Contacts of the strand formed by residues 170 - 173 (chain C) in PDB entry 7UUT
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 VAL 170 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164C ILE* 3.7 33.2 - - + -
168C ALA* 4.2 3.8 - - + +
169C THR* 1.3 79.2 - - - +
171C ALA* 1.3 73.4 + - - +
172C VAL* 4.4 3.8 - - + -
186C ALA* 4.2 10.8 - - + -
191C ALA* 3.8 19.7 - - + -
193C ARG 2.9 9.1 + - - +
194C ILE* 3.3 6.9 - - + +
195C ILE* 2.9 25.5 + - - +
236C VAL* 4.6 3.6 - - - -
238C ALA* 3.4 13.7 - - + +
240C ILE* 3.9 25.6 - - + -
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Residues in contact with ALA 171 (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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170C VAL* 1.3 75.9 - - - +
172C VAL* 1.3 56.2 + - - +
173C LEU* 4.0 4.3 - - + -
195C ILE* 3.3 11.9 - - + +
227C ILE* 4.4 10.3 - - + -
236C VAL* 3.9 20.2 - - + +
238C ALA 2.9 6.9 + - - +
239C ALA* 3.2 4.0 - - + -
240C ILE 2.8 31.2 + - - -
255C ILE* 3.9 28.3 - - + -
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Residues in contact with VAL 172 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170C VAL* 4.4 4.0 - - + -
171C ALA* 1.3 76.5 - - - +
173C LEU* 1.3 61.6 + - - +
174C GLY 3.4 17.4 + - - +
175C ILE* 4.6 1.3 - - + +
179C GLY* 3.5 24.0 - - - +
182C ALA* 3.9 15.0 - - + +
183C VAL* 3.9 30.5 - - + +
186C ALA* 5.2 0.4 - - + -
194C ILE* 4.3 13.5 - - + -
195C ILE 2.8 12.0 + - - +
196C ALA* 3.7 1.9 - - - -
197C VAL* 3.0 26.5 + - - +
240C ILE* 3.5 19.1 - - + +
242C ALA* 4.8 1.3 - - + -
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Residues in contact with LEU 173 (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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171C ALA* 4.6 3.1 - - + -
172C VAL* 1.3 69.9 - - - +
174C GLY* 1.3 60.1 + - - +
197C VAL* 3.6 28.5 - - + -
223C ILE* 4.3 10.5 - - + -
227C ILE* 4.4 1.1 - - + -
239C ALA* 4.7 5.2 - - + -
240C ILE 2.8 16.3 + - - +
241C ILE* 4.2 8.3 - - + -
242C ALA 2.9 28.1 + - - -
243C GLY 3.4 8.1 + - - +
248C ILE* 3.9 33.7 - - + -
251C THR* 4.4 2.5 - - + -
252C ALA* 3.8 36.6 - - + +
255C ILE* 4.0 22.4 - - + -
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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