Contacts of the helix formed by residues 152 - 164 (chain A) in PDB entry 1EOD
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 GLY 152 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89A ASP 5.4 3.1 - - - -
150A GLU 3.1 6.9 + - - -
151A LEU* 1.3 80.3 - - - +
153A GLU* 1.3 68.6 + - - -
154A ASN 3.4 2.9 - - - -
155A ALA* 3.2 3.3 + - - +
156A PHE* 3.1 23.1 + - - +
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Residues in contact with GLU 153 (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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152A GLY* 1.3 72.1 - - - -
154A ASN* 1.3 60.1 + - - +
155A ALA 3.0 5.7 + - - -
156A PHE* 3.2 18.2 + - - +
157A GLU* 3.1 33.1 + - - +
160A ARG* 4.3 13.3 + - - -
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Residues in contact with ASN 154 (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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152A GLY* 3.4 1.0 - - - -
153A GLU* 1.3 76.9 - - - +
155A ALA* 1.3 51.4 + - - +
157A GLU* 3.9 16.4 + - - +
158A ARG* 2.5 40.7 + - - +
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Residues in contact with ALA 155 (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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124A PHE* 4.1 18.8 - - + -
131A LEU* 3.5 13.2 - - + +
151A LEU* 4.4 10.1 - - + +
152A GLY 3.2 7.3 + - - +
153A GLU 3.1 0.6 - - - -
154A ASN* 1.3 76.6 - - - +
156A PHE* 1.3 64.2 + - - +
157A GLU 3.0 1.1 - - - -
158A ARG* 3.0 32.0 - - - +
159A TYR* 2.9 28.8 + - - +
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Residues in contact with PHE 156 (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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131A LEU* 5.0 1.3 - - - -
143A SER* 4.6 15.0 - - - -
146A ILE* 3.6 38.6 - - + -
147A LYS* 5.6 3.1 - - - -
151A LEU* 6.1 0.2 - - - +
152A GLY 3.1 16.5 + - - +
153A GLU* 3.8 19.1 - - - +
155A ALA* 1.3 78.3 - - - +
157A GLU* 1.3 57.5 + - - +
159A TYR* 3.3 15.5 - + - +
160A ARG* 2.7 71.6 + - + +
165A PHE* 5.6 4.0 - + - -
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Residues in contact with GLU 157 (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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153A GLU* 3.1 26.8 + - - +
154A ASN* 3.9 15.4 + - - +
155A ALA 3.0 0.2 - - - -
156A PHE* 1.3 74.1 - - - +
158A ARG* 1.3 67.6 + - + +
159A TYR 2.9 1.3 - - - -
160A ARG* 2.8 29.8 + - - +
161A GLU* 2.8 25.4 + - - +
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Residues in contact with ARG 158 (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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124A PHE* 3.6 8.7 - - - -
129A GLY* 2.6 31.5 + - - -
131A LEU* 4.6 7.3 - - + +
154A ASN* 2.5 47.7 + - - +
155A ALA* 3.0 30.2 + - - +
157A GLU* 1.3 76.7 - - + +
159A TYR* 1.3 60.2 + - - +
161A GLU* 3.6 5.5 + - - +
162A ASP* 2.3 39.8 + - - +
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Residues in contact with TYR 159 (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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131A LEU* 3.7 29.6 - - + +
133A ARG* 4.0 8.3 + - + -
139A LEU* 3.2 20.7 + - + +
142A PHE* 3.8 26.3 - + - -
143A SER* 2.8 25.6 + - - -
146A ILE* 3.3 28.3 - - + -
155A ALA 2.9 18.8 + - - +
156A PHE* 3.3 19.3 - + - +
158A ARG* 1.3 75.8 - - - +
160A ARG* 1.3 68.8 + - + +
162A ASP* 3.4 6.4 + - + +
163A GLU* 3.1 56.3 + - + +
165A PHE* 4.6 6.3 - + - -
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Residues in contact with ARG 160 (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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153A GLU* 4.3 7.9 + - - -
156A PHE* 2.7 86.4 + - + +
157A GLU* 2.8 32.2 + - - +
159A TYR* 1.3 76.6 - - + +
161A GLU* 1.3 66.9 + - - +
163A GLU* 3.0 11.3 + - - -
164A GLY 3.1 9.7 + - - -
165A PHE* 3.5 52.8 + - + +
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Residues in contact with GLU 161 (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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157A GLU 2.8 19.1 + - - +
158A ARG* 3.9 7.6 - - - +
160A ARG* 1.3 73.9 - - - +
162A ASP* 1.3 63.3 + - - +
163A GLU 3.3 0.3 + - - -
164A GLY* 3.5 9.0 + - - -
165A PHE* 4.6 7.8 + - - -
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Residues in contact with ASP 162 (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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131A LEU 4.8 8.9 - - - +
132A ARG* 5.0 9.0 + - - -
158A ARG* 2.3 33.7 + - - +
159A TYR* 3.6 8.1 - - + +
161A GLU* 1.3 78.6 - - - +
163A GLU* 1.3 66.8 + - + +
164A GLY 3.6 0.2 - - - -
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Residues in contact with GLU 163 (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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133A ARG* 2.7 51.8 + - - +
139A LEU* 4.0 7.9 - - + +
159A TYR* 3.2 41.1 - - + +
160A ARG 3.0 3.3 + - - +
162A ASP* 1.3 84.2 - - + +
164A GLY* 1.3 57.2 + - - +
165A PHE* 3.8 27.6 - - + -
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Residues in contact with GLY 164 (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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160A ARG 3.1 3.8 + - - -
161A GLU 3.5 8.4 + - - -
162A ASP 3.6 0.2 - - - -
163A GLU* 1.3 80.2 - - - +
165A PHE* 1.3 67.1 - - - +
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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