Contacts of the strand formed by residues 52 - 57 (chain A) in PDB entry 1OI4
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 GLU 52 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A HIS 4.8 1.1 - - - -
10A HIS* 3.6 36.4 + - - +
11A LEU* 4.6 18.7 - - + +
23A SER* 4.0 12.9 - - - -
24A LYS 2.9 14.5 + - - +
25A LYS* 4.7 7.7 - - + +
26A ILE* 3.0 31.5 + - - +
51A HIS* 1.3 73.7 - - - +
53A VAL* 1.3 69.2 + - - +
54A ILE* 4.1 19.0 - - + +
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Residues in contact with VAL 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A HIS* 3.1 37.9 + - + +
10A HIS* 3.0 25.6 - - - -
26A ILE* 3.6 5.2 - - + +
28A VAL* 3.6 25.6 - - + -
39A PHE* 4.1 12.3 - - + -
43A ALA* 4.3 15.0 - - + +
46A PHE* 4.1 32.3 - - + -
47A ARG* 5.0 1.1 - - - +
51A HIS 4.5 2.5 - - - +
52A GLU* 1.3 81.0 - - - +
54A ILE* 1.3 66.7 + - - +
55A THR 4.8 0.2 - - - +
91A LEU* 5.9 0.4 - - + -
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Residues in contact with ILE 54 (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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10A HIS* 5.1 1.1 - - + -
25A LYS* 3.6 41.1 - - + -
26A ILE 2.9 13.7 + - - +
27A ALA* 3.6 1.6 - - - -
28A VAL* 2.9 28.4 + - - -
52A GLU* 4.1 15.5 - - - +
53A VAL* 1.3 86.7 - - - +
55A THR* 1.3 63.6 + - - +
56A ILE* 3.6 6.9 + - + +
76A ASP* 3.4 20.4 - - + +
77A LYS* 4.0 20.2 - - + +
87A PHE* 3.8 25.1 - - + -
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Residues in contact with THR 55 (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 HIS* 3.7 20.9 - - + +
28A VAL* 3.7 6.5 - - + -
30A ILE* 4.0 17.9 - - + -
39A PHE* 3.8 28.7 - - + -
53A VAL* 4.0 0.4 - - + -
54A ILE* 1.3 72.3 - - - +
56A ILE* 1.3 60.7 + - - +
73A VAL* 4.6 4.5 - - + -
74A THR 2.7 24.7 + - - +
75A ILE* 3.9 5.8 - - - +
76A ASP* 2.9 45.5 + - - +
77A LYS 3.1 9.2 + - - -
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Residues in contact with ILE 56 (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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27A ALA* 3.6 30.7 - - + -
28A VAL 2.7 14.8 + - - +
29A LEU* 3.6 17.5 - - + -
30A ILE* 3.1 26.0 + - - +
54A ILE* 3.7 13.2 - - + +
55A THR* 1.3 80.8 - - - +
57A GLU* 1.3 64.0 + - - +
75A ILE* 4.2 0.4 - - - -
77A LYS* 3.4 9.2 - - + +
79A ILE* 3.6 35.2 - - + +
82A VAL* 4.1 14.6 - - + -
87A PHE* 3.8 20.2 - - + -
107A PHE* 4.2 2.3 - - + -
110A PHE* 4.2 7.4 - - + -
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Residues in contact with GLU 57 (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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30A ILE 3.1 20.4 - - - +
31A THR* 2.7 29.6 + - - +
56A ILE* 1.3 73.4 - - - +
58A LYS* 1.3 92.5 + - + +
59A GLN* 3.3 10.6 + - - +
62A LYS* 2.9 26.9 + - - +
64A VAL* 3.8 1.2 - - - +
75A ILE* 3.2 32.6 - - + +
77A LYS 3.0 8.3 + - - -
78A SER* 3.4 0.7 - - - -
79A ILE* 2.7 31.2 + - - +
101A LEU* 4.7 5.8 - - + -
107A PHE* 3.6 12.8 - - - -
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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