Contacts of the helix formed by residues 187 - 206 (chain A) 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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A LEU 3.5 7.5 + - - -
179A ARG* 3.4 35.1 - - - +
185A ALA 4.2 0.6 + - - -
186A ILE* 1.3 73.7 - - - +
188A PRO* 1.3 65.4 - - - +
189A ARG* 3.6 5.9 + - - +
190A GLU* 2.9 33.7 + - - +
191A HIS* 2.6 37.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 188 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A ARG* 3.2 23.1 - - - +
186A ILE 4.0 2.0 - - - +
187A SER* 1.3 86.3 - - - +
189A ARG* 1.3 61.7 + - - +
191A HIS* 3.3 17.5 - - + +
192A GLU* 3.3 13.2 + - - +
226A ARG* 5.6 7.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 189 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A LEU* 3.8 28.2 - - + +
187A SER* 3.1 5.1 + - - +
188A PRO* 1.3 79.5 - - - +
190A GLU* 1.3 65.3 + - - +
191A HIS 3.1 0.2 - - - -
192A GLU* 2.6 36.2 - - - +
193A ALA* 3.3 5.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 190 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A LEU* 3.9 13.5 - - + +
172A ASP 3.6 12.0 + - - +
173A ILE* 4.5 0.2 - - - +
177A LEU* 3.5 31.5 - - + +
178A HIS* 2.6 38.2 + - - -
179A ARG* 5.0 0.9 + - - +
185A ALA 3.8 0.5 - - - +
186A ILE* 3.3 6.0 - - - -
187A SER* 2.9 36.8 + - - +
189A ARG* 1.3 76.2 - - - +
191A HIS* 1.3 64.8 + - - +
193A ALA* 3.4 4.0 + - - +
194A MSE 2.9 43.5 + - + +
219A PHE* 4.5 6.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 191 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A ILE* 3.6 11.0 - - + +
187A SER 2.6 20.6 + - - +
188A PRO* 3.3 7.9 - - + +
190A GLU* 1.3 72.6 - - - +
192A GLU* 1.3 68.5 + - + +
193A ALA 3.0 0.2 - - - -
194A MSE 2.8 39.4 + - - +
195A VAL* 3.2 17.9 + - + +
226A ARG* 3.0 38.0 + - + +
227A PHE* 3.7 43.9 + + - +
230A ALA* 4.0 11.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 192 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A PRO 3.4 15.3 - - - +
189A ARG* 2.6 29.5 - - - +
191A HIS* 1.3 87.6 - - + +
193A ALA* 1.3 71.9 + - - +
194A MSE 3.2 0.2 - - - -
195A VAL* 3.8 8.9 - - + +
196A ALA* 3.0 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 193 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A LEU* 3.9 18.0 - - + +
148A ASN* 5.2 1.2 + - - +
177A LEU* 3.6 20.9 - - + -
189A ARG 3.4 10.1 - - - +
190A GLU 3.4 11.4 - - - +
191A HIS 3.0 0.4 + - - -
192A GLU* 1.3 86.6 + - - +
194A MSE 1.3 64.4 + - - +
196A ALA* 3.5 6.8 + - - +
197A ARG* 3.2 19.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 194 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A LEU* 3.4 23.1 - - + -
170A VAL* 3.6 25.3 - - + +
171A ASP* 5.6 0.2 - - - -
186A ILE* 3.0 54.3 - - + -
190A GLU* 2.9 46.0 - - + +
191A HIS* 2.8 10.0 + - - +
193A ALA* 1.3 75.3 - - - +
195A VAL* 1.3 58.5 + - - +
197A ARG* 2.7 27.2 + - - +
198A VAL* 3.0 15.3 + - - +
215A MSE 6.3 0.4 - - - -
219A PHE* 4.8 9.4 - - - -
227A PHE* 3.4 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 195 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A HIS* 3.2 35.9 + - + +
192A GLU* 3.8 9.0 - - - +
194A MSE 1.3 76.3 - - - +
196A ALA* 1.3 52.9 + - - +
198A VAL* 3.2 2.4 + - - +
199A ALA* 2.7 34.5 + - + +
227A PHE* 4.0 11.2 - - + -
230A ALA* 4.2 8.5 - - + +
231A MSE 4.2 15.5 - - + -
234A PHE* 4.0 26.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 196 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A ASN* 3.8 5.6 + - - +
192A GLU* 3.0 18.1 + - - +
193A ALA* 3.7 8.1 - - - +
194A MSE 3.0 0.2 - - - -
195A VAL* 1.3 74.2 - - - +
197A ARG* 1.3 67.4 + - - +
199A ALA* 3.7 6.9 - - - +
200A ALA* 2.9 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 197 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A ALA* 5.3 0.4 - - - +
137A HIS* 5.1 3.8 + - - -
