Contacts of the helix formed by residues 79 - 84 (chain B) in PDB entry 3BRS
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 THR 79 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B TYR* 4.6 1.9 - - - +
54B GLN* 3.8 4.0 + - - +
55B ASN* 3.3 13.9 + - - +
58B ILE* 3.7 23.8 - - + -
71B LEU* 4.0 5.4 - - + -
73B ALA* 3.7 24.0 - - + -
74B ALA* 3.2 8.3 + - - +
75B ASP* 2.8 40.9 + - - +
78B LYS* 1.3 77.1 - - - +
80B TYR* 1.3 61.8 + - - +
82B ALA* 3.0 4.5 + - - +
83B ALA* 2.9 17.4 + - + -
100B MET* 3.8 11.2 - - - -
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Residues in contact with TYR 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B GLU 4.0 1.5 + - - +
78B LYS 3.0 1.4 - - - +
79B THR* 1.3 79.2 - - - +
81B ASP* 1.3 70.4 + - - +
82B ALA 3.0 0.2 - - - -
83B ALA 3.7 3.1 - - - +
84B LYS* 2.9 57.5 + - + +
100B MET* 3.8 13.9 - - - -
102B GLN* 3.1 64.6 - - + +
104B ILE* 3.9 30.1 - - + -
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Residues in contact with ASP 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A LYS* 3.2 41.9 + - - +
51B TYR* 5.2 2.4 - - - -
55B ASN* 3.9 9.0 + - - +
77B GLU 4.4 6.2 - - - +
78B LYS* 2.7 33.1 + - - +
80B TYR* 1.3 80.0 - - - +
82B ALA* 1.3 57.3 + - - +
84B LYS* 3.6 23.8 - - - +
85B GLU* 4.7 3.1 - - - +
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Residues in contact with ALA 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B ASN* 3.5 47.8 - - + +
58B ILE* 3.8 19.1 - - + +
59B GLU* 4.6 10.1 - - + +
62B ILE* 4.2 3.1 - - - +
79B THR 3.0 2.0 + - - +
80B TYR 3.0 0.2 - - - -
81B ASP* 1.3 80.4 - - - +
83B ALA* 1.3 63.2 + - - +
84B LYS 3.1 6.3 + - - -
85B GLU* 3.3 20.6 + - - +
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Residues in contact with ALA 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B ILE* 4.3 2.4 - - + +
71B LEU* 3.8 20.2 - - + -
79B THR* 2.9 16.1 + - + +
80B TYR* 4.3 0.2 - - - -
82B ALA* 1.3 77.2 - - - +
84B LYS* 1.3 65.0 + - - +
85B GLU 3.1 0.9 + - - -
86B ILE* 3.2 37.8 + - + +
87B LYS 4.7 1.0 + - - -
93B LEU* 4.5 1.0 - - + +
100B MET* 4.0 21.5 - - + -
104B ILE* 3.4 14.0 - - + +
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Residues in contact with LYS 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A ASP* 4.5 14.1 + - - -
80B TYR* 2.9 60.0 + - + +
81B ASP* 3.6 21.6 - - - +
83B ALA* 1.3 78.5 - - - +
85B GLU* 1.3 83.5 + - + +
87B LYS* 4.4 7.7 + - - +
88B ASP* 5.0 6.9 + - - +
104B ILE* 4.3 4.4 - - - +
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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