Contacts of the helix formed by residues 53 - 61 (chain A) in PDB entry 3PSR
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 TYR 53 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A MET* 4.1 17.7 - - + -
42A PHE* 3.7 33.6 - + - -
43A LEU* 3.8 16.1 - - + +
46A CYS* 4.0 23.3 - - + -
47A ASP* 4.4 1.8 + - - -
51A THR* 3.4 12.3 + - + +
52A ASN* 1.3 72.7 - - - +
54A LEU* 1.3 62.0 + - + +
56A ASP* 3.2 17.4 - - - +
57A VAL* 3.3 38.4 + - + +
77A LEU* 4.3 11.6 - - + +
80A ASP* 3.9 25.5 + - - +
81A ILE* 4.7 1.4 - - - +
95A CYS* 4.6 4.5 - - - -
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Residues in contact with LEU 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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28A LYS* 5.3 3.5 - - - -
32A LEU* 3.8 30.0 - - + +
35A MET* 3.7 32.8 - - + -
36A LYS* 3.3 44.9 - - + +
43A LEU* 4.0 23.5 - - + +
52A ASN* 3.1 13.6 - - - +
53A TYR* 1.3 77.3 - - + +
55A ALA* 1.3 65.2 + - - +
56A ASP 3.1 1.3 + - - -
57A VAL* 3.6 19.8 - - + +
58A PHE 4.9 0.3 + - - -
59A GLU* 5.1 0.3 - - - +
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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
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28A LYS* 4.8 5.2 + - - -
52A ASN* 2.7 33.8 + - + +
54A LEU* 1.3 75.8 - - - +
56A ASP* 1.3 63.1 + - + +
59A GLU* 3.3 10.0 - - - +
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Residues in contact with ASP 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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52A ASN 4.4 3.3 - - - +
53A TYR* 3.2 13.9 - - - +
55A ALA* 1.3 80.1 - - + +
57A VAL* 1.3 65.1 + - - +
58A PHE 3.1 2.9 - - - -
59A GLU* 2.8 33.8 + - + +
60A LYS* 2.7 49.3 + - - +
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Residues in contact with VAL 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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31A LEU* 4.7 7.2 - - + -
32A LEU* 4.2 9.4 - - + -
35A MET* 5.2 4.5 - - + -
53A TYR* 3.3 32.3 + - + +
54A LEU* 3.6 29.8 - - + +
56A ASP* 1.3 82.0 + - - +
58A PHE* 1.3 65.9 + - - +
60A LYS* 3.1 6.3 + - - +
61A LYS* 2.8 36.9 + - + +
77A LEU* 3.8 34.1 - - + -
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Residues in contact with PHE 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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26A ILE 4.1 0.7 - - - -
27A ASP 4.0 3.4 - - - -
28A LYS* 3.4 63.3 - - + -
31A LEU* 3.3 30.3 - - + -
32A LEU* 5.1 2.5 - - + -
54A LEU 4.9 0.4 + - - +
56A ASP 3.1 0.4 - - - -
57A VAL* 1.3 83.0 - - + +
59A GLU* 1.3 69.2 + - - +
61A LYS* 3.2 1.6 + - - +
62A ASP* 2.9 39.7 + - + +
67A LYS* 3.3 44.6 - - + -
68A LYS* 3.9 4.3 - - - -
69A ILE* 3.4 22.9 - - + -
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Residues in contact with GLU 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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28A LYS* 3.0 33.2 + - - +
55A ALA 3.3 8.3 - - - +
56A ASP* 2.8 35.4 + - + +
58A PHE* 1.3 82.6 - - - +
60A LYS* 1.3 63.5 + - + +
62A ASP* 4.1 12.3 + - - +
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Residues in contact with LYS 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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56A ASP* 2.7 52.8 + - - +
57A VAL* 3.7 8.7 - - - +
59A GLU* 1.3 82.8 - - - +
61A LYS* 1.3 70.4 + - + +
62A ASP 3.5 0.2 - - - -
63A LYS* 4.5 15.6 + - - +
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Residues in contact with LYS 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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31A LEU* 5.6 1.1 - - + -
57A VAL* 2.8 36.0 + - + +
58A PHE* 5.0 0.4 - - - -
60A LYS* 1.3 84.7 + - + +
62A ASP* 1.3 58.0 + - - +
63A LYS* 2.8 23.2 + - - +
69A ILE* 3.9 15.3 - - + -
73A GLU* 3.4 27.9 - - - +
76A SER* 2.7 29.3 + - - -
77A LEU* 3.5 28.5 - - + +
80A ASP* 2.5 34.5 + - - +
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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