Contacts of the helix formed by residues 154 - 176 (chain A) in PDB entry 4GCK
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 154 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152A THR 4.1 0.4 + - - -
153A LEU* 1.3 73.2 - - - +
155A GLU* 1.3 66.3 + - - +
156A THR* 2.4 47.4 + - - -
157A LEU* 3.0 33.5 + - + +
158A LEU* 3.0 12.5 + - - +
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Residues in contact with GLU 155 (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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137A ARG* 4.2 8.5 - - + +
140A MET* 3.6 32.5 - - + +
141A ARG* 2.8 52.8 + - + +
151A TYR* 5.6 4.9 - - + -
153A LEU 3.3 5.9 + - - +
154A ASP* 1.3 78.7 + - - +
156A THR* 1.3 60.8 + - - +
158A LEU* 3.7 4.3 - - - +
159A ALA* 2.8 33.6 + - - +
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Residues in contact with THR 156 (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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133A GLU* 4.3 3.7 - - - +
137A ARG* 3.3 30.0 + - - +
141A ARG* 3.9 9.5 + - - -
154A ASP* 2.4 25.0 + - - -
155A GLU* 1.3 75.6 - - - +
157A LEU* 1.3 57.8 + - - +
159A ALA* 4.3 0.9 - - - +
160A SER* 3.0 26.7 + - - +
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Residues in contact with LEU 157 (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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153A LEU* 4.6 20.4 - - + -
154A ASP* 3.0 20.0 + - + +
156A THR* 1.3 80.3 - - - +
158A LEU* 1.3 62.7 + - - +
160A SER* 2.9 18.4 + - - -
161A GLN* 3.0 15.4 + - - +
185B ASP* 4.8 8.1 - - + +
188B ALA* 3.9 24.7 - - + +
189B ARG* 3.5 50.7 - - + +
192B LEU* 3.9 23.8 - - + -
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Residues in contact with LEU 158 (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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140A MET* 3.6 19.7 - - + +
151A TYR* 3.8 39.5 - - + -
153A LEU* 3.9 23.6 - - + +
154A ASP 3.0 16.5 + - - +
155A GLU* 3.2 2.4 + - - +
157A LEU* 1.3 77.5 - - + +
159A ALA* 1.3 62.3 + - - +
161A GLN* 3.1 7.2 - - + +
162A LEU* 3.0 24.9 + - - +
196A GLN* 3.7 24.2 - - + +
197A LEU* 4.3 15.7 - - + -
198A GLN 3.8 10.8 - - - +
192B LEU* 4.2 13.2 - - + -
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Residues in contact with ALA 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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133A GLU* 4.0 11.4 - - + -
136A LEU* 3.8 23.0 - - + +
137A ARG* 3.6 23.3 - - + +
140A MET* 3.6 11.1 - - + +
155A GLU 2.8 22.0 + - - +
156A THR 4.3 1.8 - - - +
158A LEU* 1.3 74.6 - - - +
160A SER* 1.3 61.7 + - - +
162A LEU* 3.1 6.4 + - - +
163A LEU* 2.9 23.4 + - - +
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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
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133A GLU* 3.5 23.0 + - - -
156A THR* 3.0 13.0 + - - -
157A LEU* 2.9 17.0 + - - -
159A ALA* 1.3 77.0 - - - +
161A GLN* 1.3 52.9 + - - +
163A LEU* 3.4 1.4 + - - +
164A ALA* 2.7 37.1 + - - +
169B MET* 6.4 0.2 - - - -
172B ARG* 3.5 19.5 - - - +
189B ARG* 3.0 30.6 + - - -
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Residues in contact with GLN 161 (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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157A LEU* 3.0 13.3 + - - +
158A LEU* 3.1 14.6 - - - +
160A SER* 1.3 78.0 + - - +
162A LEU* 1.3 62.8 + - + +
164A ALA* 3.6 4.9 - - - +
165A PHE* 3.1 22.0 + - - +
196A GLN* 2.6 45.4 - - + +
165B PHE* 3.6 16.8 - - - -
189B ARG* 2.9 39.2 + - - +
192B LEU* 4.2 15.8 - - + +
193B VAL* 3.5 22.8 - - - +
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Residues in contact with LEU 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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88A LEU* 3.9 22.4 - - + -
