Contacts of the helix formed by residues 24 - 34 (chain F) in PDB entry 2PY2
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 HIS 24 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23F LEU* 1.3 78.8 - - - +
25F TRP* 1.3 67.2 + - - +
26F ALA* 3.3 19.5 + - + +
27F ASP* 3.0 59.2 + - - +
28F ALA* 3.0 16.8 + - - +
30F GLU* 4.6 1.3 - - - -
63F TRP* 3.6 0.2 - - - -
117F CYS 3.3 12.8 - - - +
118F THR* 3.5 28.0 - - + +
119F HIS 3.4 8.7 - - - -
120F LEU* 3.3 11.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 25 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24F HIS* 1.3 69.7 - - - +
26F ALA* 1.3 70.1 + - + +
28F ALA* 3.2 3.5 + - - +
29F GLN* 3.0 34.0 + - + +
39F LEU* 3.3 18.3 - - + +
63F TRP* 3.4 30.9 - + + +
64F ILE 2.9 25.3 + - - -
65F GLY* 4.2 4.5 - - - -
66F GLY 4.2 1.0 + - - -
67F THR* 3.6 26.0 - - + +
78F MET* 3.5 45.3 - - + -
101F CYS* 3.4 34.6 - - + -
117F CYS* 2.9 22.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 26 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24F HIS* 3.3 17.3 + - + +
25F TRP* 1.3 90.0 - - + +
27F ASP* 1.3 58.0 + - - +
29F GLN* 3.3 4.1 + - - +
30F GLU* 2.9 42.4 + - + +
117F CYS* 4.7 1.6 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
23F LEU* 3.8 29.1 - - + +
24F HIS* 3.0 37.6 + - + +
26F ALA* 1.3 73.4 - - - +
28F ALA* 1.3 61.4 + - - +
30F GLU* 3.1 25.7 + - - +
31F SER* 2.8 29.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 28 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23F LEU* 3.9 17.0 - - + +
24F HIS 3.0 13.4 + - - +
25F TRP 3.5 9.4 - - - +
27F ASP* 1.3 76.4 - - - +
29F GLN* 1.3 62.0 + - - +
31F SER* 3.3 4.2 + - - -
32F CYS* 3.1 27.0 + - - -
39F LEU* 3.9 9.2 - - + -
63F TRP* 4.2 9.9 - - + -
121F HIS 5.3 0.4 - - - +
123F SER* 3.7 29.6 + - - +
125F CYS* 4.6 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 29 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25F TRP* 3.0 34.2 + - + +
26F ALA* 3.6 4.5 - - - +
28F ALA* 1.3 73.1 - - - +
30F GLU* 1.3 66.9 + - + +
32F CYS* 3.2 2.7 + - - +
33F MET* 3.0 50.7 + - - +
38F ASN* 3.0 26.3 + - - +
39F LEU* 2.9 42.9 + - + +
78F MET* 4.1 27.7 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
24F HIS* 4.6 1.2 - - - -
26F ALA* 2.9 33.5 + - + +
27F ASP* 3.1 30.3 + - - +
29F GLN* 1.3 78.0 - - + +
31F SER* 1.3 61.3 + - - +
33F MET* 3.2 14.7 + - - +
34F LYS* 3.2 28.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 31 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19F ASN* 3.5 24.6 + - - -
21F LEU* 5.7 1.7 - - - +
23F LEU* 4.3 7.3 - - - +
27F ASP 2.8 17.6 + - - -
28F ALA 3.5 6.3 - - - -
29F GLN 3.2 0.2 - - - -
30F GLU* 1.3 77.0 - - - +
32F CYS* 1.3 61.8 + - - +
34F LYS* 3.3 36.9 + - - +
35F GLU* 3.3 17.3 + - - +
125F CYS* 4.8 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 32 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28F ALA 3.1 18.5 + - - -
29F GLN 3.2 6.7 + - - +
31F SER* 1.3 77.0 - - - +
33F MET* 1.3 61.6 + - - +
35F GLU* 3.0 11.7 + - - +
36F GLY 3.4 0.2 + - - -
37F ALA* 2.8 29.2 + - - +
38F ASN 3.7 17.0 - - - +
39F LEU* 3.6 23.6 - - - -
125F CYS* 2.0 55.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 33 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29F GLN* 3.0 47.7 + - - +
30F GLU* 3.2 14.8 + - - +
32F CYS* 1.3 72.7 - - - +
34F LYS* 1.3 56.1 + - - +
35F GLU 2.9 5.2 - - - -
36F GLY* 3.0 18.8 + - - -
37F ALA 3.5 11.7 - - - +
38F ASN* 4.8 1.3 - - - +
78F MET* 6.3 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 34 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30F GLU* 3.2 11.6 + - + +
31F SER* 3.4 36.4 + - - +
32F CYS 3.2 0.4 - - - -
33F MET* 1.3 76.9 - - + +
35F GLU* 1.3 60.9 + - + +
36F GLY 3.5 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