Contacts of the helix formed by residues 36 - 46 (chain F) 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 GLY 36 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14F PHE* 3.5 18.1 - - - -
34F GLY 3.3 2.2 - - - -
35F ALA* 1.3 79.1 - - - +
37F LYS* 1.3 59.2 + - - +
38F SER 3.3 0.7 - - - -
39F VAL* 2.9 13.5 - - - +
40F PHE* 2.9 24.9 + - - +
200F MET* 3.2 16.7 - - - +
803F PO4 3.0 11.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 37 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29F LEU* 4.4 7.9 - - + +
31F GLY* 2.7 36.8 + - - +
32F PRO 3.7 8.1 + - - +
33F THR* 4.7 1.8 - - - +
35F ALA* 4.1 4.0 - - + -
36F GLY* 1.3 77.0 - - - +
38F SER* 1.3 61.6 + - - +
40F PHE* 3.2 5.2 - - - +
41F LEU* 3.1 27.5 + - - +
151F ASP* 5.6 0.4 - - + -
152F GLU* 3.4 18.5 + - - -
183F VAL* 3.0 37.8 - - + +
184F THR* 3.2 26.1 + - - +
185F HIS* 3.6 3.0 - - - +
200F MET* 3.7 21.3 - - + +
803F PO4 2.7 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 38 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37F LYS* 1.3 74.8 - - - +
39F VAL* 1.3 66.2 + - - +
41F LEU* 3.4 8.0 + - - +
42F GLU* 3.0 30.9 + - - +
74F PHE* 5.5 0.5 - - - -
151F ASP* 3.0 18.3 + - - +
703F MG 1.9 34.6 - - - -
803F PO4 3.0 8.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 39 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9F LYS* 6.1 0.4 - - + -
11F LEU* 4.0 27.1 - - + -
14F PHE* 4.1 9.9 - - + -
16F LEU* 3.4 24.2 - - + -
36F GLY* 2.9 34.5 - - - +
38F SER* 1.3 75.0 - - - +
40F PHE* 1.3 67.6 + - - +
42F GLU* 2.9 20.4 + - - +
43F LEU* 2.7 24.8 + - - +
48F VAL* 5.1 7.5 - - + +
803F PO4 4.5 1.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 40 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5F VAL* 4.0 10.8 - - + -
16F LEU* 4.2 6.3 - - + -
18F VAL* 3.6 39.7 - - + -
20F PHE* 3.6 28.3 - + + -
29F LEU* 4.0 23.3 - - + -
36F GLY 2.9 15.0 + - - +
37F LYS* 3.2 12.8 - - - +
39F VAL* 1.3 78.2 - - - +
41F LEU* 1.3 69.2 + - + +
43F LEU* 2.9 27.4 + - + +
44F ILE* 3.1 22.5 + - + +
181F LEU* 3.8 23.6 - - + -
200F MET* 4.3 7.9 - - + -
205F ILE* 3.7 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 41 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37F LYS 3.1 9.3 + - - +
38F SER* 3.7 8.7 - - - +
40F PHE* 1.3 81.1 - - + +
42F GLU* 1.3 55.4 + - - +
43F LEU 3.0 1.8 - - - -
44F ILE* 3.3 3.0 + - + -
45F ALA* 2.7 36.6 + - - +
74F PHE* 4.0 15.3 - - + -
149F LEU* 3.3 35.6 - - + +
150F LEU 3.3 41.7 - - - +
151F ASP* 3.9 12.6 - - + +
181F LEU* 3.9 15.7 - - + -
183F VAL* 3.6 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 42 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38F SER* 3.0 18.0 + - - +
39F VAL* 2.9 23.0 + - - +
41F LEU* 1.3 76.3 - - - +
43F LEU* 1.3 57.6 + - - +
45F ALA* 3.7 7.6 - - - -
46F GLY 2.9 5.4 + - - -
47F ILE* 2.7 42.2 + - + -
48F VAL* 3.4 23.5 + - + +
74F PHE* 4.5 14.6 - - + -
160H HIS* 3.3 32.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 43 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5F VAL* 5.2 2.9 - - + -
7F ALA* 4.7 14.4 - - + +
9F LYS* 4.8 4.9 - - + -
16F LEU* 3.5 37.7 - - + -
18F VAL* 5.1 2.5 - - + -
39F VAL 2.7 8.2 + - - +
40F PHE* 2.9 18.8 - - + +
42F GLU* 1.3 74.7 - - - +
44F ILE* 1.3 66.9 + - + +
46F GLY* 3.0 11.8 + - - -
48F VAL* 3.7 30.3 - - + +
50F PRO* 3.7 31.6 - - + -
55F VAL* 4.3 16.5 - - + +
70F ARG* 3.1 8.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 44 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3F LEU* 4.0 18.2 - - + -
5F VAL* 3.2 37.7 - - + -
40F PHE* 3.1 37.0 + - + +
41F LEU* 3.6 9.6 - - + +
43F LEU* 1.3 75.2 - - + +
45F ALA* 1.3 56.9 + - - +
55F VAL* 4.5 9.6 - - + +
57F LEU* 6.1 0.2 - - + -
70F ARG* 2.5 24.8 + - - +
72F ILE* 3.2 29.2 - - + +
147F LEU* 3.9 20.9 - - + -
149F LEU* 3.6 13.5 - - + -
181F LEU* 4.7 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 45 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41F LEU 2.7 22.0 + - - +
42F GLU* 3.5 12.6 - - - +
44F ILE* 1.3 74.9 - - - +
46F GLY* 1.3 57.7 + - - +
47F ILE* 4.3 12.3 - - + +
67F PRO* 3.4 24.1 - - - +
70F ARG* 3.5 6.6 - - - +
72F ILE* 4.1 12.6 - - + +
74F PHE* 3.9 24.5 - - + -
149F LEU* 3.8 3.1 - - + +
164H THR* 4.8 4.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 46 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42F GLU 2.9 4.2 + - - -
43F LEU 3.0 7.5 + - - -
44F ILE 3.0 0.2 + - - -
45F ALA* 1.3 79.5 - - - +
47F ILE* 1.3 60.2 + - - +
48F VAL 3.2 8.7 + - - -
49F LYS* 5.9 2.7 - - - +
65F LEU 5.1 0.5 - - - +
66F PRO* 4.9 0.5 - - - +
67F PRO* 3.1 26.2 - - - +
70F ARG* 3.0 31.2 - - - -
163H ARG* 5.2 0.5 + - - -
----------------------------------------------------------
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