Contacts of the helix formed by residues 173 - 180 (chain F) in PDB entry 3VZC
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 PHE 173 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171F TRP 3.9 0.4 + - - -
172F GLY* 1.3 69.2 - - - +
174F ILE* 1.3 71.5 + - + +
176F ASP* 3.2 2.1 + - - +
177F VAL* 2.8 53.8 + - + +
196F THR* 3.5 33.7 - - + -
199F ARG* 3.6 37.0 - - + +
200F LEU* 3.8 5.6 - - + -
203F LEU* 4.3 20.0 - - + -
206F TYR* 3.0 14.2 + - + +
258F VAL* 2.8 28.7 + - + +
259F LEU* 4.3 4.2 - - + +
299F LEU* 5.1 8.1 - - + -
1001F UUL 3.6 28.3 - - - -
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Residues in contact with ILE 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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170F ALA* 3.6 25.4 - - + -
171F TRP 4.5 4.3 + - - +
172F GLY 3.2 1.0 - - - -
173F PHE* 1.3 76.6 - - + +
175F ALA* 1.3 60.9 + - - +
177F VAL* 3.5 1.4 + - - +
178F ASP* 2.9 35.9 + - - +
259F LEU* 3.5 32.5 - - + +
261F LEU* 5.3 4.3 - - + -
268F LEU* 4.9 11.7 - - + -
1001F UUL 3.4 75.4 - - + +
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Residues in contact with ALA 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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170F ALA* 4.0 1.2 - - - +
171F TRP* 3.7 10.5 - - - -
172F GLY 2.8 22.9 + - - +
174F ILE* 1.3 74.1 - - - +
176F ASP* 1.3 52.7 + - - +
178F ASP* 3.1 4.0 + - - +
179F LEU* 2.8 36.8 + - - +
337F VAL* 3.4 27.8 - - + +
338F PHE* 4.1 1.7 - - - -
339F ALA* 3.9 24.6 - - - +
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Residues in contact with ASP 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 GLY* 2.8 21.7 + - - +
173F PHE 3.8 2.9 - - - +
175F ALA* 1.3 78.0 - - - +
177F VAL* 1.3 58.4 + - - +
179F LEU* 4.3 9.4 - - + -
180F GLU* 3.0 34.7 + - - +
199F ARG* 3.8 25.8 + - - +
204F ARG* 5.3 2.3 + - - -
206F TYR* 3.2 28.3 + - - +
337F VAL* 3.8 21.3 - - - +
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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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173F PHE* 2.8 49.2 + - + +
174F ILE 4.0 0.2 - - - +
176F ASP* 1.3 71.4 - - - +
178F ASP* 1.3 51.0 + - - +
180F GLU 3.7 3.8 - - - +
181F SER* 2.6 35.9 - - - -
191F ARG* 4.6 0.6 + - - +
192F PHE* 3.7 16.9 - - + +
195F GLY* 3.6 27.8 - - - +
196F THR 3.6 3.6 - - - +
199F ARG* 3.7 25.8 - - + +
1001F UUL 3.8 20.0 - - + -
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Residues in contact with ASP 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 ILE* 2.9 20.4 + - - +
175F ALA 3.3 8.7 - - - +
177F VAL* 1.3 75.7 - - - +
179F LEU* 1.3 67.4 + - - +
181F SER* 3.6 9.2 - - - -
191F ARG* 4.0 9.9 + - - +
192F PHE* 3.3 15.9 - - - -
339F ALA* 3.4 25.1 - - + +
342F GLY* 4.1 20.5 - - - +
1001F UUL 2.8 26.7 + - - -
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Residues in contact with LEU 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 ALA 2.8 19.6 + - - +
176F ASP* 3.9 9.9 - - + +
178F ASP* 1.3 75.1 - - - +
180F GLU* 1.3 77.3 + - + +
181F SER* 2.6 15.8 + - - -
182F GLU* 3.9 6.4 + - - +
337F VAL* 4.3 19.5 - - + -
344F LEU* 3.8 39.5 - - + -
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Residues in contact with GLU 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 ASP* 3.0 14.5 + - + +
177F VAL* 3.7 6.3 - - - +
179F LEU* 1.3 85.6 - - + +
181F SER* 1.3 60.0 + - - +
182F GLU* 4.5 12.6 - - - +
183F LYS* 4.3 7.8 + - - -
195F GLY* 5.6 1.7 - - - -
199F ARG* 5.3 13.0 + - - +
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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