Contacts of the helix formed by residues 48 - 58 (chain A) in PDB entry 1WH7
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 48 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A ILE* 5.5 1.1 - - - +
44A GLN 3.8 7.8 - - - +
45A LYS* 3.4 24.2 - - - +
46A HIS 3.0 3.6 + - - +
47A ASP* 1.3 76.2 - - - +
49A VAL* 1.3 73.1 + - + +
50A ALA 3.4 0.2 - - - -
51A VAL* 3.1 8.1 + - - +
52A GLU* 3.0 31.3 + - - +
62A ARG* 5.9 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A HIS 4.3 3.9 + - - +
48A ASP* 1.3 75.5 - - + +
50A ALA* 1.3 57.0 + - - +
51A VAL 2.9 1.6 - - - -
52A GLU* 2.6 17.6 + - + +
53A GLN* 2.6 49.6 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
35A PHE* 3.1 18.7 - - + -
39A LEU* 4.6 13.5 - - + -
46A HIS 4.9 3.2 + - - +
47A ASP* 4.5 15.5 - - - +
48A ASP 3.4 0.2 - - - -
49A VAL* 1.3 78.4 - - - +
51A VAL* 1.3 56.4 + - - +
53A GLN* 3.8 9.2 - - - +
54A PHE* 3.0 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A PHE* 3.8 15.0 - - + -
39A LEU* 4.7 1.1 - - + -
43A ILE* 3.7 28.7 - - + -
47A ASP* 2.7 27.6 - - + +
48A ASP* 3.1 11.1 + - - +
49A VAL 2.9 0.6 - - - -
50A ALA* 1.3 76.7 - - - +
52A GLU* 1.3 63.6 + - + +
54A PHE* 3.4 3.8 + - - +
55A CYS* 3.0 28.7 + - + +
60A VAL 5.1 0.6 - - - +
62A ARG* 3.7 38.6 - - + +
65A LEU* 4.5 7.1 - - + +
----------------------------------------------------------
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 ASP* 3.0 23.2 + - - +
49A VAL* 2.6 19.2 + - + +
51A VAL* 1.3 73.8 - - + +
53A GLN* 1.3 58.7 + - - +
55A CYS* 3.3 6.1 + - - +
56A ALA* 2.8 31.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A VAL* 2.6 32.0 + - + +
50A ALA* 3.8 9.3 - - - +
52A GLU* 1.3 73.1 - - - +
54A PHE* 1.3 64.0 + - - +
56A ALA* 3.3 10.0 + - + +
57A GLU* 3.2 19.8 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
31A LYS* 3.4 25.6 - - + -
32A MET* 3.4 42.2 - - + -
35A PHE* 3.0 68.2 - + + -
38A ARG* 5.1 3.8 - - - -
50A ALA 3.0 7.0 + - - +
51A VAL 3.4 3.4 - - - +
52A GLU 3.2 0.2 - - - -
53A GLN* 1.3 74.9 - - - +
55A CYS* 1.3 55.9 + - - +
57A GLU* 2.8 9.6 + - + +
58A THR* 2.5 60.4 + - + -
60A VAL* 4.6 10.1 - - + -
65A LEU* 4.4 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 55 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A VAL* 3.0 13.8 + - + +
52A GLU* 3.7 6.3 - - - +
54A PHE* 1.3 74.8 - - - +
56A ALA* 1.3 59.2 + - - +
57A GLU 2.7 11.9 + - - -
58A THR* 3.9 1.1 - - - -
59A GLY* 2.5 48.7 + - - +
60A VAL 3.0 28.0 - - - +
61A ARG* 4.8 13.9 - - - -
62A ARG 5.6 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 56 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A GLU 2.8 18.5 + - - +
53A GLN* 3.4 11.7 - - + +
54A PHE 3.2 0.2 - - - -
55A CYS* 1.3 77.8 - - - +
57A GLU* 1.3 59.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 57 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A LYS* 4.1 25.6 + - - -
53A GLN 3.2 9.8 + - - +
54A PHE* 2.8 10.9 + - + +
55A CYS 2.7 1.6 + - - +
56A ALA* 1.3 81.9 - - - +
58A THR* 1.3 71.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A GLU* 5.7 0.4 - - + -
28A GLN* 3.0 38.7 + - + +
31A LYS* 3.7 46.0 - - + +
54A PHE* 2.5 41.1 + - + +
57A GLU* 1.3 79.4 - - + +
59A GLY* 1.3 58.3 + - - -
60A VAL* 3.9 6.5 + - - -
----------------------------------------------------------
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