Contacts of the helix formed by residues 158 - 183 (chain A) in PDB entry 3VJR
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 PRO 158 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ARG* 3.5 17.5 - - - +
156A LYS 3.5 3.8 - - - +
157A PRO* 1.3 83.3 - - + +
159A VAL* 1.3 66.8 + - - +
160A SER* 4.5 8.5 - - - +
161A GLU* 2.9 39.1 + - + +
162A GLN* 2.9 9.9 + - - -
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Residues in contact with VAL 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A PRO 3.7 1.2 + - - -
158A PRO* 1.3 70.7 - - - +
160A SER* 1.3 58.4 + - - +
162A GLN* 3.1 16.3 + - - +
163A LYS* 2.9 60.7 + - + +
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Residues in contact with SER 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A PRO* 3.2 8.6 + - - +
159A VAL* 1.3 80.1 - - - +
161A GLU* 1.3 70.4 + - - +
163A LYS* 3.7 7.4 + - - +
164A LEU* 3.3 28.6 + - - +
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Residues in contact with GLU 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ARG* 2.8 31.4 + - - -
103A PRO* 3.8 29.8 - - + +
140A ILE 4.4 2.9 - - - +
152A PHE* 4.7 2.4 - - - -
157A PRO* 4.2 6.7 - - + -
158A PRO* 2.9 34.3 + - + +
160A SER* 1.3 74.8 + - - +
162A GLN* 1.3 66.4 + - - +
164A LEU* 3.2 7.8 + - + +
165A ILE* 2.9 29.9 + - + +
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Residues in contact with GLN 162 (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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29A TRP* 4.3 15.7 - - + -
157A PRO* 4.0 16.3 - - + +
158A PRO 2.9 11.9 + - - +
159A VAL* 3.5 25.4 - - - +
161A GLU* 1.3 78.1 - - - +
163A LYS* 1.3 72.1 + - - +
165A ILE* 3.2 12.2 + - - +
166A ASP* 2.7 56.2 + - - +
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Residues in contact with LYS 163 (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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159A VAL* 2.9 40.7 + - + +
160A SER* 4.0 7.0 - - - +
161A GLU 3.3 0.2 - - - -
162A GLN* 1.3 90.9 - - - +
164A LEU* 1.3 58.6 + - + +
166A ASP* 3.3 3.8 + - - +
167A GLU* 2.9 37.8 + - - +
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Residues in contact with LEU 164 (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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103A PRO* 3.7 19.7 - - + +
104A GLY* 3.2 27.0 - - - +
160A SER* 3.3 20.6 - - - +
161A GLU* 3.2 7.5 + - + +
163A LYS* 1.3 75.0 - - + +
165A ILE* 1.3 60.4 + - - +
167A GLU* 3.2 12.3 + - - +
168A ALA 2.9 24.8 + - - -
196A ALA* 3.9 12.8 - - + +
197A GLN* 3.6 39.9 - - - +
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Residues in contact with ILE 165 (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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23A ARG* 5.2 3.6 - - + +
26A ALA* 4.7 6.5 - - + -
29A TRP* 3.9 17.5 - - + -
103A PRO* 4.1 8.1 - - + -
104A GLY 4.2 4.7 - - - +
138A ILE* 4.0 11.9 - - + -
139A GLY 3.6 16.4 - - - +
140A ILE* 4.1 22.7 - - + +
157A PRO* 4.4 18.8 - - + -
161A GLU* 2.9 27.0 + - + +
162A GLN* 3.6 9.4 - - - +
164A LEU* 1.3 74.0 - - - +
166A ASP* 1.3 59.2 + - - +
168A ALA* 3.2 5.5 + - - +
169A ILE* 2.9 48.8 + - + +
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Residues in contact with ASP 166 (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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29A TRP* 3.9 22.0 - - - +
33A LEU* 5.4 2.9 - - - +
162A GLN* 2.7 47.1 + - - +
163A LYS* 3.7 4.9 - - - +
165A ILE* 1.3 77.4 - - - +
167A GLU* 1.3 56.7 + - - +
169A ILE* 3.9 11.2 - - - +
170A ASP* 3.0 29.1 + - - +
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Residues in contact with GLU 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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163A LYS* 2.9 21.2 + - - +
164A LEU* 3.2 18.3 + - - +
166A ASP* 1.3 74.3 - - - +
168A ALA* 1.3 65.1 + - - +
