Contacts of the strand formed by residues 83 - 90 (chain A) in PDB entry 2AIN
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 VAL 83 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A THR* 3.5 30.5 - - + -
11A LEU 3.8 4.7 - - - +
12A LYS* 4.6 18.8 - - + -
61A ASP* 2.8 23.4 - - - +
81A SER* 3.2 14.4 + - - +
82A SER* 1.3 83.1 - - - +
84A VAL* 1.3 59.0 + - - +
85A THR* 5.3 3.1 - - + +
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Residues in contact with VAL 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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9A VAL 3.0 14.1 - - - +
10A THR* 3.3 4.0 - - - -
11A LEU* 2.8 36.0 + - + +
13A LYS* 3.2 41.3 - - + -
17A MET* 5.0 6.5 - - + -
60A VAL* 4.7 1.6 - - + -
61A ASP* 3.5 5.4 - - - +
77A MET 5.3 0.9 - - - +
80A THR* 3.6 16.6 - - + +
81A SER 3.9 0.4 - - - +
82A SER 4.3 0.9 - - - +
83A VAL* 1.3 80.7 - - - +
85A THR* 1.3 63.7 + - - +
86A LEU* 3.7 35.9 - - + -
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Residues in contact with THR 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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8A THR* 3.5 20.5 - - + +
9A VAL 3.3 2.9 - - - +
10A THR* 3.9 25.8 - - + +
59A SER* 3.3 9.7 - - - +
60A VAL* 3.4 0.2 - - - -
61A ASP* 3.0 44.0 + - - +
62A GLY* 3.3 9.7 + - - -
83A VAL* 5.3 3.2 - - + +
84A VAL* 1.3 77.1 - - - +
86A LEU* 1.3 61.5 + - - +
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Residues in contact with LEU 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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7A ILE 3.5 2.6 - - - +
8A THR* 3.3 2.3 - - - -
9A VAL* 3.0 41.9 + - + +
11A LEU* 5.6 4.9 - - + -
17A MET* 3.5 34.1 - - + -
19A LEU* 5.5 0.9 - - + -
45A ALA* 5.7 0.9 - - + -
51A LEU* 4.2 23.8 - - + -
57A LEU* 4.4 15.3 - - + -
59A SER 3.6 0.9 - - - -
60A VAL* 3.3 38.6 - - + -
77A MET* 4.8 4.3 - - + -
84A VAL* 3.7 15.3 - - + -
85A THR* 1.3 71.2 - - - +
87A GLU* 1.3 60.6 + - - +
88A VAL* 3.6 4.0 + - + +
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Residues in contact with GLU 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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6A ILE* 3.1 33.9 - - + +
7A ILE* 3.2 5.3 + - - +
8A THR* 3.4 26.5 + - + +
56A GLN 3.9 0.2 - - - +
57A LEU* 3.6 5.9 - - - +
58A LEU* 3.1 49.5 + - + +
59A SER* 2.9 33.2 + - - +
86A LEU* 1.3 70.0 - - - +
88A VAL* 1.3 58.9 + - - +
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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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5A GLU 3.7 1.9 - - - +
6A ILE* 3.4 3.2 - - - -
7A ILE* 2.8 50.3 + - + +
9A VAL* 5.8 4.3 - - + -
36A VAL* 4.9 3.8 - - + -
50A ARG 5.3 3.8 - - - +
51A LEU* 4.5 25.1 - - + -
55A ASP* 3.2 39.0 - - + +
56A GLN 3.3 13.0 - - - +
57A LEU* 4.7 7.4 - - + -
86A LEU* 3.6 5.7 + - + +
87A GLU* 1.3 74.5 - - - +
89A ALA* 1.3 64.6 + - - +
90A LYS* 5.5 5.4 - - - -
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Residues in contact with ALA 89 (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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4A PRO* 4.7 8.1 - - + -
5A GLU 3.5 3.6 - - - -
6A ILE* 3.7 20.9 - - + +
55A ASP* 3.4 15.6 - - - +
56A GLN* 2.8 31.6 + - - +
88A VAL* 1.3 75.2 - - - +
90A LYS* 1.3 61.6 + - - +
91A GLN* 3.0 34.6 + - - +
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Residues in contact with LYS 90 (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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4A PRO* 3.5 6.8 - - - +
5A GLU* 2.8 65.5 + - + +
7A ILE* 5.1 15.3 - - - +
50A ARG 4.2 17.2 + - - -
55A ASP* 4.3 13.6 + - - +
88A VAL* 5.5 4.5 - - + +
89A ALA* 1.3 75.3 - - - +
91A GLN* 1.3 65.7 + - - +
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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