Contacts of the strand formed by residues 78 - 82 (chain C) in PDB entry 2PK9
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 78 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C VAL* 3.4 45.7 + - + +
39C LYS 5.1 5.6 - - - -
46C THR* 3.8 20.6 - - + -
47C PRO* 4.7 2.9 - - + -
50C ALA* 3.8 29.4 - - + -
54C ILE* 4.4 3.8 - - + -
71C VAL* 3.5 22.2 - - + -
72C ILE 3.2 9.2 - - - +
73C HIS* 3.4 20.4 - - + +
77C LYS* 1.3 74.5 - - - +
79C THR* 1.3 64.1 + - - +
80C LEU* 3.7 3.7 + - + +
168D TYR* 3.4 22.0 - - + +
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Residues in contact with THR 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C LEU* 5.2 11.1 - - + +
36C LYS 3.5 11.0 - - - -
37C GLU* 3.8 29.8 - - + +
38C VAL 5.6 0.2 - - - +
70C ASP 4.4 0.2 - - - +
71C VAL* 3.7 2.4 - - - +
72C ILE* 3.0 55.2 + - + +
77C LYS* 4.0 25.1 - - + -
78C LEU* 1.3 73.6 - - - +
80C LEU* 1.3 63.0 + - - +
81C VAL* 4.2 3.8 + - - +
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Residues in contact with LEU 80 (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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34C ALA 3.7 1.4 - - - +
35C LEU* 3.5 5.7 - - - +
36C LYS* 2.9 40.4 + - + +
38C VAL* 4.2 13.7 - - + -
50C ALA* 5.3 4.5 - - + +
53C GLU* 3.9 23.3 - - + +
54C ILE* 3.6 39.9 - - + +
68C LEU* 3.9 7.6 - - + -
70C ASP 4.1 3.4 - - - -
71C VAL* 3.7 14.6 - - + -
78C LEU* 4.0 11.0 - - + +
79C THR* 1.3 75.3 - - - +
81C VAL* 1.3 62.0 + - - +
82C PHE* 3.7 32.3 + - + -
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Residues in contact with VAL 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C PHE* 4.0 26.2 - - + -
33C VAL* 3.8 31.9 - - + -
34C ALA 3.9 1.6 - - - -
35C LEU* 3.8 19.7 - - + -
68C LEU* 3.3 7.4 - - - +
69C TYR* 2.7 41.3 + - + +
70C ASP* 3.1 30.1 + - + +
72C ILE* 4.3 13.7 - - + -
79C THR* 4.4 2.5 - - - +
80C LEU* 1.3 77.7 - - - +
82C PHE* 1.3 56.2 - - - +
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Residues in contact with PHE 82 (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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21C VAL* 6.4 0.7 - - + -
33C VAL* 3.4 8.3 - - - +
34C ALA* 2.9 42.9 + - + +
36C LYS* 3.6 35.4 - - + -
53C GLU* 4.4 14.8 - - + -
57C MET* 4.2 24.5 - - + -
66C VAL* 3.7 25.8 - - + -
67C ARG 3.4 3.6 - - - -
68C LEU* 4.2 20.0 - - + -
69C TYR* 4.3 3.6 - - - -
80C LEU* 3.7 32.3 - - + -
81C VAL* 1.3 74.3 - - - +
83C GLU* 1.3 64.0 + - - +
151C ASP* 5.9 4.7 - - - -
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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