Contacts of the helix formed by residues 222 - 232 (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 ILE 222 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A LYS* 1.3 64.3 + - + +
224A HIS* 3.3 7.0 - - - +
225A THR* 3.1 16.1 + - - -
226A GLU* 2.9 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 223 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A ILE* 1.3 76.5 - - - +
224A HIS* 1.3 66.3 + - - +
226A GLU* 3.2 18.6 + - + +
227A TYR* 2.8 63.6 + - + +
254A GLU* 3.0 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 224 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A ILE 3.3 4.1 - - - +
223A LYS* 1.3 76.5 - - - +
225A THR* 1.3 61.0 + - - +
227A TYR* 3.4 11.0 + - - +
228A MET* 2.9 49.9 + - + +
246A SER* 3.2 31.7 + - - -
249A ALA* 3.5 20.1 - - + +
250A ASP* 2.9 28.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 225 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A ILE* 3.1 16.3 + - - -
223A LYS 3.1 0.8 - - - -
224A HIS* 1.3 79.6 + - - +
226A GLU* 1.3 66.3 + - - +
228A MET* 3.3 5.6 + - + +
229A GLU* 2.8 28.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 226 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A ILE 2.9 13.6 + - - +
223A LYS* 3.6 28.5 - - + +
225A THR* 1.3 74.9 - - - +
227A TYR* 1.3 63.5 + - + +
229A GLU* 3.9 5.5 - - - +
230A PHE* 3.0 31.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 227 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A LYS* 2.8 51.8 + - + +
224A HIS* 3.6 6.3 - - - +
226A GLU* 1.3 76.5 - - + +
228A MET* 1.3 58.3 + - - +
230A PHE* 3.3 6.1 + - + +
231A LEU* 2.8 35.6 + - + +
249A ALA* 3.6 31.4 - - + -
252A LEU* 3.5 41.4 + - + +
254A GLU* 2.9 39.4 + - - +
329A LEU* 3.9 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 228 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A HIS* 2.9 41.5 + - - +
225A THR* 4.0 5.8 - - + +
227A TYR* 1.3 73.1 - - - +
229A GLU* 1.3 67.4 + - - +
231A LEU* 3.8 4.8 - - - -
232A LYS* 2.9 63.1 + - + +
242A GLU* 3.8 25.1 - - + +
245A LEU* 4.2 12.3 - - + +
246A SER* 3.9 11.0 - - - +
249A ALA* 3.9 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 229 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A THR* 2.8 21.6 + - + +
226A GLU* 3.9 4.9 - - - +
228A MET* 1.3 76.3 - - - +
230A PHE* 1.3 64.2 + - - +
232A LYS* 3.5 7.6 + - - +
233A SER* 3.4 18.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 230 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A GLU* 3.0 21.0 + - + +
227A TYR* 3.6 4.5 - - + +
229A GLU* 1.3 77.7 - - - +
231A LEU* 1.3 69.6 + - + +
233A SER* 2.6 28.9 + - - -
234A VAL* 3.5 26.6 - - + +
275A ILE* 3.7 23.8 - - + -
276A ILE 3.2 23.3 - - - -
277A SER* 3.6 21.1 - - - -
301A LYS* 4.2 23.1 - - + -
302A GLY* 4.1 3.6 - - - -
329A LEU* 3.6 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 231 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A TYR 2.8 26.8 + - - +
228A MET* 3.9 4.3 - - - +
230A PHE* 1.3 86.6 - - + +
232A LYS* 1.3 61.8 + - - +
233A SER 3.1 1.2 + - - -
234A VAL* 3.2 19.7 + - - +
237A PHE* 3.7 26.5 - - + +
245A LEU* 4.0 43.3 - - + +
248A LEU* 4.2 18.8 - - + -
249A ALA* 4.5 1.6 - - + +
252A LEU* 4.4 13.7 - - + -
275A ILE* 3.9 27.1 - - + -
329A LEU* 4.6 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 232 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A MET* 2.9 49.6 + - + +
229A GLU* 3.9 7.2 - - - +
230A PHE 3.2 0.2 - - - -
231A LEU* 1.3 74.3 - - - +
233A SER* 1.3 56.5 + - - +
234A VAL 3.5 0.4 - - - -
238A GLN* 2.8 30.8 + - - +
242A GLU* 4.1 21.1 - - - +
245A LEU* 3.7 18.8 - - + -
----------------------------------------------------------
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