Contacts of the helix formed by residues 168 - 180 (chain F) in PDB entry 5FLX
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 THR 168 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15351 U 3.5 19.1 - - - +
15981 G 4.9 9.6 - - - +
162F ALA* 3.7 9.4 - - - +
166F ILE 4.1 7.4 - - - +
167F LYS* 1.3 78.8 - - - +
169F ILE* 1.3 65.2 + - - +
170F ALA 4.3 0.4 - - - -
171F GLU* 3.6 19.2 + - - +
172F CYS* 3.7 14.2 + - - -
69Z THR* 5.6 1.0 - - - +
71Z ALA* 4.6 10.2 - - + +
105Z ALA 5.7 5.2 - - - +
106Z GLN* 3.5 31.3 + - - +
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Residues in contact with ILE 169 (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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15351 U 3.2 77.0 + - + +
76F MET* 4.9 13.0 - - + -
92F ILE* 3.6 33.9 - - + -
158F ALA* 5.0 12.4 - - + +
162F ALA* 4.6 13.7 - - + +
168F THR* 1.3 76.7 - - - +
170F ALA* 1.3 60.0 + - - +
171F GLU 3.2 0.2 - - - -
172F CYS* 3.5 2.8 + - - +
173F LEU* 2.9 38.0 + - + +
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Residues in contact with ALA 170 (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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92F ILE* 4.5 15.6 - - + +
95F HIS* 4.5 14.4 - - + -
96F ALA* 4.7 5.0 - - - +
99F ILE* 3.6 17.0 - - + +
168F THR* 3.5 1.6 + - - -
169F ILE* 1.3 79.3 - - - +
171F GLU* 1.3 57.9 - - - +
173F LEU* 4.2 5.8 - - - +
174F ALA* 2.9 33.1 + - - +
106Z GLN* 3.4 23.6 - - - +
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Residues in contact with GLU 171 (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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99F ILE* 4.8 6.2 - - - +
167F LYS* 3.3 41.8 - - + +
168F THR* 3.6 17.9 + - - +
169F ILE 3.2 0.8 - - - -
170F ALA* 1.3 78.3 - - - +
172F CYS* 1.3 59.1 + - - +
174F ALA* 4.3 1.6 - - - +
175F ASP* 2.9 33.9 + - + +
69Z THR* 5.0 8.3 - - + -
71Z ALA* 3.1 25.3 - - - +
72Z VAL* 3.2 33.5 + - + +
75Z GLU* 4.9 2.4 - - - +
106Z GLN* 4.8 0.2 - - - +
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Residues in contact with CYS 172 (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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158F ALA* 4.2 12.9 - - - +
161F ALA* 3.6 32.8 - - + +
162F ALA* 3.6 28.0 - - + -
167F LYS* 4.1 21.8 - - - -
168F THR 3.7 7.1 + - - +
169F ILE* 3.5 3.6 + - - +
171F GLU* 1.3 77.6 - - - +
173F LEU* 1.3 60.1 + - - +
175F ASP* 3.8 8.8 - - - +
176F GLU* 2.9 30.5 + - - +
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Residues in contact with LEU 173 (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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72F LEU* 5.1 16.4 - - + -
76F MET* 3.6 30.5 - - + -
89F THR* 6.1 0.2 - - - +
92F ILE* 3.9 22.9 - - + -
93F VAL* 5.4 3.4 - - + -
96F ALA* 3.6 28.0 - - + -
100F ILE* 5.0 0.2 - - + -
158F ALA* 4.5 13.6 - - + +
169F ILE* 2.9 19.6 + - + +
170F ALA* 3.9 4.9 - - - +
172F CYS* 1.3 75.6 - - - +
174F ALA* 1.3 61.3 + - - +
176F GLU* 3.2 3.1 + - - +
177F LEU* 2.9 57.9 + - + +
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Residues in contact with ALA 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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96F ALA* 4.7 2.5 - - - +
99F ILE* 3.8 23.8 - - + -
