Contacts of the strand formed by residues 43 - 47 (chain P) in PDB entry 5EEY
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 VAL 43 (chain P).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11P VAL* 3.9 23.8 - - + -
12P ILE 3.3 7.6 - - - +
13P LYS* 3.9 20.6 - - + -
38P LEU* 5.0 1.3 - - - -
41P GLY 3.7 0.2 + - - -
42P GLU* 1.3 79.3 - - - +
44P LEU* 1.3 61.5 + - - +
45P ILE* 4.0 16.2 - - + -
55Q ILE 3.9 0.7 - - - +
56Q LYS* 3.3 7.9 - - - +
57Q VAL* 2.9 37.2 + - + +
63Q ILE* 4.1 21.8 - - + -
70Q ILE* 4.7 5.8 - - + -
71Q GLU 4.4 2.2 - - - +
72Q SER* 3.7 29.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 44 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10P VAL 3.8 1.7 - - - +
11P VAL* 3.7 0.9 - - - -
12P ILE* 2.8 43.0 + - + +
21P VAL* 3.9 34.3 - - + -
36P GLU* 4.1 20.2 - - + -
38P LEU* 4.1 18.3 - - + +
42P GLU 4.2 0.2 + - - -
43P VAL* 1.3 74.1 - - - +
45P ILE* 1.3 60.8 + - - +
46P ALA* 4.1 15.9 + - + -
24Q LEU* 3.9 27.4 - - + -
54Q ALA* 4.3 6.5 - - + -
55Q ILE 3.5 18.4 - - - +
56Q LYS* 4.1 10.3 - - + -
101Q TRP* 5.5 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 45 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9P PHE* 3.5 29.6 - - + -
10P VAL 3.4 4.0 - - - +
11P VAL* 4.4 11.7 - - + -
43P VAL* 4.0 17.7 - - + -
44P LEU* 1.3 73.5 - - - +
46P ALA* 1.3 61.1 + - - +
10Q VAL* 4.1 23.6 - - + -
12Q ILE* 5.5 0.2 - - + -
48Q PHE* 3.4 27.2 - - + -
54Q ALA* 3.1 2.9 - - - -
55Q ILE* 2.8 54.1 + - + +
57Q VAL* 4.7 6.7 - - + -
63Q ILE* 4.3 20.9 - - + -
65Q THR* 4.7 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 46 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9P PHE* 3.2 5.3 - - - -
10P VAL* 2.8 44.9 + - + +
12P ILE* 5.3 3.1 - - + -
21P VAL* 5.5 0.2 - - + -
44P LEU* 4.3 15.3 - - + +
45P ILE* 1.3 76.0 - - - +
47P GLN* 1.4 61.4 + - - +
55P ILE* 4.4 6.2 - - + +
53Q SER 3.9 4.5 - - - -
54Q ALA* 4.0 6.7 - - + -
101Q TRP* 3.8 30.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 47 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5P THR 2.9 29.1 + - - -
6P ASN 4.4 0.2 - - - -
7P SER* 3.4 18.1 + - - +
8P ASP 3.3 9.0 - - - +
9P PHE* 3.8 15.5 - - + +
46P ALA* 1.4 73.8 - - - +
48P PHE* 1.3 73.7 + - - +
49P THR* 3.6 4.3 - - + +
52P THR* 4.5 1.2 - - - -
55P ILE* 4.4 3.9 - - - +
8Q ASP* 5.8 1.6 - - - +
26Q ARG* 2.8 29.4 + - - -
48Q PHE* 3.5 27.4 - - + +
53Q SER* 3.1 23.9 + - - +
101Q TRP* 2.8 26.9 + - - -
----------------------------------------------------------
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