170A ASP* 3.4 9.1 + - + +
171A GLU* 3.0 18.4 + - - +
194A PHE* 3.6 16.4 - - + -
196A ALA* 3.7 24.5 - - + +
197A GLN 5.0 3.3 + - - +
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Residues in contact with ALA 168 (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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104A GLY* 3.6 31.2 - - - +
105A VAL 3.7 16.8 - - - +
106A ALA* 4.3 8.8 - - + +
138A ILE* 5.1 4.3 - - + -
164A LEU 2.9 9.0 + - - +
165A ILE* 3.6 8.5 - - - +
167A GLU* 1.3 75.6 - - - +
169A ILE* 1.3 59.1 + - - +
171A GLU* 3.4 2.4 + - - +
172A ALA* 2.8 29.9 + - - +
191A LEU* 4.7 0.7 - - - +
194A PHE* 3.6 12.7 - - + -
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Residues in contact with ILE 169 (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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26A ALA 3.7 22.4 - - - +
29A TRP* 4.0 17.0 - - + +
30A PHE* 3.7 33.6 - - + +
33A LEU* 3.9 18.8 - - + -
138A ILE* 3.9 20.4 - - + -
165A ILE* 2.9 40.1 + - + +
166A ASP* 3.9 10.8 - - - +
168A ALA* 1.3 72.5 - - - +
170A ASP* 1.3 57.1 + - - +
172A ALA* 3.2 5.6 + - - +
173A ALA* 2.7 34.5 + - - +
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Residues in contact with ASP 170 (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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33A LEU* 3.9 18.0 - - + +
37A ARG* 4.6 4.2 + - - -
166A ASP 3.0 18.4 + - - +
167A GLU* 3.4 10.8 - - - +
169A ILE* 1.3 77.2 - - - +
171A GLU* 1.3 62.5 + - - +
173A ALA* 3.4 2.8 + - - +
174A ARG* 2.9 56.8 + - - +
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Residues in contact with GLU 171 (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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167A GLU 3.0 16.3 + - - +
168A ALA 3.8 3.8 - - - +
170A ASP* 1.3 76.1 - - - +
172A ALA* 1.3 57.9 + - - +
174A ARG* 3.3 11.1 + - - +
175A CYS* 2.9 42.6 + - - -
190A ARG* 2.6 50.2 + - - +
191A LEU* 4.3 8.5 - - + -
194A PHE* 3.5 48.7 - - + -
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Residues in contact with ALA 172 (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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30A PHE* 3.6 3.6 - - + -
106A ALA* 4.4 3.8 - - + -
108A PHE* 4.6 0.9 - - - -
136A LEU* 3.7 37.5 - - + -
138A ILE* 5.8 0.2 - - + -
168A ALA 2.8 18.5 + - - +
169A ILE* 3.6 8.7 - - + +
171A GLU* 1.3 76.6 - - - +
173A ALA* 1.3 52.4 + - - +
175A CYS* 3.4 2.3 + - - +
176A THR* 2.8 38.6 + - - -
191A LEU* 4.0 14.5 - - + +
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Residues in contact with ALA 173 (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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30A PHE* 3.4 16.9 - - + -
33A LEU* 4.2 10.8 - - + -
34A LEU* 4.1 14.1 - - + +
37A ARG* 3.8 23.8 - - - -
169A ILE 2.7 19.5 + - - +
170A ASP 3.5 5.4 - - - +
172A ALA* 1.3 73.8 - - - +
174A ARG* 1.3 60.2 + - - +
176A THR* 3.2 4.0 + - - -
177A GLU* 3.1 29.2 + - - +
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Residues in contact with ARG 174 (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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37A ARG* 3.4 39.8 - - - +
170A ASP* 2.9 40.2 + - - +
171A GLU* 3.3 17.5 + - - +
173A ALA* 1.3 74.5 - - - +
175A CYS* 1.3 58.3 + - - +
177A GLU* 3.2 12.6 + - - +
178A MET* 2.9 25.6 + - - +
190A ARG* 4.4 21.1 - - - +
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Residues in contact with CYS 175 (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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108A PHE* 4.3 7.7 - - + -
171A GLU* 2.9 39.4 + - - +
172A ALA 3.8 4.3 - - - +
174A ARG* 1.3 74.2 - - - +
176A THR* 1.3 59.9 + - - +
178A MET* 3.3 6.9 + - - -
179A TRP* 2.9 23.7 + - - +
187A ALA* 3.2 26.0 - - - +
190A ARG* 3.7 13.0 - - - -
191A LEU* 3.6 38.6 - - + -
