Contacts of the helix formed by residues 54 - 59 (chain A) in PDB entry 1PQA
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 ALA 54 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A THR* 1.4 85.0 + - - +
55A ALA* 1.3 66.0 + - - +
56A HIS* 3.5 32.5 - - + +
57A CYS* 3.0 21.6 + - - +
58A VAL* 3.9 1.7 + - - +
99A ASP* 3.3 15.7 - - - +
100A LEU* 4.9 1.1 - - - -
101A ALA 4.1 0.9 - - - -
196A GLY* 3.4 20.2 - - - +
209A ALA* 5.0 0.9 - - + -
210A VAL 3.8 5.2 - - - +
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Residues in contact with ALA 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A ALA* 1.3 70.6 - - - +
56A HIS* 1.3 61.4 + - - +
58A VAL* 3.0 2.8 + - - +
59A SER* 2.8 32.3 + - - -
89A VAL* 4.5 7.9 - - + -
93A TYR* 3.6 36.8 - - + -
99A ASP* 2.9 16.5 + - - +
100A LEU 3.5 24.8 - - - +
101A ALA* 4.0 7.4 - - - -
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Residues in contact with HIS 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A ALA* 3.2 18.1 - - + -
55A ALA* 1.3 77.2 - - - +
57A CYS* 1.3 60.4 + - - +
58A VAL 3.3 0.3 + - - -
59A SER* 4.3 4.1 + - - +
61A TYR* 3.6 17.8 + - - -
93A TYR* 3.3 19.3 - - - +
96A ASN* 6.1 0.6 + - - -
99A ASP* 2.6 32.5 + - - +
195A SEB 1.8 77.0 + + - -
211A SER* 2.8 30.2 + - - -
212A TRP* 5.8 0.2 - - - +
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Residues in contact with CYS 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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33A ILE* 5.6 1.3 - - + -
40A TRP* 2.9 22.0 + - + +
41A CYS* 2.1 54.7 - - + -
53A THR* 3.8 12.8 - - - +
54A ALA* 3.0 16.4 + - - +
55A ALA 3.0 0.2 + - - -
56A HIS* 1.3 80.0 - - - +
58A VAL* 1.4 64.3 + - + +
61A TYR* 3.4 8.3 - - - -
66A PHE* 3.5 6.1 - - - -
195A SEB 3.3 29.2 - - - -
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Residues in contact with VAL 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ILE* 5.6 2.5 - - + -
53A THR* 4.3 4.9 - - + -
54A ALA 4.0 2.9 - - - +
55A ALA* 3.0 4.5 + - - +
57A CYS* 1.4 91.8 - - + +
59A SER* 1.3 69.3 + - - +
60A GLY 3.2 1.2 + - - -
61A TYR* 3.1 25.6 + - - +
66A PHE* 4.0 27.8 - - + -
84A LEU* 5.1 1.6 - - + -
87A VAL* 3.7 25.1 - - + +
89A VAL* 4.6 1.1 - - + -
101A ALA* 3.7 30.7 - - + -
103A LEU* 4.2 21.1 - - + -
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Residues in contact with SER 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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55A ALA 2.8 21.6 + - - -
56A HIS* 4.3 4.2 + - - +
57A CYS 4.0 0.2 - - - -
58A VAL* 1.3 70.4 - - - +
60A GLY* 1.4 62.2 + - - +
61A TYR* 3.2 18.0 + - - -
87A VAL* 5.9 0.4 - - - -
89A VAL* 4.2 21.6 - - - +
93A TYR* 3.9 27.2 - - - -
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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