Contacts of the helix formed by residues 158 - 180 (chain A) in PDB entry 2HKU
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 GLY 158 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A LEU* 4.6 3.4 - - - -
157A ALA* 1.3 78.1 - - - +
159A ILE* 1.3 60.7 + - - -
160A ASP* 3.2 12.1 - - - -
161A VAL* 3.0 23.1 + - - +
162A GLU* 3.2 7.4 + - - +
303A EDO 4.1 6.4 + - - -
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Residues in contact with ILE 159 (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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141A GLU* 3.5 48.3 - - + +
145A ILE* 3.4 17.8 - - + +
146A ARG* 4.8 3.1 - - + +
149A MSE 3.8 22.4 - - + -
155A LEU* 4.1 19.9 - - + +
157A ALA 3.7 0.8 + - - -
158A GLY* 1.3 67.0 - - - -
160A ASP* 1.3 70.5 + - + +
162A GLU* 3.4 3.1 + - - +
163A SER* 3.1 17.0 + - - -
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Residues in contact with ASP 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A HIS* 5.6 0.7 - - - +
141A GLU* 3.3 23.1 - - - +
158A GLY* 3.5 14.0 - - - -
159A ILE* 1.3 77.5 + - + +
161A VAL* 1.4 78.3 + - - +
163A SER* 3.2 6.8 + - - -
164A LYS* 3.1 35.8 + - - +
190B GLU* 4.7 8.7 - - - +
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Residues in contact with VAL 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A ALA* 3.7 23.1 - - + -
158A GLY* 3.0 12.3 + - - +
160A ASP* 1.4 84.7 - - - +
162A GLU* 1.3 60.9 + - - +
164A LYS* 3.2 9.3 + - + +
165A ALA* 2.8 28.2 + - + +
190B GLU* 4.1 22.7 - - + +
193B ALA* 4.0 32.5 - - + +
194B VAL* 4.3 10.2 - - + +
197B ALA* 5.3 1.1 - - + -
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Residues in contact with GLU 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A ILE* 3.9 24.6 - - + +
153A TRP* 3.4 10.5 - - - -
155A LEU* 4.0 10.1 - - + -
156A ARG* 2.8 63.3 + - - +
157A ALA* 3.0 28.3 + - + +
158A GLY 3.2 4.1 + - - +
159A ILE 3.8 6.5 - - - +
160A ASP 3.3 0.4 - - - -
161A VAL* 1.3 77.0 - - - +
163A SER* 1.3 62.2 + - - +
165A ALA* 3.5 7.0 + - - +
166A PHE* 3.0 22.9 + - - +
199A LEU* 5.2 2.4 - - - +
197B ALA* 4.4 7.4 - - - +
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Residues in contact with SER 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A HIS* 2.6 39.1 + - - -
140A GLY* 3.2 16.7 - - - -
141A GLU* 3.7 18.8 - - - -
145A ILE* 4.0 7.3 - - - +
159A ILE 3.1 6.6 + - - -
160A ASP 3.2 8.3 + - - -
162A GLU* 1.3 78.5 - - - +
164A LYS* 1.3 56.0 + - - +
166A PHE* 3.3 5.9 + - - +
167A TRP* 2.9 30.8 + - - -
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Residues in contact with LYS 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A HIS* 3.7 44.4 + - + +
160A ASP* 3.1 27.6 + - - +
161A VAL* 3.2 8.7 + - + +
163A SER* 1.3 72.6 - - - +
165A ALA* 1.3 55.0 + - - +
167A TRP* 4.3 0.2 - - - +
168A SER* 2.8 38.3 + - - -
173B LEU* 5.3 4.3 - - + +
176B GLN* 4.9 1.9 + - - +
190B GLU* 2.5 48.4 + - + +
194B VAL* 4.5 10.3 - - + +
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Residues in contact with ALA 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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156A ARG* 5.6 0.2 - - - +
161A VAL 2.8 16.8 + - - +
162A GLU* 3.7 13.0 - - - +
163A SER 3.3 0.2 - - - -
164A LYS* 1.3 75.3 - - - +
166A PHE* 1.3 62.9 + - - +
168A SER* 3.5 0.7 + - - -
169A ALA* 3.3 23.9 + - - +
198A ASN* 4.9 0.7 - - - +
194B VAL* 3.7 30.4 - - + +
197B ALA* 5.0 4.3 - - + -
198B ASN* 3.5 27.5 + - - +
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Residues in contact with PHE 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A LEU* 3.6 21.1 - - + -
98A VAL* 3.8 11.0 - - + -
101A LEU* 3.8 6.7 - - + -
140A GLY* 5.8 0.4 - - - -
144A LEU* 3.3 28.5 - - + -
145A ILE* 5.0 3.1 - - + -
