SER 3.2 14.9 + - - +
214B HIS* 2.9 28.6 - - - +
215B VAL 3.3 20.6 - - - +
216B LEU* 3.6 16.6 - - - +
239B PHE* 3.4 25.6 - - - -
176C ALA 3.1 5.3 + - - +
177C ARG* 3.5 28.7 - - - +
179C THR* 1.3 78.5 - - - +
181C HIS* 1.3 60.6 + - + +
183C LEU* 3.2 3.8 + - - +
184C GLN* 2.8 54.9 + - - +
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Residues in contact with HIS 181 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C THR* 3.6 14.4 + - + +
65C GLU* 2.9 36.2 + - - -
66C GLU* 3.2 29.3 + - - -
69C HIS* 4.4 7.4 - + - -
148C GLU* 3.3 28.7 + - + +
177C ARG* 2.8 27.6 + - + +
178C GLU* 5.3 1.0 - - - +
180C GLN* 1.3 80.7 - - + +
182C GLN* 1.3 65.2 - - - +
184C GLN* 3.3 25.5 - - - +
185C PHE* 3.0 35.7 + - + -
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Residues in contact with GLN 182 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142B ARG* 3.3 13.3 + - - +
198B ILE 3.9 0.7 - - - +
199B ILE* 3.6 13.4 - - + -
200B VAL 3.1 43.6 + - - -
145C VAL* 4.0 6.7 - - + +
148C GLU* 3.3 37.1 + - + +
149C SER* 3.5 16.1 - - - +
152C ARG* 3.6 12.9 - - - +
178C GLU 2.9 16.5 + - - +
179C THR* 3.6 4.3 - - - +
181C HIS* 1.3 76.7 - - - +
183C LEU* 1.3 58.7 + - - +
185C PHE* 3.8 2.5 - - - -
186C MET* 2.9 42.2 + - + +
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Residues in contact with LEU 183 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198B ILE* 4.8 1.6 - - + -
199B ILE* 3.6 20.0 - - + -
213B SER 4.5 2.5 - - - +
214B HIS* 3.4 35.7 - - + +
233B ALA* 4.0 3.0 - - + +
234B LYS* 4.0 30.6 + - + +
235B ASP* 3.7 17.9 - - + +
239B PHE* 3.7 16.6 - - + -
179C THR* 2.9 32.0 + - + +
180C GLN 3.8 2.9 - - - +
182C GLN* 1.3 77.7 - - - +
184C GLN* 1.3 62.2 + - - +
186C MET* 3.3 9.6 + - - +
187C LYS* 2.9 23.7 + - - +
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Residues in contact with GLN 184 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216B LEU* 4.2 11.3 - - + +
228B PHE* 3.7 7.2 - - + -
239B PHE* 3.7 11.8 - - + -
58C LEU* 3.6 29.2 - - + +
62C THR* 2.7 29.7 + - - -
177C ARG* 5.4 0.3 + - - -
180C GLN* 2.8 45.1 + - - +
181C HIS* 3.3 29.2 - - - +
183C LEU* 1.3 73.3 - - - +
185C PHE* 1.3 77.5 + - + +
187C LYS* 3.3 4.3 + - - +
188C ALA* 3.0 26.7 + - - +
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Residues in contact with PHE 185 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C PHE* 3.6 37.5 - + - -
58C LEU* 3.9 15.5 - - + -
59C LEU* 4.1 17.0 - - + -
62C THR* 3.9 17.5 - - + -
141C MET* 3.5 26.2 - - - +
144C ASN* 3.6 20.4 - - + -
145C VAL* 3.6 17.6 - - + +
148C GLU* 4.0 7.4 - - + -
181C HIS* 3.0 24.9 + - + +
184C GLN* 1.3 100.1 - - + +
186C MET* 1.3 60.3 + - - +
188C ALA* 3.7 3.1 - - - +
189C GLN* 2.8 31.0 + - - +
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Residues in contact with MET 186 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B ARG* 3.4 25.4 - - - +
198B ILE* 3.4 43.3 - - + +
199B ILE* 4.9 0.2 - - + -
234B LYS* 4.1 20.6 - - + +
145C VAL* 3.8 18.6 - - + -
182C GLN* 2.9 36.8 + - + +
183C LEU* 3.3 12.8 + - + +
185C PHE* 1.3 77.9 - - - +
187C LYS* 1.3 56.9 + - - +
189C GLN* 3.4 8.9 + - - +
190C GLU* 2.9 44.2 + - - +
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Residues in contact with LYS 187 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228B PHE* 3.7 24.2 - - + -
231B GLN* 3.9 20.5 - - - +
232B VAL* 3.1 32.9 + - - +
233B ALA* 4.7 4.0 - - - +
234B LYS 5.5 0.9 - - - +
239B PHE* 4.2 10.3 - - + -
183C LEU 2.9 13.5 + - - +
184C GLN 3.6 7.2 - - - +
185C PHE 3.3 0.2 - - - -
186C MET* 1.3 76.5 - - - +
188C ALA* 1.3 63.2 + - - +
190C GLU* 3.2 15.9 + - + +
191C GLU* 3.0 42.4 + - + +
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Residues in contact with ALA 188 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228B PHE* 4.1 6.7 - - + -
