Contacts of the helix formed by residues 34 - 44 (chain H) in PDB entry 2ONK
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 ASN 34 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30H LEU 3.7 8.6 + - - +
31H GLN* 3.9 11.6 + - - +
32H LEU 2.9 0.6 - - - -
33H PHE* 1.3 92.8 + - - +
35H PHE* 1.3 56.4 + - - +
36H ASP* 2.9 17.7 + - - +
37H GLU* 3.0 41.7 + - + +
38H PHE* 3.1 10.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 35 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31H GLN 3.5 18.2 - - - -
32H LEU* 2.9 32.8 + - + +
33H PHE 3.7 0.2 - - - -
34H ASN* 1.3 76.1 - - - +
36H ASP* 1.3 58.3 + - - +
38H PHE* 3.8 23.6 - + - -
39H LEU* 2.9 70.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 36 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34H ASN* 2.9 4.8 + - - -
35H PHE* 1.3 78.8 + - - +
37H GLU* 1.3 69.5 + - + +
39H LEU* 3.2 10.1 + - - +
40H LYS* 2.9 32.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 37 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34H ASN* 3.0 34.8 + - + +
36H ASP* 1.3 78.5 - - + +
38H PHE* 1.3 55.5 + - - +
40H LYS* 3.0 12.0 + - - +
41H ALA* 2.7 36.0 + - - +
227H SER* 4.1 17.5 - - - +
231H PRO* 4.3 14.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 38 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28H VAL* 5.9 0.2 - - + -
31H GLN* 3.5 51.4 + - + +
34H ASN 3.1 3.5 + - - +
35H PHE* 3.7 35.4 - + - +
37H GLU* 1.3 79.0 - - - +
39H LEU* 1.3 63.0 + - + +
41H ALA* 3.3 2.6 + - - +
42H ALA* 2.8 37.0 + - + +
231H PRO* 4.3 8.7 - - - -
234H ALA* 4.2 5.2 - - + -
235H ILE* 3.7 33.2 - - + +
238H LEU* 3.8 28.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 39 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35H PHE* 2.9 60.5 + - + +
36H ASP* 3.5 7.9 - - - +
38H PHE* 1.3 78.9 - - + +
40H LYS* 1.3 56.2 + - - +
42H ALA* 3.1 12.4 + - + +
43H SER* 2.4 32.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 40 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36H ASP* 2.9 20.6 + - - +
37H GLU* 3.3 12.3 - - + +
39H LEU* 1.3 73.0 - - + +
41H ALA* 1.3 55.7 + - - +
43H SER* 2.8 11.3 + - - -
44H ASP* 2.7 34.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 41 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37H GLU 2.7 15.9 + - - +
38H PHE 3.3 8.7 - - - +
40H LYS* 1.3 71.8 - - - +
42H ALA* 1.3 63.4 + - - +
44H ASP* 2.9 28.4 + - - +
47H VAL* 4.0 7.3 - - - +
220H ARG* 5.2 5.4 - - - +
231H PRO* 3.7 20.9 - - + -
232H VAL* 4.5 10.1 - - + +
235H ILE* 3.4 20.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 42 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38H PHE* 2.8 24.4 + - + +
39H LEU* 3.1 20.2 - - + +
41H ALA* 1.3 76.7 - - - +
43H SER* 1.3 50.0 + - - +
48H TRP* 2.5 40.2 + - + +
235H ILE* 3.2 16.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 43 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39H LEU 2.4 29.3 + - - -
40H LYS* 2.9 11.7 + - - -
42H ALA* 1.3 75.6 - - - +
44H ASP* 1.3 54.1 + - - +
45H PRO* 2.7 28.2 - - - +
48H TRP* 4.1 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 44 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40H LYS 2.7 12.2 + - - +
41H ALA* 2.9 18.6 + - - +
43H SER* 1.3 73.5 - - - +
45H PRO* 1.3 64.2 - - - +
46H ALA* 2.8 31.8 + - - +
47H VAL* 2.9 29.6 + - + +
48H TRP* 3.5 6.2 - - - -
220H ARG* 2.8 32.8 + - - -
203J GLU* 4.5 0.7 - - - +
204J ARG* 5.4 1.6 + - - -
----------------------------------------------------------
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