Contacts of the helix formed by residues 23 - 33 (chain F) in PDB entry 5ZX2
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 GLU 23 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22F ASP* 1.3 75.3 + - - +
24F GLU* 1.3 73.5 + - - +
26F THR* 2.4 34.8 + - + +
27F ALA* 2.9 11.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 24 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22F ASP* 3.2 29.2 - - - +
23F GLU* 1.3 85.4 - - - +
25F LEU* 1.3 58.7 + - + +
27F ALA* 4.0 4.3 - - - +
28F ARG* 2.9 36.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 25 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22F ASP* 3.4 16.4 + - + +
23F GLU 3.2 0.2 - - - -
24F GLU* 1.3 79.1 - - + +
26F THR* 1.3 58.6 + - + +
28F ARG* 3.4 26.9 - - - +
29F PHE* 2.9 33.0 + - - +
66F TYR* 5.8 0.4 - - - -
69F PHE* 3.6 15.1 - - + +
70F ARG* 3.4 72.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 26 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22F ASP 3.8 12.8 - - - +
23F GLU* 2.4 35.9 + - + +
25F LEU* 1.3 79.1 - - + +
27F ALA* 1.3 58.5 + - - +
29F PHE* 3.3 5.7 + - - +
30F GLU* 2.9 42.8 + - - +
66F TYR* 3.3 35.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 27 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23F GLU 2.9 10.6 + - - +
24F GLU* 4.1 4.5 - - - +
26F THR* 1.3 81.4 + - - +
28F ARG* 1.3 64.2 + - - +
30F GLU* 3.1 9.4 + - - +
31F ARG* 3.0 25.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 28 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24F GLU* 2.9 20.2 + - - +
25F LEU* 3.4 30.7 - - - +
27F ALA* 1.3 76.6 - - - +
29F PHE* 1.3 57.7 + - - +
31F ARG* 3.1 22.8 - - - +
32F ASP* 2.9 45.1 + - - +
69F PHE* 3.9 28.5 + - + -
72F PHE* 3.8 26.1 + - - -
74F HIS* 3.6 60.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 29 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363D PRO* 4.0 16.2 - - + -
366D ILE* 5.5 3.8 - - + -
25F LEU 2.9 22.1 + - - +
26F THR* 3.5 4.7 - - - +
28F ARG* 1.3 77.8 - - - +
30F GLU* 1.3 59.4 + - - +
33F ALA* 2.8 56.5 + - + +
34F ILE* 3.7 17.5 + - + -
62F MET* 4.5 19.3 - - + -
65F ALA* 4.3 7.6 - - + -
66F TYR* 3.8 48.5 - + + -
69F PHE* 3.5 43.2 - + + -
82F LEU* 5.2 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 30 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363D PRO* 3.7 40.6 - - + +
364D GLU* 4.6 4.4 + - - +
365D ILE* 5.0 5.7 - - - +
26F THR* 2.9 29.0 + - - +
27F ALA* 3.7 7.0 + - - +
29F PHE* 1.3 76.3 - - - +
31F ARG* 1.3 61.3 + - - +
34F ILE* 3.5 30.9 - - + +
35F PRO* 4.2 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 31 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27F ALA 3.0 14.1 + - - +
28F ARG* 3.1 41.8 - - - +
30F GLU* 1.3 79.2 - - - +
32F ASP* 1.3 76.5 + - - +
35F PRO* 3.2 24.1 - - - +
74F HIS* 4.1 14.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 32 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28F ARG* 2.9 39.9 + - + +
29F PHE* 5.1 0.4 - - - -
31F ARG* 1.3 96.2 + - - +
33F ALA* 1.3 62.0 + - - +
35F PRO* 3.6 5.2 - - - +
36F LEU* 3.3 21.3 - - - +
69F PHE* 5.5 2.0 - - + -
74F HIS* 5.5 1.2 - - - +
78F LEU* 4.0 17.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 33 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29F PHE* 2.8 55.4 + - + +
32F ASP* 1.3 74.1 - - - +
34F ILE* 1.3 67.0 + - + +
36F LEU* 2.9 22.1 + - - +
37F LEU* 3.9 6.1 + - - +
62F MET* 5.6 3.1 - - - +
78F LEU* 3.7 19.3 - - + -
82F LEU* 4.4 12.4 - - + +
----------------------------------------------------------
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