Contacts of the strand formed by residues 138 - 143 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190B GLN* 4.5 3.8 + - - -
193B ASN* 4.5 8.1 + - - -
197B LYS* 4.6 1.9 + - - +
103C TYR* 3.8 17.7 - + + -
104C GLY 3.1 10.9 + - - -
105C LEU* 3.3 12.0 - - + -
106C VAL* 2.9 27.4 + - - +
133C ARG* 3.6 8.1 - - - +
136C LYS* 4.4 0.3 - - - +
137C ASP* 1.3 103.8 - - + +
139C ALA* 1.3 61.7 + - - +
140C VAL* 4.8 0.4 - - + -
163C ASN* 4.0 11.2 - - - -
189C GLU* 2.5 50.4 + - + +
190C GLN* 4.7 0.3 + - - -
192C TRP* 3.7 39.9 - + + +
193C ASN* 3.4 30.0 + - + -
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Residues in contact with ALA 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106C VAL* 3.3 17.9 - - + -
129C LEU* 4.1 13.9 - - + +
133C ARG* 3.7 29.0 - - - +
138C TYR* 1.3 77.1 - - - +
140C VAL* 1.3 63.9 + - - +
141C LEU 4.2 0.2 - - - -
163C ASN 4.2 1.5 + - - +
164C VAL* 3.5 17.2 - - + -
165C LEU* 3.0 25.3 + - - +
192C TRP 4.8 1.2 - - - +
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Residues in contact with VAL 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75C PHE* 4.5 6.1 - - + -
105C LEU* 4.1 17.7 - - + -
106C VAL 2.8 14.6 + - - +
107C ALA* 3.1 10.8 - - + +
108C ASP 3.0 24.3 + - - +
129C LEU* 4.0 3.6 - - - +
139C ALA* 1.3 81.5 - - - +
141C LEU* 1.3 61.0 + - - +
142C THR* 3.7 7.8 + - - +
165C LEU* 3.8 10.5 - - + -
167C PHE* 3.7 37.2 - - + -
192C TRP* 3.6 35.9 - - + -
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Residues in contact with LEU 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C ASP* 3.9 6.1 - - + -
110C LYS* 3.9 21.3 - - + -
124C PHE* 3.4 41.5 - - + +
126C VAL* 4.2 7.9 - - + -
129C LEU* 3.7 22.1 - - + +
140C VAL* 1.3 72.1 - - - +
142C THR* 1.3 59.0 + - - +
143C ALA* 3.8 23.6 - - + -
148C TYR* 3.3 6.8 + - - +
164C VAL* 4.5 2.4 - - + +
165C LEU 2.7 16.7 + - - +
166C LEU* 4.2 20.9 - - + -
167C PHE* 2.7 35.3 + - - +
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Residues in contact with THR 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71C LEU* 3.9 24.2 - - + +
107C ALA* 4.8 0.2 - - - +
108C ASP 2.8 18.1 + - - +
109C ALA* 3.6 1.5 - - - -
110C LYS* 2.8 26.9 + - - +
140C VAL* 3.7 8.5 + - - +
141C LEU* 1.3 72.1 - - - +
143C ALA* 1.3 58.4 + - - +
167C PHE* 3.7 21.6 - - + -
168C SER* 3.7 27.6 - - - +
169C TRP* 3.6 30.0 + - + +
172C LEU* 4.6 2.0 - - + -
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Residues in contact with ALA 143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110C LYS* 3.7 10.5 - - + -
112C PHE* 4.8 1.1 - - + -
124C PHE* 4.5 9.2 - - + -
141C LEU* 3.8 13.5 - - + -
142C THR* 1.3 74.9 - - - +
144C PRO* 1.4 78.5 - - + +
148C TYR* 3.7 26.7 - - + +
167C PHE 3.3 6.1 + - - +
168C SER* 3.0 22.7 - - - -
169C TRP* 3.2 8.3 + - - -
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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