Contacts of the helix formed by residues 215 - 231 (chain D) in PDB entry 1JIQ
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 215 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157D ILE* 3.6 33.4 - - + -
210D SER* 2.9 23.0 + - - -
211D LYS 5.1 0.7 + - - -
212D THR* 3.6 8.1 + - - -
213D PHE 3.8 1.0 - - - -
214D THR* 1.3 73.8 + - - +
216D GLN* 1.3 67.9 + - - +
217D GLU 3.4 1.0 + - - +
218D THR* 3.4 17.9 + - - +
219D ILE* 2.9 23.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 216 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424C ILE* 3.9 28.2 - - + +
428C ASN* 4.8 5.3 + - - +
214D THR 3.0 7.8 + - - +
215D THR* 1.3 73.1 - - - +
217D GLU* 1.3 61.3 + - + +
219D ILE* 4.1 2.1 - - - +
220D THR* 2.5 45.5 + - - +
522D ALA* 6.0 1.4 - - - +
523D LYS* 3.4 20.9 + - - +
526D GLU* 2.8 35.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 217 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385C THR* 2.6 30.7 + - - +
388C GLN* 4.3 3.8 + - - -
389C HIS* 2.5 36.0 + - - -
424C ILE* 4.8 8.7 - - + -
428C ASN* 4.4 5.9 + - - +
157D ILE* 3.9 15.9 - - + +
185D SER 4.1 4.1 - - - +
187D ILE* 3.3 41.4 + - + +
215D THR* 3.5 1.4 - - - +
216D GLN* 1.3 81.5 - - + +
218D THR* 1.3 58.2 + - - +
220D THR* 3.3 2.4 + - - -
221D ASN* 2.9 35.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 218 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155D ILE* 3.5 34.4 - - - +
156D GLY* 3.5 2.0 - - - -
157D ILE* 3.4 30.1 + - - +
208D ILE* 4.2 13.9 - - + -
209D ALA 3.7 14.7 + - - +
210D SER* 4.2 5.8 - - - -
215D THR* 3.4 22.4 + - - +
217D GLU* 1.3 78.5 - - - +
219D ILE* 1.3 56.5 + - + +
221D ASN* 3.3 5.5 + - - +
222D ALA* 2.9 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 219 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208D ILE* 3.9 24.2 - - + -
210D SER* 4.6 1.1 - - - -
213D PHE* 3.5 52.9 - - + +
214D THR* 4.0 3.6 - - - +
215D THR* 2.9 26.4 + - - +
216D GLN* 4.3 1.8 - - - +
218D THR* 1.3 74.1 - - + +
220D THR* 1.3 60.7 + - - +
222D ALA* 3.1 5.9 + - + +
223D GLU* 2.9 51.5 + - + +
256D PHE* 5.4 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 220 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417C ARG* 3.4 6.2 + - - +
420C LEU* 3.9 26.9 - - + +
421C HIS* 3.9 14.4 - - + +
424C ILE* 4.0 14.2 - - + +
187D ILE* 3.9 20.9 - - + -
216D GLN* 2.5 27.9 + - - +
217D GLU 3.6 4.5 - - - -
219D ILE* 1.3 77.4 - - - +
221D ASN* 1.3 62.2 + - - +
223D GLU* 3.3 6.2 + - - -
224D THR* 3.1 25.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 221 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421C HIS* 3.1 26.0 + - - -
155D ILE* 3.5 22.8 - - + +
184D VAL* 4.0 17.1 - - + +
185D SER* 3.8 13.1 + - - +
186D ASN 3.1 27.1 + - - +
187D ILE* 4.1 2.2 - - - +
188D ASP 5.2 0.2 - - - +
192D ILE* 3.7 18.7 - - + +
217D GLU 2.9 22.5 + - - +
218D THR* 4.8 0.8 - - - +
220D THR* 1.3 75.5 - - - +
222D ALA* 1.3 57.3 + - - +
224D THR* 3.3 3.9 + - - -
225D ALA* 3.0 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 222 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155D ILE* 4.2 6.0 - - - +
208D ILE* 3.8 35.7 - - + -
218D THR 2.9 14.1 + - - +
219D ILE* 3.1 12.3 + - + +
221D ASN* 1.3 77.2 - - - +
223D GLU* 1.3 57.6 + - - +
225D ALA* 3.1 4.0 + - - +
226D LYS 2.9 24.1 + - - -
243D PHE* 4.1 0.3 - - - -
256D PHE* 3.5 27.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 223 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417C ARG* 3.9 22.2 + - - +
