Contacts of the strand formed by residues 151 - 155 (chain C) in PDB entry 2ESN
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 PHE 151 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101C PHE* 3.7 25.1 - + - -
102C VAL 3.1 2.0 + - - -
103C PHE* 3.2 39.6 - + + -
104C ALA 3.0 11.9 + - - -
144C LEU* 3.9 2.2 - - - -
149C ILE* 2.9 21.1 - - - +
150C ASP* 1.3 90.8 - - + +
152C ALA* 1.3 60.6 + - - +
280C LEU* 3.5 37.9 - - + -
281C TYR 3.3 4.5 - - - +
282C SER* 3.9 13.0 - - - -
292C HIS* 3.8 44.2 - + - -
295C MET* 3.9 14.8 - - + -
296C ILE* 4.2 9.0 - - + -
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Residues in contact with ALA 152 (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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104C ALA* 3.5 15.0 - - + +
138C LYS 3.4 24.0 - - - +
139C LEU* 5.0 1.3 - - + -
140C SER 5.8 0.4 - - - +
144C LEU* 4.0 14.1 - - + +
149C ILE* 5.1 0.9 - - + -
151C PHE* 1.3 75.3 - - - +
153C LEU* 1.3 63.8 + - - +
280C LEU* 3.5 4.0 - - - -
281C TYR* 2.7 52.1 + - + -
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Residues in contact with LEU 153 (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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103C PHE* 3.7 21.1 - - + -
104C ALA 2.8 16.2 + - - +
105C ALA* 4.0 15.1 - - + -
106C THR* 5.3 0.5 - - - +
109C THR* 3.8 39.7 + - + +
113C LEU* 3.7 25.8 - - + -
132C LEU* 4.8 4.3 - - + -
138C LYS* 4.1 10.9 - - - +
152C ALA* 1.3 74.5 - - - +
154C GLY* 1.3 58.5 + - - +
171C TRP* 4.0 19.5 - - + +
207C TRP* 4.5 9.0 - - - -
279C ARG 3.4 2.9 - - - +
280C LEU* 3.5 30.7 - - + -
281C TYR* 4.2 3.6 - - - -
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Residues in contact with GLY 154 (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 THR* 6.2 0.4 - - - -
109C THR* 4.1 12.9 - - - +
138C LYS* 4.1 10.5 - - - -
153C LEU* 1.3 75.1 - - - +
155C TYR* 1.3 60.3 + - - +
207C TRP* 5.1 5.6 - - - -
278C LEU* 3.4 7.9 - - - +
279C ARG* 2.6 39.4 + - - +
281C TYR* 3.7 6.5 - - - -
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Residues in contact with TYR 155 (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 TYR* 5.8 5.4 - + - -
138C LYS* 2.8 28.1 + - - +
154C GLY* 1.3 74.9 - - - +
156C ASP* 1.3 88.4 + - + +
176C TYR* 2.5 40.7 + + - -
213C VAL* 3.6 24.2 - - + +
251C PRO* 6.1 1.3 - - + -
276C TYR* 3.8 25.8 - + + -
277C VAL 2.8 29.2 - - - +
278C LEU* 3.8 17.3 - - + -
279C ARG* 4.1 1.3 - - - -
281C TYR* 3.2 10.2 + - - -
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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