Contacts of the helix formed by residues 238 - 244 (chain B) in PDB entry 7REQ
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 ALA 238 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B ILE* 3.2 6.7 + - + +
237B ASP* 1.3 71.3 - - - +
239B ASN* 1.3 58.2 + - - +
241B TYR* 3.3 23.5 + - + +
242B HIS 3.5 7.1 + - - -
251B GLU* 3.6 36.9 - - + +
255B ALA* 3.8 30.1 - - + +
283B ARG 2.9 15.3 + - - +
284B VAL* 4.8 4.7 - - + -
300B LEU* 5.9 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 239 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B ASP* 3.1 14.3 + - - +
238B ALA* 1.3 71.1 - - - +
240B ILE* 1.3 54.9 + - - +
241B TYR 3.4 0.2 - - - -
242B HIS* 3.1 3.7 + - - +
243B ASN* 3.0 53.2 + - - -
251B GLU* 4.3 0.2 - - - -
283B ARG* 3.6 9.8 + - + +
285B THR* 2.7 44.2 + - - +
325B ILE* 3.6 30.6 - - + +
326B THR 5.0 1.1 + - - +
327B SER* 5.0 2.8 - - - +
328B TRP* 5.2 1.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 240 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B ARG* 5.9 1.3 - - + -
172B GLN* 6.0 2.2 - - - +
200B ASP* 4.2 1.8 - - - +
203B GLY* 4.1 23.6 - - - +
204B PHE 4.9 0.2 - - - +
206B ALA* 4.9 1.1 - - + -
207B LEU* 3.8 40.2 - - + -
237B ASP* 3.4 40.4 + - + +
239B ASN* 1.3 73.7 - - - +
241B TYR* 1.3 71.9 + - + +
244B ALA* 3.4 8.7 + - - +
488B LEU* 4.5 15.3 - - + -
490B TRP* 3.1 42.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 241 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B ILE* 4.0 11.6 + - - +
203B GLY* 4.3 6.7 + - - -
206B ALA* 3.7 14.6 - - + +
236B ILE* 6.5 0.9 - - + -
237B ASP 4.3 12.6 - - - -
238B ALA* 3.3 19.4 + - + +
240B ILE* 1.3 77.9 - - + +
242B HIS* 1.3 63.1 + - - +
244B ALA* 3.1 14.1 + - - +
245B GLY 3.3 0.7 + - - -
246B ALA* 3.0 26.4 + - + +
251B GLU* 4.9 5.4 - - - -
254B TRP* 3.6 52.0 - + + -
258B THR* 4.7 7.6 + - - -
429B MET* 3.9 10.4 - - + +
433B VAL* 3.7 19.8 - - + +
438B VAL* 4.1 11.2 - - + -
442B LEU* 4.1 1.6 - - + +
488B LEU* 3.7 26.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 242 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B ALA 3.5 4.0 + - - -
239B ASN* 3.1 9.0 + - - +
241B TYR* 1.3 73.2 - - - +
243B ASN* 1.3 74.9 + - - +
245B GLY 3.1 6.8 + - - -
246B ALA* 3.9 14.1 + - - +
247B GLY 5.5 1.6 + - - -
251B GLU* 3.3 12.4 + - - +
285B THR* 3.3 32.0 - - + +
287B THR* 3.8 26.3 - - + +
296B ARG* 5.8 0.2 + - - -
327B SER* 2.7 30.5 + - - -
329B ARG* 2.8 63.4 + - + +
330B GLU* 4.0 2.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 243 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B ARG* 5.6 1.0 - - - +
239B ASN* 3.0 30.8 + - - +
242B HIS* 1.3 89.8 - - - +
244B ALA* 1.3 55.7 + - - +
245B GLY 3.4 0.7 + - - -
328B TRP* 3.6 43.2 + - + +
329B ARG* 4.0 5.6 + - - -
490B TRP* 3.5 52.0 - - + +
491B HIS 3.6 25.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 244 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B ILE 3.4 11.4 + - - +
241B TYR 3.1 10.8 + - - +
243B ASN* 1.3 73.7 - - - +
245B GLY* 1.3 55.2 + - - +
246B ALA 3.8 0.2 - - - -
442B LEU* 3.6 27.7 - - + +
446B ASN* 3.0 20.1 + - - -
488B LEU* 3.9 17.7 - - + -
489B ALA 3.4 22.8 - - - +
490B TRP* 3.7 2.0 - - + -
491B HIS 5.8 0.4 - - - -
----------------------------------------------------------
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