Contacts of the helix formed by residues 37 - 47 (chain P) in PDB entry 3K9Q
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 37 (chain P).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36P THR* 1.3 82.3 + - - +
38P ASP* 1.3 64.3 + - - +
39P ASP* 3.6 15.6 - - - +
40P MET* 3.1 28.6 + - - +
41P LEU* 3.2 18.9 + - - +
194Q GLY* 5.8 3.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 38 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37P ASP* 1.3 72.9 - - - +
39P ASP* 1.3 66.7 + - - +
41P LEU* 3.3 9.2 + - - +
42P ALA* 2.9 28.6 + - - +
60P VAL* 3.8 22.8 - - + +
61P VAL 4.4 2.8 - - - +
63P GLY* 4.1 3.8 + - - -
64P GLY* 3.5 30.6 + - - +
65P PHE* 4.2 3.1 - - + -
74P SER* 2.4 33.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 39 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37P ASP* 3.6 18.1 - - - +
38P ASP* 1.3 76.7 - - - +
40P MET* 1.3 62.1 + - - +
42P ALA* 4.0 2.1 - - - +
43P HIS* 3.2 24.8 + - - +
60P VAL* 4.2 15.3 - - + +
194Q GLY 4.9 2.9 - - - +
196Q LYS* 2.6 39.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 40 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36P THR* 3.2 28.3 - - + +
37P ASP* 3.1 8.6 + - - +
39P ASP* 1.3 80.7 + - - +
41P LEU* 1.3 57.7 + - - +
43P HIS* 3.2 6.0 + - - +
44P LEU* 2.9 54.8 + - + +
190Q PRO* 3.8 8.7 - - + -
191Q HIS 3.9 18.8 - - - +
194Q GLY* 3.4 43.5 - - - +
195Q ASP 3.9 8.5 - - - +
196Q LYS* 4.1 13.5 - - + +
199Q ALA* 3.9 11.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 41 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10P PHE* 3.8 40.7 - - + +
32P VAL* 4.2 9.0 - - + -
34P ASP* 4.0 11.9 - - + -
36P THR* 3.5 25.6 - - + +
37P ASP 3.2 14.5 + - - +
38P ASP* 3.7 24.5 - - - +
40P MET* 1.3 72.9 - - - +
42P ALA* 1.3 66.1 + - - +
44P LEU* 3.2 6.2 + - + +
45P LEU* 3.0 23.6 + - - +
65P PHE* 4.1 15.3 - - + -
74P SER* 4.0 16.6 - - - +
75P PHE 5.3 4.0 - - - +
190Q PRO* 5.2 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 42 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38P ASP 2.9 19.8 + - - +
39P ASP 4.0 2.2 - - - +
41P LEU* 1.3 72.0 - - - +
43P HIS* 1.3 63.5 + - - +
45P LEU* 3.2 5.4 + - - +
46P LYS* 3.0 33.6 + - + +
58P VAL* 3.7 25.9 - - + +
59P GLU 5.4 0.2 - - - +
60P VAL* 3.7 22.9 - - + +
65P PHE* 4.6 11.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 43 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39P ASP 3.2 17.4 + - - +
40P MET 3.4 4.9 - - - +
42P ALA* 1.3 79.7 - - - +
44P LEU* 1.3 69.3 + - + +
46P LYS* 3.2 15.5 + - - +
47P TYR* 3.0 53.5 + + + +
196Q LYS* 3.3 50.5 + - + +
200Q ARG* 4.4 9.0 + - - -
276R ASP* 4.9 2.2 - - + +
277R GLU 3.5 38.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 44 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10P PHE 5.5 0.2 - - - +
15P ARG* 3.1 35.1 + - - +
19P ARG* 4.8 1.6 + - - -
40P MET* 2.9 36.3 + - + +
41P LEU* 4.1 4.5 - - + +
43P HIS* 1.3 80.0 - - + +
45P LEU* 1.3 63.2 + - - +
47P TYR 3.0 19.1 - - - +
48P ASP* 4.8 2.6 - - - +
188Q ASP* 4.5 6.5 - - + -
189Q ALA* 3.4 13.7 - - - +
190Q PRO* 3.4 37.5 - - + -
199Q ALA* 4.1 20.0 - - + -
200Q ARG* 4.1 20.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 45 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10P PHE* 4.1 13.5 - - + -
15P ARG* 3.9 10.5 - - + +
18P PHE* 3.7 39.5 - - + -
19P ARG* 3.0 36.8 + - + +
41P LEU 3.0 13.6 + - - +
42P ALA 3.6 7.2 - - - +
44P LEU* 1.3 77.9 - - - +
46P LYS* 1.3 58.4 + - - +
54P PHE* 3.2 25.9 - - + +
58P VAL* 3.9 18.4 - - + -
65P PHE* 4.0 13.9 - - + -
67P VAL* 3.9 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 46 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42P ALA* 3.0 25.0 + - + +
43P HIS* 3.2 13.6 + - - +
45P LEU* 1.3 77.2 - - - +
47P TYR* 1.3 81.7 + - + +
53P ARG* 3.4 6.8 - - - +
54P PHE* 2.8 34.6 + - + +
56P GLY 5.7 2.0 - - - +
58P VAL* 3.9 39.5 + - + +
276R ASP* 3.2 35.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 47 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43P HIS* 3.0 42.1 + + + +
44P LEU* 3.0 23.7 - - - +
45P LEU 3.3 0.2 - - - -
46P LYS* 1.3 103.0 - - + +
48P ASP* 1.3 59.8 + - - +
52P GLY 4.8 0.2 - - - -
53P ARG* 3.6 35.2 + - + +
188Q ASP* 3.9 5.5 - - - +
200Q ARG* 3.6 16.6 + - - +
274R THR* 4.8 1.7 + - - -
276R ASP* 2.6 34.2 + - + +
278R ILE* 3.6 19.6 - - + +
282R ASP* 3.2 30.1 - - + +
----------------------------------------------------------
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