Contacts of the helix formed by residues 164 - 188 (chain A) in PDB entry 4WTM
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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A ARG 4.5 1.0 - - - +
99A SER* 2.7 22.7 + - - -
100A LYS* 3.0 36.3 + - + +
101A TYR* 3.9 17.0 - - + -
118A HIS* 4.3 1.9 + - - -
134A ILE* 5.7 0.2 - - - +
135A PRO 4.7 3.6 + - - -
162A TYR* 5.5 0.9 - - - -
163A PRO* 1.3 77.5 - - - +
165A LEU* 1.3 67.4 + - - +
166A GLY* 3.1 19.7 + - - +
167A VAL* 2.9 24.4 + - + +
168A ARG* 3.0 10.4 + - - +
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Residues in contact with LEU 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A THR* 4.0 24.7 - - + -
96A SER* 4.1 1.8 - - - +
97A ALA 3.5 21.3 + - - +
98A ARG* 4.1 1.2 + - - -
99A SER* 3.8 24.0 - - - +
103A PHE* 4.2 6.5 - - + -
104A GLY* 3.9 26.5 - - - -
105A ALA* 4.0 3.6 - - - +
108A VAL* 3.9 16.2 - - + -
164A ASP* 1.3 75.0 + - - +
166A GLY* 1.3 63.5 + - - +
168A ARG* 3.1 33.9 + - + +
169A VAL* 3.0 29.5 + - + +
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Residues in contact with GLY 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A SER* 4.8 1.6 + - - -
103A PHE* 4.9 1.5 - - - -
118A HIS* 4.3 13.2 - - - -
119A ILE* 4.0 23.5 - - - +
122A VAL* 4.1 6.5 - - - +
164A ASP* 3.1 13.7 + - - -
165A LEU* 1.3 78.4 - - - +
167A VAL* 1.3 62.6 + - - +
169A VAL* 3.4 4.0 + - - +
170A CYS* 3.2 25.3 + - - -
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Residues in contact with VAL 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A VAL* 4.0 22.4 - - + -
126A LEU* 5.9 1.6 - - + -
134A ILE* 4.3 27.8 - - + -
163A PRO* 3.8 22.7 - - + -
164A ASP* 2.9 20.0 + - + +
166A GLY* 1.3 72.4 - - - +
168A ARG* 1.3 61.3 + - - +
170A CYS* 2.9 5.3 + - + +
171A GLU* 2.8 35.2 + - + +
256A LEU* 4.5 9.0 - - + -
260A LEU* 4.1 16.4 - - + -
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Residues in contact with ARG 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A SER* 2.7 24.0 + - - -
97A ALA* 2.7 31.1 + - - +
98A ARG 5.4 0.6 + - - -
162A TYR* 3.6 14.9 - - - -
163A PRO* 2.9 38.8 + - + +
164A ASP* 3.0 10.6 + - - +
165A LEU* 3.1 33.7 + - + +
167A VAL* 1.3 75.9 - - - +
169A VAL* 1.3 62.2 + - - +
171A GLU* 3.3 15.5 + - - +
172A LYS* 3.3 31.2 + - - +
283A GLY 4.6 1.3 - - - -
285A LEU* 5.5 0.3 - - - +
2T A 3.3 36.4 + - - -
3T G 3.5 17.0 + - - +
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Residues in contact with VAL 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A LEU 4.3 2.0 - - - +
88A ALA* 3.6 21.1 - - + +
89A CYS* 3.9 17.7 - - - +
92A THR* 3.7 22.0 - - - +
108A VAL* 4.1 9.4 - - + -
119A ILE* 4.0 33.4 - - + -
165A LEU* 3.0 21.5 + - + +
166A GLY 3.7 7.0 - - - +
167A VAL 3.2 0.2 - - - -
168A ARG* 1.3 77.7 - - - +
170A CYS* 1.3 63.4 + - - +
172A LYS* 3.1 18.9 + - - +
173A MET* 3.2 10.5 + - - +
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Residues in contact with CYS 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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119A ILE* 3.8 15.3 - - - -
122A VAL* 3.6 20.0 - - - -
123A TRP* 3.6 43.7 - - + -
126A LEU* 3.8 13.7 - - + -
166A GLY 3.2 15.6 + - - +
167A VAL* 2.9 10.8 + - - +
169A VAL* 1.3 76.1 - - - +
171A GLU* 1.3 65.6 + - - +
173A MET* 2.9 22.3 + - - +
174A ALA* 3.0 12.1 + - - +
256A LEU* 4.8 1.3 - - - -
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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
----------------------------------------------------------
163A PRO* 3.6 18.2 - - - +
167A VAL 2.8 17.6 + - - +
168A ARG* 3.6 23.2 - - - +
169A VAL 3.3 0.2 - - - -
170A CYS* 1.3 75.3 - - - +
172A LYS* 1.3 58.8 + - - +
174A ALA* 3.3 1.0 + - - +
175A LEU* 2.8 33.1 + - - +
256A LEU* 3.9 24.0 - - + +
260A LEU* 3.9 11.2 - - + -
261A TYR* 2.6 33.3 + - - +
283A GLY 4.9 0.2 - - - +
