Contacts of the helix formed by residues 160 - 182 (chain B) in PDB entry 4IA4
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 ASN 160 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B VAL* 4.6 1.1 - - - -
159B TYR* 1.3 74.8 - - - +
161B LYS* 1.3 56.2 + - - +
162B GLY* 2.9 8.2 - - - +
163B THR* 2.6 60.3 + - - +
164B ALA* 3.2 8.0 + - - +
140D PHE 4.9 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 161 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B VAL* 4.2 10.5 - - + +
159B TYR 3.9 1.6 + - - -
160B ASN* 1.3 71.4 - - - +
162B GLY* 1.3 62.1 + - - +
164B ALA* 3.4 10.2 + - - +
165B LEU* 3.2 22.3 + - - +
240B ASP* 3.7 10.5 + - - -
241B ASP* 2.6 48.5 + - - +
243B TRP* 3.5 27.5 - - + +
244B ILE* 3.9 9.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 162 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B ASN* 2.8 13.6 + - - +
161B LYS* 1.3 79.3 - - - +
163B THR* 1.3 55.2 + - - -
165B LEU* 3.5 9.8 + - - +
166B GLY* 3.0 21.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 163 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B TYR* 4.1 15.5 - - + -
160B ASN* 2.6 41.0 + - - +
162B GLY* 1.3 69.8 - - - -
164B ALA* 1.3 65.4 + - - +
166B GLY* 2.8 12.3 + - - +
167B ALA* 2.8 13.0 + - - +
216B ILE* 4.4 8.3 - - + -
139D ALA 4.4 4.0 + - - -
140D PHE* 3.6 57.3 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
155B VAL* 3.8 32.5 - - + +
159B TYR* 5.3 0.2 - - - +
160B ASN 3.2 3.0 + - - -
161B LYS 3.6 8.3 - - - +
163B THR* 1.3 78.5 - - - +
165B LEU* 1.3 58.9 + - - +
167B ALA* 3.3 2.3 + - - +
168B GLU* 2.8 32.7 + - - +
216B ILE* 4.3 6.9 - - + +
217B THR* 3.7 26.6 - - + +
244B ILE* 3.9 10.5 - - + -
245B PHE* 5.9 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 165 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B LYS 3.2 8.0 + - - +
162B GLY* 3.6 11.9 - - - +
163B THR 3.1 0.4 - - - -
164B ALA* 1.3 75.5 - - - +
166B GLY* 1.3 65.7 - - - +
168B GLU* 3.6 1.4 - - - +
169B ILE* 2.9 42.4 + - + +
243B TRP* 3.5 33.9 - - + -
244B ILE* 3.2 43.8 - - + +
247B VAL* 4.1 7.9 - - + -
248B GLY* 3.9 13.0 - - - +
251B ILE* 5.4 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 166 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B GLY 3.0 11.4 + - - -
163B THR 2.8 8.9 + - - -
165B LEU* 1.3 78.0 - - - +
167B ALA* 1.3 60.8 + - - -
169B ILE* 3.7 6.5 - - - +
170B ILE* 3.0 26.7 + - - +
140D PHE* 3.5 20.0 - - - -
----------------------------------------------------------
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 THR 2.8 16.8 + - - +
164B ALA 3.8 4.5 - - - +
166B GLY* 1.3 71.7 - - - -
168B GLU* 1.3 54.5 + - - +
170B ILE* 3.3 1.7 - - - +
171B GLY* 2.7 34.1 + - - -
213B THR* 4.4 17.7 + - + +
216B ILE* 3.9 27.4 - - + -
217B THR* 5.5 0.4 - - + -
53D TYR* 3.5 23.9 + - - +
140D PHE* 3.3 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 168 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B ALA 2.8 26.2 + - - +
165B LEU* 3.6 7.9 - - - +
166B GLY 3.2 0.2 - - - -
167B ALA* 1.3 74.3 - - - +
169B ILE* 1.3 61.9 + - - +
171B GLY* 4.9 0.4 - - - -
172B THR* 2.7 32.2 + - - -
213B THR* 4.3 4.8 - - - +
217B THR* 2.9 26.3 + - + +
