Contacts of the helix formed by residues 52 - 59 (chain A) in PDB entry 2HU2
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 52 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A PHE 3.7 9.9 - - - -
43A CYS* 3.6 38.2 + - + -
50A GLU 3.5 8.9 + - - -
51A ILE* 1.3 74.8 - - - +
53A GLU* 1.3 66.4 + - - +
54A LYS* 3.1 7.6 - - + +
55A VAL* 3.0 37.1 + - + +
56A LEU* 3.5 7.4 + - - +
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Residues in contact with GLU 53 (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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51A ILE 3.6 2.6 + - - +
52A HIS* 1.3 71.1 - - - +
54A LYS* 1.3 61.9 + - - +
56A LEU* 3.3 16.2 + - + +
57A ASN* 2.9 33.8 + - - +
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Residues in contact with LYS 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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18A LEU* 5.0 12.8 - - + -
52A HIS* 3.1 7.7 - - + +
53A GLU* 1.3 78.1 - - - +
55A VAL* 1.3 59.6 + - + +
57A ASN* 3.1 6.7 + - - -
58A GLU* 2.8 57.9 + - + +
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Residues in contact with VAL 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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18A LEU* 4.3 15.0 - - + -
20A ALA* 3.8 26.9 - - + -
22A LEU* 4.8 2.7 - - + -
41A ALA* 5.5 7.4 - - + -
43A CYS* 4.0 10.8 - - - -
51A ILE* 3.8 16.6 - - + -
52A HIS* 3.0 36.2 + - + +
54A LYS* 1.3 78.3 - - + +
56A LEU* 1.3 63.2 + - - +
59A ALA* 3.0 36.7 + - + +
78A PHE* 4.4 9.9 - - + -
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Residues in contact with LEU 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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48A THR* 4.5 12.1 - - - +
51A ILE* 3.8 37.7 - - + +
52A HIS 4.0 2.9 - - - +
53A GLU* 3.3 15.7 + - + +
54A LYS 3.3 0.4 - - - -
55A VAL* 1.3 77.5 - - - +
57A ASN* 1.3 62.1 + - - +
59A ALA 5.0 0.7 + - - +
77A LYS* 3.5 35.9 - - + +
78A PHE* 3.3 36.0 - - + +
79A LYS 3.1 25.1 + - - -
80A ALA 4.5 0.3 + - - -
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Residues in contact with ASN 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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53A GLU* 2.9 23.6 + - - +
54A LYS* 3.1 8.2 + - - +
56A LEU* 1.3 84.3 - - - +
58A GLU* 1.3 72.5 + - + +
77A LYS 5.0 1.4 + - - -
79A LYS* 3.4 35.8 - - + +
80A ALA* 3.6 18.8 + - - +
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Residues in contact with GLU 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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18A LEU* 3.8 20.4 + - + +
54A LYS* 2.8 47.7 + - + +
57A ASN* 1.3 84.0 - - + +
59A ALA* 1.3 64.8 + - - +
60A VAL* 3.3 9.5 + - - +
80A ALA* 3.5 9.9 - - - +
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Residues in contact with ALA 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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18A LEU* 3.5 22.6 - - + +
20A ALA* 4.9 2.5 - - + -
55A VAL* 3.0 36.2 + - + +
56A LEU 5.3 0.9 - - - +
57A ASN 3.8 0.4 - - - -
58A GLU* 1.3 77.6 - - - +
60A VAL* 1.3 59.6 + - - +
61A GLY 4.0 11.4 - - - +
62A ALA* 6.1 0.2 - - + -
78A PHE* 5.0 6.6 - - + -
80A ALA* 3.2 3.6 + - - +
81A LEU* 3.0 30.7 + - + +
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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