Contacts of the helix formed by residues 151 - 161 (chain D) in PDB entry 2EWY
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 THR 151 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52D SER* 4.2 15.6 + - - +
136D GLY 4.2 12.1 - - - +
137D LEU* 5.2 0.4 - - - -
138D ALA 3.9 22.8 + - - +
140D ALA* 4.0 17.0 + - - +
143D ALA* 5.1 1.0 - - - +
149D LEU 3.4 3.1 + - - -
150D GLU* 1.3 78.1 - - - +
152D PHE* 1.3 70.5 + - - +
153D PHE* 3.1 22.9 - - + +
154D ASP* 2.9 29.9 + - - +
155D SER* 3.0 18.9 + - - -
359D ARG* 5.2 1.6 - - - +
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Residues in contact with PHE 152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D MET* 3.6 23.3 - - + -
52D SER 5.5 1.2 + - - -
53D ASN 6.2 0.2 - - - -
54D PHE* 3.6 48.4 - + + +
101D VAL* 4.1 7.9 - - + -
103D ILE* 4.2 15.3 - - + -
111D PHE* 4.0 20.0 - + - -
113D VAL* 4.0 22.7 - - + +
114D ASN 5.9 1.3 - - - +
135D LEU* 3.4 34.1 - - + -
136D GLY 4.7 3.9 + - - +
137D LEU* 5.0 2.2 - - + -
150D GLU 3.8 1.4 + - - -
151D THR* 1.3 76.7 - - + +
153D PHE* 1.3 71.1 + + - +
155D SER* 3.0 15.4 + - - -
156D LEU* 3.0 25.9 + - + +
189D LEU* 5.4 2.0 - - + -
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Residues in contact with PHE 153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137D LEU* 4.4 18.3 - - + +
151D THR* 3.1 12.0 - - + +
152D PHE* 1.3 83.8 - + - +
154D ASP* 1.3 54.7 + - - +
156D LEU* 2.9 17.2 + - + +
157D VAL* 2.7 57.2 + - + +
162D ILE* 4.4 14.4 - - + -
163D PRO 4.3 1.8 - - - -
164D ASN* 3.5 12.3 - - - -
165D VAL 3.2 32.3 - - - -
166D PHE* 4.0 17.7 - + + -
189D LEU* 4.1 16.8 - - + -
190D GLY 4.4 0.4 - - - -
359D ARG* 3.5 33.9 - - - +
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Residues in contact with ASP 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140D ALA* 4.3 13.7 + - - +
150D GLU* 3.1 24.3 - - + +
151D THR* 2.9 36.1 + - - +
153D PHE* 1.3 77.8 - - - +
155D SER* 1.3 64.0 - - - +
157D VAL* 3.5 7.8 + - - +
158D THR* 3.3 20.6 + - - -
164D ASN* 5.4 1.0 - - - +
359D ARG* 3.7 19.4 + - - -
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Residues in contact with SER 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112D LEU 3.7 23.6 + - - -
113D VAL* 4.1 15.1 - - - +
114D ASN* 5.0 1.4 + - - -
150D GLU* 2.9 25.4 + - - +
151D THR 3.0 9.0 + - - -
152D PHE* 3.0 9.8 + - - -
154D ASP* 1.3 73.4 - - - +
156D LEU* 1.3 68.1 + - - +
158D THR* 2.9 6.9 + - - -
159D GLN* 2.9 34.2 + - - +
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Residues in contact with LEU 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107D PHE* 3.9 15.7 - - + -
111D PHE* 3.2 47.0 - - + -
152D PHE* 3.0 23.6 + - + +
153D PHE* 2.9 21.5 + - + +
155D SER* 1.3 78.4 - - - +
157D VAL* 1.3 58.3 + - - +
159D GLN* 5.0 0.2 - - - -
160D ALA* 2.8 46.9 + - + +
162D ILE* 4.3 9.1 - - + +
189D LEU* 3.7 34.5 - - + -
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Residues in contact with VAL 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153D PHE* 2.7 56.1 + - + +
154D ASP* 3.7 7.9 - - - +
156D LEU* 1.3 74.0 - - - +
158D THR* 1.3 61.4 + - - +
161D ASN* 2.8 30.7 + - - -
162D ILE* 3.3 21.0 + - + +
163D PRO 4.3 4.0 - - - +
164D ASN* 3.9 23.8 - - + +
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Residues in contact with THR 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150D GLU* 4.6 4.0 + - - -
154D ASP 3.3 10.6 + - - -
155D SER* 2.9 13.0 + - - -
157D VAL* 1.3 81.9 - - - +
159D GLN* 1.3 69.7 + - + +
161D ASN* 3.3 14.6 + - - +
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Residues in contact with GLN 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111D PHE* 2.9 24.7 - - + +
112D LEU* 2.7 54.3 + - - +
155D SER* 2.9 29.3 + - - +
156D LEU 4.5 0.4 - - - +
158D THR* 1.3 82.8 - - + +
160D ALA* 1.3 60.1 + - - +
161D ASN* 3.1 2.5 + - - +
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Residues in contact with ALA 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107D PHE* 4.0 12.3 - - + -
111D PHE* 5.1 4.2 - - + -
156D LEU* 2.8 40.5 + - + +
159D GLN* 1.3 73.1 - - - +
161D ASN* 1.3 72.2 + - - +
162D ILE* 3.2 21.9 + - + +
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Residues in contact with ASN 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157D VAL 2.8 14.2 + - - -
158D THR* 3.7 9.7 - - - +
159D GLN 3.1 4.8 - - - +
160D ALA* 1.3 80.9 - - - +
162D ILE* 1.3 57.8 + - - +
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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