162A GLU 3.0 14.7 + - - +
163A SER* 3.5 10.1 - - - +
164A LYS 3.2 0.2 - - - -
165A ALA* 1.3 79.3 - - - +
167A TRP* 1.3 81.2 + + - +
169A ALA* 3.6 4.1 - - - +
170A ILE* 3.0 52.4 + - + +
195A ILE* 3.8 31.2 - - + -
199A LEU* 4.8 7.6 - - + -
302A EDO 3.7 28.3 - - - -
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Residues in contact with TRP 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A VAL* 4.5 9.0 - - + -
77A GLY* 4.5 7.4 - - - -
101A LEU* 4.0 24.2 - - + -
109A VAL* 4.7 3.6 - - + -
136A LEU* 3.1 55.1 + - + -
137A HIS* 3.6 25.6 - + + +
139A SER* 4.9 0.2 - - - -
140A GLY* 4.9 0.2 - - - -
163A SER* 2.9 30.8 + - - +
164A LYS 4.3 0.2 - - - +
166A PHE* 1.3 82.8 - + - +
168A SER* 1.3 57.3 + - - +
170A ILE* 3.3 22.2 + - + +
171A PHE* 3.0 68.8 + + + -
302A EDO 2.9 38.9 + - - -
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Residues in contact with SER 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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164A LYS 2.8 23.4 + - - -
165A ALA* 3.5 8.5 + - - -
167A TRP* 1.3 73.1 - - - +
169A ALA* 1.3 56.8 + - - +
171A PHE* 3.5 10.8 + - - -
172A GLY 3.0 23.4 + - - -
168B SER 3.2 10.3 - - - +
169B ALA* 4.0 4.7 + - - +
172B GLY* 3.3 15.5 - - - -
173B LEU* 4.0 13.4 - - - +
176B GLN* 3.6 17.0 - - - +
194B VAL* 4.0 12.0 - - - +
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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
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165A ALA 3.3 17.2 + - - +
166A PHE* 3.6 1.1 - - - +
167A TRP 3.3 0.2 - - - -
168A SER* 1.3 77.3 + - - +
170A ILE* 1.3 60.4 + - - +
172A GLY 3.7 0.2 - - - -
173A LEU* 2.7 42.4 + - + +
194A VAL* 5.3 0.4 - - + -
195A ILE* 3.4 24.2 - - + -
198A ASN* 3.5 17.0 - - - +
165B ALA* 5.9 0.9 - - - +
168B SER* 4.4 13.7 - - - -
169B ALA* 4.6 2.8 - - - +
198B ASN* 4.8 3.4 - - - +
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Residues in contact with ILE 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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98A VAL* 4.6 4.0 - - + -
101A LEU* 4.2 18.4 - - + -
102A LEU* 3.9 22.4 - - + -
109A VAL* 4.2 13.0 - - + -
166A PHE* 3.0 52.7 + - + +
167A TRP* 3.3 30.5 + - + +
169A ALA* 1.3 74.6 - - - +
171A PHE* 1.3 58.4 + - - +
173A LEU* 3.8 2.9 - - - +
174A VAL* 2.9 36.9 + - + +
195A ILE* 3.9 18.8 - - + -
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Residues in contact with PHE 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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73A VAL* 4.9 0.4 - - + -
109A VAL* 3.6 21.5 - - + -
112A PHE* 4.0 18.8 - + - -
113A THR* 4.1 8.5 - - + +
116A MSE 4.0 9.9 - - + -
133A LEU* 3.8 31.6 - - + -
136A LEU* 4.0 8.7 - - + -
167A TRP* 3.0 59.5 + + + -
168A SER* 3.7 5.2 - - - +
169A ALA 3.3 0.4 - - - -
170A ILE* 1.3 73.7 - - - +
172A GLY* 1.3 57.2 + - - +
174A VAL* 3.8 1.9 - - - +
175A ILE* 2.9 36.3 + - - +
172B GLY* 3.9 18.8 - - - -
175B ILE* 3.8 16.4 - - + -
176B GLN* 3.9 10.5 - - - -
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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
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168A SER 3.0 11.3 + - - -
169A ALA 3.8 0.2 - - - -
171A PHE* 1.3 77.1 - - - +
173A LEU* 1.3 60.9 + - - +
175A ILE* 3.6 3.2 + - - +
176A GLN* 2.9 37.3 + - - +
168B SER* 3.4 25.4 - - - -
171B PHE* 4.3 8.3 - - - -
172B GLY* 4.0 7.3 - - - -
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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
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102A LEU* 4.1 13.9 - - + -
169A ALA* 2.7 28.6 + - + +
170A ILE* 3.9 3.1 - - - +
172A GLY* 1.3 71.9 - - - +
174A VAL* 1.3 59.4 + - - +
176A GLN* 4.1 0.8 - - - +
177A LYS* 2.8 35.2 + - - +
