Contacts of the helix formed by residues 188 - 206 (chain A) in PDB entry 2QNR
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 THR 188 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A LEU* 1.3 77.7 - - - +
189A LEU* 1.3 58.5 + - - +
190A LYS* 3.6 7.6 + - - +
191A GLU* 3.0 37.9 + - - +
192A ARG* 2.9 26.2 + - - +
256B ARG* 4.0 20.6 - - + +
257B LEU* 3.2 35.9 - - + +
258B TYR* 3.9 6.4 - - + +
259B PRO* 5.7 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 189 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A LEU 5.5 0.2 - - - +
188A THR* 1.3 73.4 - - - +
190A LYS* 1.3 63.9 + - - +
192A ARG* 3.2 43.1 + - - +
193A GLU* 3.1 30.1 + - + +
269A GLU 5.0 4.3 - - - +
257B LEU 4.8 2.6 + - - -
259B PRO* 3.8 32.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 190 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A THR* 3.3 7.8 + - - +
189A LEU* 1.3 79.5 - - - +
191A GLU* 1.3 62.5 + - - +
193A GLU* 3.3 5.2 + - - +
194A ARG* 3.2 38.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 191 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A THR 4.0 0.9 - - - +
187A LEU* 3.5 19.6 - - + +
188A THR* 3.0 39.8 + - - +
190A LYS* 1.3 75.8 - - - +
192A ARG* 1.3 63.5 + - - +
194A ARG* 3.4 33.6 + - - +
195A LEU* 3.1 23.0 + - - +
256B ARG* 2.9 31.1 + - - -
1401B GDP 2.5 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 192 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A ILE* 4.8 0.8 - - + +
184A ALA* 4.5 21.6 + - - +
187A LEU* 4.1 20.0 + - + +
188A THR 2.9 14.7 + - - +
189A LEU* 3.2 38.8 + - - +
191A GLU* 1.3 76.0 - - - +
193A GLU* 1.3 59.5 + - + +
195A LEU* 3.1 5.7 + - - +
196A LYS* 2.9 45.5 + - + +
238A SER* 3.0 33.7 + - - +
268A PRO 4.7 5.3 + - - -
269A GLU 5.0 2.0 + - - -
270A HIS 3.2 28.9 + - - -
271A ASN* 4.1 12.4 - - - +
272A ASP* 4.2 9.3 + - - -
260B TRP* 5.0 3.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 193 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A LEU* 3.1 18.9 + - + +
190A LYS* 3.9 4.9 - - - +
192A ARG* 1.3 75.0 - - + +
194A ARG* 1.3 60.4 + - - +
196A LYS* 3.9 12.1 - - + +
197A LYS* 3.0 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 194 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A HIS* 5.3 10.1 + - - -
190A LYS* 3.2 21.9 + - - +
191A GLU* 3.4 46.3 + - - +
193A GLU* 1.3 75.8 - - - +
195A LEU* 1.3 58.3 + - - +
197A LYS* 3.9 4.1 - - - +
198A ARG* 3.0 30.0 + - - +
1401B GDP 4.4 12.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 195 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A ILE* 5.5 0.4 - - + -
154A SER 4.3 5.4 - - - +
155A PRO* 4.1 15.9 - - + +
157A GLY 3.9 10.1 - - - +
158A HIS* 3.1 39.5 - - - +
159A GLY* 3.8 11.4 - - - +
181A ILE* 4.0 31.4 - - + -
187A LEU* 4.1 14.1 - - + -
191A GLU 3.1 13.6 + - - +
192A ARG* 3.1 8.9 + - - +
194A ARG* 1.3 73.8 - - - +
196A LYS* 1.3 62.1 + - - +
198A ARG 3.3 0.2 + - - -
199A ILE* 2.8 47.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 196 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A ILE* 3.9 13.5 - - + -
192A ARG* 2.9 34.2 + - + +
193A GLU* 3.9 10.5 - - + +
195A LEU* 1.3 72.8 - - - +
197A LYS* 1.3 66.4 + - - +
199A ILE* 3.1 2.8 + - - +
200A LEU* 2.9 31.2 + - + +
233A ALA 6.0 0.4 - - - +
234A SER* 2.7 38.2 + - - +
235A ILE 4.8 2.0 - - - +
236A PRO* 3.3 30.2 - - + +
