Contacts of the helix formed by residues 26 - 32 (chain A) in PDB entry 2I1Q
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 ASP 26 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A ILE* 1.3 97.5 - - + +
27A PHE* 1.3 68.6 + - - +
28A MET* 3.6 25.5 + - - +
29A LYS* 3.3 23.3 + - + +
30A ILE* 3.3 16.7 + - - +
247A LEU 5.3 3.8 - - - +
248A PHE* 5.9 9.1 - - + -
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Residues in contact with PHE 27 (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 LEU* 3.8 35.9 - - + -
7A ASP* 4.0 25.1 - - + -
8A LEU* 3.9 21.1 - - + -
25A ILE 4.2 0.6 + - - -
26A ASP* 1.3 76.0 - - - +
28A MET* 1.3 57.7 + - - +
30A ILE* 3.2 5.1 + - - +
31A ALA* 2.8 30.1 + - - +
56A ALA* 3.5 7.2 - - + +
59A LEU* 3.4 38.1 - - + -
60A CYS* 3.6 19.5 - - - -
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Residues in contact with MET 28 (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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26A ASP* 3.2 15.6 + - - +
27A PHE* 1.3 80.3 - - - +
29A LYS* 1.3 59.4 + - - +
31A ALA* 4.2 1.1 - - - -
32A THR* 2.9 51.1 + - + +
60A CYS* 3.8 28.3 - - - -
62A LEU* 4.0 24.5 - - + -
246A ASP 6.0 0.7 - - - +
247A LEU* 4.7 29.4 - - + +
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Residues in contact with LYS 29 (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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22A ALA 4.8 1.2 + - - -
23A GLY* 3.0 35.1 + - - +
24A TYR* 3.7 34.6 - - + -
25A ILE 5.1 0.7 - - - +
26A ASP* 3.3 21.3 + - + +
28A MET* 1.3 78.7 - - - +
30A ILE* 1.3 61.9 + - - +
32A THR* 3.4 8.8 + - - +
33A ALA* 3.3 21.7 + - - +
37A GLU* 4.7 1.5 - - - +
196A GLU* 3.1 40.0 + - - +
243A LYS* 5.1 4.2 + - - +
247A LEU* 4.6 12.0 - - + +
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Residues in contact with ILE 30 (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 LEU* 4.2 13.5 - - + -
8A LEU* 3.7 22.9 - - + -
19A LEU* 4.1 23.3 - - + -
24A TYR* 4.0 25.8 - - + +
26A ASP 3.3 13.7 + - - +
27A PHE* 3.2 6.8 + - - +
28A MET 3.2 0.2 - - - -
29A LYS* 1.3 76.0 - - - +
31A ALA* 1.3 66.7 + - - +
32A THR 3.1 0.2 - - - -
33A ALA* 3.2 14.8 + - - +
38A LEU* 4.4 5.6 - - + -
52A MET* 3.8 40.4 - - + +
53A ILE* 3.4 15.7 - - - +
56A ALA* 3.9 3.8 - - + -
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Residues in contact with ALA 31 (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 PHE 2.8 17.3 + - - +
28A MET* 3.7 8.3 - - - +
30A ILE* 1.3 76.6 - - - +
32A THR* 1.3 59.4 + - - +
33A ALA 3.4 1.1 + - - -
53A ILE* 3.8 7.5 - - - +
56A ALA* 3.5 21.7 - - + +
57A ARG* 3.3 39.3 + - - +
62A LEU* 3.8 21.5 - - + +
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Residues in contact with THR 32 (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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28A MET* 2.9 41.6 + - + +
29A LYS* 3.4 7.9 + - - -
31A ALA* 1.3 80.3 - - + +
33A ALA* 1.3 58.8 + - - +
34A THR* 5.2 2.4 - - - +
37A GLU* 4.9 0.9 - - - +
57A ARG* 6.2 0.2 - - - -
62A LEU* 4.9 5.2 - - + -
243A LYS* 3.3 35.9 + - - -
247A LEU* 4.3 8.6 - - + +
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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