219D ILE* 2.9 37.3 + - + +
220D THR* 3.8 7.1 - - - +
222D ALA* 1.3 73.4 - - - +
224D THR* 1.3 61.0 + - - +
226D LYS* 3.7 14.1 + - - +
227D GLU* 2.9 31.8 + - - +
256D PHE* 4.1 16.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 224 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416C ILE* 4.1 13.7 - - + -
417C ARG* 2.8 32.4 + - + +
421C HIS* 2.8 25.0 + - - -
192D ILE* 4.0 26.0 - - + -
196D LEU* 4.6 5.8 - - + -
220D THR 3.1 5.8 + - - -
221D ASN* 3.5 9.2 - - - -
222D ALA 3.3 0.2 - - - -
223D GLU* 1.3 76.7 - - - +
225D ALA* 1.3 62.3 + - - +
227D GLU* 3.6 4.8 + - - +
228D TRP* 3.1 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 225 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155D ILE* 4.1 12.3 - - + -
192D ILE* 4.2 4.9 - - + +
196D LEU* 4.4 11.0 - - + -
206D PHE* 4.0 26.9 - - + -
221D ASN 3.0 13.4 + - - +
222D ALA 3.4 8.1 - - - +
224D THR* 1.3 78.5 - - - +
226D LYS* 1.3 56.8 + - - +
228D TRP* 3.4 8.1 + - - +
229D PHE* 2.9 28.2 + - - +
243D PHE* 3.9 10.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 226 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222D ALA 2.9 16.3 + - - +
223D GLU* 3.7 13.1 + - - +
225D ALA* 1.3 73.7 - - - +
227D GLU* 1.3 61.5 + - - +
229D PHE* 3.0 2.6 + - - +
230D LEU* 2.8 48.2 + - + +
239D VAL* 4.1 19.5 - - + -
243D PHE* 3.6 12.5 - - + -
255D GLU 4.4 2.6 + - - -
256D PHE* 2.7 65.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 227 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417C ARG* 3.6 30.7 + - - +
223D GLU 2.9 18.4 + - - +
224D THR* 3.8 5.9 - - - +
226D LYS* 1.3 76.7 - - - +
228D TRP* 1.3 64.2 + - - +
230D LEU* 3.4 7.6 + - - +
231D GLN* 3.2 41.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 228 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196D LEU* 3.7 49.4 + - + +
199D LEU* 3.8 29.2 - - + -
200D ASN 4.3 0.2 - - - -
201D PRO* 3.5 48.6 - - + +
204D SER* 4.8 0.7 - - - -
206D PHE* 3.8 23.1 - + - -
224D THR 3.1 18.2 + - - +
225D ALA 3.5 8.7 - - - +
227D GLU* 1.3 77.0 + - - +
229D PHE* 1.3 81.1 + + + +
231D GLN* 3.4 31.5 + - - +
232D ALA* 3.9 5.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 229 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144D TYR* 4.1 13.0 - + - -
201D PRO* 3.6 26.5 - - + -
204D SER 5.5 0.2 - - - -
206D PHE* 5.4 2.5 - + - -
225D ALA 2.9 14.5 + - - +
226D LYS 3.0 6.9 + - - +
228D TRP* 1.3 89.6 - + + +
230D LEU* 1.3 71.2 + - + +
231D GLN 3.0 0.2 - - - -
232D ALA* 2.9 27.4 + - - +
233D ALA* 3.7 5.8 + - + -
238D ALA* 3.5 35.4 - - + -
239D VAL* 3.8 11.0 - - + -
242D HIS* 3.2 44.4 - + + -
243D PHE* 4.0 21.1 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 230 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226D LYS* 2.8 41.7 + - + +
227D GLU* 3.4 7.2 + - - +
229D PHE* 1.3 78.4 - - + +
231D GLN* 1.3 57.4 + - - +
232D ALA 3.2 1.6 - - - -
233D ALA 3.8 5.8 - - - +
234D LYS* 2.9 40.8 + - + +
235D ASP 3.6 41.5 - - - +
236D PRO* 4.3 6.7 - - + -
239D VAL* 3.9 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 231 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227D GLU* 3.2 29.9 + - + +
228D TRP* 3.5 26.3 + - - +
229D PHE 3.0 1.6 + - - -
230D LEU* 1.3 77.1 - - - +
232D ALA* 1.3 60.8 + - - +
233D ALA 3.4 0.2 - - - -
234D LYS* 3.7 17.9 - - - +
----------------------------------------------------------
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