Contacts of the helix formed by residues 140 - 150 (chain A) in PDB entry 2ESV
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 ALA 140 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123A TYR* 3.2 58.2 - - + +
124A LEU* 4.4 2.4 - - + +
135A ALA* 3.8 9.0 - - + -
137A ASP 3.0 10.6 + - - +
138A THR 3.0 2.0 + - - -
139A ALA* 1.3 77.0 - - - +
141A GLN* 1.3 56.4 + - - +
142A ILE 3.4 2.5 - - - -
143A SER* 3.3 3.5 + - - -
144A GLU* 2.8 28.8 + - - +
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Residues in contact with GLN 141 (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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135A ALA* 4.1 8.6 - - + +
137A ASP 4.8 0.4 + - - -
138A THR* 3.1 46.7 + - - +
139A ALA 3.3 1.2 - - - -
140A ALA* 1.3 78.0 - - - +
142A ILE* 1.3 60.5 + - + +
144A GLU* 3.4 20.8 + - - +
145A GLN* 3.1 29.6 + - - +
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Residues in contact with ILE 142 (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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84A TYR* 3.4 44.0 - - + +
139A ALA 4.6 3.8 + - - +
140A ALA 3.4 0.4 - - - -
141A GLN* 1.3 78.1 - - + +
143A SER* 1.3 56.6 + - - +
145A GLN* 3.2 18.4 - - + +
146A LYS* 3.1 39.0 + - - +
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Residues in contact with SER 143 (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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84A TYR* 3.4 2.8 - - - -
123A TYR* 2.7 38.3 + - - -
124A LEU* 4.3 4.5 - - - -
140A ALA 3.3 6.7 + - - -
142A ILE* 1.3 74.8 - - - +
144A GLU* 1.3 60.0 + - - +
146A LYS* 3.7 4.5 - - - +
147A SER* 2.9 35.9 + - - -
9P LEU* 2.7 42.3 + - - +
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Residues in contact with GLU 144 (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 LEU* 3.8 15.7 - - + +
133A TRP* 3.5 20.4 - - - +
134A THR* 3.8 8.8 - - - +
135A ALA* 3.5 26.0 + - + +
140A ALA 2.8 17.4 + - - +
141A GLN* 3.5 21.8 - - - +
143A SER* 1.3 77.5 - - - +
145A GLN* 1.3 58.6 + - - +
147A SER* 3.6 3.0 + - - -
148A ASN* 3.1 39.0 + - - +
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Residues in contact with GLN 145 (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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141A GLN 3.1 16.4 + - - +
142A ILE* 3.2 30.1 - - - +
144A GLU* 1.3 77.9 - - - +
146A LYS* 1.3 60.8 + - + +
148A ASN* 3.3 4.8 + - - +
149A ASP* 2.8 57.5 + - - +
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Residues in contact with LYS 146 (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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84A TYR* 4.0 17.9 - - - -
142A ILE* 3.1 26.0 + - - +
143A SER* 3.7 5.4 - - - +
145A GLN* 1.3 79.3 - - + +
147A SER* 1.3 61.6 + - - +
149A ASP* 3.9 5.4 - - - +
150A ALA* 3.1 27.5 + - - +
28E GLY 4.8 3.4 + - - -
30E ASP* 3.7 29.0 + - - +
51E LYS* 5.4 4.0 - - - +
96E GLN* 4.3 22.5 + - - +
8P ILE 3.9 22.2 - - - +
9P LEU* 4.2 8.5 - - - +
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Residues in contact with SER 147 (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 LEU* 4.0 1.4 - - - +
133A TRP* 3.5 33.2 - - - -
143A SER* 2.9 22.1 + - - -
144A GLU 3.9 2.7 - - - -
146A LYS* 1.3 77.9 - - - +
148A ASN* 1.3 60.3 + - - +
151A SER* 3.5 2.4 + - - -
152A GLU* 3.2 38.6 + - - +
153A ALA 4.5 0.2 + - - -
7P LEU* 3.4 26.5 - - - +
8P ILE 5.6 1.6 + - - -
9P LEU* 5.2 1.6 - - - +
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Residues in contact with ASN 148 (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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132A SER* 3.5 14.9 - - - -
133A TRP* 2.9 45.2 + - - -
144A GLU* 3.1 28.4 + - - +
145A GLN* 3.3 5.9 + - - +
147A SER* 1.3 75.9 - - - +
149A ASP* 1.3 66.6 + - - +
151A SER* 3.6 12.0 + - - +
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Residues in contact with ASP 149 (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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145A GLN* 2.8 44.8 + - - +
146A LYS* 3.9 5.6 - - - +
148A ASN* 1.3 82.9 - - - +
150A ALA* 1.3 57.6 + - - +
151A SER* 3.3 5.6 + - - -
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Residues in contact with ALA 150 (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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146A LYS 3.1 17.6 + - - +
148A ASN 3.4 0.2 - - - -
149A ASP* 1.3 75.1 - - + +
151A SER* 1.3 71.0 + - - +
152A GLU* 3.3 20.5 + - + +
96E GLN* 4.2 10.5 - - + +
97E ASP* 3.7 40.6 - - + +
99E ASP* 4.2 7.3 - - - +
5P ARG* 5.3 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