141A GLY* 3.2 34.4 + - - +
142A LEU* 3.8 22.3 + - + +
147A SER* 4.0 7.7 + - - -
148A ASN* 3.0 36.6 + - - +
151A TYR* 3.2 45.5 + - + -
168A LEU* 4.3 13.2 - - + -
169A ASP* 3.9 20.4 + - - -
170A VAL* 4.4 13.5 - - + +
171A ASP 5.2 3.4 + - - -
172A ASP* 6.1 0.2 - - - +
193A ALA 3.2 9.5 + - - +
194A MSE 2.7 16.6 + - - +
196A ALA* 1.3 76.7 - - - +
198A VAL* 1.3 65.5 + - + +
200A ALA* 3.6 2.1 + - - +
201A VAL* 3.4 21.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 198 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A LEU* 5.7 2.2 - - + -
170A VAL* 3.9 17.9 - - + -
194A MSE 3.0 12.4 + - - +
195A VAL 3.4 7.6 - - - +
197A ARG* 1.3 74.1 - - + +
199A ALA* 1.3 67.2 + - - +
200A ALA 3.0 0.9 + - - -
201A VAL* 3.1 7.4 + - - +
202A ARG* 3.0 21.3 + - + +
211A VAL* 6.2 0.7 - - + -
213A ILE* 3.3 37.0 - - + -
227A PHE* 4.6 1.6 - - + -
231A MSE 3.8 27.1 - - + -
234A PHE* 4.0 20.2 - - + -
236A LEU* 4.3 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 199 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A VAL* 2.7 22.2 + - + +
196A ALA* 3.7 8.1 - - - +
198A VAL* 1.3 72.6 - - - +
200A ALA* 1.3 62.7 + - - +
202A ARG* 3.2 4.2 + - - +
203A GLU* 3.1 22.7 + - - +
234A PHE* 3.5 28.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 200 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A ASN* 4.0 13.9 - - + +
152A ILE* 4.1 20.9 - - + +
196A ALA 2.9 17.9 + - - +
197A ARG 3.7 6.1 - - - +
199A ALA* 1.3 76.1 - - - +
201A VAL* 1.3 63.3 + - - +
203A GLU* 3.3 6.8 + - - +
204A ALA* 3.1 21.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 201 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A ASN* 5.3 0.9 - - - +
151A TYR* 4.5 11.0 - - + -
152A ILE* 4.2 18.2 - - + +
155A ALA* 4.4 10.8 - - + -
166A ILE* 4.2 25.4 - - + -
168A LEU* 3.9 30.5 - - + -
197A ARG* 3.4 15.7 - - + +
198A VAL* 3.1 6.8 + - - +
200A ALA* 1.3 72.8 - - + +
202A ARG* 1.3 66.8 + - - +
204A ALA* 4.2 6.3 - - - -
205A VAL* 3.0 30.0 + - + +
211A VAL* 5.2 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 202 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A VAL* 3.0 14.1 + - + +
199A ALA* 3.4 10.5 - - - +
200A ALA 3.2 0.2 - - - -
201A VAL* 1.3 78.8 - - - +
203A GLU* 1.3 56.4 + - - +
205A VAL* 5.3 0.9 - - - -
206A GLY* 2.8 37.9 + - - +
207A PRO* 4.6 18.1 - - - +
208A GLU 5.6 0.6 - - - +
209A VAL 3.4 14.1 + - - +
210A GLU* 5.4 0.4 - - - +
211A VAL* 3.0 35.8 - - - +
234A PHE* 2.9 50.3 + - + +
235A GLY* 3.2 14.4 + - - -
236A LEU* 6.1 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 203 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A ALA 3.1 8.7 + - - +
200A ALA* 3.3 7.6 + - - +
202A ARG* 1.3 78.5 - - - +
204A ALA* 1.3 67.8 + - - +
206A GLY* 3.4 10.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 204 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A ILE* 3.2 36.6 - - + -
156A ARG* 3.4 30.8 + - + +
200A ALA 3.1 14.6 + - - +
201A VAL* 3.3 5.8 + - - +
203A GLU* 1.3 81.0 - - - +
205A VAL* 1.3 64.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 205 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A ILE 5.8 0.2 - - - +
155A ALA* 4.1 26.5 - - + -
156A ARG* 5.2 4.0 - - + +
159A VAL* 4.5 15.9 - - + -
166A ILE* 4.2 13.5 - - + -
201A VAL* 3.0 18.3 + - + +
202A ARG* 5.3 0.9 - - - -
204A ALA* 1.3 79.4 - - + +
206A GLY* 1.3 63.5 + - - +
207A PRO 3.9 1.0 - - - +
209A VAL* 3.1 51.0 - - + +
211A VAL* 6.4 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 206 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A ARG* 2.8 31.3 + - - +
203A GLU* 3.4 8.0 + - - -
204A ALA 3.3 3.2 - - - -
205A VAL* 1.3 91.6 - - - +
207A PRO* 1.3 72.2 - - - +
209A VAL* 4.1 2.9 - - - +
----------------------------------------------------------
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