Contacts of the strand formed by residues 163 - 167 (chain A) in PDB entry 3IE7
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 PHE 163 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131A LYS 4.5 1.2 + - - -
133A ASP 3.1 12.9 + - - +
134A MSE 3.6 35.0 - - + -
135A VAL* 2.9 30.3 + - - +
136A VAL* 6.0 0.2 - - + -
161A GLY 3.8 1.0 + - - -
162A ALA* 1.3 75.2 - - - +
164A LEU* 1.3 66.2 + - - +
165A GLY 4.1 1.8 - - - -
182A ASP* 3.5 28.5 - - + -
183A PHE* 3.8 26.7 - - + -
215A TYR* 3.8 23.3 - + - -
258A ILE* 4.0 14.1 - - + -
261A LEU* 3.7 22.9 - - + -
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Residues in contact with LEU 164 (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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135A VAL* 3.5 9.6 - - + +
137A ILE* 4.0 22.2 - - + -
154A LEU* 4.1 16.2 - - + +
157A VAL* 3.7 30.3 - - + -
158A LYS* 4.1 23.3 - - + -
162A ALA 4.3 3.1 - - - +
163A PHE* 1.3 78.5 - - - +
165A GLY* 1.3 69.5 + - - +
166A CYS* 4.2 2.5 - - - -
180A GLY 4.6 0.9 - - - +
181A VAL* 3.6 29.1 - - + +
182A ASP* 2.8 44.6 + - - +
183A PHE 3.2 3.5 + - - -
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Residues in contact with GLY 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A VAL 2.9 11.2 + - - +
136A VAL* 3.4 10.4 - - - -
137A ILE 2.9 25.3 + - - -
163A PHE* 4.1 6.0 - - - -
164A LEU* 1.3 75.8 - - - +
166A CYS* 1.3 64.7 + - - -
167A ASP 4.3 0.2 - - - -
183A PHE* 3.3 26.2 - - - -
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Residues in contact with CYS 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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137A ILE* 3.3 9.2 - - - -
150A PHE* 5.0 0.4 - - - -
154A LEU* 3.7 29.4 - - - -
164A LEU* 4.2 6.7 - - - -
165A GLY* 1.3 78.8 - - - -
167A ASP* 1.3 60.8 + - - +
168A ASN* 3.5 19.9 + - + +
173A LEU* 4.9 2.3 - - + +
176A ALA* 3.9 16.8 - - + -
181A VAL* 3.9 17.0 - - + -
183A PHE* 2.8 14.6 + - - +
184A ILE* 3.3 30.7 - - + +
185A LYS 3.9 0.7 + - - -
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Residues in contact with ASP 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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39A LYS* 2.6 48.3 + - - +
136A VAL* 5.4 1.9 - - + +
137A ILE 2.9 8.9 + - - -
138A ALA* 3.5 12.4 - - + +
139A GLY 3.2 14.7 + - - -
166A CYS* 1.3 70.6 - - - +
168A ASN* 1.3 59.6 + - - +
183A PHE* 5.6 1.1 - - + -
185A LYS* 3.6 31.5 - - + +
190A GLU* 4.4 5.9 - - - +
250A GLY 4.4 0.7 - - - +
251A ASP* 4.3 4.9 - - - +
254A VAL* 3.4 34.1 - - + +
319A MG 4.1 8.5 - - - -
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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