Contacts of the helix formed by residues 236 - 250 (chain A) in PDB entry 4FK8
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 236 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A THR* 3.4 9.1 + - - -
235A GLY* 1.3 75.1 - - - +
237A THR* 1.3 60.1 + - - +
238A ALA* 3.8 8.7 + - - +
239A MET* 3.2 24.6 + - - +
240A LEU* 2.9 28.2 + - - +
269A PHE* 3.8 33.4 - - - -
271A ASP* 5.3 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 237 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A GLY 3.8 0.6 + - - -
236A SER* 1.3 72.5 - - - +
238A ALA* 1.3 57.6 + - - +
240A LEU* 3.5 7.6 + - + +
241A LYS* 2.9 30.4 + - + +
267A ARG* 3.2 35.5 + - - +
269A PHE* 4.2 5.6 + - - -
271A ASP* 3.1 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 238 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A SER* 3.1 8.6 + - - +
237A THR* 1.3 76.9 - - - +
239A MET* 1.3 59.1 + - - +
241A LYS* 3.3 6.0 + - - +
242A ASP* 3.0 40.8 + - - +
271A ASP* 5.7 0.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 239 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A LEU* 3.7 41.3 - - + +
129A SER 5.1 0.2 - - - -
130A THR* 3.8 21.1 - - + -
203A GLU 5.8 0.4 - - - -
204A GLY* 4.9 11.2 - - - -
206A ILE* 3.8 18.8 - - + -
207A THR* 4.2 6.5 + - - +
233A LEU* 4.1 9.6 - - + -
235A GLY* 4.2 12.1 - - - -
236A SER* 3.2 22.2 + - - +
238A ALA* 1.3 78.9 - - - +
240A LEU* 1.3 75.3 + - - +
242A ASP* 4.9 1.1 - - - -
243A THR* 2.7 52.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 240 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A LEU* 3.5 46.4 - - + +
235A GLY 4.0 7.2 - - - +
236A SER 2.9 17.8 + - - +
237A THR* 3.6 6.5 - - - +
239A MET* 1.3 85.9 - - - +
241A LYS* 1.3 51.4 + - - +
244A THR* 2.7 43.2 + - + +
265A ILE* 4.2 20.9 - - + -
266A GLU* 3.6 29.8 - - - +
267A ARG* 3.6 21.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 241 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A THR* 2.9 20.1 + - + +
238A ALA* 3.3 8.0 + - - +
240A LEU* 1.3 74.6 - - - +
242A ASP* 1.3 67.2 + - - +
244A THR* 3.1 16.5 + - - -
245A GLU* 3.3 12.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 242 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A THR* 3.7 26.8 + - + +
238A ALA* 3.0 25.7 + - - +
239A MET* 4.8 0.6 - - - -
241A LYS* 1.3 80.0 - - - +
243A THR* 1.3 61.3 + - - +
245A GLU* 3.5 17.7 - - - +
246A LEU* 3.5 14.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 243 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A LEU* 3.9 17.0 - - + -
206A ILE* 4.4 1.3 - - + +
207A THR* 3.0 21.3 + - - -
210A ILE* 3.7 29.2 - - + -
233A LEU* 4.0 17.0 - - + -
239A MET* 2.7 34.9 + - + +
242A ASP* 1.3 74.7 - - - +
244A THR* 1.3 65.9 + - - +
246A LEU* 3.1 7.3 + - - +
247A LEU* 3.0 25.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 244 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A LEU* 3.5 20.2 - - + -
240A LEU 2.7 29.9 + - - +
241A LYS* 3.1 11.3 + - - -
243A THR* 1.3 77.3 - - - +
245A GLU* 1.3 51.7 + - - +
247A LEU* 3.6 8.3 - - - +
248A LYS* 2.8 47.3 + - - +
263A TYR* 3.6 31.9 - - + +
265A ILE* 3.7 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 245 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A LYS 3.3 10.4 + - - +
242A ASP* 3.5 13.0 - - - +
243A THR 3.2 0.4 - - - -
244A THR* 1.3 81.3 + - - +
246A LEU* 1.3 59.8 + - + +
248A LYS* 3.4 10.4 + - - +
249A LYS* 3.0 39.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 246 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A THR* 3.4 39.9 - - + +
210A ILE* 3.6 28.5 - - + -
211A ALA* 3.8 17.0 - - + +
224A PHE* 5.8 1.7 - - - -
242A ASP 3.6 12.1 - - - +
243A THR* 3.1 8.8 + - + +
245A GLU* 1.3 76.9 - - + +
247A LEU* 1.3 64.8 + - + +
249A LYS* 3.4 28.4 + - + +
250A ALA* 3.0 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 247 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A ILE* 5.2 0.4 - - + -
224A PHE* 3.6 38.4 - - + -
231A VAL* 4.0 25.1 - - + -
233A LEU* 4.1 16.8 - - + -
243A THR* 3.0 24.9 + - + +
244A THR* 3.1 7.4 + - - +
246A LEU* 1.3 77.2 - - + +
248A LYS* 1.3 61.3 + - - +
250A ALA* 3.1 12.2 + - - +
251A GLY 3.3 0.2 + - - -
252A LEU* 2.9 32.3 + - + +
263A TYR* 3.7 46.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 248 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A THR* 2.8 32.8 + - - +
245A GLU* 3.7 8.7 - - - +
247A LEU* 1.3 73.4 - - - +
249A LYS* 1.3 58.3 + - + +
251A GLY* 2.9 19.8 + - - -
252A LEU 3.5 14.5 - - - +
253A VAL* 6.0 0.2 - - - -
254A GLU* 5.9 1.1 - - - -
263A TYR* 3.3 24.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 249 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A GLU* 3.0 27.2 + - + +
246A LEU* 3.8 27.3 - - + +
247A LEU 3.3 0.2 - - - -
248A LYS* 1.3 73.4 - - + +
250A ALA* 1.3 58.1 + - - +
251A GLY* 3.0 6.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 250 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A PHE* 3.6 31.1 - - + +
225A SER* 4.5 0.3 - - - -
226A PRO* 3.2 20.6 - - - +
246A LEU 3.0 13.1 + - - +
247A LEU* 3.1 9.3 + - - +
249A LYS* 1.3 74.8 - - - +
251A GLY* 1.3 56.9 + - - +
252A LEU* 3.4 9.9 - - + -
----------------------------------------------------------
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