Contacts of the helix formed by residues 218 - 234 (chain B) in PDB entry 4DJH
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 ASP 218 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B PRO* 3.6 12.1 - - + +
216B ASP 3.0 6.5 + - - +
217B ASP* 1.3 76.9 - - + +
219B TYR* 1.3 63.5 + - - +
220B SER* 3.3 3.1 - - - -
221B TRP* 3.2 30.6 + - - +
222B TRP* 3.2 43.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 219 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B SER* 3.7 13.0 + - - -
212B LEU* 2.2 27.5 + - - +
213B GLN* 3.9 13.6 + - - -
214B PHE* 3.3 55.5 - + + -
215B PRO 3.1 10.3 + - - +
216B ASP* 4.1 19.5 - - + +
217B ASP 3.3 4.2 - - - +
218B ASP* 1.3 77.3 - - - +
220B SER* 1.3 68.2 + - - +
221B TRP 3.1 0.7 + - - -
222B TRP* 3.4 1.7 + - - +
223B ASP* 3.2 28.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 220 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B ASP 4.8 4.9 + - - -
218B ASP 4.7 1.2 - - - -
219B TYR* 1.3 82.7 - - - +
221B TRP* 1.3 76.7 + - - +
223B ASP* 3.8 6.0 - - - +
224B LEU* 3.4 19.2 + - - +
1304B PEG 3.8 27.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 221 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B ASP 5.1 3.1 - - - -
218B ASP* 3.2 26.4 + - - +
219B TYR 3.2 0.8 - - - -
220B SER* 1.3 88.4 + - - +
222B TRP* 1.3 55.5 + - - +
223B ASP 3.2 1.3 - - - -
224B LEU* 3.1 26.5 + - + +
225B PHE* 2.7 35.5 + - - +
1304B PEG 3.8 38.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 222 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B PHE* 3.7 28.7 - + + -
215B PRO* 3.6 35.6 - - + +
218B ASP* 3.2 42.7 + - + +
219B TYR 3.9 2.5 - - - +
221B TRP* 1.3 75.8 - - - +
223B ASP* 1.3 65.9 + - - +
225B PHE* 3.0 35.3 + + + +
226B MET* 2.9 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 223 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B LEU* 5.6 3.1 - - - +
214B PHE* 3.8 24.0 - - + -
219B TYR* 3.2 23.7 + - + +
220B SER* 3.8 7.3 - - - +
222B TRP* 1.3 78.5 - - - +
224B LEU* 1.3 55.1 + - - +
226B MET* 3.0 2.6 + - - +
227B LYS* 2.8 76.8 + - - +
298B ALA* 5.0 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 224 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B SER 3.4 10.4 + - - +
221B TRP* 3.1 36.2 + - + +
223B ASP* 1.3 81.4 + - - +
225B PHE* 1.3 65.2 + - - +
227B LYS* 4.4 4.0 - - - -
228B ILE* 2.9 47.6 + - + +
295B LEU* 5.5 0.2 - - + -
298B ALA* 3.8 28.0 - - + +
299B LEU* 3.4 33.0 - - + -
1304B PEG 4.6 12.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 225 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B TRP 2.7 16.7 + - - +
222B TRP* 3.2 36.6 - + + +
224B LEU* 1.3 75.7 - - - +
226B MET* 1.3 65.2 + - + +
228B ILE* 3.5 6.8 + - - +
229B CYS* 3.2 38.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 226 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B TYR* 4.3 13.2 - - - +
189B VAL* 5.7 10.5 - - + -
192B SER* 5.1 9.6 - - - +
196B LEU* 4.5 10.5 - - + -
212B LEU* 3.9 25.4 - - + -
214B PHE* 3.9 24.2 - - + -
222B TRP 2.9 11.6 + - - +
223B ASP* 3.6 6.7 - - - +
225B PHE* 1.3 77.8 - - + +
227B LYS* 1.3 58.3 + - + +
229B CYS* 3.2 7.1 + - + +
230B VAL* 2.7 52.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 227 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B TYR* 6.1 0.7 - - - +
223B ASP* 2.8 55.8 + - - +
224B LEU* 3.2 5.8 + - - +
226B MET* 1.3 74.9 - - + +
228B ILE* 1.3 56.6 + - + +
230B VAL* 3.3 2.1 + - - +
231B PHE* 2.8 29.5 + - - +
294B ILE* 3.4 29.6 + - + +
295B LEU* 4.3 7.2 - - + +
297B GLU* 3.2 28.3 + - - +
298B ALA* 3.7 20.6 - - + +
1300B JDC 3.7 24.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 228 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B LEU* 2.9 48.3 + - + +
225B PHE* 3.7 6.1 - - - +
227B LYS* 1.3 75.9 - - - +
229B CYS* 1.3 61.1 + - - +
231B PHE* 2.9 6.5 + - + +
232B ILE* 2.9 40.4 + - + +
295B LEU* 4.1 19.1 - - + -
299B LEU* 4.7 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 229 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B PHE* 3.2 36.1 + - - +
226B MET* 3.2 10.6 + - + +
228B ILE* 1.3 81.9 - - - +
230B VAL* 1.3 63.1 + - + +
232B ILE* 3.3 4.6 + - - +
233B PHE* 2.9 52.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 230 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B TYR* 4.4 8.7 - - + -
142B MET* 3.7 22.9 - - + -
143B PHE* 3.9 28.9 - - + -
189B VAL* 5.3 3.4 - - + -
226B MET* 2.7 40.0 + - + +
227B LYS 3.6 1.1 - - - +
229B CYS* 1.3 73.2 - - + +
231B PHE* 1.3 58.2 + - - +
234B ALA* 2.8 36.1 + - + +
291B HIS* 4.5 3.0 - - + -
1300B JDC 3.4 37.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 231 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B LYS 2.8 14.7 + - - +
228B ILE* 2.9 8.9 + - + +
230B VAL* 1.3 78.5 - - - +
232B ILE* 1.3 74.3 + - + +
235B PHE* 3.2 48.9 + + + +
236B VAL* 3.2 29.0 + - + -
291B HIS* 4.4 33.9 - - + +
292B ILE* 4.8 9.9 - - + -
295B LEU* 3.6 38.8 - - + -
1300B JDC 6.3 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 232 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B ILE* 2.9 32.2 + - + +
229B CYS* 3.8 6.5 - - - +
231B PHE* 1.3 93.6 - - + +
233B PHE* 1.3 70.3 + - + +
236B VAL* 3.4 15.6 + - + -
237B ILE* 3.0 51.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 233 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B PHE* 4.3 15.0 - + + -
147B PHE* 3.4 20.7 - + + -
229B CYS* 2.9 48.8 + - + +
232B ILE* 1.3 85.4 - - + +
234B ALA* 1.3 58.0 + - - +
235B PHE 3.3 1.6 - - - -
237B ILE* 3.8 25.1 - - + +
238B PRO* 3.2 17.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 234 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B MET* 4.3 15.4 - - + +
143B PHE* 3.8 28.5 - - + -
146B ILE* 3.7 25.0 - - + +
230B VAL* 2.8 29.4 + - + +
233B PHE* 1.3 72.9 - - - +
235B PHE* 1.3 62.2 + - - +
238B PRO* 3.7 6.7 - - - -
283B PHE* 5.8 0.9 - - - -
291B HIS* 3.7 12.2 + - + -
----------------------------------------------------------
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