Contacts of the helix formed by residues 118 - 124 (chain A) in PDB entry 1EZF
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 ASP 118 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49A GLN 4.7 3.5 - - - +
50A THR* 4.1 26.4 - - + +
77A ARG* 2.7 43.7 + - + +
81A THR* 3.8 19.2 + - - +
116A GLU* 4.2 3.7 - - + +
117A LYS* 1.3 94.4 - - - +
119A ARG* 1.3 63.7 + - - +
120A GLN* 3.4 2.9 - - - -
121A VAL* 3.4 21.6 + - + +
122A LEU* 3.6 4.5 - - - +
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Residues in contact with ARG 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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112A MET* 4.7 9.5 + - - +
114A SER* 3.2 29.7 + - - +
115A LYS* 4.8 5.9 - - - +
116A GLU 2.9 29.8 - - - +
117A LYS 3.2 6.3 + - - +
118A ASP* 1.3 73.8 - - - +
120A GLN* 1.3 63.2 + - + +
122A LEU* 2.7 36.2 + - - +
123A GLU* 2.9 38.8 + - + +
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Residues in contact with GLN 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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46A TYR* 4.4 22.2 + - + +
49A GLN* 4.9 10.1 - - - +
117A LYS 6.1 0.2 - - - +
118A ASP* 3.4 1.5 - - - -
119A ARG* 1.3 90.1 - - + +
121A VAL* 1.3 57.2 + - - +
123A GLU* 2.8 43.4 + - - +
124A ASP* 2.8 36.6 + - - +
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Residues in contact with VAL 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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46A TYR* 4.9 7.6 - - + -
50A THR* 4.9 7.6 - - + -
74A LEU* 3.6 32.3 - - + +
77A ARG* 4.3 6.7 - - + -
78A ALA* 3.4 31.0 - - + +
81A THR* 4.3 1.8 - - - +
118A ASP* 3.4 22.3 + - + +
119A ARG 2.9 1.4 + - - -
120A GLN* 1.3 77.4 - - - +
122A LEU* 1.3 68.7 + - + +
125A PHE* 3.4 28.2 + - - +
128A ILE* 3.3 31.9 - - + +
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Residues in contact with LEU 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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78A ALA* 3.6 30.3 - - + +
81A THR* 3.4 35.4 - - + -
82A LEU* 4.0 24.7 - - + -
100A PHE* 5.2 0.2 - - + -
109A TRP* 4.3 16.2 - - + -
110A ARG* 3.6 0.7 - - - -
111A PHE* 3.2 37.9 + - + +
114A SER* 4.4 6.3 - - - +
118A ASP 3.6 5.2 - - - +
119A ARG 2.7 14.6 + - - +
121A VAL* 1.3 85.8 - - + +
123A GLU* 1.3 63.7 + - - +
124A ASP 3.2 0.2 - - - -
125A PHE* 3.1 18.0 + - - +
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Residues in contact with GLU 123 (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 ARG* 3.4 25.6 - - - +
111A PHE 3.6 12.8 - - - +
112A MET* 3.5 40.8 - - + +
114A SER* 4.6 2.1 - - - +
119A ARG* 2.9 55.9 + - + +
120A GLN* 2.8 35.0 + - - +
122A LEU* 1.3 78.4 - - - +
124A ASP* 1.3 57.1 + - + +
125A PHE 3.4 0.2 - - - -
126A PRO* 4.4 0.5 - - - +
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Residues in contact with ASP 124 (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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42A THR* 4.0 5.0 - - - +
46A TYR* 2.5 33.4 + - + +
120A GLN* 2.8 19.2 + - + +
121A VAL 4.0 2.7 - - - -
123A GLU* 1.3 76.8 - - + +
125A PHE* 1.3 65.7 + - - +
126A PRO* 3.2 7.7 - - - +
127A THR* 2.7 43.0 + - - -
128A ILE* 3.8 3.9 + - - +
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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