Contacts of the helix formed by residues 166 - 194 (chain A) in PDB entry 2GER
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 LEU 166 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A VAL* 3.3 30.3 - - + -
163A GLU* 2.9 6.7 + - + +
165A ASP* 1.3 94.0 + - - +
167A ILE* 1.3 57.4 + - - +
169A ALA* 2.9 24.6 + - + +
170A VAL* 2.8 23.8 + - + +
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Residues in contact with ILE 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A ARG* 3.9 39.4 + - + +
120A CYS 5.2 1.1 - - - +
121A MET* 3.8 27.6 - - + -
134A VAL* 3.8 24.0 - - + -
135A TYR* 4.5 1.6 - - - -
136A ALA* 3.9 21.3 - - + +
162A VAL* 4.5 4.9 - - + +
163A GLU 4.6 1.1 - - - +
164A GLU* 2.7 40.5 + - - +
166A LEU* 1.3 70.0 - - - +
168A ASP* 1.3 56.6 + - - +
170A VAL* 3.6 8.1 - - + -
171A THR* 2.7 24.8 + - + +
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Residues in contact with ASP 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A ARG* 3.1 22.7 + - - -
164A GLU 4.1 0.4 + - - -
165A ASP* 3.5 9.2 + - - +
166A LEU 3.0 1.8 + - - -
167A ILE* 1.3 75.5 - - - +
169A ALA* 1.3 64.3 + - - +
171A THR* 2.5 18.8 + - - -
172A GLY 3.6 3.1 + - - -
262A CYS* 3.5 17.2 - - - +
265A THR* 3.0 26.4 - - + +
266A ARG* 3.2 34.1 + - + +
269A GLN* 3.1 27.8 + - - +
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Residues in contact with ALA 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A ASP 4.5 0.8 + - - +
166A LEU* 2.9 15.3 + - + +
168A ASP* 1.3 77.2 - - - +
170A VAL* 1.3 58.5 + - + +
172A GLY* 2.6 30.7 + - - -
173A LEU* 3.2 5.5 + - - +
258A VAL* 5.5 3.9 - - + +
262A CYS* 3.6 18.2 - - - +
266A ARG* 4.8 6.0 - - - +
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Residues in contact with VAL 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A MET* 4.8 4.5 - - + -
134A VAL* 4.2 28.5 - - + -
162A VAL* 4.9 7.0 - - + -
166A LEU* 2.8 33.0 - - + +
167A ILE* 3.6 12.1 - - + +
169A ALA* 1.3 76.2 - - + +
171A THR* 1.3 62.9 + - - +
172A GLY 3.1 0.9 + - - -
173A LEU* 3.1 16.9 + - + +
174A SER* 3.1 33.8 + - - +
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Residues in contact with THR 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A ALA* 5.0 7.9 - - + -
98A GLY 5.3 2.9 - - - +
119A ARG* 5.6 0.4 - - - +
121A MET* 2.9 53.6 - - + -
167A ILE* 2.7 14.9 + - + +
168A ASP* 2.5 27.2 + - - -
170A VAL* 1.3 77.4 - - - +
172A GLY* 1.3 63.4 + - - +
175A GLY* 3.1 6.4 + - - +
176A SER* 3.1 23.0 + - - -
261A SER* 3.8 2.4 + - - -
265A THR* 4.0 18.3 + - - +
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Residues in contact with GLY 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A ASP 3.6 1.6 + - - -
169A ALA 2.6 17.9 + - - -
171A THR* 1.3 77.7 + - - +
173A LEU* 1.3 66.3 + - - +
176A SER* 3.4 4.0 - - - -
180A TYR* 3.3 20.3 + - - -
258A VAL* 4.0 13.2 - - - -
261A SER* 3.2 24.7 - - - -
262A CYS* 4.0 4.2 - - - +
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Residues in contact with LEU 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A ALA 3.2 7.1 + - - +
170A VAL* 3.1 10.9 + - + +
172A GLY* 1.3 83.0 - - - +
174A SER* 1.3 59.1 + - - +
175A GLY 2.9 2.5 + - - -
177A GLY* 2.7 28.1 + - - -
180A TYR* 5.3 1.1 - - + -
258A VAL* 3.2 30.9 - - + +
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Residues in contact with SER 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A MET* 5.1 4.5 + - - +
123A ASN* 2.9 25.7 - - - +
132A ALA* 3.7 32.6 + - - -
170A VAL* 3.1 25.4 + - - +
171A THR* 5.0 0.3 - - - -
173A LEU* 1.3 81.9 - - - +
175A GLY* 1.3 64.3 + - - +
177A GLY* 4.7 1.1 - - - +
178A PRO* 3.2 8.3 - - - +
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Residues in contact with GLY 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A MET* 4.3 15.5 - - - -
