Contacts of the helix formed by residues 159 - 176 (chain J) 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 PRO 159 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16J LYS* 5.7 2.2 - - - -
18J CYS* 3.7 9.1 - - - -
158J ASP* 1.3 88.2 - - + +
160J ASP* 1.3 58.0 + - - +
162J LEU* 3.8 10.3 - - + -
163J PHE* 2.9 34.1 + - - +
188J ILE* 3.5 17.6 - - + +
190J GLU* 3.5 34.3 - - - +
193J LYS* 3.5 27.8 - - - +
195J THR* 5.4 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 160 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206I LYS* 3.8 13.7 - - + +
207I GLY 5.1 0.2 + - - -
158J ASP* 3.5 22.9 - - - +
159J PRO* 1.3 87.8 - - - +
161J HIS* 1.3 58.0 + - - +
163J PHE* 4.2 4.4 - - - +
164J GLU* 3.1 24.6 + - - +
193J LYS* 4.2 11.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 161 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203I ARG* 4.5 16.1 + - + -
204I CYS 3.7 23.4 + - - -
205I GLU* 5.1 1.3 - - - -
206I LYS* 4.1 22.7 - - + +
154J GLU* 2.2 40.2 + - - +
156J ASN 4.3 0.2 - - - -
157J MET* 2.2 48.8 - - + +
158J ASP* 2.7 27.1 + - - +
160J ASP* 1.3 71.0 - - - +
162J LEU* 1.3 57.4 + - - +
163J PHE 3.2 2.2 - - - -
164J GLU* 2.9 18.7 + - - +
165J THR* 3.0 18.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 162 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13J MET* 3.3 29.3 - - + +
15J GLY* 3.6 24.2 - - - +
18J CYS* 3.2 39.3 - - + +
20J ALA* 3.5 28.0 - - + +
157J MET* 3.7 24.2 - - + -
158J ASP 2.9 12.1 + - - +
159J PRO* 3.2 11.2 + - + +
161J HIS* 1.3 76.6 - - - +
163J PHE* 1.3 61.5 + - - +
166J ILE* 3.1 26.4 + - - +
188J ILE* 4.1 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 163 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159J PRO 2.9 13.3 + - - +
160J ASP* 4.2 7.2 - - - +
162J LEU* 1.3 74.8 - - - +
164J GLU* 1.3 71.2 + - + +
166J ILE* 3.4 4.3 - - - +
167J SER* 2.8 52.8 + - - -
186J VAL* 4.6 19.1 - - + -
188J ILE* 3.3 27.3 - - + +
195J THR* 4.8 11.4 - - - -
196J THR 5.1 15.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 164 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204I CYS* 4.0 18.9 - - - +
205I GLU 4.4 4.0 - - - +
206I LYS* 3.6 14.2 - - + -
207I GLY* 2.9 30.0 + - - +
160J ASP 3.1 21.0 - - - +
161J HIS* 2.9 9.2 + - - +
163J PHE* 1.3 89.2 - - + +
165J THR* 1.3 60.5 + - - +
167J SER* 3.9 4.4 - - - -
168J GLN* 3.0 38.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 165 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204I CYS* 4.4 14.5 + - - +
13J MET* 4.0 17.7 - - - -
149J CYS* 5.5 3.1 - - + +
152J LEU* 4.2 34.4 + - + +
153J TRP* 4.9 1.3 - - - +
154J GLU* 4.7 0.2 + - - -
157J MET* 3.4 35.3 - - + +
161J HIS* 3.0 16.8 + - - -
164J GLU* 1.3 73.5 - - - +
166J ILE* 1.4 60.1 + - - +
168J GLN* 3.2 3.8 + - - +
169J ALA* 2.9 29.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 166 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11J MET* 4.1 21.5 - - + -
13J MET* 3.9 22.1 - - + +
20J ALA* 3.5 24.9 - - + -
21J ILE* 3.6 29.2 - - - +
22J ALA* 3.7 13.5 - - + +
162J LEU 3.1 20.4 + - - +
163J PHE* 3.4 8.3 - - - +
165J THR* 1.4 76.4 - - - +
167J SER* 1.4 60.3 + - - +
169J ALA* 3.8 4.0 - - - -
170J MET* 2.9 27.4 + - - +
186J VAL* 3.8 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 167 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163J PHE* 2.8 46.9 + - - -
164J GLU* 4.0 6.7 - - - -
166J ILE* 1.4 72.2 - - - +
168J GLN* 1.3 63.1 + - - +
170J MET* 4.2 4.9 - - - -
171J LEU* 2.9 46.1 + - - +
