Contacts of the helix formed by residues 176 - 195 (chain B) in PDB entry 2GER
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).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B THR* 3.0 6.6 + - - +
175B GLY* 1.3 70.7 - - - +
177B GLY* 1.3 53.1 + - - +
178B PRO* 2.5 5.5 - - - +
179B ALA* 2.4 44.6 + - - +
180B TYR* 3.2 32.9 + - - -
261B SER* 3.1 19.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 177 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B LEU* 2.7 26.2 + - - -
174B SER* 4.5 1.6 - - - -
176B SER* 1.3 68.7 - - - +
178B PRO* 1.3 68.1 - - - +
180B TYR* 2.9 33.3 + - - +
181B ALA* 3.1 11.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 178 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B ASN* 3.9 23.6 - - + +
124B THR* 5.0 6.7 - - - +
125B PRO* 4.1 16.4 - - + -
174B SER* 2.9 24.5 - - - +
175B GLY 3.5 3.4 - - - +
176B SER 2.5 4.6 - - - +
177B GLY* 1.3 86.3 - - - +
179B ALA* 1.3 55.1 + - - +
181B ALA* 3.5 7.0 - - + +
182B PHE* 3.0 49.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 179 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B SER* 2.4 32.8 + - - +
178B PRO* 1.3 67.2 - - - +
180B TYR* 1.3 73.9 + - + +
182B PHE* 3.3 10.6 + - - +
183B THR* 3.0 26.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 180 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B GLY 3.0 25.6 + - - -
173B LEU* 4.1 4.7 - - + -
176B SER* 3.2 33.0 - - - -
177B GLY* 3.2 23.6 - - - +
179B ALA* 1.3 79.9 - - + +
181B ALA* 1.3 52.3 + - - +
183B THR* 3.1 9.0 + - - +
184B ALA* 2.6 35.3 + - - +
254B LEU* 5.0 16.6 - - + -
257B ALA* 3.5 39.6 + - + -
258B VAL* 4.6 2.7 - - + -
261B SER* 3.7 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 GLY 3.1 7.9 + - - +
178B PRO* 3.5 12.6 - - + +
180B TYR* 1.3 75.7 - - - +
182B PHE* 1.3 64.3 + - + +
183B THR 2.9 1.3 - - - -
184B ALA* 2.8 10.6 + - - +
185B LEU* 2.7 43.7 + - + +
210B LEU* 5.9 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 182 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B THR* 6.1 5.6 - - - -
125B PRO* 6.5 2.0 - - + -
178B PRO* 3.0 31.4 + - + +
179B ALA* 3.3 8.9 + - - +
181B ALA* 1.3 80.2 - - + +
183B THR* 1.3 57.2 + - - +
185B LEU* 3.6 14.7 - - + +
186B ASP* 3.1 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 183 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B ALA 3.0 12.7 + - - -
180B TYR* 3.2 11.4 - - - +
181B ALA 2.9 0.4 - - - -
182B PHE* 1.3 75.6 - - - +
184B ALA* 1.3 70.1 + - - +
185B LEU 2.9 1.6 - - - -
186B ASP* 3.4 4.6 + - - +
187B ALA* 2.8 30.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 184 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B TYR 2.6 18.1 + - - +
181B ALA* 3.2 14.8 - - - +
183B THR* 1.3 75.0 - - - +
185B LEU* 1.3 57.6 + - + +
187B ALA* 3.1 7.6 - - - +
188B LEU* 3.0 38.3 + - + +
210B LEU* 5.1 7.9 - - + -
250B PHE* 6.4 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 185 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B ALA* 2.7 27.2 + - + +
182B PHE* 3.6 16.4 - - + +
183B THR 2.9 0.8 + - - -
184B ALA* 1.3 67.0 - - - +
186B ASP* 1.3 69.9 + - - +
187B ALA 2.5 2.8 + - - -
188B LEU* 2.8 16.4 + - + +
189B ALA* 2.9 14.2 + - + +
203B VAL* 4.3 14.8 - - + +
206B GLY* 3.5 7.6 - - - -
207B ALA* 3.5 33.7 - - + +
210B LEU* 3.0 34.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 186 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B PHE 3.1 14.4 + - - +
183B THR* 4.0 4.5 - - - +
185B LEU* 1.3 77.9 - - - +
187B ALA* 1.3 63.3 + - - +
