Contacts of the helix formed by residues 176 - 195 (chain A) in PDB entry 2IZZ
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 SER 176 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A THR 2.8 13.0 + - - -
172A GLY 3.9 0.4 - - - -
175A GLY* 1.3 72.9 - - - +
177A GLY* 1.3 64.3 + - - +
178A PRO* 3.4 1.8 - - - -
179A ALA* 2.9 23.4 + - - +
180A TYR* 3.2 36.3 + - - -
261A SER* 2.7 23.6 + - - -
1273A EDO 4.4 1.6 - - - -
231B VAL* 4.4 0.9 - - - -
237B ALA* 4.4 1.6 - - - +
238B THR* 2.8 30.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 177 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A LEU 2.9 25.0 + - - -
174A SER 3.6 0.9 + - - -
175A GLY 3.4 0.2 - - - -
176A SER* 1.3 76.4 - - - +
178A PRO* 1.3 67.6 - - - +
180A TYR* 3.2 16.9 + - - +
181A ALA* 3.1 21.0 + - - +
188B LEU* 6.2 1.8 - - - -
209B ALA* 4.2 11.7 - - - -
210B LEU* 4.7 4.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 178 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A ASN* 3.8 13.5 - - + +
124A THR* 4.2 5.2 - - - +
125A PRO* 3.6 31.0 - - + -
174A SER 3.1 15.5 - - - +
175A GLY 3.6 5.8 - - - +
176A SER 3.5 4.3 - - - -
177A GLY* 1.3 88.1 - - - +
179A ALA* 1.3 55.2 + - - +
181A ALA* 3.2 3.1 + - - +
182A PHE* 2.8 51.3 + - + -
209B ALA* 4.4 6.3 - - + +
213B ALA* 3.8 17.9 - - + -
231B VAL* 4.3 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 179 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A SER 2.9 12.4 + - - +
178A PRO* 1.3 74.8 - - - +
180A TYR* 1.3 60.4 + - - +
182A PHE* 3.5 11.4 + - - +
183A THR* 2.9 32.2 + - - -
228B LYS* 4.1 8.6 - - + +
231B VAL* 3.8 15.2 - - + +
238B THR* 3.5 26.9 - - + -
242B LEU* 4.0 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 180 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A GLY 2.7 29.1 + - - -
173A LEU 4.2 1.3 - - - -
176A SER* 3.2 22.6 - - - -
177A GLY* 3.2 22.8 + - - +
179A ALA* 1.3 75.6 - - - +
181A ALA* 1.3 58.1 + - - +
183A THR* 3.4 3.9 + - - -
184A ALA* 2.9 29.0 + - - +
254A LEU* 4.7 11.0 - - + -
257A ALA* 3.3 31.0 + - + -
258A VAL* 4.3 1.6 - - + -
261A SER* 3.6 1.2 - - - -
188B LEU* 3.8 31.6 - - + -
210B LEU* 5.7 1.3 - - + -
238B THR* 4.9 2.0 - - + -
241B ALA* 3.4 23.2 - - + +
242B LEU* 4.2 6.7 - - + -
245B LEU* 3.8 28.9 - - + -
250B PHE* 4.0 4.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 181 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A GLY 3.1 11.2 + - - +
178A PRO* 3.5 7.9 - - + +
180A TYR* 1.3 74.5 - - - +
182A PHE* 1.3 59.1 + - - +
184A ALA* 3.3 7.1 + - - +
185A LEU* 2.8 37.5 + - + +
210A LEU* 4.0 12.1 - - + -
210B LEU* 3.8 23.7 - - + +
213B ALA* 3.5 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 182 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A THR* 4.6 2.0 - - - -
178A PRO* 2.8 39.3 + - + +
179A ALA* 3.9 3.6 - - - +
181A ALA* 1.3 73.0 - - - +
183A THR* 1.3 58.5 + - - +
185A LEU* 3.3 11.2 + - + +
186A ASP* 3.0 29.6 + - - +
213B ALA* 3.3 35.0 - - + -
