Contacts of the strand formed by residues 76 - 80 (chain E) in PDB entry 4DHJ
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 76 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50E PHE* 3.6 31.9 - - + +
72E LEU* 2.9 30.7 + - + +
73E SER* 3.2 19.6 - - - +
75E VAL* 1.3 98.3 - - + +
77E GLY* 1.3 58.8 + - - +
230E ARG* 4.0 5.4 - - - -
232E GLU* 2.5 39.5 + - + -
260E THR* 3.3 35.9 + - + +
271E ILE* 3.8 17.3 - - + -
272E TYR 3.4 21.3 - - - +
273E LYS* 3.7 22.0 - - + +
274E LYS* 3.7 3.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 77 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49E PRO* 3.7 4.2 - - - +
50E PHE* 2.8 22.6 + - - +
76E TYR* 1.3 73.3 - - - +
78E GLU* 1.3 75.8 + - - +
272E TYR 2.9 7.9 + - - -
274E LYS* 3.8 21.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 78 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47E LEU* 4.3 30.2 - - + +
48E ALA 3.2 18.4 - - - +
49E PRO* 4.9 1.3 - - + -
50E PHE* 3.7 8.9 - - - +
77E GLY* 1.3 89.1 - - - +
79E ILE* 1.3 61.4 + - - +
271E ILE* 3.4 5.5 - - - +
272E TYR* 3.0 51.0 + - + +
273E LYS 4.3 6.1 - - - +
274E LYS* 5.4 1.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 79 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46E THR 4.3 0.5 - - - +
47E LEU* 4.0 0.8 - - - -
48E ALA* 3.1 38.1 + - + +
49E PRO 3.9 13.0 - - - +
50E PHE* 4.2 10.1 - - + -
52E ILE* 5.2 0.2 - - + -
53E LEU* 4.1 18.4 - - + +
78E GLU* 1.3 78.4 - - - +
80E ARG* 1.3 70.4 + - - +
81E TYR* 3.7 36.7 + - + +
262E LEU* 3.8 28.7 - - + -
269E ASP* 4.2 6.1 - - + -
270E VAL 3.4 10.1 - - - +
271E ILE* 3.8 11.4 - - + -
272E TYR* 4.8 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 80 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44E VAL* 3.6 19.7 - - + +
45E ALA 2.9 39.4 + - - +
46E THR* 3.8 15.7 - - - +
47E LEU* 3.5 32.0 - - + +
79E ILE* 1.3 73.9 - - - +
81E TYR* 1.3 67.2 + - - +
82E ILE* 3.4 7.7 + - + +
95E VAL* 3.8 9.0 - - - -
99E GLU* 2.9 21.3 + - - -
157E TYR* 3.5 29.7 + - - -
269E ASP* 3.5 1.2 - - - +
270E VAL* 2.7 39.1 + - + +
272E TYR* 3.0 28.2 + - + +
----------------------------------------------------------
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