Contacts of the helix formed by residues 172 - 195 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168B ASP* 2.8 29.7 + - - +
169B SER* 3.1 11.3 + - - +
171B PRO* 1.3 80.0 - - + +
173B LEU* 1.3 64.1 + - + +
174B PRO* 3.5 0.9 - - - -
175B LYS* 3.5 21.6 + - + +
176B ALA* 3.3 19.2 + - - +
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Residues in contact with LEU 173 (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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169B SER* 3.7 14.1 - - - +
170B LEU* 3.2 31.2 + - + +
172B GLN* 1.3 77.2 - - + +
174B PRO* 1.3 61.6 - - + +
176B ALA* 3.0 6.5 + - + +
177B PHE* 2.7 35.9 + - - +
207B PHE* 3.6 36.8 - - + -
232B CYS* 3.8 29.4 - - - +
233B LYS* 4.6 13.9 - - + -
235B LEU* 4.3 2.0 - - + -
236B VAL* 3.7 19.6 - - + +
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Residues in contact with PRO 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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170B LEU 3.6 6.1 - - - +
171B PRO* 3.4 17.9 - - + +
172B GLN 3.6 0.4 - - - -
173B LEU* 1.3 93.6 - - + +
175B LYS* 1.3 60.5 + - - +
177B PHE* 3.3 11.2 + - + +
178B GLU* 3.4 18.2 + - - +
203B TYR* 3.9 35.6 + - + -
207B PHE* 3.7 22.2 - - + -
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Residues in contact with LYS 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B PRO 5.2 0.6 + - - +
172B GLN* 3.5 24.7 + - - +
173B LEU 3.2 0.4 - - - -
174B PRO* 1.3 78.7 - - - +
176B ALA* 1.3 61.9 + - - +
178B GLU* 3.4 9.7 + - - +
179B GLN* 3.3 25.7 + - - +
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Residues in contact with ALA 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B GLN 3.3 10.4 + - - +
173B LEU* 3.0 14.2 + - + +
175B LYS* 1.3 78.7 - - - +
177B PHE* 1.3 59.0 + - - +
179B GLN* 3.3 14.5 + - - +
180B TYR* 2.8 50.0 + - + -
233B LYS* 6.3 3.1 - - + -
236B VAL* 4.1 11.0 - - + -
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Residues in contact with PHE 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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173B LEU 2.7 17.1 + - - +
174B PRO* 3.5 12.1 - - + +
175B LYS 3.3 0.2 - - - -
176B ALA* 1.3 71.8 - - - +
178B GLU* 1.3 64.5 + - + +
181B LEU* 3.1 42.6 + - + +
189B LEU* 6.0 0.9 - - + -
192B LEU* 4.9 1.1 - - + -
201B LEU* 3.4 23.6 - - + -
203B TYR* 3.9 20.0 - + + -
206B TRP* 3.8 12.3 - + - -
207B PHE* 4.3 6.7 - - + -
236B VAL* 3.7 14.5 - - + +
239B ALA* 3.7 44.9 - - + -
240B VAL* 3.8 16.1 - - + +
243B LEU* 3.8 25.1 - - + -
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Residues in contact with GLU 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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174B PRO 3.4 13.2 + - - +
175B LYS* 3.4 9.5 + - - +
176B ALA 3.2 0.6 - - - -
177B PHE* 1.3 84.6 - - + +
179B GLN* 1.3 57.1 + - - +
181B LEU* 3.1 5.0 + - - +
182B ASN* 2.8 36.6 + - - +
189B LEU* 3.9 17.3 - - + +
193B ARG* 3.1 29.2 + - - +
198B ALA* 3.7 25.6 - - - +
203B TYR* 4.1 8.6 + - - +
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Residues in contact with GLN 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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175B LYS* 3.3 15.4 + - - +
176B ALA* 3.4 17.5 - - - +
178B GLU* 1.3 79.3 - - - +
180B TYR* 1.3 86.7 + - + +
182B ASN* 3.4 8.0 + - - +
183B LEU* 3.3 35.3 + - + +
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Residues in contact with TYR 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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176B ALA* 2.8 39.5 + - + +
