Contacts of the strand formed by residues 83 - 87 (chain A) in PDB entry 2A79
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 LEU 83 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A VAL* 4.2 11.4 - - + -
50A SER* 4.2 3.8 - - - +
53A GLY* 3.3 9.2 - - - -
54A LEU 2.9 26.0 + - - -
81A ILE* 3.6 3.5 - - - +
82A ASN* 1.3 83.1 + - - +
84A PHE* 1.3 73.2 + - - +
114A VAL* 3.5 18.8 - - + +
116A THR* 3.8 17.7 - - + +
241A MET* 3.4 40.2 - - + -
319A SER* 3.3 30.1 - - - +
321A LEU* 4.1 14.5 - - + +
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Residues in contact with PHE 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A LEU* 3.4 31.9 - - + +
56A THR* 5.9 1.3 - - + -
60A PHE* 6.1 0.4 - + - -
73A MET* 3.4 51.1 - - + -
76A ALA* 4.1 10.8 - - + -
77A TYR* 4.4 7.4 - - + -
81A ILE* 3.6 23.8 - - + -
82A ASN* 3.5 26.9 - - - -
83A LEU* 1.3 78.0 - - - +
85A ASP* 1.3 56.1 + - - +
99A LEU* 4.4 15.0 - - + -
113A LEU* 3.9 15.3 - - + -
114A VAL 3.1 5.7 + - - -
115A ILE* 3.5 18.6 - - + +
116A THR* 2.7 34.5 + - - +
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Residues in contact with ASP 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A LEU 3.4 6.7 + - - -
55A GLY* 3.6 1.4 - - - -
56A THR* 3.0 29.6 + - - +
83A LEU 4.2 0.2 - - - -
84A PHE* 1.3 73.8 - - - +
86A THR* 1.3 69.3 + - - +
99A LEU* 5.3 0.2 - - - -
116A THR* 2.7 24.7 + - - +
118A LYS* 2.7 32.9 + - - +
214A GLN* 3.2 24.9 + - - +
321A LEU* 3.5 23.9 - - + +
1001A NAP 2.7 17.6 + - - +
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Residues in contact with THR 86 (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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56A THR* 2.9 19.8 + - - -
85A ASP* 1.3 75.5 - - - +
87A ALA* 1.3 72.8 + - - +
90A TYR* 3.7 7.4 - - - -
95A ALA* 3.8 16.6 - - - +
96A GLU* 3.6 22.8 + - + +
99A LEU* 4.2 20.4 - - + -
115A ILE* 5.3 0.4 - - + -
116A THR 2.9 16.4 + - - +
117A THR* 3.3 18.4 - - - +
118A LYS* 3.0 25.5 + - - +
147A LEU* 4.5 5.2 - - + -
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Residues in contact with ALA 87 (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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86A THR* 1.3 86.4 + - - +
88A GLU* 1.3 66.2 + - - +
89A VAL 3.0 2.9 - - - +
90A TYR* 3.0 47.0 + - + +
93A GLY 5.2 0.2 + - - -
95A ALA* 5.0 0.3 - - - +
96A GLU* 3.5 9.7 - - - +
117A THR* 3.3 8.5 - - - -
118A LYS* 3.5 21.8 - - + +
158A ASN* 4.1 7.9 - - - +
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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