Contacts of the helix formed by residues 172 - 195 (chain A) in PDB entry 5EJC
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 GLN 172 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A ASP* 2.8 29.5 + - - +
169A SER* 3.1 11.1 + - - +
171A PRO* 1.3 78.4 - - + +
173A LEU* 1.3 65.2 + - + +
174A PRO 3.5 1.6 - - - -
175A LYS* 3.5 21.8 + - + +
176A ALA* 3.3 19.1 + - - +
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Residues in contact with LEU 173 (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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169A SER* 3.7 15.3 - - - +
170A LEU* 3.2 30.5 + - + +
172A GLN* 1.3 76.7 - - + +
174A PRO* 1.3 61.7 - - + +
176A ALA* 3.0 7.6 + - + +
177A PHE* 2.7 35.5 + - - +
207A PHE* 3.6 37.2 - - + -
232A CYS* 3.8 28.5 - - - +
233A LYS* 4.6 14.1 - - + -
235A LEU* 4.3 2.2 - - + -
236A VAL* 3.7 20.9 - - + +
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Residues in contact with PRO 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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170A LEU 3.6 6.5 - - - +
171A PRO* 3.4 18.8 - - + +
172A GLN 3.6 0.4 - - - -
173A LEU* 1.3 92.5 - - + +
175A LYS* 1.3 62.3 + - - +
177A PHE* 3.4 11.2 + - + +
178A GLU* 3.5 17.4 + - - +
203A TYR* 3.8 41.8 + - + -
207A PHE* 3.7 16.1 - - + -
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Residues in contact with LYS 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A PRO 5.2 0.4 + - - +
172A GLN* 3.5 23.7 + - - +
173A LEU 3.2 0.4 - - - -
174A PRO* 1.3 79.0 - - - +
176A ALA* 1.3 62.1 + - - +
178A GLU* 3.4 9.9 + - - +
179A GLN* 3.3 52.0 + - + +
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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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172A GLN 3.3 10.5 + - - +
173A LEU* 3.0 15.3 + - + +
175A LYS* 1.3 75.1 - - - +
177A PHE* 1.3 59.9 + - - +
179A GLN* 3.6 14.7 + - - +
180A TYR* 2.8 51.7 + - + +
233A LYS* 6.3 2.2 - - + -
236A VAL* 4.1 11.0 - - + -
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Residues in contact with PHE 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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173A LEU 2.7 16.6 + - - +
174A PRO* 3.5 12.3 - - + +
175A LYS 3.3 0.2 - - - -
176A ALA* 1.3 73.6 - - - +
178A GLU* 1.3 63.0 + - + +
181A LEU* 3.1 42.4 + - + +
189A LEU* 6.0 0.9 - - + -
192A LEU* 4.9 1.6 - - + -
201A LEU* 3.4 22.0 - - + -
203A TYR* 3.9 20.9 - + + -
206A TRP* 3.8 12.3 - + - -
207A PHE* 4.3 6.7 - - + -
236A VAL* 3.7 13.4 - - + +
239A ALA* 3.7 44.2 - - + -
240A VAL* 3.8 16.5 - - + +
243A LEU* 3.8 25.4 - - + -
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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
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174A PRO 3.7 13.7 - - - +
175A LYS* 3.4 9.3 + - - +
176A ALA 3.2 0.4 - - - -
177A PHE* 1.3 85.7 - - + +
179A GLN* 1.3 58.5 + - + +
181A LEU* 3.1 4.4 + - - +
182A ASN* 2.8 36.5 + - - +
189A LEU* 3.9 18.5 - - + +
193A ARG* 3.1 29.0 + - - +
198A ALA* 3.7 25.0 - - + +
203A TYR* 4.1 8.4 + - - +
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Residues in contact with GLN 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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175A LYS* 3.3 44.9 + - + +
176A ALA* 3.6 17.0 - - - +
178A GLU* 1.3 80.6 - - + +
180A TYR* 1.3 63.3 + - + +
182A ASN* 3.4 8.4 + - - +
183A LEU* 3.3 31.6 + - + +
