Contacts of the helix formed by residues 165 - 187 (chain A) in PDB entry 1E3S
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 GLN 165 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A VAL 4.9 5.2 - - - +
97A ALA* 6.2 0.9 - - + -
157A ALA* 3.7 19.1 - - - +
160A GLU 4.5 0.5 - - - +
161A GLY* 3.8 0.6 - - - -
162A GLN* 2.9 57.9 + - + +
163A VAL 4.6 1.6 - - - +
164A GLY* 1.3 79.7 - - - +
166A ALA* 1.3 64.7 + - - +
167A ALA 3.4 2.7 - - - -
168A TYR* 3.3 33.9 + - + +
169A SER* 2.9 30.5 + - - +
259A MET* 5.8 0.9 - - - +
181B PRO* 4.2 2.0 - - - -
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Residues in contact with ALA 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A ILE 4.9 5.5 + - - +
100A THR* 4.0 12.1 - - - +
109A HIS* 5.3 1.3 - - + -
114A PHE* 4.0 2.1 - - - -
164A GLY 3.6 3.8 + - - +
165A GLN* 1.3 74.7 - - - +
167A ALA* 1.3 63.1 + - - +
170A ALA* 3.0 25.3 + - - +
126B PHE* 4.2 14.1 - - + -
178B MET* 3.8 5.6 - - + +
181B PRO* 4.1 15.3 - - + +
182B ILE* 3.8 28.3 - - + -
185B ASP* 4.4 5.3 + - - +
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Residues in contact with ALA 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A VAL* 4.4 9.0 - - + -
109A HIS* 4.2 16.9 + - + +
114A PHE* 3.7 33.0 - - + +
117A VAL* 3.7 31.2 - - + +
118A ILE* 4.1 3.1 - - - +
164A GLY 5.3 0.6 + - - -
165A GLN 3.4 0.6 - - - -
166A ALA* 1.3 77.7 - - - +
168A TYR* 1.3 63.3 + - - +
170A ALA* 3.4 2.9 + - - +
171A SER* 3.1 18.7 + - - -
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Residues in contact with TYR 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A ILE 3.6 24.7 - - - -
95A ALA* 4.0 19.3 - - + -
96A VAL* 4.8 13.1 + - - +
117A VAL* 3.9 6.1 - - + +
121A ASN* 3.8 6.3 - - - -
155A SER* 3.7 22.2 - - - -
157A ALA* 3.8 10.1 - - + -
165A GLN* 3.3 33.9 + - - +
167A ALA* 1.3 77.6 - - - +
169A SER* 1.3 55.6 + - - +
171A SER* 2.9 21.9 + - - -
172A LYS* 3.0 30.8 + - + +
301A NAD 2.7 51.2 + + - -
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Residues in contact with SER 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A ALA* 2.8 36.3 + - - +
158A ALA* 4.5 1.2 - - - -
161A GLY* 3.3 17.0 - - - -
165A GLN* 2.9 23.0 + - - +
166A ALA 4.0 1.3 - - - -
168A TYR* 1.3 69.9 - - - +
170A ALA* 1.3 60.2 + - - +
172A LYS* 3.8 1.1 - - - -
173A GLY* 2.8 29.5 + - - -
177B GLY* 3.5 21.7 - - - -
181B PRO* 3.6 9.2 - - - +
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Residues in contact with ALA 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A PHE* 3.8 23.6 - - + -
118A ILE* 4.0 6.3 - - + -
122A LEU* 4.8 0.2 - - - +
166A ALA 3.0 20.2 + - - +
167A ALA 3.7 4.7 - - - +
169A SER* 1.3 75.9 - - - +
171A SER* 1.3 62.5 + - - +
174A GLY* 3.1 19.4 + - - -
122B LEU* 4.2 7.6 - - + +
174B GLY* 3.3 28.0 - - - +
178B MET* 4.0 9.3 - - - +
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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
----------------------------------------------------------
117A VAL* 4.0 7.9 - - - -
118A ILE* 3.8 18.3 - - - +
121A ASN* 3.1 40.5 + - - +
122A LEU* 3.9 12.2 - - - +
167A ALA 3.1 14.1 + - - -
168A TYR* 2.9 15.9 + - - -
170A ALA* 1.3 77.0 - - - +
172A LYS* 1.3 60.8 + - - +
174A GLY* 3.5 2.3 + - - -
175A ILE* 3.4 24.0 + - - +
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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
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92A ALA 5.4 1.0 + - - -
93A GLY* 5.3 0.2 - - - -
121A ASN* 4.1 14.3 - - - +
153A THR 3.1 17.2 + - - -
154A ALA* 3.5 18.5 + - - +
155A SER* 3.8 27.4 - - - +
158A ALA* 4.0 11.9 - - + +
168A TYR* 3.0 39.6 + - + +
169A SER* 4.2 2.0 - - - +
171A SER* 1.3 77.5 + - - +
173A GLY* 1.3 64.8 + - - +
174A GLY 3.3 0.2 - - - -
175A ILE* 3.3 20.9 + - + +
176A VAL* 3.1 25.5 + - - +
