Contacts of the helix formed by residues 166 - 187 (chain F) in PDB entry 2AJQ
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 GLU 166 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139F TYR* 3.8 11.9 - - + -
142F ASP* 4.9 16.2 - - - +
143F PHE* 3.9 23.6 - - - -
146F MET* 4.4 21.3 - - - +
164F ASN* 2.7 32.5 + - - +
165F GLU* 1.3 75.1 - - - +
167F MET* 1.3 62.4 + - - +
168F MET 3.3 0.7 - - - -
169F ASP* 3.2 22.5 + - + +
170F TYR* 3.4 17.5 + - + -
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Residues in contact with MET 167 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7F ALA* 4.1 5.8 - - + -
19F HIS* 3.5 44.4 - - + -
20F CYS* 3.9 9.0 - - - -
139F TYR* 3.6 15.9 - - + +
159F GLU 3.6 14.6 - - - +
160F TRP* 3.5 37.6 - - + -
162F ASN 3.6 17.9 - - - +
163F PHE* 4.0 11.2 - - + -
164F ASN* 2.7 22.4 + - - +
166F GLU* 1.3 77.8 - - - +
168F MET* 1.3 54.0 + - - +
169F ASP 3.0 4.7 - - - -
170F TYR* 3.6 1.9 + - - +
171F ASN* 3.0 28.6 + - - +
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Residues in contact with MET 168 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20F CYS* 3.3 19.0 - - + -
21F GLY 3.3 23.8 - - - +
22F VAL* 3.9 8.7 - - + -
33F SER* 3.6 26.5 - - - +
34F TYR 3.3 30.7 - - - +
35F ARG* 3.8 25.6 - - - +
163F PHE* 3.9 13.9 - - + -
164F ASN 3.5 2.0 + - - -
165F GLU* 3.7 20.6 + - - +
166F GLU 3.3 0.2 - - - -
167F MET* 1.3 76.4 - - - +
169F ASP* 1.3 60.2 + - - +
171F ASN* 3.9 12.3 - - - +
172F VAL* 3.2 20.6 - - - +
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Residues in contact with ASP 169 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136F LYS* 5.8 1.7 + - - -
165F GLU 3.7 10.0 + - - +
166F GLU* 3.2 20.1 - - + +
167F MET 3.0 0.2 - - - -
168F MET* 1.3 78.9 - - - +
170F TYR* 1.3 67.9 + - + +
171F ASN 3.1 3.4 - - - -
172F VAL* 3.2 16.5 + - - +
173F GLN* 3.2 10.9 + - - +
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Residues in contact with TYR 170 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136F LYS* 4.0 18.8 + - + -
137F GLY* 3.1 37.5 - - - -
138F GLU* 3.2 20.4 + - - -
139F TYR* 3.5 34.3 - + + -
142F ASP* 3.5 38.9 + - + +
166F GLU* 3.4 18.7 + - + +
167F MET 4.4 2.0 - - - +
169F ASP* 1.3 79.9 - - + +
171F ASN* 1.3 60.5 + - - +
172F VAL 3.2 0.2 - - - -
173F GLN* 3.5 24.8 - - + +
174F ASP* 2.9 34.4 + - - +
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Residues in contact with ASN 171 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5F ALA* 3.9 14.5 + - - +
6F ILE 3.7 22.9 + - - -
7F ALA* 4.7 3.0 - - + +
20F CYS* 3.2 24.5 - - - +
21F GLY* 3.3 24.4 + - - -
22F VAL* 3.7 9.6 - - + +
167F MET 3.0 19.7 + - - +
168F MET* 3.9 9.9 - - - +
169F ASP 3.1 0.2 - - - -
170F TYR* 1.3 79.3 - - - +
172F VAL* 1.3 62.6 + - - +
174F ASP* 3.4 6.6 + - - +
175F VAL* 3.2 21.3 + - - +
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Residues in contact with VAL 172 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22F VAL* 3.8 23.1 - - + -
31F TYR* 4.2 22.9 - - + -
33F SER* 4.3 11.0 - - - +
168F MET 3.2 18.8 - - - +
169F ASP* 3.2 9.1 + - - +
171F ASN* 1.3 75.7 - - - +
173F GLN* 1.3 67.4 + - - +
175F VAL* 3.0 14.0 + - - +
176F VAL* 3.0 19.6 + - + +
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Residues in contact with GLN 173 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134F GLU 4.6 3.1 - - - +
