Contacts of the helix formed by residues 168 - 192 (chain A) in PDB entry 2BAP
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 VAL 168 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A PRO* 1.3 76.0 - - + +
169A SER* 1.3 70.2 + - - +
170A TRP 3.3 0.7 - - - -
171A VAL* 3.2 16.6 + - - +
172A GLN* 3.3 25.3 + - - +
218A ASN* 3.5 31.6 + - + +
219A LYS* 5.9 1.6 - - + +
220A PHE* 5.0 6.5 - - + +
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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
----------------------------------------------------------
167A PRO* 3.8 13.5 - - - +
168A VAL* 1.3 81.5 - - - +
170A TRP* 1.3 63.5 + - - +
172A GLN* 3.3 32.3 + - - +
173A THR* 3.2 14.2 + - - +
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Residues in contact with TRP 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A SER* 3.7 33.2 - - - -
136A ALA* 3.8 25.6 - - + +
139A TYR* 4.2 21.8 - + - -
159A LEU* 5.5 2.7 - - + -
162A SER* 4.0 26.5 - - - -
163A LEU* 4.2 20.4 - - + -
166A ASN* 3.3 38.7 - - + +
167A PRO* 3.8 25.2 - - + +
168A VAL 3.3 0.4 - - - -
169A SER* 1.3 80.9 + - - +
171A VAL* 1.3 66.3 + - + +
173A THR* 2.6 22.5 + - - -
174A PHE* 3.6 13.5 + + + -
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Residues in contact with VAL 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A LEU* 4.1 27.6 - - + +
167A PRO 3.2 23.1 - - - +
168A VAL* 3.2 11.6 + - - +
170A TRP* 1.3 82.1 - - + +
172A GLN* 1.3 64.5 + - - +
174A PHE* 3.2 8.0 + - - +
175A GLY* 3.1 15.9 + - - -
214A ALA 5.6 1.3 - - - +
215A PHE* 3.5 42.5 - - + +
218A ASN* 4.3 14.8 - - - +
220A PHE* 4.3 5.9 - - + -
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Residues in contact with GLN 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A VAL* 3.3 23.1 + - - +
169A SER* 3.4 29.2 - - - +
170A TRP 3.3 0.4 - - - -
171A VAL* 1.3 77.3 - - - +
173A THR* 1.3 55.1 + - + +
175A GLY* 2.7 26.2 + - - -
177A GLU* 5.1 0.5 - - - +
220A PHE* 3.6 44.5 - - + +
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Residues in contact with THR 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A SER* 5.2 5.7 + - - +
136A ALA* 3.8 19.3 - - - +
137A MET* 6.0 1.0 - - - +
140A ILE* 3.9 10.9 - - - +
169A SER 3.2 8.3 + - - +
170A TRP* 2.6 31.9 + - - -
172A GLN* 1.3 76.4 - - + +
174A PHE* 1.3 59.1 + - - +
177A GLU* 3.9 10.6 - - - +
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Residues in contact with PHE 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A ALA* 4.1 12.7 - - + +
139A TYR* 3.9 19.7 - - + -
140A ILE* 3.8 25.6 - - + +
143A LEU* 3.9 11.7 - - + -
159A LEU* 3.9 20.0 - - + -
163A LEU* 4.7 19.5 - - + -
170A TRP* 3.6 12.4 + + + +
171A VAL* 3.2 14.9 + - - +
172A GLN 3.1 0.2 - - - -
173A THR* 1.3 79.1 + - - +
175A GLY* 1.3 68.2 + - - +
177A GLU* 3.8 3.8 + - - +
178A GLY* 2.8 56.2 + - - -
179A LEU* 3.6 6.7 - - - -
182A LEU* 3.9 18.6 - - + -
215A PHE* 4.9 9.9 - + - -
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Residues in contact with GLY 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A VAL 3.1 6.5 + - - -
172A GLN 2.7 20.6 + - - -
174A PHE* 1.3 84.5 - - - +
176A ALA* 1.3 60.9 + - - -
177A GLU* 4.2 6.1 - - - -
179A LEU* 3.4 17.8 + - - +
215A PHE* 4.2 6.8 - - - -
220A PHE* 4.0 19.7 - - - -
224A THR* 4.9 2.5 - - - -
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Residues in contact with ALA 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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175A GLY* 1.3 72.4 - - - -
