Contacts of the helix formed by residues 169 - 193 (chain A) in PDB entry 4EVI
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 ALA 169 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A CYS 4.4 2.0 + - - -
167A GLU 3.9 2.6 + - - -
168A ASP* 1.3 73.4 + - - +
170A ASN* 1.3 58.5 + - - +
172A SER* 3.7 6.9 - - - -
173A GLN* 2.9 29.7 + - - +
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Residues in contact with ASN 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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124A HIS* 4.9 9.9 + - - -
168A ASP* 3.3 7.5 + - - +
169A ALA* 1.3 75.1 - - - +
171A PHE* 1.3 82.2 + - - +
173A GLN* 3.0 15.2 + - - +
174A LEU* 3.1 30.9 + - - +
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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
----------------------------------------------------------
121A CYS* 3.8 40.2 - - - -
124A HIS* 3.9 17.7 - + + +
126A HIS* 3.8 37.0 - + + -
127A LEU* 4.0 20.6 - - + -
152A PHE* 5.3 0.9 - + - -
161A VAL* 4.2 22.9 - - + -
164A VAL* 4.6 10.5 - - + -
165A CYS* 4.3 11.9 - - - -
168A ASP* 3.0 26.2 + - - +
170A ASN* 1.3 84.9 - - - +
172A SER* 1.3 63.7 + - - +
174A LEU* 3.3 10.5 + - + +
175A PHE* 3.1 22.5 + + + +
329A PHE* 5.9 0.7 - + - -
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Residues in contact with SER 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A CYS* 3.2 43.5 + - - +
168A ASP 2.9 20.1 + - - -
169A ALA* 3.7 7.9 - - - -
171A PHE* 1.3 79.6 - - - +
173A GLN* 1.3 57.0 + - - +
175A PHE* 3.3 2.4 + - - +
176A SER* 3.0 31.8 + - - -
234A HIS* 3.8 15.2 + - - -
235A VAL* 5.7 0.3 - - - +
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Residues in contact with GLN 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A ALA 2.9 19.7 + - - +
170A ASN* 3.0 8.0 + - - +
172A SER* 1.3 75.4 - - - +
174A LEU* 1.3 61.0 + - + +
176A SER* 3.3 7.1 + - - -
177A GLU* 2.8 50.5 + - - +
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Residues in contact with LEU 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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117A SER* 3.5 36.2 - - - +
120A PHE* 3.9 31.2 - - + +
121A CYS* 3.9 21.4 - - + +
124A HIS* 4.7 10.1 - - + -
170A ASN* 3.1 35.4 + - - +
171A PHE* 3.3 11.9 + - + +
173A GLN* 1.3 76.1 - - + +
175A PHE* 1.3 56.2 + - - +
177A GLU* 4.5 3.8 - - - +
178A GLY* 2.8 26.7 + - - -
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Residues in contact with PHE 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A LEU* 5.0 1.6 - - + -
121A CYS* 3.9 14.8 - - - -
161A VAL* 4.8 3.4 - - + -
162A TYR* 3.8 30.7 - + - -
165A CYS* 4.1 19.5 - - - -
171A PHE* 3.1 13.1 + + + +
172A SER* 3.7 9.2 - - - +
174A LEU* 1.3 79.4 - - - +
176A SER* 1.3 57.2 + - - +
178A GLY* 3.3 1.7 + - - -
179A MET* 3.0 57.2 + - + +
329A PHE* 4.0 30.7 - + - -
330A LEU* 5.1 0.2 - - + -
401A SAH 4.8 2.0 - - - -
402A C9M 3.9 36.3 - + + -
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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 SER* 3.0 19.5 + - - -
173A GLN* 3.3 9.7 + - - -
175A PHE* 1.3 72.8 - - - +
177A GLU* 1.3 64.2 + - - +
179A MET* 3.3 8.3 + - - +
180A ALA* 2.9 28.6 + - - +
210A GLY* 6.4 0.9 - - - -
211A THR* 4.7 18.5 + - - +
235A VAL* 5.3 13.9 - - - -
401A SAH 6.1 0.9 - - - -
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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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114A ASN 5.4 1.2 - - - +
117A SER* 2.7 36.4 + - - +
173A GLN* 2.8 36.5 + - + +
174A LEU* 4.4 5.0 - - - +
176A SER* 1.3 73.7 - - - +
178A GLY* 1.3 57.9 + - - +
180A ALA* 3.2 8.0 + - - +
181A GLY* 2.9 26.7 + - - -
-7B GLY 4.8 11.3 + - - -
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Residues in contact with GLY 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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114A ASN 6.0 1.3 - - - -
