Contacts of the helix formed by residues 7 - 21 (chain R) in PDB entry 2DYS
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 THR 7 (chain R).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304O PSC 4.4 0.7 - - - -
6R GLU* 1.3 79.2 - - - +
8R ASP* 1.3 67.2 + - - +
9R GLU* 3.4 18.5 + - - +
10R GLU* 3.1 36.3 + - - +
11R PHE* 3.1 21.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 8 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304O PSC 3.6 23.0 - - - -
6R GLU 4.9 0.2 - - - +
7R THR* 1.3 75.7 - - - +
9R GLU* 1.3 65.5 + - - +
11R PHE* 3.8 0.3 - - - +
12R ASP* 2.7 40.5 + - - +
10V ARG* 3.1 42.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 9 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7R THR* 3.2 22.9 + - - +
8R ASP* 1.3 87.2 + - - +
10R GLU* 1.3 61.7 + - + +
12R ASP* 3.5 8.1 + - - +
13R ALA* 2.9 29.2 + - - +
46R LYS* 5.3 6.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 10 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6R GLU* 3.4 21.6 - - - +
7R THR* 3.1 37.1 + - - +
9R GLU* 1.3 77.4 - - + +
11R PHE* 1.3 64.7 + - - +
13R ALA* 3.7 5.7 - - - +
14R ARG* 3.0 29.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 11 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304O PSC 3.3 46.9 - - - -
5R HIS* 5.5 2.0 - + - -
6R GLU* 3.4 27.7 + - - +
7R THR 3.1 11.4 + - - +
8R ASP 3.8 0.2 - - - +
10R GLU* 1.3 79.9 - - - +
12R ASP* 1.3 74.4 + - - +
14R ARG* 3.3 15.5 + - - +
15R TRP* 3.3 50.6 + + - -
36R LEU* 3.9 7.2 - - + -
39R TYR* 3.8 33.9 - + - -
41R LEU* 3.9 22.9 - - + -
47R ILE* 4.5 5.4 - - + -
10V ARG* 5.1 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 12 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8R ASP* 2.7 27.8 + - - +
9R GLU* 3.6 6.7 - - - +
11R PHE* 1.3 80.9 - - - +
13R ALA* 1.3 61.5 + - - +
15R TRP 3.4 1.0 + - - -
16R VAL* 3.0 28.9 + - - +
44R GLU* 3.3 28.9 + - - +
46R LYS* 4.2 24.7 + - + +
47R ILE* 3.7 18.3 - - + +
10V ARG* 2.6 25.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 13 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9R GLU 2.9 17.9 + - - +
10R GLU* 3.7 7.6 - - - +
12R ASP* 1.3 75.1 - - - +
14R ARG* 1.3 55.7 + - + +
16R VAL* 3.0 7.8 + - - +
17R THR* 2.8 41.1 + - - +
46R LYS* 5.6 1.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 14 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5R HIS* 5.5 2.8 - - - -
6R GLU* 3.2 35.3 + - - +
10R GLU* 3.0 14.8 + - + +
11R PHE* 3.5 23.7 - - - +
13R ALA* 1.3 80.0 - - + +
15R TRP* 1.3 79.1 + - - +
17R THR* 3.6 8.0 - - - +
18R TYR* 3.1 24.8 + - - +
39R TYR* 4.5 6.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 15 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11R PHE* 3.3 55.7 + + - +
13R ALA 3.2 0.4 - - - -
14R ARG* 1.3 98.2 - - - +
16R VAL* 1.3 64.9 + - - +
17R THR 3.2 0.2 - - - -
18R TYR* 3.2 20.5 + + + +
19R PHE* 3.1 49.1 + + - -
32R GLY* 3.3 42.6 - - - -
35R THR* 3.9 17.9 - - + -
36R LEU* 3.9 14.6 - - + -
39R TYR* 3.9 22.2 - + - -
47R ILE* 3.8 25.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 16 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12R ASP 3.0 20.4 + - - +
13R ALA* 3.5 5.8 - - - +
15R TRP* 1.3 75.8 - - - +
17R THR* 1.3 65.4 + - - +
19R PHE 3.5 0.2 + - - -
20R ASN* 3.0 45.4 + - - +
46R LYS* 3.4 48.9 - - + +
47R ILE* 3.8 7.0 - - + +
50R ALA* 3.8 10.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 17 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13R ALA* 2.8 22.6 + - - +
14R ARG* 3.6 9.0 - - - +
16R VAL* 1.3 79.0 - - - +
18R TYR* 1.3 63.2 + - - +
20R ASN* 3.3 14.9 + - - +
21R LYS* 3.3 12.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 18 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14R ARG 3.1 18.6 + - - +
15R TRP* 3.2 24.7 + + + +
17R THR* 1.3 79.7 - - - +
19R PHE* 1.3 81.0 + + - +
21R LYS* 3.5 12.7 + - - +
24R ILE* 3.5 18.9 - - + +
27R TRP* 5.3 1.0 - - - -
28R GLU* 2.4 48.5 + - + +
31R LYS* 3.9 7.8 - - - +
32R GLY* 3.5 24.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 19 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15R TRP* 3.1 38.1 + + - +
18R TYR* 1.3 92.6 - + - +
20R ASN* 1.3 58.0 + - - +
21R LYS 3.3 0.8 - - - +
24R ILE* 4.0 12.1 - - + +
29R LEU* 4.0 25.8 - - + -
32R GLY* 3.7 18.6 - - - -
33R MET* 3.6 27.8 - - + -
36R LEU* 4.0 5.8 - - + -
47R ILE* 3.9 20.4 - - + -
50R ALA* 3.5 27.3 - - + +
51R ALA* 3.8 18.2 - - + -
54R ALA* 3.5 10.0 - - + +
57R ARG* 2.8 21.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 20 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16R VAL* 3.0 38.3 + - - +
17R THR* 3.7 7.4 - - - +
18R TYR 3.2 0.6 - - - -
19R PHE* 1.3 78.3 - - - +
21R LYS* 1.3 65.9 + - - +
22R PRO* 2.9 10.9 - - - +
50R ALA* 3.3 24.1 - - - +
53R ARG* 4.9 6.9 - - - -
57R ARG* 3.7 12.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 21 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17R THR 3.3 10.0 + - - +
18R TYR* 3.7 13.5 - - - +
19R PHE 3.3 1.4 - - - -
20R ASN* 1.3 73.1 - - - +
22R PRO* 1.3 76.3 - - + +
23R ASP* 3.4 30.1 + - - +
24R ILE* 3.2 26.3 + - + +
28R GLU* 2.8 37.6 + - - -
57R ARG* 3.0 13.5 + - - -
----------------------------------------------------------
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