Contacts of the strand formed by residues 166 - 170 (chain A) in PDB entry 5J1T
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 166 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87A ILE* 5.8 1.3 - - + -
115A ILE* 5.2 0.9 - - + -
116A ALA* 4.8 8.1 - - + -
119A ILE* 3.7 31.6 - - + -
120A TYR* 4.0 22.9 - - + -
128A TYR 3.0 9.3 + - - +
129A VAL* 3.5 16.9 - - + -
130A HIS* 2.8 31.2 + - - -
164A ARG 4.1 7.9 - - - +
165A SER* 1.3 77.3 - - - +
167A PHE* 1.3 63.1 + - - +
168A ILE* 4.3 11.7 - - + -
202A MET* 3.4 24.5 - - + +
204A ILE* 4.2 24.0 - - + -
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Residues in contact with PHE 167 (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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130A HIS* 3.5 34.3 - + + +
132A PHE* 3.9 12.6 - + + -
154A TRP* 4.6 4.3 - + - -
155A ILE* 4.0 32.8 - - + -
158A ASN* 4.3 7.4 - - + -
159A VAL* 3.5 32.5 - - + -
165A SER* 3.6 23.3 - - - -
166A ILE* 1.3 74.1 - - - +
168A ILE* 1.3 63.2 + - - +
169A PHE* 4.0 12.4 + - + -
201A ALA* 4.6 1.1 - - + -
202A MET 2.8 13.2 + - - -
203A PHE* 3.3 38.6 - + + +
204A ILE* 2.8 26.2 + - - +
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Residues in contact with ILE 168 (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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112A SER* 4.4 18.4 - - - +
116A ALA* 5.3 1.1 - - + -
124A LEU* 3.7 29.6 - - + -
129A VAL* 3.9 16.2 - - + -
130A HIS 2.8 11.7 + - - +
131A LEU* 3.5 24.4 - - + -
132A PHE* 2.8 34.5 + - - +
166A ILE* 4.3 6.5 - - + -
167A PHE* 1.3 77.4 - - - +
169A PHE* 1.3 60.3 + - - +
204A ILE* 3.3 28.9 - - + +
206A LEU* 4.1 25.6 - - + -
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Residues in contact with PHE 169 (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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132A PHE* 3.5 38.8 - + + -
138A PHE* 4.5 2.0 - + - -
151A LEU* 4.0 11.4 - - + -
155A ILE* 4.1 17.0 - - + -
167A PHE* 4.0 24.0 - - + -
168A ILE* 1.3 74.1 - - - +
170A ASP* 1.3 63.7 + - - +
172A MET* 4.1 6.6 - - + +
175A MET* 3.8 40.6 - - + -
183A ILE* 3.9 20.0 - - + -
203A PHE* 4.0 9.0 - + - -
204A ILE 2.8 8.7 + - - -
205A PHE* 3.5 29.4 - + + -
206A LEU 2.9 26.9 + - - +
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Residues in contact with ASP 170 (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 ASN* 3.1 33.9 + - - +
131A LEU* 4.2 12.6 - - + -
132A PHE 2.8 16.0 + - - +
133A VAL* 4.1 18.0 - - + +
134A ALA* 3.0 25.6 + - - +
168A ILE 3.8 1.2 - - - -
169A PHE* 1.3 74.1 - - - +
171A GLN* 1.3 92.4 + - - +
172A MET* 3.4 0.7 + - - -
175A MET* 5.7 0.3 - - - +
206A LEU* 3.5 23.2 - - + +
402A MG 3.9 2.4 - - - -
383B ASP* 5.5 1.9 - - - +
386B ASN* 5.1 2.6 + - - -
449B ARG* 5.5 0.9 + - - -
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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