Contacts of the helix formed by residues 425 - 430 (chain F) in PDB entry 1FPY
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 425 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421F LEU 3.2 17.1 + - - +
422F ASP* 2.7 43.8 + - - +
423F LEU 2.5 13.9 + - - +
424F ASP* 1.3 72.2 - - - +
426F GLU* 1.3 73.1 + - - +
427F PHE 3.4 0.4 - - - -
428F LEU* 3.1 21.9 + - - +
429F LYS* 3.4 25.9 + - + +
436F ASP* 3.1 36.7 + - - +
439F ILE* 4.0 20.7 - - + +
440F ASP* 3.0 38.6 + - - -
443F ILE* 4.4 4.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 426 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423F LEU 4.9 4.9 - - - +
424F ASP* 3.1 5.1 - - - +
425F ARG* 1.3 85.6 - - + +
427F PHE* 1.3 65.6 + - - +
428F LEU 3.0 1.4 + - - -
429F LYS* 3.0 48.8 + - - +
430F ALA* 3.5 8.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 427 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304F HIS* 3.5 39.7 - + + +
307F ALA* 4.2 10.3 - - + -
308F ILE* 4.5 6.7 - - + -
373F ALA* 3.7 4.5 - - + -
376F MET* 3.6 15.8 - - - +
377F ALA* 3.4 44.0 - - + -
380F ASP* 4.0 20.0 - - + +
424F ASP* 3.0 40.3 + - - -
426F GLU* 1.3 76.3 - - - +
428F LEU* 1.3 94.1 + - + +
429F LYS 3.5 0.2 - - - -
430F ALA* 3.5 18.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 428 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307F ALA* 5.3 0.9 - - + +
311F LEU* 5.6 1.6 - - + -
373F ALA* 3.9 20.6 - - + -
376F MET* 3.7 17.8 - - + +
421F LEU* 3.5 32.8 - - + -
425F ARG* 3.1 10.9 + - - +
426F GLU 3.0 1.0 + - - -
427F PHE* 1.3 121.9 - - + +
429F LYS* 1.3 59.8 + - - +
430F ALA 3.1 10.9 + - - +
433F VAL* 3.6 3.1 - - - +
434F PHE* 3.0 58.3 + - + +
439F ILE* 4.2 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 429 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425F ARG* 3.5 30.8 - - + +
426F GLU* 3.0 34.5 + - - +
428F LEU* 1.3 72.9 - - - +
430F ALA* 1.3 68.2 + - - +
431F GLY 3.5 0.2 + - - -
432F GLY* 2.9 19.4 + - - -
434F PHE 3.1 20.1 - - - +
435F THR* 4.8 2.7 - - - +
436F ASP* 3.0 39.7 + - - +
439F ILE* 4.2 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 430 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114F TYR* 3.6 25.1 - - + +
376F MET* 3.4 4.2 - - + +
383F LYS* 5.7 3.4 - - - +
426F GLU 3.5 7.0 + - - +
427F PHE* 3.5 21.1 - - - +
428F LEU 3.1 0.4 - - - -
429F LYS* 1.3 79.8 - - - +
431F GLY* 1.3 59.7 + - - +
432F GLY 2.9 5.5 + - - -
433F VAL* 3.1 19.1 + - - +
----------------------------------------------------------
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