179B GLN* 1.3 93.9 + - + +
181B LEU* 1.3 64.9 + - - +
182B ASN 3.3 0.2 - - - -
183B LEU* 3.3 22.5 + - + +
184B GLU* 3.2 27.6 + - + +
233B LYS* 3.7 25.8 + - - -
236B VAL* 4.3 7.6 - - + -
237B PHE* 3.6 36.6 - + + -
240B VAL* 4.3 14.3 - - + +
285B HIS* 3.7 36.4 + + + -
286B CYS* 4.4 3.6 - - - -
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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
----------------------------------------------------------
177B PHE* 3.1 32.0 + - + +
178B GLU* 3.6 3.6 - - - +
180B TYR* 1.3 72.5 - - - +
182B ASN* 1.3 59.0 + - - +
184B GLU* 3.1 1.2 + - + +
185B ASP* 2.7 52.8 + - + +
188B LEU* 4.5 16.6 - - + -
189B LEU* 4.2 17.0 - - + +
192B LEU* 3.8 29.8 - - + -
240B VAL* 4.1 24.3 - - + +
243B LEU* 3.8 18.2 - - + -
244B LEU* 4.6 6.3 - - + -
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Residues in contact with ASN 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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178B GLU 2.8 17.4 + - - +
179B GLN* 3.4 9.9 + - - +
181B LEU* 1.3 78.4 - - - +
183B LEU* 1.3 65.9 + - - +
184B GLU 3.4 0.5 + - - -
185B ASP 3.8 0.3 + - - -
186B GLY* 3.5 26.4 + - - +
189B LEU* 3.6 24.5 - - + +
193B ARG* 5.6 0.4 + - - -
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Residues in contact with LEU 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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179B GLN* 3.3 25.8 + - + +
180B TYR* 3.6 33.2 - - + +
181B LEU 3.2 0.6 - - - -
182B ASN* 1.3 80.9 - - + +
184B GLU* 1.3 66.1 + - - +
285B HIS* 4.3 18.5 - - + +
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Residues in contact with GLU 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 TYR 3.2 15.0 + - - +
181B LEU* 3.1 4.0 + - - +
182B ASN 4.4 0.2 - - - -
183B LEU* 1.3 83.3 - - - +
185B ASP* 1.3 62.9 + - - +
237B PHE* 6.4 0.4 - - + -
240B VAL* 4.5 8.3 - - + -
244B LEU* 4.2 27.3 - - + +
281B LEU* 3.6 27.0 - - + +
284B LYS* 3.1 18.6 + - - -
285B HIS* 2.8 30.3 + - + +
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Residues in contact with ASP 185 (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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181B LEU* 2.7 21.5 + - + +
182B ASN 3.8 0.2 + - - -
184B GLU* 1.3 77.1 - - - +
186B GLY* 1.3 62.2 + - - +
187B ARG* 3.0 27.2 + - - +
188B LEU* 3.2 21.6 + - + +
189B LEU* 3.3 9.5 + - - +
244B LEU* 3.8 21.1 - - + +
247B LYS* 2.7 37.6 + - - +
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Residues in contact with GLY 186 (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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182B ASN* 3.5 29.9 + - - +
185B ASP* 1.3 71.7 + - - +
187B ARG* 1.3 53.5 + - - +
188B LEU 3.3 0.2 - - - -
189B LEU* 3.3 6.2 + - - +
190B THR* 2.7 36.9 + - - -
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Residues in contact with ARG 187 (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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185B ASP* 3.0 24.2 + - - +
186B GLY* 1.3 72.9 - - - +
188B LEU* 1.3 61.1 + - - +
190B THR* 3.4 9.7 + - - -
191B HIS* 2.9 26.2 + - - +
247B LYS* 4.0 20.9 - - - +
251B MSE 4.5 21.6 - - + +
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Residues in contact with LEU 188 (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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181B LEU* 4.5 10.8 - - + -
185B ASP* 3.2 28.3 + - + +
