Contacts of the strand formed by residues 166 - 170 (chain C) in PDB entry 2OQH
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 ALA 166 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130C ILE 4.5 2.2 + - - -
131C THR* 3.4 11.5 - - + +
132C ALA 3.1 20.3 + - - -
164C PHE* 3.4 6.9 - - - +
165C ASP* 1.3 82.8 - - - +
167C VAL* 1.3 69.2 + - - +
192C VAL* 3.7 1.3 - - - -
193C ASN* 3.2 21.5 - - + +
195C ARG* 3.7 28.9 - - - +
322C ALA* 4.0 9.2 - - + -
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Residues in contact with VAL 167 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131C THR* 3.9 2.5 - - - -
132C ALA* 3.3 17.9 - - + +
134C ILE* 4.0 35.9 - - + -
155C ALA* 4.8 6.5 - - + +
158C VAL* 6.0 0.2 - - + -
159C VAL* 3.5 31.9 - - + -
166C ALA* 1.3 81.1 - - - +
168C LYS* 1.3 63.3 + - - +
169C LEU 4.3 0.2 - - - -
185C VAL* 5.2 0.7 - - + -
189C LEU* 4.7 5.6 - - + -
192C VAL* 4.0 9.2 - - + -
193C ASN 2.9 7.8 + - - +
194C LEU* 3.5 20.0 - - + +
195C ARG* 3.0 26.3 + - - +
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Residues in contact with LYS 168 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131C THR* 4.2 13.0 - - + -
132C ALA 2.9 11.0 + - - +
133C LEU* 3.2 23.5 - - + +
134C ILE* 2.9 28.9 + - - -
167C VAL* 1.3 75.6 - - - +
169C LEU* 1.3 71.5 + - - +
170C LYS* 6.2 0.2 - - - +
195C ARG* 3.4 24.9 - - + +
196C VAL 5.0 0.2 - - - -
197C ASP* 3.8 22.9 + - + -
223C GLU* 3.3 25.1 + - - +
297C HIS* 5.3 5.1 + - - -
324C ASP* 2.7 35.2 + - - +
326C MSE 5.5 6.7 - - - +
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Residues in contact with LEU 169 (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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134C ILE* 3.4 23.3 - - + +
135C THR* 4.6 1.1 - - - -
136C ARG* 5.2 1.3 - - + +
151C MSE 3.4 33.0 - - + -
167C VAL* 4.9 0.2 - - - +
168C LYS* 1.3 78.3 - - - +
170C LYS* 1.3 72.1 + - - +
171C GLY 3.3 0.3 + - - -
178C ASP* 4.0 17.7 - - + +
181C ILE* 3.9 26.7 - - + -
182C LEU* 3.9 26.0 - - + -
185C VAL* 6.5 0.2 - - + -
194C LEU* 5.6 1.1 - - + +
195C ARG 2.9 14.5 + - - +
196C VAL* 4.2 11.2 - - + -
197C ASP* 2.8 27.0 + - - +
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Residues in contact with LYS 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133C LEU* 4.2 11.9 - - + +
134C ILE 3.0 8.6 + - - +
135C THR* 3.8 36.4 - - + -
136C ARG* 5.2 3.8 + - - +
168C LYS 3.9 0.8 + - - -
169C LEU* 1.3 81.3 - - - +
171C GLY* 1.3 72.6 + - - +
172C THR* 4.0 11.8 - - + +
178C ASP* 4.7 1.0 - - - +
197C ASP* 3.7 5.4 - - - -
199C ASN* 3.9 23.5 - - - +
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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