Contacts of the helix formed by residues 176 - 195 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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231A VAL* 4.5 0.4 - - - -
237A ALA* 4.4 1.6 - - - +
238A THR* 2.7 32.0 + - - -
1272A EDO 4.4 2.3 - - - -
171B THR 2.8 11.9 + - - -
172B GLY 3.9 0.9 - - - -
175B GLY* 1.3 72.0 - - - +
177B GLY* 1.3 64.9 + - - +
178B PRO* 3.4 1.6 - - - -
179B ALA* 3.0 18.6 + - - +
180B TYR* 3.3 38.8 + - - -
261B SER* 2.7 23.5 + - - -
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Residues in contact with GLY 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A LEU* 6.1 2.3 - - - +
209A ALA* 4.2 12.5 - - - -
173B LEU 2.8 25.3 + - - -
174B SER 3.7 0.6 + - - -
175B GLY 3.4 0.4 - - - -
176B SER* 1.3 76.0 - - - +
178B PRO* 1.3 67.6 - - - +
180B TYR* 3.1 17.3 + - - +
181B ALA* 3.1 20.7 + - - +
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Residues in contact with PRO 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A ALA* 4.5 5.6 - - + +
213A ALA* 3.8 17.9 - - + -
231A VAL* 4.4 4.5 - - + -
123B ASN* 3.9 13.2 - - + +
124B THR* 4.2 8.7 - - - +
125B PRO* 3.7 27.4 - - + -
174B SER 3.2 15.5 - - - +
175B GLY 3.5 6.1 - - - +
176B SER 3.5 4.7 - - - -
177B GLY* 1.3 89.1 - - - +
179B ALA* 1.3 56.1 + - - +
181B ALA* 3.1 4.2 + - - +
182B PHE* 2.8 50.9 + - + -
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Residues in contact with ALA 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A LYS* 4.4 9.1 - - + +
231A VAL* 4.1 13.3 - - + +
238A THR* 3.4 33.4 - - + -
242A LEU* 3.9 16.3 - - + +
176B SER 3.0 5.4 + - - +
178B PRO* 1.3 74.4 - - - +
180B TYR* 1.3 65.1 + - - +
182B PHE* 3.9 11.7 - - - +
183B THR* 3.0 27.9 + - - -
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Residues in contact with TYR 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A LEU* 3.8 32.3 - - + -
238A THR* 5.0 1.6 - - + -
241A ALA* 3.5 23.7 - - + +
242A LEU* 4.2 6.3 - - + -
245A LEU* 3.9 27.1 - - + -
250A PHE* 4.1 4.7 - - - -
172B GLY 2.7 29.4 + - - -
173B LEU 4.1 1.3 - - - -
176B SER* 3.3 22.7 - - - -
177B GLY* 3.1 23.3 + - - +
179B ALA* 1.3 77.3 - - + +
181B ALA* 1.3 57.7 + - - +
183B THR* 3.6 3.1 - - - -
184B ALA* 3.0 28.3 + - - +
254B LEU* 4.7 11.2 - - + -
257B ALA* 3.4 29.5 + - + -
258B VAL* 4.4 1.6 - - + -
261B SER* 3.5 1.6 - - - -
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Residues in contact with ALA 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A LEU* 3.6 31.0 - - + +
213A ALA* 3.5 24.2 - - + -
177B GLY 3.1 10.5 + - - +
178B PRO 3.4 8.5 - - - +
180B TYR* 1.3 74.7 - - - +
182B PHE* 1.3 59.7 + - - +
184B ALA* 3.3 6.8 + - - +
185B LEU* 2.9 38.2 + - + +
210B LEU* 4.7 2.5 - - + -
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Residues in contact with PHE 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A ALA* 3.3 30.5 - - + -
216A MET* 3.9 24.7 - - + -
217A LEU* 4.6 5.6 - - + -
224A PRO* 3.5 24.4 - - + +
227A LEU* 3.6 43.7 - - + -
228A LYS* 3.5 24.5 - - + +
231A VAL* 4.2 6.1 - - + -
