Contacts of the helix formed by residues 26 - 36 (chain F) in PDB entry 5ITZ
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 GLN 26 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21F ALA* 3.0 14.4 + - + +
24F ALA* 3.9 26.5 + - + -
25F GLY* 1.3 77.8 + - - +
27F ASP* 1.3 65.6 + - - +
28F ASP 3.3 2.7 - - - -
29F GLU* 3.2 27.7 + - + +
30F VAL* 2.9 24.1 + - - +
62F ILE* 3.9 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 27 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25F GLY 3.1 18.7 + - - +
26F GLN* 1.3 73.6 - - - +
28F ASP* 1.3 66.2 + - - +
30F VAL* 3.4 2.9 + - - +
31F ARG* 3.2 27.5 + - - +
59F HIS* 5.7 0.9 - - - +
61F GLU* 3.6 24.3 - - + +
62F ILE* 3.2 27.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 28 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26F GLN 3.3 0.4 - - - -
27F ASP* 1.3 75.3 - - - +
29F GLU* 1.3 66.0 + - - +
31F ARG* 2.7 45.9 + - - +
32F ILE* 3.0 36.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 29 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17F LYS* 5.2 3.8 - - - +
21F ALA* 3.8 9.7 - - + +
26F GLN* 3.2 32.9 + - + +
28F ASP* 1.3 79.3 - - - +
30F VAL* 1.3 63.7 + - - +
32F ILE* 3.9 14.2 - - - +
33F LEU* 2.8 53.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 30 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18F LEU* 3.9 19.2 - - + +
21F ALA* 3.9 20.4 - - + +
22F ALA* 4.0 2.2 - - - +
26F GLN 2.9 17.8 + - - +
27F ASP 3.6 7.9 - - - +
29F GLU* 1.3 74.0 - - - +
31F ARG* 1.3 63.1 + - - +
33F LEU* 3.8 1.9 - - - +
34F MET* 3.0 45.2 + - - +
62F ILE* 3.7 41.5 - - + -
65F VAL* 4.3 12.1 - - + -
66F LEU* 4.6 3.1 - - + -
----------------------------------------------------------
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 ASP* 3.2 13.7 + - - +
28F ASP* 2.7 48.7 + - - +
30F VAL* 1.3 79.8 - - - +
32F ILE* 1.3 59.6 + - - +
34F MET* 3.1 10.0 + - - +
35F ALA* 2.8 35.8 + - + +
65F VAL* 5.8 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 32 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28F ASP* 3.0 24.7 + - + +
29F GLU* 4.0 15.3 - - - +
31F ARG* 1.3 83.8 - - + +
33F LEU* 1.3 64.1 + - + +
35F ALA* 3.0 13.5 + - + +
36F ASN* 2.9 36.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 33 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14F LEU* 3.9 22.7 - - + +
17F LYS* 3.6 49.4 - - + +
18F LEU* 3.6 14.6 - - + +
21F ALA* 3.8 8.7 - - + -
29F GLU* 2.8 47.2 + - - +
30F VAL* 3.8 3.8 - - - +
32F ILE* 1.3 73.6 - - + +
34F MET* 1.3 61.9 + - - +
36F ASN* 3.1 14.5 + - - +
37F GLY 3.3 0.5 + - - -
38F ALA* 3.0 29.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 34 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18F LEU* 4.6 11.4 - - + -
30F VAL* 3.0 41.6 + - - +
31F ARG* 3.5 5.2 - - - +
33F LEU* 1.3 74.0 - - - +
35F ALA* 1.3 64.0 + - - +
37F GLY* 2.9 15.6 + - - -
38F ALA 4.0 7.8 - - - +
40F VAL* 3.6 25.6 - - + -
65F VAL* 4.0 14.4 - - - +
66F LEU* 4.4 9.9 - - + -
69F HIS* 3.4 46.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 35 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31F ARG* 2.8 19.4 + - + +
32F ILE* 3.0 13.7 + - + +
34F MET* 1.3 73.3 - - - +
36F ASN* 1.3 63.6 + - - +
37F GLY 3.5 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 36 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14F LEU* 3.3 26.3 - - + +
32F ILE* 2.9 37.7 + - - +
33F LEU* 3.1 11.1 + - - +
35F ALA* 1.3 80.9 - - - +
37F GLY* 1.3 57.7 + - - +
38F ALA 3.6 0.2 - - - -
----------------------------------------------------------
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