Contacts of the helix formed by residues 153 - 159 (chain F) in PDB entry 1FZB
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 CYS 153 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152F ASP* 1.3 74.1 - - - +
154F GLN* 1.3 50.9 + - - +
156F ILE* 3.3 5.6 + - - +
157F ALA* 2.7 34.0 + - - +
180F VAL* 3.9 9.2 - - - -
182F CYS* 2.0 54.5 - - + +
184F ILE* 5.2 1.4 - - - +
190F GLY* 3.5 9.2 - - - +
191F TRP 3.5 11.7 - - - +
192F THR* 2.9 40.0 - - - +
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Residues in contact with GLN 154 (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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152F ASP* 3.1 6.8 + - - +
153F CYS* 1.3 71.5 - - - +
155F ASP* 1.3 67.5 + - - +
157F ALA* 2.8 16.7 + - - +
158F ASN* 2.9 33.8 + - - +
188F GLY 3.0 21.6 + - - -
190F GLY* 2.5 37.1 + - - +
192F THR* 4.7 0.2 - - - +
387F ILE* 3.2 9.4 - - - +
388F PRO* 3.6 32.1 - - + -
391F ARG* 3.2 33.1 + - + +
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Residues in contact with ASP 155 (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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150F GLY* 3.2 5.9 - - - -
151F LYS* 2.8 50.3 + - + +
152F ASP* 2.9 26.6 + - - +
154F GLN* 1.3 78.3 - - - +
156F ILE* 1.3 63.2 + - - +
158F ASN* 3.1 23.8 + - - +
159F LYS* 3.1 31.8 + - - +
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Residues in contact with ILE 156 (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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148F ILE* 3.4 26.7 - - + +
149F THR 3.8 3.6 - - - -
150F GLY* 3.7 19.7 - - - +
152F ASP 2.9 13.3 + - - +
153F CYS* 3.4 10.5 - - - +
154F GLN 3.1 0.2 - - - -
155F ASP* 1.3 74.9 - - - +
157F ALA* 1.3 64.8 + - - +
159F LYS* 3.1 23.9 + - - +
160F GLY 3.4 4.7 + - - -
161F ALA* 3.4 24.9 + - + +
167F TYR* 3.5 39.9 - - + -
168F PHE 4.2 0.2 - - - +
169F ILE* 3.8 19.5 - - + -
182F CYS* 4.3 5.6 - - - -
184F ILE* 5.1 0.9 - - + -
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Residues in contact with ALA 157 (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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153F CYS 2.7 18.1 + - - +
154F GLN* 2.8 27.1 + - - +
156F ILE* 1.3 72.1 - - - +
158F ASN* 1.3 62.2 + - - +
160F GLY* 3.5 8.0 + - - -
161F ALA* 3.8 19.5 + - - +
184F ILE* 4.7 9.6 - - + -
188F GLY* 3.6 15.8 - - - +
189F ASN 4.3 0.7 - - - -
190F GLY* 3.8 12.3 - - - +
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Residues in contact with ASN 158 (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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154F GLN* 2.9 39.9 + - - +
155F ASP* 3.3 21.2 + - - +
157F ALA* 1.3 76.1 - - - +
159F LYS* 1.3 65.3 + - + +
160F GLY* 2.8 8.0 + - - -
188F GLY 4.8 0.7 - - - +
391F ARG* 4.9 4.5 + - - -
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Residues in contact with LYS 159 (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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148F ILE* 4.0 20.0 - - + -
149F THR 3.5 21.6 + - - +
150F GLY* 4.3 0.2 - - - -
151F LYS* 3.9 11.7 - - - +
155F ASP* 3.2 38.9 + - - +
156F ILE* 3.1 14.1 + - - +
158F ASN* 1.3 77.6 - - + +
160F GLY* 1.3 56.8 + - - +
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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