Contacts of the strand formed by residues 164 - 168 (chain A) in PDB entry 4A69
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 VAL 164 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A ILE* 4.0 24.2 - - + -
157A LEU* 4.1 20.2 - - + -
158A LEU* 3.9 20.6 - - + -
161A HIS* 4.0 16.8 - - + -
163A ARG* 1.3 77.1 - - - +
165A LEU* 1.3 69.5 + - - +
186A ARG 3.0 9.1 + - - +
187A VAL* 3.2 8.3 - - + +
188A MET 2.9 25.8 + - - -
247A TYR* 3.5 3.7 + - - -
251A CYS* 3.5 11.7 - - + +
253A VAL* 4.1 19.5 - - + -
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Residues in contact with LEU 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A VAL* 1.3 73.7 - - - +
166A TYR* 1.3 60.9 + - - +
167A ILE* 3.8 27.8 - - + -
188A MET* 3.4 21.5 - - + +
190A VAL* 3.9 11.2 - - + -
240A ILE* 5.2 1.8 - - + -
243A VAL* 3.7 34.3 - - + -
244A VAL* 4.1 21.3 - - + -
247A TYR* 4.4 4.0 - - + -
249A PRO* 3.7 22.4 - - + +
251A CYS 3.0 9.5 + - - +
252A ILE* 3.3 11.6 - - + +
253A VAL 2.8 32.1 + - - +
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Residues in contact with TYR 166 (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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134A HIS* 3.6 3.5 - - - +
150A ILE* 3.3 42.7 - - + +
154A ILE* 4.1 12.8 - - + -
164A VAL 3.8 1.0 + - - -
165A LEU* 1.3 72.2 - - - +
167A ILE* 1.3 57.4 + - - +
168A ASP* 2.6 45.3 + - + -
174A GLY* 5.0 4.7 - - - -
177A VAL* 3.9 26.7 - - + -
187A VAL* 4.4 2.7 - - + -
188A MET 2.7 15.8 + - - +
189A THR* 3.9 20.6 - - + -
190A VAL* 2.7 36.0 + - - +
191A SER* 5.8 1.6 - - - -
253A VAL* 3.5 28.0 - - + +
255A GLN* 3.4 14.5 - - + +
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Residues in contact with ILE 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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165A LEU* 3.8 31.6 - - + -
166A TYR* 1.3 77.0 - - - +
168A ASP* 1.3 62.8 + - - +
169A ILE* 4.0 15.7 - - + -
190A VAL* 3.5 5.8 - - + +
192A PHE* 4.8 2.5 - - + -
236A PHE* 4.0 12.1 - - + -
240A ILE* 3.8 27.8 - - + -
252A ILE* 3.9 18.2 - - + -
253A VAL 2.8 10.8 + - - +
254A LEU* 3.4 22.6 - - + +
255A GLN* 2.9 27.0 + - - +
283A VAL* 4.0 18.8 - - + -
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Residues in contact with ASP 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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134A HIS* 2.4 30.2 + - - -
166A TYR* 2.6 31.0 + - + -
167A ILE* 1.3 74.1 - - - +
169A ILE* 1.3 60.3 + - - +
170A ASP* 3.2 17.8 + - - +
174A GLY* 3.5 6.0 - - - -
190A VAL 2.9 13.7 + - - +
191A SER* 4.0 8.3 - - - +
192A PHE* 3.2 20.1 + - - -
255A GLN* 3.8 6.5 - - - -
503A K 2.5 37.1 - - - -
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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