Contacts of the helix formed by residues 159 - 180 (chain F) in PDB entry 3A2C
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 159 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157F ALA* 4.3 9.2 - - + +
158F PHE* 1.3 77.6 - - - +
160F GLU* 1.3 65.1 + - - +
161F ARG* 3.4 8.8 + - - +
162F GLU* 2.9 46.2 + - - +
163F ALA 3.0 9.0 + - - -
333F GLN* 3.7 36.2 + - + +
334F THR 3.4 11.4 - - - +
335F PRO* 4.8 3.4 - - + -
336F LEU* 3.3 8.4 - - - +
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Residues in contact with GLU 160 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159F THR* 1.3 70.9 - - - +
161F ARG* 1.3 56.8 + - - +
163F ALA* 3.0 7.3 - - - +
164F SER 2.9 23.2 + - - -
257F LEU* 3.9 18.4 - - + -
293F GLU 4.4 0.7 - - - +
294F VAL* 4.3 15.9 - - - +
295F SER* 3.3 23.3 + - - -
298F VAL* 3.4 5.4 - - - +
324F TRP* 2.9 30.8 + - + +
331F VAL* 3.9 1.1 - - + -
332F PRO* 3.8 14.0 + - - +
334F THR* 2.8 45.2 + - + +
336F LEU* 3.1 16.3 - - + +
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Residues in contact with ARG 161 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159F THR* 3.0 8.8 + - - +
160F GLU* 1.3 76.5 - - - +
162F GLU* 1.3 60.7 + - + +
164F SER* 3.3 3.1 + - - -
165F GLU* 3.0 44.0 + - - +
328F SER 3.2 19.3 - - - +
329F THR* 3.3 24.9 + - - +
330F LYS* 4.4 1.6 - - - +
331F VAL* 3.0 39.0 + - + +
332F PRO* 3.4 8.9 + - - +
333F GLN* 2.9 45.9 + - + +
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Residues in contact with GLU 162 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153F ARG* 3.0 40.3 + - - -
157F ALA 3.5 4.9 - - - +
158F PHE* 3.4 15.8 - - + -
159F THR* 2.9 35.4 + - - +
161F ARG* 1.3 74.7 - - + +
163F ALA* 1.3 67.0 + - - +
165F GLU* 3.7 16.5 - - - +
166F ILE* 3.0 31.9 + - + +
333F GLN* 5.8 2.2 - - - +
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Residues in contact with ALA 163 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158F PHE* 3.7 19.8 - - + -
159F THR 3.0 8.0 + - - +
160F GLU* 3.0 16.6 - - - +
162F GLU* 1.3 78.6 - - - +
164F SER* 1.3 55.4 + - - +
166F ILE* 3.2 4.1 + - - +
167F MET* 2.9 31.1 + - + +
256F LEU* 4.2 10.2 - - + +
257F LEU* 3.7 28.9 - - + -
324F TRP* 3.8 6.3 - - + -
336F LEU* 4.6 0.9 - - + -
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Residues in contact with SER 164 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160F GLU 2.9 8.7 + - - -
161F ARG 3.3 7.4 + - - -
163F ALA* 1.3 73.8 - - - +
165F GLU* 1.3 59.8 - - - +
167F MET* 3.3 1.6 + - - +
168F LYS* 2.8 25.1 + - - +
324F TRP* 2.5 59.0 + - - -
325F ILE* 4.3 1.7 - - - +
328F SER* 2.8 25.5 + - - -
331F VAL* 4.0 9.9 - - - -
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Residues in contact with GLU 165 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161F ARG* 3.0 42.5 + - - +
162F GLU* 3.7 17.5 - - - +
163F ALA 3.3 0.2 - - - -
164F SER* 1.3 74.8 - - - +
166F ILE* 1.3 64.5 + - + +
168F LYS* 3.0 15.8 + - - +
169F SER* 3.2 13.7 + - - -
328F SER* 3.7 20.2 - - - -
329F THR* 5.3 7.9 - - + +
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Residues in contact with ILE 166 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146F LEU* 3.8 25.6 - - + -
150F ILE* 4.2 3.4 - - + -
158F PHE* 3.5 35.0 - - + -
162F GLU* 3.0 13.9 + - + +
163F ALA 3.5 3.4 - - - +
165F GLU* 1.3 77.4 - - + +
167F MET* 1.3 59.8 + - - +
169F SER* 2.9 21.1 + - - -