92A VAL* 4.2 18.5 - - + +
136A LEU* 4.2 17.7 - - + -
140A MET* 3.3 32.8 - - + -
158A LEU 3.0 8.7 + - - +
159A ALA 3.5 6.5 - - - +
161A GLN* 1.3 78.1 - - + +
163A LEU* 1.3 61.5 + - - +
165A PHE* 3.2 10.5 + - - +
166A CYS* 3.1 25.7 + - - -
190A TRP* 4.7 4.0 - - + -
193A VAL* 3.5 29.4 - - + -
196A GLN* 4.6 4.9 - - - +
197A LEU* 4.0 19.5 - - + -
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Residues in contact with LEU 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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95A ILE* 4.6 6.7 - - + -
129A PHE* 3.6 42.4 - - + +
132A ILE* 4.0 21.5 - - + -
133A GLU* 3.4 32.3 - - + +
136A LEU* 4.5 6.4 - - + +
159A ALA 2.9 15.2 + - - +
160A SER* 3.8 1.3 - - - +
162A LEU* 1.3 74.0 - - - +
164A ALA* 1.3 57.4 + - - +
166A CYS* 3.1 14.1 + - + +
167A GLU* 2.8 47.7 + - + +
172B ARG* 3.4 17.0 - - - +
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Residues in contact with ALA 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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160A SER 2.7 23.9 + - - +
161A GLN* 3.6 7.4 - - - +
163A LEU* 1.3 72.4 - - - +
165A PHE* 1.3 57.4 + - - +
167A GLU* 4.6 0.4 - - - -
168A GLY* 2.9 25.1 + - - -
164B ALA 4.1 1.7 - - - +
165B PHE* 4.6 12.6 - - + -
168B GLY* 3.2 13.4 - - - -
169B MET* 3.9 29.6 - - + -
172B ARG* 4.2 15.4 - - - +
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Residues in contact with PHE 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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92A VAL* 3.9 28.3 - - + -
96A LEU* 4.1 12.6 - - + -
161A GLN 3.1 10.9 + - - +
162A LEU* 3.3 12.3 - - - +
163A LEU 3.1 0.4 - - - -
164A ALA* 1.3 80.4 - - - +
166A CYS* 1.3 63.9 + - - +
168A GLY* 3.3 1.9 + - - -
169A MET* 3.0 55.5 + - + +
182A PRO 5.8 0.2 - - - -
186A PHE* 5.0 6.1 - + - -
189A ARG* 4.3 19.3 - - + -
193A VAL* 4.0 28.9 - - + -
196A GLN* 5.8 1.8 - - - +
161B GLN* 3.5 35.4 - - - -
164B ALA* 4.8 9.9 - - + +
165B PHE* 5.4 6.2 - - - +
196B GLN* 5.6 2.2 - - - +
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Residues in contact with CYS 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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92A VAL* 3.8 39.9 - - - -
95A ILE* 4.2 24.7 - - + -
96A LEU* 3.9 19.6 - - + +
129A PHE* 6.3 0.2 - - + -
136A LEU* 6.4 0.9 - - - -
162A LEU 3.1 19.8 + - - -
163A LEU* 3.1 15.9 + - + +
165A PHE* 1.3 78.3 - - - +
167A GLU* 1.3 57.4 + - + +
169A MET* 3.2 3.1 + - - +
170A LEU* 2.9 34.8 + - + +
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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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110A THR* 5.1 2.0 - - - +
129A PHE* 4.1 24.9 - - + -
163A LEU* 2.8 26.7 + - + +
164A ALA 3.9 3.6 - - - +
166A CYS* 1.3 72.4 - - + +
168A GLY* 1.3 59.2 + - - +
170A LEU* 3.9 6.8 - - - +
171A SER* 2.9 31.2 + - - -
168B GLY* 4.1 10.1 - - - +
171B SER* 3.3 20.4 + - - +
172B ARG* 3.2 25.8 + - - +
175B ARG* 2.8 48.5 + - - -
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Residues in contact with GLY 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 ALA 2.9 12.8 + - - -
165A PHE 3.3 1.1 + - - -
167A GLU* 1.3 77.8 - - - +
169A MET* 1.3 61.1 + - - +
171A SER* 3.4 3.2 + - - -
172A ARG* 3.1 31.8 + - - +
164B ALA* 3.3 28.0 - - - -
167B GLU* 4.2 3.6 - - - +
168B GLY* 3.5 11.2 - - - -
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Residues in contact with MET 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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96A LEU* 4.2 14.6 - - + -
165A PHE* 3.0 44.8 + - + +
166A CYS 3.7 3.8 - - - +
168A GLY* 1.3 77.5 - - - +
170A LEU* 1.3 57.6 + - - +
172A ARG* 3.3 14.2 + - + +
173A PHE* 3.0 29.2 + - - +
180A TYR 4.6 2.6 - - - +
181A ARG 4.6 5.2 - - - +
