Contacts of the helix formed by residues 168 - 185 (chain a) in PDB entry 5A0Q
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 LEU 168 (chain a).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20a PHE* 2.9 41.1 - - + -
22a ILE* 5.5 2.0 - - + +
166a LEU 3.0 3.4 + - - -
167a SER* 1.3 72.5 - - - +
169a ASP* 1.4 62.2 + - - +
171a ALA* 3.5 3.1 - - + +
172a MET* 2.9 41.4 + - + +
197a ILE* 5.6 0.4 - - + -
199a THR* 4.7 7.2 - - + -
204a ARG* 3.5 35.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 169 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167a SER* 3.6 0.6 - - - -
168a LEU* 1.4 80.7 - - - +
170a ARG* 1.3 62.3 + - - +
172a MET* 3.3 10.0 + - - +
173a ARG* 3.1 21.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 170 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202I TYR* 3.3 29.1 + - + +
152a GLN* 3.3 44.3 + - - +
164a VAL* 3.4 31.3 - - - +
167a SER* 3.6 20.3 + - - +
168a LEU 3.5 0.2 - - - -
169a ASP* 1.3 78.0 + - - +
171a ALA* 1.4 52.0 + - - +
173a ARG* 3.3 9.6 + - + +
174a LEU* 2.8 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 171 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202I TYR* 4.9 0.2 - - - -
15a ILE* 4.8 5.5 - - + +
20a PHE* 4.7 6.3 - - + -
22a ILE* 4.4 15.3 - - + -
166a LEU 4.7 3.8 - - - +
167a SER* 2.7 25.5 + - - +
168a LEU* 3.5 7.0 - - - +
169a ASP 3.2 0.2 - - - -
170a ARG* 1.4 73.4 - - - +
172a MET* 1.3 58.5 + - - +
174a LEU* 3.6 11.0 - - + +
175a VAL* 2.9 33.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 172 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22a ILE* 4.7 10.5 - - + -
168a LEU* 2.9 31.7 + - + +
169a ASP* 3.5 11.9 - - - +
171a ALA* 1.3 74.1 - - - +
173a ARG* 1.3 64.4 + - - +
175a VAL* 3.3 4.9 + - - +
176a LYS* 2.9 60.3 + - - +
195a ILE* 4.7 11.4 - - + -
197a ILE* 3.8 37.7 - - + -
204a ARG* 4.4 9.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 173 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202I TYR* 6.2 3.6 - - + -
169a ASP 3.1 9.9 + - - +
170a ARG* 3.6 11.0 - - + +
171a ALA 3.3 0.2 - - - -
172a MET* 1.3 80.2 - - - +
174a LEU* 1.3 55.9 + - - +
176a LYS* 3.2 18.6 + - - +
177a ASP* 2.9 41.6 + - + +
180a ILE* 4.4 20.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 174 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202I TYR* 2.4 70.2 + - + +
15a ILE* 5.8 1.8 - - + -
148a LEU* 4.7 7.4 - - + -
149a LEU* 5.2 5.5 - - + +
152a GLN* 3.6 12.1 - - + +
153a VAL* 3.2 35.9 - - + -
170a ARG* 2.8 12.2 + - - +
171a ALA* 3.6 11.9 - - + +
172a MET 3.2 0.2 - - - -
173a ARG* 1.3 73.8 - - - +
175a VAL* 1.4 62.0 + - + +
177a ASP* 4.7 3.5 - - + +
178a VAL* 3.3 30.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 175 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13a LEU* 4.0 17.7 - - + -
15a ILE* 2.9 40.6 - - + -
22a ILE* 4.0 22.9 - - + +
24a ALA* 4.0 23.6 - - + -
149a LEU* 5.5 1.1 - - + -
171a ALA 2.9 17.4 + - - +
172a MET* 3.7 5.2 - - - +
174a LEU* 1.4 73.8 - - - +
176a LYS* 1.3 68.0 + - - +
178a VAL* 3.3 19.9 - - - +
179a PHE* 3.9 8.3 + - - +
193a LEU* 4.7 1.4 - - + +
195a ILE* 4.6 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 176 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172a MET* 2.9 53.7 + - - +
173a ARG* 3.2 23.8 + - - +
175a VAL* 1.3 76.9 - - - +
177a ASP* 1.4 60.8 + - - +
179a PHE* 3.3 15.9 + - - +
180a ILE* 3.4 17.2 + - + +
193a LEU* 4.4 11.8 - - + +
195a ILE* 3.8 30.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 177 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202I TYR 5.8 1.7 + - - -
151J SER* 4.5 15.2 - - - +
