Contacts of the strand formed by residues 82 - 88 (chain A) in PDB entry 2AOT
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 CYS 82 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52A SER 4.2 13.2 + - - +
53A GLU* 3.4 19.2 - - + +
54A ILE 3.0 23.4 + - - -
80A GLY 3.6 4.0 + - - -
81A VAL* 1.3 76.4 - - - +
83A ILE* 1.3 69.1 + - - +
84A ASN* 5.6 0.2 - - - -
110A ASN* 3.6 14.1 - - - -
112A LYS* 5.1 9.2 - - - -
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Residues in contact with ILE 83 (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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54A ILE* 3.3 23.6 - - + +
56A ILE* 4.0 13.7 - - + -
71A LEU* 3.7 26.9 - - + -
74A VAL* 4.0 18.2 - - + -
75A GLN* 3.5 34.3 - - + +
78A TYR* 5.8 0.7 - - + +
81A VAL 3.7 10.1 - - - +
82A CYS* 1.3 81.4 - - - +
84A ASN* 1.3 66.1 + - - +
85A ASN 4.2 0.2 - - - +
110A ASN* 3.1 7.8 + - + +
111A VAL* 3.4 16.0 - - + +
112A LYS* 2.8 34.3 + - - +
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Residues in contact with ASN 84 (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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53A GLU* 3.9 26.2 + - - +
54A ILE 2.8 10.4 + - - +
55A LYS* 3.5 14.4 - - + +
56A ILE 2.8 28.2 + - - +
82A CYS* 4.2 1.3 - - - -
83A ILE* 1.3 71.6 - - - +
85A ASN* 1.3 59.7 + - - +
86A GLU* 3.0 28.0 + - - +
112A LYS* 2.8 45.4 + - + +
136A TRP* 4.0 10.8 - - - -
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Residues in contact with ASN 85 (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 ILE* 3.4 26.4 - - - +
58A SER* 4.7 3.6 - - - -
67A ASP* 4.4 4.2 + - - +
71A LEU* 3.6 25.9 - - + +
83A ILE* 3.7 1.5 + - + -
84A ASN* 1.3 71.9 + - - +
86A GLU* 1.3 61.9 + - - +
87A VAL* 3.5 11.6 + - - +
98A TYR* 3.3 24.7 + - - -
111A VAL* 4.0 17.5 - - + -
112A LYS 2.8 14.5 + - - +
113A PHE* 3.5 12.3 - - + -
114A ALA 3.3 18.2 + - - +
140A HIS* 5.1 2.4 - - - -
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Residues in contact with GLU 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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55A LYS* 5.5 0.2 - - - -
56A ILE 2.9 8.4 + - - +
57A LEU* 3.5 8.2 - - + +
58A SER* 2.8 26.3 + - - -
84A ASN* 3.0 29.5 + - - +
85A ASN* 1.3 73.8 - - - +
87A VAL* 1.3 60.1 + - - +
112A LYS* 3.6 9.4 + - - -
114A ALA* 3.2 23.1 - - + +
116A HIS* 2.6 34.7 + - + +
123A TYR* 4.7 2.9 + - - -
136A TRP* 3.4 28.9 - - + -
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Residues in contact with VAL 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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58A SER* 3.4 14.6 - - - +
61A GLY* 4.1 7.4 - - - +
67A ASP* 4.1 2.9 - - - +
85A ASN* 3.5 12.6 - - - +
86A GLU* 1.3 78.5 - - - +
88A VAL* 1.3 62.1 + - - +
89A GLU* 3.8 17.6 + - + +
98A TYR* 3.5 44.4 - - + +
113A PHE* 5.1 0.4 - - + -
114A ALA 2.7 10.5 + - - +
115A TRP* 3.5 25.1 - - + +
116A HIS* 2.7 35.4 + - - +
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Residues in contact with VAL 88 (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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57A LEU* 4.0 9.2 - - + -
58A SER 2.8 9.7 + - - +
59A ILE* 3.7 26.2 - - + -
60A GLY 2.7 31.5 + - - -
61A GLY 4.0 0.3 + - - -
87A VAL* 1.3 73.3 - - - +
89A GLU* 1.3 59.2 + - - +
90A PRO* 4.6 0.2 - - - -
116A HIS* 3.6 6.1 - - + -
118A GLU* 3.5 20.6 - - + +
119A THR 3.6 21.5 - - - +
120A SER* 4.0 6.5 - - - +
123A TYR* 3.5 40.6 - - + -
500A SAH 4.2 2.4 - - + -
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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