Contacts of the helix formed by residues 166 - 182 (chain F) in PDB entry 2CEA
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 ALA 166 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163F VAL* 4.4 17.5 - - + -
164F GLY 3.1 10.0 - - - +
165F GLY* 1.3 79.7 - - - +
167F GLU* 1.3 55.6 + - - +
168F GLU* 3.4 6.3 - - - +
169F ALA* 3.5 14.5 + - + +
170F ILE* 2.7 46.0 + - + +
210F LEU* 5.0 6.5 - - + -
328F VAL* 6.1 4.9 - - + -
1607F ADP 5.4 2.5 - - - +
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Residues in contact with GLU 167 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165F GLY* 3.8 20.0 + - - +
166F ALA* 1.3 77.8 - - - +
168F GLU* 1.3 76.6 + - + +
170F ILE* 3.4 12.1 + - + +
171F GLU* 3.0 30.1 + - + +
332F ASP* 5.8 0.5 - - - +
334F LEU* 5.8 2.9 - - - +
335F GLY* 5.3 2.9 + - - -
338F LYS* 5.7 3.3 - - - +
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Residues in contact with GLU 168 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165F GLY 4.8 7.0 - - - +
166F ALA* 4.9 2.0 - - - -
167F GLU* 1.3 103.4 + - + +
169F ALA* 1.3 61.3 + - - +
171F GLU* 3.5 6.4 + - - +
172F GLU* 3.3 26.9 + - - +
327F VAL 5.7 1.8 - - - +
329F ASP* 5.2 8.3 - - - +
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Residues in contact with ALA 169 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166F ALA* 3.5 11.4 + - + +
167F GLU 3.4 0.4 - - - -
168F GLU* 1.3 77.0 + - - +
170F ILE* 1.3 66.7 + - - +
172F GLU* 3.5 2.7 + - - +
173F LEU* 3.3 26.7 + - - +
210F LEU* 3.8 25.1 - - + -
326F ILE* 3.9 26.9 - - + +
327F VAL 4.5 10.1 + - - +
328F VAL* 4.6 5.4 - - + -
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Residues in contact with ILE 170 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160F PHE* 4.1 43.7 - - + +
163F VAL* 4.2 20.4 - - + +
166F ALA* 2.7 39.0 + - + +
167F GLU* 3.5 13.0 - - + +
169F ALA* 1.3 77.6 - - - +
171F GLU* 1.3 64.2 + - + +
173F LEU* 2.9 5.4 + - - +
174F LYS* 2.9 46.6 + - + +
210F LEU* 4.8 5.4 - - + -
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Residues in contact with GLU 171 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167F GLU* 3.0 17.8 + - + +
168F GLU* 3.7 7.9 - - - +
169F ALA 3.3 0.2 - - - -
170F ILE* 1.3 80.7 - - + +
172F GLU* 1.3 62.8 + - + +
174F LYS* 3.2 54.9 + - - +
175F GLU* 4.2 8.1 + - - +
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Residues in contact with GLU 172 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168F GLU 3.3 15.9 + - - +
169F ALA 3.7 4.5 - - - +
170F ILE 3.2 0.8 - - - -
171F GLU* 1.3 78.0 - - - +
173F LEU* 1.3 63.8 + - - +
174F LYS 3.6 0.3 + - - -
175F GLU* 4.0 22.1 + - - +
176F VAL* 4.3 3.6 - - - +
324F LYS* 4.4 23.4 + - - +
325F LYS 5.8 0.2 - - - +
326F ILE* 3.6 38.2 - - + +
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Residues in contact with LEU 173 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160F PHE* 4.6 4.3 - - + -
169F ALA 3.3 13.6 + - - +
170F ILE* 2.9 5.5 + - - +
172F GLU* 1.3 75.8 - - - +
174F LYS* 1.3 65.5 + - - +
175F GLU 3.2 2.5 - - - -
176F VAL* 3.0 17.7 + - + +
177F VAL* 3.1 15.8 + - - +
197F ILE* 3.4 12.3 - - + -
199F LEU* 4.8 5.2 - - + -
210F LEU* 3.9 23.3 - - + -
214F VAL* 3.6 25.9 - - + +
303F MET* 3.2 40.2 - - + -
326F ILE* 3.2 29.8 - - + -
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Residues in contact with LYS 174 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160F PHE* 4.5 13.5 - - + -
170F ILE* 2.9 35.8 + - + +
171F GLU* 3.2 36.5 + - - +
173F LEU* 1.3 78.8 - - - +
175F GLU* 1.3 57.4 + - + +
177F VAL* 3.2 11.0 + - - +
