Contacts of the strand formed by residues 164 - 168 (chain C) in PDB entry 4QKB
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 LEU 164 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C VAL 3.9 0.7 - - - +
35C VAL* 3.6 1.6 - - - -
36C ARG* 2.7 44.5 + - - +
39C PHE* 3.6 41.5 - - + -
92C VAL* 4.0 22.7 - - + -
95C ALA* 4.4 12.3 - - + -
96C ALA* 5.3 0.9 - - + -
133C ALA* 4.6 3.6 - - + -
134C GLY 3.3 16.4 - - - +
135C LEU* 3.7 25.6 - - + -
159C LEU* 5.6 0.2 - - - -
163C SER* 1.3 78.9 - - - +
165C TYR* 1.3 68.7 + - - +
166C ILE* 4.4 16.2 - - + +
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Residues in contact with TYR 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C VAL 3.2 10.3 - - - +
35C VAL* 4.2 5.4 - - + -
132C ILE* 4.1 20.5 - - + +
133C ALA* 3.3 4.2 - - - +
134C GLY* 2.8 73.3 + - - -
136C SER* 4.8 1.6 - - - -
143C MSE 3.6 22.0 - - + +
157C LEU* 5.1 3.6 - - + -
159C LEU* 3.8 35.2 - - + +
163C SER 4.4 0.2 - - - -
164C LEU* 1.3 75.9 - - - +
166C ILE* 1.3 66.5 + - - +
167C LEU* 3.8 31.8 - - + +
177C HIS* 5.4 1.4 - - - -
197C ARG* 4.4 2.7 - - - -
201C ILE* 4.4 3.8 - - - +
302C AKG 2.8 39.8 + - - +
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Residues in contact with ILE 166 (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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32C ALA 3.3 6.1 - - - +
34C VAL* 2.9 49.8 + - + +
36C ARG* 5.1 7.2 - - + -
95C ALA* 3.8 15.3 - - + +
96C ALA* 3.7 28.5 - - + +
131C THR* 3.9 17.9 - - + -
132C ILE 3.4 3.8 - - - +
133C ALA* 4.6 0.7 - - + -
164C LEU* 4.4 17.7 - - + +
165C TYR* 1.3 78.5 - - - +
167C LEU* 1.3 68.6 + - - +
168C ARG* 3.6 36.8 - - + +
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Residues in contact with LEU 167 (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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32C ALA 3.5 1.3 - - - -
33C ALA* 4.0 23.1 - - + -
130C ALA 3.6 1.6 - - - +
131C THR* 3.4 2.5 - - - -
132C ILE* 2.7 51.9 + - + +
143C MSE 4.0 8.1 - - - -
145C LEU* 3.9 28.3 - - + -
157C LEU* 4.4 10.1 - - + -
165C TYR* 3.8 25.4 - - + -
166C ILE* 1.3 80.3 - - - +
168C ARG* 1.3 60.2 + - - +
171C ALA* 4.2 12.3 - - + +
172C ARG* 3.9 5.5 - - - +
177C HIS* 3.9 28.5 - - + +
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Residues in contact with ARG 168 (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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31C ASP 3.2 23.3 + - - +
32C ALA* 3.1 26.5 + - - +
34C VAL* 4.9 6.1 - - - +
95C ALA 5.1 2.0 + - - -
96C ALA* 2.7 32.7 + - - +
97C PHE* 4.9 1.6 - - - +
98C GLY* 5.1 3.6 - - - +
101C GLN* 5.4 2.0 - - - +
130C ALA* 3.4 10.5 - - + +
131C THR* 4.1 15.3 + - + +
166C ILE* 3.6 30.1 - - + +
167C LEU* 1.3 75.2 - - - +
169C GLY* 1.3 67.8 + - - +
170C SER 3.2 0.5 + - - -
171C ALA* 3.2 14.4 + - - +
172C ARG* 3.6 3.3 + - - +
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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