Contacts of the strand formed by residues 70 - 74 (chain C) in PDB entry 2E3V
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 ILE 70 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C GLN* 4.3 22.2 - - + +
27C VAL 3.3 11.2 - - - +
28C GLN* 3.1 33.0 - - + +
29C PHE* 3.7 1.5 - - - -
60C TYR* 5.6 0.3 - - - -
65C ALA* 3.1 27.7 + - - +
68C GLU* 3.4 37.2 - - + +
69C GLY* 1.3 76.1 - - - +
71C VAL* 1.3 80.1 + - - +
72C THR* 4.0 11.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 71 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C VAL* 2.8 49.4 + - + +
29C PHE* 3.9 16.4 - - + -
43C TYR* 4.4 8.1 - - + -
45C ALA* 4.4 2.9 - - + -
60C TYR* 3.5 51.6 - - + +
65C ALA* 4.2 4.7 - - + -
70C ILE* 1.3 81.1 - - - +
72C THR* 1.3 59.1 + - - +
73C ILE* 5.2 1.8 - - + -
86C LEU* 3.9 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 72 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B GLU* 4.6 21.2 + - - +
24C THR* 4.4 8.5 - - + -
25C ALA 3.4 10.8 - - - +
26C GLN* 3.6 24.0 - - + +
58C LYS* 4.8 4.2 + - - +
60C TYR* 2.8 27.7 + - - -
70C ILE* 4.0 7.1 - - - +
71C VAL* 1.3 74.8 - - - +
73C ILE* 1.3 70.3 + - - +
74C VAL* 4.0 18.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 73 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C THR* 3.0 8.0 - - - -
25C ALA* 2.8 37.1 + - + +
27C VAL* 4.0 15.3 - - + -
45C ALA* 4.5 7.2 - - + -
47C TRP* 3.5 51.1 - - + -
60C TYR* 3.9 13.0 - - - +
71C VAL* 5.2 1.8 - - + +
72C THR* 1.3 74.9 - - - +
74C VAL* 1.3 62.2 + - - +
76C LEU* 3.6 23.8 - - + -
84C VAL* 3.5 33.2 - - + -
103C PHE* 4.8 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 74 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B GLU* 5.5 5.6 - - - +
66B SER* 3.5 45.5 - - - +
67B MSE 3.3 22.8 + - - +
23C SER 3.6 4.5 - - - -
24C THR* 3.8 17.3 - - + -
58C LYS* 4.3 7.7 - - + +
72C THR* 4.0 17.4 + - + +
73C ILE* 1.3 87.6 - - - +
75C GLY* 1.3 66.0 + - - +
76C LEU* 3.3 5.2 + - - +
----------------------------------------------------------
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