55C TYR* 3.7 33.8 + - + -
58C LEU* 4.4 2.0 - - + -
141C MET* 3.9 22.9 - - + -
184C GLN 3.0 16.9 + - - +
185C PHE 3.7 4.3 - - - +
187C LYS* 1.3 76.5 - - - +
189C GLN* 1.3 64.6 + - - +
191C GLU* 3.2 2.6 + - - +
192C LEU* 2.9 29.7 + - - +
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Residues in contact with GLN 189 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145B VAL* 6.1 0.4 - - - +
189B GLN* 5.7 4.9 - - - +
138C VAL* 4.6 4.0 - - - +
141C MET* 4.0 15.1 - - + +
142C ARG* 3.5 34.3 - - + +
145C VAL* 3.7 22.5 - - - +
185C PHE 2.8 19.9 + - - +
186C MET* 3.5 9.1 - - - +
188C ALA* 1.3 73.3 - - - +
190C GLU* 1.3 60.3 + - - +
192C LEU* 3.3 5.9 + - - +
193C GLU* 2.9 60.9 + - + +
234C LYS* 5.5 3.8 - - - +
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Residues in contact with GLU 190 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234B LYS* 2.9 48.5 + - - +
186C MET* 2.9 25.3 + - - +
187C LYS* 3.2 17.0 + - + +
189C GLN* 1.3 80.6 - - + +
191C GLU* 1.3 65.1 - - + +
193C GLU* 3.3 17.4 + - - +
194C GLU* 2.9 38.4 + - + +
234C LYS* 5.9 2.9 - - - +
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Residues in contact with GLU 191 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231B GLN* 2.9 31.0 + - - +
54C LYS* 2.8 24.1 + - - +
55C TYR* 2.7 38.6 + - - +
187C LYS* 3.0 32.1 + - + +
188C ALA* 3.7 1.4 - - - +
190C GLU* 1.3 75.8 - - + +
192C LEU* 1.3 62.0 + - - +
194C GLU* 3.3 19.4 + - - +
195C LYS* 3.1 21.3 + - - +
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Residues in contact with LEU 192 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C TYR* 3.7 33.2 - - + -
137C LEU* 3.5 32.8 - - + +
138C VAL* 3.9 15.9 - - + -
141C MET* 3.8 15.3 - - + -
188C ALA 2.9 22.4 + - - +
189C GLN* 3.7 3.8 - - - +
191C GLU* 1.3 77.4 - - - +
193C GLU* 1.3 55.3 + - - +
195C LYS* 3.1 3.7 + - + +
196C TYR* 2.9 47.1 + - + +
264D HIS 4.7 1.6 - - - +
265D GLN* 4.1 4.0 - - - -
266D GLY* 3.7 26.9 - - - +
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Residues in contact with GLU 193 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B MET* 5.6 0.3 - - - +
138C VAL* 3.9 11.9 - - + -
142C ARG* 2.7 31.0 + - - +
189C GLN* 2.9 45.1 + - - +
190C GLU* 3.6 23.8 - - - +
192C LEU* 1.3 75.2 - - - +
194C GLU* 1.3 61.2 + - + +
197C GLY* 2.8 42.3 + - - +
198C ILE* 3.5 25.5 + - + +
234C LYS* 4.6 6.9 + - - -
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Residues in contact with GLU 194 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190C GLU* 2.9 28.2 + - - +
191C GLU* 3.5 20.4 - - - +
192C LEU 3.2 0.2 - - - -
193C GLU* 1.3 79.7 - - + +
195C LYS* 1.3 59.8 + - - +
197C GLY 4.8 0.5 + - - -
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Residues in contact with LYS 195 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191C GLU 3.1 12.6 + - - +
192C LEU* 3.1 8.3 + - + +
194C GLU* 1.3 78.7 - - - +
196C TYR* 1.3 100.5 + - + +
266D GLY* 3.7 21.5 + - - +
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Residues in contact with TYR 196 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138C VAL* 3.9 15.7 - - + -
192C LEU* 2.9 31.8 + - + +
195C LYS* 1.3 111.7 - - + +
197C GLY* 1.3 59.9 + - - +
202C GLY* 3.2 27.8 - - - +
264D HIS* 3.5 55.4 - + + +
265D GLN 3.6 3.1 + - - -
266D GLY* 2.9 39.1 + - - -
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Residues in contact with GLY 197 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138C VAL* 4.3 7.8 - - - +
193C GLU* 2.8 37.0 + - - +
194C GLU 4.7 0.4 - - - -
195C LYS 3.8 0.6 - - - -
196C TYR* 1.3 76.2 - - - +
198C ILE* 1.3 64.6 + - - -
199C ILE 3.3 10.3 + - - +
202C GLY* 4.5 2.7 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il