Contacts of the strand formed by residues 43 - 48 (chain E) in PDB entry 1Y8R
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 HIS 43 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16E ALA 3.3 26.1 + - - -
17E GLY* 4.2 11.0 - - - -
18E GLY 3.5 19.7 + - - +
19E ARG* 3.3 25.2 - - + +
20E VAL* 2.9 24.8 + - - +
41E PHE* 3.8 0.4 - - - +
42E SER* 1.3 83.3 - - - +
44E ILE* 1.3 62.5 + - - +
45E ASP* 4.6 0.2 - - - -
88E ASN* 3.2 32.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 44 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20E VAL* 3.6 21.1 - - + +
22E VAL* 4.3 3.6 - - + -
33E LEU* 3.9 27.6 - - + +
36E LEU* 3.7 34.5 - - + -
37E VAL* 4.0 22.7 - - + -
41E PHE* 4.0 11.0 - - + +
42E SER 3.6 2.2 + - - +
43E HIS* 1.3 84.5 - - - +
45E ASP* 1.3 75.1 + - - +
46E LEU* 4.6 0.4 - - + +
88E ASN 3.2 8.9 + - - +
89E ILE* 3.2 19.2 - - + +
90E VAL 2.9 22.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 45 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19E ARG* 2.9 52.3 + - - +
20E VAL 2.9 7.9 + - - +
21E LEU* 3.2 13.3 - - + +
22E VAL* 2.9 26.9 + - - +
44E ILE* 1.3 78.6 + - - +
46E LEU* 1.3 59.0 + - - +
90E VAL* 3.5 11.4 - - - +
92E TYR* 3.0 24.3 + - + -
109E PHE* 3.2 29.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 46 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22E VAL* 3.4 36.8 - - + +
24E GLY 3.8 8.7 - - - +
25E ALA* 3.6 18.6 - - + -
29E GLY 5.4 1.3 - - - +
33E LEU* 3.7 34.8 - - + -
44E ILE* 3.8 1.0 + - + -
45E ASP* 1.3 74.5 - - - +
47E ILE* 1.3 64.9 + - - +
73E ALA* 3.6 34.5 - - + +
76E ALA* 4.5 2.9 - - + -
77E LYS* 5.9 0.4 - - + +
89E ILE* 4.5 10.5 - - + -
90E VAL 2.7 14.7 + - - +
91E ALA* 3.5 2.6 - - - -
92E TYR* 3.0 28.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 47 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21E LEU* 4.5 9.4 - - + -
22E VAL 3.1 7.5 + - - +
23E VAL* 3.5 31.0 - - + -
24E GLY* 2.8 30.0 + - - -
46E LEU* 1.3 80.7 - - - +
48E ASP* 1.3 65.0 + - - +
92E TYR* 3.6 19.3 - - + +
94E ASP 3.6 10.5 - - - +
95E SER 3.8 4.7 - - - -
96E ILE* 3.4 46.0 - - + +
101E TYR* 4.0 21.3 - - + -
105E PHE* 6.1 1.6 - - + -
801E ATP 4.1 3.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 48 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25E ALA* 2.7 32.5 + - + -
47E ILE* 1.3 75.4 - - - +
49E LEU* 1.3 60.4 + - - +
50E ASP 2.9 20.1 + - - +
72E LYS* 3.4 22.3 - - + +
73E ALA* 3.9 9.1 + - + +
92E TYR 3.3 8.5 + - - +
93E HIS* 3.5 7.4 + - - -
94E ASP 3.2 18.4 + - - -
801E ATP 2.4 56.3 + - - -
----------------------------------------------------------
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