Contacts of the strand formed by residues 113 - 118 (chain A) in PDB entry 4GR0
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 TYR 113 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111A LYS* 3.2 27.2 - - + +
112A HIS* 1.3 76.9 - - - +
114A ILE* 1.3 61.0 + - - +
115A THR* 4.3 14.5 + - + -
148A LYS* 3.6 41.2 - - + +
150A SER* 3.5 32.6 + - - -
158A ASP* 4.1 0.7 - - - +
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Residues in contact with ILE 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A TRP* 3.7 39.3 - - + -
111A LYS* 4.0 11.0 - - + +
112A HIS 4.2 1.1 - - - +
113A TYR* 1.3 80.5 - - - +
115A THR* 1.3 74.2 + - - +
147A LEU* 3.8 28.3 - - + -
148A LYS 2.9 8.9 + - - -
149A PHE* 3.2 31.9 - - + +
150A SER 2.9 22.9 + - - -
158A ASP* 3.5 15.3 - - + +
159A ILE* 3.9 23.6 - - + -
224A LEU* 4.2 2.9 - - + -
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Residues in contact with THR 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A TYR* 4.3 14.8 - - + +
114A ILE* 1.3 80.3 - - - +
116A TYR* 1.3 61.7 + - - +
150A SER* 3.2 21.1 - - - +
152A ILE* 4.1 20.9 - - + -
156A MET 4.0 4.0 + - - +
157A ALA* 3.3 7.9 - - - -
158A ASP* 2.9 40.4 + - - +
159A ILE* 3.0 21.8 + - - +
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Residues in contact with TYR 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A THR* 1.3 75.8 - - - +
117A ARG* 1.3 66.9 + - - +
118A ILE* 4.5 9.0 - - + -
131A ASP 5.0 0.9 + - - -
134A ILE* 3.7 19.5 - - + -
135A ARG* 3.8 26.9 + - - +
138A PHE* 3.4 51.4 - + + -
149A PHE* 4.4 13.0 - - + -
150A SER 3.0 15.1 + - - -
151A LYS* 3.5 45.2 - - + +
152A ILE* 2.8 29.5 + - - +
157A ALA* 3.6 5.2 - - - -
159A ILE* 3.1 15.7 - - + +
161A VAL* 4.9 2.7 - - + -
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Residues in contact with ARG 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A TYR* 1.3 78.0 - - - +
118A ILE* 1.3 73.5 + - - +
119A ASN* 3.5 19.1 + - - +
151A LYS* 5.4 0.2 - - - -
152A ILE* 3.4 22.2 - - + +
153A ASN 3.5 29.6 - - - +
154A THR* 4.0 4.5 - - - +
155A GLY* 2.8 32.6 + - - +
156A MET* 5.4 0.4 - - - +
157A ALA* 3.6 8.7 - - + +
159A ILE 3.0 6.7 + - - -
160A LEU* 3.5 31.0 - - + +
161A VAL* 2.9 24.3 + - - +
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Residues in contact with ILE 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A TYR* 4.5 11.9 - - + -
117A ARG* 1.3 83.6 + - - +
119A ASN* 1.3 62.8 + - - +
120A ASN 3.3 23.3 + - - +
121A TYR* 3.8 33.0 - - + +
130A VAL* 4.4 4.7 - - + -
131A ASP* 3.3 32.3 - - - +
134A ILE* 4.2 25.4 - - + -
151A LYS* 4.3 13.6 - - - +
152A ILE 4.6 1.2 + - - -
161A VAL* 3.8 22.4 - - + +
163A PHE* 5.0 0.2 - - + -
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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