Contacts of the helix formed by residues 206 - 227 (chain A) in PDB entry 1JQO
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 206 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A ASP 4.7 5.2 - - - +
205A ILE* 1.3 80.0 - - - +
207A ASP* 1.3 65.6 + - - +
208A ASP* 3.6 5.7 + - - +
209A ASP* 2.9 34.5 + - - +
210A LYS* 3.3 18.9 + - - +
122B ARG* 5.5 11.2 - - + +
262B ARG* 4.8 2.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 207 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A THR* 1.3 75.7 - - - +
208A ASP* 1.3 69.6 + - - +
210A LYS* 3.3 7.4 + - - +
211A GLN* 3.0 24.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 208 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A THR* 3.6 3.5 + - - +
207A ASP* 1.3 79.7 - - - +
209A ASP* 1.3 71.1 + - - +
211A GLN* 3.2 13.0 + - - +
212A GLU* 3.1 23.3 + - - +
142B ASP* 5.6 1.2 - - - +
144B GLU* 3.3 18.9 - - - +
262B ARG* 3.7 33.6 + - - +
265B THR* 3.4 12.7 - - + +
269B ASN* 3.0 25.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 209 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A ILE* 3.9 17.2 - - + +
206A THR* 2.9 43.9 + - - +
208A ASP* 1.3 80.8 - - - +
210A LYS* 1.3 62.9 + - - +
212A GLU* 3.1 11.6 + - - +
213A LEU* 3.0 20.9 + - + +
262B ARG* 3.2 24.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 210 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A LEU* 3.6 30.6 - - + +
201A ASN* 5.7 0.2 - - - +
202A ALA 4.6 4.9 + - - -
203A LYS* 5.8 4.0 - - - +
205A ILE* 3.1 32.1 + - + +
206A THR 3.3 8.1 + - - +
207A ASP* 3.3 9.5 + - - +
209A ASP* 1.3 76.9 - - - +
211A GLN* 1.3 66.0 + - - +
213A LEU* 2.9 22.3 + - - +
214A ASP* 2.9 13.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 211 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A ASP 3.0 12.3 + - - +
208A ASP* 3.4 26.7 - - - +
210A LYS* 1.3 77.4 - - - +
212A GLU* 1.3 62.9 + - + +
214A ASP* 3.5 7.7 - - - +
215A GLU* 3.3 29.9 + - + +
265B THR* 4.2 13.1 - - - +
268B LYS* 4.2 22.1 - - - +
269B ASN* 4.1 15.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 212 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A ASP 3.1 11.9 + - - +
209A ASP* 3.1 7.1 + - - +
210A LYS 3.1 0.6 - - - -
211A GLN* 1.3 77.3 - - + +
213A LEU* 1.3 66.0 + - - +
214A ASP 3.1 1.8 - - - -
215A GLU* 3.1 18.9 + - - +
216A ALA* 2.9 21.2 + - - +
219A ARG* 5.5 0.5 + - - -
258B LYS 5.5 0.5 - - - +
261B ARG* 4.6 22.2 - - + +
262B ARG* 2.8 45.3 + - - +
265B THR* 2.7 30.2 + - - +
275B ARG* 6.0 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 213 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A CYS* 4.1 15.9 - - - +
199A GLN* 3.6 45.5 - - + +
200A LEU* 3.5 13.6 - - + +
205A ILE* 4.1 20.0 - - + -
209A ASP* 3.0 36.8 + - + +
210A LYS* 2.9 11.6 + - - +
212A GLU* 1.3 77.9 - - + +
214A ASP* 1.3 61.7 + - - +
216A ALA* 2.9 22.7 - - - +
217A LEU* 3.0 10.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 214 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ARG* 2.8 39.6 + - - -
