Contacts of the helix formed by residues 175 - 199 (chain A) in PDB entry 2PU1
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 SER 175 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A ALA* 3.5 2.6 - - - +
174A THR* 1.3 83.2 + - - +
176A PHE* 1.3 59.8 + - - +
177A SER* 3.6 5.4 + - - -
178A GLU* 3.1 25.1 + - - +
179A ALA* 2.9 28.4 + - - +
414A GLU* 3.5 11.7 - - - -
423A PHE* 3.5 13.0 - - - -
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Residues in contact with PHE 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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143A LEU* 3.9 22.4 - - + +
144A PRO* 3.4 28.3 - - + -
146A PRO* 3.9 20.9 - - + -
175A SER* 1.3 72.0 - - - +
177A SER* 1.3 61.1 + - - +
179A ALA* 3.2 0.7 + - - +
180A LEU* 2.8 40.5 + - + +
407A LEU* 3.4 35.9 - - + -
410A LEU* 3.4 42.0 - - + -
411A LEU* 3.9 21.5 - - + -
414A GLU* 3.1 14.2 + - - +
423A PHE* 3.3 12.5 - + - +
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Residues in contact with SER 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A SER* 3.9 5.2 - - - -
176A PHE* 1.3 74.9 - - - +
178A GLU* 1.3 58.1 - - - +
180A LEU* 3.8 2.1 - - - +
181A ARG* 3.0 29.9 + - - +
411A LEU* 3.6 18.6 - - - +
414A GLU* 2.5 32.6 + - - -
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Residues in contact with GLU 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A LYS 4.6 0.9 - - - +
173A ALA* 3.3 6.1 - - - -
174A THR* 3.0 33.4 + - - +
175A SER* 3.1 18.7 + - - +
177A SER* 1.3 77.3 - - - +
179A ALA* 1.3 60.3 + - - +
181A ARG* 3.4 28.4 + - - +
182A MET* 2.9 45.6 + - - +
237A LYS* 5.8 2.5 + - - -
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Residues in contact with ALA 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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146A PRO* 3.9 10.1 - - + -
148A PHE* 4.1 0.9 - - - -
170A PRO* 3.4 28.1 - - + +
173A ALA* 3.5 11.1 - - + +
175A SER 2.9 19.0 + - - +
176A PHE* 3.2 5.8 + - - +
178A GLU* 1.3 76.3 - - - +
180A LEU* 1.3 56.5 + - - +
182A MET* 3.5 0.5 + - - +
183A GLY* 2.9 25.1 + - - -
423A PHE* 3.5 27.1 - - + -
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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
----------------------------------------------------------
146A PRO* 4.8 0.8 - - - +
148A PHE* 3.9 17.3 - - + -
176A PHE* 2.8 30.0 + - + +
177A SER* 3.8 3.8 - - - +
179A ALA* 1.3 69.5 - - - +
181A ARG* 1.3 66.1 + - - +
183A GLY* 3.3 1.4 + - - -
184A SER* 3.0 24.2 + - - -
398A PRO* 4.7 6.5 - - + -
407A LEU* 3.7 47.1 - - + -
408A ASN* 4.8 3.1 - - - +
411A LEU* 3.8 35.7 - - + -
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Residues in contact with ARG 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A SER 3.0 17.6 + - - +
178A GLU* 3.8 31.9 + - - +
180A LEU* 1.3 75.9 - - - +
182A MET* 1.3 61.0 + - - +
184A SER* 3.2 6.8 + - - -
185A GLU* 2.8 70.2 + - + +
234A HIS* 4.4 8.5 - - - -
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Residues in contact with MET 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A PRO* 3.6 13.7 - - + -
173A ALA* 4.2 13.7 - - + +
178A GLU* 2.9 42.8 + - + +
179A ALA 3.8 2.5 - - - +
181A ARG* 1.3 80.7 - - - +
183A GLY* 1.3 58.2 + - - +
185A GLU* 3.3 1.8 + - - +
186A VAL* 2.9 35.0 + - - +
234A HIS* 3.7 31.6 - - + -
237A LYS* 3.2 34.3 - - + +
238A PHE* 3.1 31.2 - - + -
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Residues in contact with GLY 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A PHE* 3.6 30.1 - - - -
168A ILE* 4.3 4.7 - - - +
179A ALA 2.9 11.3 + - - -