122A THR 4.6 1.9 - - - +
123A ASN* 3.7 14.5 - - - +
170A VAL 3.4 1.2 + - - -
171A THR* 3.1 20.4 + - - -
173A LEU 2.9 3.4 + - - -
174A SER* 1.3 82.6 + - - +
176A SER* 1.3 58.9 + - - +
178A PRO* 3.5 9.2 - - - +
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Residues in contact with SER 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A THR 3.1 4.8 + - - -
172A GLY 3.4 3.8 - - - -
173A LEU 3.2 0.4 + - - -
175A GLY* 1.3 72.7 - - - +
177A GLY* 1.3 55.8 + - - +
178A PRO* 3.0 3.9 - - - +
179A ALA* 2.4 42.8 + - - +
180A TYR* 3.2 33.9 + - - -
261A SER* 2.9 19.6 + - - -
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Residues in contact with GLY 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A GLY 3.9 0.8 + - - -
173A LEU 2.7 23.3 + - - -
174A SER* 4.8 0.9 - - - -
176A SER* 1.3 70.8 - - - +
178A PRO* 1.3 69.6 - - - +
180A TYR* 2.8 30.9 + - - +
181A ALA* 2.9 12.7 + - - +
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Residues in contact with PRO 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A ASN* 3.4 32.1 - - + +
124A THR* 4.0 8.3 - - - +
125A PRO* 3.5 21.8 - - + -
174A SER 3.2 16.8 - - - +
175A GLY 3.5 4.9 - - - +
176A SER 2.8 6.3 - - - +
177A GLY* 1.3 87.6 - - - +
179A ALA* 1.3 55.5 + - - +
181A ALA* 3.0 23.0 - - + +
182A PHE* 3.1 27.8 + - + -
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Residues in contact with ALA 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A SER* 2.4 30.8 + - - +
178A PRO* 1.3 67.8 - - - +
180A TYR* 1.3 67.6 + - + +
181A ALA 3.0 1.8 - - - -
182A PHE* 3.8 14.4 - - + +
183A THR* 3.2 24.4 + - - -
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Residues in contact with TYR 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A GLY 3.3 10.7 + - - -
173A LEU* 4.9 1.1 - - - -
176A SER* 3.2 37.7 - - - -
177A GLY* 2.8 21.5 + - - +
179A ALA* 1.3 76.3 - - + +
181A ALA* 1.3 57.5 + - - +
183A THR* 3.3 8.0 + - - -
184A ALA* 3.0 26.2 + - - +
254A LEU* 4.7 23.7 - - + +
257A ALA* 2.8 49.0 + - + -
258A VAL* 4.3 10.5 - - + -
261A SER* 3.2 10.2 - - - -
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Residues in contact with ALA 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A GLY 2.9 9.5 + - - +
178A PRO* 3.0 15.0 - - + +
180A TYR* 1.3 76.2 - - - +
182A PHE* 1.3 66.5 + - + +
184A ALA* 2.8 24.7 + - - +
185A LEU* 2.9 20.0 + - + +
210A LEU* 4.7 15.0 - - + -
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Residues in contact with PHE 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A THR* 5.1 8.1 - - - -
125A PRO* 5.9 2.2 - - + -
178A PRO* 3.1 31.6 + - + -
179A ALA* 3.4 14.1 + - + +
181A ALA* 1.3 79.3 - - + +
183A THR* 1.3 61.9 + - - +
185A LEU* 4.1 8.4 - - + +
186A ASP* 3.1 25.1 + - - +
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Residues in contact with THR 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A ALA 3.2 10.7 + - - -
180A TYR* 3.7 9.6 - - - -
181A ALA 3.0 0.8 - - - -
182A PHE* 1.3 76.7 - - - +
184A ALA* 1.3 71.4 + - - +
185A LEU 3.2 0.2 + - - -
186A ASP* 3.4 4.9 + - - +
187A ALA* 3.1 22.3 + - + +
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Residues in contact with ALA 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A TYR 3.0 13.9 + - - +
181A ALA* 2.8 14.8 + - - +
183A THR* 1.3 76.2 - - - +
185A LEU* 1.3 64.6 + - + +
187A ALA* 2.9 27.4 - - - +
188A LEU* 2.9 18.3 + - + +
210A LEU* 5.0 5.4 - - + -
250A PHE* 6.5 0.9 - - + -
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Residues in contact with LEU 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A ALA* 2.9 15.8 + - + +
182A PHE* 4.1 8.1 - - + +
184A ALA* 1.3 77.7 - - + +
186A ASP* 1.3 68.1 + - - +
187A ALA 2.8 2.4 + - - -
188A LEU* 2.9 25.5 + - + -
189A ALA* 2.6 27.9 + - - +