177A GLU* 1.3 66.2 + - - +
179A LEU* 3.4 7.8 + - + +
180A ALA* 2.7 37.0 + - - +
220A PHE* 5.3 0.2 - - - -
224A THR* 4.1 23.0 - - + +
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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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140A ILE* 4.3 12.0 - - + +
144A ARG* 4.0 24.5 + - - +
172A GLN 5.1 0.5 - - - +
173A THR 3.9 17.3 - - - +
174A PHE 4.0 4.0 - - - +
175A GLY* 4.2 2.4 - - - -
176A ALA* 1.3 94.1 + - + +
178A GLY* 1.3 57.8 + - - +
180A ALA* 3.0 23.4 - - - +
181A SER* 3.1 10.2 + - - -
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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
----------------------------------------------------------
140A ILE* 4.0 8.6 - - - +
143A LEU* 4.2 0.2 - - - +
174A PHE* 2.8 50.8 + - - -
177A GLU* 1.3 73.9 - - - +
179A LEU* 1.3 64.3 + - - +
180A ALA 3.1 1.6 - - - -
181A SER* 2.6 22.3 + - - -
182A LEU* 3.4 6.6 + - - +
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Residues in contact with LEU 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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174A PHE* 3.6 10.0 - - - -
175A GLY 3.4 19.1 + - - +
176A ALA* 3.6 4.9 - - + +
178A GLY* 1.3 72.1 - - - +
180A ALA* 1.3 68.0 + - - +
182A LEU* 3.0 19.7 + - - +
183A LEU* 3.3 22.6 + - + +
212A LEU* 3.7 25.1 - - + -
215A PHE* 3.2 34.1 - - + -
224A THR* 3.4 33.9 - - + +
225A MET* 3.9 8.3 - - + -
228A THR* 3.9 10.3 - - + -
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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
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176A ALA 2.7 17.3 + - - +
177A GLU* 3.0 16.4 - - - +
179A LEU* 1.3 73.1 - - - +
181A SER* 1.3 55.4 + - - +
183A LEU* 2.9 27.2 + - - +
184A ASP* 2.5 24.7 + - - +
228A THR* 6.3 0.9 - - - -
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Residues in contact with SER 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A ILE* 4.4 4.5 - - - +
143A LEU* 3.5 28.3 - - - +
144A ARG* 4.8 15.5 - - - -
177A GLU 3.1 10.0 + - - -
178A GLY* 2.6 19.9 + - - -
180A ALA* 1.3 75.1 - - - +
182A LEU* 1.3 60.3 + - - +
184A ASP* 3.3 13.2 + - - +
185A ILE* 3.2 31.1 + - - +
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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
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143A LEU* 4.0 10.3 - - + -
156A LEU* 4.0 10.3 - - + -
159A LEU* 3.8 25.1 - - + -
163A LEU* 5.4 2.2 - - + -
174A PHE* 3.9 24.7 - - + -
178A GLY 3.4 8.0 + - - +
179A LEU* 3.0 14.6 + - + +
181A SER* 1.3 78.5 - - - +
183A LEU* 1.3 63.1 + - - +
185A ILE* 3.6 6.6 + - + +
186A LEU* 3.3 15.1 + - - +
208A ILE* 3.3 36.3 - - + +
211A CYS* 4.2 20.9 - - + +
212A LEU* 4.5 17.5 - - + -
215A PHE* 5.7 3.8 - - + -
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Residues in contact with LEU 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 LEU* 3.5 28.3 - - + +
180A ALA* 2.9 10.5 + - - +
182A LEU* 1.3 73.7 - - - +
184A ASP* 1.3 66.4 + - - +
186A LEU* 3.1 32.4 + - + +
187A LYS* 3.2 16.9 + - - +
212A LEU* 4.2 10.8 - - + -
225A MET* 3.8 24.2 - - + -
228A THR* 4.0 22.9 - - + -
230A GLU* 5.0 1.3 - - + -
231A GLY* 4.2 15.5 - - - +
234A LEU* 3.9 20.6 - - + +
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Residues in contact with ASP 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A ALA* 2.5 30.4 - - - +
181A SER* 3.3 16.1 + - - +
183A LEU* 1.3 76.5 - - - +
