Contacts of the strand formed by residues 42 - 48 (chain E) in PDB entry 4XH9
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 TYR 42 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300D ARG* 5.7 1.8 - - - +
302D LEU* 4.3 3.1 - - - +
25E ASN 4.6 1.2 + - - -
26E SER* 3.7 40.9 + - - -
39E PHE* 3.5 21.3 - + + -
40E GLU 3.3 1.7 + - - +
41E ASN* 1.3 77.0 - - - +
43E VAL* 1.3 84.7 + - - +
44E ALA* 3.7 17.2 - - + +
45E ASP 5.5 0.5 + - - -
57E LEU* 2.8 47.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 43 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300D ARG 3.8 6.6 + - - +
301D LYS* 3.4 46.5 - - + +
302D LEU* 3.6 21.7 - - + +
42E TYR* 1.3 91.2 + - - +
44E ALA* 1.3 63.5 + - - +
45E ASP* 4.0 6.0 + - - +
54E GLU* 3.6 40.4 - - + +
55E LEU 3.4 3.1 - - - +
56E ALA* 4.1 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 44 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25E ASN* 3.9 22.9 - - - +
42E TYR* 3.7 20.5 + - + -
43E VAL* 1.3 73.8 - - - +
45E ASP* 1.3 63.0 + - - +
46E ILE* 3.6 14.3 + - + -
53E VAL 3.4 1.6 - - - +
54E GLU* 3.7 1.0 - - - -
55E LEU* 2.8 43.0 + - + +
57E LEU* 4.3 9.0 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
301D LYS* 2.7 35.6 + - - +
42E TYR* 5.5 0.6 + - - -
43E VAL 4.7 3.5 - - - +
44E ALA* 1.3 73.8 - - - +
46E ILE* 1.3 61.6 + - - +
47E GLU 4.4 0.2 + - - -
52E GLN* 4.9 14.5 - - + +
53E VAL 3.6 3.5 - - - +
54E GLU* 3.8 15.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 46 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25E ASN* 4.7 5.2 - - - +
44E ALA* 4.2 19.3 - - + +
45E ASP* 1.3 78.8 - - - +
47E GLU* 1.3 62.2 - - - +
48E VAL* 4.0 19.5 + - + -
51E LYS 3.5 1.7 - - - +
52E GLN* 3.8 4.7 + - - -
53E VAL* 2.9 38.9 + - - +
55E LEU* 3.7 13.7 - - + -
168E ARG 5.7 0.2 - - - +
171E PHE* 3.6 32.3 - - + +
172E GLU* 4.3 13.5 - - + -
175E THR* 3.6 28.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 47 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45E ASP 4.4 0.6 + - - -
46E ILE* 1.3 73.1 - - - +
48E VAL* 1.3 70.1 + - - +
50E GLY* 5.0 10.6 - - - +
51E LYS 3.4 15.3 - - - +
52E GLN* 3.1 39.0 + - - +
172E GLU* 4.7 8.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 48 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46E ILE* 4.0 5.6 - - + -
47E GLU* 1.3 79.7 - - - +
49E ASP* 1.3 70.7 + - - +
50E GLY 3.2 2.2 - - - -
51E LYS* 2.9 21.7 + - - +
172E GLU* 3.7 41.7 - - + +
175E THR* 3.5 28.3 - - + -
176E ARG* 3.9 29.2 - - + +
179E LEU* 3.6 17.2 - - + +
----------------------------------------------------------
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