Contacts of the helix formed by residues 183 - 189 (chain F) in PDB entry 2ZU6
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 GLU 183 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108F PRO* 3.3 19.5 - - + +
112F LEU* 3.4 28.7 - - + +
182F ASP* 1.3 89.9 + - - +
184F ALA* 1.3 60.3 + - - +
185F ASP* 3.5 10.7 - - - +
186F GLU* 3.2 26.9 - - + +
187F MET* 3.1 25.1 + - - +
212F LEU* 3.3 11.3 + - - +
213F SER* 4.8 1.6 - - - +
214F ALA* 6.1 0.7 - - - +
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Residues in contact with ALA 184 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181F LEU* 4.8 5.8 - - + +
182F ASP 3.5 1.7 - - - -
183F GLU* 1.3 69.8 - - - +
185F ASP* 1.3 63.6 + - - +
187F MET* 3.8 9.3 - - - +
188F LEU* 3.1 35.2 + - + +
211F LEU* 3.4 28.9 - - + -
212F LEU 2.6 16.1 + - - +
213F SER* 3.1 10.8 - - - +
220F VAL* 3.8 13.2 - - + -
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Residues in contact with ASP 185 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183F GLU* 3.6 10.5 - - - +
184F ALA* 1.3 75.3 + - - +
186F GLU* 1.3 83.2 + - - +
188F LEU* 4.2 0.9 - - - +
189F SER* 3.1 30.0 + - - -
213F SER* 2.5 27.5 + - - +
214F ALA* 3.2 14.0 + - - +
215F THR* 3.0 44.2 + - - +
217F PRO* 4.9 5.4 - - + -
220F VAL* 4.0 10.2 - - - +
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Residues in contact with GLU 186 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108F PRO* 3.8 24.5 - - + -
183F GLU* 3.2 33.4 + - - +
184F ALA 3.4 0.2 - - - -
185F ASP* 1.3 89.9 + - - +
187F MET* 1.3 61.6 + - - +
189F SER* 4.0 7.0 + - - -
190F ARG* 3.2 48.6 + - - +
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Residues in contact with MET 187 (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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106F LEU* 3.6 18.6 - - + +
107F ALA 3.8 5.4 - - - +
108F PRO* 3.9 17.3 - - + -
159F PRO* 3.5 28.9 - - - -
181F LEU* 3.8 22.4 - - + -
182F ASP 3.0 37.2 - - - +
183F GLU 3.1 18.0 + - - +
184F ALA* 3.8 7.6 - - + +
185F ASP 3.3 0.4 - - - -
186F GLU* 1.3 75.4 - - - +
188F LEU* 1.3 64.9 + - - +
190F ARG 3.1 9.4 + - - -
191F GLY 3.4 0.2 + - - -
192F PHE* 3.2 33.9 + - + +
196F ILE* 4.3 13.0 - - + -
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Residues in contact with LEU 188 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184F ALA* 3.1 20.7 + - + +
185F ASP 4.3 0.9 - - - +
187F MET* 1.3 77.6 - - - +
189F SER* 1.3 55.3 + - - +
191F GLY* 2.8 26.7 + - - -
192F PHE 3.7 2.4 + - - +
193F LYS* 3.3 53.1 + - + +
196F ILE* 3.6 21.5 - - + -
219F ASP* 3.4 29.8 - - + +
220F VAL* 3.4 31.0 - - + -
223F VAL* 4.4 12.1 - - + -
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Residues in contact with SER 189 (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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421E HIS* 3.8 10.7 - - - -
185F ASP 3.1 19.9 + - - -
186F GLU* 4.1 8.8 + - - -
188F LEU* 1.3 75.4 - - - +
190F ARG* 1.3 56.7 + - - +
191F GLY 3.2 3.4 - - - -
219F ASP* 5.6 1.1 - - - -
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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