Contacts of the strand formed by residues 52 - 56 (chain p) in PDB entry 5Z58
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 ALA 52 (chain p).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9p ILE 3.7 0.5 - - - +
10p TYR* 3.6 2.6 - - - -
11p ILE* 2.8 41.1 + - + +
40p ILE* 6.1 2.2 - - + -
41p VAL 3.4 11.7 - - - +
42p ALA* 4.0 10.1 - - + -
51p GLN* 1.3 79.6 - - - +
53p PHE* 1.3 65.5 + - - +
54p VAL* 5.7 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 53 (chain p).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165H A 3.7 36.3 - - + +
8p THR* 5.4 6.5 - - - -
9p ILE 3.3 8.3 - - - +
10p TYR* 4.7 2.9 - - + +
39p ASP 4.1 0.5 - - - +
40p ILE* 3.4 6.2 - - - +
41p VAL* 2.9 34.4 + - + +
52p ALA* 1.3 75.6 - - - +
54p VAL* 1.3 60.0 + - - +
55p ILE* 4.2 0.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 54 (chain p).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7p HIS 3.8 1.7 - - - +
8p THR* 3.2 3.9 - - - -
9p ILE* 2.9 38.5 + - + +
27p LEU* 6.1 5.4 - - + -
31p PHE* 5.3 13.5 - - + -
37p VAL* 6.0 4.7 - - + -
39p ASP 4.0 3.6 - - - -
40p ILE* 4.7 5.4 - - + +
52p ALA* 4.1 2.3 + - + -
53p PHE* 1.3 71.4 - - - +
55p ILE* 1.3 59.6 + - - +
56p PHE 4.0 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 55 (chain p).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7p HIS* 3.9 5.4 - - + -
8p THR* 4.3 10.1 - - - +
37p VAL* 3.3 7.5 - - - +
38p VAL* 2.7 36.3 + - + -
39p ASP* 3.0 29.7 + - + +
53p PHE 4.1 0.9 - - - +
54p VAL* 1.3 71.5 - - - +
56p PHE* 1.3 55.6 + - - +
88p SER* 5.0 12.6 - - - -
90p ILE* 5.9 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 56 (chain p).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7p HIS* 3.1 32.7 + - - +
35p GLY 5.7 0.4 - - - -
36p HIS 3.4 11.4 - - - +
37p VAL* 4.3 1.3 - - - +
38p VAL* 4.7 3.8 - - - -
54p VAL 4.0 0.4 + - - -
55p ILE* 1.3 74.6 - - - +
57p LYS* 1.3 65.5 + - - +
58p GLU 3.3 20.4 - - - +
61p SER* 4.2 13.2 - - - -
62p SER* 4.4 6.7 - - - +
----------------------------------------------------------
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