Contacts of the helix formed by residues 160 - 171 (chain B) in PDB entry 1EE8
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 GLY 160 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B GLU* 2.8 32.8 + - - -
52B LYS* 3.8 9.9 - - - -
151B LEU* 3.9 9.9 - - - -
158B GLY 3.6 1.4 + - - -
159B VAL* 1.3 74.5 - - - +
161B ASN* 1.3 57.1 + - - -
164B ALA* 3.0 31.7 + - - +
253B ARG* 4.7 4.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 161 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B GLU* 3.4 4.5 + - - +
147B LYS* 3.3 24.3 + - - +
160B GLY* 1.3 69.4 - - - -
162B ILE* 1.3 68.2 + - + +
165B ASP* 2.9 31.9 + - - +
231B TYR* 4.5 14.1 - - + +
253B ARG* 2.6 54.2 + - - +
254B GLY 3.8 10.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 162 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B PRO 6.4 0.2 - - - -
2B GLU* 3.0 18.1 + - - +
5B GLU* 5.0 5.4 - - - +
161B ASN* 1.3 77.2 - - + +
163B TYR* 1.3 83.9 + - + +
165B ASP* 3.6 1.7 - - - +
166B GLU* 2.9 34.2 + - + +
207B SER* 4.3 19.1 - - - +
209B LEU* 4.5 7.9 - - + -
228B HIS* 3.7 26.7 - - + +
231B TYR* 3.6 43.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 163 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B GLU* 2.9 27.4 + - + +
4B PRO* 3.6 20.5 - - + +
5B GLU* 2.5 39.8 + - - -
158B GLY 5.5 0.4 - - - -
159B VAL* 4.5 8.3 - - + -
160B GLY 4.9 0.7 - - - +
162B ILE* 1.3 90.0 - - + +
164B ALA* 1.3 61.3 + - - +
166B GLU* 4.2 0.8 - - - +
167B ALA* 2.9 31.4 + - - +
194B LEU* 4.3 2.0 - - + +
197B VAL* 3.5 24.7 - - + +
198B LEU* 3.7 22.4 - - + -
201B ALA* 3.3 27.0 - - + +
207B SER* 2.8 21.1 + - - -
224B PHE* 3.7 16.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 164 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B LYS* 3.6 26.2 - - + -
150B LEU* 4.4 13.2 - - + -
151B LEU* 3.8 9.6 - - + -
159B VAL* 3.9 13.1 - - + +
160B GLY 3.0 21.5 + - - +
163B TYR* 1.3 76.4 - - - +
165B ASP* 1.3 58.1 + - - +
167B ALA* 3.8 3.2 - - - +
168B LEU* 2.9 37.7 + - - +
194B LEU* 4.8 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 165 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B LYS* 2.9 29.6 + - - +
161B ASN* 2.9 20.8 + - - +
162B ILE 3.6 3.4 - - - +
164B ALA* 1.3 76.5 - - - +
166B GLU* 1.3 61.5 + - - +
168B LEU* 3.5 6.2 + - - +
169B PHE* 3.1 23.7 + - - +
175B PRO* 6.1 0.2 - - - -
230B VAL* 3.7 12.2 - - + +
231B TYR* 3.8 10.0 - - + -
254B GLY 4.4 1.4 - - - +
255B THR* 3.5 8.0 - - - +
256B HIS* 2.8 53.9 + - - +
262B GLN* 4.6 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 166 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B ILE* 2.9 24.5 + - + +
163B TYR 4.2 0.2 - - - +
165B ASP* 1.3 75.1 - - - +
167B ALA* 1.3 58.8 + - - +
169B PHE* 3.5 3.4 + - - +
170B ARG* 2.9 36.5 + - - +
197B VAL* 4.1 21.8 - - + -
224B PHE* 4.6 6.5 - - + -
227B ARG 3.7 4.3 - - - +
228B HIS* 3.5 20.9 - - + -
229B ALA* 2.8 29.6 + - - +
230B VAL* 2.9 13.3 + - - +
231B TYR* 2.8 36.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 167 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B TYR 2.9 20.0 + - - +
164B ALA 3.8 1.8 - - - +
166B GLU* 1.3 73.6 - - - +
168B LEU* 1.3 61.0 + - + +
170B ARG* 3.2 3.6 + - - +
171B ALA* 2.9 27.7 + - - +
190B LEU* 4.2 6.1 - - + -
193B ALA* 3.4 8.8 - - + +
194B LEU* 3.5 43.3 - - + +
197B VAL* 4.0 11.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 168 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B LEU* 3.5 34.3 - - + -
147B LYS* 4.0 24.5 - - + -
150B LEU* 4.3 7.2 - - + -
164B ALA 2.9 22.8 + - - +
165B ASP* 3.9 4.5 - - - +
167B ALA* 1.3 76.8 - - - +
169B PHE* 1.3 57.4 + - - +
171B ALA* 3.5 1.1 + - - -
172B ARG 2.9 7.4 + - - -
173B LEU* 2.9 38.9 + - + +
174B SER 4.5 0.9 - - - +
175B PRO* 3.5 31.6 - - + -
190B LEU* 3.6 19.3 - - + -
262B GLN* 3.4 15.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 169 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B ASP 3.1 17.4 + - - +
166B GLU* 3.8 5.2 - - - +
168B LEU* 1.3 74.3 - - - +
170B ARG* 1.3 66.6 + - - +
172B ARG* 2.7 56.3 + - - -
229B ALA* 3.5 24.0 - - + -
230B VAL* 3.5 29.6 - - + -
238B CYS* 3.6 26.0 - - - -
239B PRO* 3.7 20.9 - - + -
240B ALA* 4.0 8.7 - - + -
258B CYS* 4.2 6.5 - - + -
261B CYS* 4.2 9.0 - - + -
262B GLN* 3.4 25.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 170 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B GLU* 2.9 21.9 + - - +
167B ALA* 3.4 6.1 - - - +
169B PHE* 1.3 85.9 - - - +
171B ALA* 1.3 59.0 + - - +
172B ARG* 3.2 15.7 + - - +
193B ALA* 3.7 16.1 + - + +
196B GLU* 3.8 24.0 + - - +
197B VAL* 3.5 25.0 - - - +
200B GLU* 2.6 40.6 + - - -
224B PHE* 6.0 2.2 - - - -
227B ARG 6.0 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 171 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B ALA 2.9 17.0 + - - +
168B LEU 4.2 0.7 - - - +
170B ARG* 1.3 75.3 - - - +
172B ARG* 1.3 67.8 + - - +
173B LEU* 3.5 14.1 + - + +
189B ARG* 2.9 66.0 + - + +
190B LEU* 3.7 11.9 - - + +
193B ALA* 3.9 2.0 - - + +
----------------------------------------------------------
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