186A TYR* 3.4 24.6 - - + -
191A ALA* 3.7 29.2 - - + +
194A VAL* 3.9 20.2 - - + -
195A ILE* 3.6 34.8 - - + -
168B SER* 3.3 19.7 - - - +
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Residues in contact with VAL 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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101A LEU 4.3 1.8 - - - +
102A LEU* 3.8 19.1 - - + -
106A ALA* 3.7 27.1 - - + +
109A VAL* 3.7 24.5 - - + -
110A GLU* 3.6 38.1 - - + +
113A THR* 5.5 0.2 - - + -
170A ILE* 2.9 22.0 + - + +
171A PHE 3.8 3.6 - - - +
173A LEU* 1.3 76.0 - - - +
175A ILE* 1.3 65.7 + - + +
177A LYS* 4.0 7.0 + - - +
178A THR* 3.2 21.9 + - - -
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Residues in contact with ILE 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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113A THR* 3.9 22.4 - - + +
117A LEU* 6.1 0.2 - - + -
171A PHE 2.9 26.6 + - - +
172A GLY* 4.0 7.9 - - - +
173A LEU 3.3 0.2 - - - -
174A VAL* 1.3 78.6 - - + +
176A GLN* 1.3 57.3 + - + +
178A THR* 2.9 26.9 - - - +
179A ALA* 3.0 10.4 + - - +
113B THR* 4.5 8.3 - - - +
116B MSE 3.8 39.5 - - + -
117B LEU* 4.3 14.1 - - + -
171B PHE* 4.8 7.2 - - + +
175B ILE* 3.8 39.0 - - + -
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Residues in contact with GLN 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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172A GLY 2.9 23.5 + - - +
173A LEU 4.1 0.2 - - - +
175A ILE* 1.3 73.9 - - - +
177A LYS* 1.3 58.1 + - - +
179A ALA* 4.4 1.1 - - - -
180A THR* 2.5 40.5 + - - +
186A TYR* 3.3 28.3 + - + -
116B MSE 3.9 24.5 - - + -
133B LEU* 3.5 13.0 - - + +
137B HIS* 3.3 29.3 - - - -
168B SER* 3.1 31.5 + - - +
171B PHE* 3.5 15.4 - - + -
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Residues in contact with LYS 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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102A LEU* 2.7 46.9 + - - +
106A ALA* 3.9 13.1 - - - +
173A LEU 2.8 22.0 + - - +
174A VAL* 4.0 5.6 + - - +
176A GLN* 1.3 79.4 - - - +
178A THR* 1.3 57.6 - - - +
180A THR* 3.1 6.7 + - - -
182A GLU* 2.7 60.8 + - + +
186A TYR* 3.4 24.3 - - + +
187A SER 3.9 1.8 - - - +
188A LEU* 3.9 21.9 - - + +
191A ALA* 4.4 11.2 - - + -
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Residues in contact with THR 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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110A GLU* 3.1 29.1 + - - +
174A VAL* 3.2 15.0 + - - +
175A ILE* 2.9 19.1 - - - +
177A LYS* 1.3 74.6 - - - +
179A ALA* 1.3 72.3 + - + +
181A GLY* 3.3 11.5 + - - -
182A GLU* 5.8 1.6 - - - -
116B MSE 4.5 3.6 - - - +
117B LEU* 4.1 20.6 - - + -
119B THR* 4.9 3.2 + - - -
126B ARG* 4.0 8.1 + - - -
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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
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175A ILE 3.0 12.2 + - - +
176A GLN* 4.1 3.8 - - - +
178A THR* 1.3 83.4 - - - +
180A THR* 1.3 57.5 + - + +
181A GLY 3.2 0.9 - - - -
116B MSE 3.4 47.8 - - + +
119B THR* 4.2 11.1 + - + +
126B ARG* 3.3 25.5 + - - +
129B ILE* 4.0 10.9 - - + +
130B THR* 4.5 1.7 - - - +
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Residues in contact with THR 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A GLN 2.5 28.8 + - - +
177A LYS* 3.1 11.1 + - - -
178A THR 3.3 0.2 - - - -
179A ALA* 1.3 75.0 - - - +
181A GLY* 1.3 62.1 + - - +
182A GLU 3.4 2.8 + - - -
183A SER* 3.2 30.8 + - - +
184A PHE* 3.6 26.2 - - + +
186A TYR* 3.8 8.1 - - + +
126B ARG* 3.9 9.8 + - - -
129B ILE* 5.6 0.2 - - + -
130B THR* 4.1 17.9 - - + -
133B LEU* 3.6 28.5 - - + -
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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