216B MET* 3.9 23.6 - - + -
217B LEU* 4.5 4.5 - - + -
224B PRO* 3.5 29.0 - - + +
227B LEU* 3.5 40.4 - - + -
228B LYS* 3.5 25.1 - - + -
231B VAL* 4.1 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 183 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A ALA 2.9 17.9 + - - -
180A TYR* 3.5 7.2 - - - -
182A PHE* 1.3 78.0 - - - +
184A ALA* 1.3 62.1 + - - +
186A ASP* 3.4 6.4 + - - +
187A ALA* 3.1 22.2 + - - +
228B LYS* 4.0 13.3 - - - +
242B LEU* 3.5 17.3 - - + +
245B LEU* 5.0 4.5 - - + -
246B GLU* 4.5 6.2 + - - +
250B PHE* 3.8 23.6 - - + -
251B ARG* 3.9 32.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 184 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A TYR 2.9 17.9 + - - +
181A ALA* 3.3 8.5 + - - +
183A THR* 1.3 76.2 - - - +
185A LEU* 1.3 59.0 + - + +
187A ALA* 3.4 1.7 + - - +
188A LEU* 2.8 40.7 + - + +
210A LEU* 6.0 4.5 - - + -
250A PHE* 6.4 0.4 - - + -
250B PHE* 3.9 8.9 - - + -
254B LEU* 3.5 26.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 185 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A ALA 2.8 23.8 + - - +
182A PHE* 3.7 9.6 - - + +
184A ALA* 1.3 75.0 - - + +
186A ASP* 1.3 59.5 + - - +
188A LEU* 3.5 11.5 + - + +
189A ALA* 3.0 30.7 + - - +
199A ARG* 5.3 0.2 - - - -
203A VAL* 5.3 2.5 - - - +
206A GLY* 3.5 29.1 - - - +
207A ALA* 3.5 15.7 - - + +
210A LEU* 4.2 25.6 - - + -
213B ALA 4.9 0.2 - - - -
214B ALA* 4.3 19.1 - - - +
217B LEU* 3.7 32.3 - - + -
224B PRO* 5.0 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 186 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A PHE 3.0 17.0 + - - +
183A THR* 3.6 6.5 - - - +
184A ALA 3.4 0.2 - - - -
185A LEU* 1.3 76.0 - - - +
187A ALA* 1.3 57.3 + - - +
189A ALA 3.4 0.9 + - - -
190A ASP* 2.9 29.0 + - - -
199A ARG* 2.8 34.2 + - - +
223B HIS* 3.6 20.4 - - - -
224B PRO* 4.3 8.6 - - + +
225B GLY* 5.2 4.4 + - - +
251B ARG* 2.8 26.5 + - - +
225C GLY* 5.8 0.7 - - - -
228C LYS* 4.4 13.3 + - - -
229C ASP* 4.7 0.2 - - - +
251C ARG* 4.7 1.9 + - - -
186D ASP* 5.7 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 187 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A THR 3.1 16.9 + - - +
184A ALA 3.7 3.8 - - - +
186A ASP* 1.3 74.3 - - - +
188A LEU* 1.3 59.8 + - - +
190A ASP* 3.2 9.6 + - - -
191A GLY* 2.9 24.1 + - - -
251B ARG* 3.5 44.6 - - + +
254B LEU* 4.0 11.2 - - + -
255B ILE* 3.4 12.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 188 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A ALA* 2.8 29.2 + - + +
185A LEU* 3.9 17.3 - - + +
187A ALA* 1.3 76.6 - - - +
189A ALA* 1.3 56.1 + - - +
191A GLY* 3.2 2.9 + - - -
192A GLY 3.0 22.9 + - - -
206A GLY* 5.1 8.3 - - - +
209A ALA* 6.5 0.9 - - + -
210A LEU* 6.0 5.6 - - + -
173B LEU* 3.4 26.0 - - + +
177B GLY* 6.1 2.2 - - - +
180B TYR* 3.8 29.2 - - + -
254B LEU* 3.9 26.7 - - + +
258B VAL* 3.6 26.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 189 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A LEU 3.0 17.7 + - - +