124B THR* 4.7 1.6 - - - -
178B PRO* 2.8 43.8 + - + +
179B ALA* 3.4 4.7 + - - +
181B ALA* 1.3 73.2 - - - +
183B THR* 1.3 57.7 + - - +
185B LEU* 3.4 10.4 + - + +
186B ASP* 3.0 28.8 + - - +
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Residues in contact with THR 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A LYS* 4.3 13.0 - - - +
242A LEU* 3.6 16.6 - - + +
245A LEU* 5.0 5.2 - - + -
246A GLU* 4.7 5.6 - - - +
250A PHE* 3.8 23.3 - - + -
251A ARG* 3.9 32.5 + - + +
179B ALA 3.0 18.0 + - - -
180B TYR* 3.6 6.7 - - - -
182B PHE* 1.3 74.0 - - - +
184B ALA* 1.3 63.3 - - - +
186B ASP* 3.4 7.5 + - - +
187B ALA* 3.1 22.3 + - - +
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Residues in contact with ALA 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A LEU* 6.1 0.4 - - + -
250A PHE* 3.9 10.5 - - + -
254A LEU* 3.5 25.2 - - + +
180B TYR 3.0 17.9 + - - +
181B ALA* 3.3 8.3 + - - +
183B THR* 1.3 76.3 - - - +
185B LEU* 1.3 57.4 + - - +
187B ALA* 3.3 1.7 + - - +
188B LEU* 2.8 41.7 + - + +
210B LEU* 4.9 7.4 - - + -
250B PHE* 6.4 0.2 - - + -
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Residues in contact with LEU 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A ALA* 4.3 22.9 - - - +
217A LEU* 3.4 34.5 - - + -
224A PRO* 5.2 1.3 - - - -
181B ALA* 2.9 26.2 + - + +
182B PHE* 3.8 8.7 - - + +
184B ALA* 1.3 73.3 - - - +
186B ASP* 1.3 60.5 + - - +
188B LEU* 3.9 5.4 - - + +
189B ALA* 2.9 30.7 + - - +
203B VAL* 5.6 3.1 - - + +
206B GLY* 3.5 6.5 - - - +
207B ALA* 3.5 26.9 - - + +
210B LEU* 3.4 36.1 - - + -
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Residues in contact with ASP 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A HIS* 3.5 22.3 + - - -
224A PRO* 4.2 9.3 - - + +
225A GLY* 5.2 3.9 + - - +
251A ARG* 2.9 25.5 + - - +
182B PHE 3.0 17.6 + - - +
183B THR* 3.7 7.2 - - - +
185B LEU* 1.3 75.9 - - - +
187B ALA* 1.3 57.3 + - - +
189B ALA 3.4 0.2 + - - -
190B ASP* 3.0 32.6 + - - +
199B ARG* 2.8 38.5 + - - +
186E ASP* 5.6 1.4 - - - +
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Residues in contact with ALA 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251A ARG* 3.6 43.9 - - + +
254A LEU* 4.0 12.1 - - + -
255A ILE* 3.4 9.2 + - - +
183B THR 3.1 16.2 + - - +
184B ALA 3.7 3.8 - - - +
186B ASP* 1.3 75.8 - - - +
188B LEU* 1.3 60.0 + - - +
190B ASP* 3.2 12.9 + - - +
191B GLY* 2.9 24.3 + - - -
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Residues in contact with LEU 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A LEU* 3.6 26.4 - - + +
177A GLY* 6.0 1.8 - - - +
180A TYR* 3.8 26.9 - - + -
254A LEU* 3.9 25.8 - - + +
258A VAL* 3.6 26.4 - - + +
184B ALA* 2.8 31.1 + - + +
185B LEU* 3.9 8.5 - - + +
187B ALA* 1.3 71.4 - - - +
189B ALA* 1.3 57.8 + - - +
191B GLY* 3.1 2.8 + - - -
192B GLY 2.9 23.2 + - - -
206B GLY* 5.1 6.3 - - - +
209B ALA* 6.5 0.4 - - + -
210B LEU* 4.2 27.1 - - + -
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Residues in contact with ALA 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A LEU* 4.6 0.2 - - - +
