Contacts of the helix formed by residues 124 - 134 (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 124 (chain A).
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Specific contacts
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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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Residues in contact with PHE 125 (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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75A VAL* 4.1 17.9 - - + -
78A ALA* 4.0 13.7 - - + -
100A PHE* 3.8 24.7 - + - -
103A PHE* 3.7 25.8 - - + -
104A LEU* 3.8 22.4 - - + -
106A GLN 5.6 0.2 - - - -
109A TRP* 3.4 36.1 - + + +
121A VAL 3.4 17.3 + - - +
122A LEU* 3.1 17.3 + - - +
124A ASP* 1.3 77.0 - - - +
126A PRO* 1.4 68.7 - - + +
128A ILE* 2.9 14.6 + - + +
129A SER* 2.8 37.4 + - - -
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Residues in contact with PRO 126 (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 PRO 3.1 22.9 - - - +
108A ASP* 3.7 12.6 - - - +
109A TRP 3.2 21.8 - - - +
110A ARG* 3.8 12.6 - - + -
123A GLU 4.4 1.1 - - - +
124A ASP* 3.2 10.5 - - - +
125A PHE* 1.4 88.6 - - - +
127A THR* 1.3 56.8 + - - +
129A SER* 2.9 11.4 + - - +
130A LEU* 2.8 31.7 + - - +
133A ARG* 4.4 1.9 + - - -
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Residues in contact with THR 127 (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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39A SER* 3.8 35.6 - - - +
42A THR* 3.9 17.7 - - + +
43A CYS* 3.9 4.4 - - - +
46A TYR* 5.0 2.0 - - + -
124A ASP* 2.7 38.7 + - - +
126A PRO* 1.3 78.4 - - - +
128A ILE* 1.3 63.7 + - - +
130A LEU* 3.4 10.9 - - + +
131A GLU* 3.2 23.4 + - - +
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Residues in contact with ILE 128 (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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43A CYS* 4.0 16.2 - - - -
46A TYR* 4.1 19.7 - - + -
71A ILE* 4.2 10.2 - - + +
74A LEU* 4.0 25.1 - - + +
75A VAL* 3.9 26.5 - - + +
121A VAL* 3.3 47.8 - - + +
124A ASP 4.5 3.8 - - - +
125A PHE* 2.9 14.6 + - + +
127A THR* 1.3 75.0 - - - +
129A SER* 1.3 60.2 + - - +
131A GLU* 3.3 4.3 + - - +
132A PHE* 2.9 24.6 + - - +
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Residues in contact with SER 129 (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 PHE 4.4 2.0 - - - -
104A LEU* 3.5 12.5 - - - +
106A GLN 4.5 2.8 + - - -
107A PRO 4.4 2.1 + - - -
125A PHE* 2.8 31.1 + - - -
126A PRO* 2.9 27.9 + - - +
128A ILE* 1.3 74.3 - - - +
130A LEU* 1.3 64.4 + - - +
132A PHE* 3.2 9.1 + - - +
133A ARG* 2.9 49.2 + - - +
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Residues in contact with LEU 130 (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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39A SER* 4.3 23.1 - - - +
126A PRO 2.8 18.8 + - - +
127A THR* 3.4 9.2 - - - +
129A SER* 1.3 75.3 + - - +
131A GLU* 1.3 58.3 + - - +
133A ARG* 3.0 42.6 + - + +
134A ASN* 3.2 24.6 + - - +
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Residues in contact with GLU 131 (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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39A SER* 2.7 25.3 + - - +
40A LEU* 3.3 36.7 + - + +
43A CYS* 3.7 19.3 - - - -
71A ILE* 3.6 23.8 - - + -
127A THR 3.2 8.0 + - - +
128A ILE 3.8 2.9 - - - +
130A LEU* 1.3 80.1 - - - +
132A PHE* 1.3 60.9 + - - +
134A ASN* 3.2 37.8 + - - +
135A LEU* 3.4 18.2 + - - +
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Residues in contact with PHE 132 (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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71A ILE* 3.7 18.6 - - + +
75A VAL* 5.0 4.9 - - + -
104A LEU* 3.6 46.2 - - + -
105A TYR* 3.5 39.5 - + - -
128A ILE 2.9 15.0 + - - +
129A SER* 3.4 10.1 - - - +
130A LEU 3.1 0.2 - - - -
131A GLU* 1.3 76.1 - - - +
133A ARG* 1.3 66.1 + - + +
135A LEU* 3.2 20.3 + - + +
140A GLN* 3.2 43.0 - - + +
143A ILE* 3.6 36.3 - - + -
144A ALA* 4.5 0.9 - - + -
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Residues in contact with ARG 133 (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 LEU 2.9 29.6 + - - +
105A TYR* 4.4 22.2 - - + +
107A PRO* 3.7 45.8 + - - +
126A PRO 4.4 1.2 + - - -
129A SER* 2.9 33.8 + - - +
130A LEU* 3.0 39.5 + - + +
132A PHE* 1.3 82.2 - - + +
134A ASN* 1.3 59.6 + - - +
135A LEU 3.7 0.5 - - - +
140A GLN* 2.8 22.2 + - - +
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Residues in contact with ASN 134 (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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130A LEU* 3.2 22.0 + - - +
131A GLU* 3.3 39.9 + - - +
132A PHE 3.1 0.6 - - - -
133A ARG* 1.3 75.5 - - - +
135A LEU* 1.3 67.0 + - - +
136A ALA 3.8 0.3 + - - -
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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