Contacts of the helix formed by residues 239 - 249 (chain B) in PDB entry 2H8R
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 GLY 239 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B ASN* 4.0 16.4 - - - -
237B LYS* 3.3 4.9 + - - -
238B TRP* 1.3 73.7 - - - +
240B PRO* 1.3 65.3 - - - +
241B ALA 3.1 2.0 - - - -
242B SER* 3.4 8.6 + - - -
243B GLN* 2.8 33.9 + - - +
272B GLU* 3.7 15.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 240 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B GLN* 5.3 12.8 - - + +
133B ASN* 4.9 2.9 - - - +
239B GLY* 1.3 81.7 - - - +
241B ALA* 1.3 61.2 + - + +
243B GLN* 2.9 19.8 - - + +
244B GLN* 2.8 33.7 + - - +
275B GLN* 3.5 22.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 241 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B PRO* 1.3 75.6 - - + +
242B SER* 1.3 64.7 + - - +
243B GLN 3.0 1.1 - - - -
244B GLN* 3.3 21.5 + - - +
245B ILE* 3.5 14.8 - - - +
271B ALA* 4.8 15.9 - - + +
272B GLU* 3.3 8.7 - - - +
275B GLN* 3.1 25.8 - - + +
----------------------------------------------------------
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 TRP* 4.2 14.8 - - - -
239B GLY 3.4 9.5 + - - -
241B ALA* 1.3 76.7 - - - +
243B GLN* 1.3 65.1 + - - +
244B GLN 3.3 0.2 + - - -
245B ILE* 3.4 9.1 + - - +
246B LEU* 3.0 26.8 + - - +
268B CYS* 3.2 31.4 - - - +
272B GLU* 2.6 37.6 + - - +
291B VAL* 4.6 3.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 243 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B LYS* 5.3 5.3 - - - +
238B TRP* 3.9 25.5 + - + +
239B GLY 2.8 16.5 + - - +
240B PRO* 2.9 23.3 - - + +
241B ALA 3.0 0.4 - - - -
242B SER* 1.3 77.5 - - - +
244B GLN* 1.4 53.3 - - - +
246B LEU* 2.7 26.8 + - - +
247B TYR* 2.8 43.6 + - + +
299B TRP* 3.8 19.0 + - - +
15E C 4.8 4.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 244 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B PRO 2.8 12.2 + - - +
241B ALA* 3.3 15.3 - - - +
243B GLN* 1.4 71.4 - - - +
245B ILE* 1.3 72.1 + - + +
246B LEU 3.1 0.7 + - - -
247B TYR* 3.1 8.1 + - - +
248B GLN* 2.9 54.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 245 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B ALA 3.5 16.8 - - - +
242B SER* 3.6 13.2 - - - +
244B GLN* 1.3 79.2 - - + +
246B LEU* 1.3 61.7 + - + +
248B GLN* 2.9 16.8 + - + +
249B ALA* 2.9 34.4 + - + +
264B LEU* 3.6 27.8 - - + -
267B GLU* 3.6 30.3 - - + +
268B CYS* 4.4 13.0 - - - +
271B ALA* 4.2 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 246 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B TRP* 4.1 24.5 - - + -
242B SER 3.0 20.1 + - - +
243B GLN* 2.7 11.4 + - - +
245B ILE* 1.3 78.4 - - + +
247B TYR* 1.3 56.6 + - - +
249B ALA* 3.6 6.1 + - - +
250B TYR* 2.8 32.1 + - - +
264B LEU* 4.2 18.8 - - + -
268B CYS* 4.5 9.2 - - - -
296B VAL* 5.1 4.9 - - + -
299B TRP* 3.7 34.6 - - + +
300B PHE* 3.9 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 247 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B GLN* 2.8 35.5 + - + -
244B GLN* 3.4 11.9 - - - +
246B LEU* 1.3 77.9 - - - +
248B GLN* 1.4 53.0 + - + +
249B ALA 3.1 0.2 - - - -
250B TYR* 2.8 36.0 + + - +
251B ASP* 3.6 9.8 + - - +
299B TRP* 3.7 25.8 + + - -
303B ARG* 4.0 24.0 + - - +
306B GLU* 3.6 19.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 248 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B GLN* 2.9 43.9 + - - +
245B ILE* 2.9 22.4 + - + +
247B TYR* 1.4 71.1 - - + +
249B ALA* 1.3 58.9 + - + +
250B TYR 3.0 9.7 + - - -
251B ASP* 4.3 14.9 + - - +
267B GLU* 6.0 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 249 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B ILE* 2.9 20.3 + - + +
246B LEU 3.8 4.9 - - - +
248B GLN* 1.3 78.6 - - + +
250B TYR* 1.3 59.3 + - - +
253B GLN* 2.8 23.2 - - - +
264B LEU* 4.1 27.6 - - + +
300B PHE* 4.8 3.5 - - - -
----------------------------------------------------------
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