Contacts of the helix formed by residues 39 - 55 (chain A) in PDB entry 2KOQ
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 ASP 39 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ALA* 6.2 0.2 - - - -
33A THR* 3.0 21.1 - - - +
37A ASP* 5.6 0.2 + - - -
38A VAL* 1.3 79.1 - - - +
40A SER* 1.3 64.8 + - - +
41A LEU* 2.7 35.0 + - - +
42A SER* 3.4 26.6 + - - +
43A MET* 3.3 12.8 + - - +
101A SHW 5.8 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 40 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A THR* 4.5 3.1 - - - -
39A ASP* 1.3 80.3 + - - +
41A LEU* 1.3 67.3 + - - +
43A MET* 3.2 19.4 - - - +
44A VAL* 3.8 10.6 - - - +
101A SHW 1.6 71.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 41 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ASP* 2.7 11.0 + - - +
40A SER* 1.3 92.3 - - - +
42A SER* 1.3 63.1 + - - +
43A MET 3.1 1.9 + - - -
44A VAL* 3.4 17.2 + - + +
45A GLU* 3.8 13.2 - - - +
101A SHW 4.3 6.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ILE* 3.1 40.6 + - - +
19A ALA* 4.9 0.4 - - - -
38A VAL* 4.0 10.8 - - - -
39A ASP* 3.4 26.3 + - - +
41A LEU* 1.3 75.8 - - - +
43A MET* 1.3 64.3 + - - +
45A GLU* 3.1 23.6 + - - -
46A VAL* 3.3 4.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A PHE* 3.5 20.9 - - + -
33A THR* 3.2 31.2 - - + +
38A VAL* 3.7 16.6 - - + +
39A ASP 3.3 10.5 + - - +
40A SER* 3.2 15.3 - - - +
41A LEU 3.1 0.2 - - - -
42A SER* 1.3 79.1 - - - +
44A VAL* 1.3 58.9 + - + +
46A VAL* 2.9 32.0 + - + +
47A VAL* 3.1 16.7 + - + +
101A SHW 3.4 59.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A SER 3.8 14.6 - - - +
41A LEU* 3.4 11.9 + - + +
42A SER 3.2 0.6 - - - -
43A MET* 1.3 78.5 - - + +
45A GLU* 1.3 58.2 + - + +
47A VAL* 3.4 8.1 + - + +
48A VAL* 2.9 32.1 + - + +
60A ASP* 3.8 37.0 - - + +
64A LYS* 5.4 1.6 - - - +
101A SHW 6.0 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ILE* 3.5 28.5 - - + +
41A LEU 3.8 10.8 - - - +
42A SER* 3.1 29.1 + - - +
44A VAL* 1.3 75.8 - - + +
46A VAL* 1.3 61.2 + - - +
48A VAL* 3.2 11.0 - - + +
49A ALA* 2.9 32.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU* 4.7 3.4 - - + +
14A ILE* 3.5 28.8 - - + +
15A VAL* 4.1 27.8 - - + -
18A ILE* 4.1 14.4 - - + -
32A PHE* 4.5 4.7 - - + -
38A VAL* 4.8 7.6 - - + -
42A SER 3.4 14.8 - - - +
43A MET* 3.2 18.6 - - + +
45A GLU* 1.3 78.3 - - - +
47A VAL* 1.3 52.1 + - - +
49A ALA* 3.7 1.6 - - - +
50A ALA* 2.8 36.4 + - - +
101A SHW 3.9 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A MET* 3.2 20.9 - - + +
44A VAL* 3.5 13.2 - - + +
46A VAL* 1.3 75.8 - - - +
48A VAL* 1.3 64.8 + - - +
50A ALA* 3.0 21.4 + - - +
51A GLU* 3.2 12.4 + - - +
58A ILE* 3.3 26.6 - - + +
60A ASP* 4.0 12.1 - - + +
63A VAL* 3.5 48.2 - - + -
101A SHW 4.1 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A VAL* 2.9 22.4 + - + +
45A GLU* 3.2 20.9 - - + +
47A VAL* 1.3 72.9 - - - +
49A ALA* 1.3 67.7 + - + +
51A GLU* 3.1 37.2 - - - +
52A GLU* 4.0 3.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ILE* 4.0 21.3 - - + -
18A ILE* 4.6 4.3 - - + -
45A GLU 2.9 19.4 + - - +
46A VAL 3.8 3.1 - - - +
48A VAL* 1.3 78.4 - - + +
50A ALA* 1.3 60.3 + - - +
52A GLU* 3.1 9.2 + - - +
53A ARG* 2.9 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU* 5.1 0.4 - - + -
14A ILE* 3.9 7.6 - - + +
46A VAL* 2.8 18.8 + - + +
47A VAL 3.0 9.6 + - - +
49A ALA* 1.3 75.9 - - - +
51A GLU* 1.3 56.5 + - - +
54A PHE* 2.8 60.5 + - + +
56A VAL* 4.1 1.9 - - - +
58A ILE* 4.4 9.4 - - + -
101A SHW 4.1 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A VAL* 3.2 11.7 + - - +
48A VAL* 3.1 37.5 - - - +
50A ALA* 1.3 76.3 - - - +
52A GLU* 1.3 57.5 + - - +
55A ASP* 3.2 5.4 + - - -
56A VAL* 2.8 44.3 + - - +
57A LYS* 2.7 41.9 + - + +
58A ILE* 3.4 32.7 + - + +
59A PRO* 4.5 2.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A VAL 4.9 2.7 - - - +
49A ALA* 3.1 10.1 + - - +
51A GLU* 1.3 77.6 - - - +
53A ARG* 1.3 66.3 + - - +
54A PHE 3.3 0.9 - - - -
55A ASP* 3.3 21.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A GLY* 3.8 12.8 - - - +
13A GLU* 2.8 48.4 + - - -
14A ILE* 3.6 25.8 - - + -
49A ALA* 2.9 17.2 + - + +
50A ALA 3.8 2.9 - - - +
52A GLU* 1.3 79.8 + - - +
54A PHE* 1.3 67.6 + - + +
55A ASP* 4.6 3.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 54 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A GLU 4.8 0.2 - - - -
7A ILE* 3.0 50.7 - - + -
10A GLY* 3.5 16.4 - - - -
11A LEU* 3.3 28.3 - - + -
14A ILE* 4.3 1.1 - - + -
50A ALA* 2.8 46.5 + - + +
53A ARG* 1.3 86.0 - - + +
55A ASP* 1.3 73.1 + - - +
56A VAL* 3.6 15.4 - - + +
76A ILE* 3.5 26.6 - - + +
80A GLN* 4.7 11.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 55 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A GLU 3.2 9.9 + - - -
52A GLU* 3.3 15.1 + - - +
53A ARG 4.6 3.1 - - - +
54A PHE* 1.3 83.6 - - - +
56A VAL* 1.3 61.4 + - - +
80A GLN* 5.5 0.3 - - - -
81A ALA* 3.4 25.9 + - + +
----------------------------------------------------------
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