Contacts of the strand formed by residues 138 - 143 (chain B) in PDB entry 2E52
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 TYR 138 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B TYR* 3.8 19.1 - + + -
104B GLY 3.0 11.1 + - - -
105B LEU* 3.2 12.5 - - + -
106B VAL* 2.9 25.5 + - - +
133B ARG* 3.6 9.2 - - - +
136B LYS* 4.4 0.2 - - - +
137B ASP* 1.3 103.8 - - + +
139B ALA* 1.3 62.0 + - - +
140B VAL* 4.9 0.2 - - + -
163B ASN* 4.1 10.3 - - - -
189B GLU* 2.6 46.9 + - + +
190B GLN* 4.8 0.7 + - - -
192B TRP* 3.6 41.7 - - + +
193B ASN* 3.4 31.4 - - + +
190C GLN* 4.8 1.0 + - - -
193C ASN* 4.6 7.3 + - - -
197C LYS* 4.0 4.7 - - - -
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Residues in contact with ALA 139 (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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106B VAL* 3.3 19.7 - - + -
129B LEU* 4.1 14.1 - - + +
133B ARG* 3.7 29.7 - - - +
138B TYR* 1.3 75.8 - - - +
140B VAL* 1.3 62.9 + - - +
141B LEU 4.2 0.4 - - - -
163B ASN 4.1 2.1 + - - +
164B VAL* 3.5 16.5 - - + -
165B LEU* 3.0 24.1 + - - +
192B TRP 4.7 1.8 + - - +
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Residues in contact with VAL 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B PHE* 4.7 3.8 - - + -
105B LEU* 4.2 15.5 - - + -
106B VAL 2.9 11.5 + - - +
107B ALA* 3.1 11.7 - - + +
108B ASP 2.8 26.9 + - - +
129B LEU* 4.0 4.5 - - - +
139B ALA* 1.3 79.9 - - - +
141B LEU* 1.3 61.8 + - - +
142B THR* 3.7 11.4 - - - +
165B LEU* 3.7 13.5 - - + -
167B PHE* 3.6 33.0 - - + -
192B TRP* 3.6 37.5 - - + -
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Residues in contact with LEU 141 (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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108B ASP* 3.9 5.2 - - + +
110B LYS* 3.9 18.6 - - + -
124B PHE* 3.5 43.5 - - + +
126B VAL* 4.1 7.6 - - + -
129B LEU* 3.8 20.8 - - + +
139B ALA 4.2 0.2 - - - -
140B VAL* 1.3 71.1 - - - +
142B THR* 1.3 58.5 + - - +
143B ALA* 3.6 28.0 - - + -
148B TYR* 3.4 8.2 + - - +
164B VAL* 4.4 2.5 - - + -
165B LEU 2.8 15.3 + - - +
166B LEU* 4.0 20.2 - - + -
167B PHE* 2.7 35.0 + - - +
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Residues in contact with THR 142 (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 LEU* 3.8 23.7 - - + +
108B ASP 2.9 18.3 + - - -
109B ALA* 3.6 1.2 - - - -
110B LYS 2.8 26.0 + - - -
140B VAL* 3.7 17.7 + - - +
141B LEU* 1.3 74.4 - - - +
143B ALA* 1.3 59.4 + - - +
167B PHE* 3.7 13.0 - - + -
168B SER 3.9 18.2 - - - +
169B TRP* 3.6 36.4 + - + -
172B LEU* 4.6 2.5 - - + -
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Residues in contact with ALA 143 (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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110B LYS* 3.8 11.0 - - + -
112B PHE* 4.9 1.1 - - + -
124B PHE* 4.5 8.3 - - + -
141B LEU* 3.6 21.3 - - + -
142B THR* 1.3 75.0 - - - +
144B PRO* 1.3 76.4 - - + +
148B TYR* 3.6 17.5 - - + +
167B PHE 3.3 7.5 + - - +
168B SER* 3.0 24.3 - - - -
169B TRP* 3.3 8.4 + - - -
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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