Contacts of the helix formed by residues 118 - 124 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49B GLN* 4.6 5.6 + - - +
50B THR* 3.7 29.7 - - + +
77B ARG* 3.0 45.8 + - + +
81B THR* 3.5 21.8 + - - +
116B GLU* 3.4 2.0 - - - +
117B LYS* 1.3 95.7 - - - +
119B ARG* 1.3 63.8 + - - +
120B GLN* 2.9 6.2 + - - -
121B VAL* 3.0 22.7 + - + +
122B LEU* 4.0 2.3 + - - +
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Residues in contact with ARG 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B THR* 4.3 2.0 - - - +
111B PHE 4.7 0.5 - - - +
112B MET 5.4 4.9 + - - -
114B SER* 3.3 45.8 + - - +
115B LYS* 4.6 3.6 - - - +
116B GLU 3.1 21.7 + - - +
117B LYS 4.1 5.8 - - - +
118B ASP* 1.3 76.2 - - - +
120B GLN* 1.3 61.6 + - + +
122B LEU* 2.8 22.1 + - - +
123B GLU* 2.9 27.5 + - + +
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Residues in contact with GLN 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B LYS* 5.3 0.9 + - - -
46B TYR* 2.6 36.0 + - + -
49B GLN* 3.9 26.2 - - - +
117B LYS 4.9 0.8 + - - +
118B ASP 2.9 2.1 + - - +
119B ARG* 1.3 84.0 - - + +
121B VAL* 1.3 55.3 + - - +
123B GLU* 3.0 42.9 + - - +
124B ASP* 2.8 36.1 + - - +
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Residues in contact with VAL 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B TYR* 4.2 16.2 - - + -
50B THR* 4.5 11.0 - - + -
74B LEU* 4.1 24.5 - - + +
77B ARG* 4.4 4.5 - - + -
78B ALA* 3.5 39.5 - - + +
118B ASP* 3.0 14.8 + - + +
120B GLN* 1.3 78.3 - - - +
122B LEU* 1.3 65.3 + - + +
124B ASP 4.2 0.4 - - - -
125B PHE* 3.4 26.7 + - - -
128B ILE* 3.5 25.5 - - + +
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Residues in contact with LEU 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B ALA* 3.6 32.5 - - + +
81B THR* 3.8 21.5 - - + -
82B LEU* 4.0 25.8 - - + -
100B PHE* 4.8 0.4 - - + -
109B TRP* 3.9 28.3 - - + -
110B ARG* 3.6 0.2 - - - -
111B PHE* 3.1 35.7 + - + +
114B SER* 4.7 6.3 - - - -
118B ASP 4.2 2.9 - - - +
119B ARG* 2.8 10.1 + - - +
121B VAL* 1.3 92.1 - - + +
123B GLU* 1.3 64.8 + - - +
124B ASP 3.3 0.4 - - - -
125B PHE* 3.3 14.9 + - + +
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Residues in contact with GLU 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B ARG* 3.6 24.5 + - - +
111B PHE 3.4 10.9 + - - +
112B MET* 3.5 33.0 - - + +
119B ARG* 2.9 26.4 + - + +
120B GLN* 3.0 29.0 + - - +
122B LEU* 1.3 78.9 - - - +
124B ASP* 1.3 57.7 + - + +
125B PHE 3.3 1.8 + - - -
126B PRO* 4.1 0.9 - - - +
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Residues in contact with ASP 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B THR* 3.8 6.8 - - - +
46B TYR* 2.6 36.8 + - + +
120B GLN* 2.8 17.9 + - - +
121B VAL 4.0 3.8 - - - -
123B GLU* 1.3 76.2 - - + +
125B PHE* 1.3 63.9 + - - +
126B PRO* 3.2 6.8 - - - +
127B THR* 2.6 39.7 + - - -
128B ILE* 3.7 6.0 + - - +
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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