Contacts of the strand formed by residues 183 - 187 (chain V) in PDB entry 5A0Q
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 GLY 183 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40V ARG* 5.7 0.2 - - - +
178V ALA 4.5 0.2 - - - -
179V ILE 3.8 0.3 - - - -
180V ALA* 3.0 34.3 + - - +
181V GLU 3.4 0.8 - - - -
182V SER* 1.4 77.9 - - - +
184V VAL* 1.3 65.6 + - - +
185V GLU* 4.1 11.9 - - - -
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Residues in contact with VAL 184 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39V ASP* 4.2 23.1 - - - +
42V PHE* 4.3 16.8 - - + -
177V ALA* 4.8 0.4 - - + -
178V ALA 2.7 21.5 - - - +
179V ILE* 4.0 22.0 - - + -
180V ALA 5.3 0.9 - - - +
183V GLY* 1.3 76.4 - - - +
185V GLU* 1.3 66.5 + - - +
186V ARG* 3.6 28.4 + - + -
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Residues in contact with GLU 185 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176V LEU* 3.8 4.7 - - - +
177V ALA 3.8 0.3 - - - -
178V ALA* 2.8 39.2 + - + +
183V GLY* 4.1 7.6 - - - -
184V VAL* 1.3 81.1 + - - +
186V ARG* 1.3 61.5 + - - +
187V GLN* 3.5 3.9 + - - +
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Residues in contact with ARG 186 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32V ASP* 1.9 52.6 + - - -
34V LEU* 3.5 17.0 + - + +
36V PRO* 3.8 6.8 - - - +
42V PHE* 2.9 45.4 - - - -
175V ARG* 6.4 0.9 - - + +
176V LEU 3.0 16.2 - - - +
177V ALA* 3.5 17.0 - - + -
184V VAL* 3.6 14.3 + - + +
185V GLU* 1.3 71.9 - - - +
187V GLN* 1.3 61.8 + - - +
188V VAL* 4.8 4.3 - - + +
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Residues in contact with GLN 187 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153V LEU* 4.2 22.4 - - - +
157V ALA* 4.3 16.6 - - - +
174V ILE* 5.2 8.3 + - - +
175V ARG* 3.7 0.7 - - - +
176V LEU* 3.0 68.9 + - + +
185V GLU 3.5 4.0 + - - +
186V ARG* 1.3 74.7 - - - +
188V VAL* 1.3 76.5 + - - +
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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