Contacts of the strand formed by residues 56 - 61 (chain A) in PDB entry 2E3V
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 HIS 56 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A GLU* 3.1 6.6 - - - +
47A TRP* 2.8 72.1 + + + +
48A ARG* 5.3 2.9 - - - -
49A ALA 5.8 0.9 - - - -
52A GLU* 6.0 5.2 - - + +
54A VAL* 4.9 12.2 + - + +
55A TRP* 1.3 77.3 + - - +
57A SER* 1.3 62.1 + - - +
82A TYR* 5.8 3.8 - + - -
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Residues in contact with SER 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A LYS* 3.7 28.8 + - - -
45A ALA 3.0 13.9 - - - -
46A GLU* 3.9 8.5 - - - -
47A TRP* 3.5 8.6 - - - -
55A TRP 4.1 1.3 + - - -
56A HIS* 1.3 78.4 - - - +
58A LYS* 1.3 64.7 + - - +
59A TRP* 5.6 1.0 + - - -
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Residues in contact with LYS 58 (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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44A LYS* 3.5 2.4 - - - -
45A ALA 2.9 31.0 + - - -
47A TRP* 3.5 16.5 - - + -
57A SER* 1.3 77.3 - - - +
59A TRP* 1.3 78.0 + - - +
60A TYR* 3.3 34.4 - - + +
72A THR 4.8 5.1 + - - +
74A VAL* 4.3 25.9 - - + +
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Residues in contact with TRP 59 (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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42A LYS* 3.7 19.3 - - + -
43A TYR 3.4 18.8 - - - -
44A LYS* 3.5 42.4 - - + +
57A SER* 5.6 1.1 - - - -
58A LYS* 1.3 92.2 - - - +
60A TYR* 1.3 68.4 + - - +
89A LEU* 3.6 35.7 - - + -
94A LEU* 4.0 24.2 - - + -
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Residues in contact with TYR 60 (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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42A LYS* 3.3 8.2 - - - +
43A TYR* 2.8 40.9 + - + +
45A ALA* 3.6 20.8 - - + +
47A TRP* 4.6 0.3 - - - -
58A LYS* 3.3 53.1 - - + +
59A TRP* 1.3 78.8 - - - +
61A ASP* 1.3 64.8 + - - +
65A ALA* 5.0 1.3 - - + -
71A VAL* 3.4 40.6 - - + -
72A THR* 2.7 34.7 + - - -
73A ILE* 3.8 12.1 - - - +
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Residues in contact with ASP 61 (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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41A LEU 3.8 3.1 - - - +
42A LYS* 2.9 34.3 + - - +
60A TYR* 1.3 73.8 - - - +
62A ALA* 1.3 66.0 + - - +
63A LYS* 3.2 15.3 + - - +
64A GLU* 3.2 33.6 + - + +
65A ALA* 3.1 22.6 + - - +
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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