Contacts of the helix formed by residues 173 - 185 (chain F) in PDB entry 5GJQ
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 173 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36F THR* 4.1 18.2 + - + -
171F GLY 3.4 0.6 - - - -
172F SER* 1.3 78.5 + - - +
174F SER* 1.3 62.8 + - - +
175F GLU* 3.4 2.5 - - - -
176F GLY* 4.3 3.4 - - - +
177F ALA* 3.1 24.4 + - - +
205F VAL* 3.6 36.8 - - + +
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Residues in contact with SER 174 (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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169F ALA* 3.0 29.5 + - - +
170F ILE* 4.0 2.1 - - - -
171F GLY 3.1 25.5 + - - +
172F SER 3.1 4.6 + - - -
173F ALA* 1.3 79.2 - - - +
175F GLU* 1.3 60.7 + - - +
177F ALA* 3.8 0.9 - - - +
178F GLN* 2.9 34.0 + - - +
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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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172F SER 5.3 4.3 - - - +
173F ALA* 3.4 0.6 - - - -
174F SER* 1.3 82.8 - - - +
176F GLY* 1.3 63.8 + - - +
178F GLN* 3.2 7.1 + - - +
179F SER* 3.0 24.1 + - - -
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Residues in contact with GLY 176 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173F ALA* 3.9 4.7 + - - +
174F SER 3.4 0.2 - - - -
175F GLU* 1.3 78.2 - - - +
177F ALA* 1.3 58.2 + - - +
179F SER* 3.1 8.6 + - - -
180F SER* 2.9 32.8 + - - -
205F VAL* 5.1 6.5 - - - -
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Residues in contact with ALA 177 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36F THR* 4.7 6.5 - - - +
38F ILE* 4.5 8.3 - - + -
169F ALA* 3.8 18.2 - - + -
173F ALA 3.1 21.2 + - - +
176F GLY* 1.3 75.0 - - - +
178F GLN* 1.3 57.3 + - - +
180F SER* 3.5 2.4 + - - -
181F LEU* 2.9 32.9 + - - +
201F ILE* 3.7 24.4 - - + +
205F VAL* 4.5 10.8 - - + +
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Residues in contact with GLN 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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167F ALA 3.3 21.7 + - - -
168F ARG* 3.4 14.0 - - - +
169F ALA* 2.8 31.7 + - - +
174F SER* 2.9 21.2 + - - +
175F GLU* 3.2 6.5 + - - +
177F ALA* 1.3 73.1 - - - +
179F SER* 1.3 62.0 + - - +
181F LEU* 3.2 9.3 + - - +
182F GLN* 2.9 47.4 + - - +
54G SER* 3.2 26.3 + - - +
56G LEU* 4.5 3.2 - - - +
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Residues in contact with SER 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 13.3 + - - -
176F GLY* 3.1 9.6 + - - -
178F GLN* 1.3 76.0 - - - +
180F SER* 1.3 63.3 + - - +
182F GLN* 3.0 17.3 + - - +
183F GLU* 2.9 38.2 + - - +
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Residues in contact with SER 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 GLY 2.9 17.6 + - - -
177F ALA 3.6 5.4 - - - -
179F SER* 1.3 76.0 - - - +
181F LEU* 1.3 60.8 + - - +
183F GLU* 3.4 25.1 + - - +
184F VAL* 3.3 21.7 + - - +
201F ILE* 3.7 26.3 - - - +
204F GLN* 3.7 20.9 + - - -
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Residues in contact with LEU 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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38F ILE* 4.1 15.3 - - + -
40F ILE* 4.0 31.0 - - + -
167F ALA* 4.2 12.6 - - + -
168F ARG 3.8 37.0 - - - +
169F ALA* 4.0 7.6 - - + -
177F ALA 2.9 19.5 + - - +
178F GLN* 3.3 17.9 - - - +
179F SER 3.2 0.2 - - - -
180F SER* 1.3 75.6 - - - +
182F GLN* 1.3 63.0 + - - +
184F VAL* 3.1 17.4 + - + +
185F TYR* 3.1 21.9 + - + +
198F SER* 5.8 0.2 - - - -
201F ILE* 3.8 19.1 - - + -
56G LEU* 4.4 1.1 - - + -
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Residues in contact with GLN 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 GLN* 2.9 27.4 + - - +
179F SER* 3.0 16.6 + - - +
181F LEU* 1.3 76.0 - - - +
183F GLU* 1.3 63.9 + - + +
184F VAL 3.2 1.4 + - - -
185F TYR 3.8 9.9 + - - +
54G SER* 3.0 39.2 + - - -
55G GLU* 2.7 46.5 - - + +
56G LEU* 3.8 15.2 - - + +
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Residues in contact with GLU 183 (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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179F SER* 2.9 31.5 + - - +
180F SER* 3.5 19.4 + - - +
181F LEU 3.2 0.2 - - - -
182F GLN* 1.3 76.6 - - + +
184F VAL* 1.3 64.9 + - + +
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Residues in contact with VAL 184 (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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180F SER 3.3 20.0 - - - +
181F LEU* 3.1 14.3 + - + +
183F GLU* 1.3 89.7 - - + +
185F TYR* 1.3 61.8 + - + +
186F HIS* 4.0 9.2 + - - -
189F MET* 3.9 13.3 - - + +
197F SER* 4.5 19.1 + - - +
201F ILE* 4.5 10.1 - - + -
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Residues in contact with TYR 185 (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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40F ILE* 4.0 11.2 - - + -
41F GLN* 3.2 28.2 + - - +
42F THR* 4.9 1.3 - - - -
166F ASP* 2.6 49.6 + - + +
167F ALA* 4.0 12.1 - - + -
181F LEU* 3.1 17.6 + - + +
182F GLN 3.8 6.7 + - - +
183F GLU 3.8 1.2 - - - -
184F VAL* 1.3 79.9 - - + +
186F HIS* 1.3 80.6 + - - +
187F LYS* 4.1 12.1 - - + +
189F MET* 3.6 18.6 - - + -
56G LEU* 3.3 35.5 - - + +
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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