189B ALA* 3.5 8.1 + - - -
190B ASP* 2.7 36.7 + - - +
199B ARG* 3.4 24.9 + - - +
203B VAL* 5.9 1.5 - - - +
223D HIS* 6.1 0.3 - - - -
225D GLY* 4.6 14.6 - - - -
228D LYS* 3.9 6.4 + - - -
251D ARG* 5.3 7.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 187 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B THR* 2.8 19.1 + - + +
184B ALA* 3.1 15.0 - - - +
185B LEU 2.5 6.7 + - - -
186B ASP* 1.3 77.1 + - - +
188B LEU* 1.3 60.9 + - + +
190B ASP* 3.1 6.5 + - - +
191B GLY* 3.0 22.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 188 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B ALA* 3.0 17.5 - - + +
185B LEU* 2.8 12.4 + - + +
187B ALA* 1.3 74.3 - - + +
189B ALA* 1.3 55.7 + - + +
190B ASP 2.8 11.2 + - - -
191B GLY* 3.1 3.4 + - - +
192B GLY* 3.0 22.5 + - - -
202B ALA* 5.1 1.2 - - - +
206B GLY* 4.9 14.6 - - - -
209B ALA* 6.5 0.2 - - + -
210B LEU* 4.5 28.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 189 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B LEU* 2.9 17.8 + - + +
186B ASP* 3.6 5.4 - - - +
188B LEU* 1.3 73.8 - - - +
190B ASP* 1.3 52.9 + - - +
193B VAL* 3.2 16.3 - - - +
199B ARG* 2.7 28.6 + - - +
202B ALA* 3.8 13.0 + - + -
203B VAL* 3.3 46.9 - - + +
206B GLY* 6.1 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 190 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B ASP* 2.7 23.7 - - - +
187B ALA* 3.1 11.1 - - - +
189B ALA* 1.3 72.4 - - - +
191B GLY* 1.3 73.3 + - - +
192B GLY 3.1 0.9 - - - -
193B VAL* 2.8 10.1 + - - +
194B LYS* 2.7 24.7 + - - +
199B ARG* 2.6 22.7 + - - -
228D LYS* 2.7 34.4 + - - -
229D ASP* 4.0 0.7 - - - +
232D SER* 6.1 0.7 - - - -
239D ILE* 4.4 11.9 - - + +
242D LEU* 5.5 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 191 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B ALA 3.0 13.4 + - - -
188B LEU* 3.1 5.0 + - - -
190B ASP* 1.3 75.3 - - - +
192B GLY* 1.3 55.9 + - - +
194B LYS* 2.8 33.2 + - - +
195B MET* 3.1 12.6 + - - +
243D HIS* 6.5 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 192 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B LEU 3.0 13.5 + - - -
191B GLY* 1.3 72.0 - - - +
193B VAL* 1.3 63.5 + - - +
194B LYS 3.1 0.9 - - - -
195B MET* 3.1 19.8 + - - +
196B GLY 3.2 0.9 + - - -
197B LEU* 3.2 33.8 + - - +
202B ALA* 4.8 3.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 193 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B ALA 3.2 26.2 - - - +
190B ASP* 2.8 16.0 + - - +
192B GLY* 1.3 72.3 - - - +
194B LYS* 1.3 51.4 + - - +
196B GLY* 2.7 14.0 + - - -
197B LEU 3.3 14.1 - - - +
198B PRO 3.8 6.3 - - - +
199B ARG* 3.8 33.0 - - + +
202B ALA* 4.1 2.0 - - + +
232D SER* 4.4 13.9 - - - +
234D PRO* 2.7 43.2 - - + +
239D ILE* 4.6 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 194 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B ASP 2.7 10.6 + - - +
191B GLY* 2.8 19.7 - - - +
193B VAL* 1.3 78.4 - - - +
195B MET* 1.3 77.2 + - + +
196B GLY 3.3 3.1 + - - -
234D PRO 3.6 8.1 - - - +
235D GLY 3.8 9.9 - - - +
239D ILE* 3.9 21.9 - - + +
240D HIS* 3.0 48.2 + - + +
243D HIS* 3.3 45.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 195 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B GLY 3.1 11.8 + - - +
192B GLY* 3.1 16.6 + - - +
193B VAL 3.0 1.0 - - - -
194B LYS* 1.3 112.5 - - + +
196B GLY* 1.3 54.6 + - - -
197B LEU* 3.7 5.6 + - + +
240D HIS* 5.1 5.4 - - + -
----------------------------------------------------------
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