Contacts of the helix formed by residues 410 - 415 (chain F) in PDB entry 1XPU
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 ASP 410 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406F THR* 3.4 30.8 - - + +
407F LYS* 4.2 29.8 + - - +
408F THR 3.3 0.4 - - - +
409F ASN* 1.3 84.2 + - - +
411F ASP* 1.3 57.7 + - - +
412F PHE 3.1 1.3 - - - -
413F PHE* 3.2 7.0 + - - +
414F GLU* 2.8 32.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 411 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164F LEU* 4.2 11.3 - - + +
383F LEU* 3.6 23.4 - - - +
399F LEU* 4.8 4.5 - - - +
402F LYS* 3.5 25.7 - - - +
403F LEU* 3.6 22.1 + - + +
406F THR* 3.4 14.4 + - - +
408F THR* 3.5 18.7 + - - +
409F ASN 3.4 0.2 - - - -
410F ASP* 1.3 77.2 - - - +
412F PHE* 1.3 58.0 + - - +
413F PHE 3.2 1.2 + - - -
414F GLU* 4.6 7.4 - - - +
415F MET* 3.3 32.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 412 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164F LEU* 3.6 32.8 - - + -
376F GLU* 4.1 27.1 - - + -
379F LYS* 3.2 57.4 - - + +
380F MET* 3.6 23.8 - - + -
383F LEU* 3.8 26.2 - - + -
408F THR* 3.5 14.6 + - - -
409F ASN* 3.6 20.2 - - - +
410F ASP 3.1 0.8 - - - -
411F ASP* 1.3 77.9 - - - +
413F PHE* 1.3 62.9 + - - +
415F MET* 5.3 0.4 - - - -
416F MET* 3.3 28.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 413 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379F LYS* 3.5 32.1 - - - -
409F ASN* 4.2 9.6 - - - +
410F ASP* 3.2 9.9 + - - +
412F PHE* 1.3 81.4 - - - +
414F GLU* 1.3 65.4 + - - +
415F MET 3.3 1.3 - - - -
416F MET* 4.0 4.7 - - + +
417F LYS* 3.1 26.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 414 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402F LYS* 3.8 23.3 - - - +
405F MET* 3.4 35.0 - - - +
406F THR* 4.4 12.4 - - + +
410F ASP 2.8 18.2 + - - +
411F ASP* 4.6 6.5 - - - +
413F PHE* 1.3 76.0 - - - +
415F MET* 1.3 71.5 + - - +
417F LYS* 3.6 16.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 415 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383F LEU* 5.0 11.7 - - + -
386F ILE* 4.5 18.4 - - + -
398F PHE* 4.4 11.7 - - + -
402F LYS* 3.5 50.5 - - + +
411F ASP* 3.3 25.3 + - - +
412F PHE* 5.3 0.4 - - - -
413F PHE 3.3 0.6 - - - -
414F GLU* 1.3 87.9 - - - +
416F MET* 1.3 63.0 + - + +
417F LYS* 3.1 19.4 + - - +
----------------------------------------------------------
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