180A LEU 3.7 1.1 - - - -
181A ARG 3.2 0.2 - - - -
182A MET* 1.3 77.8 - - - +
184A SER* 1.3 55.9 + - - +
186A VAL* 3.9 1.9 - - - +
187A TYR* 3.0 28.2 + - - +
238A PHE* 3.8 11.8 - - - -
398A PRO* 3.9 7.4 - - - +
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Residues in contact with SER 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A LEU* 3.0 17.9 + - - -
181A ARG* 3.6 7.2 - - - -
183A GLY* 1.3 75.5 - - - +
185A GLU* 1.3 64.9 + - - +
187A TYR* 3.3 2.1 + - - +
188A HIS* 2.9 50.3 + - - -
398A PRO* 3.8 23.6 + - - +
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Residues in contact with GLU 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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181A ARG* 2.8 57.6 + - + +
182A MET 3.3 3.8 + - - +
184A SER* 1.3 74.4 - - - +
186A VAL* 1.3 58.6 + - - +
188A HIS* 3.3 8.6 + - - +
189A SER* 3.0 30.1 + - - -
232A ALA* 3.8 10.7 - - + +
234A HIS* 2.6 41.4 + - + +
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Residues in contact with VAL 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A ILE* 3.5 28.5 - - + -
182A MET 2.9 20.7 + - - +
183A GLY 3.9 0.2 - - - +
185A GLU* 1.3 72.7 - - - +
187A TYR* 1.3 55.1 + - - +
189A SER* 3.1 2.6 + - - -
190A LEU* 2.7 34.7 + - + +
225A LEU* 4.8 1.1 - - + +
228A ALA* 3.7 7.4 - - + -
229A ILE* 3.7 36.6 - - + +
232A ALA* 3.7 20.9 - - + -
234A HIS* 3.9 4.0 - - + -
238A PHE* 3.6 23.6 - - + -
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Residues in contact with TYR 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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150A VAL* 3.9 22.7 - - + -
168A ILE* 4.6 1.0 - - - +
183A GLY 3.0 18.6 + - - +
184A SER 3.4 4.7 - - - +
186A VAL* 1.3 74.8 - - - +
188A HIS* 1.3 80.1 + + - +
190A LEU* 3.2 9.2 + - - +
191A ARG* 3.0 27.5 + - - +
205A VAL* 3.4 12.0 - - - +
209A GLY 2.7 28.9 + - - -
210A GLY* 4.3 2.9 - - - -
211A PHE* 3.4 39.8 - + - -
397A ALA* 3.8 8.3 - - + -
398A PRO* 3.6 23.8 - - + -
399A CYS* 3.3 27.3 - - + -
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Residues in contact with HIS 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A SER* 2.9 43.7 + - - +
185A GLU* 3.7 7.9 + - - +
186A VAL 3.2 0.2 - - - -
187A TYR* 1.3 93.0 - + - +
189A SER* 1.3 64.4 + - - +
191A ARG* 3.3 22.6 + - - +
192A GLY* 3.4 9.5 + - - -
398A PRO 5.7 3.5 + - - -
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Residues in contact with SER 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 GLU 3.0 13.9 + - - -
186A VAL 3.4 7.6 - - - -
188A HIS* 1.3 74.6 - - - +
190A LEU* 1.3 63.4 + - - +
192A GLY* 3.2 4.0 + - - -
193A ILE* 3.1 27.6 + - - +
228A ALA* 3.8 20.0 - - - -
231A GLU* 3.9 24.1 + - - +
232A ALA* 3.5 19.1 + - - +
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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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150A VAL* 3.7 37.0 - - + +
151A ILE* 3.9 10.3 - - + -
168A ILE* 6.0 0.7 - - + -
186A VAL* 2.7 20.7 + - + +
187A TYR* 3.4 7.2 - - - +
188A HIS 3.2 0.2 - - - -
189A SER* 1.3 71.9 - - - +
191A ARG* 1.3 60.0 + - - +
193A ILE* 3.2 4.0 + - + +
194A ILE* 2.9 37.1 + - + +
211A PHE* 3.6 26.5 - - + -
224A ILE* 3.4 35.0 - - + +
225A LEU* 4.2 4.3 - - + -
228A ALA* 3.7 19.2 - - + +
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Residues in contact with ARG 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A TYR* 3.0 11.4 + - - +
188A HIS* 3.6 21.1 - - + +
189A SER 3.3 0.2 - - - -
190A LEU* 1.3 76.6 - - - +
192A GLY* 1.3 57.4 + - - +
