Contacts of the helix formed by residues 28 - 37 (chain B) in PDB entry 2EZX
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 GLU 28 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B GLY* 5.8 2.9 - - - -
27B GLY* 1.3 72.9 - - - -
29B VAL* 1.3 66.2 + - + +
31B GLY* 3.5 2.0 + - - -
32B LYS* 3.2 21.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 29 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B GLY* 3.2 1.4 - - - -
28B GLU* 1.3 78.7 - - + +
30B LEU* 1.3 69.5 + - + +
32B LYS* 3.2 21.2 + - + +
33B LYS* 3.4 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 30 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B GLY 4.1 6.1 - - - +
26B ILE* 3.9 13.5 - - + -
27B GLY* 3.2 23.6 + - - +
29B VAL* 1.3 77.6 - - + +
31B GLY* 1.3 68.1 + - - +
32B LYS 3.0 2.5 + - - -
33B LYS* 3.1 24.7 + - + +
34B LEU* 3.2 16.6 + - + +
67B CYS* 3.9 33.0 - - + +
68B GLY 5.1 1.3 - - - -
69B ALA* 4.6 13.7 - - + +
73B GLN* 3.1 34.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 31 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B VAL* 3.7 20.3 - - - +
21B GLY* 4.4 6.3 - - - -
26B ILE* 3.4 17.4 - - - +
27B GLY 2.7 19.1 + - - -
28B GLU* 4.0 2.2 - - - -
30B LEU* 1.3 74.1 - - - +
32B LYS* 1.3 61.0 + - - +
34B LEU* 3.9 2.0 - - - +
35B GLU* 3.1 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 32 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B GLU 3.2 14.2 + - - +
29B VAL* 3.3 13.9 - - - +
30B LEU 3.0 0.2 - - - -
31B GLY* 1.3 79.9 - - - +
33B LYS* 1.3 64.3 + - + +
35B GLU* 3.2 17.6 + - - +
36B GLU* 3.1 34.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 33 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B VAL* 3.7 33.0 - - - +
30B LEU* 3.1 14.4 + - + +
32B LYS* 1.3 76.9 - - + +
34B LEU* 1.3 64.9 + - - +
36B GLU* 3.1 11.5 + - - +
37B ARG* 3.1 25.6 + - + +
66B THR 5.2 2.2 - - - +
67B CYS* 3.9 38.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 34 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B VAL* 3.8 24.5 - - + -
26B ILE* 4.0 25.8 - - + -
30B LEU* 3.2 15.1 + - + +
31B GLY 3.9 4.9 - - - +
33B LYS* 1.3 76.7 - - - +
35B GLU* 1.3 59.1 + - - +
37B ARG* 2.8 22.8 + - - +
39B PHE* 3.0 33.6 + - + +
45B VAL* 5.4 4.5 - - + -
62B TRP* 3.9 22.0 - - + -
63B LEU* 4.2 12.3 - - + -
66B THR* 3.8 27.1 - - + -
67B CYS* 4.9 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 35 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B VAL* 4.9 3.8 - - + +
31B GLY 3.1 16.1 + - - +
32B LYS* 3.4 20.6 - - - +
33B LYS 3.1 0.2 - - - -
34B LEU* 1.3 77.3 - - - +
36B GLU* 1.3 62.4 + - - +
38B GLY* 3.1 14.2 + - - -
39B PHE 3.6 13.6 + - - +
40B ASP* 4.3 23.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 36 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B LYS* 3.1 25.8 + - + +
33B LYS* 3.1 12.1 + - - +
35B GLU* 1.3 77.5 - - + +
37B ARG* 1.3 62.4 + - + +
38B GLY 3.2 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 37 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B LYS* 3.1 18.5 - - - +
34B LEU* 2.8 12.6 + - - +
36B GLU* 1.3 82.2 - - + +
38B GLY* 1.3 58.2 + - - +
39B PHE* 3.5 24.3 - - + -
65B ASP 4.1 5.3 + - - -
66B THR* 3.1 47.5 + - + +
----------------------------------------------------------
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