Contacts of the helix formed by residues 187 - 206 (chain B) in PDB entry 2QQ6
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 187 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B LEU* 3.0 11.9 + - - +
179B ARG* 5.2 17.5 - - - -
185B ALA 4.1 1.0 + - - -
186B ILE* 1.3 74.1 - - - +
188B PRO* 1.3 78.7 - - - +
189B ARG* 3.9 3.2 + - - +
190B GLU* 2.8 43.0 + - - +
191B HIS* 2.9 23.9 + - - +
226B ARG* 4.9 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 188 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B ILE 4.6 1.1 - - - +
187B SER* 1.3 90.4 - - - +
189B ARG* 1.3 57.5 + - + +
191B HIS* 3.2 9.9 - - - +
192B GLU* 3.0 27.2 - - - +
226B ARG* 4.1 20.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 189 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B LEU* 3.2 34.2 - - + +
187B SER* 3.3 3.3 + - - +
188B PRO* 1.3 77.1 - - + +
190B GLU* 1.3 59.2 + - - +
191B HIS 3.1 1.8 - - - -
192B GLU* 3.4 10.6 + - + +
193B ALA* 3.0 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 190 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B LEU* 5.5 5.4 - - + -
172B ASP* 4.7 8.5 + - + +
173B ILE* 5.2 0.3 - - - +
177B LEU* 3.3 35.9 - - + +
178B HIS* 3.0 35.4 + - - +
179B ARG 4.8 0.3 + - - -
185B ALA 3.7 4.0 - - - +
186B ILE* 3.3 16.6 - - + +
187B SER* 2.8 39.7 + - - +
189B ARG* 1.3 77.3 - - - +
191B HIS* 1.3 61.1 + - - +
193B ALA* 3.4 3.0 - - - +
194B MSE 3.1 35.5 + - + +
219B PHE* 4.4 7.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 191 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B ILE* 3.6 18.5 - - + +
187B SER 2.9 12.8 + - - +
188B PRO* 3.2 13.2 - - + +
189B ARG 3.1 0.2 - - - -
190B GLU* 1.3 75.1 - - - +
192B GLU* 1.3 83.8 + - - +
194B MSE 3.2 7.6 + - - +
195B VAL* 3.2 39.1 + - + +
226B ARG* 3.7 56.4 + - + +
227B PHE* 3.8 25.4 + + - +
230B ALA* 4.2 8.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 192 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B PRO* 3.0 22.0 + - - +
189B ARG* 3.4 11.4 + - + +
191B HIS* 1.3 93.4 - - - +
193B ALA* 1.3 64.4 + - - +
195B VAL* 3.3 6.9 + - - +
196B ALA* 2.9 24.7 + - - +
226B ARG* 3.8 12.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 193 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B LEU* 3.9 23.8 - - + +
143B PHE* 5.2 3.6 - - + -
148B ASN* 5.4 0.3 - - - +
177B LEU* 3.9 20.4 - - + -
189B ARG* 3.0 14.6 + - + +
190B GLU* 3.4 11.0 - - - +
192B GLU* 1.3 77.3 - - - +
194B MSE 1.3 62.2 + - - +
196B ALA* 3.2 9.3 - - - +
197B ARG 3.1 16.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 194 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B LEU* 3.7 16.6 - - + -
170B VAL* 3.1 48.3 - - + +
171B ASP* 5.5 0.7 - - - -
172B ASP 6.1 0.2 - - - -
186B ILE* 3.8 40.4 - - + -
190B GLU* 3.1 25.4 + - - +
191B HIS* 3.2 7.4 + - - +
193B ALA* 1.3 74.9 - - - +
195B VAL* 1.3 65.0 + - - +
197B ARG* 3.1 14.1 + - - +
198B VAL* 3.1 18.0 + - - +
215B MSE 5.0 1.6 - - - -
219B PHE* 4.5 13.5 - - + -
227B PHE* 3.6 26.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 195 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B HIS* 3.2 35.5 + - + +
192B GLU* 3.8 8.3 - - - +
194B MSE 1.3 76.0 - - - +
196B ALA* 1.3 57.0 + - - +
198B VAL* 3.1 8.7 + - - +
199B ALA* 2.8 30.0 + - + +
227B PHE* 4.0 13.2 - - + -
230B ALA* 4.4 8.5 - - + +
231B MSE 4.2 6.1 - - + -
234B PHE* 3.8 29.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 196 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B ASN* 4.3 8.5 - - - +
192B GLU 2.9 13.4 + - - +
193B ALA* 3.2 14.8 - - - +
195B VAL* 1.3 78.7 - - - +
197B ARG* 1.3 63.4 + - - +
199B ALA* 3.3 5.5 + - - +
