Contacts of the helix formed by residues 160 - 182 (chain C) in PDB entry 2B5F
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 ASN 160 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155C VAL* 4.6 3.7 - - - +
159C TYR* 1.3 76.0 - - - +
161C LYS* 1.3 63.7 + - - +
162C GLY* 3.1 6.1 + - - +
163C THR* 2.9 31.5 + - - -
164C ALA* 3.1 21.9 + - - +
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Residues in contact with LYS 161 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155C VAL* 4.6 10.5 - - + +
160C ASN* 1.3 76.2 - - - +
162C GLY* 1.3 57.0 + - - +
164C ALA* 3.4 7.7 + - - +
165C LEU* 2.9 29.7 + - - +
240C ASP* 5.6 3.1 - - - -
241C ASP* 3.3 27.7 + - - +
243C TRP* 4.6 22.0 - - + +
244C ILE* 4.3 18.9 - - + +
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Residues in contact with GLY 162 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A PHE* 5.4 0.2 - - - -
160C ASN* 3.1 7.5 + - - +
161C LYS* 1.3 77.9 - - - +
163C THR* 1.3 58.6 + - - +
165C LEU* 3.5 8.1 + - - +
166C GLY* 3.0 23.7 + - - -
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Residues in contact with THR 163 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A ALA 5.0 1.2 + - - -
140A PHE* 3.3 52.9 + - + +
159C TYR* 3.6 28.6 - - + +
160C ASN* 2.9 25.4 + - - -
162C GLY* 1.3 73.0 - - - +
164C ALA* 1.3 60.4 + - - +
166C GLY 3.2 0.9 + - - -
167C ALA* 2.9 27.0 + - - +
216C ILE* 4.3 7.2 - - + -
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Residues in contact with ALA 164 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155C VAL* 4.4 18.8 - - + -
160C ASN 3.1 11.4 + - - +
161C LYS* 3.7 10.5 - - - +
163C THR* 1.3 77.7 - - - +
165C LEU* 1.3 64.9 + - - +
167C ALA* 3.2 2.6 + - - +
168C GLU* 2.9 27.7 + - - +
216C ILE* 4.1 8.5 - - + +
217C THR* 4.0 22.7 - - + +
244C ILE* 4.2 12.8 - - + -
245C PHE* 5.6 0.4 - - + -
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Residues in contact with LEU 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161C LYS 2.9 18.6 + - - +
162C GLY* 3.9 7.9 - - - +
163C THR 3.2 0.2 - - - -
164C ALA* 1.3 77.0 - - - +
166C GLY* 1.3 62.5 + - - +
168C GLU* 3.2 3.2 + - - +
169C ILE* 2.9 39.8 + - + +
243C TRP* 4.2 25.8 - - + -
244C ILE* 3.9 18.8 - - + +
247C VAL* 4.3 13.5 - - + -
248C GLY* 3.5 35.7 - - - +
251C ILE* 5.5 2.7 - - + -
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Residues in contact with GLY 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A PHE* 3.4 20.6 - - - -
162C GLY 3.0 14.8 + - - -
163C THR 3.2 3.5 + - - -
165C LEU* 1.3 76.6 - - - +
167C ALA* 1.3 55.2 + - - +
169C ILE* 3.3 12.6 + - - +
170C ILE* 3.0 30.3 + - - +
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Residues in contact with ALA 167 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A TYR* 3.8 16.3 + - - +
140A PHE* 3.2 13.9 - - + -
163C THR 2.9 16.3 + - - +
164C ALA* 3.7 5.8 - - - +
166C GLY* 1.3 77.1 - - - +
168C GLU* 1.3 57.3 + - - +
170C ILE* 3.9 2.5 - - - +
171C GLY* 2.9 28.4 + - - -
213C THR* 4.5 20.6 + - + +
216C ILE* 4.3 17.7 - - + -
217C THR* 4.8 1.1 - - + -
221C ILE* 5.3 0.2 - - - +
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Residues in contact with GLU 168 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164C ALA 2.9 20.6 + - - +
165C LEU 3.7 4.3 - - - +
167C ALA* 1.3 74.6 - - - +
169C ILE* 1.3 59.6 + - - +
