Contacts of the strand formed by residues 54 - 57 (chain A) in PDB entry 2UUY
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 TRP 54 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49A LEU* 3.6 3.1 - - - +
50A ILE* 3.0 36.4 + - + +
51A ASN* 3.0 41.6 + - - +
52A SER 3.8 0.2 - - - -
53A GLN* 1.3 92.5 + - + +
55A VAL* 1.3 63.4 - - - +
89A LYS* 5.0 0.2 - - + -
91A ILE* 4.1 11.4 - - + -
107A LEU* 3.8 34.8 - - + -
108A ILE 3.3 19.7 - - - -
109A LYS* 3.7 45.4 - - + +
110A LEU* 4.4 0.6 - - - +
239A THR* 4.3 4.7 - - + -
240A ILE* 3.6 36.3 + - + +
243A ASN* 3.8 34.7 + - + -
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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
----------------------------------------------------------
36A VAL* 3.8 16.4 - - + -
38A LEU* 4.7 3.1 - - + -
47A GLY* 4.0 3.1 - - - -
48A SER 3.3 17.0 - - - +
49A LEU* 3.9 20.2 - - + -
54A TRP* 1.3 78.8 - - - +
56A VAL* 1.3 78.7 + - - +
57A SER* 4.0 0.6 + - - -
68A VAL* 4.2 22.0 - - + -
106A MET 3.8 0.2 - - - +
107A LEU* 3.4 6.8 - - - +
108A ILE* 2.8 53.6 + - + +
110A LEU* 4.2 9.6 - - + -
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Residues in contact with VAL 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A GLY* 3.2 3.8 - - - -
48A SER* 2.8 36.1 + - - +
50A ILE* 3.8 35.0 - - + -
54A TRP 4.5 0.2 + - - -
55A VAL* 1.3 71.9 - - - +
57A SER* 1.3 65.0 + - - +
105A ILE* 4.3 10.5 - - + -
106A MET 3.5 3.1 - - - -
107A LEU* 3.8 12.3 - - + -
198A GLY 3.5 2.5 - - - +
207A LEU* 4.2 17.0 - - + -
210A ILE* 3.4 34.3 - - + -
229A VAL* 5.2 1.1 - - + -
236A ILE* 4.6 13.7 - - + -
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Residues in contact with SER 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A LEU* 3.5 19.6 - - - +
46A GLY 2.8 24.8 + - - -
47A GLY* 4.3 1.3 - - - -
55A VAL* 4.0 0.6 + - - -
56A VAL* 1.3 74.8 - - - +
58A ALA* 1.3 67.4 + - - +
61A CYS* 4.0 6.4 - - - +
105A ILE* 3.4 6.1 - - - +
106A MET* 2.9 39.2 + - - -
108A ILE* 4.5 6.5 - - - -
198A GLY* 3.4 11.8 - - - -
210A ILE* 3.6 14.6 - - - +
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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