Contacts of the helix formed by residues 162 - 184 (chain B) in PDB entry 4DHI
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 162 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158B THR* 3.2 12.0 + - + +
159B ILE* 3.2 12.0 + - - +
161B ASN* 1.3 76.5 - - - +
163B ASP* 1.3 68.6 + - - +
164B GLY* 3.1 6.3 + - - -
165B SER* 3.1 31.9 + - - +
166B ALA* 2.7 24.7 + - - +
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Residues in contact with ASP 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B LEU* 3.5 27.0 - - - +
83B ARG* 4.2 13.7 + - - -
161B ASN 3.6 5.0 + - - -
162B ASP* 1.3 72.2 + - - +
164B GLY* 1.3 58.5 + - - +
167B ASN* 2.9 47.8 + - - +
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Residues in contact with GLY 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B ASP* 3.2 8.1 + - - -
163B ASP* 1.3 78.7 - - - +
165B SER* 1.3 61.5 + - - +
167B ASN* 4.0 1.9 - - - +
168B TYR* 3.1 32.7 + - - -
64D MET* 5.7 2.6 - - - +
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Residues in contact with SER 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B PHE* 3.6 26.1 - - - -
159B ILE* 3.7 32.3 - - - +
162B ASP* 3.1 19.8 + - - -
164B GLY* 1.3 74.9 - - - +
166B ALA* 1.3 64.1 + - - +
168B TYR* 3.3 2.8 + - - +
169B ILE* 3.0 28.8 + - - +
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Residues in contact with ALA 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B LEU* 3.8 9.2 - - + -
91B ARG* 3.7 17.1 + - - +
94B LEU* 5.1 1.6 - - - +
159B ILE 3.7 2.9 + - - -
160B LEU* 3.3 33.9 - - + +
162B ASP 2.7 23.4 + - - +
163B ASP 4.1 0.2 - - - +
165B SER* 1.3 74.7 - - - +
167B ASN* 1.3 57.9 + - - +
169B ILE* 3.4 9.2 + - - +
170B LEU* 2.9 27.4 + - - +
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Residues in contact with ASN 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B LEU* 5.1 1.8 - - - +
87B ASN* 4.4 0.5 + - - -
91B ARG* 3.1 30.0 + - - +
163B ASP* 2.9 36.7 + - - +
164B GLY 4.2 1.6 - - - +
166B ALA* 1.3 74.3 - - - +
168B TYR* 1.3 61.1 + - - +
170B LEU* 3.8 4.0 - - - +
171B MET* 2.9 29.3 + - - +
209B MET* 3.7 22.5 - - + +
210B TRP* 4.0 24.5 - - - -
64D MET* 3.7 21.6 - - + +
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Residues in contact with TYR 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B ASP* 4.8 13.3 - - + +
135B PHE* 3.3 48.0 - + - +
138B PHE* 3.7 41.5 - + + -
164B GLY* 3.1 22.0 + - - +
165B SER 3.3 8.0 + - - +
167B ASN* 1.3 75.6 - - - +
169B ILE* 1.3 62.7 + - - +
171B MET* 3.3 11.8 + - - +
172B PHE* 3.4 10.0 + - - +
7D ARG* 4.5 12.8 - - - +
63D PRO* 3.6 28.6 - - + +
64D MET* 3.7 16.8 - - + -
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Residues in contact with ILE 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B LEU* 4.1 26.7 - - + -
98B ILE* 4.8 1.6 - - + -
138B PHE* 4.0 17.3 - - + -
139B PHE* 3.8 35.2 - - + -
142B PHE* 3.8 32.1 - - + -
159B ILE* 4.1 18.6 - - + -
160B LEU* 4.2 9.2 - - + -
165B SER 3.0 22.2 + - - +
166B ALA* 3.7 4.9 - - - +
167B ASN 3.2 0.2 - - - -
168B TYR* 1.3 72.1 - - - +
170B LEU* 1.3 67.2 + - - +
172B PHE* 3.2 15.4 + - - +
173B PHE* 3.4 13.7 - - + -
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Residues in contact with LEU 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B ASN* 3.6 23.1 - - + +
90B TYR* 3.8 16.2 - - + -
91B ARG* 3.6 55.9 - - + +
94B LEU* 3.8 12.3 - - + +