182A PRO* 3.4 33.9 - - + +
184A ASP 4.8 0.9 - - - +
189A ARG* 3.9 34.1 - - - +
160B SER* 5.5 0.7 - - - +
164B ALA* 3.9 20.2 - - + -
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Residues in contact with LEU 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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95A ILE* 4.2 23.8 - - + +
96A LEU* 4.5 5.8 - - + -
99A GLY* 4.2 19.1 - - - -
106A THR* 4.0 15.4 - - + +
109A LEU* 4.1 29.6 - - + -
110A THR* 3.7 15.5 - - + -
129A PHE* 5.2 9.6 - - + -
166A CYS* 2.9 22.6 + - + +
167A GLU* 3.9 6.7 - - - +
169A MET* 1.3 74.8 - - - +
171A SER* 1.3 64.2 + - - +
173A PHE* 3.2 5.9 + - - +
174A VAL* 3.0 27.0 + - - +
182A PRO* 4.2 18.6 - - + -
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Residues in contact with SER 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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110A THR* 3.9 14.8 - - - +
112A HIS* 4.9 10.2 - - - -
167A GLU 2.9 19.3 + - - -
168A GLY* 3.7 7.0 - - - -
169A MET 3.3 0.2 - - - -
170A LEU* 1.3 77.8 - - - +
172A ARG* 1.3 56.1 + - - +
174A VAL* 3.3 4.5 + - - +
175A ARG* 2.9 35.8 + - - +
110B THR* 4.9 9.2 + - - +
167B GLU* 3.9 19.5 + - - +
171B SER* 4.9 12.5 - - - -
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Residues in contact with ARG 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 GLY 3.1 21.2 + - - +
169A MET* 3.6 14.9 - - + +
170A LEU 3.2 0.2 - - - -
171A SER* 1.3 73.1 - - - +
173A PHE* 1.3 59.0 + - - +
175A ARG* 3.2 21.2 - - - +
176A SER* 2.7 38.2 + - - -
180A TYR* 3.9 35.1 - - + +
133B GLU* 3.1 34.8 + - - -
160B SER* 3.8 18.8 + - - -
163B LEU* 3.8 15.2 - - - +
164B ALA* 4.0 20.6 - - - +
167B GLU* 3.0 40.2 + - - +
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Residues in contact with PHE 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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99A GLY 3.4 22.9 - - - -
100A GLU* 3.6 20.6 - - - -
103A PRO* 4.1 8.5 - - + -
106A THR* 4.0 17.5 - - + -
169A MET 3.0 13.2 + - - +
170A LEU 3.4 7.9 - - - +
172A ARG* 1.3 74.7 - - - +
174A VAL* 1.3 59.8 + - - +
176A SER* 3.1 4.0 + - - -
178A PHE* 2.7 89.4 + + + -
180A TYR 3.4 24.4 + - - +
181A ARG* 3.8 24.0 - - - -
182A PRO* 3.5 20.0 - - + -
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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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106A THR* 3.7 23.3 - - + -
107A ARG* 4.1 33.1 + - + +
110A THR* 3.7 15.7 - - + +
112A HIS* 3.9 28.5 - - + +
170A LEU 3.0 16.7 + - - +
171A SER* 3.6 7.9 - - - +
173A PHE* 1.3 77.5 - - - +
175A ARG* 1.3 64.0 - - - +
177A GLU* 3.2 17.5 + - - +
178A PHE* 3.9 16.5 + - + -
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Residues in contact with ARG 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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112A HIS* 6.1 0.2 - - - -
171A SER* 2.9 37.0 + - - +
172A ARG* 3.2 31.7 - - - +
174A VAL* 1.3 76.1 - - - +
176A SER* 1.3 56.8 - - - +
177A GLU* 3.2 11.8 + - - +
180A TYR* 4.4 14.9 - - - -
109B LEU 5.4 0.9 - - - -
110B THR 6.0 3.4 - - - +
122B GLN* 3.5 22.5 - - - +
126B ASN* 2.8 59.9 + - - +
129B PHE* 3.7 41.1 - - - +
130B GLU* 4.9 4.4 + - - -
133B GLU* 4.9 1.6 + - - -
167B GLU* 2.5 41.4 + - - +
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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
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172A ARG 2.7 22.7 + - - -
173A PHE 3.1 7.1 + - - -
175A ARG* 1.3 76.8 - - - +
177A GLU* 1.3 72.6 + - - +
179A LYS* 3.2 33.0 + - - +
180A TYR* 3.0 48.4 + - - +
126B ASN* 4.5 4.9 - - - +
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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
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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