Contacts of the strand formed by residues 138 - 149 (chain A) in PDB entry 2ESR
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 LEU 138 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110A ARG* 2.8 26.5 + - - -
111A PHE* 3.9 1.1 - - + -
114A VAL* 3.9 28.7 - - + -
129A ILE* 4.8 3.1 - - + +
132A LEU* 4.0 35.7 - - + +
133A ALA* 4.3 11.4 - - - +
136A ASN* 3.4 1.8 - - - +
137A LEU* 1.3 85.4 - - - +
139A SER* 1.3 66.1 + - - +
140A GLU* 5.4 0.5 - - - +
142A VAL* 3.9 18.4 - - + -
144A VAL* 4.4 4.7 - - + -
161A LEU* 4.0 37.5 - - + -
179A ASN* 5.0 4.7 - - - +
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Residues in contact with SER 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A ARG* 4.2 17.9 - - - +
111A PHE 2.9 24.6 + - - +
112A ASP* 3.5 23.9 + - - +
138A LEU* 1.3 77.9 - - - +
140A GLU* 1.3 65.5 + - - +
141A GLN* 3.5 6.1 + - - +
142A VAL* 3.0 32.8 + - - +
179A ASN* 3.3 6.8 - - - +
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Residues in contact with GLU 140 (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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110A ARG* 5.4 4.4 + - - +
138A LEU 3.8 1.3 + - - +
139A SER* 1.3 73.4 - - - +
141A GLN* 1.3 74.7 + - + +
142A VAL 3.4 1.4 + - - -
179A ASN* 3.1 35.1 + - - +
181A GLY 5.3 0.3 - - - -
182A HIS* 4.9 2.3 + - - -
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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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112A ASP* 4.1 5.1 - - - +
139A SER* 3.2 7.5 + - - +
140A GLU* 1.3 87.7 - - + +
142A VAL* 1.3 66.1 + - - +
143A MSE 3.7 4.0 + - - +
181A GLY 3.1 24.9 + - - -
182A HIS* 3.3 24.0 + - + +
183A HIS* 2.9 53.0 + - + +
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Residues in contact with VAL 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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111A PHE 3.4 18.6 - - - +
112A ASP 3.3 12.1 - - - +
114A VAL* 4.2 4.0 - - + -
138A LEU* 3.9 33.9 - - + -
139A SER* 3.0 24.6 + - - +
140A GLU 3.3 1.0 + - - -
141A GLN* 1.3 80.2 - - - +
143A MSE 1.3 72.9 + - - +
144A VAL* 4.1 3.8 - - + -
161A LEU* 4.5 11.2 - - + -
178A VAL* 3.7 11.1 - - - -
179A ASN* 3.8 17.2 + - - +
182A HIS* 3.6 12.0 + - - -
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Residues in contact with MSE 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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36A ILE* 3.6 37.5 - - + +
40A PHE* 4.1 18.2 - - + -
112A ASP 3.1 9.9 + - - +
113A LEU* 3.4 21.8 - - + +
114A VAL 2.9 24.6 + - - -
141A GLN 4.4 2.2 - - - +
142A VAL* 1.3 75.0 - - - +
144A VAL* 1.3 61.8 + - - +
145A VAL* 3.8 1.6 - - + -
164A TRP* 4.0 7.2 - - + -
176A VAL* 4.1 8.3 - - + -
177A TYR 3.6 4.3 - - - -
178A VAL* 4.2 7.4 - - + -
182A HIS* 3.7 22.2 - - + +
185A HIS* 3.4 27.4 - - + -
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Residues in contact with VAL 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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114A VAL* 3.4 15.5 - - + +
116A LEU* 3.7 33.9 - - + -
129A ILE* 3.8 17.9 - - + -
132A LEU* 5.4 1.8 - - + -
138A LEU* 4.4 10.8 - - + -
142A VAL* 4.1 14.8 - - + -
143A MSE 1.3 73.5 - - - +
145A VAL* 1.3 60.3 + - - +
146A CYS* 3.8 3.3 + - - -
161A LEU* 3.7 24.2 - - + -
175A THR 3.5 2.4 - - - +
176A VAL* 3.3 2.6 - - - -
177A TYR* 2.8 47.9 + - + +
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Residues in contact with VAL 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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32A ILE* 4.4 10.8 - - + -
36A ILE* 3.9 25.1 - - + -
55A LEU* 5.7 2.6 - - + +
113A LEU* 3.8 26.0 - - + -
114A VAL 2.7 8.5 + - - +
115A PHE* 3.4 25.6 - - + -
116A LEU 2.8 26.5 + - - +
143A MSE 4.4 0.9 - - - +
144A VAL* 1.3 73.2 - - - +
146A CYS* 1.3 65.1 + - - +
147A GLU* 4.1 2.4 + - + +
174A VAL* 3.8 26.2 - - + -
175A THR 3.6 2.7 - - - -
176A VAL* 4.2 9.2 - - + +
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Residues in contact with CYS 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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116A LEU* 3.3 10.8 - - - -
125A ILE* 3.8 45.3 - - + -
144A VAL* 4.2 13.9 - - - -
145A VAL* 1.3 80.0 - - - +
147A GLU* 1.3 60.1 + - - +
148A THR* 4.1 1.8 - - + +
154A LEU* 4.2 9.6 - - + -
173A LYS 3.5 1.7 - - - +
174A VAL* 3.2 5.2 - - - +
175A THR* 2.7 44.9 + - - +
177A TYR* 4.0 19.3 - - - -
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Residues in contact with GLU 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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28A VAL* 3.7 24.8 - - - +
32A ILE* 3.8 15.0 - - + +
55A LEU* 4.2 20.6 - - + +
116A LEU 3.2 6.8 + - - -
117A ASP* 3.2 45.8 - - + +
118A PRO* 5.2 0.2 - - - +
121A ALA* 5.8 0.2 - - - +
145A VAL* 4.1 2.8 + - + -
146A CYS* 1.3 72.3 - - - +
148A THR* 1.3 69.4 + - - +
172A SER* 4.2 18.5 + - - -
173A LYS 3.4 7.2 - - - +
174A VAL* 4.5 10.9 - - + +
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Residues in contact with THR 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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117A ASP* 5.0 1.8 - - - -
121A ALA* 4.1 13.7 - - + -
125A ILE* 3.6 30.5 - - + -
146A CYS 4.5 2.9 - - - +
147A GLU* 1.3 84.3 - - - +
149A ASP* 1.3 73.6 + - - +
152A VAL* 3.6 23.0 - - + +
154A LEU* 4.5 7.4 - - + +
172A SER* 3.4 8.1 - - - -
173A LYS* 2.9 41.8 + - - +
175A THR* 5.4 0.5 + - - -
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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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148A THR* 1.3 91.5 + - - +
150A LYS* 1.3 66.9 + - + +
151A THR* 4.2 11.2 - - - +
152A VAL* 3.2 23.4 + - + +
171A ILE 4.1 10.5 - - - +
173A LYS* 3.9 2.4 - - - +
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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