186B GLY 3.3 0.2 - - - -
187B ARG* 1.3 75.7 - - - +
189B LEU* 1.3 64.3 + - - +
191B HIS* 3.2 3.6 + - + +
192B LEU* 3.0 29.1 + - + +
243B LEU* 3.7 48.0 - - + +
244B LEU* 4.4 3.4 - - - +
247B LYS* 4.2 14.4 - - + -
250B VAL* 3.9 27.6 - - + -
251B MSE 3.9 28.7 - - + -
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Residues in contact with LEU 189 (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 PHE* 6.0 1.1 - - + -
178B GLU* 3.9 28.9 - - + +
181B LEU* 4.2 19.8 - - + +
182B ASN* 3.6 37.5 - - + +
185B ASP 3.3 10.0 + - - +
186B GLY* 3.4 8.7 - - - +
188B LEU* 1.3 75.7 - - - +
190B THR* 1.3 64.6 + - - +
192B LEU* 3.3 15.9 + - + +
193B ARG* 3.0 62.3 + - + +
198B ALA* 5.4 2.0 - - + -
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Residues in contact with THR 190 (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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186B GLY 2.7 27.0 + - - -
187B ARG* 3.4 13.3 - - - -
189B LEU* 1.3 74.0 - - - +
191B HIS* 1.3 52.3 + - - +
193B ARG* 3.1 9.9 + - + +
194B MSE 2.8 54.7 + - + +
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Residues in contact with HIS 191 (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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187B ARG 2.9 13.5 + - - +
188B LEU 3.5 7.6 - - - +
190B THR* 1.3 75.6 - - - +
192B LEU* 1.3 64.6 + - - +
194B MSE 3.3 7.7 + - - +
195B CYS* 3.1 48.8 + - - -
250B VAL* 3.4 28.3 + - + -
251B MSE 3.7 36.2 + - + +
253B LEU 2.9 29.1 + - - -
254B ASN* 4.6 3.6 - - + -
259B ILE* 4.3 5.0 - - + +
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Residues in contact with LEU 192 (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 PHE* 4.9 0.9 - - + -
181B LEU* 3.8 17.5 - - + -
188B LEU* 3.0 19.4 + - + +
189B LEU* 3.5 11.9 - - + +
190B THR 3.2 0.2 - - - -
191B HIS* 1.3 76.0 - - - +
193B ARG* 1.3 61.1 + - - +
195B CYS* 3.3 6.0 + - - -
197B ALA* 2.8 36.2 + - + +
198B ALA* 4.1 13.9 - - + +
201B LEU* 4.6 18.4 - - + -
243B LEU* 3.6 31.4 - - + -
250B VAL* 4.4 17.5 - - + -
259B ILE* 4.2 26.7 - - + -
263B LEU* 5.8 0.2 - - + -
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Residues in contact with ARG 193 (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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178B GLU* 3.1 30.5 + - - +
182B ASN* 5.6 0.8 + - - -
189B LEU* 3.0 47.8 + - + +
190B THR* 3.6 10.1 - - - +
192B LEU* 1.3 76.2 - - - +
194B MSE 1.3 68.5 + - + +
196B SER* 3.2 14.2 + - - +
198B ALA* 4.2 17.7 - - + -
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Residues in contact with MSE 194 (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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190B THR* 2.8 40.1 + - + +
191B HIS* 3.9 9.0 - - - +
192B LEU 3.2 0.4 - - - -
193B ARG* 1.3 82.0 - - + +
195B CYS* 1.3 59.7 + - - +
196B SER* 3.3 0.9 + - - -
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Residues in contact with CYS 195 (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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191B HIS* 3.1 45.8 + - - +
192B LEU* 3.3 4.7 + - - +
194B MSE 1.3 76.2 - - - +
196B SER* 1.3 75.1 + - - +
197B ALA* 3.1 7.5 + - + -
254B ASN* 4.0 21.1 - - - +
255B SER* 4.2 4.9 - - - +
256B ALA* 3.4 27.9 + - - +
259B ILE* 5.2 3.6 - - + -
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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
------------------------------------------------------------
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