173a ARG* 2.9 30.4 + - - +
174a LEU* 4.8 4.5 - - + +
175a VAL 3.5 0.2 - - - -
176a LYS* 1.4 73.8 - - - +
178a VAL* 1.3 65.0 + - + +
180a ILE* 3.1 26.6 + - + +
181a SER* 2.9 31.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 178 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151J SER* 5.8 0.7 - - - +
13a LEU* 3.9 21.5 - - + -
145a LEU* 3.3 29.3 - - + +
148a LEU* 3.3 36.1 - - + -
149a LEU* 4.1 12.1 - - + -
174a LEU* 3.3 21.1 - - + +
175a VAL 3.3 18.4 - - - +
177a ASP* 1.3 79.5 - - + +
179a PHE* 1.4 56.2 + - + +
181a SER* 3.4 8.5 + - - -
182a ALA 2.9 22.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 179 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11a THR* 3.7 24.7 - - + -
13a LEU* 3.6 31.9 - - + -
24a ALA* 4.1 18.2 - - + -
25a SER* 4.2 0.4 - - - -
26a ASP* 3.8 15.9 - - + -
145a LEU* 4.2 10.1 - - + -
175a VAL 3.9 11.7 - - - -
176a LYS 3.3 10.4 + - - +
177a ASP 3.2 0.8 - - - -
178a VAL* 1.4 78.1 - - + +
180a ILE* 1.3 61.1 + - - +
182a ALA* 3.9 3.8 - - + +
183a ALA* 3.1 28.9 + - - +
189a THR* 3.6 29.2 - - + -
190a GLY 6.1 0.2 - - - -
193a LEU* 3.3 38.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 180 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173a ARG* 4.4 15.5 - - - +
176a LYS* 3.5 14.4 - - + +
177a ASP* 3.3 30.1 - - - +
179a PHE* 1.3 75.8 - - - +
181a SER* 1.3 62.6 + - - +
183a ALA* 3.5 4.4 + - - +
184a GLU* 3.3 34.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 181 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147J GLY 4.9 5.6 - - - -
150J GLU* 2.7 47.7 - - - +
151J SER* 3.3 26.8 + - - -
145a LEU* 5.8 0.9 - - - -
148a LEU* 5.3 2.0 - - - -
177a ASP* 2.9 14.8 + - - -
178a VAL* 3.5 10.6 - - - -
180a ILE* 1.3 74.0 - - - +
182a ALA* 1.4 62.6 + - - +
184a GLU* 3.6 1.9 + - - -
185a ARG* 3.2 10.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 182 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150J GLU* 4.7 0.7 - - - -
141a ALA* 4.0 16.2 - - + -
144a MET* 5.0 7.0 - - + -
145a LEU* 4.0 19.5 - - + +
178a VAL 2.9 18.0 + - - +
179a PHE* 4.2 3.6 - - - +
180a ILE 3.5 0.2 - - - -
181a SER* 1.4 71.6 - - - +
183a ALA* 1.3 61.2 + - - +
184a GLU 3.4 0.2 - - - -
185a ARG* 4.5 4.3 - - - +
186a ASP* 2.9 33.5 + - - +
189a THR* 3.8 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 183 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19I ARG* 4.7 5.2 + - - -
28a ARG* 4.8 2.4 + - - -
179a PHE 3.1 20.2 + - - +
180a ILE* 3.8 4.5 - - - +
181a SER 3.3 0.2 - - - -
182a ALA* 1.3 77.4 - - - +
184a GLU* 1.4 72.7 + - - +
186a ASP 3.2 12.5 - - - +
187a VAL* 5.3 0.2 - - - -
189a THR* 3.4 24.6 - - + +
190a GLY* 3.9 15.6 - - - +
191a ASP 5.9 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 184 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19I ARG* 3.7 19.4 + - - +
26I VAL* 4.6 1.6 - - - +
29I LYS* 3.7 30.4 - - + +
150J GLU* 4.7 4.7 - - - +
180a ILE* 3.3 24.5 + - + +
181a SER* 4.0 2.7 - - - +
182a ALA 3.4 0.2 - - - -
183a ALA* 1.4 89.0 - - - +
185a ARG* 1.3 57.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 185 (chain a).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25I VAL* 4.1 1.6 - - + -
26I VAL* 3.1 59.6 + - - +
27I ALA 5.7 2.0 - - - -
29I LYS* 3.4 47.0 - - - +
134J ASP* 4.8 0.8 + - - -
135J PHE* 3.8 14.5 - - - -
146J TYR* 3.2 33.9 + - + +
150J GLU* 3.0 55.8 + - - +
144a MET* 3.6 27.1 - - + -
181a SER 3.2 6.4 + - - +
184a GLU* 1.3 78.9 - - - +
186a ASP* 1.3 59.5 + - - +
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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