Contacts of the helix formed by residues 124 - 134 (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 124 (chain B).
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Specific contacts
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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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Residues in contact with PHE 125 (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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75B VAL* 4.2 6.7 - - + -
78B ALA* 3.8 13.9 - - + -
100B PHE* 3.5 33.2 - + - -
103B PHE 4.0 12.3 - - - -
104B LEU* 3.5 25.1 - - + -
109B TRP* 3.5 36.3 - + + +
121B VAL 3.4 18.2 + - - -
122B LEU* 3.3 16.7 + - - +
123B GLU 3.3 1.4 - - - -
124B ASP* 1.3 76.8 - - - +
126B PRO* 1.4 63.3 - - + +
128B ILE* 2.8 25.0 + - + +
129B SER* 2.8 44.4 + - - -
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Residues in contact with PRO 126 (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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107B PRO 3.3 22.3 - - - +
108B ASP* 4.2 7.0 - - - +
109B TRP 3.3 20.2 - - - +
110B ARG* 3.7 17.9 - - + -
123B GLU 4.1 1.3 - - - +
124B ASP* 3.2 9.6 - - - +
125B PHE* 1.4 89.4 - - + +
127B THR* 1.3 56.5 - - - +
129B SER* 3.1 10.4 + - - +
130B LEU* 3.0 30.9 + - - +
133B ARG* 4.6 0.9 + - - -
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Residues in contact with THR 127 (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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39B SER* 3.6 37.0 - - - +
42B THR* 3.9 19.7 - - + -
43B CYS* 3.8 3.8 - - - +
46B TYR* 5.0 2.2 - - + -
124B ASP* 2.6 35.5 + - - -
126B PRO* 1.3 78.2 - - - +
128B ILE* 1.3 60.8 + - - +
130B LEU* 3.4 8.9 - - - +
131B GLU* 3.4 22.0 + - - +
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Residues in contact with ILE 128 (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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43B CYS* 3.9 7.9 - - - -
46B TYR* 4.1 17.5 - - + -
71B ILE* 4.4 8.2 - - + +
74B LEU* 4.2 32.5 - - + +
75B VAL* 4.2 21.5 - - + -
121B VAL* 3.5 49.8 - - + +
124B ASP 4.2 7.0 - - - +
125B PHE* 2.8 18.2 + - + +
127B THR* 1.3 76.1 - - - +
129B SER* 1.3 59.4 + - - +
131B GLU* 3.0 6.8 + - - +
132B PHE* 2.9 24.3 + - - +
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Residues in contact with SER 129 (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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103B PHE 4.3 2.9 - - - -
104B LEU* 3.4 20.2 - - - +
106B GLN 4.2 6.3 + - - -
107B PRO* 4.3 0.9 - - - +
125B PHE* 2.8 35.8 + - - -
126B PRO* 3.1 15.9 + - - +
128B ILE* 1.3 70.4 - - - +
130B LEU* 1.3 62.4 + - - +
132B PHE* 3.1 10.8 + - - +
133B ARG* 2.8 46.4 + - - +
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Residues in contact with LEU 130 (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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39B SER* 3.9 26.5 - - - +
126B PRO 3.0 20.4 + - - +
127B THR* 3.4 7.6 - - - +
128B ILE 3.1 0.2 - - - -
129B SER* 1.3 80.1 + - - +
131B GLU* 1.3 60.0 + - - +
133B ARG* 3.3 34.4 + - + +
134B ASN* 3.3 23.3 + - - +
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Residues in contact with GLU 131 (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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37B SER* 3.1 12.7 + - - -
39B SER* 2.7 30.4 + - - +
40B LEU* 3.4 27.1 + - + +
43B CYS* 3.6 20.2 - - - -
71B ILE* 3.6 22.6 - - + +
127B THR 3.4 5.6 + - - +
128B ILE 3.0 9.4 + - - +
130B LEU* 1.3 76.5 - - - +
132B PHE* 1.3 65.1 + - - +
134B ASN* 3.2 35.5 + - - +
135B LEU* 3.5 16.6 + - - +
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Residues in contact with PHE 132 (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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71B ILE* 3.9 22.6 - - + +
75B VAL* 5.0 0.7 - - + -
104B LEU* 3.5 48.5 - - + -
105B TYR* 3.8 30.5 - + - -
128B ILE 2.9 12.8 + - - +
129B SER* 3.3 11.9 - - - +
131B GLU* 1.3 77.2 - - - +
133B ARG* 1.3 61.5 + - + +
135B LEU* 3.1 32.4 + - + +
140B GLN* 3.5 50.7 + - + +
143B ILE* 3.8 28.7 - - + -
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Residues in contact with ARG 133 (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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104B LEU 3.6 12.7 + - - +
105B TYR* 4.1 22.0 - - + +
106B GLN 4.1 0.4 - - - -
107B PRO* 3.5 43.2 + - - +
126B PRO 4.6 1.2 + - - -
129B SER* 2.8 44.5 + - - +
130B LEU* 3.3 41.0 - - + +
131B GLU 3.3 0.4 - - - -
132B PHE* 1.3 83.3 - - + +
134B ASN* 1.3 60.4 + - - +
135B LEU 3.2 1.8 - - - +
137B GLU* 5.2 0.5 - - - +
140B GLN* 2.9 23.1 + - - +
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Residues in contact with ASN 134 (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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130B LEU* 3.3 19.9 + - - +
131B GLU* 3.2 37.3 + - - +
132B PHE 3.2 1.2 - - - -
133B ARG* 1.3 78.4 - - - +
135B LEU* 1.3 64.8 + - - +
136B ALA 4.0 0.2 + - - -
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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