203A VAL* 5.0 10.3 - - + +
206A GLY* 4.0 5.8 - - - +
207A ALA* 3.6 34.3 - - + +
210A LEU* 3.5 33.7 - - + -
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Residues in contact with ASP 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A PHE 3.1 17.5 + - - +
183A THR* 3.8 5.6 - - - +
185A LEU* 1.3 77.8 - - - +
187A ALA* 1.3 67.2 + - - +
189A ALA* 3.5 4.9 - - - +
190A ASP* 3.1 29.3 + - - +
199A ARG* 3.2 21.3 + - - +
225E GLY* 5.7 5.0 - - - -
228E LYS* 5.2 3.6 + - - +
229E ASP* 5.0 1.6 - - - +
251E ARG* 4.7 13.0 + - - -
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Residues in contact with ALA 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A THR* 3.1 13.6 + - + +
184A ALA* 2.9 17.3 - - - +
185A LEU 2.8 0.6 + - - -
186A ASP* 1.3 78.4 + - - +
188A LEU* 1.3 52.5 + - + +
190A ASP* 2.5 34.0 + - - +
191A GLY* 2.9 10.4 + - - -
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Residues in contact with LEU 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A ALA* 2.9 15.5 + - + +
185A LEU* 2.9 38.6 + - + +
187A ALA* 1.3 72.5 - - + +
189A ALA* 1.3 53.6 + - - +
191A GLY* 3.4 2.8 - - - +
192A GLY* 2.5 36.2 + - - -
202A ALA* 4.7 1.3 - - - +
206A GLY* 4.8 18.2 - - - +
210A LEU* 5.3 5.6 - - + -
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Residues in contact with ALA 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A LEU 2.6 20.2 + - - +
186A ASP* 3.5 4.0 - - - +
188A LEU* 1.3 70.6 - - - +
190A ASP* 1.3 52.2 + - - +
192A GLY 3.1 0.7 + - - -
193A VAL* 2.7 39.0 + - - +
199A ARG* 3.0 28.3 - - - +
202A ALA* 3.4 14.5 + - + +
203A VAL* 3.5 31.1 - - + +
206A GLY* 6.0 0.2 - - - -
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Residues in contact with ASP 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A ASP* 3.1 17.2 + - - +
187A ALA* 2.5 18.5 + - - +
189A ALA* 1.3 72.6 - - - +
191A GLY* 1.3 49.9 - - - +
193A VAL* 3.1 3.7 + - - -
194A LYS* 2.6 32.8 + - - +
199A ARG* 2.3 44.7 + - - +
228E LYS* 3.7 28.0 + - - +
229E ASP* 4.2 3.1 - - - +
239E ILE* 3.0 20.1 - - + +
242E LEU* 5.4 1.9 - - - +
246E GLU* 5.2 1.9 - - - +
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Residues in contact with GLY 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A ALA 2.9 10.2 + - - -
188A LEU* 3.4 4.5 - - - -
190A ASP* 1.3 73.1 - - - +
192A GLY* 1.3 68.9 + - - +
194A LYS* 3.3 14.9 + - - +
195A MET* 3.3 17.7 - - - +
243E HIS* 6.1 3.6 - - - -
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Residues in contact with GLY 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A LEU 2.5 21.7 + - - -
189A ALA 3.4 1.6 - - - -
191A GLY* 1.3 79.1 - - - +
193A VAL* 1.3 60.8 + - - +
195A MET* 2.9 19.3 + - - +
197A LEU* 3.7 24.2 - - - +
202A ALA* 4.0 9.6 - - - -
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Residues in contact with VAL 193 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A ALA 2.7 22.8 + - - +
190A ASP 3.3 6.1 - - - +
192A GLY* 1.3 66.2 - - - +
194A LYS* 1.3 54.4 + - - +
195A MET 2.7 9.6 + - - -
196A GLY 3.1 1.7 + - - -
197A LEU 3.1 17.0 - - - +
198A PRO 3.9 10.5 - - - +
199A ARG* 3.8 32.3 - - - +
202A ALA* 4.0 1.2 - - + +
232E SER* 5.1 4.7 - - - +
233E SER 4.3 2.0 - - - -
234E PRO* 2.5 57.9 - - + +
239E ILE* 3.2 16.6 - - + -
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Residues in contact with LYS 194 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A ASP 2.6 19.3 + - - +
191A GLY* 3.9 10.8 - - - +
192A GLY 3.1 1.4 + - - -
193A VAL* 1.3 71.6 - - - +
195A MET* 1.3 79.0 + - - +
234E PRO 4.4 1.8 - - - -
235E GLY 4.9 4.5 - - - +
239E ILE* 3.3 38.6 - - + +
240E HIS* 3.7 38.4 + - + +
243E HIS* 3.4 45.0 + - + +
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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