Contacts of the strand formed by residues 160 - 164 (chain F) in PDB entry 2WNU
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 LYS 160 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209E GLU* 3.5 37.3 + - - +
210E GLY* 5.0 3.6 - - - +
153F LEU* 3.6 31.6 - - + +
154F LEU 3.6 5.6 - - - +
155F TYR* 3.4 23.5 - - + +
159F VAL* 1.3 79.7 - - - +
161F VAL* 1.3 63.2 + - - +
162F VAL 4.5 4.5 - - - +
163F THR* 3.6 25.6 + - - +
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Residues in contact with VAL 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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100E THR* 5.5 0.5 - - - +
119E ILE* 4.3 18.1 - - + +
212E ASN* 4.5 2.8 + - - +
154F LEU* 2.8 27.3 + - + +
156F ARG* 3.7 25.8 - - + +
159F VAL* 3.4 18.8 - - + +
160F LYS* 1.3 74.8 - - - +
162F VAL* 1.3 68.8 + - + +
179F VAL* 4.2 17.3 - - + -
181F LEU* 4.2 23.1 - - + -
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Residues in contact with VAL 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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100E THR* 4.2 13.2 - - + -
119E ILE* 4.2 20.0 - - + -
212E ASN* 3.1 11.4 - - - +
214E ILE* 4.3 6.7 - - + -
142F TYR* 6.5 0.4 - - + -
152F VAL 3.8 0.7 - - - +
153F LEU* 3.3 4.2 - - - +
154F LEU* 2.9 46.5 + - + +
160F LYS* 3.8 2.4 - - - +
161F VAL* 1.3 91.3 - - + +
163F THR* 1.3 63.4 + - - +
164F PHE* 3.7 29.1 - - + -
178F GLY 4.8 2.5 - - - +
179F VAL* 4.5 13.9 - - + -
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Residues in contact with THR 163 (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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210E GLY* 3.6 36.5 + - - +
211E ALA* 3.8 1.4 - - - -
212E ASN* 2.5 41.7 + - - +
151F CYS* 4.2 2.2 - - + -
152F VAL 3.4 3.6 - - - +
153F LEU* 3.7 25.4 - - + +
160F LYS* 3.6 25.6 + - - +
162F VAL* 1.3 76.0 + - - +
164F PHE* 1.3 70.9 + - - +
165F CYS* 4.1 11.9 - - - -
194F ASN* 4.6 3.8 - - - +
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Residues in contact with PHE 164 (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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146E HIS* 3.8 18.2 - - + -
148E SER* 4.0 3.6 - - - -
180E VAL* 3.9 20.4 - - + -
211E ALA* 5.2 0.4 - - - +
212E ASN* 3.1 38.1 - - + -
214E ILE* 3.6 24.7 - - + -
142F TYR* 3.5 16.6 - + - +
152F VAL 2.8 34.3 + - - -
162F VAL* 3.7 35.9 - - + -
163F THR* 1.3 75.0 - - - +
165F CYS* 1.3 62.3 + - - +
175F ASN* 3.0 11.7 + - - +
176F SER 3.8 9.2 - - - +
177F GLY* 3.6 24.0 - - - -
178F GLY 3.9 3.4 - - - -
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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