301A NAD 2.9 42.6 + - - -
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Residues in contact with GLY 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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158A ALA* 4.0 13.9 - - - +
169A SER 2.8 17.2 + - - -
170A ALA 4.0 0.4 - - - -
172A LYS* 1.3 77.1 - - - +
174A GLY* 1.3 57.2 + - - +
176A VAL* 3.6 5.6 - - - +
177A GLY 3.0 22.5 + - - -
173B GLY* 3.3 25.7 - - - +
177B GLY* 4.4 5.8 - - - -
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Residues in contact with GLY 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A LEU* 3.7 16.6 - - - -
170A ALA 3.1 13.4 + - - -
171A SER 3.9 4.3 - - - -
172A LYS 3.3 0.4 - - - -
173A GLY* 1.3 74.1 - - - +
175A ILE* 1.3 63.8 + - - +
177A GLY 3.4 0.3 + - - -
178A MET* 3.1 25.1 + - - +
170B ALA* 3.3 29.2 - - - +
173B GLY 4.1 0.4 - - - -
174B GLY 3.7 2.6 - - - +
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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
----------------------------------------------------------
121A ASN 3.7 21.5 - - - +
122A LEU* 4.2 11.9 - - + -
125A THR* 4.5 15.9 - - + +
152A ASN* 3.9 30.7 + - + +
153A THR 3.7 19.7 - - - +
154A ALA* 4.3 4.9 - - + -
171A SER 3.4 15.9 + - - +
172A LYS* 3.3 25.8 + - + +
174A GLY* 1.3 75.8 - - - +
176A VAL* 1.3 63.1 + - - +
178A MET* 3.4 11.7 + - + +
179A THR* 2.9 23.4 + - - -
195A THR* 4.0 15.0 - - + +
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Residues in contact with VAL 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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154A ALA* 4.1 13.9 - - + -
158A ALA* 3.9 19.1 - - + -
159A PHE* 4.1 25.6 - - + -
172A LYS 3.1 14.5 + - - +
173A GLY* 3.6 8.7 - - - +
175A ILE* 1.3 76.3 - - - +
177A GLY* 1.3 63.8 + - - +
179A THR* 3.1 22.2 + - - -
180A LEU 4.6 1.4 + - - -
195A THR* 5.1 0.4 - - - -
250A VAL* 4.3 23.7 - - + +
158B ALA 5.4 3.1 - - - +
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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
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173A GLY 3.0 16.8 + - - -
174A GLY 3.4 2.0 + - - -
176A VAL* 1.3 75.4 - - - +
178A MET* 1.3 59.2 + - - +
180A LEU* 4.5 0.5 + - - +
181A PRO* 3.5 14.9 - - - +
157B ALA 4.2 3.6 - - - +
158B ALA 3.7 21.2 - - - +
159B PHE 6.0 0.3 - - - -
161B GLY 5.2 0.5 + - - -
169B SER* 3.5 25.7 - - - -
173B GLY* 4.3 3.6 - - - -
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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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122A LEU* 4.1 18.4 - - + -
125A THR* 4.1 25.8 - - + -
126A PHE* 4.1 20.2 - - + +
129A ILE* 4.2 10.3 - - + -
152A ASN* 5.9 1.8 - - - +
174A GLY 3.1 14.1 + - - +
175A ILE* 3.7 13.5 - - + +
176A VAL 3.3 0.2 - - - -
177A GLY* 1.3 75.9 - - - +
179A THR* 1.3 65.2 + - - +
180A LEU 3.5 0.4 - - - -
181A PRO* 3.4 8.2 - - + +
182A ILE* 3.1 43.9 + - + +
114B PHE* 4.0 24.2 - - - -
166B ALA 3.8 16.6 - - - +
169B SER* 4.5 0.9 - - - -
170B ALA* 4.0 9.6 - - + +
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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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152A ASN* 4.4 2.6 + - - +
175A ILE 2.9 18.2 + - - -
176A VAL* 3.1 14.0 + - - -
178A MET* 1.3 77.2 - - - +
180A LEU* 1.3 58.7 + - - +
182A ILE* 4.0 2.2 - - - +
183A ALA* 3.1 26.9 + - - +
193A VAL* 4.1 18.9 - - + +
195A THR* 2.7 32.9 + - - +
248A GLY* 3.9 17.0 - - - +
249A GLU 3.9 21.3 - - - +
250A VAL* 4.6 4.3 - - + -
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Residues in contact with LEU 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 VAL 4.6 1.2 + - - -
177A GLY 4.5 0.6 + - - +
179A THR* 1.3 76.8 - - - +
181A PRO* 1.3 66.3 - - + +
183A ALA* 3.3 4.0 + - + -
184A ARG* 2.9 60.2 + - + +