166B ALA 2.9 17.8 + - - +
167B ASN* 3.8 8.1 - - - +
168B TYR 3.3 0.2 - - - -
169B ILE* 1.3 77.0 - - - +
171B MET* 1.3 63.2 + - - +
173B PHE* 3.0 13.9 + - - +
174B ARG* 3.1 36.6 + - + +
209B MET* 3.9 9.4 - - + -
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Residues in contact with MET 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B PHE* 3.9 33.9 - - + -
167B ASN 2.9 18.2 + - - +
168B TYR 3.6 6.3 - - - +
169B ILE 3.2 0.4 - - - -
170B LEU* 1.3 76.6 - - - +
172B PHE* 1.3 62.4 + - - +
174B ARG* 3.1 10.6 + - + +
175B LEU* 2.9 51.5 + - + +
207B GLU* 3.3 27.4 - - - +
209B MET* 3.9 15.3 - - - +
64D MET* 4.4 1.3 - - + -
96D SER* 3.7 15.7 - - - +
97D PRO* 3.7 22.2 - - + -
98D ALA* 4.4 5.2 - - + +
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Residues in contact with PHE 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B PHE* 5.2 1.8 - + - -
115B SER* 3.7 38.4 - - - -
118B TRP* 4.4 2.2 - + + -
135B PHE* 4.3 8.4 - - - +
136B CYS* 3.8 42.0 - - - -
139B PHE* 3.3 44.0 - + + -
140B ILE* 5.5 0.4 - - + -
168B TYR 3.4 4.5 + - - +
169B ILE 3.2 10.8 + - - +
171B MET* 1.3 77.3 - - - +
173B PHE* 1.3 69.6 + + - +
175B LEU* 3.2 12.5 + - + +
176B ILE* 3.0 64.2 + - + +
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Residues in contact with PHE 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B TYR* 4.3 13.9 - - + +
93B ILE* 5.5 1.1 - - + -
94B LEU* 3.6 35.2 - - + -
97B LEU* 3.8 25.1 - - + -
98B ILE* 5.9 1.6 - - + -
111B PHE* 4.2 14.6 - + - -
139B PHE* 3.6 39.3 - + - -
169B ILE* 3.4 17.7 - - + -
170B LEU* 3.0 8.9 + - - +
172B PHE* 1.3 80.7 - + - +
174B ARG* 1.3 64.4 + - - +
176B ILE* 3.6 18.6 - - + +
177B THR* 2.7 30.5 + - - -
221B LEU* 3.8 24.9 - - + -
225B ALA* 4.5 1.3 - - + -
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Residues in contact with ARG 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B GLY 3.1 10.7 + - - -
87B ASN* 2.9 28.5 + - - -
90B TYR* 3.4 38.1 + - + -
170B LEU* 3.1 17.8 + - + +
171B MET* 3.1 18.0 + - + +
173B PHE* 1.3 75.7 - - - +
175B LEU* 1.3 63.7 + - - +
177B THR* 3.4 0.9 + - - -
178B SER* 3.0 20.1 + - - -
206B ILE* 2.9 42.7 + - - +
207B GLU* 4.0 6.9 - - - +
208B PRO 3.1 20.1 + - - -
209B MET* 3.7 19.0 - - - +
211B LYS* 2.9 35.5 + - - +
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Residues in contact with LEU 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B LEU* 3.9 19.9 - - + +
127B PHE* 4.0 16.7 - - + -
132B CYS* 3.8 41.7 - - + +
135B PHE* 4.0 31.6 - - + -
136B CYS* 5.0 1.8 - - - -
171B MET* 2.9 35.9 + - + +
172B PHE* 3.2 10.5 + - + +
174B ARG* 1.3 76.4 - - - +
176B ILE* 1.3 58.1 + - + +
178B SER* 3.3 5.7 + - - -
179B ALA* 2.8 28.6 + - - +
207B GLU* 5.1 5.4 - - + -
98D ALA* 4.5 5.6 - - + -
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Residues in contact with ILE 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B PHE* 5.7 2.2 - - + -
118B TRP* 3.5 41.9 - - + +
122B LEU* 5.3 3.8 - - + -
172B PHE* 3.0 51.0 + - + +
173B PHE* 3.6 26.5 - - + +
175B LEU* 1.3 74.5 - - + +
177B THR* 1.3 64.2 + - - +
179B ALA* 3.7 6.9 - - - +
180B PHE* 2.9 30.8 + - - +
221B LEU* 5.0 1.1 - - + -
224B ALA* 3.6 31.7 - - + +
225B ALA* 4.2 7.4 - - + +
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Residues in contact with THR 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B TYR* 3.7 11.3 - - - +
173B PHE 2.7 22.8 + - - -
174B ARG 3.6 4.7 - - - -
