Contacts of the helix formed by residues 44 - 53 (chain O) in PDB entry 2DFS
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 44 (chain O).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
799M ARG* 3.4 33.4 - - - +
37O ARG* 3.7 1.5 + - - -
43O PRO* 1.3 76.0 - - - +
45O GLU* 1.4 57.7 + - - +
46O ALA* 3.0 16.1 + - - +
47O GLU* 2.9 28.8 + - + +
48O LEU* 3.0 27.2 + - - +
82O GLU* 3.5 12.5 + - - +
114O GLU* 4.6 10.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 45 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
802M ARG* 2.7 39.0 + - - +
33O GLY* 5.0 0.3 - - - -
37O ARG* 2.7 44.9 + - - +
44O THR* 1.4 72.8 - - - +
46O ALA* 1.3 56.3 + - - +
48O LEU* 3.1 24.8 - - + +
49O GLN* 3.0 27.1 + - - +
114O GLU* 5.0 7.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 46 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44O THR* 3.0 11.9 + - - +
45O GLU* 1.3 75.0 - - - +
47O GLU* 1.3 51.0 + - - +
49O GLN* 2.9 10.0 + - - +
50O ASP* 2.8 46.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 47 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43O PRO* 3.2 25.9 - - - +
44O THR* 2.9 33.4 + - + +
46O ALA* 1.3 70.9 - - - +
48O LEU* 1.3 61.5 + - - +
50O ASP* 3.4 14.0 + - - +
51O MET* 3.1 30.3 + - - +
75O LYS* 2.6 39.8 + - - +
78O ASP* 3.2 22.7 - - - +
79O THR* 4.9 5.5 + - - -
82O GLU* 4.6 8.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 48 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29O THR 5.2 1.1 - - - +
30O LYS* 4.9 7.6 - - - +
32O LEU* 3.9 20.6 - - + +
33O GLY* 3.1 39.5 - - - +
36O MET* 4.7 7.6 - - - -
37O ARG* 5.1 0.9 - - - +
43O PRO* 5.1 1.9 - - + +
44O THR 3.0 15.5 + - - +
45O GLU* 3.1 33.0 - - + +
47O GLU* 1.3 75.4 + - - +
49O GLN* 1.3 67.8 + - + +
51O MET* 3.3 9.9 + - - +
52O ILE* 2.7 42.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 49 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45O GLU 3.0 16.8 + - - +
46O ALA* 2.9 15.3 + - - +
48O LEU* 1.3 79.5 - - + +
50O ASP* 1.3 59.4 + - - +
51O MET 3.4 0.9 + - - -
52O ILE* 3.4 19.1 - - - +
53O ASN* 2.9 29.4 + - - +
58O ASP* 5.6 1.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 50 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46O ALA* 2.8 33.7 + - - +
47O GLU* 3.6 13.4 + - + +
48O LEU 3.3 0.2 - - - -
49O GLN* 1.3 70.1 - - - +
51O MET* 1.4 57.7 + - - +
53O ASN* 3.0 23.3 + - - +
75O LYS* 5.7 4.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 51 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32O LEU* 4.7 4.2 - - + +
36O MET* 3.5 32.5 - - + +
47O GLU* 3.1 23.9 + - - +
48O LEU* 3.8 7.6 - - - +
50O ASP* 1.4 78.4 - - - +
52O ILE* 1.4 63.3 + - - +
53O ASN 3.4 9.5 - - - +
71O MET* 3.8 52.9 - - + +
72O MET* 4.7 2.0 - - - +
74O ARG* 5.9 4.2 - - - +
75O LYS* 3.7 54.1 - - + -
79O THR* 4.7 6.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 52 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29O THR* 4.1 38.4 - - + +
32O LEU* 3.7 27.8 - - + -
48O LEU* 2.7 28.8 + - + +
49O GLN* 3.4 33.4 - - - +
51O MET* 1.4 69.6 - - - +
53O ASN* 1.4 68.9 + - - +
57O ALA* 3.5 24.4 - - + +
58O ASP* 3.3 20.9 + - - +
63O ILE* 5.0 4.0 - - + -
67O GLU* 5.3 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 53 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49O GLN* 2.9 26.8 + - - +
50O ASP* 3.0 28.8 + - - +
51O MET* 3.4 12.5 - - - +
52O ILE* 1.4 85.3 - - + +
54O GLU* 1.3 63.8 + - - +
58O ASP* 3.3 23.8 - - - +
74O ARG* 5.5 1.7 + - - -
----------------------------------------------------------
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