238A SER* 3.4 18.8 - - - -
272A ASP* 2.8 20.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 197 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A GLU 3.0 19.1 + - - +
194A ARG* 4.0 5.2 - - - +
196A LYS* 1.3 75.9 - - - +
198A ARG* 1.3 62.8 + - - +
200A LEU* 3.4 8.5 + - - +
201A ASP* 3.1 33.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 198 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A HIS* 3.2 48.8 + - - +
159A GLY 4.9 0.6 - - - +
194A ARG 3.0 19.7 + - - +
195A LEU 3.8 0.9 - - - +
197A LYS* 1.3 78.9 - - - +
199A ILE* 1.3 61.5 + - - +
201A ASP* 3.5 7.5 + - + +
202A GLU* 3.2 46.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 199 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A ILE* 4.0 24.5 - - + -
159A GLY* 4.3 6.7 - - - -
160A LEU* 3.8 26.0 - - + +
168A MSE 6.2 0.2 - - + -
179A PRO* 5.2 1.1 - - + -
181A ILE* 3.9 23.3 - - + -
195A LEU* 2.8 46.2 + - + +
196A LYS 3.8 3.4 - - - +
198A ARG* 1.3 75.2 - - - +
200A LEU* 1.3 58.9 + - - +
202A GLU* 3.3 7.6 + - - +
203A ILE* 2.9 42.3 + - + +
236A PRO* 4.0 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 200 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A LYS* 2.9 22.5 + - + +
197A LYS* 3.8 7.0 - - - +
199A ILE* 1.3 74.5 - - - +
201A ASP* 1.3 65.6 + - - +
203A ILE* 3.1 23.1 + - + +
204A GLU* 3.0 24.2 + - - +
210A ILE* 5.0 3.4 - - + -
232A LYS 6.1 0.2 - - - +
235A ILE* 3.7 36.6 - - + +
236A PRO* 4.0 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 201 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A LYS* 3.1 26.0 + - - +
198A ARG* 3.8 7.5 - - + +
199A ILE 3.3 0.2 - - - -
200A LEU* 1.3 78.6 - - - +
202A GLU* 1.3 58.4 + - + +
204A GLU* 3.3 7.6 + - - +
205A GLU* 2.8 31.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 202 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A GLY* 3.5 7.0 - - - -
160A LEU* 3.1 49.4 + - + +
198A ARG* 3.2 46.6 + - + +
199A ILE* 3.8 3.5 - - - +
201A ASP* 1.3 75.0 - - + +
203A ILE* 1.3 66.7 + - - +
205A GLU* 4.0 18.4 - - - +
206A HIS* 3.0 45.7 + - + +
208A ILE* 4.5 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 203 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A LEU* 4.7 8.3 - - + -
168A MSE 5.5 3.1 - - + -
179A PRO* 4.4 8.5 - - + -
199A ILE* 2.9 35.6 + - + +
200A LEU* 3.1 21.7 + - + +
202A GLU* 1.3 78.5 - - - +
204A GLU* 1.3 63.7 + - + +
207A ASN* 3.2 1.2 + - - -
208A ILE* 3.0 60.4 + - + +
210A ILE* 3.8 41.1 - - + -
212A HIS* 6.3 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 204 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A LEU 3.0 14.2 + - - +
201A ASP* 3.3 9.8 + - - +
203A ILE* 1.3 78.6 - - + +
205A GLU* 1.3 67.3 + - - +
207A ASN* 2.9 16.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 205 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A ASP* 2.8 21.0 + - - +
202A GLU* 3.8 23.0 - - - +
204A GLU* 1.3 73.3 - - - +
206A HIS* 1.3 75.6 + - + +
207A ASN* 3.6 1.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 206 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A VAL* 4.0 35.6 - - + +
169A LYS* 4.4 9.7 - - + +
202A GLU* 3.0 41.8 + - + +
205A GLU* 1.3 92.6 - - + +
207A ASN* 1.3 72.5 + - - +
208A ILE* 3.3 18.3 + - + +
----------------------------------------------------------
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