Contacts of the helix formed by residues 181 - 186 (chain F) in PDB entry 2ZXX
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 PRO 181 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118D HIS* 3.6 26.5 - - + +
113E GLU* 3.9 2.5 - - - +
180F ALA* 1.3 87.7 - - + +
182F ALA* 1.3 62.9 + - - +
183F TYR* 3.4 29.4 - - + +
184F GLN* 3.0 29.7 + - + +
185F ARG 2.9 23.0 + - - -
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Residues in contact with ALA 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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111D LEU* 3.9 6.5 - - + +
114D ASN* 3.3 23.0 + - - +
110E ALA* 4.4 12.6 - - - -
113E GLU* 3.1 18.5 + - + +
181F PRO* 1.3 67.4 - - - +
183F TYR* 1.3 54.8 + - - +
184F GLN 2.6 17.3 + - - -
185F ARG* 3.5 13.5 - - - +
186F PHE* 2.9 42.8 + - + -
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Residues in contact with TYR 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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111D LEU* 3.6 43.2 - - + +
114D ASN* 3.0 26.5 + - - +
115D GLU* 3.3 45.3 - - + +
118D HIS* 4.1 12.8 - - + +
181F PRO* 3.4 23.5 - - + +
182F ALA* 1.3 73.8 - - - +
184F GLN* 1.3 77.6 + - + +
187F HIS* 3.7 24.3 - - - +
201F TYR* 3.5 28.7 + + - -
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Residues in contact with GLN 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 ALA* 5.3 5.3 - - + +
181F PRO* 3.0 28.5 + - + +
182F ALA 2.6 4.8 + - - -
183F TYR* 1.3 110.4 + - + +
185F ARG* 1.3 67.6 + - - +
186F PHE 3.0 1.3 - - - -
187F HIS* 2.9 13.9 + - - +
201F TYR* 3.4 46.3 - - + +
202F LYS* 5.6 2.8 - - - +
350F ASP* 3.2 14.5 - - - +
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Residues in contact with ARG 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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109E GLU* 3.8 17.6 + - - +
113E GLU* 2.7 29.7 + - - -
179F LYS 3.6 14.6 + - - -
180F ALA* 2.9 50.5 + - + +
181F PRO 2.9 13.3 + - - +
182F ALA* 3.5 10.9 - - - +
184F GLN* 1.3 71.8 - - - +
186F PHE* 1.3 99.4 + - + +
348F ASN* 4.7 7.1 - - - +
350F ASP* 3.2 27.4 - - - +
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Residues in contact with PHE 186 (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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107D LEU* 4.3 4.2 - - + +
111D LEU* 3.3 26.1 - - + +
106E ALA* 3.6 36.8 - - + -
109E GLU* 3.8 28.5 - - + -
110E ALA 4.9 0.2 - - - -
182F ALA* 2.9 29.2 + - + +
185F ARG* 1.3 123.5 - - + +
187F HIS* 1.3 65.3 + - - +
188F ALA 3.6 1.8 - - - -
189F LEU* 3.6 16.5 + - + +
190F ALA* 3.5 10.6 + - - +
350F ASP* 3.7 0.9 - - - -
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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