185B LEU 2.9 19.8 + - - +
186B ASP 3.6 0.7 - - - +
188B LEU* 1.3 77.2 - - - +
190B ASP* 1.3 55.8 + - - +
192B GLY* 3.2 2.1 + - - -
193B VAL* 2.9 32.4 + - - +
199B ARG* 3.4 31.2 - - - +
202B ALA* 3.6 14.3 + - + +
203B VAL* 3.8 24.7 - - + +
206B GLY* 6.0 0.2 - - - -
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Residues in contact with ASP 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251A ARG* 4.9 5.7 + - - +
255A ILE* 4.0 20.5 - - + +
186B ASP* 3.0 24.6 + - - +
187B ALA* 3.3 13.1 - - - +
189B ALA* 1.3 74.4 - - - +
191B GLY* 1.3 57.0 + - - +
193B VAL* 3.5 7.1 + - - +
194B LYS* 2.9 28.1 + - - +
199B ARG* 3.1 18.2 + - - +
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Residues in contact with GLY 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255A ILE* 3.9 23.2 - - - +
258A VAL* 3.5 18.6 - - - -
259A GLU* 5.1 0.3 + - - +
187B ALA 2.9 13.1 + - - -
188B LEU 3.1 4.9 + - - -
190B ASP* 1.3 74.3 - - - +
192B GLY* 1.3 63.0 + - - +
194B LYS* 3.3 2.6 + - - +
195B MET* 3.2 28.8 + - - +
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Residues in contact with GLY 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A ALA 5.3 0.2 - - - -
173A LEU* 4.4 6.1 - - - -
258A VAL* 3.7 10.4 - - - +
188B LEU 2.9 13.3 + - - -
189B ALA 3.2 3.8 + - - -
191B GLY* 1.3 76.0 - - - +
193B VAL* 1.3 58.5 + - - +
195B MET* 3.2 4.9 + - - +
196B GLY 3.1 6.4 + - - -
197B LEU* 2.9 47.8 + - - +
202B ALA* 4.4 0.9 - - - -
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Residues in contact with VAL 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189B ALA 2.9 19.6 + - - +
190B ASP* 3.8 8.5 - - - +
192B GLY* 1.3 70.5 - - - +
194B LYS* 1.3 67.8 + - - +
196B GLY* 3.0 14.6 + - - -
197B LEU 3.3 20.4 - - - +
198B PRO 4.3 0.2 - - - -
199B ARG* 3.6 38.8 - - + +
202B ALA* 4.3 1.8 - - + -
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Residues in contact with LYS 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255A ILE* 4.3 18.4 - - + +
259A GLU* 2.8 35.9 + - + +
190B ASP 2.9 18.1 + - - +
191B GLY* 3.3 8.5 + - - +
193B VAL* 1.3 78.9 - - - +
195B MET* 1.3 69.5 + - - +
196B GLY* 3.3 0.9 + - - -
264E ARG* 5.5 5.0 + - - -
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Residues in contact with MET 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A ASP 5.7 0.5 - - - +
169A ALA* 3.5 24.4 - - + +
258A VAL* 4.3 4.7 - - + -
259A GLU* 3.8 40.4 - - + +
262A CYS* 3.7 22.2 - - + -
263A ILE* 4.1 20.6 - - + -
266A ARG* 3.4 44.8 + - - +
191B GLY 3.2 16.8 + - - +
192B GLY* 3.2 4.0 + - - +
193B VAL 3.1 0.6 - - - -
194B LYS* 1.3 89.3 - - - +
196B GLY* 1.3 55.8 + - - +
197B LEU 3.8 0.4 - - - -
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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
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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) + - + + + + + -
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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