Contacts of the helix formed by residues 108 - 118 (chain F) in PDB entry 5GJQ
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 108 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99F HIS* 6.3 0.2 - - + -
105F GLU* 5.4 0.7 - - - +
106F THR 4.8 2.7 - - - +
107F MET* 1.3 76.1 - - - +
109F VAL* 1.3 66.3 + - - +
110F GLU* 4.0 5.6 + - - +
111F SER* 2.8 45.3 + - - -
112F VAL* 3.1 12.2 + - - +
147F ASP* 3.5 13.5 - - - +
148F GLU* 3.5 31.0 - - - +
149F LYS* 6.2 4.0 - - + -
79f ASN* 3.8 17.2 + - + +
81f LYS* 3.9 17.7 - - + +
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Residues in contact with VAL 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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74F ILE* 3.8 21.5 - - + -
107F MET 3.8 0.4 + - - -
108F THR* 1.3 71.6 - - - +
110F GLU* 1.3 57.5 + - - +
112F VAL* 3.3 2.3 + - + +
113F THR* 2.8 38.8 + - - +
143F PHE* 4.5 13.7 - - + +
144F GLY 4.8 0.4 - - - -
145F GLY* 3.6 45.1 - - - +
146F VAL 3.8 3.8 - - - +
147F ASP* 3.0 16.8 + - + +
152F GLN* 3.9 13.7 - - + +
154F PHE* 3.8 20.6 - - + -
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Residues in contact with GLU 110 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108F THR* 3.1 6.2 - - - +
109F VAL* 1.3 80.8 - - - +
111F SER* 1.3 57.5 + - - +
113F THR* 3.8 3.8 - - - -
114F GLN* 2.9 30.2 + - + +
149F LYS* 4.1 19.5 + - + +
152F GLN* 4.1 8.6 + - - +
154F PHE* 3.7 36.4 - - + -
162F PHE* 4.1 13.0 - - + -
164F GLN* 5.2 2.9 - - - +
61G LYS* 5.3 9.6 + - - -
79f ASN 5.5 1.2 - - - +
80f ASN* 4.3 21.8 + - - +
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Residues in contact with SER 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 MET* 3.8 22.1 - - - +
108F THR* 2.8 26.0 + - - -
110F GLU* 1.3 77.4 - - - +
112F VAL* 1.3 65.0 + - - +
114F GLN* 3.3 7.2 + - - +
115F ALA* 3.0 23.0 + - - +
78f SER* 2.5 33.9 + - - -
79f ASN* 3.0 12.7 + - - -
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Residues in contact with VAL 112 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70F ILE* 4.4 7.2 - - + -
74F ILE* 3.7 17.0 - - + -
92F ALA* 4.1 26.7 - - + +
95F GLU* 5.8 0.4 - - + -
96F THR* 3.6 20.9 - - + -
107F MET* 3.5 38.1 - - + +
108F THR 3.1 6.6 + - - +
109F VAL* 3.7 4.9 - - + +
111F SER* 1.3 73.9 - - - +
113F THR* 1.3 66.6 + - - +
115F ALA* 3.0 14.2 + - + +
116F VAL* 3.0 16.8 + - + +
143F PHE* 4.8 9.2 - - + -
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Residues in contact with THR 113 (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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109F VAL* 2.8 24.3 + - - +
110F GLU* 3.8 5.6 - - - -
112F VAL* 1.3 78.4 - - - +
114F GLN* 1.3 53.2 + - - +
116F VAL* 3.4 8.8 + - - +
117F SER* 2.8 37.6 + - - +
143F PHE* 3.8 34.4 - - + +
154F PHE* 3.9 19.3 - - + +
156F MET* 5.0 3.1 - - + -
162F PHE* 3.5 35.7 - - + -
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Residues in contact with GLN 114 (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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110F GLU* 2.9 20.6 + - - +
111F SER 3.5 5.3 - - - +
112F VAL 3.1 0.2 - - - -
113F THR* 1.3 78.0 - - - +
115F ALA* 1.3 62.1 + - - +
117F SER* 3.1 3.2 + - - -
118F ASN* 3.0 41.1 + - - +
162F PHE* 3.9 29.1 - - + -
82G ARG* 4.1 18.5 - - - +
89G ARG* 5.5 7.4 - - - +
77f HIS 5.0 6.1 + - - -
78f SER* 3.9 30.2 + - - +
80f ASN* 5.9 3.4 - - - +
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Residues in contact with ALA 115 (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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91F LYS* 3.8 15.2 + - + +
92F ALA* 6.2 0.2 - - - -
95F GLU* 4.0 36.6 - - + +
107F MET* 4.8 1.8 - - + -
111F SER 3.0 13.1 + - - +
112F VAL* 3.0 11.8 + - + +
114F GLN* 1.3 75.9 - - - +
116F VAL* 1.3 63.6 + - + +
118F ASN* 3.0 27.6 + - - +
119F LEU* 3.9 2.6 + - - +
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Residues in contact with VAL 116 (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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88F LEU* 3.9 32.1 - - + +
91F LYS* 5.0 5.1 - - - +
92F ALA* 3.7 31.0 - - + -
112F VAL* 3.0 17.2 + - + +
113F THR 3.6 6.1 - - - +
115F ALA* 1.3 73.9 - - - +
117F SER* 1.3 62.9 + - - +
119F LEU* 3.2 23.3 + - + +
120F ALA 4.2 1.2 + - - -
141F LEU* 4.3 0.7 - - + -
143F PHE* 3.8 23.8 - - + -
156F MET* 4.0 23.0 - - + +
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Residues in contact with SER 117 (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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113F THR 2.8 20.8 + - - -
114F GLN 3.1 6.3 + - - -
116F VAL* 1.3 75.7 - - - +
118F ASN* 1.3 61.3 + - - +
119F LEU 3.2 0.4 - - - -
120F ALA* 3.0 27.6 - - - +
156F MET* 2.8 30.6 - - - +
160F GLY* 3.3 19.2 + - - +
162F PHE* 3.5 11.2 - - - +
82G ARG* 3.7 16.8 + - - -
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Residues in contact with ASN 118 (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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91F LYS* 5.5 2.2 - - - +
114F GLN* 3.0 25.6 + - - +
115F ALA* 3.0 17.3 + - - +
117F SER* 1.3 75.7 - - - +
119F LEU* 1.3 60.6 + - + +
120F ALA* 3.0 7.9 + - - +
121F LEU 4.8 0.7 + - - -
122F GLN* 3.3 17.8 + - - +
82G ARG* 3.1 31.3 + - - +
83G LEU* 5.9 2.6 - - - +
86G ASN* 4.7 16.1 + - - +
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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