185A ILE* 1.3 63.2 + - + +
187A LYS* 3.3 25.9 + - - +
188A ARG* 3.1 27.4 + - - +
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Residues in contact with ILE 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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143A LEU* 3.8 44.4 - - + +
152A LEU* 4.2 19.5 - - + -
156A LEU* 5.8 0.7 - - + -
181A SER 3.2 19.6 + - - +
182A LEU* 3.9 9.9 - - + +
183A LEU 3.2 0.2 - - - -
184A ASP* 1.3 74.0 - - + +
186A LEU* 1.3 56.2 + - - +
188A ARG* 3.4 34.8 + - - +
189A LEU* 2.7 57.7 + - + +
208A ILE* 4.0 12.8 - - + -
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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
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182A LEU 3.3 10.6 + - - +
183A LEU* 3.1 27.0 + - + +
185A ILE* 1.3 76.0 - - - +
187A LYS* 1.3 52.4 + - - +
189A LEU* 2.8 8.6 + - - +
190A HIS* 2.7 63.7 + - + +
205A GLN* 4.2 24.0 - - + +
208A ILE* 4.3 14.1 - - + +
209A ILE* 4.4 20.9 - - + -
212A LEU* 4.4 15.7 - - + -
234A LEU* 4.1 27.4 - - + +
235A LEU 5.3 0.2 - - - +
238A ALA* 5.5 1.3 - - + -
246A MET* 5.8 0.2 - - - -
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Residues in contact with LYS 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 LEU 3.2 8.4 + - - +
184A ASP* 3.3 31.0 + - - +
186A LEU* 1.3 76.7 - - - +
188A ARG* 1.3 65.5 + - - +
190A HIS* 3.0 13.7 + - - +
191A ASP* 2.8 42.8 + - - +
230A GLU* 3.6 25.9 + - - +
234A LEU* 3.9 17.2 - - + +
237A ARG* 4.9 4.5 - - - +
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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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143A LEU 5.7 1.6 + - - -
146A GLY* 5.9 2.0 - - - -
147A LEU 4.3 17.6 + - - +
148A ARG* 6.3 0.6 - - - +
152A LEU* 4.6 5.9 - - - +
184A ASP 3.1 16.9 + - - +
185A ILE* 3.4 42.2 - - - +
187A LYS* 1.3 83.1 - - + +
189A LEU* 1.3 66.1 + - - +
191A ASP* 3.5 23.0 - - - +
192A GLU* 3.7 13.3 - - + +
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Residues in contact with LEU 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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152A LEU* 4.5 5.4 - - + -
185A ILE* 2.7 40.5 + - + +
186A LEU* 3.2 8.5 - - - +
188A ARG* 1.3 77.1 - - - +
190A HIS* 1.3 64.5 + - - +
192A GLU* 3.7 21.7 + - + +
201A ASP* 4.7 13.9 - - + +
204A ASN* 4.4 25.8 - - + +
205A GLN* 4.1 29.6 - - + +
208A ILE* 4.6 4.5 - - + -
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Residues in contact with HIS 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A LEU* 2.7 45.9 + - + +
187A LYS 3.2 7.2 - - - +
189A LEU* 1.3 72.5 - - - +
191A ASP* 1.3 67.6 + - - +
192A GLU 3.0 11.6 + - - +
205A GLN* 3.8 15.9 + - - -
234A LEU* 3.4 29.4 - - + +
237A ARG* 3.6 64.7 + - + +
238A ALA* 4.2 4.9 + - - -
246A MET* 6.1 1.0 - - - +
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Residues in contact with ASP 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A LYS* 2.8 30.5 + - - +
188A ARG* 3.5 15.8 - - - +
190A HIS* 1.3 73.1 - - - +
192A GLU* 1.3 63.0 + - + +
193A LYS* 3.7 12.3 + - - +
237A ARG* 5.0 5.0 + - - +
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Residues in contact with GLU 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A ARG* 3.7 16.2 - - + +
189A LEU* 3.7 21.2 + - + +
190A HIS 3.0 14.3 + - - +
191A ASP* 1.3 76.5 - - + +
193A LYS* 1.3 69.1 + - - +
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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