Contacts of the strand formed by residues 155 - 159 (chain C) in PDB entry 2WWR
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 THR 155 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153C GLN 5.0 0.7 + - - -
154C SER* 1.3 76.9 + - - +
156C VAL* 1.3 64.1 - - - +
178C GLN* 5.7 2.8 + - - +
179C ARG* 3.5 32.3 - - + +
181C LEU* 4.1 21.3 - - + -
208C GLN* 3.9 18.1 + - + +
209C SER* 3.6 13.1 - - - -
210C ASP* 2.7 39.1 + - - +
211C PHE* 3.2 6.9 + - - -
235C LYS* 5.5 0.9 + - - -
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Residues in contact with VAL 156 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151C LEU* 3.9 17.7 - - + -
154C SER* 4.3 0.7 - - - +
155C THR* 1.3 78.1 - - - +
157C GLY* 1.3 63.7 + - - +
158C ILE* 4.1 19.0 + - + +
172C LEU* 4.0 22.4 - - + -
177C VAL* 3.8 28.3 - - + -
179C ARG 3.0 7.1 + - - -
180C PHE* 3.4 19.1 - - + +
181C LEU* 3.0 25.6 + - - +
209C SER* 4.1 3.1 - - - -
211C PHE* 3.4 18.4 - - + +
213C VAL* 4.8 6.7 - - + -
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Residues in contact with GLY 157 (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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156C VAL* 1.3 71.6 - - - +
158C ILE* 1.3 63.3 + - - -
181C LEU* 3.5 7.0 - - - -
205C LEU* 3.8 24.0 - - - -
209C SER* 3.7 7.2 - - - -
211C PHE 2.7 15.1 + - - -
212C ILE* 3.3 7.0 - - - +
213C VAL 2.8 28.4 + - - +
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Residues in contact with ILE 158 (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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156C VAL* 4.3 12.3 - - + +
157C GLY* 1.3 73.2 - - - +
159C ILE* 1.3 65.4 + - - +
160C GLY 3.8 0.6 + - - -
161C LEU* 4.0 41.0 + - + +
165C GLY* 4.0 17.0 - - - +
168C ILE* 5.3 5.4 - - + -
169C ALA* 4.0 29.4 - - + +
172C LEU* 5.9 0.2 - - + -
180C PHE* 4.1 19.3 - - + -
181C LEU 2.8 14.3 + - - +
182C TYR* 3.3 5.7 - - - +
183C THR 3.2 21.8 + - - -
205C LEU* 4.3 1.4 - - - +
213C VAL* 3.5 15.0 - - + +
215C ALA* 5.3 3.1 - - + -
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Residues in contact with ILE 159 (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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158C ILE* 1.3 72.1 - - - +
160C GLY* 1.3 65.7 + - - +
183C THR* 4.2 16.6 - - + +
202C THR* 4.6 11.9 - - + -
205C LEU* 4.2 22.2 - - + -
212C ILE* 4.3 9.6 - - + -
213C VAL 2.8 13.7 + - - +
214C VAL* 4.2 24.5 - - + -
215C ALA* 3.0 27.9 + - - +
216C CYS* 3.5 5.0 + - - -
225C LEU* 5.0 14.8 - - + -
226C CYS* 5.5 2.0 - - - -
230C PHE* 4.1 28.9 - - + -
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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