Contacts of the strand formed by residues 114 - 119 (chain F) in PDB entry 2J3W
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 THR 114 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107F GLN* 3.7 2.8 - - - +
108F ALA* 2.9 40.2 + - + +
111F ASP* 2.4 28.2 + - - +
112F ASP 3.4 0.8 - - - -
113F LYS* 1.3 75.7 - - - +
115F TYR* 1.3 71.4 + - - +
116F TYR* 3.8 30.3 - - + +
171F MET* 3.9 19.6 - - + -
172F ILE 3.4 3.8 - - - +
173F LYS* 2.9 19.4 + - - +
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Residues in contact with TYR 115 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82F VAL* 4.1 13.2 - - + +
83F LEU* 6.1 1.8 - - + -
86F LEU* 3.2 37.0 - - + -
105F LEU* 4.5 8.3 - - + -
106F GLU 3.2 9.2 - - - +
107F GLN* 3.6 43.4 + - + +
112F ASP 3.6 22.1 + - - -
113F LYS 4.4 0.2 - - - -
114F THR* 1.3 77.7 - - - +
116F TYR* 1.3 73.4 + - - +
171F MET* 3.9 0.2 - - - -
172F ILE* 2.9 37.2 + - + +
174F PHE* 3.7 30.5 - + - -
179F ILE* 4.7 2.8 - - + +
182F ASP* 5.2 2.3 + - - -
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Residues in contact with TYR 116 (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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104F LYS 3.5 1.0 - - - +
105F LEU* 3.4 6.0 - - - +
106F GLU* 2.5 65.0 + - + +
107F GLN 4.6 0.7 - - - -
108F ALA* 4.0 28.8 - - - +
109F ASN* 5.8 1.6 - - - -
114F THR* 3.8 15.1 - - + +
115F TYR* 1.3 82.6 - - - +
117F ILE* 1.3 63.2 + - - +
118F ILE* 3.7 15.0 + - + +
163F HIS* 5.9 0.7 - + - -
165F HIS* 6.0 6.1 - + - -
169F THR* 4.1 20.6 - - + -
170F LEU 3.6 1.6 - - - -
171F MET* 3.8 34.1 - - + -
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Residues in contact with ILE 117 (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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86F LEU* 4.5 6.5 - - + +
89F ILE* 4.7 7.9 - - + -
90F LYS* 4.0 25.1 - - + +
94F TRP* 3.8 33.0 - - + -
102F ALA* 3.9 14.6 - - + -
104F LYS 3.5 4.0 - - - +
105F LEU* 3.9 27.8 - - + -
115F TYR 4.3 0.2 - - - -
116F TYR* 1.3 73.4 - - - +
118F ILE* 1.3 60.9 + - - +
119F GLU 4.2 0.2 + - - -
168F THR 3.8 1.0 - - - +
169F THR* 3.5 2.8 - - - -
170F LEU* 2.9 47.4 + - + +
172F ILE* 3.6 24.9 - - + -
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Residues in contact with ILE 118 (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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102F ALA* 4.4 1.0 - - - +
103F ASP* 3.4 11.0 + - - +
104F LYS* 2.8 52.2 + - + +
106F GLU* 3.1 40.4 - - + +
116F TYR* 3.9 18.6 - - + +
117F ILE* 1.3 79.6 - - - +
119F GLU* 1.3 64.1 + - - +
120F LYS 4.3 0.7 - - - +
165F HIS* 3.7 5.6 - - + +
166F LYS* 3.6 46.4 - - + +
168F THR 3.5 1.6 - - - +
169F THR* 3.6 18.4 - - - +
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Residues in contact with GLU 119 (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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94F TRP* 3.4 42.5 + - + +
98F PHE* 5.9 1.2 - - - +
100F LYS* 2.7 38.9 + - - +
102F ALA* 4.9 0.4 - - - -
103F ASP* 2.9 30.1 + - - +
117F ILE 4.2 0.2 + - - -
118F ILE* 1.3 73.5 - - - +
120F LYS* 1.3 60.1 + - - +
121F GLU* 4.1 12.1 + - - +
123F LEU* 3.5 20.5 - - + +
166F LYS 3.9 2.9 - - - -
167F GLY 3.4 0.5 - - - -
168F THR* 2.5 48.8 + - + +
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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