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Residues in contact with THR 176 (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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9A ILE* 4.1 26.2 - - + -
30A PHE* 3.4 17.3 - - + -
34A LEU* 4.4 12.6 - - + -
57A LEU* 5.8 1.1 - - + -
93A LEU* 4.2 13.9 - - + +
108A PHE* 3.9 17.7 - - - -
136A LEU* 4.8 0.2 - - - +
172A ALA 2.8 24.0 + - - -
173A ALA* 3.2 5.8 + - - -
175A CYS* 1.3 75.7 - - - +
177A GLU* 1.3 62.8 + - - +
179A TRP* 3.2 23.7 - - + +
180A PHE* 3.2 21.0 - - + -
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Residues in contact with GLU 177 (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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34A LEU* 4.4 11.4 - - + +
37A ARG* 2.7 48.9 + - - +
38A LEU* 4.0 24.7 - - + +
57A LEU* 4.9 10.2 - - + +
173A ALA 3.1 12.1 + - - +
174A ARG* 3.5 8.1 - - - +
176A THR* 1.3 75.6 - - + +
178A MET* 1.3 62.3 + - - +
180A PHE* 3.1 20.6 + - - +
181A THR* 3.3 17.4 + - + +
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Residues in contact with MET 178 (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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174A ARG 2.9 13.9 + - - +
175A CYS* 3.5 10.1 - - - +
176A THR 3.3 0.2 - - - -
177A GLU* 1.3 72.9 - - - +
179A TRP* 1.3 58.5 + - - +
181A THR* 3.9 7.2 - - - -
182A ASP* 2.8 53.7 + - + +
183A GLY 3.4 3.6 + - - +
186A LYS* 4.1 42.0 - - + +
187A ALA* 4.1 9.0 - - + +
190A ARG* 3.8 30.5 - - + -
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Residues in contact with TRP 179 (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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5A THR* 5.6 6.2 - - - +
6A ILE* 3.6 30.2 - - + +
93A LEU* 3.9 25.6 - - + -
108A PHE* 3.9 30.7 - + + -
134A HIS* 3.5 42.8 - + + -
175A CYS 2.9 11.6 + - - +
176A THR* 3.2 17.3 - - + +
178A MET* 1.3 75.8 - - - +
180A PHE* 1.3 66.5 + + + +
183A GLY* 2.9 24.8 + - - -
184A LEU* 3.6 46.7 - - + +
187A ALA* 3.6 11.2 - - + +
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Residues in contact with PHE 180 (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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5A THR* 5.3 3.4 - - - -
6A ILE* 3.4 53.4 - - + -
9A ILE* 4.2 3.4 - - + -
57A LEU* 3.6 42.2 - - + -
58A GLY* 3.8 26.0 - - - +
62A VAL* 3.6 21.1 - - + -
93A LEU* 6.1 0.4 - - + -
176A THR* 3.2 38.4 - - + -
177A GLU 3.1 8.3 + - - +
179A TRP* 1.3 87.8 - + + +
181A THR* 1.3 60.2 + - + +
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Residues in contact with THR 181 (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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58A GLY* 4.9 11.0 - - - +
177A GLU* 3.3 15.2 + - + +
178A MET* 3.8 7.1 + - - -
180A PHE* 1.3 81.4 - - + +
182A ASP* 1.3 82.6 + - - +
183A GLY 3.9 0.4 - - - -
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Residues in contact with ASP 182 (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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178A MET* 2.8 35.8 + - + +
181A THR* 1.3 101.9 + - - +
183A GLY* 1.3 58.7 + - - +
186A LYS* 4.0 34.8 + - + +
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Residues in contact with GLY 183 (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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178A MET 3.4 1.3 + - - +
179A TRP* 2.9 21.1 + - - -
180A PHE 4.7 0.2 - - - -
181A THR 3.9 0.4 - - - -
182A ASP* 1.3 79.2 - - - +
184A LEU* 1.3 64.8 + - - -
185A THR* 3.3 4.0 - - - -
186A LYS 3.3 3.7 + - - -
187A ALA* 3.1 21.3 + - - +
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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
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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) + - + + + + + -
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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