Contacts of the helix formed by residues 178 - 188 (chain F) in PDB entry 4GTU
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 PRO 178 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175F ASP 4.2 2.8 - - - +
176F ALA 3.5 8.9 - - - +
177F PHE* 1.3 85.4 - - - +
179F ASN* 1.3 70.2 + - + +
181F LYS* 3.0 20.3 + - + +
182F ASP* 2.8 28.0 + - - +
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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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138F SER* 2.5 54.0 + - - +
141F LEU* 3.4 19.3 - - - +
142F GLY* 3.0 29.4 - - - +
178F PRO* 1.3 85.2 - - + +
180F LEU* 1.3 60.7 + - - +
182F ASP* 3.4 6.8 + - - +
183F PHE 3.2 14.0 + - - -
186F ARG* 5.1 2.3 + - - -
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Residues in contact with LEU 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 MET* 3.6 44.6 - - + +
137F PHE* 4.0 15.0 - - + +
138F SER* 3.6 27.4 - - - +
141F LEU* 3.5 24.7 - - + -
147F PHE* 4.4 11.9 - - + -
163F LEU* 4.4 13.2 - - + +
174F LEU* 3.5 19.1 - - + -
177F PHE* 3.0 9.4 + - + +
179F ASN* 1.3 73.9 - - - +
181F LYS* 1.3 62.0 + - - +
183F PHE* 2.9 24.4 + - - +
184F ILE* 3.3 10.6 + - - +
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Residues in contact with LYS 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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174F LEU* 3.4 26.2 - - + +
175F ASP* 3.0 47.7 + - + +
177F PHE 3.2 3.0 + - - +
178F PRO* 3.0 19.3 + - + +
180F LEU* 1.3 78.4 - - - +
182F ASP* 1.3 60.6 + - - +
184F ILE* 3.2 24.4 - - + +
185F SER* 3.4 11.3 + - - -
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Residues in contact with ASP 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 PRO 2.8 15.4 + - - +
179F ASN* 3.7 6.7 - - - +
180F LEU 3.1 0.4 - - - -
181F LYS* 1.3 75.1 - - - +
183F PHE* 1.3 65.7 + - - +
185F SER* 3.3 7.3 + - - -
186F ARG* 3.0 38.8 + - - +
181G LYS* 3.6 28.4 + - - -
185G SER* 5.3 2.1 + - - -
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Residues in contact with PHE 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* 3.6 27.4 - - + -
145F PRO 3.3 19.7 - - - -
146F TRP* 3.5 21.8 - + - -
147F PHE* 3.9 15.7 - + - -
156F ASP* 3.4 49.4 - - + -
159F ALA* 4.2 4.9 - - + -
160F TYR* 4.3 9.6 - - + -
163F LEU* 3.7 24.5 - - + -
179F ASN 3.2 4.8 + - - -
180F LEU* 2.9 12.7 + - - +
182F ASP* 1.3 75.5 - - - +
184F ILE* 1.3 62.9 + - + +
186F ARG* 2.8 34.8 + - - +
187F PHE* 3.2 11.3 + + - +
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Residues in contact with ILE 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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160F TYR* 3.3 34.9 - - + -
163F LEU* 3.8 28.0 - - + -
164F ASP 4.9 1.1 - - - +
167F ARG* 4.3 33.0 - - + +
174F LEU* 4.3 21.3 - - + -
180F LEU 3.5 8.7 - - - +
181F LYS* 3.2 26.9 - - + +
183F PHE* 1.3 80.0 - - + +
185F SER* 1.3 55.8 + - - +
187F PHE* 2.9 21.2 + - - +
188F GLU* 3.2 18.3 + - - +
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Residues in contact with SER 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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167F ARG* 6.3 0.2 - - - +
181F LYS 3.4 13.0 + - - -
182F ASP* 3.3 14.1 + - - -
183F PHE 3.3 0.4 - - - -
184F ILE* 1.3 78.1 - - - +
186F ARG* 1.3 60.3 + - - +
187F PHE 3.3 0.9 + - - -
188F GLU* 3.6 16.7 + - - +
189F GLY 3.6 2.6 + - - -
181G LYS* 4.7 9.3 + - - -
182G ASP* 3.4 28.5 + - - +
185G SER* 3.0 38.9 + - - -
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Residues in contact with ARG 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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141F LEU* 4.8 4.6 - - - +
144F ARG 4.6 1.0 + - - -
145F PRO* 3.0 50.8 + - - +
146F TRP* 3.4 27.5 - - + -
179F ASN* 5.1 2.2 + - - -
182F ASP* 3.0 27.0 + - - +
183F PHE* 2.8 33.1 + - - +
185F SER* 1.3 78.6 - - - +
187F PHE* 1.3 57.7 + - - +
189F GLY* 4.2 3.5 + - - -
190F LEU* 3.5 18.0 + - + +
185G SER* 4.1 11.4 + - - +
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Residues in contact with PHE 187 (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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18F LEU* 4.9 4.3 - - + -
146F TRP* 4.2 11.9 - + - -
152F ILE* 4.8 7.0 - - + -
156F ASP* 4.0 24.5 - - + -
157F PHE* 3.2 41.7 - + - -
160F TYR* 3.2 42.0 - + + -
183F PHE* 3.2 8.9 + + + +
184F ILE* 2.9 15.5 + - - +
186F ARG* 1.3 75.6 - - - +
188F GLU* 1.3 57.6 + - - +
189F GLY 3.0 4.5 - - - -
190F LEU* 2.9 45.6 + - + +
193F ILE* 3.7 34.1 - - + +
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Residues in contact with GLU 188 (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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160F TYR* 3.6 21.8 - - + +
167F ARG* 3.2 33.8 + - - -
184F ILE 3.2 14.0 + - - +
185F SER* 3.6 8.5 + - - +
187F PHE* 1.3 74.8 - - - +
189F GLY* 1.3 57.7 + - - +
190F LEU 3.4 1.3 - - - -
193F ILE* 4.6 3.1 - - - -
194F SER* 4.0 20.4 + - - -
197F MET* 3.7 27.8 - - + +
182G ASP* 4.5 17.4 - - - +
186G ARG* 5.6 4.0 + - - -
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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