135F MET* 3.2 26.9 - - + +
136F LYS* 3.1 38.3 - - + +
137F GLY 3.0 26.8 + - - +
169F ASP 3.2 4.8 + - - +
170F TYR* 3.5 27.7 - - + +
172F VAL* 1.3 79.7 - - - +
174F ASP* 1.3 71.2 + - - +
176F VAL* 2.9 19.8 + - + +
177F VAL* 2.8 30.5 + - + +
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Residues in contact with ASP 174 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5F ALA* 4.8 9.0 - - + -
125F LEU* 3.4 29.8 - - + +
126F GLU* 5.6 1.9 + - - -
135F MET* 4.9 4.5 - - - +
160F TRP* 6.1 0.9 - - - -
170F TYR* 2.9 20.4 + - - +
171F ASN* 3.8 7.9 - - - +
172F VAL 3.3 0.2 - - - -
173F GLN* 1.3 91.2 - - - +
175F VAL* 1.3 51.9 + - - +
177F VAL* 3.8 5.1 - - - +
178F THR* 2.7 35.9 + - - -
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Residues in contact with VAL 175 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3F VAL* 4.0 16.1 - - + +
4F SER 4.2 0.4 - - - -
5F ALA* 3.4 23.8 - - + +
22F VAL* 3.6 30.7 - - + +
24F TYR* 4.2 18.2 - - + -
31F TYR* 4.0 19.1 - - + -
171F ASN 3.2 14.3 + - - +
172F VAL 3.0 8.9 + - - +
173F GLN 3.0 1.0 - - - -
174F ASP* 1.3 75.6 - - - +
176F VAL* 1.3 62.1 + - - +
178F THR* 2.9 9.3 + - - -
179F LYS* 2.7 28.1 + - + +
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Residues in contact with VAL 176 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31F TYR* 3.2 36.6 - - + +
134F GLU* 4.2 15.6 - - + +
172F VAL* 3.0 21.7 + - + +
173F GLN* 2.9 20.1 + - + +
175F VAL* 1.3 76.1 - - - +
177F VAL* 1.3 69.1 + - + +
179F LYS* 3.3 7.7 + - - +
180F ALA* 2.8 30.0 + - - +
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Residues in contact with VAL 177 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125F LEU* 3.4 34.1 - - + +
128F TRP* 4.7 4.7 - - + -
129F GLY* 4.0 13.5 - - - +
132F LEU* 4.6 3.5 - - + +
134F GLU* 3.8 20.2 - - + +
135F MET* 3.4 28.7 - - + -
173F GLN* 2.8 20.4 + - + +
174F ASP* 3.9 7.6 - - - +
176F VAL* 1.3 81.9 - - + +
178F THR* 1.3 59.9 + - - +
180F ALA* 3.8 5.4 - - - +
181F LEU* 2.9 27.2 + - - +
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Residues in contact with THR 178 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3F VAL* 3.4 21.5 - - + -
4F SER 4.5 8.3 + - - +
5F ALA* 5.0 2.1 - - - +
57F VAL* 4.1 16.2 - - + -
59F HIS* 3.9 19.1 + - - +
91F THR* 4.1 11.0 - - + +
125F LEU* 3.6 17.8 - - - +
174F ASP 2.7 19.5 + - - -
175F VAL* 2.9 13.1 + - - -
177F VAL* 1.3 78.3 - - - +
179F LYS* 1.3 61.1 + - - +
181F LEU* 3.3 5.1 + - - +
182F LEU* 3.0 22.9 + - - +
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Residues in contact with LYS 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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3F VAL* 4.0 15.2 - - + +
24F TYR* 3.3 51.8 + - + -
26F TYR* 3.2 19.5 - - + +
31F TYR* 4.5 10.8 - - - +
175F VAL* 2.7 16.9 + - + +
176F VAL* 3.6 9.9 - - - +
178F THR* 1.3 75.1 - - - +
180F ALA* 1.3 57.4 + - - +
182F LEU* 3.5 5.5 + - - +
183F GLU* 2.9 57.4 + - - +
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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
----------------------------------------------------------
132F LEU* 3.6 15.8 - - + +
134F GLU* 4.1 24.2 - - + +
176F VAL 2.8 16.9 + - - +
177F VAL 3.8 3.8 - - - +
178F THR 3.2 0.2 - - - -
