Contacts of the helix formed by residues 89 - 96 (chain F) in PDB entry 3EXH
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 ALA 89 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59F GLU* 3.6 27.1 - - + +
60F MET* 3.8 8.3 - - - +
63F ALA* 3.6 16.2 - - + -
80F PHE* 3.7 22.4 - - + -
86F SER* 2.8 4.7 + - - +
88F GLN* 1.3 79.1 - - - +
90F ILE* 1.3 59.0 + - - +
91F ASP 3.1 3.4 - - - -
92F GLN* 2.7 23.0 + - + +
93F VAL* 3.1 10.0 + - - +
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Residues in contact with ILE 90 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86F SER* 2.9 12.2 + - - +
87F MET* 3.9 15.9 - - + +
88F GLN 3.5 1.8 - - - -
89F ALA* 1.3 78.4 - - - +
91F ASP* 1.3 65.8 + - - +
93F VAL* 3.0 6.0 + - + +
94F ILE* 2.8 27.3 + - + +
132F PHE* 5.2 0.7 - - + -
135F TRP* 4.0 22.0 - - + -
136F TYR* 3.4 41.5 - - + +
87H MET* 3.8 26.5 - - + +
90H ILE* 4.1 9.0 - - + -
135H TRP* 3.7 28.5 - - + -
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Residues in contact with ASP 91 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137E ILE* 3.4 35.9 - - - +
140E ALA* 3.8 13.5 - - - +
60F MET* 4.5 9.7 - - + +
88F GLN 5.2 0.4 + - - -
89F ALA 3.1 0.8 - - - -
90F ILE* 1.3 81.4 - - - +
92F GLN* 1.3 60.3 + - - +
95F ASN* 2.9 53.7 + - - +
96F SER* 3.5 4.2 + - - -
84H ASN 4.4 4.0 - - - +
87H MET* 3.7 23.1 + - + +
88H GLN* 4.4 18.4 + - + +
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Residues in contact with GLN 92 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140E ALA* 3.0 28.8 + - - +
143E PRO* 3.9 8.1 - - - +
144E LEU* 3.7 10.9 - - - +
174E GLN* 2.9 24.0 + - - -
60F MET* 3.6 31.3 - - - +
63F ALA* 4.3 8.7 - - + +
64F GLY* 3.6 19.4 - - - +
67F VAL* 4.3 6.0 - - + +
89F ALA 2.7 14.6 + - - +
91F ASP* 1.3 75.4 - - - +
93F VAL* 1.3 61.5 + - - +
96F SER* 2.7 35.7 + - - -
97F ALA* 3.2 22.3 + - - +
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Residues in contact with VAL 93 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63F ALA* 5.5 0.2 - - + -
80F PHE* 4.3 15.0 - - + -
89F ALA* 3.1 11.2 + - + +
90F ILE* 3.0 12.8 + - - +
92F GLN* 1.3 79.0 - - + +
94F ILE* 1.3 64.9 + - + +
97F ALA* 3.2 5.2 - - - +
98F ALA* 2.9 26.2 + - - +
114F PHE* 3.9 48.2 - - + -
136F TYR* 3.9 30.5 - - + +
142F LEU* 4.3 12.9 - - + +
168F VAL* 4.4 2.0 - - + -
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Residues in contact with ILE 94 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90F ILE* 2.8 20.7 + - + +
93F VAL* 1.3 84.9 - - + +
95F ASN* 1.3 63.3 + - - +
98F ALA* 3.3 22.3 + - + +
99F LYS* 3.4 23.1 + - - +
136F TYR* 4.3 7.9 - - + -
139F CYS* 3.8 28.3 - - + -
142F LEU* 3.8 24.7 - - + -
87H MET* 4.1 9.6 - - + -
130H GLN* 3.7 26.2 - - - +
135H TRP* 4.0 21.1 - - + -
266H TRP* 5.0 1.1 - - + -
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Residues in contact with ASN 95 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137E ILE* 3.9 15.0 - - + +
91F ASP* 2.9 32.4 + - - +
94F ILE* 1.3 73.8 - - - +
96F SER* 1.3 59.1 + - - +
99F LYS* 2.7 36.7 + - - +
100F THR* 4.1 5.5 + - - -
103F MET* 4.2 3.8 - - - +
84H ASN* 4.5 4.6 + - - +
87H MET* 2.8 31.6 - - - +
127H GLN* 2.6 54.7 + - - +
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Residues in contact with SER 96 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135E ASN* 5.5 1.2 + - - -
140E ALA* 4.1 10.4 - - - +
144E LEU* 4.0 27.9 - - - +
67F VAL* 4.1 4.2 - - - +
71F MET* 3.4 12.0 - - - +
91F ASP* 3.5 2.7 + - - -
92F GLN* 2.7 41.4 + - - -
95F ASN* 1.3 77.8 - - - +
97F ALA* 1.3 60.2 + - - +
100F THR* 2.5 26.7 + - - -
110F VAL* 4.3 0.3 - - - +
127H GLN* 4.5 3.7 + - - +
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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