Contacts of the helix formed by residues 103 - 111 (chain F) in PDB entry 5A31
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 HIS 103 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101F LYS 3.2 8.1 + - - -
102F SER* 1.3 85.5 - - - +
104F ASP* 1.3 57.2 + - - +
105F ASP 3.2 1.3 - - - +
106F ILE* 3.1 22.4 + - + +
107F VAL* 2.9 32.3 + - - +
118F LEU* 4.1 17.6 - - + +
121F LEU* 5.2 1.6 - - + -
125F TYR* 5.1 8.3 - + - -
133F LYS* 5.1 8.8 + - + +
136F GLU* 4.7 12.7 + - + +
137F CYS* 4.1 35.4 + - + -
140F LYS* 3.8 34.3 - - + +
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Residues in contact with ASP 104 (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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102F SER* 3.1 24.5 + - - +
103F HIS* 1.3 69.1 - - - +
105F ASP* 1.3 61.7 + - - +
107F VAL* 3.3 11.1 + - - +
108F THR* 2.9 37.4 + - + +
140F LYS* 4.2 12.9 + - - +
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Residues in contact with ASP 105 (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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100F GLN 4.5 1.6 - - - +
101F LYS* 3.5 21.9 - - + +
102F SER* 3.0 36.0 + - - +
103F HIS 3.2 0.2 - - - -
104F ASP* 1.3 77.4 - - - +
106F ILE* 1.3 58.3 + - - +
108F THR* 2.4 24.8 + - - -
109F GLU* 2.9 23.8 + - + +
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Residues in contact with ILE 106 (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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92F LEU* 4.4 10.8 - - + +
93F SER* 4.9 3.8 - - - -
101F LYS* 4.0 33.0 - - + +
103F HIS* 3.1 23.6 + - + +
105F ASP* 1.3 73.6 - - - +
107F VAL* 1.3 63.7 + - - +
109F GLU* 3.1 3.5 + - - +
110F PHE* 2.9 55.1 + - + +
114F ALA* 4.8 1.6 - - + +
117F THR* 4.1 9.0 - - - +
118F LEU* 3.7 25.8 - - + -
121F LEU* 4.0 25.8 - - + -
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Residues in contact with VAL 107 (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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103F HIS 2.9 19.8 + - - +
104F ASP* 3.3 14.1 + - - +
106F ILE* 1.3 73.8 - - - +
108F THR* 1.3 61.2 + - + +
111F GLY* 2.8 31.7 + - - +
114F ALA* 3.7 12.5 - - + +
118F LEU* 4.7 9.0 - - + -
140F LYS* 5.2 7.4 - - + +
144F LEU* 4.2 37.0 - - + -
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Residues in contact with THR 108 (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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104F ASP* 2.9 21.4 + - + +
105F ASP* 2.4 32.5 + - - -
107F VAL* 1.3 82.0 - - + +
109F GLU* 1.3 63.6 + - - +
111F GLY* 4.0 4.9 + - - -
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Residues in contact with GLU 109 (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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69F PRO* 3.6 18.7 - - + +
72F LYS* 4.7 13.4 + - - +
101F LYS* 3.3 40.1 + - - +
105F ASP* 2.9 23.5 + - + +
106F ILE* 3.7 4.4 - - - +
108F THR* 1.3 81.7 + - - +
110F PHE* 1.3 79.6 + - + +
111F GLY 3.8 0.2 + - - -
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Residues in contact with PHE 110 (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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69F PRO* 3.5 43.7 - - + +
72F LYS* 3.9 21.5 - - + -
73F TYR 4.2 1.1 - - - -
92F LEU* 3.4 45.8 - - + -
106F ILE* 2.9 45.8 + - + +
109F GLU* 1.3 92.4 - - + +
111F GLY* 1.3 65.1 + - - +
112F ASP 3.1 2.4 + - - -
113F SER* 3.0 23.6 + - - +
114F ALA* 3.7 17.7 - - - -
117F THR* 3.8 16.6 - - + +
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Residues in contact with GLY 111 (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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107F VAL* 2.8 21.0 + - - +
108F THR* 4.0 4.2 + - - -
109F GLU 3.5 2.0 - - - -
110F PHE* 1.3 73.6 - - - +
112F ASP* 1.3 63.7 + - - +
114F ALA* 3.0 19.6 - - - +
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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