Contacts of the helix formed by residues 173 - 186 (chain F) in PDB entry 5OF4
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 GLN 173 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130F GLU* 3.1 37.4 + - - +
131F THR* 4.3 11.1 + - - +
134F ALA* 4.2 10.4 - - - +
170F SER 4.3 0.8 + - - -
171F ALA* 3.2 2.9 - - - +
172F LEU* 1.3 80.3 - - + +
174F TYR* 1.3 65.3 + - - +
175F MET 3.4 2.0 - - - +
176F ASN* 3.0 37.7 + - + +
177F PHE* 3.0 26.5 + - + -
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Residues in contact with TYR 174 (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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171F ALA* 3.9 18.8 + - + +
172F LEU 3.8 2.8 + - - -
173F GLN* 1.3 77.0 - - - +
175F MET* 1.4 73.2 + - + +
177F PHE* 4.0 1.7 - - - +
178F MET* 3.0 75.9 + - + +
202F LEU* 4.2 21.8 - - + -
205F GLN* 4.7 2.8 + - - -
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Residues in contact with MET 175 (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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173F GLN* 3.4 0.6 - - - +
174F TYR* 1.4 93.5 - - + +
176F ASN* 1.3 59.4 + - - +
178F MET* 3.8 4.9 - - - +
179F ASN* 2.9 33.6 + - + +
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Residues in contact with ASN 176 (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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134F ALA* 5.2 7.2 - - + -
173F GLN* 3.0 47.8 + - + +
174F TYR 3.3 0.4 - - - -
175F MET* 1.3 76.6 - - - +
177F PHE* 1.3 69.0 + - + +
179F ASN* 3.4 11.7 + - - +
180F VAL* 2.9 32.5 + - + +
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Residues in contact with PHE 177 (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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130F GLU* 3.2 48.0 - - + -
133F LEU* 3.6 10.5 - - + -
134F ALA* 3.6 20.6 - - + -
137F LEU* 6.6 0.2 - - + -
165F LYS* 4.1 6.7 - - - -
169F ASP* 3.2 35.0 - - - -
170F SER 3.9 5.6 - - - -
173F GLN* 3.0 24.3 + - + +
174F TYR 3.5 3.0 + - - +
175F MET 3.4 0.2 - - - -
176F ASN* 1.3 79.6 - - - +
178F MET* 1.3 63.0 + - - +
180F VAL* 3.2 8.3 + - + +
181F ILE* 3.0 35.0 + - + +
202F LEU* 3.9 28.7 - - + -
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Residues in contact with MET 178 (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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174F TYR* 3.0 63.7 + - + +
175F MET* 3.8 5.8 - - - +
177F PHE* 1.3 77.6 - - + +
179F ASN* 1.3 57.0 + - - +
181F ILE* 3.0 16.5 + - + +
182F PHE* 2.9 58.7 + - + -
202F LEU* 4.1 8.5 - - + -
205F GLN* 3.4 35.4 - - + +
209F ILE* 4.8 11.4 - - + -
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Residues in contact with ASN 179 (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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175F MET* 2.9 20.3 + - + +
176F ASN* 3.6 13.1 + - - +
178F MET* 1.3 74.0 - - - +
180F VAL* 1.3 63.1 + - - +
182F PHE* 3.3 11.9 + - - +
183F ALA* 2.9 29.7 + - - +
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Residues in contact with VAL 180 (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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134F ALA* 4.8 5.4 - - + +
137F LEU* 3.8 37.0 - - + -
138F ALA* 4.6 20.4 - - + +
141F LEU* 3.7 20.4 - - + +
176F ASN* 2.9 24.4 + - + +
177F PHE* 3.7 7.6 - - + +
178F MET 3.2 0.2 - - - -
179F ASN* 1.3 80.3 - - + +
181F ILE* 1.3 63.5 + - + +
183F ALA* 3.3 5.1 + - - -
184F ALA* 2.9 26.9 + - + +
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Residues in contact with ILE 181 (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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137F LEU* 5.9 2.7 - - + -
177F PHE* 3.0 25.2 + - + +
178F MET* 3.0 21.6 + - + +
180F VAL* 1.3 77.9 - - + +
182F PHE* 1.3 61.1 + - + +
184F ALA* 3.2 7.8 + - - +
185F GLN* 3.0 25.3 + - - +
191F ILE* 5.1 4.0 - - + -
202F LEU* 4.2 7.9 - - + +
205F GLN 4.7 2.2 - - - -
206F ALA* 3.7 36.3 - - + +
209F ILE* 3.9 28.0 - - + -
210F THR* 3.6 22.8 - - + +
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Residues in contact with PHE 182 (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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178F MET* 2.9 55.3 + - + -
179F ASN* 3.6 11.0 - - - +
181F ILE* 1.3 77.6 - - + +
183F ALA* 1.3 65.4 + - - +
185F GLN* 3.1 33.4 - - - +
186F LYS* 3.0 41.8 + - + +
209F ILE* 4.4 20.9 - - + -
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Residues in contact with ALA 183 (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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141F LEU* 4.1 14.1 - - + -
179F ASN* 2.9 19.9 + - - +
180F VAL* 3.8 6.5 - - + +
182F PHE* 1.3 76.9 - - - +
184F ALA* 1.3 62.2 + - - +
186F LYS* 3.8 8.1 - - - +
187F GLN* 3.2 26.4 + - - +
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Residues in contact with ALA 184 (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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141F LEU* 4.1 23.5 - - + +
180F VAL* 2.9 17.5 + - + +
181F ILE 3.4 5.4 - - - +
182F PHE 3.1 0.2 - - - -
183F ALA* 1.3 76.5 - - - +
185F GLN* 1.3 62.7 + - - +
187F GLN* 3.6 3.6 + - - -
189F ILE* 3.3 33.8 + - + +
191F ILE* 3.6 33.0 - - + -
210F THR* 4.6 2.0 - - + -
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Residues in contact with GLN 185 (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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181F ILE 3.0 10.1 + - - +
182F PHE* 3.1 44.8 + - - +
184F ALA* 1.3 76.5 - - - +
186F LYS* 1.3 77.0 + - + +
187F GLN 3.1 2.0 - - - -
188F ASN* 3.3 20.1 + - - +
189F ILE 5.0 3.1 - - - +
209F ILE* 3.3 30.4 - - - +
210F THR* 4.8 14.8 - - + +
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Residues in contact with LYS 186 (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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97E ASP* 3.3 44.0 + - - +
98E GLN* 4.7 6.2 + - - +
182F PHE* 3.0 33.5 + - + +
183F ALA* 3.4 7.2 + - - +
184F ALA 3.3 0.2 - - - -
185F GLN* 1.3 97.4 - - + +
187F GLN* 1.3 57.6 + - - +
188F ASN* 3.4 6.1 + - - -
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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