Contacts of the strand formed by residues 188 - 191 (chain C) in PDB entry 1Q90
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 188 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80C GLN 3.0 15.0 - - - +
81C ALA* 3.6 22.7 - - + +
82C ALA 4.0 0.7 - - - +
178C HIS 3.4 2.4 - - - +
179C CYS* 3.6 2.8 - - - -
180C ASP* 3.3 36.4 + - - +
186C LEU* 3.5 11.9 + - + +
187C VAL* 1.3 82.3 - - - +
189C PHE* 1.3 62.7 + - - +
190C SER* 4.5 4.3 + - - -
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Residues in contact with PHE 189 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C GLN* 2.7 34.7 + - + +
81C ALA 5.2 0.4 - - - -
82C ALA* 3.2 26.4 - - + +
107C SER* 4.1 5.2 - - - -
108C GLN 2.9 26.5 - - - -
109C GLY* 3.5 17.9 - - - -
110C LEU* 3.3 28.4 - - + +
115C THR* 3.9 19.5 - - + -
117C LEU* 3.2 36.8 - - + -
129C GLY* 4.3 4.9 - - - -
177C ALA* 4.6 9.6 - - + -
178C HIS 3.1 11.7 - - - -
179C CYS* 4.1 15.9 - - + -
187C VAL* 5.4 0.4 - - + -
188C THR* 1.3 74.3 - - - +
190C SER* 1.3 61.5 + - - +
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Residues in contact with SER 190 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C GLN 5.2 1.2 + - - +
110C LEU* 3.5 4.5 - - - -
177C ALA* 3.1 8.8 - - - +
178C HIS* 2.6 59.8 + - - -
180C ASP* 3.7 15.1 + - - -
188C THR* 4.5 5.7 + - - -
189C PHE* 1.3 78.3 + - - +
191C THR* 1.3 61.2 + - - +
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Residues in contact with THR 191 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C LEU* 3.6 19.1 - - + +
178C HIS* 3.0 16.8 + - - -
190C SER* 1.3 72.7 - - - +
192C TRP* 1.3 72.7 + - - +
193C THR* 3.9 10.2 + - - +
205C TRP* 5.4 7.4 - - + +
206C ALA* 6.3 2.0 - - + -
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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
------------------------------------------------------------
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