Contacts of the strand formed by residues 64 - 70 (chain F) in PDB entry 1PQ3
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 HIS 64 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24F HIS 3.3 8.1 + - - +
25F SER* 3.3 20.9 - - - +
26F VAL 2.8 27.5 + - - +
62F GLY 3.7 1.5 + - - +
63F CYS* 1.3 73.0 - - - +
65F LEU* 1.3 71.0 + - - +
111F TYR* 4.5 11.5 - + - -
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Residues in contact with LEU 65 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26F VAL* 3.3 17.5 - - + +
28F VAL* 5.2 2.7 - - + -
55F MET* 3.3 36.6 - - + +
58F LEU* 3.9 16.6 - - + -
59F SER* 3.3 28.0 - - - +
63F CYS* 3.6 26.3 + - + +
64F HIS* 1.3 91.8 + - - +
66F LYS* 1.3 64.3 + - - +
67F ASP* 4.0 2.2 - - + +
111F TYR* 4.9 0.7 - - - -
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Residues in contact with LYS 66 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26F VAL 3.1 6.4 + - - +
27F ALA* 3.4 1.0 - - - -
28F VAL* 3.3 14.2 + - - +
55F MET* 5.6 0.2 - - - -
65F LEU* 1.3 74.3 - - - +
67F ASP* 1.3 68.0 + - - +
68F PHE* 3.2 56.1 - - + -
109F ASP* 5.3 5.0 + - - -
111F TYR* 3.0 48.7 - - + +
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Residues in contact with ASP 67 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28F VAL 3.5 6.3 - - - +
50F ARG* 2.7 36.4 + - - -
55F MET* 3.1 26.4 - - + +
65F LEU* 4.0 2.7 - - + +
66F LYS* 1.3 76.5 - - - +
68F PHE* 1.3 61.3 + - - +
69F GLY* 2.6 30.2 + - - -
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Residues in contact with PHE 68 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27F ALA* 3.7 20.2 - - + -
28F VAL 2.9 17.9 + - - +
29F ILE* 4.2 13.7 - - + -
66F LYS* 3.2 52.3 - - + -
67F ASP* 1.3 72.6 - - - +
69F GLY* 1.3 64.5 + - - +
70F ASP 5.0 0.3 - - - -
71F LEU* 4.4 10.9 - - + +
102F VAL* 3.4 37.0 - - + -
105F ARG* 4.9 8.5 - - + -
106F ALA* 3.6 24.0 - - + -
109F ASP* 5.1 3.4 - - - -
111F TYR* 5.1 3.1 - + - -
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Residues in contact with GLY 69 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29F ILE* 3.9 3.3 - - - +
30F GLY 3.0 20.1 + - - -
50F ARG* 3.7 5.2 + - - -
67F ASP* 2.6 19.3 + - - -
68F PHE* 1.3 85.7 - - - +
70F ASP* 1.3 65.7 + - - -
71F LEU 3.7 1.0 + - - -
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Residues in contact with ASP 70 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30F GLY* 3.3 15.6 - - - -
32F PRO* 4.0 14.9 - - + +
46F PRO* 3.8 16.8 - - - +
47F ALA* 4.5 5.5 + - - +
50F ARG* 2.7 38.8 + - - -
68F PHE 5.0 0.2 - - - -
69F GLY* 1.3 71.6 - - - -
71F LEU* 1.3 65.9 + - - +
72F SER* 3.7 2.8 + - - -
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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