220B GLY* 3.3 13.2 + - - -
221B ILE* 3.0 28.8 + - - +
244B ILE* 4.2 8.5 - - + +
245B PHE* 3.5 27.6 - - + -
248B GLY* 4.2 14.6 - - - -
249B PRO* 4.0 9.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 169 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B LEU* 2.9 31.5 + - + +
166B GLY* 3.7 5.8 - - - +
168B GLU* 1.3 71.0 - - - +
170B ILE* 1.3 72.6 + - + +
171B GLY 2.9 2.6 + - - -
172B THR* 2.9 14.7 + - - -
173B PHE* 2.9 13.0 + - + +
248B GLY* 3.4 28.0 - - - +
251B ILE* 3.5 34.1 - - + -
252B GLY* 3.9 15.8 - - - +
255B VAL* 5.4 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 170 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B GLY 3.0 13.6 + - - +
167B ALA* 3.3 7.0 - - - +
169B ILE* 1.3 83.7 - - + +
171B GLY* 1.3 66.7 + - - +
173B PHE* 3.4 16.5 + - + +
174B VAL* 3.5 9.0 + - + +
49D LEU* 5.3 3.4 - - + -
50D LEU* 3.5 30.3 - - + -
53D TYR* 3.2 50.0 - - + +
136D LEU* 4.1 22.0 - - + -
140D PHE* 4.5 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 171 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B ALA 2.7 24.8 + - - -
168B GLU 3.9 0.7 - - - -
169B ILE 2.9 1.2 + - - -
170B ILE* 1.3 75.4 - - - +
172B THR* 1.3 55.1 + - - -
174B VAL* 2.9 29.1 + - - +
175B LEU* 3.4 3.8 + - - +
209B VAL* 3.7 24.6 - - - +
213B THR* 5.1 1.6 - - - -
221B ILE* 4.0 9.0 - - - -
53D TYR* 5.4 3.1 - - - -
54D ILE* 5.5 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 172 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B ALA* 4.1 10.5 - - + -
168B GLU 2.7 18.3 + - - -
169B ILE 2.9 3.9 + - - -
171B GLY* 1.3 71.3 - - - +
173B PHE* 1.3 65.0 + - - +
174B VAL 3.0 0.2 - - - -
175B LEU* 3.7 11.9 - - + +
176B VAL* 3.1 39.7 + - + +
221B ILE* 3.5 24.0 - - - +
249B PRO* 3.4 39.9 - - + +
252B GLY* 4.5 2.2 - - - -
253B ALA 4.2 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 173 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B ILE* 2.9 13.2 + - + +
170B ILE* 3.5 16.8 - - + +
171B GLY 3.1 0.4 - - - -
172B THR* 1.3 76.9 - - - +
174B VAL* 1.3 59.4 + - - +
177B TYR* 2.9 49.5 + + + +
252B GLY* 3.9 12.5 - - - +
255B VAL* 3.7 18.8 - - + -
256B ALA* 3.3 42.0 - - + -
259B TYR* 3.7 32.5 - + + -
46D ILE* 4.1 11.4 - - + -
50D LEU* 3.9 26.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 174 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B ILE* 3.6 12.6 - - + +
171B GLY 2.9 10.3 + - - +
173B PHE* 1.3 79.7 - - - +
175B LEU* 1.3 55.9 - - - +
177B TYR* 4.2 3.4 - - - +
178B THR* 2.6 34.5 + - - +
205B ALA* 4.3 12.7 - - + +
209B VAL* 3.6 21.3 - - + -
50D LEU* 3.5 35.9 - - + -
54D ILE* 4.5 13.7 - - + -
84D MET* 4.8 18.4 - - + -
87D VAL* 5.2 4.7 - - + -
88D LEU* 6.2 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 175 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B ASN* 3.6 27.4 - - - +
104B VAL* 3.8 18.2 - - + -
171B GLY 3.4 2.7 + - - +
172B THR* 3.2 16.9 + - + +
174B VAL* 1.3 80.0 - - - +
176B VAL* 1.3 61.4 + - + +
178B THR* 3.1 8.0 + - - -
179B VAL* 3.0 24.2 + - + +
202B ILE* 4.2 22.0 - - + +
205B ALA* 4.3 10.3 - - + -
206B VAL* 3.8 30.7 - - + -
209B VAL* 4.7 3.5 - - + +