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Residues in contact with TYR 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* 2.8 41.3 + - + +
179A GLN* 1.3 76.7 - - + +
181A LEU* 1.3 64.0 + - - +
182A ASN 3.3 0.2 - - - -
183A LEU* 3.3 22.0 + - + +
184A GLU* 3.2 27.2 + - - +
233A LYS* 3.7 25.5 + - - -
236A VAL* 4.3 7.0 - - + -
237A PHE* 3.6 38.4 - + + -
240A VAL* 4.3 14.0 - - + +
285A HIS* 3.7 35.0 + + + -
286A CYS* 4.4 3.8 - - - -
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Residues in contact with LEU 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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177A PHE* 3.1 32.7 + - + +
178A GLU* 3.1 3.6 + - - +
180A TYR* 1.3 73.8 - - - +
182A ASN* 1.3 57.2 + - - +
184A GLU 3.1 0.4 + - - +
185A ASP* 2.7 53.5 + - + +
188A LEU* 4.5 16.4 - - + -
189A LEU* 4.2 17.0 - - + +
192A LEU* 3.8 29.4 - - + -
240A VAL* 4.1 23.5 - - + +
243A LEU* 3.8 17.7 - - + -
244A LEU* 4.6 6.3 - - + -
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Residues in contact with ASN 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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178A GLU 2.8 17.0 + - - +
179A GLN* 3.4 9.5 + - - +
181A LEU* 1.3 78.1 - - - +
183A LEU* 1.3 66.0 + - - +
184A GLU 3.4 0.7 + - - -
185A ASP 3.8 0.2 + - - -
186A GLY* 3.6 26.4 + - - -
189A LEU* 3.6 24.9 - - + +
193A ARG* 5.6 0.4 + - - -
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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 GLN* 3.3 17.8 + - + +
180A TYR* 3.6 32.3 - - + +
181A LEU 3.2 0.8 - - - -
182A ASN* 1.3 82.6 - - + +
184A GLU* 1.3 64.5 + - - +
285A HIS* 4.2 18.4 - - + +
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Residues in contact with GLU 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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180A TYR 3.2 14.9 + - - +
181A LEU 3.1 3.8 + - - +
183A LEU* 1.3 84.1 - - - +
185A ASP* 1.3 63.0 + - - +
186A GLY 4.3 0.2 - - - -
237A PHE* 6.4 0.4 - - + -
240A VAL* 4.5 8.7 - - + -
244A LEU* 4.2 27.7 - - + +
281A LEU* 3.6 26.8 - - + +
284A LYS* 3.1 17.8 + - - -
285A HIS* 2.8 30.5 + - + +
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Residues in contact with ASP 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 LEU* 2.7 22.1 + - + +
182A ASN 3.8 0.4 + - - -
184A GLU* 1.3 76.9 - - - +
186A GLY* 1.3 63.1 + - - +
187A ARG* 3.4 18.2 + - - +
188A LEU* 3.2 31.4 + - + +
189A LEU* 3.3 9.5 + - - +
244A LEU* 3.8 21.1 - - + +
247A LYS* 2.7 39.8 + - - +
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Residues in contact with GLY 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 ASN* 3.6 29.7 + - - +
185A ASP* 1.3 73.7 + - - +
187A ARG* 1.3 51.5 + - - +
189A LEU* 3.3 7.7 + - - +
190A THR* 2.7 36.7 + - - -
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Residues in contact with ARG 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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185A ASP* 3.3 12.7 + - - +
186A GLY* 1.3 73.8 - - - +
188A LEU* 1.3 60.7 + - - +
190A THR* 3.3 9.3 + - - -
191A HIS* 2.9 26.5 + - - +
247A LYS* 3.7 21.6 - - - +
251A MSE 4.5 16.4 - - + +
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Residues in contact with LEU 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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181A LEU* 4.5 9.2 - - + -
185A ASP* 3.2 25.7 + - + +
