Contacts of the helix formed by residues 161 - 181 (chain B) in PDB entry 4AUP
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 161 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B ARG* 2.8 20.7 + - + +
160B PHE* 1.3 76.4 - - - +
162B GLU* 1.3 54.1 + - - +
163B ALA* 3.7 7.7 + - - +
164B ASN* 3.1 28.1 + - - +
165B ARG* 2.7 35.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 162 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B PHE* 5.4 2.8 - - - +
161B THR* 1.3 75.9 - - - +
163B ALA* 1.3 56.4 + - - +
165B ARG* 2.8 48.3 + - - +
166B LYS* 2.9 29.6 + - - +
206B ARG* 4.8 6.8 + - - +
210B TRP* 3.6 16.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 163 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B THR* 3.3 8.1 + - - +
162B GLU* 1.3 76.2 - - - +
164B ASN* 1.3 62.8 + - - +
166B LYS* 3.5 6.7 + - - +
167B ARG* 3.3 40.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 164 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B TYR* 4.5 0.3 + - - -
154B TYR* 3.5 29.0 + - + -
159B ARG* 2.9 36.9 + - - +
160B PHE* 5.0 0.7 - - - -
161B THR* 3.1 21.1 + - - +
163B ALA* 1.3 75.0 - - - +
165B ARG* 1.3 63.5 + - - +
167B ARG* 3.2 32.5 + - - +
168B ILE* 3.0 26.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 165 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B TYR* 3.2 24.4 + - + +
160B PHE* 3.4 32.6 - - + -
161B THR 2.7 19.8 + - - +
162B GLU* 2.8 42.0 + - - +
164B ASN* 1.3 72.8 - - - +
166B LYS* 1.3 57.0 + - - +
168B ILE* 3.2 10.3 + - - +
169B ASP* 2.8 49.1 + - - +
205B VAL 2.8 27.7 + - - -
206B ARG* 2.8 35.9 + - - +
209B GLY* 3.4 10.9 - - - -
210B TRP* 3.6 20.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 166 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B GLU 2.9 17.3 + - - +
163B ALA* 3.8 6.7 - - - +
164B ASN 3.2 0.2 - - - -
165B ARG* 1.3 77.2 - - - +
167B ARG* 1.3 52.3 + - - +
169B ASP* 3.3 0.7 + - - +
170B ASP* 2.7 71.6 + - - +
202B TYR* 4.9 4.0 + - - -
206B ARG* 3.4 39.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 167 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B TYR* 3.6 33.6 - - + +
154B TYR* 5.4 0.7 - - - -
163B ALA* 3.3 32.9 + - - +
164B ASN* 3.2 34.3 + - - +
166B LYS* 1.3 78.5 - - - +
168B ILE* 1.3 56.9 + - - +
170B ASP* 3.5 7.5 + - - +
171B ASN* 3.0 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 168 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B LEU* 4.4 9.6 - - + -
102B TYR* 3.8 14.4 - - - +
147B HIS* 3.7 38.5 - - + +
150B GLY* 3.7 34.5 - - - +
151B TYR* 3.8 13.0 - - + +
154B TYR* 3.7 24.0 - - + -
160B PHE* 4.6 3.1 - - + -
164B ASN 3.0 23.0 + - - +
165B ARG* 3.7 7.2 - - - +
167B ARG* 1.3 75.3 - - - +
169B ASP* 1.3 57.8 + - - +
171B ASN* 3.2 8.4 + - + +
172B PHE* 2.9 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 169 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B HIS* 2.9 13.4 + - - -
151B TYR* 2.7 20.1 + - - -
165B ARG* 2.8 36.5 + - - +
166B LYS 3.7 3.8 - - - +
168B ILE* 1.3 69.9 - - - +
170B ASP* 1.3 64.9 + - - +
172B PHE* 3.2 9.6 + - - +
173B LYS 3.1 17.8 + - - -
202B TYR* 3.5 11.6 - - + -
205B VAL* 3.3 18.9 - - + +
206B ARG* 2.7 41.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 170 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B LYS* 2.7 55.8 + - - +
167B ARG* 3.9 6.9 + - - +
169B ASP* 1.3 71.9 - - - +
171B ASN* 1.3 61.7 + - - +
173B LYS* 3.3 5.5 + - - +
174B LYS* 3.0 23.3 + - - +
202B TYR* 2.9 29.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 171 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B LEU* 3.0 33.3 + - + +
102B TYR* 3.8 26.7 + - + +
146B ARG* 4.1 9.3 + - - +
167B ARG 3.0 18.9 + - - +
168B ILE* 3.5 6.2 - - - +
170B ASP* 1.3 77.0 - - - +
172B PHE* 1.3 56.6 + - - +
