Contacts of the helix formed by residues 49 - 56 (chain A) in PDB entry 2EXG
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 49 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A LYS* 5.8 0.2 - - - -
21A ASN* 3.9 14.8 - - - -
23A MET 3.3 18.2 - - - -
24A GLY* 4.1 4.2 - - - -
48A GLY* 1.3 74.0 - - - +
50A ALA* 1.3 60.3 + - - -
52A ASP* 2.9 11.2 + - - +
53A VAL* 2.9 32.0 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
16A THR 3.8 7.5 - - - +
17A LEU* 3.6 19.5 - - + -
18A LYS* 4.0 1.9 - - - +
19A LYS* 3.5 30.7 - - - +
20A GLN 3.7 9.2 - - - +
21A ASN* 4.2 3.4 + - - +
22A GLY 2.9 19.4 + - - +
49A GLY* 1.3 71.1 - - - -
51A ALA* 1.3 57.1 + - - +
53A VAL* 3.6 9.7 - - - +
54A ASP* 3.3 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A VAL* 3.6 28.9 - - + +
16A THR 4.0 8.7 + - - +
23A MET* 3.0 35.8 + - + +
25A LEU* 3.7 16.7 - - + +
50A ALA* 1.3 75.9 - - - +
52A ASP* 1.3 60.1 + - - +
55A GLY* 2.9 27.8 + - - +
56A ARG 3.4 1.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A MET 3.1 5.0 + - - +
24A GLY 3.2 22.0 - - - +
25A LEU* 3.8 2.1 - - - +
45A VAL* 3.3 28.1 - - + +
47A LYS* 3.1 19.5 + - - -
48A GLY* 2.7 27.3 + - - -
49A GLY 2.9 15.1 + - - +
51A ALA* 1.3 74.8 - - - +
53A VAL* 1.3 67.9 + - - +
56A ARG* 3.0 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A LYS* 5.2 2.5 - - + -
19A LYS* 4.7 22.9 - - + +
49A GLY 2.9 23.7 + - - +
50A ALA* 3.6 12.6 - - - +
52A ASP* 1.3 81.0 - - - +
54A ASP* 1.3 64.8 + - + +
56A ARG* 2.8 25.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 54 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A THR* 5.4 3.6 + - - +
18A LYS* 2.7 62.5 + - + +
50A ALA 3.3 4.8 + - - +
53A VAL* 1.3 78.7 - - + +
55A GLY* 1.3 60.9 + - - +
56A ARG* 2.8 52.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 55 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A THR 5.7 0.7 - - - -
15A VAL* 3.4 20.3 - - - +
16A THR 5.8 0.4 + - - -
50A ALA 4.2 0.8 + - - -
51A ALA 2.9 18.0 + - - -
54A ASP* 1.3 77.0 - - - +
56A ARG* 1.3 68.1 + - - +
57A LEU* 3.1 13.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 56 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A LYS* 5.3 6.9 + - - -
45A VAL* 4.3 4.0 - - - -
51A ALA 3.4 1.8 + - - -
52A ASP 3.0 19.5 + - - +
53A VAL 2.8 31.7 + - - +
54A ASP* 2.8 49.3 + - - -
55A GLY* 1.3 74.4 + - - +
57A LEU* 1.3 65.8 + - - +
58A ALA* 4.7 0.9 - - - +
----------------------------------------------------------
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