Contacts of the strand formed by residues 54 - 59 (chain A) in PDB entry 4DQ0
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 54 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A GLY 3.1 12.6 + - - +
33A LYS* 3.5 27.8 + - + +
34A THR 2.7 31.6 + - - +
52A GLY 3.7 2.4 + - - -
53A TYR* 1.3 69.9 - - - +
55A VAL* 1.3 55.9 + - - +
56A ASP* 4.0 1.6 + - - +
79A ASN* 3.6 25.6 - - + +
81A HIS* 4.1 15.9 + - - -
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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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34A THR* 3.3 13.7 - - + +
36A ASP* 4.5 4.5 - - + +
45A SER* 3.5 27.8 - - - +
48A LEU* 3.8 17.0 - - + -
49A ALA* 3.8 25.8 - - + +
53A TYR* 3.9 9.6 - - + +
54A ASP* 1.3 74.1 - - - +
56A ASP* 1.3 78.1 + - - +
79A ASN 2.9 12.8 + - - +
80A LEU* 3.5 19.7 - - + -
81A HIS* 2.9 27.7 + - - -
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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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33A LYS* 3.8 17.1 + - - -
34A THR 2.7 13.2 + - - +
35A LEU* 3.4 15.2 - - + +
36A ASP 2.9 27.5 + - - -
54A ASP* 4.7 1.8 - - - +
55A VAL* 1.3 77.2 - - - +
57A ALA* 1.3 60.7 + - - +
58A TRP* 3.7 21.1 - - - +
81A HIS* 3.3 21.8 + - - +
83A ARG* 5.8 1.5 + - - -
96A TYR* 2.8 26.9 + - - +
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Residues in contact with ALA 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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36A ASP 4.0 2.5 - - - -
39A CYS* 3.7 13.2 - - - -
45A SER* 3.1 34.3 - - - +
55A VAL* 3.8 0.6 - - - +
56A ASP* 1.3 71.4 - - - +
58A TRP* 1.3 62.0 + - - +
65A ILE* 4.0 1.6 - - - +
68A VAL* 5.2 2.7 - - + -
80A LEU* 4.0 12.1 - - + -
81A HIS 2.7 10.8 + - - +
82A THR* 3.1 14.5 - - + -
83A ARG 2.9 23.2 + - - +
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Residues in contact with TRP 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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35A LEU* 3.6 27.6 - - + -
36A ASP 3.2 10.1 + - - +
37A LEU* 3.9 14.8 - - + -
38A GLY 2.8 14.9 + - - +
39A CYS* 2.8 26.4 + - - -
56A ASP* 3.7 16.1 - - - +
57A ALA* 1.3 88.4 - - - +
59A ASP* 1.3 61.6 + - - +
81A HIS 4.7 1.2 + - - -
82A THR 4.4 0.4 - - - -
83A ARG* 3.1 50.2 - - + +
85A VAL* 3.5 20.6 - - + -
90A LEU* 4.5 12.6 - - + -
92A PHE* 3.8 42.6 - + + -
93A ASP 5.3 2.5 - - - -
96A TYR* 3.9 20.4 - - - -
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Residues in contact with ASP 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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38A GLY* 3.6 13.2 - - - -
39A CYS* 3.8 13.7 - - - -
40A GLY* 3.1 33.9 + - - +
58A TRP* 1.3 74.7 - - - +
60A LYS* 1.3 63.7 + - - +
61A ASN* 3.0 34.5 + - - +
64A SER* 4.6 0.6 + - - -
65A ILE* 3.9 11.7 - - + +
83A ARG 3.1 5.1 + - - -
84A VAL* 3.1 10.7 - - - +
85A VAL* 2.8 25.1 + - - +
87A LEU* 5.9 1.8 - - - -
144B THR 5.0 3.7 - - - +
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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