194A ILE* 3.4 0.4 + - - -
195A LYS* 2.9 48.4 + - - +
203A VAL* 3.5 42.0 + - + +
204A ASN* 5.9 0.8 + - - -
211A PHE* 3.4 33.7 - - + -
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Residues in contact with GLY 192 (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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188A HIS 3.4 5.7 + - - -
189A SER* 3.2 7.4 + - - -
191A ARG* 1.3 78.6 - - - +
193A ILE* 1.3 57.2 + - - +
195A LYS* 3.4 7.7 + - - +
196A LYS* 3.0 30.3 + - - +
231A GLU* 5.9 0.9 - - - -
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Residues in contact with ILE 193 (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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189A SER 3.1 15.9 + - - +
190A LEU* 3.6 7.2 - - - +
192A GLY* 1.3 74.4 - - - +
194A ILE* 1.3 62.5 + - - +
196A LYS* 3.5 6.2 + - - +
197A LYS* 3.1 29.2 + - + +
224A ILE* 4.0 23.1 - - + -
227A GLU* 3.5 35.9 - - + +
228A ALA* 3.4 41.3 - - + +
231A GLU* 3.5 26.0 - - - +
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Residues in contact with ILE 194 (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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151A ILE* 4.4 7.6 - - + -
190A LEU* 2.9 33.3 + - + +
191A ARG 3.8 3.6 - - - +
193A ILE* 1.3 72.5 - - - +
195A LYS* 1.3 61.3 + - - +
198A TYR* 2.8 43.0 + - + +
199A GLY 3.7 0.5 + - - +
202A ALA* 3.5 32.3 - - + +
203A VAL* 3.8 8.5 - - + -
211A PHE* 3.4 40.2 - - + -
213A PRO* 3.9 21.1 - - + -
224A ILE* 4.4 9.0 - - + -
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Residues in contact with LYS 195 (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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191A ARG* 2.9 38.1 + - - +
192A GLY* 3.7 8.3 - - - +
193A ILE 3.4 0.2 - - - -
194A ILE* 1.3 76.9 - - - +
196A LYS* 1.3 58.5 + - - +
199A GLY* 2.8 36.3 + - - -
200A GLN* 4.1 31.6 + - - +
203A VAL* 3.6 11.3 - - + +
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Residues in contact with LYS 196 (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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192A GLY 3.0 17.6 + - - +
193A ILE* 3.9 5.8 - - - +
194A ILE 3.3 0.2 - - - -
195A LYS* 1.3 78.0 - - - +
197A LYS* 1.3 61.6 + - - +
199A GLY* 4.6 1.0 + - - -
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Residues in contact with LYS 197 (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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193A ILE* 3.1 22.6 + - + +
196A LYS* 1.3 79.5 - - - +
198A TYR* 1.3 102.9 + - + +
220A GLU* 4.2 9.0 - - - -
224A ILE* 4.1 17.5 - - + -
227A GLU* 6.2 0.4 - - - +
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Residues in contact with TYR 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A ILE* 2.8 32.6 + - + +
197A LYS* 1.3 104.4 - - + +
199A GLY* 1.3 61.5 + - - +
201A ASP* 5.3 2.3 + - - +
202A ALA* 3.4 22.7 + - + +
213A PRO* 4.0 4.3 - - + -
214A PRO* 3.7 32.0 - - + +
215A ILE* 3.4 24.2 - - + +
220A GLU* 2.7 28.9 + - - -
224A ILE* 3.2 29.2 - - + +
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Residues in contact with GLY 199 (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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194A ILE 3.7 0.2 + - - -
195A LYS* 2.8 28.0 + - - +
196A LYS 4.5 1.0 + - - -
197A LYS 3.7 1.2 - - - -
198A TYR* 1.3 77.2 - - - +
200A GLN* 1.3 65.6 + - - -
201A ASP* 3.1 3.4 - - - -
202A ALA* 3.1 17.5 + - - +
203A VAL* 4.5 0.3 - - - +
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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