200A LEU* 4.1 15.6 - - + +
210A LYS 2.9 10.4 + - - +
211A GLN* 3.5 13.0 - - - +
213A LEU* 1.3 73.2 - - - +
215A GLU* 1.3 68.0 + - - +
216A ALA 2.9 1.3 - - - -
217A LEU* 2.8 22.2 + - - +
218A GLN* 2.6 43.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 215 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A GLN* 3.4 22.4 + - + +
212A GLU* 3.1 16.3 + - - +
214A ASP* 1.3 78.8 - - - +
216A ALA* 1.3 62.6 + - - +
218A GLN* 3.4 16.2 + - - +
219A ARG* 3.1 43.2 + - - +
261B ARG* 5.4 0.5 + - - -
265B THR* 5.6 1.5 + - - -
268B LYS* 2.8 30.4 + - - -
275B ARG* 3.2 27.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 216 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A CYS* 3.6 20.4 - - - -
212A GLU 2.9 11.7 + - - +
213A LEU* 2.9 16.4 - - - +
215A GLU* 1.3 76.4 - - - +
217A LEU* 1.3 67.6 + - - +
218A GLN 3.1 0.7 + - - -
219A ARG* 3.2 20.0 + - - +
220A GLU* 3.1 25.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 217 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A LEU* 5.3 4.3 - - + -
41A LEU* 4.1 15.3 - - + -
44A ARG* 4.8 9.0 - - + -
193A ILE* 4.1 14.4 - - + +
196A CYS* 4.1 12.5 - - + -
197A LEU* 4.0 29.2 - - + +
200A LEU* 3.7 28.0 - - + -
213A LEU 3.0 6.9 + - - +
214A ASP* 2.8 17.6 + - - +
216A ALA* 1.3 75.6 - - - +
218A GLN* 1.3 62.3 + - + +
220A GLU* 3.5 5.7 + - - +
221A ILE* 3.1 53.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 218 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ARG* 3.8 29.9 - - + +
47A ASN* 5.8 2.8 - - - +
48A ILE* 3.3 25.7 - - + +
214A ASP* 2.6 34.2 + - - +
215A GLU* 3.7 17.8 - - - +
216A ALA 3.1 0.2 - - - -
217A LEU* 1.3 75.7 - - + +
219A ARG* 1.3 61.7 + - - +
221A ILE* 3.0 7.5 + - - +
222A GLN* 2.8 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 219 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A GLU 5.5 0.6 + - - -
215A GLU* 3.1 37.8 + - - +
216A ALA* 3.3 26.1 - - - +
218A GLN* 1.3 78.9 - - - +
220A GLU* 1.3 62.5 + - - +
222A GLN* 3.6 10.1 - - - +
223A ALA* 2.6 37.0 + - - +
261B ARG* 3.4 27.9 - - - +
275B ARG* 4.3 3.0 - - - +
329B GLU* 5.4 4.9 - - - +
430B ALA* 2.9 41.3 + - + +
431B ILE* 4.2 8.4 - - - +
433B ASP* 3.9 6.4 + - - +
434B GLY* 3.6 30.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 220 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A GLN* 3.7 4.5 - - - +
189A LYS* 3.5 33.0 - - + +
192A ARG* 3.4 55.2 + - + -
193A ILE* 4.0 11.4 - - + +
196A CYS* 6.3 1.3 - - - -
216A ALA 3.1 18.1 + - - +
217A LEU* 3.8 5.8 - - - +
219A ARG* 1.3 79.6 - - - +
221A ILE* 1.3 65.8 + - - +
223A ALA* 3.6 4.7 - - - +
224A ALA* 2.9 25.8 + - - +
329B GLU* 3.8 16.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 221 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A LEU* 4.1 11.7 - - - +
44A ARG* 4.0 22.2 - - + -
45A PHE* 3.9 27.3 - - + -
48A ILE* 3.4 16.8 - - + -
104A HIS* 5.7 0.2 + - - -