284A VAL* 3.5 3.7 - - - +
285A LEU* 2.8 39.7 + - + -
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Residues in contact with LYS 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A LEU* 3.9 4.7 - - + +
88A ALA* 4.0 18.4 - - + +
91A LEU* 3.9 40.7 + - + -
92A THR* 4.3 8.5 - - - +
93A PRO* 5.0 3.6 - - - +
168A ARG* 3.4 20.2 + - - +
169A VAL* 3.1 8.2 + - - +
170A CYS 3.1 0.6 - - - -
171A GLU* 1.3 76.9 - - - +
173A MET* 1.3 67.3 + - - +
176A TYR* 3.0 36.5 + - + +
285A LEU* 3.7 19.5 - - + +
3T G 3.2 21.4 + - - -
4T G 3.0 28.5 + - - +
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Residues in contact with MET 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A ARG 4.3 1.2 - - - +
82A LEU* 3.5 12.8 - - + -
83A LEU* 3.1 42.9 + - - +
84A THR* 5.2 0.2 - - - -
85A LEU* 3.7 42.8 - - + +
88A ALA* 3.5 20.9 - - + -
119A ILE* 4.6 3.1 - - - -
123A TRP* 3.8 40.6 - - + +
169A VAL* 3.2 3.1 + - - +
170A CYS* 2.9 28.3 + - - +
172A LYS* 1.3 79.8 - - - +
174A ALA* 1.3 61.0 + - - +
176A TYR 4.8 0.2 + - - -
177A ASP 5.7 0.2 + - - -
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Residues in contact with ALA 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A ARG 4.7 6.1 - - - +
82A LEU* 4.1 9.9 - - - -
123A TRP* 4.0 11.4 - - + -
170A CYS 3.0 10.5 + - - +
171A GLU 3.7 6.7 - - - +
173A MET* 1.3 81.0 - - - +
175A LEU* 1.3 64.4 + - + +
177A ASP 5.4 0.2 + - - -
178A ILE* 4.2 5.4 - - - +
249A ALA* 4.5 7.4 - - - +
252A ALA* 4.1 11.7 - - + -
253A ILE* 3.9 19.6 - - + +
256A LEU* 3.9 20.4 - - + -
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Residues in contact with LEU 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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171A GLU 2.8 16.3 + - - +
174A ALA* 1.3 76.5 - - - +
176A TYR* 1.3 65.6 + - - +
177A ASP 3.2 2.9 - - - -
178A ILE* 3.1 23.8 + - + +
179A THR* 3.0 21.6 + - + +
240A TYR* 4.0 23.8 - - + -
253A ILE* 3.8 31.2 - - + -
256A LEU* 4.1 17.7 - - + -
261A TYR* 3.4 38.6 - - + +
285A LEU* 3.8 10.5 - - + -
286A THR* 4.1 10.3 - - + -
289A MET* 4.6 0.9 - - + -
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Residues in contact with TYR 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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83A LEU* 3.7 26.2 - - + -
91A LEU* 4.0 29.8 - - + +
172A LYS* 3.0 35.9 + - + +
173A MET 4.8 0.2 + - - -
175A LEU* 1.3 77.6 - - - +
177A ASP* 1.3 65.5 + - - +
179A THR* 2.5 26.7 + - - -
180A GLN* 3.2 43.0 + - + +
285A LEU* 3.9 10.2 - - + +
4T G 4.2 25.2 + - - -
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Residues in contact with ASP 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ALA* 3.2 3.4 - - + -
81A ARG* 2.8 57.2 + - - +
83A LEU* 4.3 11.6 - - + +
175A LEU 3.2 0.8 - - - -
176A TYR* 1.3 83.6 - - - +
178A ILE* 1.3 62.7 + - - +
180A GLN* 3.2 15.7 + - - +
181A LYS* 2.8 52.1 + - - +
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Residues in contact with ILE 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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78A VAL* 5.6 1.1 - - + -
80A ALA* 3.5 20.2 - - + -
174A ALA 4.2 7.9 - - - +
175A LEU* 3.1 17.1 + - + +
177A ASP* 1.3 73.3 - - + +
179A THR* 1.3 65.7 + - - +
180A GLN 3.0 1.3 - - - -
181A LYS* 2.9 2.8 + - - +
182A LEU* 2.8 50.3 + - + +
240A TYR* 4.3 13.0 - - + +
243A CYS* 4.7 7.4 - - - -
245A LEU* 3.8 24.7 - - + -
253A ILE* 3.9 22.7 - - + -
289A MET* 3.6 23.8 - - + -
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Residues in contact with THR 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 LEU* 3.0 19.4 + - + +
176A TYR* 2.5 27.9 + - - -
178A ILE* 1.3 74.9 - - - +
180A GLN* 1.3 72.5 + - - +
181A LYS 3.6 0.2 + - - -
183A PRO* 3.8 15.1 - - - +
191A TYR* 5.1 3.5 + - - -
285A LEU* 4.3 31.9 - - + +
289A MET* 3.7 32.9 - - + +
4T G 5.1 9.4 + - - -