115A ALA* 6.4 0.7 - - - -
117A SER* 3.9 0.8 - - - -
118A LEU* 3.8 36.5 - - - +
174A LEU 2.8 18.5 + - - -
175A PHE 3.6 2.0 - - - -
176A SER 3.2 0.4 - - - -
177A GLU* 1.3 78.7 - - - +
179A MET* 1.3 69.2 + - - +
181A GLY* 3.5 1.4 + - - -
182A ASP* 3.4 19.8 + - - +
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Residues in contact with MET 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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118A LEU* 3.8 15.9 - - + -
175A PHE* 3.0 42.3 + - + +
176A SER* 3.7 7.6 - - - +
177A GLU 3.3 0.4 - - - -
178A GLY* 1.3 73.3 - - - +
180A ALA* 1.3 61.0 + - - +
182A ASP* 3.3 5.0 + - - +
183A SER 2.9 24.1 + - - -
268A TRP* 3.5 29.4 - - + -
401A SAH 3.2 56.9 - - + +
402A C9M 3.7 28.5 - - + +
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Residues in contact with ALA 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A PRO 5.1 0.7 - - - -
176A SER 2.9 17.7 + - - +
177A GLU* 3.2 9.2 + - - +
179A MET* 1.3 76.4 - - - +
181A GLY* 1.3 62.6 + - - +
183A SER* 3.3 6.1 + - - -
184A TRP* 3.0 24.4 + - - +
211A THR* 3.7 13.5 - - - +
213A ASN* 3.5 26.1 - - - +
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Residues in contact with GLY 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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112A PRO 3.9 18.4 - - - -
113A TYR* 3.8 16.6 - - - +
114A ASN 4.3 10.8 - - - -
177A GLU 2.9 15.6 + - - -
178A GLY 3.5 2.0 + - - -
179A MET 3.3 0.2 - - - -
180A ALA* 1.3 79.7 - - - +
182A ASP* 1.3 62.1 + - - +
184A TRP* 3.4 13.5 + - - +
185A LEU* 3.6 4.9 + - - +
13B GLN* 4.4 3.5 - - - +
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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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118A LEU* 5.8 2.2 - - + -
178A GLY 3.4 10.2 + - - +
179A MET 3.3 5.6 + - - +
180A ALA 3.3 0.2 - - - -
181A GLY* 1.3 76.6 - - - +
183A SER* 1.3 56.7 + - - +
185A LEU* 3.1 4.2 + - - +
186A PHE* 2.8 26.6 + - - +
267A LYS* 2.8 20.1 + - - -
268A TRP* 3.5 21.3 - - + -
361A ARG* 2.7 47.2 + - - -
10B LEU* 4.0 0.7 - - - +
13B GLN* 2.9 32.3 + - - +
17B TRP* 3.7 4.6 - - + -
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Residues in contact with SER 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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179A MET 2.9 11.9 + - - -
180A ALA* 3.3 6.7 + - - -
182A ASP* 1.3 76.6 - - - +
184A TRP* 1.3 59.0 + - - +
186A PHE* 4.4 0.2 - - - -
187A SER* 2.8 33.3 + - - -
209A GLY 5.8 0.2 + - - -
213A ASN* 3.8 15.0 - - - +
214A THR* 3.1 19.6 + - - -
267A LYS* 3.2 11.7 + - - +
401A SAH 2.4 34.4 + - - -
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Residues in contact with TRP 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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112A PRO* 3.6 45.0 - - + +
113A TYR* 3.5 32.1 - + + -
180A ALA 3.0 11.7 + - - +
181A GLY 3.4 12.1 - - - +
182A ASP 3.2 0.2 - - - -
183A SER* 1.3 78.4 - - - +
185A LEU* 1.3 65.6 + - + +
187A SER* 3.3 4.9 + - - -
188A ARG* 2.8 75.3 + - - +
213A ASN* 3.4 24.4 - - - +
241A GLN* 5.5 1.8 - - - -
1B MET* 3.8 33.9 - - + -
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Residues in contact with LEU 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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106A LEU* 4.2 7.2 - - + -
113A TYR* 3.6 25.6 - - + -
181A GLY 3.6 1.5 + - - +
182A ASP 3.1 5.9 + - - +
184A TRP* 1.3 101.1 - - + +
186A PHE* 1.3 65.8 + - - +
188A ARG* 3.3 6.4 + - - +
189A ALA* 3.2 20.6 + - - +
6B ALA* 3.9 17.3 - - - +
9B LEU* 3.6 45.1 - - + +
10B LEU* 3.9 13.2 - - + +
13B GLN* 3.8 29.6 - - + +