108A LEU* 4.3 16.2 - - + -
193A ILE* 4.3 17.7 - - + +
217A LEU* 3.1 39.9 + - + +
218A GLN* 3.0 8.9 + - - +
220A GLU* 1.3 77.7 - - - +
222A GLN* 1.3 59.0 + - - +
224A ALA* 3.3 4.5 + - - +
225A PHE* 2.9 27.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 222 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A ILE* 3.8 29.6 - - + +
52A LEU* 4.0 15.8 - - + +
218A GLN 2.8 14.7 + - - +
219A ARG* 3.6 6.3 - - - +
221A ILE* 1.3 76.1 - - - +
223A ALA* 1.3 54.6 + - - +
225A PHE* 3.1 8.4 + - - +
226A ARG* 2.7 36.6 + - - +
427B GLY 4.1 4.8 + - - -
428B ASP* 3.1 42.8 + - - +
430B ALA* 3.8 20.6 - - - +
431B ILE* 3.9 10.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 223 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A LYS* 4.0 17.3 - - + -
219A ARG 2.6 22.5 + - - +
220A GLU* 3.6 11.9 - - - +
222A GLN* 1.3 72.4 - - - +
224A ALA* 1.3 62.6 + - - +
226A ARG* 3.1 9.4 + - - +
227A THR* 3.0 21.7 + - - -
329B GLU* 5.8 4.7 - - + +
332B MET* 3.7 8.1 - - + +
431B ILE* 3.5 25.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 224 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A HIS* 3.5 17.9 - - + +
186A LEU* 4.2 18.2 - - + +
189A LYS* 3.8 29.8 - - + +
193A ILE* 5.2 3.8 - - + -
220A GLU 2.9 17.3 + - - +
221A ILE* 3.5 6.3 - - - +
223A ALA* 1.3 75.8 - - - +
225A PHE* 1.3 63.9 + - - +
226A ARG 3.2 0.5 + - - -
227A THR* 3.3 19.2 + - - +
229A GLU* 4.9 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 225 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A PHE* 3.6 31.2 - + + -
48A ILE* 5.1 3.8 - - + -
49A LEU* 3.8 22.2 - - + -
52A LEU* 3.8 23.3 - - + -
53A HIS* 3.7 30.1 - + - -
97A LEU* 4.4 13.5 - - + -
100A SER* 4.0 16.7 + - - -
101A SER* 4.3 9.2 - - - -
104A HIS* 3.6 24.4 + + + -
221A ILE 2.9 14.6 + - - +
222A GLN* 3.4 11.0 - - - +
224A ALA* 1.3 77.6 - - - +
226A ARG* 1.3 64.1 + - - +
227A THR 3.6 4.7 + - - +
229A GLU* 4.2 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 226 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A LEU* 3.2 48.3 + - - +
53A HIS* 5.5 7.2 + - - -
222A GLN* 2.7 21.1 + - - +
223A ALA 3.5 6.7 - - - +
224A ALA 3.1 0.8 - - - -
225A PHE* 1.3 82.5 - - - +
227A THR* 1.3 58.0 + - - +
332B MET* 3.7 22.7 - - + +
333B TRP* 3.5 23.7 + - - +
334B ARG* 3.1 34.4 - - - +
426B CYS 3.9 12.9 + - - -
427B GLY* 4.9 1.0 - - - -
428B ASP* 3.0 37.0 + - - +
431B ILE* 4.2 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 227 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A ARG* 4.2 12.8 - - - +
185A SER* 4.3 9.6 - - - -
189A LYS* 4.1 4.1 - - - -
223A ALA 3.0 16.2 + - - -
224A ALA* 3.3 9.6 + - - +
225A PHE 4.0 1.7 - - - +
226A ARG* 1.3 79.3 - - - +
228A ASP* 1.3 72.3 + - - +
229A GLU* 3.0 23.0 - - - +
331B SER* 2.7 50.7 + - - +
332B MET* 3.9 2.0 - - - +
333B TRP* 4.4 1.6 - - - -
----------------------------------------------------------
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