174B LYS* 3.4 23.2 - - - +
175B ASP* 2.9 42.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 172 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B SER* 3.5 26.7 - - - -
144B CYS* 3.7 41.3 - - - -
147B HIS* 3.5 28.5 - + + +
168B ILE 2.9 12.6 + - - +
169B ASP 3.3 8.5 - - - +
171B ASN* 1.3 74.3 + - - +
173B LYS* 1.3 60.6 + - - +
175B ASP* 3.1 7.4 + - - +
176B LEU* 2.9 56.2 + - + +
201B TYR* 4.2 20.0 - + + -
202B TYR* 4.7 4.7 - - - -
205B VAL* 4.1 30.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 173 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B ASP 3.1 7.4 + - - +
170B ASP* 3.3 7.6 + - - +
172B PHE* 1.3 74.1 - - - +
174B LYS* 1.3 53.8 + - - +
176B LEU* 3.2 10.5 + - + -
177B TYR* 2.8 62.9 + - + -
198B ALA 5.1 1.8 - - - +
199B ASN* 3.4 25.0 + - - +
202B TYR* 3.5 53.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 174 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B TYR 5.9 2.2 + - - -
170B ASP 3.0 13.4 + - - +
171B ASN* 3.4 24.9 - - - +
173B LYS* 1.3 77.4 - - - +
175B ASP* 1.4 59.0 + - - +
177B TYR* 3.4 5.9 + - - +
178B ASN* 2.9 50.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 175 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B MET* 3.6 19.7 - - + +
143B SER* 3.1 26.7 + - - +
146B ARG* 2.9 49.6 + - - +
171B ASN* 2.9 25.1 + - - +
172B PHE* 3.1 8.0 + - - +
174B LYS* 1.4 74.5 - - - +
176B LEU* 1.3 65.3 + - - +
178B ASN* 3.5 16.7 + - - +
179B GLU* 3.1 18.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 176 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B ASN 5.2 0.4 - - - +
140B PHE* 3.5 39.7 - - + -
143B SER* 3.5 23.8 - - - +
172B PHE* 2.9 48.3 + - + +
173B LYS* 3.6 9.4 - - - +
175B ASP* 1.3 76.9 - - - +
177B TYR* 1.3 56.2 + - - +
179B GLU* 2.9 9.1 + - + +
180B CYS* 2.9 32.8 + - - -
198B ALA* 3.9 36.8 - - + +
201B TYR* 4.1 7.4 - - + -
202B TYR 4.8 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 177 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B LYS* 2.8 49.3 + - + +
174B LYS* 3.8 6.3 - - - +
176B LEU* 1.3 72.0 - - - +
178B ASN* 1.3 53.0 + - - +
180B CYS* 3.3 6.8 + - - +
181B ALA* 2.8 36.1 + - - +
195B ARG* 3.6 36.2 + - + +
198B ALA* 4.1 18.6 - - + -
199B ASN* 2.6 39.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 178 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B MET* 6.6 0.7 - - + -
146B ARG* 5.8 0.2 - - - +
174B LYS* 2.9 42.7 + - - +
175B ASP* 3.5 19.6 + - - +
177B TYR* 1.3 77.7 - - - +
179B GLU* 1.3 60.0 + - - +
181B ALA* 3.6 15.1 + - - +
182B LYS* 3.7 14.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 179 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B ASN* 3.3 53.0 + - + +
140B PHE* 5.5 2.0 - - + -
142B ASP* 5.9 1.6 - - - +
143B SER* 5.1 2.5 - - - +
175B ASP 3.1 11.1 + - - +
176B LEU* 2.9 12.0 + - - +
178B ASN* 1.3 71.6 - - - +
180B CYS* 1.3 67.3 + - - +
182B LYS* 2.8 58.1 + - - +
183B TYR* 3.9 18.1 + - + -
194B CYS* 5.3 4.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 180 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B PHE* 4.6 1.8 - - - -
176B LEU 2.9 21.8 + - - -
177B TYR* 3.7 6.5 - - - +
179B GLU* 1.3 77.7 - - - +
181B ALA* 1.3 60.1 + - - +
182B LYS 3.1 1.8 + - - -
183B TYR* 3.2 23.3 + - - +
191B GLY* 3.9 8.7 - - - +
194B CYS* 2.1 67.1 - - + -
195B ARG* 3.5 25.6 + - + +
198B ALA* 4.4 4.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 181 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B TYR 2.8 21.7 + - - +
178B ASN* 3.7 11.7 - - - +
179B GLU 3.2 0.4 - - - -
180B CYS* 1.3 70.7 - - - +
182B LYS* 1.3 61.1 + - - +
183B TYR 3.2 7.4 + - - +
184B SER* 4.7 5.9 + - - -
195B ARG* 4.6 7.6 - - - +
----------------------------------------------------------
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