172C THR* 2.7 37.8 + - - -
213C THR* 4.1 3.2 - - - +
217C THR* 2.5 31.0 + - + -
220C GLY* 2.9 15.8 + - - -
221C ILE* 2.7 33.6 + - - +
244C ILE* 4.3 8.3 - - + +
245C PHE* 3.6 26.0 - - + -
248C GLY* 4.1 16.3 - - - +
249C PRO* 4.1 4.9 - - + +
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Residues in contact with ILE 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165C LEU* 2.9 36.7 + - + +
166C GLY* 3.3 12.1 + - - +
168C GLU* 1.3 77.7 - - - +
170C ILE* 1.3 61.1 + - + +
172C THR 3.4 0.7 + - - -
173C PHE* 2.9 26.5 + - + +
248C GLY* 3.6 25.1 - - - +
251C ILE* 4.0 28.7 - - + +
252C GLY* 3.3 19.2 - - - -
255C VAL* 5.2 5.6 - - + -
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Residues in contact with ILE 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A LEU* 4.7 3.8 - - + -
50A LEU* 3.1 36.6 - - + -
53A TYR* 3.4 50.7 - - + +
136A LEU* 4.9 12.3 - - + -
140A PHE* 5.6 2.5 - - + -
166C GLY 3.0 10.9 + - - +
167C ALA 3.9 4.7 - - - +
169C ILE* 1.3 79.0 - - + +
171C GLY* 1.3 70.3 + - - +
173C PHE* 3.2 11.3 + - + +
174C VAL* 3.0 27.9 + - + +
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Residues in contact with GLY 171 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A TYR* 5.8 1.3 - - - -
54A ILE* 5.9 0.9 - - - -
167C ALA 2.9 18.3 + - - -
168C GLU 4.0 0.4 - - - -
170C ILE* 1.3 79.3 - - - +
172C THR* 1.3 61.2 + - - +
174C VAL* 3.4 2.6 + - - -
175C LEU* 3.3 18.2 + - - +
209C VAL* 3.6 35.4 - - - +
213C THR* 5.1 0.9 - - - -
221C ILE* 3.9 8.6 - - - +
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Residues in contact with THR 172 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103C ALA* 4.0 13.0 - - + -
168C GLU 2.7 23.1 + - - -
169C ILE 3.8 2.5 - - - -
171C GLY* 1.3 71.5 - - - +
173C PHE* 1.3 61.2 + - - +
175C LEU* 3.2 5.4 + - + +
176C VAL* 2.9 37.9 + - + +
221C ILE* 3.4 28.2 - - - +
249C PRO* 3.3 43.9 - - + +
252C GLY* 4.3 3.1 - - - -
253C ALA 4.1 1.3 - - - +
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Residues in contact with PHE 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A ILE* 4.5 10.8 - - + -
50A LEU* 3.5 32.1 - - + -
169C ILE* 2.9 16.3 + - + +
170C ILE* 3.3 15.0 - - + +
172C THR* 1.3 75.1 - - - +
174C VAL* 1.3 62.7 + - - +
177C TYR* 2.8 48.6 + + + +
252C GLY* 3.7 11.1 + - - +
255C VAL* 3.6 25.8 - - + -
256C ALA* 3.5 37.5 - - + -
259C TYR* 4.3 26.5 - + + -
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Residues in contact with VAL 174 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A LEU* 3.5 34.3 - - + -
54A ILE* 4.4 16.2 - - + -
84A MET* 4.7 18.6 - - + -
87A VAL* 5.1 5.4 - - + -
88A LEU* 6.4 0.9 - - + -
170C ILE* 3.0 20.7 + - + +
171C GLY* 3.6 8.7 - - - +
172C THR 3.3 0.2 - - - -
173C PHE* 1.3 76.8 - - - +
175C LEU* 1.3 57.9 + - - +
177C TYR* 3.7 5.8 - - + +
178C THR* 2.6 38.8 + - - +
205C ALA* 4.3 10.1 - - + +
208C MET* 5.7 0.4 - - + -
209C VAL* 3.8 17.5 - - + -
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Residues in contact with LEU 175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C ASN* 3.5 29.2 - - - +
104C VAL* 4.2 10.1 - - + -
171C GLY 3.3 9.6 + - - +
172C THR* 3.2 9.3 + - + +
174C VAL* 1.3 78.1 - - - +
176C VAL* 1.3 66.0 + - + +
178C THR* 3.1 7.3 + - - -
179C VAL* 2.9 32.2 + - + +
202C ILE* 3.7 31.6 - - + -
205C ALA* 4.5 10.9 + - + +
206C VAL* 3.8 11.7 - - + -
