Contacts of the strand formed by residues 110 - 114 (chain F) in PDB entry 4OA5
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 ILE 110 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71F ALA* 3.7 36.1 - - + +
72F ILE* 4.0 5.8 - - - +
75F ALA* 3.8 18.8 - - + -
83F HIS* 4.0 0.2 - - - -
84F ILE* 3.3 11.7 - - + +
86F THR* 3.8 23.6 - - + -
98F ASN* 5.7 0.3 - - - +
101F ILE* 3.7 41.8 - - + +
106F LEU* 3.1 19.3 + - + +
107F GLU* 3.2 20.9 - - - +
109F LYS* 1.3 85.1 - - - +
111F THR* 1.3 65.4 + - - +
112F VAL* 4.2 0.7 + - - +
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Residues in contact with THR 111 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83F HIS* 2.7 29.2 + - - -
84F ILE 2.8 7.7 + - - -
85F TYR* 3.5 21.3 - - + +
86F THR* 2.9 26.1 + - - +
107F GLU 5.1 0.9 + - - -
110F ILE* 1.3 73.0 + - - +
112F VAL* 1.3 65.8 + - - +
113F LEU* 3.8 20.9 + - + +
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Residues in contact with VAL 112 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65F THR* 4.2 14.6 - - + +
86F THR* 3.3 20.2 - - + +
88F GLU* 4.6 1.3 - - + -
94F VAL* 3.9 37.6 - - + +
97F ALA* 4.3 8.7 - - + -
98F ASN* 3.5 31.4 + - - +
101F ILE* 3.6 25.4 - - + -
110F ILE 5.5 0.2 - - - +
111F THR* 1.3 75.2 - - - +
113F LEU* 1.3 69.4 + - - +
114F HIS 4.0 1.4 + - - -
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Residues in contact with LEU 113 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85F TYR* 4.3 13.2 - - + -
86F THR 2.7 14.8 + - - +
87F ILE* 3.4 12.7 - - + +
88F GLU* 3.0 26.2 + - - -
111F THR* 4.1 17.5 - - + +
112F VAL* 1.3 80.9 - - - +
114F HIS* 1.3 61.1 + - - +
115F GLY 3.6 0.7 + - - -
120F GLN* 3.6 27.8 - - + +
123F THR* 4.4 5.2 - - - +
124F LEU* 3.8 41.1 - - + -
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Residues in contact with HIS 114 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88F GLU 3.3 9.2 - - - -
89F LYS 3.0 30.2 + - - -
91F TYR* 3.5 37.8 + + + +
94F VAL* 3.8 26.4 - - + +
112F VAL 4.0 2.8 + - - -
113F LEU* 1.3 70.5 - - - +
115F GLY* 1.3 61.6 + - - +
120F GLN* 3.6 15.1 + - - +
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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