Contacts of the strand formed by residues 57 - 64 (chain A) in PDB entry 2YYU
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 57 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A LEU 2.7 9.9 + - - +
32A PHE* 3.5 28.7 - - + -
33A VAL* 2.9 29.1 + - - +
56A HIS* 1.3 75.3 - - - +
58A VAL* 1.3 60.0 + - - +
84A ASP* 3.3 15.3 - - + +
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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
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32A PHE* 3.9 4.0 - - - -
33A VAL* 3.5 4.5 - - + +
35A VAL* 4.0 23.3 - - + -
48A VAL* 4.5 23.1 - - + +
51A LEU* 3.7 31.4 - - + -
52A LYS* 4.5 12.6 - - + -
56A HIS 4.0 7.9 - - - +
57A ALA* 1.3 78.8 - - - +
59A PHE* 1.3 70.8 + - - +
60A LEU* 3.8 5.5 + - + +
83A ALA* 4.1 1.7 - - - -
84A ASP* 2.7 43.9 + - - +
85A LEU 3.1 6.9 + - - +
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Residues in contact with PHE 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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8A ILE* 4.3 12.6 - - + -
32A PHE* 3.8 14.8 - - + -
33A VAL 2.8 16.6 + - - +
34A LYS* 3.3 32.3 - - + -
35A VAL 2.9 25.6 + - - -
58A VAL* 1.3 72.9 - - - +
60A LEU* 1.3 71.2 + - - +
61A ASP* 3.2 10.8 + - + -
85A LEU* 3.3 38.4 - - + -
86A VAL 4.0 6.1 - - - -
87A ASN* 3.6 29.8 - - - -
118A ILE* 3.9 18.8 - - + -
161A VAL* 4.9 3.8 - - + -
181A VAL* 4.6 11.2 - - + -
213A VAL* 5.2 0.9 - - + -
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Residues in contact with LEU 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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35A VAL* 3.8 22.2 - - + +
40A TYR* 3.5 41.7 - - + +
48A VAL* 4.3 7.6 - - + -
58A VAL* 3.8 5.5 + - + -
59A PHE* 1.3 69.8 - - - +
61A ASP* 1.3 59.8 + - - +
62A LEU* 3.3 23.4 + - + +
64A LEU* 5.9 0.3 - - - +
78A LEU* 3.5 36.2 - - + +
81A VAL* 4.4 6.1 - - + -
83A ALA* 4.1 20.4 - - + -
85A LEU 2.8 12.0 + - - +
86A VAL* 3.5 23.6 - - + +
87A ASN* 3.7 2.6 + - - +
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Residues in contact with ASP 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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34A LYS* 3.1 49.3 + - + +
35A VAL 2.9 10.6 + - - +
36A GLY* 3.5 18.3 - - - -
37A MET* 3.8 5.5 + - - +
59A PHE* 3.2 10.3 + - + -
60A LEU* 1.3 67.4 - - - +
62A LEU* 1.3 61.8 + - - +
63A LYS* 2.8 30.3 + - - +
87A ASN* 2.6 33.6 + - - -
1301A C5P 3.8 4.0 + - - -
66B ASP* 4.6 1.4 - - - +
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Residues in contact with LEU 62 (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 GLY 4.3 0.7 - - - -
37A MET* 3.6 29.3 - - + +
40A TYR* 3.7 41.3 - - + -
41A TYR* 4.0 17.0 + - + -
60A LEU* 3.3 31.6 + - + +
61A ASP* 1.3 80.9 - - - +
63A LYS* 1.3 73.6 + - - +
64A LEU* 3.2 16.7 + - + -
78A LEU* 4.0 7.0 - - + -
87A ASN* 3.2 4.0 + - - -
41B TYR* 3.9 33.6 + - + +
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Residues in contact with LYS 63 (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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37A MET* 4.7 1.9 - - + +
61A ASP* 2.8 39.9 + - - +
62A LEU* 1.3 80.1 - - - +
64A LEU* 1.3 66.7 + - - +
65A HIS* 3.3 3.3 + - - +
87A ASN* 2.9 25.9 + - - +
88A VAL* 4.2 2.0 - - - +
89A HIS* 3.3 31.5 + - + +
120A VAL* 3.9 17.9 - - + -
123A LEU* 3.9 15.0 - - + -
161A VAL* 6.2 2.5 - - - -
1301A C5P 4.4 7.9 + - - -
63B LYS 5.4 2.1 - - - +
65B HIS* 3.6 14.8 - - - +
66B ASP* 2.6 42.3 + - - +
67B ILE* 5.7 0.9 - - - -
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Residues in contact with LEU 64 (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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60A LEU 5.9 0.4 - - - +
62A LEU* 3.6 28.3 - - + +
63A LYS* 1.3 72.6 - - - +
65A HIS* 1.3 57.7 + - - +
66A ASP 4.2 0.9 - - - -
71A VAL* 4.4 13.0 - - + -
74A ALA* 3.6 31.2 - - + -
75A MET* 4.1 19.7 - - + -
78A LEU* 4.0 16.4 - - + -
86A VAL* 5.9 0.2 - - + -
87A ASN 3.4 19.0 + - - +
88A VAL* 3.3 14.1 - - + +
89A HIS 3.1 22.2 + - - -
96A MET* 4.0 4.2 - - - +
37B MET* 4.0 21.8 - - + -
41B TYR* 4.1 10.8 - - + +
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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