221C ILE* 3.7 27.1 - - + +
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Residues in contact with VAL 176 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103C ALA 4.2 12.6 - - - +
104C VAL* 4.5 9.2 - - + +
107C GLY* 4.7 5.6 - - - -
108C LEU* 6.5 0.2 - - + -
172C THR* 2.9 31.3 + - + +
175C LEU* 1.3 77.3 - - + +
177C TYR* 1.3 66.5 + - - +
179C VAL* 3.2 9.4 + - + +
180C PHE* 3.0 42.9 + - + -
253C ALA* 4.0 28.7 - - + +
256C ALA* 3.6 20.4 - - + -
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Residues in contact with TYR 177 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A ALA* 5.3 3.6 + - - +
46A ILE* 4.9 11.6 - - + +
47A ALA* 6.0 3.1 - - + -
50A LEU* 5.0 8.3 - - + -
88A LEU* 5.0 12.3 - - + -
91A CYS* 3.6 39.7 + - + +
92A THR* 4.4 10.7 - - + +
95A ILE* 5.8 2.4 - - - +
173C PHE* 2.8 40.9 + + + +
174C VAL* 3.7 5.4 - - - +
176C VAL* 1.3 77.5 - - - +
178C THR* 1.3 59.8 + - - +
180C PHE* 3.5 6.4 + - + +
181C SER* 2.9 41.2 + - - -
256C ALA* 3.8 9.6 - - + +
259C TYR* 3.8 38.3 + + + -
260C HIS* 5.6 5.4 - + - -
263C VAL* 6.3 0.9 - - + -
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Residues in contact with THR 178 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A VAL* 3.8 17.2 - - + +
90A TYR* 4.9 3.2 - - + -
91A CYS* 4.1 19.0 - - - -
174C VAL* 2.6 22.0 + - - +
175C LEU 3.1 7.6 + - - -
177C TYR* 1.3 76.1 - - - +
179C VAL* 1.3 51.5 + - - +
181C SER* 3.1 4.5 + - - -
182C ALA* 2.7 35.1 + - - +
201C PRO* 3.8 28.0 - - + +
202C ILE* 4.4 4.5 - - + +
205C ALA* 3.4 27.7 - - + +
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Residues in contact with VAL 179 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104C VAL* 4.2 31.6 - - + -
108C LEU* 4.5 17.0 - - + -
175C LEU* 2.9 27.2 + - + +
176C VAL* 3.2 12.1 + - + +
178C THR* 1.3 76.2 - - - +
180C PHE* 1.3 57.9 + - + +
182C ALA* 2.5 33.0 + - - +
183C THR* 3.0 7.5 + - - +
197C LEU* 4.0 22.6 - - + +
202C ILE* 3.7 24.2 - - + +
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Residues in contact with PHE 180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107C GLY 3.4 27.1 - - - -
108C LEU* 3.9 21.5 - - + -
111C ALA* 3.8 22.9 - - + -
113C LYS* 4.7 9.4 - - - -
176C VAL* 3.0 42.5 + - + +
177C TYR* 3.9 5.4 - - - +
179C VAL* 1.3 73.1 - - + +
181C SER* 1.3 65.5 + - - +
183C THR* 3.2 25.3 - - - +
256C ALA 4.5 2.2 - - - -
257C ALA* 3.5 28.0 - - + -
260C HIS* 3.0 54.5 + + + +
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Residues in contact with SER 181 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A TYR* 3.4 21.9 + - - -
91A CYS* 4.0 26.3 + - - +
192A SER* 4.9 10.9 + - - +
193A HIS* 6.1 0.3 - - - +
177C TYR* 2.9 29.2 + - - -
178C THR 3.1 7.4 + - - -
180C PHE* 1.3 81.2 - - - +
182C ALA* 1.3 55.4 + - - +
183C THR 3.1 9.1 + - - +
260C HIS* 4.9 3.8 + - - -
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Residues in contact with ALA 182 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A TYR* 4.0 13.5 - - + +
178C THR* 2.7 14.8 + - + +
179C VAL* 2.5 29.9 + - - +
181C SER* 1.3 70.7 - - - +
183C THR* 1.3 59.0 + - - +
184C ASP* 5.0 1.2 - - - +
196C ILE 3.3 0.5 - - - +
197C LEU* 2.9 36.7 - - + -
198C ALA* 3.3 24.2 + - - +
201C PRO* 5.1 1.3 - - + -
202C ILE* 4.6 7.4 - - + -
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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