248A GLY* 4.2 9.4 - - - +
159B PHE 4.0 20.0 - - - +
160B GLU* 4.0 8.7 - - - -
161B GLY 4.3 1.1 - - - +
256C ALA* 3.8 34.8 - - + +
258C ARG* 3.9 37.2 - - + +
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Residues in contact with PRO 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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177A GLY 3.5 19.5 - - - +
178A MET* 3.4 16.6 - - - +
180A LEU* 1.3 95.4 - - + +
182A ILE* 1.3 55.0 + - - +
184A ARG* 3.4 4.1 + - + +
185A ASP* 2.9 35.8 + - - +
161B GLY* 3.6 21.8 - - - +
162B GLN 3.5 21.9 - - - +
165B GLN 4.3 0.7 - - - +
166B ALA* 4.2 16.8 - - - +
169B SER* 3.7 17.0 - - - +
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Residues in contact with ILE 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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126A PHE* 4.0 19.5 - - + -
129A ILE* 4.0 26.5 - - + -
152A ASN* 6.2 0.2 - - - +
178A MET* 3.1 47.2 + - + +
179A THR* 4.1 2.2 - - - +
181A PRO* 1.3 71.6 - - - +
183A ALA* 1.3 64.5 + - - +
185A ASP* 3.1 6.2 + - - +
186A LEU* 3.0 36.0 + - + +
193A VAL* 4.0 22.4 - - + -
100B THR* 3.7 17.9 - - - +
166B ALA* 3.8 11.9 - - + -
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Residues in contact with ALA 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A THR 3.1 18.3 + - - +
180A LEU 3.3 3.8 + - - +
182A ILE* 1.3 73.0 - - - +
184A ARG* 1.3 61.4 + - - +
186A LEU 3.4 1.6 + - - +
187A ALA* 3.1 24.1 + - - +
191A ILE 4.7 3.7 - - - +
193A VAL* 4.0 15.8 - - + +
247A ASN* 3.5 31.6 + - - +
248A GLY* 4.0 15.0 - - - -
222C PRO* 5.3 1.4 - - - +
256C ALA* 4.6 7.0 - - + -
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Residues in contact with ARG 184 (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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180A LEU* 2.9 39.2 + - + +
181A PRO* 3.7 4.9 - - + +
183A ALA* 1.3 76.8 - - - +
185A ASP* 1.3 60.9 + - - +
186A LEU 3.5 0.2 + - - -
187A ALA* 3.5 15.7 + - - +
188A PRO* 3.8 4.7 - - - +
160B GLU* 3.3 16.8 + - - +
161B GLY 2.9 31.3 + - - -
162B GLN* 3.9 2.2 - - - +
163B VAL* 3.9 21.2 - - + +
259B MET 3.0 23.8 + - - -
260B GLN* 3.8 9.7 + - - +
261B PRO* 3.4 40.8 - - + +
222C PRO* 4.7 13.7 - - + +
256C ALA* 4.9 3.4 + - + -
258C ARG* 3.9 26.9 - - - +
260C GLN* 5.3 0.8 - - - +
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Residues in contact with ASP 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A PRO 2.9 19.4 + - - +
182A ILE* 3.1 8.2 + - - +
184A ARG* 1.3 75.3 - - - +
186A LEU* 1.3 63.5 + - + +
188A PRO* 3.5 16.5 - - - +
189A ILE* 5.6 0.5 - - - +
98B ILE 4.7 0.2 - - - +
99B LYS* 3.8 13.0 - - + +
100B THR* 2.8 46.6 + - - +
101B TYR 4.5 7.9 - - - +
162B GLN 5.4 0.2 - - - -
163B VAL* 3.4 17.1 - - - +
164B GLY 3.0 28.8 + - - -
166B ALA* 4.3 7.8 - - - +
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Residues in contact with LEU 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A ILE* 5.0 0.7 - - + -
133A ALA* 4.2 28.0 - - + -
150A ILE* 4.2 6.1 - - + -
182A ILE* 3.0 35.9 + - + +
183A ALA 3.7 2.0 - - - +
185A ASP* 1.3 78.9 - - + +
187A ALA* 1.3 64.6 + - - +
188A PRO* 3.5 2.2 - - - -
189A ILE* 3.1 26.2 + - + +
190A GLY 3.4 7.4 + - - -
191A ILE* 3.5 45.7 + - + +
193A VAL* 4.1 7.0 - - + -
100B THR* 4.3 14.1 - - + -
101B TYR* 4.3 19.3 - - + +
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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 ALA 3.1 16.5 + - - +
184A ARG 3.7 6.5 - - - +
185A ASP 3.4 0.2 - - - -
186A LEU* 1.3 76.4 - - - +
188A PRO* 1.3 69.3 - - + +
190A GLY* 3.0 15.3 + - - +
191A ILE 5.0 2.0 - - - -
247A ASN* 5.9 0.4 - - - +
222C PRO* 3.6 37.4 - - + +
223C PHE* 3.9 20.5 - - + -
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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