Contacts of the helix formed by residues 241 - 252 (chain A) in PDB entry 5JAX
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 PRO 241 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A SER 3.9 6.1 - - - +
240A LEU* 1.3 90.4 - - + +
242A GLU* 1.3 69.2 + - - +
243A GLU* 4.4 7.4 - - + +
244A ILE* 3.0 40.5 + - + +
245A LEU* 3.1 9.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 242 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A MET* 3.8 7.3 - - + +
232A LYS* 4.1 27.8 - - - +
240A LEU 3.5 3.1 + - - -
241A PRO* 1.3 76.7 - - - +
243A GLU* 1.3 64.4 + - + +
245A LEU* 3.3 11.3 + - - +
246A SER* 2.8 28.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 243 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A PRO* 3.2 5.2 - - + +
242A GLU* 1.3 85.9 - - + +
244A ILE* 1.3 63.8 + - + +
246A SER* 3.4 10.6 + - - -
247A LYS* 3.1 45.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 244 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A LEU* 4.2 21.1 - - + -
241A PRO* 3.0 38.1 + - + +
243A GLU* 1.3 77.2 - - + +
245A LEU* 1.3 66.2 + - - +
247A LYS* 3.2 15.8 + - - +
248A LEU* 3.0 22.9 + - + +
338A HIS 6.1 0.2 - - - +
339A LEU* 3.9 48.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 245 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A MET* 4.4 11.7 - - + -
231A LEU* 4.0 24.7 - - + +
232A LYS* 3.7 36.1 - - + +
237A PHE* 3.6 29.4 - - + +
238A GLN* 5.3 1.6 - - - +
240A LEU* 3.9 30.1 - - + +
241A PRO 3.1 14.4 + - - +
242A GLU* 3.3 12.8 + - - +
244A ILE* 1.3 75.7 - - - +
246A SER* 1.3 58.2 + - - +
248A LEU* 3.2 12.3 + - + +
249A ALA* 2.9 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 246 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A HIS* 3.2 27.1 + - - -
228A MET* 3.9 18.5 - - - +
242A GLU 2.8 17.6 + - - -
243A GLU* 3.6 17.0 + - - -
244A ILE 3.2 0.2 - - - -
245A LEU* 1.3 77.0 - - - +
247A LYS* 1.3 57.7 + - - +
249A ALA 3.2 0.7 + - - -
250A ASP* 3.0 29.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 247 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A GLU* 3.1 37.5 + - - +
244A ILE* 3.2 14.8 + - - +
246A SER* 1.3 77.7 - - - +
248A LEU* 1.3 61.5 + - - +
250A ASP* 3.2 21.6 + - - +
251A VAL* 3.2 21.4 + - + +
338A HIS* 4.1 22.2 - - - -
339A LEU* 4.2 25.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 248 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A LEU* 4.2 12.8 - - + -
237A PHE* 5.5 3.4 - - + -
240A LEU* 4.2 19.3 - - + -
244A ILE* 3.0 21.3 + - + +
245A LEU* 3.2 16.1 + - + +
247A LYS* 1.3 75.1 - - - +
249A ALA* 1.3 57.5 + - - +
251A VAL* 3.2 3.7 + - + +
252A LEU* 2.9 38.4 + - + +
331A ILE* 4.0 24.7 - - + -
335A SER* 4.5 4.3 - - - -
339A LEU* 3.8 22.2 - - + -
340A ILE* 3.9 37.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 249 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A HIS* 3.5 27.3 - - + +
227A TYR* 3.6 38.7 - - + -
228A MET* 3.9 12.6 - - + +
231A LEU* 4.5 2.0 - - + +
245A LEU 2.9 17.0 + - - +
246A SER 3.5 1.8 - - - +
248A LEU* 1.3 77.4 - - - +
250A ASP* 1.3 61.6 + - - +
252A LEU* 3.8 15.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 250 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A HIS* 2.9 25.9 + - - -
246A SER* 3.0 20.2 + - - +
247A LYS* 3.4 17.4 - - - +
248A LEU 3.2 0.6 - - - -
249A ALA* 1.3 78.3 - - - +
251A VAL* 1.3 64.8 + - + +
252A LEU 3.7 2.3 - - - +
253A GLU* 5.7 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 251 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A LYS* 3.4 19.1 - - + +
248A LEU* 3.2 12.1 + - + +
250A ASP* 1.3 83.1 - - + +
252A LEU* 1.3 72.4 + - - +
253A GLU* 3.7 13.5 + - - +
330A VAL 4.7 0.5 - - - +
331A ILE* 5.3 3.1 - - + -
332A ASP* 5.0 11.6 + - - +
335A SER* 3.4 33.9 - - - +
339A LEU* 5.6 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 252 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A TYR* 3.5 46.5 + - + -
231A LEU* 4.4 11.2 - - + -
248A LEU* 2.9 24.9 + - + +
249A ALA* 3.8 18.8 - - - +
250A ASP 3.7 3.2 - - - +
251A VAL* 1.3 83.5 - - - +
253A GLU* 1.3 71.0 + - - +
275A ILE* 6.2 0.2 - - + -
329A LEU* 4.0 32.8 - - + -
330A VAL 3.4 15.9 - - - +
331A ILE* 4.2 15.9 - - + +
----------------------------------------------------------
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