200B ALA* 2.9 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 197 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B ASN* 5.2 0.8 - - - +
142B LEU* 2.8 56.8 + - + +
147B SER* 3.3 17.0 - - - -
148B ASN* 3.5 25.5 + - - +
151B TYR* 3.4 47.1 - - - -
168B LEU* 4.7 6.3 - - + -
169B ASP 4.1 22.0 + - - +
170B VAL* 4.6 6.0 - - + +
193B ALA 3.1 8.2 + - - +
194B MSE 3.1 10.4 + - - +
196B ALA* 1.3 80.0 - - - +
198B VAL* 1.3 67.0 + - - +
200B ALA* 3.5 1.3 + - - +
201B VAL* 3.0 36.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 198 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B LEU* 6.4 0.2 - - - -
170B VAL* 4.2 9.9 - - + -
194B MSE 3.1 17.9 + - - +
195B VAL 3.1 5.6 + - - +
197B ARG* 1.3 79.5 - - - +
199B ALA* 1.3 67.3 + - - +
201B VAL* 3.0 11.9 + - - +
202B ARG* 3.0 12.4 + - + +
211B VAL* 6.2 0.9 - - + -
213B ILE* 3.4 35.4 - - + -
227B PHE* 4.4 2.7 - - + -
231B MSE 3.7 31.9 - - + -
234B PHE* 3.9 20.4 - - + -
236B LEU* 4.0 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 199 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B VAL* 2.8 20.6 + - + +
196B ALA* 3.8 6.5 - - - +
198B VAL* 1.3 72.4 - - - +
200B ALA* 1.3 63.7 + - - +
202B ARG* 3.1 2.3 + - - +
203B GLU* 3.0 29.7 + - - +
234B PHE* 3.5 27.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 200 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B ASN* 4.2 25.6 - - + +
152B ILE* 3.4 25.1 - - + +
196B ALA 2.9 18.4 + - - +
197B ARG 3.6 4.7 - - - +
199B ALA* 1.3 77.6 - - - +
201B VAL* 1.3 63.9 + - + +
203B GLU* 4.4 5.1 - - - +
204B ALA* 3.5 12.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 201 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B TYR* 4.7 9.2 - - + +
152B ILE* 4.6 7.4 - - + -
155B ALA* 4.0 24.0 - - + -
166B ILE* 5.0 5.8 - - + -
168B LEU* 3.5 36.3 - - + -
197B ARG* 3.0 28.7 - - - +
198B VAL* 3.0 6.6 + - - +
200B ALA* 1.3 77.4 - - + +
202B ARG* 1.3 65.8 + - - +
204B ALA* 3.3 4.1 + - - +
205B VAL* 3.1 26.1 + - + +
211B VAL* 5.2 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 202 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B VAL* 3.0 13.6 + - + +
199B ALA 3.6 5.8 - - - +
201B VAL* 1.3 77.6 - - - +
203B GLU* 1.3 65.8 + - - +
204B ALA 3.0 0.3 + - - -
205B VAL* 5.4 1.3 - - - +
206B GLY* 2.9 50.0 + - - +
207B PRO* 3.7 14.7 + - - +
209B VAL* 3.1 19.2 + - - +
210B GLU* 5.2 0.4 - - - +
211B VAL* 2.9 38.1 - - + +
234B PHE* 3.1 50.0 + - + +
235B GLY 3.4 14.8 + - - -
236B LEU* 4.4 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 203 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B ALA* 3.0 18.4 + - - +
200B ALA* 4.4 4.7 - - - +
202B ARG* 1.3 77.9 - - - +
204B ALA* 1.3 61.3 + - - +
206B GLY* 4.3 3.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 204 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B ILE* 3.3 37.2 - - + -
156B ARG* 3.8 25.8 + - - +
200B ALA 3.5 14.2 + - - +
201B VAL 3.3 4.9 + - - +
202B ARG 3.0 0.8 - - - -
203B GLU* 1.3 83.5 - - - +
205B VAL* 1.3 66.6 + - + +
206B GLY 3.6 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 205 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B ALA* 3.7 32.8 - - + -
156B ARG* 4.8 7.0 - - + +
159B VAL* 3.7 17.7 - - + -
166B ILE* 5.9 3.1 - - + -
201B VAL* 3.1 21.2 + - + +
202B ARG* 4.5 1.1 - - - +
204B ALA* 1.3 79.5 - - + +
206B GLY* 1.3 61.1 + - - +
209B VAL* 3.2 44.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 206 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B ARG* 2.9 36.5 + - - -
203B GLU 4.3 3.3 + - - -
204B ALA 3.4 3.2 + - - -
205B VAL* 1.3 82.4 - - - +
207B PRO* 1.3 72.7 - - - +
208B GLU 3.4 3.8 + - - -
209B VAL* 3.9 7.0 + - - +
----------------------------------------------------------
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