184J VAL* 5.5 2.5 - - - +
186J VAL* 4.1 15.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 168 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204I CYS* 3.7 31.2 - - + -
148J MET* 4.7 0.9 - - + -
164J GLU* 3.0 26.5 + - - +
165J THR 3.7 3.6 - - - +
167J SER* 1.3 79.6 - - - +
169J ALA* 1.3 57.4 + - - +
171J LEU* 4.9 9.6 - - - +
172J ASN* 2.9 64.8 + - - +
151a ASN* 3.7 19.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 169 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11J MET* 4.0 11.9 - - + +
13J MET* 6.2 0.7 - - - -
148J MET* 3.7 18.9 - - + +
149J CYS* 3.5 35.2 - - + -
152J LEU* 5.4 1.3 - - + +
165J THR* 2.9 18.7 + - + +
166J ILE* 3.9 4.7 - - - +
168J GLN* 1.3 74.8 - - - +
170J MET* 1.3 60.8 + - - +
173J ALA* 3.1 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 170 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9J ALA* 5.2 2.7 - - + -
11J MET* 3.7 28.2 - - + +
22J ALA* 4.6 5.4 - - + -
23J ALA* 3.6 11.0 - - - -
24J ASP* 3.3 44.0 - - + +
166J ILE 2.9 19.5 + - - +
167J SER* 3.7 7.4 - - - +
169J ALA* 1.3 76.5 - - - +
171J LEU* 1.3 63.9 + - - +
174J VAL* 3.1 54.4 + - + +
184J VAL* 3.7 38.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 171 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167J SER* 2.9 28.8 + - - +
168J GLN* 4.1 11.4 - - - +
170J MET* 1.3 80.4 - - + +
172J ASN* 1.3 61.2 + - - +
174J VAL* 5.0 2.0 - - + -
175J ASP* 3.0 39.5 + - + +
184J VAL* 3.8 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 172 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148J MET* 3.1 26.2 - - + +
168J GLN* 2.9 45.3 + - - +
171J LEU* 1.3 78.0 - - - +
173J ALA* 1.3 65.8 + - - +
174J VAL 3.5 0.2 + - - -
175J ASP* 4.8 1.8 - - - +
176J ARG* 3.8 14.2 + - - +
147a PRO* 3.6 24.5 + - + +
151a ASN* 3.7 20.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 173 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141J CYS* 5.0 0.2 - - - -
144J GLN* 3.2 48.1 + - + +
145J MET* 3.7 22.9 - - + -
148J MET* 4.9 2.2 - - + +
169J ALA 3.1 18.4 + - - +
170J MET* 4.2 1.3 - - - +
172J ASN* 1.3 79.3 - - - +
174J VAL* 1.3 61.3 + - + +
177J ASP* 3.4 21.7 + - - +
147a PRO* 4.3 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 174 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9J ALA* 4.0 23.3 - - + -
24J ASP* 4.5 0.2 - - + -
141J CYS* 4.8 4.9 - - - -
145J MET* 5.1 2.5 - - - -
170J MET* 3.1 43.6 + - + +
171J LEU* 4.6 2.0 - - + +
173J ALA* 1.3 80.2 - - + +
175J ASP* 1.4 63.8 + - - +
176J ARG 3.2 1.3 - - - -
177J ASP* 2.9 23.3 + - - +
180J SER* 3.3 12.1 - - - +
181J GLY* 3.2 37.5 - - - +
184J VAL* 5.8 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 175 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171J LEU* 3.0 27.3 + - + +
172J ASN* 4.8 1.8 - - - +
174J VAL* 1.4 76.9 - - - +
176J ARG* 1.3 61.2 + - - +
177J ASP 3.6 1.4 - - - +
181J GLY* 5.9 1.1 - - - -
19Z ARG* 3.4 23.6 + - - -
29Z GLN* 5.0 2.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 176 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144J GLN* 3.6 24.5 - - - +
172J ASN 3.8 12.2 + - - +
173J ALA 3.9 0.2 - - - +
174J VAL 3.2 0.2 - - - -
175J ASP* 1.3 77.2 - - - +
177J ASP* 1.3 54.6 + - - +
25Z TYR* 3.5 17.6 + - + -
26Z ILE* 2.4 61.4 + - + +
27Z ALA 4.7 3.6 + - - -
29Z GLN* 3.3 28.9 + - - +
146a GLN* 2.7 72.6 + - - +
147a PRO* 3.2 7.8 - - + +
150a ASP* 3.9 16.1 + - - +
----------------------------------------------------------
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