170F ILE* 3.2 22.9 + - + +
194F TYR* 3.7 21.5 - - - +
203F LEU* 4.2 7.4 - - + -
256F LEU* 3.7 18.6 - - + -
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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
----------------------------------------------------------
163F ALA* 2.9 20.0 + - + +
164F SER 3.8 1.6 - - - +
166F ILE* 1.3 73.2 - - - +
168F LYS* 1.3 66.7 + - - +
170F ILE* 4.1 11.2 - - + +
171F GLY 3.1 16.8 + - - -
249F LEU* 3.4 46.0 - - + +
252F ILE* 3.8 9.4 - - + -
253F MET* 3.7 34.3 - - + -
256F LEU* 3.7 22.9 - - + -
319F PHE* 3.7 21.6 - - + -
324F TRP* 4.2 6.3 - - + -
325F ILE* 3.8 18.4 - - + -
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Residues in contact with LYS 168 (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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164F SER 2.8 14.1 + - - +
165F GLU* 3.0 10.9 + - - +
167F MET* 1.3 78.5 - - - +
169F SER* 1.3 57.5 + - - +
171F GLY 3.7 0.2 + - - -
172F GLU* 3.2 45.9 + - - +
320F MET* 3.8 12.5 + - + +
325F ILE* 3.3 34.1 + - + +
326F MET* 3.7 26.2 + - - +
328F SER* 3.7 13.2 - - - +
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Residues in contact with SER 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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116F HIS* 3.4 39.4 - - - +
165F GLU 3.2 9.9 + - - -
166F ILE* 2.9 18.2 + - - -
167F MET 3.2 0.2 - - - -
168F LYS* 1.3 77.9 - - - +
170F ILE* 1.3 65.2 + - - +
172F GLU* 3.6 8.7 - - - -
173F ALA* 3.3 13.5 + - - +
203F LEU* 4.8 15.1 - - - +
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Residues in contact with ILE 170 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146F LEU* 4.4 0.9 - - + -
166F ILE* 3.2 33.9 + - + +
167F MET* 4.1 12.6 - - + +
169F SER* 1.3 76.1 + - - +
171F GLY* 1.3 64.0 + - - +
173F ALA* 3.0 19.1 + - + +
174F ILE* 3.0 16.0 + - + +
187F VAL* 4.6 8.7 - - + -
192F LEU* 3.9 36.3 - - + -
203F LEU* 4.1 16.4 - - + -
205F LEU* 6.1 1.1 - - + -
249F LEU* 3.8 25.4 - - + -
252F ILE* 4.0 19.3 - - + -
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Residues in contact with GLY 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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167F MET 3.1 15.4 + - - -
170F ILE* 1.3 76.1 - - - +
172F GLU* 1.3 55.6 + - - +
174F ILE* 4.2 2.9 - - - -
175F GLN* 2.7 36.6 + - - +
249F LEU* 4.4 4.2 - - - +
316F ILE* 3.5 17.2 - - - +
319F PHE* 4.1 6.3 - - - -
320F MET* 3.6 15.9 - - - -
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Residues in contact with GLU 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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114F CYS* 4.7 2.1 - - - -
116F HIS* 3.2 28.9 + - + -
168F LYS* 3.2 45.2 + - - +
169F SER* 3.6 11.4 - - - +
170F ILE 3.2 0.2 - - - -
171F GLY* 1.3 76.1 - - - +
173F ALA* 1.3 63.2 + - - +
175F GLN* 3.2 13.2 + - - +
176F TYR* 3.0 22.9 + - - +
320F MET* 3.8 14.9 - - + +
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Residues in contact with ALA 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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114F CYS* 4.2 12.3 - - - -
116F HIS* 3.8 25.7 - - + +
117F ILE* 4.1 15.6 - - + +
169F SER 3.3 4.0 + - - +
170F ILE* 3.0 12.5 + - + +
172F GLU* 1.3 79.2 - - - +
174F ILE* 1.3 63.0 + - - +
176F TYR* 3.3 3.8 + - - +
177F LEU* 3.1 26.5 + - - +
205F LEU* 4.7 13.9 - - + -
