Contacts of the helix formed by residues 101 - 111 (chain A) in PDB entry 2FQ4
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 101 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95A LEU 4.0 6.3 - - - +
96A ILE* 4.1 9.0 - - - +
97A SER 3.0 19.3 + - - +
98A ARG* 2.6 46.1 + - - +
100A GLY* 1.3 72.5 - - - +
102A ILE* 1.3 64.9 + - - +
103A ILE 3.1 0.9 + - - -
104A ASN* 3.4 24.9 + - - +
105A GLU* 3.4 22.0 + - - +
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Residues in contact with ILE 102 (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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22A TYR* 3.4 39.5 - - + +
25A LEU* 4.0 16.2 - - + -
26A LEU* 4.0 17.5 - - + -
64A PHE* 3.7 19.7 - - + -
98A ARG 4.6 3.6 - - - +
99A GLU* 3.1 24.2 - - - +
100A GLY 3.1 0.2 - - - -
101A THR* 1.3 75.6 + - - +
103A ILE* 1.3 65.1 + - - +
105A GLU* 3.2 17.6 + - + +
106A LEU* 2.9 45.2 + - + +
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Residues in contact with ILE 103 (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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61A MSE 6.2 0.2 - - + -
64A PHE* 3.4 35.4 - - + -
94A PHE* 4.5 1.8 - - + -
95A LEU* 4.1 14.6 - - + -
100A GLY 3.1 16.9 + - - +
102A ILE* 1.3 77.5 - - - +
104A ASN* 1.3 63.3 + - - +
106A LEU* 3.3 9.5 + - + +
107A VAL* 2.9 39.4 + - + +
120A TYR* 6.1 1.8 - - + -
124A TYR* 3.9 26.2 - - + -
125A PHE* 4.3 7.0 - - + -
163A PHE* 4.3 16.2 - - + -
166A LEU* 4.2 15.9 - - + -
167A LEU* 5.7 0.2 - - + -
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Residues in contact with ASN 104 (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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95A LEU 5.0 0.4 + - - -
100A GLY 4.5 0.8 + - - -
101A THR* 3.5 23.3 + - - +
102A ILE 3.3 0.2 - - - -
103A ILE* 1.3 75.0 - - - +
105A GLU* 1.3 62.8 + - + +
107A VAL* 3.5 1.7 + - - +
108A GLY* 2.8 26.9 + - - -
166A LEU* 3.1 53.7 - - - +
167A LEU* 4.1 18.7 - - + +
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Residues in contact with GLU 105 (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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101A THR* 3.4 24.2 + - - +
102A ILE* 3.2 18.2 + - + +
104A ASN* 1.3 84.8 - - + +
106A LEU* 1.3 59.3 + - + +
108A GLY* 3.4 1.5 + - - -
109A GLU* 3.0 34.3 + - + +
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Residues in contact with LEU 106 (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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25A LEU* 4.5 14.4 - - + -
30A PHE* 4.1 30.1 - - + -
60A VAL* 4.8 3.4 - - + -
61A MSE 3.5 26.5 - - - -
64A PHE* 4.3 15.5 - - + -
102A ILE* 2.9 41.9 + - + +
103A ILE* 3.8 9.0 - - + +
105A GLU* 1.3 73.7 - - + +
107A VAL* 1.3 61.8 + - + +
109A GLU* 3.3 1.1 + - - -
110A GLY 2.8 23.6 + - - -
116A LEU* 3.4 15.3 - - + +
120A TYR* 3.4 20.9 - - + -
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Residues in contact with VAL 107 (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 ILE* 2.9 26.9 + - + +
104A ASN 3.9 2.9 - - - +
106A LEU* 1.3 74.1 - - + +
108A GLY* 1.3 66.4 + - - +
110A GLY* 3.1 8.3 + - - -
111A GLN* 3.0 35.1 + - + +
120A TYR* 3.7 19.5 + - + +
125A PHE* 4.0 31.2 - - + -
163A PHE* 6.1 0.4 - - + -
167A LEU* 3.8 33.4 - - + -
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Residues in contact with GLY 108 (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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104A ASN 2.8 18.7 + - - -
105A GLU* 3.7 2.7 - - - -
107A VAL* 1.3 80.1 - - - +
109A GLU* 1.3 62.1 + - - +
111A GLN* 3.3 15.9 + - - +
112A PHE* 3.5 17.5 - - - -
167A LEU* 5.3 0.6 - - - +
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Residues in contact with GLU 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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30A PHE* 4.0 28.9 + - + +
31A LYS* 3.7 37.1 + - - +
105A GLU* 3.0 19.3 + - + +
106A LEU* 3.6 1.6 - - - +
108A GLY* 1.3 74.6 - - - +
110A GLY* 1.3 58.0 + - - +
112A PHE* 3.0 26.5 + - - +
113A ASP* 3.2 13.7 + - + +
116A LEU* 3.6 20.6 - - + -
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Residues in contact with GLY 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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106A LEU 2.8 12.6 + - - -
107A VAL 3.1 1.2 + - - -
109A GLU* 1.3 71.8 - - - +
111A GLN* 1.3 63.3 + - - +
112A PHE 3.1 2.8 + - - -
113A ASP 3.3 26.5 + - - +
114A SER* 4.2 1.4 + - - -
116A LEU* 4.4 3.1 - - - -
117A ALA* 3.9 9.5 - - - +
120A TYR* 3.3 28.3 - - - -
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Residues in contact with GLN 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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107A VAL* 3.0 34.2 + - + +
108A GLY* 3.5 14.1 - - - +
109A GLU 3.2 0.6 - - - -
110A GLY* 1.3 76.0 - - - +
112A PHE* 1.3 73.3 + - + +
120A TYR* 4.1 5.7 + - - -
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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