Contacts of the helix formed by residues 237 - 245 (chain B) in PDB entry 3E88
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 237 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B GLY 3.8 1.2 + - - -
236B GLU* 1.3 71.4 - - - +
238B PHE* 1.3 56.7 + - - +
240B HIS* 3.2 5.9 + - + +
241B LEU* 2.9 32.6 + - - +
247B PHE* 4.4 12.6 - - + -
255B TYR* 4.0 18.6 - - + -
259B ILE* 5.2 0.2 - - + -
278B LEU* 3.8 17.3 - - + +
281B LEU* 2.8 39.3 + - + +
282B MET* 4.3 0.2 - - - +
283B LEU* 3.7 38.4 - - + -
289B ILE* 3.8 20.2 - - + -
343B MET* 4.3 21.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 238 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B GLU* 3.1 20.4 - - - +
237B LEU* 1.3 76.5 - - - +
239B PHE* 1.3 58.4 + - - +
241B LEU* 4.0 1.0 - - + +
242B SER* 2.7 54.4 + - - -
278B LEU* 3.1 36.2 + - + +
279B GLU* 4.0 8.7 - - + +
4D ARG* 3.5 64.8 - - + -
6D ARG* 4.0 41.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 239 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B GLU* 3.1 19.6 + - + +
238B PHE* 1.3 82.2 - - - +
240B HIS* 1.3 65.2 + + - +
242B SER* 3.6 5.1 - - - -
243B ARG* 3.1 70.0 + - - +
437B ARG 3.5 16.8 - - - -
438B TYR* 3.7 33.7 - + + +
439B PHE* 3.8 22.4 - - - -
440B ASP* 3.8 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 240 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B GLY 2.6 27.6 + - - -
236B GLU 3.1 24.9 - - - -
237B LEU* 3.2 7.5 + - + +
239B PHE* 1.3 78.4 - + + +
241B LEU* 1.3 59.9 + - - +
243B ARG* 3.2 14.1 + - - +
244B GLU* 2.8 44.4 + - - +
247B PHE* 4.1 15.3 - - + -
251B ARG* 4.6 2.7 - - - +
283B LEU* 3.7 23.1 - - + +
426B PHE* 3.6 28.1 - + - -
438B TYR* 3.5 28.1 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 241 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B LEU 2.9 16.5 + - - +
238B PHE* 4.3 2.0 - - + +
240B HIS* 1.3 77.1 - - - +
242B SER* 1.3 54.9 + - - +
245B ARG* 2.7 53.1 + - - +
246B VAL* 4.0 9.9 - - - -
247B PHE* 3.8 32.4 - - + -
278B LEU* 3.3 34.8 - - + -
342B GLU* 3.7 25.4 - - + +
343B MET* 3.8 16.8 - - - +
346B GLY* 5.4 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 242 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B PHE* 2.7 51.4 + - - -
239B PHE* 3.6 6.5 - - - -
241B LEU* 1.3 78.9 - - - +
243B ARG* 1.3 56.8 + - - +
245B ARG* 3.1 24.7 + - - +
3D GLY* 5.0 16.5 - - - -
4D ARG 5.0 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 243 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B PHE* 3.1 55.7 + - - +
240B HIS* 3.2 16.4 + - - +
242B SER* 1.3 77.5 - - - +
244B GLU* 1.3 62.9 + - + +
245B ARG* 2.7 20.1 + - - +
426B PHE* 6.1 0.4 - - - -
437B ARG* 5.2 3.2 + - - +
438B TYR* 4.2 18.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 244 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B HIS* 2.8 26.4 + - - +
243B ARG* 1.3 78.2 + - + +
245B ARG* 1.3 70.9 + - - +
246B VAL* 2.9 24.2 + - - +
247B PHE* 3.8 13.1 - - + -
251B ARG* 2.9 41.7 + - - -
426B PHE* 4.8 7.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 245 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B LEU* 2.7 31.0 + - - +
242B SER* 3.1 17.3 + - - +
243B ARG* 2.7 32.3 + - - +
244B GLU* 1.3 75.7 - - - +
246B VAL* 1.3 60.1 + - + +
346B GLY* 3.3 25.9 - - - +
3D GLY* 5.4 9.0 - - - +
----------------------------------------------------------
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