Contacts of the strand formed by residues 36 - 40 (chain E) in PDB entry 2JG7
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 36 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21E ASP* 4.3 7.9 - - - +
34E GLY 4.2 8.1 - - - +
35E GLU* 1.3 73.8 - - - +
37E ILE* 1.3 61.6 + - - +
38E THR* 4.2 1.8 + - - +
50E ARG* 3.8 37.7 - - + -
51E VAL 3.6 9.0 - - - +
52E THR* 4.2 16.2 - - + +
53E GLN* 4.4 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 37 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35E GLU 3.6 1.2 + - - -
36E VAL* 1.3 73.9 - - - +
38E THR* 1.3 71.3 + - - +
39E SER* 4.0 0.4 + - - -
50E ARG* 3.3 4.6 - - - +
51E VAL* 2.9 42.0 + - + +
53E GLN* 3.5 33.0 - - + +
192E PRO* 3.7 28.0 - - + +
193E THR* 5.6 2.2 - - + -
195E PRO* 3.8 28.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 38 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3E LEU* 4.7 3.8 - - + -
36E VAL* 4.2 1.6 + - - +
37E ILE* 1.3 82.8 - - - +
39E SER* 1.3 61.4 + - - +
40E TYR* 3.2 38.2 - - + +
47E PRO* 3.7 30.3 - - + -
49E ALA 3.8 9.4 - - - +
50E ARG* 3.3 24.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 39 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37E ILE* 4.0 1.2 + - - +
38E THR* 1.3 72.2 - - - +
40E TYR* 1.3 55.4 + - - +
47E PRO* 3.7 0.9 - - - +
48E ILE* 2.8 36.3 + - - +
49E ALA 3.0 8.8 + - - -
51E VAL* 6.0 0.4 - - - -
106E GLU* 2.6 42.2 + - - +
193E THR* 3.7 7.6 + - - +
195E PRO* 4.3 13.7 - - - -
196E LEU* 3.7 18.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 40 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38E THR* 3.2 45.9 + - + +
39E SER* 1.3 76.2 + - - +
41E CYS* 1.3 62.5 + - - +
42E PRO* 3.3 12.7 - - + +
45E ASN* 3.6 23.8 - - + +
46E GLU 3.5 1.3 - - - -
47E PRO* 3.5 35.5 - - + +
48E ILE* 3.8 3.9 - - - +
106E GLU 3.9 7.8 - - - +
193E THR 5.3 2.0 + - - +
344E HIS* 5.7 0.5 - - - +
----------------------------------------------------------
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