Contacts of the strand formed by residues 112 - 117 (chain F) in PDB entry 4ILW
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 HIS 112 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110F LYS* 3.0 26.3 - - + +
111F THR* 1.3 99.4 + - - +
113F LEU* 1.3 60.0 + - - +
114F THR* 5.6 1.3 - - - +
147F THR* 3.3 27.1 - - - +
149F SER* 5.9 2.2 - - - +
157F ASP* 4.5 0.5 - - - +
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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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108F TRP* 3.6 58.1 - - + +
110F LYS* 3.9 20.9 - - + +
111F THR 4.8 2.0 - - - +
112F HIS* 1.3 74.6 - - - +
114F THR* 1.3 65.8 + - - +
146F LEU* 4.2 15.5 - - + -
147F THR 2.9 6.6 + - - +
148F PHE* 3.1 37.3 - - + -
149F SER* 2.9 27.2 + - - -
157F ASP* 3.5 15.7 - - + +
158F ILE* 5.0 2.7 - - + -
223F LEU* 3.8 8.7 - - + -
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Residues in contact with THR 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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112F HIS 5.6 1.3 - - - +
113F LEU* 1.3 75.6 - - - +
115F TYR* 1.3 62.9 + - - +
148F PHE* 5.4 0.7 - - - -
149F SER* 3.3 25.4 - - - +
151F LEU* 4.0 22.5 - - + +
155F GLU 4.8 0.2 + - - -
156F ALA* 3.3 12.4 - - - -
157F ASP* 2.8 41.4 + - - +
158F ILE* 2.8 27.1 + - - +
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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
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114F THR* 1.3 75.6 - - - +
116F ARG* 1.3 65.5 + - - +
117F ILE* 4.3 9.4 - - + -
133F ILE* 4.2 11.4 - - + -
134F GLU* 3.5 31.2 + - - +
137F LEU* 3.4 36.8 - - + -
148F PHE* 4.1 15.5 - - + -
149F SER* 3.2 13.1 + - - -
150F ARG* 3.5 42.7 - - + +
151F LEU 2.8 26.0 + - - -
156F ALA* 3.3 5.6 - - - +
158F ILE* 3.2 25.4 - - + +
160F ILE* 4.2 15.9 - - + -
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Residues in contact with ARG 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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115F TYR* 1.3 76.5 - - - +
117F ILE* 1.3 72.5 + - - +
118F VAL* 3.4 36.4 + - + +
150F ARG* 5.2 0.7 - - - -
151F LEU* 3.1 25.1 - - + +
152F TYR* 3.8 10.6 + - - +
153F GLU* 3.8 17.6 - - - +
154F GLY* 2.8 46.2 + - - +
155F GLU* 5.1 3.0 + - - -
156F ALA* 3.4 4.2 - - + +
158F ILE 3.0 7.7 + - - +
159F MET* 3.1 22.5 - - + +
160F ILE* 2.9 27.6 + - - +
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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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115F TYR* 4.3 14.3 - - + -
116F ARG* 1.3 77.1 + - - +
118F VAL* 1.3 63.9 + - - +
119F ASN 3.5 15.4 + - - +
120F TYR* 3.5 37.2 + - + +
129F VAL* 4.1 8.1 - - + -
130F ASP* 3.5 26.2 - - - +
133F ILE* 3.6 40.8 - - + -
150F ARG* 4.1 17.9 + - - +
151F LEU 4.6 1.0 + - - -
160F ILE* 3.7 11.4 - - + +
162F PHE* 5.2 1.8 - - + -
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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