Contacts of the strand formed by residues 35 - 41 (chain F) in PDB entry 1O94
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 LYS 35 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1F SER 3.0 7.7 + - - +
2F LYS* 3.3 25.2 - - + +
3F ILE* 2.9 26.9 + - - +
29F LYS* 6.0 0.4 - - - +
33F GLU 3.7 4.0 + - - +
34F ASP* 1.3 74.7 - - - +
36F VAL* 1.3 64.1 + - - +
37F VAL 3.9 0.6 + - - -
58F ASP* 3.4 17.0 - - + +
59F GLU* 5.0 6.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 36 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3F ILE* 3.5 11.2 - - + +
5F VAL* 4.1 11.2 - - + -
22F ILE* 5.1 3.6 - - + +
25F ALA* 3.9 33.2 - - + +
26F ASN* 3.9 20.9 - - - +
29F LYS* 4.2 15.0 - - + -
35F LYS* 1.3 76.3 - - - +
37F VAL* 1.3 61.3 - - - +
38F VAL* 4.4 11.2 - - + -
56F GLY 3.3 23.8 - - - +
57F VAL* 3.9 1.2 - - - -
58F ASP* 2.7 39.0 + - - +
59F GLU 3.2 6.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 37 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2F LYS* 3.9 29.6 - - + -
3F ILE 2.9 14.4 + - - +
4F LEU* 3.3 26.5 - - + +
5F VAL* 2.9 25.8 + - - +
36F VAL* 1.3 73.7 - - - +
38F VAL* 1.3 63.1 + - - +
59F GLU* 3.3 22.0 - - + +
61F VAL* 4.0 26.0 - - + -
82F LEU* 5.6 0.2 - - + -
86F HIS* 4.0 19.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 38 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5F VAL* 3.4 17.3 - - + +
7F ALA* 4.2 8.7 - - + +
22F ILE* 3.8 27.8 - - + -
36F VAL* 4.4 5.8 - - + -
37F VAL* 1.3 77.7 - - - +
39F ALA* 1.3 64.3 + - - +
52F LEU* 4.2 20.4 - - + -
57F VAL* 3.8 27.1 - - + -
59F GLU 2.8 6.1 + - - -
60F LEU* 3.4 18.8 - - + +
61F VAL* 2.8 32.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 39 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4F LEU* 4.4 4.3 - - + -
5F VAL 2.9 7.7 + - - +
6F ILE* 3.7 14.2 - - + +
7F ALA* 2.9 28.1 + - - +
37F VAL 4.2 0.2 + - - -
38F VAL* 1.3 75.6 - - - +
40F VAL* 1.3 60.4 + - - +
41F ILE* 5.0 4.0 - - + -
60F LEU* 4.9 0.2 - - - -
61F VAL* 3.2 10.8 - - + +
63F VAL* 4.6 3.8 - - + -
82F LEU* 3.4 40.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 40 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7F ALA* 4.1 11.4 - - + +
9F HIS* 3.7 25.1 - - + +
14F LEU* 5.3 1.6 - - + -
39F ALA* 1.3 74.9 - - - +
41F ILE* 1.3 65.8 + - - +
45F ALA* 3.5 22.8 - - + +
48F PHE* 3.9 18.6 - - + -
52F LEU* 3.7 30.1 - - + -
60F LEU* 4.4 3.6 - - + -
61F VAL 3.0 13.4 + - - +
62F VAL* 4.2 12.3 - - + -
63F VAL 2.9 22.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 41 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6F ILE* 4.1 10.8 - - + -
7F ALA 5.6 1.4 + - - -
9F HIS* 2.9 21.6 + - - -
39F ALA* 5.0 1.8 - - + -
40F VAL* 1.3 82.7 - - - +
42F GLY* 1.3 60.4 + - - +
45F ALA* 4.0 1.1 - - - -
63F VAL* 3.4 26.0 - - + +
65F GLY 5.2 1.6 - - - +
68F ILE 4.5 0.5 - - - +
69F ASP 5.8 0.7 - - - -
74F VAL* 4.2 12.1 - - + -
75F PHE* 3.6 55.0 - - + -
78F SER* 4.0 24.9 - - - +
79F VAL* 3.8 26.0 - - + -
82F LEU* 4.7 5.6 - - + -
----------------------------------------------------------
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