Contacts of the helix formed by residues 232 - 239 (chain B) in PDB entry 3C98
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 ARG 232 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ARG* 4.9 1.4 - - - +
42A SER* 4.0 15.7 + - - +
45A CYS 5.8 0.2 - - - -
46A LYS* 4.0 13.2 - - - +
261A ASN* 3.1 47.3 + - - +
262A ASP* 4.1 9.5 + - - -
263A VAL* 3.8 11.5 - - - +
280A LEU* 3.6 39.3 - - + +
228B GLU 3.9 1.7 + - - +
229B MET* 2.9 23.5 + - + +
230B ILE 3.4 0.2 - - - -
231B ASP* 1.3 77.4 - - - +
233B ILE* 1.3 69.2 + - - +
234B GLU* 3.8 27.4 + - - +
235B TYR* 2.8 27.1 + - + +
236B ASN* 3.3 8.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 233 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A VAL* 6.1 0.2 - - + -
38A MET* 4.8 7.4 - - + +
41A LEU* 3.6 39.0 - - + +
42A SER* 4.0 12.5 + - - -
45A CYS* 3.7 28.9 + - + +
46A LYS 4.2 1.8 - - - +
47A MET* 3.8 32.7 - - - +
50A ILE* 4.1 12.3 - - + -
58A VAL* 4.3 15.7 - - + -
231B ASP 3.6 2.8 + - - -
232B ARG* 1.3 70.3 - - - +
234B GLU* 1.3 60.7 + - - +
236B ASN* 2.9 23.6 + - - +
237B VAL* 3.2 24.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 234 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A MET* 3.6 31.7 - - + +
39A ARG* 3.1 36.0 + - - +
42A SER* 3.3 22.5 + - - +
261A ASN* 3.0 30.3 + - - +
232B ARG* 3.2 18.1 + - + +
233B ILE* 1.3 79.2 - - - +
235B TYR* 1.3 57.1 + - - +
237B VAL* 3.9 1.4 - - - +
238B GLU* 3.1 37.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 235 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A GLU* 5.1 8.6 + - - -
229B MET* 3.4 54.1 - - + +
230B ILE* 4.2 11.2 - - + -
232B ARG* 2.8 28.3 + - + +
234B GLU* 1.3 73.9 - - - +
236B ASN* 1.3 66.8 + - - +
238B GLU* 4.8 5.4 - - - -
239B HIS* 3.3 58.7 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 236 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A MET* 3.3 36.0 - - + +
58A VAL* 5.5 4.9 - - + +
114B ARG* 5.0 6.5 + - - +
118B THR* 4.1 15.8 - - - +
230B ILE* 3.2 33.8 + - - +
232B ARG 3.3 6.2 + - - +
233B ILE 2.9 7.7 + - - +
235B TYR* 1.3 81.5 - - - +
237B VAL* 1.3 66.6 + - + +
239B HIS* 3.6 2.6 + - - -
240B ALA* 3.3 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 237 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A VAL* 4.7 2.7 - - + -
38A MET* 4.0 33.4 - - + -
58A VAL* 3.6 39.0 - - + +
60A ASP* 3.7 37.9 - - + +
63A LYS* 3.5 13.7 + - - +
233B ILE* 3.2 16.0 + - + +
234B GLU 4.2 3.1 - - - +
236B ASN* 1.3 75.8 - - - +
238B GLU* 1.3 65.0 + - - +
240B ALA* 3.5 16.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 238 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A MET* 5.4 4.7 - - + +
63A LYS* 4.7 9.3 + - - +
261A ASN* 5.3 4.2 + - - -
234B GLU* 3.1 30.7 + - + +
235B TYR* 4.5 5.3 - - - +
237B VAL* 1.3 81.1 - - - +
239B HIS* 1.3 81.1 + - + +
240B ALA 3.3 5.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 239 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B TYR* 3.3 63.5 + + + +
236B ASN* 3.9 3.6 - - - +
237B VAL 3.3 0.6 - - - -
238B GLU* 1.3 98.7 + - + +
240B ALA* 1.3 58.8 + - - +
241B VAL* 3.9 2.4 + - - +
----------------------------------------------------------
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