Contacts of the helix formed by residues 43 - 56 (chain J) 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 LEU 43 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39J HIS* 3.9 8.5 - - + +
40J ALA* 3.4 12.5 + - + +
41J GLY 3.3 0.8 - - - -
42J SER* 1.3 78.9 + - - +
44J THR* 1.3 57.7 + - - +
46J PRO* 3.6 14.8 - - + -
47J MET* 2.8 41.5 + - + +
50J PHE* 5.3 1.8 - - + -
88J ALA* 3.1 42.4 - - + +
110J PHE* 3.5 26.9 - - + -
285J TYR* 3.4 34.1 - - + -
315J LEU* 4.5 1.6 - - + -
320J GLN* 4.0 13.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 44 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223I SER* 4.2 23.9 - - - +
224I GLU* 4.4 7.2 - - + -
39J HIS* 3.5 18.9 - - + -
41J GLY* 2.5 28.1 + - - -
42J SER 2.9 4.9 + - - -
43J LEU* 1.3 75.1 - - - +
45J GLU* 1.3 82.5 + - - +
47J MET* 3.3 3.8 + - - +
48J LYS* 3.1 23.6 + - + +
67J ALA* 3.9 7.5 - - + +
219J MET* 4.3 6.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 45 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224I GLU* 3.4 18.8 - - - +
42J SER 4.2 0.6 + - - -
44J THR* 1.3 81.5 - - - +
46J PRO* 1.3 67.0 - - + +
48J LYS* 2.6 64.8 + - - +
49J ALA* 3.3 2.4 + - - +
219J MET* 5.0 2.0 - - + +
242J GLN* 3.1 35.4 - - + +
243J HIS* 3.9 15.6 - - + -
318J LEU* 3.5 21.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 46 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42J SER 3.7 7.2 - - - +
43J LEU* 3.6 17.7 - - + +
44J THR 3.5 2.5 - - - -
45J GLU* 1.3 95.6 - - + +
47J MET* 1.3 63.8 + - - +
49J ALA* 2.9 16.5 + - - +
50J PHE* 2.9 34.1 + - + -
242J GLN* 4.1 6.3 - - - +
314J ILE* 4.4 3.6 - - + -
315J LEU* 3.9 14.6 - - + -
318J LEU* 3.5 19.7 - - + -
320J GLN* 3.8 22.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 47 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37J VAL* 3.9 20.2 - - + -
39J HIS* 3.7 28.3 - - + +
43J LEU* 2.8 45.9 + - + +
44J THR 3.6 4.7 - - - +
46J PRO* 1.3 71.9 - - - +
48J LYS* 1.3 62.9 + - - +
50J PHE* 3.5 24.8 - - + +
51J LYS* 2.9 24.4 + - - +
63J VAL* 6.2 0.7 - - - -
65J THR* 4.7 14.2 - - + +
88J ALA* 4.7 7.4 - - + -
110J PHE* 5.9 0.2 - - + -
287J ILE* 5.4 1.8 - - + -
302J PHE* 3.5 39.4 - - + -
306J VAL* 4.9 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 48 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224I GLU* 2.6 34.6 + - - +
44J THR* 3.1 13.5 + - + +
45J GLU* 2.6 52.1 + - - +
47J MET* 1.3 70.4 - - - +
49J ALA* 1.3 59.2 + - - +
51J LYS* 3.1 24.1 + - + +
52J ARG* 3.1 25.1 + - - +
65J THR* 6.0 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 49 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45J GLU 3.3 2.4 + - - +
46J PRO* 2.9 11.6 + - + +
48J LYS* 1.3 76.0 - - - +
50J PHE* 1.3 67.0 + - - +
51J LYS 2.9 3.1 + - - -
52J ARG* 3.3 21.7 + - - +
53J ALA* 3.0 24.4 + - - +
314J ILE* 3.5 33.9 - - + -
318J LEU* 5.2 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 50 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43J LEU* 5.3 4.0 - - + -
46J PRO* 2.9 46.7 + - + -
47J MET* 3.5 27.1 - - + +
49J ALA* 1.3 75.7 - - - +
51J LYS* 1.3 57.3 + - - +
54J PHE* 2.9 32.4 + - - +
110J PHE* 5.2 1.3 - + - -
302J PHE* 3.5 24.6 - + + -
305J LEU* 3.6 15.0 - - + +
306J VAL* 3.6 44.9 - - + -
311J GLY* 3.9 16.8 - - - -
314J ILE* 4.2 15.0 - - + -
315J LEU* 4.1 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 51 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47J MET 2.9 14.2 + - - +
48J LYS* 3.1 14.6 - - + +
49J ALA 2.9 1.2 + - - -
50J PHE* 1.3 74.2 - - - +
52J ARG* 1.3 68.5 + - - +
54J PHE* 3.2 4.3 + - - +
55J GLU* 2.8 60.0 + - - +
62J GLU* 4.2 6.8 - - - +
63J VAL* 2.5 48.9 + - + +
65J THR* 4.5 12.3 - - + -
302J PHE* 4.9 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 52 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48J LYS* 3.1 20.7 + - - +
49J ALA* 3.3 30.5 - - - +
51J LYS* 1.3 81.1 - - - +
53J ALA* 1.3 78.5 + - + +
55J GLU* 3.1 7.6 + - - +
56J GLU* 2.7 39.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 53 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49J ALA 3.0 14.9 + - - +
50J PHE* 3.8 3.4 - - - +
52J ARG* 1.3 83.7 - - + +
54J PHE* 1.3 56.2 + - - +
56J GLU* 2.7 37.8 + - - +
57J LYS* 3.2 6.1 + - - +
305J LEU* 3.8 20.4 - - + -
310J GLU* 4.6 13.9 - - - +
314J ILE* 4.8 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 54 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35J LEU* 3.8 16.4 - - + -
50J PHE 2.9 23.9 + - - +
51J LYS 3.7 2.2 - - - +
53J ALA* 1.3 72.5 - - - +
55J GLU* 1.3 59.4 + - + +
57J LYS* 3.2 24.0 + - + +
58J HIS* 3.2 32.5 + + + -
61J VAL* 4.5 14.4 - - + -
63J VAL* 3.5 22.0 - - + -
298J LEU* 3.4 23.8 - - + -
301J GLU* 3.5 14.1 - - + -
302J PHE* 3.3 48.7 - + + -
305J LEU* 3.5 12.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 55 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51J LYS* 2.8 51.3 + - - +
52J ARG* 3.7 6.1 - - - +
54J PHE* 1.3 69.5 - - - +
56J GLU* 1.3 56.1 + - - +
57J LYS 2.8 5.6 + - - -
58J HIS 4.1 5.8 - - - +
59J PRO* 2.8 37.8 - - + +
61J VAL 3.0 11.6 - - - +
62J GLU* 2.9 17.3 - - - +
63J VAL* 2.8 35.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 56 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52J ARG* 2.7 28.5 + - - +
53J ALA* 3.0 17.5 - - - +
55J GLU* 1.3 77.0 - - - +
57J LYS* 1.3 55.8 + - - +
59J PRO* 4.0 12.1 - - - +
----------------------------------------------------------
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