Contacts of the strand formed by residues 54 - 58 (chain R) in PDB entry 1TQE
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 LEU 54 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46R ILE* 4.1 12.8 - - + -
47R ILE 3.3 13.9 - - - +
48R PHE* 3.4 19.1 - - + -
52R ASN 3.4 0.6 + - - -
53R ARG* 1.3 72.1 - - - +
55R PHE* 1.3 87.0 + - - +
56R GLN* 4.6 0.9 - - + -
69S TYR* 3.5 28.5 - - + -
72S TYR* 2.9 41.2 + - + +
76S HIS* 3.0 58.7 - - + +
77S GLU 3.8 2.6 + - - -
114Y LYS* 6.4 0.2 - - - +
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Residues in contact with PHE 55 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21R PHE* 3.9 24.2 - + - -
25R LYS* 3.6 20.6 - - + -
29R MET* 4.8 1.6 - - + -
47R ILE* 2.7 52.1 + - + +
49R ASN* 3.2 22.0 - - - -
53R ARG* 3.0 51.4 - - + -
54R LEU* 1.3 77.4 - - - +
56R GLN* 1.3 61.6 + - - +
77S GLU* 3.0 39.9 - - + +
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Residues in contact with GLN 56 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29R MET* 3.0 19.6 - - - +
45R LEU 3.2 11.9 - - - +
46R ILE* 4.7 4.0 - - + -
54R LEU* 4.6 4.3 - - + -
55R PHE* 1.3 77.5 - - - +
57R TYR* 1.3 60.4 + - - +
58R ALA* 5.5 1.0 - - - +
62R MET* 3.7 24.0 - - + +
69S TYR* 2.5 34.6 + - - -
76S HIS* 3.2 12.3 - - + -
77S GLU 3.2 6.4 + - - +
78S SER* 3.5 26.5 + - - +
79S ARG* 3.1 18.8 + - - +
109Y ALA* 2.8 29.0 - - - +
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Residues in contact with TYR 57 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29R MET* 3.2 35.2 - - + -
32R ALA* 3.5 18.4 - - + -
33R TYR* 3.0 22.2 + - + -
36R SER* 3.7 5.7 - - - -
43R ILE* 3.8 14.8 - - + -
45R LEU* 3.0 38.9 + - + -
56R GLN* 1.3 73.0 - - - +
58R ALA* 1.3 75.5 + - - +
59R SER* 3.5 17.1 - - - -
62R MET* 2.8 20.0 - - - +
79S ARG* 3.6 8.5 - - + -
80S THR* 3.8 13.2 - - - -
81S ASN* 2.4 47.4 + - - -
84S ILE* 4.4 3.4 - - + -
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Residues in contact with ALA 58 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43R ILE 3.3 9.2 - - - +
44R ALA* 5.1 0.7 - - + -
56R GLN* 5.5 0.9 - - - +
57R TYR* 1.3 84.9 - - - +
59R SER* 1.3 66.6 + - - +
60R THR 3.1 1.1 + - - +
61R ASP* 3.7 10.1 - - - +
62R MET* 3.4 39.0 - - + +
65R VAL* 5.8 1.8 - - + -
79S ARG 3.4 5.9 + - - +
80S THR* 3.2 23.5 - - - +
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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