100F ILE* 3.8 32.1 - - + -
170F ALA 2.9 17.4 + - - +
171F GLU* 4.3 1.6 - - - +
173F LEU* 1.3 78.2 - - + +
175F ASP* 1.3 57.9 + - - +
177F LEU* 4.5 0.4 - - - +
178F ILE* 2.9 41.2 + - + +
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Residues in contact with ASP 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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171F GLU* 2.9 23.7 + - + +
172F CYS* 3.9 8.7 - - - +
174F ALA* 1.3 77.3 - - - +
176F GLU* 1.3 60.6 + - - +
178F ILE* 4.8 2.5 - - - -
179F ASN* 2.7 65.3 + - - +
186F ASN* 5.2 3.1 + - - -
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Residues in contact with GLU 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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153F LEU 4.7 2.4 - - - +
154F LEU* 4.3 28.9 - - + +
157F GLY* 4.9 7.1 - - - +
158F ALA* 4.8 8.1 - - + +
161F ALA* 5.7 3.1 - - + +
172F CYS 2.9 21.0 + - - +
173F LEU* 3.2 4.9 + - - +
175F ASP* 1.3 78.2 - - - +
177F LEU* 1.3 64.5 + - + +
179F ASN* 4.9 1.6 - - - -
180F ALA* 3.3 26.9 + - - +
187F SER* 3.7 9.9 - - - -
188F TYR* 3.0 39.6 + - - +
189F ALA* 3.1 20.3 + - - +
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Residues in contact with LEU 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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72F LEU* 5.3 9.4 - - + -
97F PHE* 6.3 1.8 - - + -
100F ILE* 3.9 21.5 - - + -
111F VAL* 4.0 14.2 - - + +
112F LEU* 3.8 33.0 - - + -
115F ALA* 4.0 18.3 - - + +
154F LEU* 3.9 30.7 - - + -
173F LEU* 2.9 42.2 + - + +
174F ALA* 4.1 3.6 - - - +
176F GLU* 1.3 78.1 - - + +
178F ILE* 1.3 63.0 + - + +
180F ALA 3.7 0.2 + - - -
181F ALA* 3.7 12.6 + - - +
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Residues in contact with ILE 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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99F ILE* 5.2 2.2 - - + +
100F ILE* 4.4 29.2 - - + -
103F LEU* 3.7 54.3 - - + -
111F VAL* 5.2 9.9 - - + -
174F ALA* 2.9 27.4 + - + +
175F ASP* 4.3 3.1 - - - +
177F LEU* 1.3 76.6 - - + +
179F ASN* 1.3 73.0 + - - +
181F ALA* 3.1 21.2 + - + +
182F LYS* 3.7 13.0 - - - -
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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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175F ASP* 2.7 52.8 + - - +
176F GLU* 5.2 0.2 - - - +
178F ILE* 1.3 84.2 - - - +
180F ALA* 1.3 58.6 + - - +
181F ALA 3.4 0.9 + - - -
182F LYS* 4.1 8.6 + - - +
183F GLY 3.7 2.4 + - - -
184F SER* 3.0 45.1 + - - +
186F ASN* 4.4 16.6 - - - +
187F SER* 3.8 20.0 + - - +
99z A 4.0 12.2 + - - -
100z G 5.8 1.0 - - - +
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Residues in contact with ALA 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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114F ASN 4.2 1.4 - - - +
115F ALA* 4.2 16.5 - - + +
118F ASN* 3.2 20.3 - - - +
119F SER* 5.5 0.2 - - - +
154F LEU* 5.3 2.7 - - + -
176F GLU* 3.3 20.3 + - - +
177F LEU 3.7 4.5 + - - +
178F ILE 3.2 1.2 - - - -
179F ASN* 1.3 76.0 - - - +
181F ALA* 1.3 65.2 + - - +
183F GLY 4.0 4.1 + - - -
187F SER* 3.7 15.0 - - - +
189F ALA* 4.6 14.1 - - + -
190F ILE* 4.2 13.1 - - + +
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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