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Residues in contact with PHE 186 (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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182A ASP* 2.8 24.3 + - - +
183A SER 4.2 0.4 - - - +
185A LEU* 1.3 73.2 - - - +
187A SER* 1.3 60.6 + - - +
189A ALA* 3.2 3.5 + - - +
190A LEU* 2.8 45.4 + - + +
214A THR* 5.7 0.4 - - + -
267A LYS* 3.5 28.9 - - + -
301A ALA* 3.6 32.1 - - + -
357A VAL* 3.7 33.0 - - + -
358A GLY 3.9 2.2 - - - -
361A ARG* 3.9 39.5 - - + -
362A VAL 4.5 5.6 - - - -
10B LEU* 3.8 23.5 - - + +
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Residues in contact with SER 187 (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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183A SER* 2.8 22.7 + - - +
184A TRP 3.3 4.9 + - - -
186A PHE* 1.3 80.8 - - - +
188A ARG* 1.3 65.0 + - - +
190A LEU* 3.2 10.1 + - - +
191A VAL* 3.1 30.0 + - - +
213A ASN 3.5 2.4 + - - -
214A THR* 3.7 30.5 - - - -
217A VAL* 3.3 28.9 - - - +
218A ILE* 5.7 0.2 - - - -
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Residues in contact with ARG 188 (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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184A TRP* 2.8 84.6 + - - +
185A LEU 3.3 3.9 + - - +
187A SER* 1.3 83.6 + - - +
189A ALA* 1.3 61.2 + - - +
191A VAL* 3.6 6.1 - - - +
192A SER* 3.5 19.2 + - - -
213A ASN* 5.2 0.6 + - - -
217A VAL* 3.4 29.4 - - + +
220A GLU* 5.0 2.6 + - - -
403A GOL 3.8 29.6 + - - +
1B MET* 5.0 13.2 + - - +
3B ALA* 4.6 7.6 - - - +
6B ALA* 3.7 23.8 - - + -
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Residues in contact with ALA 189 (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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185A LEU 3.2 9.6 + - - +
186A PHE 3.5 7.2 - - - +
188A ARG* 1.3 77.2 - - - +
190A LEU* 1.3 57.0 + - - +
192A SER* 3.2 3.1 + - - -
193A LYS* 2.8 34.0 + - - +
357A VAL* 3.5 10.5 - - + +
6B ALA* 4.5 1.6 - - - +
7B VAL* 3.8 30.5 - - + +
10B LEU* 3.5 28.7 - - + -
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Residues in contact with LEU 190 (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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186A PHE* 2.8 38.3 + - + +
187A SER* 3.2 7.6 + - - +
189A ALA* 1.3 77.8 - - - +
191A VAL* 1.3 57.6 + - - +
194A CYS* 2.8 58.2 + - + +
198A PHE* 3.9 23.1 - - + -
214A THR* 4.7 17.7 - - + -
218A ILE* 4.7 7.0 - - + -
265A LEU* 5.3 7.4 - - + -
301A ALA* 5.2 5.8 - - + -
357A VAL* 3.6 17.9 - - + +
363A LEU* 4.2 20.4 - - + -
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Residues in contact with VAL 191 (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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187A SER 3.1 19.1 + - - +
188A ARG* 3.6 9.0 - - - +
190A LEU* 1.3 77.9 - - + +
192A SER* 1.3 62.7 + - - +
195A ARG* 3.4 25.2 + - - +
198A PHE* 4.4 10.8 - - + -
217A VAL* 3.9 17.7 - - + -
218A ILE* 4.2 21.5 - - + -
221A THR* 3.7 26.7 - - + +
222A PHE* 3.9 26.0 - - + -
403A GOL 4.4 8.1 - - - +
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Residues in contact with SER 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A ARG 3.6 11.2 - - - -
189A ALA* 3.2 8.0 + - - -
190A LEU 3.1 0.6 - - - -
191A VAL* 1.3 83.2 - - - +
193A LYS* 1.3 70.0 + - - +
194A CYS 3.3 0.6 + - - -
195A ARG* 3.8 9.6 + - - +
3B ALA* 3.6 26.6 - - - +
7B VAL* 5.6 1.8 - - - +
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Residues in contact with LYS 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A ALA 2.8 20.7 + - - +
192A SER* 1.3 79.1 - - - +
194A CYS* 1.3 64.9 + - - +
195A ARG 3.6 0.8 + - - -
355A THR* 3.9 12.1 - - + +
356A PRO* 4.0 26.2 + - - +
357A VAL* 3.0 33.5 + - - +
358A GLY* 5.2 0.6 - - - -
7B VAL* 4.2 28.0 - - + +
11B ASP* 5.3 1.8 + - - -
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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