Contacts of the helix formed by residues 161 - 167 (chain A) in PDB entry 4XJO
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 THR 161 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125A SER* 3.5 19.5 - - - -
129A GLU* 2.6 32.9 + - - +
160A ASP* 1.3 78.8 - - - +
162A PHE* 1.3 60.0 + - - +
163A LEU 3.4 0.7 - - - -
164A ALA* 3.2 5.5 + - - +
165A MET* 2.8 25.8 + - - +
126B VAL* 4.0 30.7 - - + -
129B GLU* 3.5 27.4 - - + +
161B THR* 4.4 9.0 - - + -
315B HIS* 4.4 3.8 - - + -
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Residues in contact with PHE 162 (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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160A ASP 5.1 0.2 - - - -
161A THR* 1.3 73.4 - - - +
163A LEU* 1.3 61.6 + - - +
165A MET* 3.6 16.6 - - - +
166A SER* 3.4 17.8 + - - -
178A TRP* 4.0 16.8 - + - -
181A VAL* 3.9 26.2 - - + +
182A LEU* 3.8 25.4 - - + +
183A ALA* 5.3 0.9 + - - +
129B GLU* 2.9 55.4 + - + +
132B ALA* 4.5 9.6 - - + -
133B LYS* 4.0 35.9 - - + -
136B LEU* 4.8 3.4 - - + -
162B PHE* 6.3 0.2 - - + -
163B LEU* 4.1 25.1 - - + +
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Residues in contact with LEU 163 (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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128A VAL* 4.7 12.3 - - + +
129A GLU* 3.0 23.3 + - - +
132A ALA* 3.6 27.6 - - + -
150A LEU* 4.0 13.9 - - + -
162A PHE* 1.3 73.8 - - - +
164A ALA* 1.3 71.2 + - - +
166A SER* 2.6 36.5 + - - +
167A ILE* 3.8 3.5 + - + +
183A ALA* 4.8 8.3 - - + -
185A GLN* 3.8 13.9 - - - +
162B PHE* 4.1 26.6 - - + +
163B LEU 5.9 0.2 - - - +
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Residues in contact with ALA 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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125A SER 4.6 1.8 - - - +
128A VAL* 4.2 19.3 - - + -
129A GLU* 3.1 6.4 + - - +
158A HIS* 3.3 26.5 - - - +
159A GLY* 3.7 13.0 - - - -
161A THR* 3.5 21.1 - - - +
163A LEU* 1.3 78.4 - - - +
165A MET* 1.3 60.8 + - - +
166A SER 3.3 0.7 + - - -
167A ILE* 3.3 17.5 + - - +
168A CYS* 3.3 12.8 - - - -
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Residues in contact with MET 165 (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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25A TYR* 6.1 0.7 - - - +
159A GLY 3.8 1.8 + - - +
160A ASP* 3.3 28.7 - - - +
161A THR 2.8 18.5 + - - +
162A PHE* 3.6 22.9 - - + +
163A LEU 3.2 0.2 - - - -
164A ALA* 1.3 75.6 - - - +
166A SER* 1.3 57.3 + - - +
168A CYS* 3.1 18.1 + - - +
173A GLY 5.2 4.0 - - - +
175A HIS* 2.7 29.4 + - + +
178A TRP* 3.3 45.1 - - + +
182A LEU* 3.9 17.0 - - + -
133B LYS* 3.4 19.3 - - - +
314B MET* 5.4 1.3 - - + +
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Residues in contact with SER 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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162A PHE 3.4 8.8 + - - -
163A LEU* 2.6 23.0 + - - +
165A MET* 1.3 79.4 - - - +
167A ILE* 1.3 57.8 + - - +
168A CYS 3.5 0.4 - - - -
175A HIS* 3.9 5.0 - - - -
182A LEU* 4.1 10.1 - - - +
183A ALA* 3.5 34.6 - - - +
185A GLN* 3.0 33.1 + - - +
187A PHE* 3.3 20.6 - - - -
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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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128A VAL* 4.3 12.6 - - + -
150A LEU* 3.9 37.9 - - + -
152A THR* 3.5 28.2 + - + +
153A TRP 5.1 0.2 - - - +
156A GLY* 4.7 2.9 - - - +
158A HIS* 3.4 39.8 + - + -
163A LEU* 4.1 7.0 - - + +
164A ALA 3.4 13.5 - - - +
166A SER* 1.3 78.1 - - - +
168A CYS* 1.3 64.8 + - - +
169A ASP 3.9 0.7 + - - -
185A GLN* 3.9 14.6 - - + -
187A PHE* 3.9 5.3 - - - -
218A VAL* 3.9 26.9 - - + -
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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