Contacts of the strand formed by residues 44 - 48 (chain F) in PDB entry 4LOU
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 44 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35F TYR* 3.4 2.5 - - - -
36F GLN* 3.0 37.8 + - + +
41F THR* 4.7 10.2 + - + +
42F SER* 3.7 18.7 + - - +
43F PRO* 1.3 74.1 + - - +
45F ARG* 1.3 69.3 + - - +
46F TRP* 3.0 29.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 45 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107E TYR* 3.5 48.9 + - - -
108E PHE 3.9 9.4 + - - +
109E ASP* 3.1 38.3 + - - +
111E TRP* 5.0 1.6 - - - +
33F HIS* 5.7 0.4 - - + -
34F TRP 4.5 2.2 - - - +
35F TYR* 3.4 26.9 - - + -
43F PRO 4.2 0.6 + - - -
44F LYS* 1.3 71.5 - - - +
46F TRP* 1.3 60.1 + - - +
47F ILE 4.8 0.7 - - - +
48F TYR* 3.2 44.7 - - + -
54F THR* 2.7 50.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 46 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34F TRP* 2.8 19.4 + - + +
35F TYR 4.4 0.2 - - - -
36F GLN* 3.4 52.5 - - + +
38F LYS* 5.7 1.1 - - - -
44F LYS* 3.0 30.0 + - + +
45F ARG* 1.3 73.9 - - - +
47F ILE* 1.3 68.4 + - + +
53F LEU 3.9 0.3 - - - -
54F THR* 2.8 31.2 + - - -
56F GLY 5.0 3.6 - - - -
57F VAL* 3.3 30.8 - - + +
58F PRO* 4.1 22.7 - - + -
61F PHE* 3.3 46.4 - + - -
72F LEU* 4.8 3.6 - - + -
81F ASP* 5.6 0.9 - - - -
85F TYR* 4.3 8.3 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 47 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33F HIS* 3.2 2.1 - - - +
34F TRP* 2.6 51.1 + - + +
45F ARG* 4.8 0.7 - - - +
46F TRP* 1.3 90.9 + - + +
48F TYR* 1.3 64.6 + - - +
50F THR 3.5 28.3 - - - +
51F SER* 4.2 2.9 - - - +
52F LYS 3.4 10.8 - - - +
53F LEU* 4.0 15.3 - - + -
54F THR* 4.9 0.2 - - - -
61F PHE* 4.5 4.0 - - + -
62F SER* 3.5 40.6 - - - +
63F GLY* 3.6 2.2 - - - +
72F LEU* 4.0 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 48 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A HIS* 4.3 9.0 - - - -
235A GLU* 4.3 8.5 + - - -
102E GLY* 4.2 10.5 - - - -
107E TYR* 3.7 25.4 - + + -
33F HIS* 3.6 15.3 - - + +
45F ARG* 3.2 30.5 - - - +
47F ILE* 1.3 75.5 - - - +
49F ASP* 1.3 74.6 + - - +
50F THR 3.1 2.9 - - - -
52F LYS* 2.8 90.5 + - + +
53F LEU 4.1 4.4 + - - -
54F THR* 4.1 15.5 - - - -
----------------------------------------------------------
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