Contacts of the helix formed by residues 37 - 48 (chain A) in PDB entry 1OVX
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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A VAL* 5.4 0.6 - - - +
25A ARG* 5.2 2.8 + - - -
26A LYS* 3.6 39.7 + - + +
28A ILE* 6.3 0.4 - - - -
36A CYS* 1.3 74.9 - - - +
38A GLU* 1.3 59.7 + - + +
40A VAL* 3.2 3.3 - - - +
41A ASP* 2.3 80.5 + - - +
44B ASN* 5.5 1.6 - - - -
47B ILE* 6.0 2.0 - - + +
48B ARG* 2.5 26.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A CYS* 4.5 12.3 - - - +
19A LYS* 3.8 28.8 + - - -
24A VAL* 5.3 9.6 - - + +
36A CYS* 3.4 1.9 - - + +
37A ASP* 1.3 79.5 - - + +
39A CYS* 1.3 58.3 + - - +
41A ASP* 4.2 6.1 - - - +
42A LEU* 2.8 49.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A CYS* 3.9 4.0 - - - -
16A PHE* 4.3 14.1 - - + -
17A CYS* 3.8 7.4 - - - -
35A ILE* 3.1 19.3 - - + -
36A CYS* 2.6 42.0 - - - -
38A GLU* 1.3 74.9 - - - +
40A VAL* 1.3 49.1 + - - +
42A LEU* 5.0 1.1 - - - -
43A CYS* 2.6 46.8 + - - -
61A ZN 2.3 36.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 40 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ILE* 3.7 24.7 - - + -
36A CYS 3.6 14.1 - - - +
37A ASP* 3.2 14.4 - - - +
39A CYS* 1.3 72.4 - - - +
41A ASP* 1.3 73.1 + - - +
43A CYS* 4.2 3.1 - - - -
44A ASN* 2.5 53.5 + - - +
28B ILE* 5.2 0.7 - - - -
40B VAL* 3.4 28.0 - - + -
44B ASN* 3.4 26.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 41 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ASP* 2.3 44.5 + - - +
38A GLU* 3.8 6.4 - - - +
40A VAL* 1.3 87.0 - - - +
42A LEU* 1.3 66.2 + - + +
44A ASN* 4.2 3.1 + - - +
45A ASP* 2.9 32.9 + - - +
48B ARG* 2.4 29.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A GLU* 2.8 37.7 + - + +
39A CYS* 4.2 1.1 - - - +
41A ASP* 1.3 75.6 - - + +
43A CYS* 1.3 68.5 + - - +
45A ASP* 3.5 10.8 + - - +
46A ILE* 3.2 31.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A PHE* 4.3 24.2 - - - -
35A ILE* 5.9 0.9 - - + -
39A CYS* 2.6 44.0 + - - +
40A VAL 4.2 0.2 - - - +
42A LEU* 1.3 73.1 - - - +
44A ASN* 1.3 65.4 + - - +
46A ILE* 3.0 12.0 + - - +
47A ILE* 2.9 26.0 + - - +
28B ILE* 3.4 41.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A VAL* 2.5 48.0 + - - +
41A ASP* 4.1 4.5 + - - +
43A CYS* 1.3 71.0 - - - +
45A ASP* 1.3 60.4 + - - +
47A ILE* 3.6 8.3 - - - +
48A ARG* 2.8 68.2 + - - +
28B ILE* 3.6 17.5 - - - +
37B ASP* 4.9 1.4 - - - +
40B VAL* 3.3 23.6 - - - +
44B ASN* 3.7 7.9 - - - +
48B ARG* 5.4 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A ASP* 2.9 24.9 + - - +
42A LEU* 3.7 12.3 - - - +
43A CYS 3.1 0.8 - - - -
44A ASN* 1.3 83.6 - - - +
46A ILE* 1.3 63.6 + - + +
48A ARG* 3.7 16.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A LEU* 3.2 21.1 - - + +
43A CYS* 3.0 11.7 + - - +
45A ASP* 1.3 78.4 - - + +
47A ILE* 1.3 67.5 + - - +
48A ARG 3.3 3.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A CYS 2.9 18.2 + - - +
44A ASN* 3.3 19.5 - - - +
46A ILE* 1.3 76.1 - - - +
48A ARG* 1.3 73.4 + - + +
26B LYS* 3.6 27.8 - - + +
27B LEU 3.3 48.5 - - - +
28B ILE* 3.5 16.8 - - + -
37B ASP* 6.0 2.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ASN* 2.8 59.0 + - - +
45A ASP* 3.8 16.6 + - - +
46A ILE 4.0 3.1 - - - -
47A ILE* 1.3 91.0 - - + +
26B LYS* 4.1 23.7 + - + +
37B ASP* 2.5 23.1 + - - -
40B VAL* 3.8 0.2 - - - +
41B ASP* 2.4 34.2 + - - -
44B ASN* 5.3 0.2 - - - +
----------------------------------------------------------
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