179F LYS* 1.3 74.9 - - - +
181F LEU* 1.3 64.2 + - - +
183F GLU* 4.1 9.4 - - - +
184F LYS* 3.2 23.9 + - - +
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Residues in contact with LEU 181 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59F HIS* 3.7 29.6 - - + +
91F THR* 3.9 13.2 - - - +
95F SER* 4.8 0.9 - - - -
125F LEU* 4.6 5.8 - - + -
128F TRP* 3.8 55.6 - - + +
132F LEU* 3.8 7.6 - - + +
177F VAL 2.9 17.7 + - - +
178F THR* 3.7 6.1 - - - +
180F ALA* 1.3 75.8 - - - +
182F LEU* 1.3 59.2 + - - +
184F LYS* 3.4 4.2 + - + +
185F LEU* 2.9 58.7 + - + +
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Residues in contact with LEU 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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1F MET* 3.8 21.1 - - + -
3F VAL* 4.3 10.8 - - + -
26F TYR* 4.4 8.7 - - - +
57F VAL* 3.7 31.4 - - + -
89F ILE* 4.7 7.9 - - + -
91F THR* 4.1 19.2 - - + +
94F LEU* 4.4 14.4 - - + -
178F THR 3.0 16.1 + - - +
179F LYS 3.6 4.7 - - - +
180F ALA 3.3 0.2 - - - -
181F LEU* 1.3 75.2 - - - +
183F GLU* 1.3 54.6 + - - +
185F LEU* 3.0 5.5 + - - +
186F LEU* 2.7 65.9 + - + +
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Residues in contact with GLU 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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26F TYR* 2.8 32.7 + - - +
179F LYS* 2.9 44.5 + - - +
180F ALA* 4.1 8.0 - - - +
182F LEU* 1.3 75.5 - - + +
184F LYS* 1.3 62.4 + - - +
186F LEU* 3.8 7.7 - - - +
187F SER* 3.1 26.3 + - - -
199F THR* 4.5 12.5 - - + +
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Residues in contact with LYS 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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99F HIS* 3.5 34.4 + - - +
128F TRP* 4.9 6.8 - - + -
132F LEU* 3.5 30.1 - - + -
180F ALA 3.2 20.8 + - - +
181F LEU* 3.5 7.9 - - + +
182F LEU 3.2 0.2 - - - -
183F GLU* 1.3 76.2 - - - +
185F LEU* 1.3 60.5 + - + +
187F SER* 3.2 19.8 + - - +
188F ASP* 4.4 3.8 + - - +
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Residues in contact with LEU 185 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91F THR* 3.9 17.9 - - - +
94F LEU* 3.7 31.0 - - + -
95F SER* 4.0 8.3 - - - +
98F ILE* 3.7 23.8 - - + +
99F HIS* 3.7 33.4 - - + +
181F LEU* 2.9 47.2 + - + +
182F LEU* 3.0 7.5 + - - +
184F LYS* 1.3 77.8 - - + +
186F LEU* 1.3 61.1 + - - +
187F SER 3.1 5.2 + - - -
188F ASP* 3.3 17.1 + - - +
192F PHE* 3.5 14.4 - - - -
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Residues in contact with LEU 186 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1F MET* 4.8 2.0 - - + -
94F LEU* 5.0 1.6 - - + -
182F LEU* 2.7 53.8 + - + +
183F GLU* 3.3 6.7 + - - +
185F LEU* 1.3 73.4 - - - +
187F SER* 1.3 58.3 + - - +
188F ASP 3.2 2.1 + - - -
189F LYS* 5.7 0.7 + - - +
192F PHE* 3.6 56.1 - - + +
198F PHE* 4.1 25.0 - - + +
199F THR* 3.6 32.5 - - + +
206F PHE* 4.3 6.7 - - + -
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Residues in contact with SER 187 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183F GLU 3.1 13.5 + - - -
184F LYS* 3.2 20.0 + - - +
185F LEU 3.1 0.4 - - - -
186F LEU* 1.3 77.8 - - - +
188F ASP* 1.3 58.4 + - - +
189F LYS* 3.1 30.9 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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