Contacts of the helix formed by residues 239 - 246 (chain F) in PDB entry 3JSX
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 LYS 239 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226F SER* 2.8 32.5 + - - +
227F LEU 3.1 13.3 + - - +
228F PHE 3.4 16.1 + - - -
229F ASP* 3.4 34.3 - - - +
237F LEU 3.5 1.0 + - - -
238F MET* 1.3 76.1 - - - +
240F LYS* 1.3 59.4 + - - +
241F GLU* 3.6 25.6 - - + +
242F VAL* 3.2 15.5 + - + +
243F GLN* 2.9 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 240 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B LYS* 3.2 48.3 - - - +
229F ASP* 4.9 0.8 + - - -
238F MET 3.7 1.6 + - - -
239F LYS* 1.3 68.5 - - - +
241F GLU* 1.3 80.1 + - + +
243F GLN* 3.0 13.8 + - + +
244F ASP* 3.0 45.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 241 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229F ASP* 5.5 0.2 - - - +
239F LYS* 3.6 24.9 - - + +
240F LYS* 1.3 91.6 + - + +
242F VAL* 1.3 64.0 + - + +
244F ASP* 3.4 15.1 + - - +
245F GLU* 3.5 18.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 242 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226F SER 5.1 0.2 - - - +
227F LEU* 3.8 55.4 - - + +
238F MET* 3.4 20.0 - - + -
239F LYS* 3.2 21.4 + - + +
241F GLU* 1.3 82.9 - - + +
243F GLN* 1.3 62.8 + - - +
245F GLU* 3.2 25.1 + - + +
246F GLU* 3.3 18.0 + - + +
253F LEU* 5.3 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 243 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237F LEU* 5.8 0.5 - - - +
238F MET* 3.7 30.9 - - + +
239F LYS 2.9 14.0 + - - +
240F LYS* 3.0 14.0 + - + +
242F VAL* 1.3 77.0 - - - +
244F ASP* 1.3 65.4 + - - +
246F GLU* 3.1 14.1 + - + +
247F LYS* 3.5 21.4 + - + +
259F LEU* 6.1 0.9 - - + -
158H GLN* 3.1 44.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 244 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B LYS* 5.5 0.2 + - - -
240F LYS* 3.0 45.7 + - - +
241F GLU* 3.6 10.2 - - - +
242F VAL 3.3 0.2 - - - -
243F GLN* 1.3 76.9 - - - +
245F GLU* 1.3 61.7 + - + +
246F GLU 3.3 0.7 + - - -
247F LYS* 3.4 23.0 + - - +
248F ASN* 4.8 2.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 245 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241F GLU* 3.5 14.7 + - - +
242F VAL* 3.2 20.1 + - + +
244F ASP* 1.3 78.8 - - + +
246F GLU* 1.3 61.1 + - + +
247F LYS 3.4 1.7 + - - -
248F ASN* 3.9 6.4 - - - +
249F LYS* 3.2 20.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 246 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238F MET* 5.2 2.2 - - + -
242F VAL* 3.3 15.1 + - + +
243F GLN* 3.1 12.5 + - + +
245F GLU* 1.3 81.6 - - + +
247F LYS* 1.3 57.3 + - - +
248F ASN 3.7 0.2 - - - -
249F LYS* 3.2 29.1 - - - +
251F PHE 3.2 19.1 - - - +
252F GLY 5.1 0.3 - - - +
253F LEU* 3.0 39.7 - - + +
259F LEU* 3.9 15.2 - - + +
261F LYS* 2.8 31.0 + - - +
----------------------------------------------------------
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