Contacts of the helix formed by residues 225 - 234 (chain A) in PDB entry 5EWL
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 LEU 225 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A PHE* 3.6 38.6 - - + -
222A THR* 3.6 30.5 - - + +
223A LYS 4.5 0.4 - - - +
224A ASN* 1.3 73.9 - - - +
226A THR* 1.4 60.2 + - - +
227A ALA* 3.2 3.4 - - - +
228A LEU* 3.3 16.9 + - + +
229A LEU* 2.9 32.5 + - + +
248A ASP 4.6 0.2 - - - +
251A ALA* 3.6 34.5 - - + +
252A VAL* 3.6 26.9 - - + +
255A SER* 3.7 12.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 226 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A ASN* 3.1 29.1 + - - +
225A LEU* 1.4 75.3 - - - +
227A ALA* 1.3 59.3 + - - +
230A LEU* 2.9 41.4 + - - +
255A SER* 3.8 20.2 - - - +
258A MET* 5.7 4.5 - - + -
259A LEU* 3.9 26.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 227 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A ASN 5.1 1.8 + - - +
225A LEU* 3.2 1.7 - - - +
226A THR* 1.3 78.0 + - - +
228A LEU* 1.4 63.8 + - - +
230A LEU* 3.5 5.9 + - - +
231A GLU* 3.3 25.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 228 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A ILE* 3.7 27.1 - - + -
216A LEU* 3.6 34.8 - - + +
217A GLN 3.5 26.5 - - - +
218A PHE* 3.8 22.7 - - + -
225A LEU* 3.4 26.8 - - + +
227A ALA* 1.4 78.7 - - - +
229A LEU* 1.3 68.6 + - + +
231A GLU* 3.3 13.0 - - - +
232A ALA 3.2 15.1 + - - -
252A VAL* 5.3 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 229 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A ILE* 4.0 26.9 - - + -
225A LEU* 2.9 15.7 + - + +
228A LEU* 1.3 80.9 - - + +
230A LEU* 1.3 58.8 + - - +
232A ALA* 3.4 3.3 + - + -
233A LYS 3.0 21.7 + - - -
252A VAL* 3.6 23.1 - - + +
255A SER* 3.5 20.4 - - - -
256A ALA* 3.4 36.1 - - + +
259A LEU* 3.4 18.8 - - + -
261A MET* 3.3 29.1 - - + +
268A TRP* 4.3 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 230 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A THR* 2.9 30.1 + - - +
227A ALA* 4.0 5.8 - - - +
229A LEU* 1.3 72.8 - - - +
231A GLU* 1.3 64.6 + - - +
233A LYS* 3.2 16.8 + - + +
234A GLU* 3.2 23.6 + - - +
259A LEU* 3.8 25.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 231 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A LEU* 3.4 27.0 - - + +
227A ALA 3.3 13.3 + - - +
228A LEU* 3.3 14.6 - - - +
230A LEU* 1.3 79.8 - - - +
232A ALA* 1.4 59.4 + - - +
234A GLU* 3.7 15.2 + - - +
235A LEU* 3.7 14.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 232 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A ILE* 3.5 31.1 - - + +
166A ILE* 4.7 10.5 - - + -
216A LEU* 3.7 19.9 - - + +
228A LEU 3.2 5.5 + - - +
229A LEU* 3.5 11.2 - - - +
231A GLU* 1.4 76.6 - - - +
233A LYS* 1.3 64.4 + - - +
235A LEU* 3.4 20.6 + - - +
237A ALA 4.5 0.7 - - - +
240A ILE* 5.6 1.8 - - + -
261A MET* 4.1 12.1 - - + +
266A TYR* 5.5 1.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 233 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A LEU 3.0 16.8 + - - +
230A LEU* 3.2 20.6 + - + +
232A ALA* 1.3 75.8 - - - +
234A GLU* 1.4 60.2 + - - +
235A LEU 3.4 8.7 + - - +
238A ARG* 5.1 5.0 + - - -
259A LEU* 2.8 33.4 + - + +
260A ASP* 4.7 8.8 - - - +
261A MET* 3.6 24.9 - - + +
266A TYR* 3.3 27.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 234 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A LEU 3.2 11.8 + - - +
231A GLU* 3.7 13.2 - - - +
232A ALA 3.3 0.4 - - - -
233A LYS* 1.4 76.8 - - - +
235A LEU* 1.3 61.5 + - + +
236A GLU 4.1 0.2 + - - -
----------------------------------------------------------
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