Contacts of the helix formed by residues 108 - 119 (chain F) in PDB entry 3E5Q
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 SER 108 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33F LEU* 6.1 0.2 - - - +
51F THR 4.1 4.9 - - - -
52F SER* 3.8 19.5 - - - +
106F TRP 3.8 3.5 + - - -
107F PHE* 1.3 72.8 - - - +
109F GLU* 1.3 58.7 + - - +
110F LYS* 4.0 10.9 - - - +
111F SER* 2.3 46.9 + - - -
112F LEU* 2.6 12.2 + - - -
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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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124E PHE* 3.2 34.7 - - - +
51F THR 4.6 3.5 + - - +
87F LEU* 3.4 32.1 - - + +
88F TYR* 2.9 40.2 + - + +
108F SER* 1.3 71.7 - - - +
110F LYS* 1.3 55.8 + - + +
112F LEU* 2.8 24.7 + - - +
113F ARG* 2.9 32.5 + - - +
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Residues in contact with LYS 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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108F SER* 2.8 12.1 + - - +
109F GLU* 1.3 80.1 + - - +
111F SER* 1.3 60.3 + - - +
113F ARG* 3.9 24.1 + - - +
114F THR* 3.8 12.9 + - - +
117F ARG* 5.2 6.1 - - - +
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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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31F MET* 3.8 22.0 + - - +
32F GLY* 4.6 1.6 - - - -
33F LEU* 6.5 0.4 - - - -
106F TRP 4.8 0.4 - - - -
107F PHE* 3.3 33.6 - - - +
108F SER* 2.3 42.3 + - - -
110F LYS* 1.3 69.3 - - - +
112F LEU* 1.3 60.4 + - - -
114F THR* 3.0 22.2 + - - -
115F VAL* 3.4 11.1 + - - +
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Residues in contact with LEU 112 (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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124E PHE* 3.7 16.4 - - + -
127E PHE* 5.2 6.5 - - + -
25F LEU* 5.4 4.7 - - + -
53F MET* 4.4 18.6 - - + -
87F LEU* 4.4 10.8 - - + -
107F PHE* 3.9 26.0 - - + -
108F SER 2.6 14.4 + - - +
109F GLU 2.8 17.6 + - - +
111F SER* 1.3 70.2 + - - +
113F ARG* 1.3 65.7 + - - +
114F THR 3.2 0.3 + - - -
115F VAL* 3.2 32.0 + - + +
116F PHE* 3.0 40.0 + - + -
126F ILE* 4.8 7.6 - - + -
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Residues in contact with ARG 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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120E GLU* 3.0 44.7 + - - +
121E ASP* 2.7 29.7 + - - +
123E ILE* 6.3 0.9 - - + -
124E PHE* 3.4 39.5 - - + +
109F GLU* 2.9 32.0 + - - +
110F LYS* 4.2 21.1 - - - +
111F SER 3.5 0.4 - - - -
112F LEU* 1.3 72.0 - - - +
114F THR* 1.3 56.7 + - - +
116F PHE* 3.2 7.4 + - - +
117F ARG* 3.1 51.8 + - - +
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Residues in contact with THR 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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31F MET* 3.7 15.2 + - - +
110F LYS* 3.8 16.1 + - - +
111F SER* 3.0 14.0 + - - -
112F LEU 3.2 0.4 - - - -
113F ARG* 1.3 73.0 - - - +
115F VAL* 1.3 68.7 + - - +
117F ARG* 4.0 19.7 - - + +
118F THR* 3.0 23.6 + - - +
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Residues in contact with VAL 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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25F LEU* 4.9 8.3 - - + -
28F TYR* 3.8 32.1 - - + -
31F MET* 4.2 20.2 - - + -
107F PHE* 4.8 5.2 - - + -
111F SER* 3.4 20.4 - - - +
112F LEU* 3.2 27.1 + - + +
114F THR* 1.3 75.0 - - - +
116F PHE* 1.3 54.7 + - + +
118F THR* 2.7 30.1 + - - -
119F ASP 2.7 13.7 + - - -
122F MET* 4.0 22.9 - - + -
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Residues in contact with PHE 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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120E GLU* 5.8 1.1 - - - +
123E ILE* 3.8 29.4 - - + -
124E PHE* 3.8 26.0 - + - -
127E PHE* 5.9 3.6 - + - -
112F LEU* 3.0 35.2 - - + -
113F ARG* 3.2 8.2 + - - +
115F VAL* 1.3 80.0 - - + +
117F ARG* 1.3 60.7 + - + +
119F ASP 3.3 17.8 - - - -
120F GLU* 3.5 12.6 + - - +
122F MET* 3.4 12.1 - - + -
123F ILE* 3.1 49.1 - - + +
126F ILE* 3.3 33.4 - - + -
127F PHE* 6.4 0.4 - + - -
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Residues in contact with ARG 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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120E GLU* 3.0 32.7 + - - +
110F LYS* 5.2 6.3 - - - +
113F ARG* 3.1 44.8 + - - +
114F THR* 3.8 18.4 + - + +
115F VAL 2.9 0.4 + - - -
116F PHE* 1.3 74.5 - - - +
118F THR* 1.3 67.8 + - - +
119F ASP* 3.1 1.2 - - - -
120F GLU 5.1 0.9 + - - -
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Residues in contact with THR 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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28F TYR* 3.6 26.7 - - + -
31F MET* 3.6 20.6 - - + +
114F THR* 3.0 16.1 + - - +
115F VAL 2.7 15.5 + - - -
117F ARG* 1.3 76.9 - - - +
119F ASP* 1.3 56.7 + - + +
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Residues in contact with ASP 119 (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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24F LYS* 5.3 6.8 - - - +
28F TYR* 2.5 38.6 + - + +
115F VAL 2.7 5.8 + - - +
116F PHE* 3.3 12.3 - - - -
117F ARG 3.1 0.2 - - - -
118F THR* 1.3 80.3 - - + +
120F GLU* 1.3 72.1 + - - +
121F ASP* 3.0 22.4 + - - +
122F MET* 3.2 28.9 - - + +
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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