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Residues in contact with ILE 174 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170F ILE* 3.0 16.0 + - + +
171F GLY 3.7 5.4 - - - +
173F ALA* 1.3 74.7 - - - +
175F GLN* 1.3 61.6 + - - +
177F LEU* 3.2 9.4 + - + +
178F HIS* 2.8 61.4 + - + +
187F VAL* 3.8 30.5 - - + -
205F LEU* 4.0 16.2 - - + -
245F ASP* 4.0 13.9 - - + +
246F MET* 4.7 2.9 - - - -
249F LEU* 3.9 21.3 - - + -
316F ILE* 3.9 14.4 - - + -
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Residues in contact with GLN 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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281D MET* 3.6 17.2 - - + +
283D GLN* 5.5 5.4 + - - +
171F GLY 2.7 16.6 + - - +
172F GLU* 3.5 13.6 + - - +
174F ILE* 1.3 79.0 - - - +
176F TYR* 1.3 55.5 + - - +
179F SER* 2.9 32.0 + - - -
316F ILE* 3.5 21.0 - - + +
317F THR* 4.8 9.5 + - - +
320F MET* 3.8 33.7 - - + +
321F ASN* 5.6 1.2 + - - -
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Residues in contact with TYR 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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110F ARG 3.9 11.6 + - - -
111F ALA* 4.0 11.9 - - - -
113F GLN* 2.5 36.4 + - + -
114F CYS* 3.5 33.2 - - + -
117F ILE* 4.5 2.9 - - + -
172F GLU 3.0 13.1 + - - +
173F ALA 3.6 7.6 - - - +
175F GLN* 1.3 75.0 - - - +
177F LEU* 1.3 67.0 + - - +
179F SER* 2.6 28.0 + - - -
180F ILE* 3.3 43.1 - - + +
130G GLY* 4.9 1.9 + - - -
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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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111F ALA* 3.3 35.0 - - + -
117F ILE* 3.9 8.5 - - + -
173F ALA 3.1 14.8 + - - +
174F ILE* 3.2 12.3 + - + +
176F TYR* 1.3 78.1 - - + +
178F HIS* 1.3 63.0 + - + +
180F ILE* 3.2 7.7 + - + +
181F ASN 3.1 4.3 + - - -
182F ILE* 2.9 50.3 + - + +
184F HIS* 4.0 20.0 - - + +
205F LEU* 4.0 26.0 - - + -
208F PHE* 3.8 13.2 - - + -
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Residues in contact with HIS 178 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280D ARG* 5.5 1.6 - - - -
281D MET* 4.0 9.6 - - + +
174F ILE* 2.8 39.7 + - + +
175F GLN 4.2 0.2 - - - +
177F LEU* 1.3 69.5 - - + +
179F SER* 1.3 64.6 + - - +
180F ILE 3.0 2.0 - - - -
181F ASN* 3.0 12.5 + - - -
182F ILE 3.3 16.4 - - - -
183F ALA* 4.4 0.2 - - - -
242F LYS* 3.1 72.7 + - + +
245F ASP* 2.9 25.4 + - + +
246F MET* 4.3 8.3 - - + -
316F ILE* 3.8 27.7 + - + +
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Residues in contact with SER 179 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277D THR* 3.8 27.7 + - - +
280D ARG* 5.9 2.0 - - - -
281D MET* 3.7 21.0 - - - +
283D GLN* 5.4 2.5 - - - -
175F GLN* 2.9 17.5 + - - -
176F TYR* 2.6 32.4 + - - -
178F HIS* 1.3 76.4 - - - +
180F ILE* 1.3 63.8 + - - +
181F ASN* 3.5 2.2 + - - +
129G ALA 5.5 0.3 - - - +
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Residues in contact with ILE 180 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110F ARG* 3.9 31.3 + - + +
111F ALA* 4.7 1.6 - - - -
176F TYR* 3.3 48.9 - - + +
177F LEU* 3.3 9.4 - - - +
178F HIS 3.0 0.2 - - - -
179F SER* 1.3 87.6 + - - +
181F ASN* 1.3 71.8 + - - +
182F ILE* 3.5 20.8 + - + +
213F GLU* 4.7 0.2 - - - +
129G ALA 4.1 7.6 - - - +
130G GLY* 3.7 32.3 - - - +
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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