Contacts of the helix formed by residues 78 - 82 (chain A) in PDB entry 4UHX
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 ILE 78 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A LEU* 3.4 21.5 - - + +
9A PHE* 4.6 6.0 - - + -
18A GLU* 4.8 1.1 - - + -
21A VAL* 3.6 28.3 - - + -
25A THR* 3.1 34.1 + - + +
26A MET 3.8 7.4 - - - +
27A LEU* 3.6 39.3 - - + +
30A TYR* 4.0 28.7 - - + -
77A PRO* 1.3 71.5 - - - +
79A CYS* 1.3 62.3 + - - +
81A LEU* 3.0 34.1 + - + +
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Residues in contact with CYS 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A LEU* 3.8 10.6 - - - +
21A VAL* 3.6 30.7 - - - -
22A ASP 4.5 1.6 - - - -
23A PRO* 3.7 27.3 + - + +
77A PRO* 3.2 0.8 + - - +
78A ILE* 1.3 78.1 - - - +
80A SER* 1.3 57.6 + - - +
81A LEU 3.2 1.8 + - - -
82A TYR* 3.9 14.1 + - - +
234A ARG* 4.7 2.1 + - - -
236A PHE* 3.8 25.7 - - + -
243A TRP* 3.6 33.5 + - + +
245A SER* 4.4 3.5 + - - -
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Residues in contact with SER 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ARG* 3.1 23.8 + - - -
76A ILE* 4.0 7.8 - - - +
77A PRO* 2.8 33.8 + - - +
79A CYS* 1.3 76.6 - - - +
81A LEU* 1.3 60.9 + - - +
82A TYR* 3.4 1.6 + - - -
234A ARG* 5.8 2.4 + - - +
243A TRP* 3.9 16.3 - - - +
245A SER* 5.6 0.9 - - - -
265A ILE* 5.6 3.4 - - - -
266A MET 5.6 4.7 - - - -
287A SER* 4.3 9.9 - - - -
289A ASP* 5.6 1.0 - - - +
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Residues in contact with LEU 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A LEU* 4.5 0.2 - - - -
9A PHE* 3.3 28.5 - - + +
27A LEU* 3.8 32.1 - - + -
56A ILE* 3.9 25.4 - - + -
58A ARG* 4.7 8.1 - - - +
76A ILE* 3.7 24.0 - - + -
78A ILE* 3.0 25.7 + - + +
80A SER* 1.3 78.1 - - - +
82A TYR* 1.3 66.8 + - - +
83A GLY 3.1 0.7 + - - -
84A ALA* 2.8 28.5 + - + +
86A VAL* 3.8 14.4 - - + -
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Residues in contact with TYR 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A GLU 3.4 22.0 - - - -
7A LEU* 3.9 15.5 - - + +
8A LEU* 3.5 31.4 - - + +
58A ARG* 3.6 11.8 + - - -
79A CYS 3.9 4.0 + - - +
80A SER 3.4 3.3 - - - +
81A LEU* 1.3 75.9 - - - +
83A GLY* 1.3 62.3 + - - +
84A ALA 3.4 0.3 + - - -
225A MET* 3.3 34.4 - - + +
234A ARG* 3.4 61.2 + - - +
236A PHE* 4.7 1.8 - + + -
289A ASP* 4.9 5.5 - - - +
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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