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Residues in contact with GLN 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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176A TYR* 3.4 48.7 + - + +
177A ASP* 3.2 14.1 + - - +
178A ILE 3.0 1.0 - - - -
179A THR* 1.3 95.1 + - - +
181A LYS* 1.3 64.6 + - + +
183A PRO* 5.1 0.4 - - - -
184A GLN* 5.5 3.6 - - - +
4T G 3.9 15.4 + - - -
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Residues in contact with LYS 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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78A VAL* 4.1 17.9 - - + -
79A SER 3.1 25.1 + - - +
80A ALA* 4.1 0.9 - - - +
81A ARG* 4.8 3.6 - - - +
177A ASP* 2.8 47.3 + - - +
178A ILE 2.9 5.4 + - - +
179A THR 3.4 0.2 - - - -
180A GLN* 1.3 85.7 - - + +
182A LEU* 1.3 63.9 + - - +
183A PRO* 3.6 1.6 - - - -
184A GLN* 3.7 8.5 + - - +
185A ALA* 3.1 23.2 + - - +
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Residues in contact with LEU 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A ALA* 3.7 23.6 - - + -
78A VAL* 4.4 5.8 - - + +
178A ILE* 2.8 30.6 + - + +
181A LYS* 1.3 70.0 - - - +
183A PRO* 1.4 73.8 - - + +
185A ALA* 2.7 16.1 + - - +
186A VAL* 2.9 22.6 + - + +
239A ILE* 4.1 10.3 - - + -
240A TYR* 3.7 33.9 - - + -
243A CYS* 3.7 22.4 - - - -
289A MET* 4.1 1.3 - - - -
293A ILE* 3.8 20.6 - - + -
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Residues in contact with PRO 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A ILE 3.7 7.4 - - - +
179A THR 3.8 14.8 - - - +
180A GLN 5.1 0.2 - - - -
181A LYS 3.9 1.1 - - - -
182A LEU* 1.4 93.5 - - + +
184A GLN* 1.3 62.9 + - - +
186A VAL* 3.3 7.3 + - + -
187A MET* 3.0 35.8 + - - +
191A TYR* 3.6 39.9 - - + +
289A MET* 3.9 28.7 - - + -
292A THR* 5.5 1.3 - - + -
293A ILE* 4.6 6.7 - - + -
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Residues in contact with GLN 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A GLN 5.5 2.7 - - - +
181A LYS* 3.7 10.6 + - - +
182A LEU 3.2 0.8 - - - -
183A PRO* 1.3 79.7 - - - +
185A ALA* 1.3 59.3 + - - +
188A GLY* 2.9 42.1 + - - +
191A TYR* 4.2 16.0 - - + -
194A GLN* 3.2 39.8 + - - +
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Residues in contact with ALA 185 (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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74A ALA* 3.9 19.7 - - - +
77A LYS* 6.2 0.7 - - + -
78A VAL* 3.4 28.9 - - + -
181A LYS 3.1 14.6 + - - +
182A LEU 2.7 10.3 + - - +
184A GLN* 1.3 81.8 - - - +
186A VAL* 1.3 62.4 + - + +
188A GLY* 4.7 1.2 + - - -
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Residues in contact with VAL 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ILE* 3.7 43.6 - - + +
74A ALA* 4.0 9.7 - - + +
75A ALA* 3.8 10.1 - - + +
182A LEU* 2.9 32.5 + - + +
183A PRO* 3.6 4.7 - - + +
185A ALA* 1.3 79.6 - - - +
187A MET* 1.3 72.6 + - + +
188A GLY 3.9 0.2 - - - -
239A ILE* 5.0 1.8 - - + -
293A ILE* 4.3 21.5 - - + -
296A TYR* 3.7 19.7 + - + -
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Residues in contact with MET 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A PRO* 3.0 18.7 + - - +
186A VAL* 1.3 90.9 - - + +
188A GLY* 1.3 65.8 + - - +
189A ALA 3.3 0.9 + - - -
190A SER* 3.0 35.4 + - - +
191A TYR* 3.9 19.5 - - + +
292A THR* 3.7 26.2 - - + +
293A ILE* 4.8 3.6 - - - -
296A TYR* 3.6 49.5 + - + -
315A VAL* 3.7 24.9 - - + -
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Residues in contact with GLY 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A GLN* 2.9 34.3 + - - -
185A ALA 4.6 0.8 + - - -
186A VAL 3.9 0.4 - - - -
187A MET* 1.3 77.2 - - - +
189A ALA* 1.3 61.9 - - - -
190A SER 3.1 1.2 + - - -
191A TYR* 3.1 10.7 + - - +
194A GLN* 2.9 17.5 + - - -
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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