221B ILE* 4.0 18.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 176 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B ALA 4.1 11.7 - - - +
104B VAL* 4.5 15.0 - - + +
107B GLY* 4.5 5.2 - - - -
108B LEU* 6.0 0.4 - - + -
172B THR* 3.1 33.7 + - + +
175B LEU* 1.3 74.6 - - + +
177B TYR* 1.3 60.6 + - - +
178B THR 3.0 2.0 - - - -
179B VAL* 3.4 10.9 - - + +
180B PHE* 2.9 51.1 + - + -
253B ALA* 3.8 27.6 - - + +
256B ALA* 4.0 8.3 - - + -
----------------------------------------------------------
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 PHE* 2.9 42.9 + + + +
174B VAL* 4.2 3.8 - - - +
176B VAL* 1.3 76.0 - - - +
178B THR* 1.3 56.8 + - - +
180B PHE* 3.4 6.3 + - - +
181B SER* 2.9 38.6 + - - -
256B ALA* 3.9 13.7 - - + +
259B TYR* 3.7 35.0 + + - -
260B HIS* 4.9 13.5 - + + -
264B LEU* 4.1 12.7 - - + +
43D ALA* 5.1 0.9 - - - +
46D ILE* 4.8 3.1 - - + -
47D ALA* 6.1 1.6 - - - -
50D LEU* 4.3 17.3 - - + -
88D LEU* 5.9 2.7 - - + -
91D CYS* 3.8 21.2 + - + -
92D THR* 3.6 25.3 - - + +
95D ILE* 5.5 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 178 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B VAL* 2.6 20.2 + - - +
175B LEU 3.1 8.9 + - - -
176B VAL 3.0 0.4 - - - -
177B TYR* 1.3 77.8 - - - +
179B VAL* 1.3 55.2 + - - +
180B PHE 3.1 0.2 - - - -
181B SER 3.0 1.2 + - - -
182B ALA* 2.7 37.0 + - - +
201B PRO* 3.4 43.1 - - + +
202B ILE* 4.1 5.6 - - + +
205B ALA* 3.9 5.6 - - - +
87D VAL* 3.7 13.6 - - + +
90D TYR* 4.6 2.2 - - + -
91D CYS* 3.7 25.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 179 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B VAL* 3.6 38.6 - - + -
108B LEU* 4.1 18.8 - - + -
175B LEU* 3.0 22.9 + - + +
176B VAL* 3.1 12.8 + - + +
178B THR* 1.3 74.9 - - - +
180B PHE* 1.3 64.5 + - - +
182B ALA* 3.0 9.2 + - - -
183B THR* 3.1 14.0 + - - +
197B LEU* 3.5 26.1 - - + +
202B ILE* 3.9 26.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 180 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B GLY 3.3 26.7 - - - -
108B LEU* 3.2 28.0 - - + -
111B ALA* 3.6 17.5 - - + -
113B LYS* 5.1 3.8 - - + -
176B VAL* 2.9 38.2 + - + -
177B TYR* 3.6 7.6 - - - +
179B VAL* 1.3 77.6 - - + +
181B SER* 1.3 58.6 + - - +
182B ALA 2.9 5.4 + - - -
183B THR* 3.0 26.2 + - + -
256B ALA 4.4 1.6 - - - -
257B ALA* 3.2 38.8 - - + -
260B HIS* 3.5 47.6 + + + +
261B GLN* 4.5 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 181 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B TYR* 2.9 41.0 + - - -
178B THR 3.0 3.5 + - - -
180B PHE* 1.3 74.4 - - - +
182B ALA* 1.3 57.0 + - - +
183B THR 4.9 1.7 - - - +
260B HIS* 4.8 6.0 - - - -
90D TYR* 3.3 19.2 + - - +
91D CYS* 3.3 39.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 182 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B THR* 2.7 15.7 + - + +
179B VAL 3.6 5.4 - - - +
180B PHE 2.9 0.6 - - - -
181B SER* 1.3 79.1 - - - +
183B THR* 1.3 66.1 + - - +
184B ASP* 3.6 1.4 + - - +
196B ILE 3.8 0.5 - - - +
197B LEU* 3.7 3.3 - - + -
198B ALA* 3.2 48.4 + - + +
201B PRO* 5.2 0.4 - - + -
202B ILE* 4.0 11.7 - - + -
90D TYR* 3.7 12.7 + - + +
----------------------------------------------------------
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