Contacts of the strand formed by residues 158 - 162 (chain F) in PDB entry 2Q5E
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 GLU 158 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91F LEU* 5.1 0.2 - - - +
94F VAL* 3.7 20.5 - - - +
95F THR 5.2 0.3 + - - -
98F ASP* 3.8 28.3 - - + +
101F ARG* 4.1 6.7 - - + +
102F ILE 3.1 12.2 + - - +
103F CYS* 3.5 13.3 + - - +
104F VAL 3.0 25.1 + - - +
157F PHE* 1.3 73.3 - - - +
159F CYS* 1.3 62.4 + - - +
160F VAL* 3.7 11.7 + - + +
184F ARG* 5.8 4.4 + - + -
208F ARG* 2.8 47.5 + - - -
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Residues in contact with CYS 159 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104F VAL* 3.7 4.7 - - - -
106F ILE* 4.6 8.3 - - + -
153F MET* 3.7 37.5 - - - -
154F GLY* 4.0 2.0 - - - -
157F PHE* 3.9 6.9 + - - -
158F GLU* 1.3 77.5 - - - +
160F VAL* 1.3 64.1 + - - +
182F VAL* 3.3 50.3 + - + +
183F PHE* 3.8 21.8 - - + -
184F ARG* 3.9 6.9 + - - +
185F ALA 4.2 1.9 + - - -
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Residues in contact with VAL 160 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91F LEU* 4.0 20.9 - - + -
103F CYS* 3.6 24.9 - - - -
104F VAL 3.0 10.5 + - - +
105F VAL* 4.0 17.0 - - + -
106F ILE* 2.8 28.6 + - - +
158F GLU* 4.1 11.9 - - + +
159F CYS* 1.3 80.1 - - - +
161F LEU* 1.3 71.6 + - - +
162F PHE* 4.7 0.4 - - + -
183F PHE* 4.0 2.9 - - - -
185F ALA* 3.9 15.7 - - + +
187F LEU* 4.2 18.8 - - + -
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Residues in contact with LEU 161 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106F ILE 3.6 15.0 - - - +
107F ASP 4.6 1.6 - - - +
108F LEU* 4.0 26.9 - - + +
112F LEU* 5.5 0.2 - - + -
160F VAL* 1.3 76.8 - - - +
162F PHE* 1.3 60.6 + - - +
163F THR* 4.3 19.7 - - + -
170F ALA* 4.4 9.6 - - + -
174F THR* 3.4 25.4 - - + +
183F PHE* 3.6 32.1 - - + -
185F ALA 3.2 15.1 + - - +
186F ARG* 3.5 26.6 - - + -
187F LEU* 2.9 24.2 + - - +
188F PHE* 4.5 2.0 - - + -
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Residues in contact with PHE 162 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90F LEU* 4.4 6.3 - - + -
105F VAL* 3.8 33.7 - - + -
106F ILE 2.9 19.0 + - - +
107F ASP* 3.6 6.9 - - - -
160F VAL* 4.5 1.3 - - + +
161F LEU* 1.3 76.8 - - - +
163F THR* 1.3 62.9 + - - +
187F LEU* 3.5 24.7 - - + -
188F PHE 4.3 0.4 - - - -
191F SER* 3.5 36.6 - - - -
192F CYS* 3.7 22.0 - - - -
201F LYS* 3.5 48.3 - - + +
202F ASP 4.8 2.5 - - - -
203F LEU* 5.0 1.6 - - + -
206F LEU* 3.7 24.9 - - + -
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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