Contacts of the strand formed by residues 105 - 112 (chain B) in PDB entry 5ES4
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 ILE 105 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103B TYR 4.5 0.2 - - - +
104B PRO* 1.3 78.8 - - - +
106B ASP* 1.3 78.2 + - - +
107B LEU* 5.6 1.8 - - + -
135B LEU* 4.2 25.4 - - + -
139B THR* 3.1 37.9 - - + +
141B SER 4.6 3.2 + - - +
142B GLY* 3.6 12.6 - - - -
143B ARG* 3.2 20.3 + - - +
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Residues in contact with ASP 106 (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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104B PRO* 5.8 1.0 - - - +
105B ILE* 1.3 88.5 + - - +
107B LEU* 1.3 61.4 + - - +
108B TYR* 4.4 0.6 + - - -
143B ARG* 3.9 22.6 + - - +
188B LEU* 3.7 32.4 - - + +
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Residues in contact with LEU 107 (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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105B ILE* 4.2 2.9 - - + -
106B ASP* 1.3 75.3 - - - +
108B TYR* 1.3 69.6 + - - +
109B TYR* 4.2 10.5 - - + +
131B LEU* 3.7 38.4 - - + -
135B LEU* 4.6 20.6 - - + -
143B ARG 3.0 14.3 + - - +
144B ILE* 3.3 6.7 - - + +
145B GLY 2.9 24.4 + - - +
188B LEU* 3.3 3.1 - - - +
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Residues in contact with TYR 108 (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 ASP 4.3 0.6 - - - -
107B LEU* 1.3 84.5 - - - +
109B TYR* 1.3 66.9 + - - +
110B LEU* 3.8 24.7 + - + +
145B GLY* 3.7 3.4 - - - -
146B PHE 2.9 30.9 + - - -
147B GLY* 3.1 24.9 + - - -
182B PHE* 3.6 12.8 - + - -
184B HIS* 3.4 19.5 - + - -
186B LEU 4.6 10.8 - - - -
187B LYS* 5.9 0.2 - - - -
188B LEU* 3.8 25.6 - - + -
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Residues in contact with TYR 109 (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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107B LEU* 4.2 11.3 - - + +
108B TYR* 1.3 72.7 - - - +
110B LEU* 1.3 71.3 + - - +
111B MET* 4.0 23.1 - - + -
124B VAL* 3.7 28.7 - - + +
131B LEU* 5.5 10.3 - - + -
144B ILE* 6.0 2.5 - - + -
145B GLY 3.1 10.1 + - - +
146B PHE* 3.6 31.6 - + + -
147B GLY 2.9 28.8 + - - +
195B PHE* 6.3 1.3 - + + -
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Residues in contact with LEU 110 (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 TYR* 3.8 27.1 + - + +
109B TYR* 1.3 80.4 - - - +
111B MET* 1.3 59.7 + - - +
112B ASP 4.0 1.0 + - - -
147B GLY 3.3 1.8 - - - +
148B SER 5.0 0.4 - - - +
149B PHE* 3.8 23.2 - - + -
182B PHE* 3.8 31.0 - - + -
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Residues in contact with MET 111 (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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109B TYR* 4.0 20.4 - - + -
110B LEU* 1.3 70.8 - - - +
112B ASP* 1.3 76.5 + - - +
113B LEU* 3.3 21.6 + - + -
117B MET* 3.9 19.1 - - + +
120B ASP* 4.0 6.1 - - + -
121B LEU* 3.7 41.7 - - + +
124B VAL* 4.1 11.9 - - - -
146B PHE* 3.4 29.6 - - + -
147B GLY 3.1 7.4 + - - +
148B SER* 3.3 5.9 - - - +
149B PHE* 2.9 30.6 + - - -
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Residues in contact with ASP 112 (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 LEU 4.0 1.2 + - - -
111B MET* 1.3 81.6 - - - +
113B LEU* 1.3 62.0 + - - +
114B SER* 3.1 23.0 + - - -
116B SER* 4.5 1.9 + - - -
117B MET* 3.2 49.3 - - + +
149B PHE* 3.5 35.4 - - + +
150B VAL* 4.9 3.8 - - - +
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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