186A ASP 3.6 0.4 - - - +
188A LEU* 1.3 74.0 - - - +
190A ASP* 1.3 59.8 + - - +
192A GLY 3.1 1.2 + - - -
193A VAL* 2.9 33.4 + - - +
199A ARG* 3.4 31.9 - - - +
202A ALA* 3.6 15.4 + - + +
203A VAL* 3.8 24.2 - - + +
206A GLY* 6.0 0.2 - - - -
173B LEU* 4.6 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 190 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A ASP* 2.9 17.3 + - - +
187A ALA* 3.2 12.7 + - - +
189A ALA* 1.3 75.0 - - - +
191A GLY* 1.3 56.0 + - - +
193A VAL* 3.4 3.5 + - - +
194A LYS* 2.8 29.6 + - - +
199A ARG* 3.2 15.0 + - - +
251B ARG* 5.2 4.0 + - - +
255B ILE* 3.9 22.8 - - + +
228C LYS* 3.0 34.0 + - - -
229C ASP* 4.5 0.3 - - - +
232C SER* 6.1 0.3 - - - -
239C ILE* 3.6 24.2 - - + +
242C LEU* 5.8 2.0 - - - +
246C GLU* 4.8 7.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 191 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A ALA 2.9 14.2 + - - -
188A LEU 3.5 4.3 - - - -
189A ALA 3.2 0.2 - - - -
190A ASP* 1.3 74.5 - - - +
192A GLY* 1.3 62.8 + - - +
194A LYS* 3.3 2.9 + - - +
195A MET* 3.2 28.2 + - - +
255B ILE* 3.9 22.6 - - - +
258B VAL* 3.6 17.9 - - - -
259B GLU* 5.9 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 192 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A LEU 3.0 14.0 + - - -
189A ALA 3.1 3.7 + - - -
191A GLY* 1.3 74.1 - - - +
193A VAL* 1.3 60.6 + - - +
195A MET* 3.2 4.4 + - - +
196A GLY 3.1 7.1 + - - -
197A LEU* 2.9 49.3 + - - +
202A ALA* 4.3 3.4 - - - -
169B ALA 5.4 0.2 - - - -
173B LEU* 4.3 2.7 - - - -
258B VAL* 3.7 10.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 193 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A ALA 2.9 19.3 + - - +
190A ASP* 3.7 7.2 - - - +
192A GLY* 1.3 73.6 - - - +
194A LYS* 1.3 61.6 + - - +
196A GLY 3.0 5.4 + - - -
197A LEU 3.3 17.7 - - - +
199A ARG* 3.6 38.4 - - + +
202A ALA* 4.2 2.0 - - + -
232C SER* 3.5 26.7 - - - +
233C SER 4.3 0.9 - - - +
234C PRO* 3.3 13.6 - - + +
235C GLY 2.8 25.3 + - - -
239C ILE* 4.1 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 194 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A ASP 2.8 18.3 + - - +
191A GLY* 3.3 8.7 + - - +
193A VAL* 1.3 77.0 - - - +
195A MET* 1.3 65.2 + - - +
196A GLY 3.2 0.2 - - - -
255B ILE* 4.3 9.0 - - + -
259B GLU* 2.7 33.0 + - + +
235C GLY* 3.4 18.5 - - - -
239C ILE* 3.7 19.7 - - + +
240C HIS* 3.6 51.2 + - + +
243C HIS* 2.8 37.7 + - + +
264D ARG* 5.6 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 195 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A GLY 3.2 16.3 + - - +
192A GLY* 3.2 5.5 + - - +
194A LYS* 1.3 87.2 - - - +
196A GLY* 1.3 56.0 + - - +
197A LEU 3.7 0.4 - - - -
165B ASP 5.7 0.2 - - - +
169B ALA* 3.5 24.9 - - + +
258B VAL* 4.2 5.2 - - + -
259B GLU* 3.7 39.9 - - + +
262B CYS* 3.7 21.3 - - + -
263B ILE* 4.2 18.8 - - + -
266B ARG* 3.3 47.7 + - - +
235C GLY* 5.0 0.2 - - - -
----------------------------------------------------------
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