186A GLY 3.3 0.2 - - - -
187A ARG* 1.3 77.5 - - - +
189A LEU* 1.3 64.8 + - - +
191A HIS* 3.2 3.1 + - + +
192A LEU* 3.0 29.4 + - + +
243A LEU* 3.7 48.0 - - + +
244A LEU* 4.4 3.4 - - - +
247A LYS* 4.2 15.7 - - + -
250A VAL* 3.9 27.4 - - + -
251A MSE 3.8 30.4 - - + +
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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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177A PHE* 6.0 0.9 - - + -
178A GLU* 3.9 26.7 - - + +
181A LEU* 4.2 20.3 - - + +
182A ASN* 3.6 38.4 - - + +
185A ASP 3.3 10.1 + - - +
186A GLY* 3.4 8.7 - - - +
188A LEU* 1.3 79.3 - - - +
190A THR* 1.3 61.0 + - - +
192A LEU* 3.3 14.2 + - + +
193A ARG* 3.0 62.9 + - + +
198A ALA* 5.4 2.2 - - + -
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Residues in contact with THR 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 GLY 2.7 26.8 + - - -
187A ARG* 3.3 13.8 - - - -
188A LEU 3.2 0.2 - - - -
189A LEU* 1.3 74.4 - - - +
191A HIS* 1.3 52.1 + - - +
193A ARG* 3.0 10.2 + - + +
194A MSE 2.8 55.9 + - + +
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Residues in contact with HIS 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 ARG 2.9 14.8 + - - +
188A LEU 3.2 8.5 + - - +
190A THR* 1.3 75.7 - - - +
192A LEU* 1.3 64.4 + - - +
194A MSE 3.2 18.9 - - + +
195A CYS* 3.1 43.9 - - - -
250A VAL* 3.4 28.2 + - + -
251A MSE 3.7 34.0 + - - -
253A LEU 2.9 29.5 + - - -
254A ASN* 4.7 2.9 - - + -
259A ILE* 4.3 4.8 - - + +
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Residues in contact with LEU 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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177A PHE* 4.9 1.1 - - + -
181A LEU* 3.8 18.2 - - + -
188A LEU* 3.0 19.0 + - + +
189A LEU* 3.5 11.9 - - + +
190A THR 3.2 0.2 - - - -
191A HIS* 1.3 76.1 - - - +
193A ARG* 1.3 61.3 + - - +
195A CYS* 3.3 6.2 + - - -
197A ALA* 2.8 37.0 + - + +
198A ALA* 4.2 14.4 - - + +
201A LEU* 4.6 18.2 - - + -
243A LEU* 3.6 31.0 - - + -
250A VAL* 4.4 17.3 - - + -
259A ILE* 4.2 28.0 - - + -
263A LEU* 5.8 0.2 - - + -
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Residues in contact with ARG 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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178A GLU* 3.1 30.5 + - - +
182A ASN* 5.6 0.8 + - - -
189A LEU* 3.0 47.6 + - + +
190A THR* 3.0 10.5 + - + +
192A LEU* 1.3 74.0 - - - +
194A MSE 1.3 62.6 + - - +
196A SER* 3.2 17.2 + - - +
198A ALA* 4.2 17.2 - - + +
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Residues in contact with MSE 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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190A THR* 2.8 36.4 + - + +
191A HIS* 3.2 20.4 - - - +
192A LEU 3.2 0.2 - - - -
193A ARG* 1.3 75.4 - - - +
195A CYS* 1.3 64.8 + - - +
196A SER* 3.3 3.3 + - - -
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Residues in contact with CYS 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 HIS* 3.1 43.3 + - - -
192A LEU* 3.3 5.6 + - - +
193A ARG 3.3 0.2 - - - -
194A MSE 1.3 81.8 - - - +
196A SER* 1.3 71.9 + - - +
197A ALA* 3.1 6.6 + - + -
254A ASN* 3.9 21.5 - - - -
255A SER* 4.2 5.4 - - - +
256A ALA* 3.4 29.2 + - - +
259A ILE* 5.1 3.8 - - - -
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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
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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