Contacts of the strand formed by residues 157 - 160 (chain C) in PDB entry 3IKH
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 157 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130C GLY* 4.2 10.2 + - - -
131C ASP 2.8 11.7 + - - -
132C ILE* 3.2 20.5 - - + +
133C LEU* 2.9 25.8 + - - +
155C GLY 4.2 0.4 + - - -
156C MSE 1.3 73.0 - - - +
158C THR* 1.3 68.2 + - - +
159C VAL* 4.7 5.8 - - + -
177C ASP* 3.3 23.5 + - + +
178C ILE* 4.8 9.9 - - + -
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Residues in contact with THR 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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133C LEU 3.5 3.6 - - - +
148C PHE* 3.6 34.8 - - + +
151C ALA* 3.9 22.2 - - + -
152C ARG* 4.5 5.9 + - + -
156C MSE 4.2 5.4 - - - +
157C THR* 1.3 76.8 - - - +
159C VAL* 1.3 64.3 + - - +
175C LEU 2.6 27.1 + - - +
176C ILE* 3.4 2.5 - - - -
177C ASP* 2.9 25.0 + - - +
178C ILE 3.0 23.7 + - - -
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Residues in contact with VAL 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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132C ILE* 3.6 24.5 - - + -
133C LEU 3.0 9.0 + - - +
134C LEU* 3.5 25.4 - - + +
135C GLN 3.1 23.6 + - - -
148C PHE* 3.7 4.7 - - - -
157C THR* 4.7 2.9 - - + -
158C THR* 1.3 79.2 - - - +
160C PHE* 1.3 66.5 + - - +
178C ILE* 3.2 39.9 - - + +
180C VAL* 5.1 3.1 - - + -
235C LEU* 4.9 11.4 - - + -
238C MSE 6.0 1.1 - - + -
239C LEU* 4.5 17.3 - - + -
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Residues in contact with PHE 160 (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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135C GLN 3.6 6.3 - - - -
136C GLN 3.3 22.4 - - - -
144C THR* 4.0 11.4 - - + -
148C PHE* 3.6 15.3 - + + -
159C VAL* 1.3 78.3 - - - +
161C ASN* 1.3 65.8 + - - +
162C PRO* 3.6 33.6 - - + +
169C PHE* 3.8 26.0 - + + -
172C LEU* 3.9 25.4 - - + -
173C TRP* 3.8 24.7 - + + -
176C ILE* 3.6 31.9 - - + -
178C ILE 2.9 9.7 + - - -
179C ALA* 3.4 3.6 - - - -
180C VAL* 3.0 25.4 + - - -
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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