Contacts of the strand formed by residues 83 - 88 (chain A) in PDB entry 2AIA
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 83 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A VAL* 3.9 13.5 - - + -
41A GLU* 4.4 9.6 - - + +
44A LEU* 4.1 18.4 - - + -
45A GLY* 4.5 9.2 - - - +
48A MET* 3.7 17.9 - - - +
73A ALA* 4.3 0.2 - - - +
74A ALA* 3.0 33.3 + - + -
81A LYS* 2.8 29.7 + - + +
82A ARG* 1.3 79.8 - - - +
84A ILE* 1.3 72.4 + - - +
107A ILE* 4.7 1.1 - - + -
108A MET 3.4 7.2 - - - +
109A TYR* 3.7 39.3 - - + -
178A ILE* 4.3 1.1 - - - +
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Residues in contact with ILE 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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48A MET* 4.0 4.0 - - - -
72A LEU 3.4 8.7 - - - +
73A ALA* 3.9 12.3 - - + -
83A ILE* 1.3 82.7 - - - +
85A ALA* 1.3 60.8 + - - +
86A VAL* 4.4 9.4 - - + -
106A ALA 4.0 0.2 - - - +
107A ILE* 3.5 5.7 - - - +
108A MET* 2.8 68.5 + - + +
111A PRO* 3.9 19.3 - - + -
171A VAL* 4.6 4.3 - - + -
174A GLU* 3.9 26.9 - - + +
175A ILE* 4.2 9.9 - - + +
178A ILE* 3.9 22.0 - - + -
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Residues in contact with ALA 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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45A GLY 4.7 0.4 - - - +
48A MET* 4.0 26.2 - - + +
49A MET* 4.1 14.8 - - + +
52A LEU* 3.6 15.2 - - + +
71A GLY* 3.2 3.3 - - - -
72A LEU* 2.8 33.8 + - + +
84A ILE* 1.3 75.1 - - - +
86A VAL* 1.3 65.8 + - - +
106A ALA 3.4 7.9 - - - +
107A ILE* 4.7 6.1 - - + -
174A GLU* 4.2 0.3 - - - +
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Residues in contact with VAL 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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49A MET* 3.4 5.3 - - - +
52A LEU* 4.1 0.9 - - - -
70A VAL 3.6 6.1 - - - +
84A ILE* 4.4 10.5 - - + -
85A ALA* 1.3 80.7 - - - +
87A LEU* 1.3 60.0 + - - +
88A VAL* 5.4 0.9 - - + -
104A LEU* 3.8 27.8 - - + -
105A GLU* 3.4 3.5 - - - -
106A ALA* 2.8 56.3 + - + +
108A MET* 4.2 9.2 - - + -
170A VAL* 4.1 12.1 - - + -
171A VAL* 4.1 17.0 - - + -
174A GLU* 4.0 20.9 - - + -
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Residues in contact with LEU 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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49A MET* 3.9 11.4 - - - -
52A LEU* 3.8 15.5 - - + -
53A LYS* 3.5 43.1 - - + +
56A GLN* 3.0 34.0 + - - +
70A VAL* 2.8 21.8 + - - +
86A VAL* 1.3 74.1 - - - +
88A VAL* 1.3 58.7 + - - +
102A TYR* 3.5 48.2 - - + -
104A LEU 3.2 1.6 - - - +
105A GLU* 3.9 20.2 - - + +
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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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70A VAL* 4.4 1.8 - - + -
87A LEU* 1.3 75.9 - - - +
89A PRO* 1.3 64.7 - - - +
102A TYR* 3.4 5.3 - - - +
103A ASP* 2.5 41.4 + - + +
104A LEU* 2.8 21.6 + - + +
166A TYR* 3.2 27.8 - - + -
167A ASN* 3.2 30.1 - - - +
170A VAL* 3.7 39.3 - - + -
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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