176B ILE* 1.3 77.6 - - - +
178B SER* 1.3 61.8 + - - +
180B PHE* 3.4 3.4 + - - +
181B LEU* 3.2 23.4 + - + +
206B ILE* 3.8 23.3 - - + -
217B ALA 3.7 11.9 - - - +
220B SER* 3.8 6.8 - - - -
221B LEU* 3.4 40.3 - - + +
224B ALA* 4.4 7.4 - - - -
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Residues in contact with SER 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B PHE* 3.5 4.9 - - - -
174B ARG 3.0 16.8 + - - -
175B LEU 3.6 4.0 - - - -
177B THR* 1.3 74.7 - - - +
179B ALA* 1.3 58.4 + - - +
181B LEU* 3.1 4.7 + - - +
182B LYS* 2.9 35.9 + - - +
202B CYS* 3.2 21.0 - - - +
206B ILE* 3.7 8.2 - - - +
207B GLU* 2.6 39.3 + - - -
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Residues in contact with ALA 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B TRP* 3.5 23.6 - - + -
122B LEU* 3.5 24.0 - - + -
125B LEU* 3.5 16.0 - - + +
127B PHE* 3.7 8.4 - - - -
175B LEU 2.8 20.5 + - - +
176B ILE* 3.7 2.5 - - - +
178B SER* 1.3 71.3 + - - +
180B PHE* 1.3 57.0 + - - +
182B LYS* 3.2 1.2 + - - +
183B GLN* 2.8 32.7 + - - +
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Residues in contact with PHE 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B TRP* 3.9 16.3 - + + -
176B ILE 2.9 22.5 + - - +
177B THR 3.7 4.5 - - - +
178B SER 3.3 0.2 - - - -
179B ALA* 1.3 73.4 - - - +
181B LEU* 1.3 64.4 + - - +
183B GLN* 4.5 1.8 - - - -
184B ASN* 2.9 51.6 + - - +
188B TYR* 3.7 31.6 - + - -
220B SER* 4.0 26.0 - - - +
223B LYS* 3.6 37.5 - - + -
224B ALA* 3.8 19.7 - - + -
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Residues in contact with LEU 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177B THR 3.2 12.5 + - - +
178B SER 3.1 8.1 + - - +
180B PHE* 1.3 80.5 - - - +
182B LYS* 1.3 56.9 + - - +
184B ASN 3.2 4.0 - - - +
185B SER* 2.9 29.5 + - - -
188B TYR* 3.8 34.1 - - + -
198B VAL* 3.7 10.7 - - + +
201B TYR* 3.7 27.1 - - + +
202B CYS* 3.7 16.8 - - - -
206B ILE* 4.2 11.9 - - + -
216B LEU* 4.0 17.0 - - + +
220B SER* 3.3 30.1 - - - +
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Residues in contact with LYS 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B LEU* 4.5 21.0 + - + +
127B PHE* 3.8 29.9 - - + +
178B SER* 2.9 28.6 + - - +
179B ALA* 3.8 4.5 - - - +
181B LEU* 1.3 75.3 - - - +
183B GLN* 1.3 62.6 + - - +
185B SER* 3.4 23.7 + - - -
198B VAL* 4.4 2.0 - - + -
199B ALA* 4.3 22.1 - - + +
202B CYS* 3.8 18.8 - - - -
203B GLU* 4.9 10.3 + - - +
207B GLU* 3.0 21.2 + - - -
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Residues in contact with GLN 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B TRP* 4.1 14.0 - - - -
121B THR* 3.6 30.2 + - - +
124B GLU* 5.5 2.0 + - - -
125B LEU* 4.1 19.1 - - + +
179B ALA 2.8 17.5 + - - +
180B PHE* 3.9 5.0 - - - +
182B LYS* 1.3 77.5 - - - +
184B ASN* 1.3 71.3 + - - +
185B SER 3.5 0.7 + - - -
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Residues in contact with ASN 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180B PHE* 2.9 56.5 + - - +
181B LEU 3.2 4.3 - - - -
183B GLN* 1.3 91.9 + - - +
185B SER* 1.3 61.7 + - - +
186B GLU* 3.3 3.4 - - - -
187B GLU* 3.0 26.7 + - + +
188B TYR* 3.2 30.5 + - + -
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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) + - + + + + + -
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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