Contacts of the helix formed by residues 112 - 122 (chain A) in PDB entry 1FIU
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 112 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106A ALA 3.3 13.9 - - - +
108A TYR 3.0 7.2 + - - +
109A GLN 3.5 7.5 + - - +
111A TYR* 1.3 77.6 - - - +
113A HIS* 1.3 61.5 + - - +
114A LEU 3.2 1.2 + - - -
115A THR* 3.3 21.3 + - - -
116A ALA* 4.3 0.5 + - - +
177A MET* 3.3 43.5 - - + -
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Residues in contact with HIS 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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109A GLN 5.1 1.2 + - - -
110A GLN 3.3 18.7 + - - -
111A TYR* 3.7 10.0 - - - -
112A ALA* 1.3 75.9 + - - +
114A LEU* 1.3 79.1 + - + +
115A THR 3.1 0.7 - - - -
116A ALA* 3.2 11.0 + - - +
117A LEU* 3.1 24.9 + - + +
208A ASN* 2.9 33.0 + - - +
210A LYS* 3.7 34.1 - - + +
126C GLU* 3.5 24.0 - - + +
130C ALA* 3.8 18.7 - - + +
235D THR* 4.9 2.6 + - - +
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Residues in contact with LEU 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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103A LEU* 4.4 11.4 - - + +
105A ILE* 3.6 23.6 - - + -
106A ALA* 4.4 6.7 - - + -
111A TYR* 3.0 28.3 + - + +
113A HIS* 1.3 90.9 - - + +
115A THR* 1.3 57.7 + - - +
117A LEU* 3.6 26.6 - - + +
118A ALA* 2.9 30.7 + - - +
135A TYR* 3.2 46.9 - - + +
137A ILE* 4.6 2.5 - - + -
208A ASN* 4.4 12.6 - - + +
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Residues in contact with THR 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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103A LEU* 4.5 13.4 - - + +
106A ALA* 3.3 24.3 + - - +
112A ALA 3.3 9.0 + - - -
113A HIS 3.1 0.4 - - - -
114A LEU* 1.3 79.4 - - - +
116A ALA* 1.3 57.7 + - - +
118A ALA* 3.4 5.5 + - - +
119A LYS* 2.9 59.9 + - + +
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Residues in contact with ALA 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 ALA 4.3 0.4 + - - -
113A HIS* 3.2 13.9 + - - +
115A THR* 1.3 80.1 - - - +
117A LEU* 1.3 59.2 + - + +
119A LYS* 3.3 9.3 + - - +
120A ALA* 2.9 31.5 + - - +
126C GLU* 5.1 15.3 - - + -
127C LEU* 5.2 4.3 - - + -
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Residues in contact with LEU 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 HIS* 3.1 25.1 + - + +
114A LEU* 3.6 32.5 - - + +
116A ALA* 1.3 77.6 - - + +
118A ALA* 1.3 57.5 + - - +
120A ALA* 3.2 3.0 + - - +
121A ALA* 2.9 30.8 + - - +
131A LEU* 4.5 21.5 - - + +
135A TYR* 3.9 18.4 - - + +
208A ASN* 5.3 4.0 - - - +
126C GLU* 4.5 7.6 - - - +
127C LEU* 3.0 34.1 - - + -
130C ALA* 4.6 5.6 - - + -
131C LEU* 4.5 15.5 - - + -
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Residues in contact with ALA 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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103A LEU* 4.2 21.5 - - + -
114A LEU 2.9 17.9 + - - +
115A THR 3.7 4.0 - - - +
117A LEU* 1.3 76.9 - - - +
119A LYS* 1.3 62.8 + - + +
121A ALA* 3.3 3.3 + - - +
122A GLU* 3.0 26.2 + - - +
135A TYR* 3.3 23.1 + - + +
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Residues in contact with LYS 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 THR* 2.9 42.8 + - + +
116A ALA* 3.7 7.9 - - - +
118A ALA* 1.3 76.1 - - + +
120A ALA* 1.3 58.9 + - - +
122A GLU* 2.7 40.2 - - - +
123A GLU* 3.5 11.7 - - - +
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Residues in contact with ALA 120 (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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116A ALA 2.9 17.2 + - - +
117A LEU* 3.7 5.4 - - - +
119A LYS* 1.3 75.1 - - - +
121A ALA* 1.3 66.3 + - - +
123A GLU* 3.2 20.6 + - - +
124A ASN* 3.3 13.2 + - - +
127A LEU* 3.7 15.8 - - + +
131A LEU* 6.3 0.2 - - + -
124C ASN* 5.8 5.8 - - - +
127C LEU* 4.5 17.5 - - + -
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Residues in contact with ALA 121 (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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117A LEU 2.9 16.6 + - - +
118A ALA 3.7 5.2 - - - +
120A ALA* 1.3 72.5 - - - +
122A GLU* 1.3 52.8 + - - +
123A GLU 2.5 18.1 + - - -
124A ASN* 2.7 23.8 + - - +
127A LEU* 4.0 4.4 - - - +
128A ALA* 4.3 28.7 - - + +
131A LEU* 4.5 8.3 - - + -
132A GLY 6.0 0.9 - - - +
135A TYR* 4.4 10.1 - - - +
267B ILE* 5.8 2.4 - - - +
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Residues in contact with GLU 122 (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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118A ALA 3.0 12.0 + - - +
119A LYS* 2.7 46.9 - - - +
121A ALA* 1.3 73.6 - - - +
123A GLU* 1.3 70.8 + - + +
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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