Contacts of the strand formed by residues 53 - 58 (chain F) in PDB entry 4ZHF
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 53 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30F LYS* 4.1 18.6 - - + -
31F TRP 3.3 11.4 - - - +
32F TYR* 4.1 11.2 - - + +
33F VAL* 4.7 0.4 - - - +
52F TYR* 1.3 77.0 - - - +
54F THR* 1.3 64.3 + - - +
55F ILE* 5.1 2.5 - - + -
67F THR 3.9 0.4 - - - +
68F SER* 3.2 4.5 - - - -
69F VAL* 2.8 36.3 + - + +
176F ILE* 4.0 23.7 - - + +
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Residues in contact with THR 54 (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 GLY 3.8 1.7 - - - +
31F TRP* 2.8 37.4 + - - +
33F VAL* 4.3 1.3 - - - +
52F TYR* 3.8 5.0 - - - -
53F ALA* 1.3 74.8 - - - +
55F ILE* 1.3 64.2 + - - +
56F TYR* 3.6 17.3 - - + -
66F VAL* 3.5 30.1 - - + -
67F THR 3.3 3.8 - - - +
68F SER* 2.5 17.7 + - - +
81F ARG* 4.0 0.9 - - - +
138F TYR* 4.1 9.2 - - - +
203F SO4 2.3 33.5 + - - +
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Residues in contact with ILE 55 (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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21D ASN* 6.2 1.1 - - - -
29F GLY* 3.4 15.7 - - - +
30F LYS* 4.1 33.2 - - + +
53F ALA 5.1 1.1 - - - -
54F THR* 1.3 78.9 - - - +
56F TYR* 1.3 67.7 + - - +
57F GLU* 4.3 21.0 - - + +
65F ASN 3.3 2.8 - - - +
66F VAL* 3.3 5.6 - - - -
67F THR* 2.7 49.2 + - + +
69F VAL* 4.4 19.5 - - + -
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Residues in contact with TYR 56 (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 PHE* 3.9 23.9 - + - +
28F GLN* 3.1 16.3 - - - +
29F GLY* 2.8 39.1 + - - +
31F TRP* 3.9 19.3 - + - -
54F THR* 3.6 21.3 - - + +
55F ILE* 1.3 75.5 - - - +
57F GLU* 1.3 63.4 - - - +
64F TYR* 3.9 30.5 - + + -
65F ASN 3.6 3.1 - - - -
66F VAL* 4.0 12.5 - - + +
81F ARG* 5.6 0.2 + - - -
83F PHE* 3.8 32.7 - + - -
92F PHE* 6.2 1.6 - + - -
108F VAL* 5.5 0.8 - - + +
121F VAL* 4.9 3.1 - - - +
123F PHE* 4.3 5.5 - - - -
138F TYR* 2.8 35.8 + + - -
203F SO4 5.4 0.2 + - - -
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Residues in contact with GLU 57 (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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21D ASN* 4.7 16.7 - - - +
28F GLN* 4.0 3.1 - - - +
55F ILE* 4.3 18.0 - - + +
56F TYR* 1.3 76.3 - - - +
58F LEU* 1.3 64.0 + - - +
59F LYS* 3.4 3.3 + - + +
64F TYR* 3.2 5.7 - - - -
65F ASN* 2.8 57.7 + - + +
67F THR* 5.5 3.5 + - - -
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Residues in contact with LEU 58 (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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24F ASP* 3.7 36.1 - - + +
25F ASN* 3.8 27.6 - - + +
28F GLN* 3.0 25.0 + - - +
57F GLU* 1.3 70.9 - - - +
59F LYS* 1.3 68.2 + - - +
62F LYS* 3.7 43.7 - - - +
63F SER 3.8 2.5 - - - +
64F TYR* 3.7 24.4 - - + -
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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