178F GLU* 3.0 31.9 + - + +
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Residues in contact with GLU 175 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171F GLU 4.7 7.1 - - - +
172F GLU* 4.0 17.7 + - - +
173F LEU 3.2 0.4 - - - -
174F LYS* 1.3 76.8 - - + +
176F VAL* 1.3 59.9 + - + +
178F GLU* 3.3 9.2 + - - +
179F PHE* 3.0 28.2 + - - +
186F PHE* 4.0 13.2 - - + -
193F MET* 5.0 13.3 - - - +
324F LYS* 5.8 4.8 + - - +
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Residues in contact with VAL 176 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172F GLU 4.3 4.3 - - - +
173F LEU* 3.2 37.7 - - + +
175F GLU* 1.3 78.7 - - + +
177F VAL* 1.3 57.3 + - - +
179F PHE* 3.3 6.4 + - - +
180F LEU* 2.9 42.3 + - + +
193F MET* 4.0 13.7 - - + -
197F ILE* 3.6 13.7 - - + -
214F VAL* 3.9 9.9 - - + -
256F ILE* 5.3 0.4 - - + -
301F ILE* 2.9 37.9 - - + -
303F MET* 4.1 10.3 - - + -
324F LYS* 5.4 2.0 - - - +
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Residues in contact with VAL 177 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160F PHE* 3.5 37.2 - - + -
173F LEU 3.1 8.3 + - - +
174F LYS* 3.2 9.4 + - - +
176F VAL* 1.3 74.9 - - - +
178F GLU* 1.3 70.9 + - - +
180F LEU* 3.4 7.3 + - - +
181F LYS* 3.2 33.7 + - + +
214F VAL* 3.6 16.8 - - + +
217F GLU* 3.8 36.8 - - + +
218F ALA* 4.3 1.1 - - - +
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Residues in contact with GLU 178 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174F LYS* 3.0 18.3 + - + +
175F GLU* 3.3 11.0 + - - +
177F VAL* 1.3 82.0 - - + +
179F PHE* 1.3 62.6 + - - +
181F LYS* 3.8 13.3 + - - +
182F ASP* 3.5 17.7 + - - +
185F LYS* 5.5 1.2 - - - +
186F PHE* 3.8 19.6 - - + -
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Residues in contact with PHE 179 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175F GLU 3.0 13.7 + - - +
176F VAL* 3.5 8.7 - - - +
178F GLU* 1.3 76.2 - - - +
180F LEU* 1.3 62.7 + - + +
182F ASP 3.1 0.7 + - - -
183F PRO* 2.8 54.5 - - + +
186F PHE* 3.7 33.6 - + + -
187F ASN* 4.6 7.6 - - - -
191F ALA 5.5 0.9 - - - -
193F MET* 3.9 34.5 - - + -
296F SER* 3.2 26.5 - - - -
297F LYS* 4.7 0.4 - - - -
299F GLY* 3.5 30.1 - - - -
300F ILE 4.4 1.1 - - - -
301F ILE* 3.9 24.2 - - + -
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Residues in contact with LEU 180 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176F VAL* 2.9 29.3 + - + +
177F VAL 3.4 0.4 + - - +
179F PHE* 1.3 80.1 - - + +
181F LYS* 1.3 60.6 + - - +
182F ASP 3.5 0.3 + - - -
183F PRO* 3.7 2.8 - - - +
214F VAL* 3.8 19.7 - - + +
215F ALA* 5.3 0.9 - - - -
218F ALA* 3.5 24.0 - - + -
220F VAL* 4.0 11.8 - - + +
254F PRO* 3.6 26.5 - - + +
255F CYS* 4.4 11.2 - - - +
256F ILE* 4.3 11.4 - - + -
299F GLY 3.7 16.6 - - - +
301F ILE* 2.7 40.2 - - + -
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Residues in contact with LYS 181 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177F VAL* 3.2 25.3 + - + +
178F GLU* 4.2 14.2 + - - +
179F PHE 3.2 0.4 - - - -
180F LEU* 1.3 77.4 - - - +
182F ASP* 1.3 62.4 + - + +
183F PRO* 3.9 0.8 - - - +
217F GLU 3.7 18.7 + - - +
218F ALA* 3.5 26.0 - - - +
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Residues in contact with ASP 182 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178F GLU 3.5 9.8 + - - +
179F PHE 3.1 4.9 + - - +
181F LYS* 1.3 83.3 - - + +
183F PRO* 1.3 60.7 - - - +
184F SER* 2.1 41.8 + - - -
185F LYS* 2.6 50.2 + - + +
186F PHE* 4.1 1.7 - - - -
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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