Contacts of the helix formed by residues 108 - 119 (chain A) in PDB entry 1FX8
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 TYR 108 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A GLY* 3.4 28.6 + - - -
30A ALA* 4.0 5.2 - - + -
31A ALA* 3.4 29.9 - - - +
34A VAL* 4.0 17.7 - - + -
35A ALA* 4.1 11.6 - - + +
104A VAL* 3.0 33.9 + - + +
105A TYR 3.5 0.7 - - - -
107A LEU* 1.3 82.9 - - + +
109A TYR* 1.3 65.7 + - - +
110A ASN 3.4 2.0 - - - -
111A LEU* 2.9 34.1 + - + +
112A PHE* 3.3 25.7 + - + -
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Residues in contact with TYR 109 (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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105A TYR* 2.7 40.1 + + - +
106A GLY* 3.5 13.7 - - - +
107A LEU 3.3 1.8 - - - +
108A TYR* 1.3 70.5 - - - +
110A ASN* 1.3 83.0 + - - +
112A PHE* 3.1 17.2 + - - +
113A PHE* 3.4 52.1 - + + -
473A BOG 3.6 17.4 + - - -
475A BOG 3.9 21.1 - - - +
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Residues in contact with ASN 110 (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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108A TYR 3.1 1.2 + - - -
109A TYR* 1.3 98.8 - - - +
111A LEU* 1.3 66.0 + - + +
113A PHE* 3.4 4.3 + - - +
114A ASP* 2.9 43.7 + - - +
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Residues in contact with LEU 111 (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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34A VAL* 3.7 25.1 - - + +
35A ALA* 3.6 31.4 - - + -
107A LEU 5.2 2.9 - - - +
108A TYR* 2.9 34.5 + - + +
110A ASN* 1.3 80.8 - - + +
112A PHE* 1.3 62.8 + - - +
114A ASP* 4.2 5.3 - - - +
115A PHE* 3.0 26.9 + - - +
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Residues in contact with PHE 112 (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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30A ALA* 4.5 6.5 - - + -
34A VAL* 4.1 22.2 - - + -
104A VAL* 5.1 1.1 - - + -
105A TYR* 3.9 26.0 - + + -
108A TYR* 3.3 38.5 + - + -
109A TYR 3.1 8.8 + - - +
111A LEU* 1.3 78.2 - - - +
113A PHE* 1.3 58.1 + - - +
115A PHE* 3.7 1.6 - - - +
116A GLU* 3.0 35.8 + - - +
123A ARG* 4.0 12.8 - - - +
131A LEU* 4.3 10.7 - - + +
134A THR* 3.8 37.5 - - + -
135A PHE* 3.8 12.1 - + - -
219A TRP* 3.9 30.7 - + - -
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Residues in contact with PHE 113 (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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105A TYR* 3.2 20.4 - + - -
109A TYR* 3.4 49.8 - + + -
110A ASN* 3.4 7.0 + - - +
112A PHE* 1.3 81.3 - - + +
114A ASP* 1.3 60.8 + - - +
116A GLU* 3.4 9.4 + - + +
117A GLN* 2.9 32.0 + - - +
123A ARG* 3.4 17.9 - - - -
473A BOG 3.2 27.4 - - - -
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Residues in contact with ASP 114 (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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110A ASN* 2.9 30.3 + - - +
111A LEU* 4.2 5.8 - - - +
113A PHE* 1.3 78.7 - - - +
115A PHE* 1.3 57.1 + - - +
117A GLN* 3.7 14.9 - - - +
118A THR* 2.8 37.0 + - - +
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Residues in contact with PHE 115 (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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33A LYS 3.2 23.3 - - - -
34A VAL* 4.0 19.1 - - + +
111A LEU 3.0 19.7 + - - +
112A PHE 3.7 3.6 - - - +
114A ASP* 1.3 75.1 - - - +
116A GLU* 1.3 60.6 + - - +
118A THR* 3.3 1.5 + - - -
119A HIS* 2.9 67.0 + + - +
121A ILE* 3.5 27.6 - - + -
130A ASP* 6.0 1.3 - - - -
131A LEU* 4.0 23.1 - - + -
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Residues in contact with GLU 116 (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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112A PHE* 3.0 16.3 + - - +
113A PHE* 3.8 13.0 - - - +
115A PHE* 1.3 77.1 - - - +
117A GLN* 1.3 56.9 + - - +
120A HIS* 2.9 9.7 + - - -
121A ILE* 2.8 54.2 + - + +
123A ARG* 2.8 65.2 + - - +
131A LEU* 3.6 25.4 - - + +
219A TRP* 4.1 3.7 + - - -
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Residues in contact with GLN 117 (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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113A PHE* 2.9 19.2 + - - +
114A ASP* 3.7 16.3 - - - +
116A GLU* 1.3 76.3 - - - +
118A THR* 1.3 64.2 + - - +
120A HIS* 3.3 21.0 + - - +
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Residues in contact with THR 118 (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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114A ASP* 2.8 24.8 + - - +
115A PHE* 3.7 4.5 - - - -
117A GLN* 1.3 81.1 + - - +
119A HIS* 1.3 79.4 + - + +
120A HIS* 3.3 16.2 + - - -
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Residues in contact with HIS 119 (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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115A PHE* 2.9 63.8 + + - +
118A THR* 1.3 91.3 + - + +
120A HIS* 1.3 75.5 + - - +
121A ILE* 3.3 23.4 + - + +
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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