Contacts of the helix formed by residues 88 - 92 (chain F) in PDB entry 4DHZ
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 88 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79F ASN* 5.0 0.4 - - - +
86F ILE* 3.4 16.6 + - + -
87F CYS* 1.3 78.1 - - - +
89F ASP* 1.3 85.7 + - - +
90F ILE* 3.4 12.3 - - + -
91F LEU* 3.1 28.8 + - + +
92F LYS* 3.5 8.1 + - - +
104F VAL* 4.7 1.1 - - + +
107F SER* 3.5 32.5 - - - +
108F ILE* 4.1 15.5 - - + -
111F LEU* 3.9 39.0 - - + -
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Residues in contact with ASP 89 (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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88F LEU* 1.3 88.9 - - - +
90F ILE* 1.3 79.7 + - - +
91F LEU 3.1 5.1 + - - -
92F LYS* 3.1 9.3 + - - +
93F ASP* 3.2 6.5 + - + +
94F LYS* 2.9 57.3 + - + +
107F SER* 5.0 0.9 + - - -
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Residues in contact with ILE 90 (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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88F LEU* 4.1 16.2 - - + -
89F ASP* 1.3 90.0 + - - +
91F LEU* 1.3 62.9 + - + +
92F LYS 3.5 0.2 - - - -
94F LYS* 3.8 25.8 - - + +
95F TRP* 3.1 33.0 - - + +
99F LEU* 4.3 13.5 - - + -
103F THR* 3.9 26.9 - - + +
104F VAL* 4.3 8.1 - - + -
107F SER* 3.7 29.6 - - - +
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Residues in contact with LEU 91 (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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66F ALA* 3.5 17.4 - - - +
67F PRO* 3.7 26.1 - - + +
69F VAL* 3.9 26.0 - - + +
86F ILE* 4.2 22.9 - - + +
88F LEU* 3.1 32.7 + - + +
89F ASP 3.1 0.6 - - - -
90F ILE* 1.3 85.5 - - + +
92F LYS* 1.3 61.2 + - - +
104F VAL* 3.7 34.5 - - + -
108F ILE* 5.0 0.9 - - + -
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Residues in contact with LYS 92 (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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27A MET* 3.7 30.3 - - + -
66F ALA* 5.4 0.2 - - - +
88F LEU 3.5 6.4 + - - +
89F ASP* 3.1 5.8 + - - +
91F LEU* 1.3 80.0 - - - +
93F ASP* 1.3 71.3 + - + +
94F LYS 3.4 0.9 + - - -
95F TRP* 3.5 14.0 + - - +
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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