Contacts of the helix formed by residues 22 - 29 (chain B) in PDB entry 2F44
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 HIS 22 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B LEU* 4.1 6.5 - - + -
19B LEU* 2.9 25.9 + - + +
21B GLU* 1.3 96.8 + - + +
23B ARG* 1.3 61.5 + - - +
24B ASP 3.3 3.3 + - - -
25B ARG* 3.5 6.9 + - - +
26B PHE* 2.9 45.2 + - + -
47B LEU 4.5 3.6 + - - -
48B GLY* 3.2 34.0 + - - -
49B VAL* 3.9 19.2 - - + +
54B HIS* 4.9 0.4 - - + -
58B ILE* 5.3 2.9 - - + -
256B ZN 2.1 36.3 - - - -
257B CL 3.4 5.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 23 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B PHE* 3.5 30.7 + - - +
11B GLY* 3.6 35.5 - - - +
12B ASP* 3.1 28.3 + - - -
14B LEU* 4.1 9.6 - - + +
15B GLU* 2.6 46.0 + - - -
19B LEU 4.1 1.6 + - - -
20B GLY* 3.2 20.6 + - - +
22B HIS* 1.3 79.2 - - - +
24B ASP* 1.3 69.0 + - - +
26B PHE* 3.9 1.4 - - - +
27B GLU* 2.9 39.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 24 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B GLY 4.8 1.4 + - - +
21B GLU 4.9 4.3 + - - +
22B HIS 3.3 1.0 - - - -
23B ARG* 1.3 86.7 - - - +
25B ARG* 1.3 55.4 + - - +
27B GLU* 3.2 18.6 + - - +
28B ASP* 2.6 43.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 25 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B GLU 5.5 1.1 + - - +
22B HIS* 3.5 10.2 + - - +
23B ARG 3.4 0.4 - - - -
24B ASP* 1.3 79.5 - - - +
26B PHE* 1.3 62.9 + - - +
28B ASP* 3.0 11.1 + - - +
29B HIS* 3.0 47.2 + - - -
45B VAL 5.5 0.2 + - - -
46B GLU 2.8 16.9 + - - -
47B LEU* 2.7 56.1 + - - +
48B GLY* 2.9 9.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 26 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B LYS* 5.7 1.3 - - - +
10B VAL* 4.3 10.8 - - + -
11B GLY* 6.2 0.9 - - - +
13B TRP* 6.2 0.4 - + - -
14B LEU* 3.9 25.4 - - + -
22B HIS* 2.9 40.9 + - + +
23B ARG 4.0 3.4 - - - +
25B ARG* 1.3 79.7 - - - +
27B GLU* 1.3 56.4 + - - +
29B HIS* 3.4 1.3 + - - -
30B GLU 3.1 7.3 + - - -
31B ILE* 3.0 59.9 + - + +
36B LEU* 4.9 4.5 - - + -
39B LEU* 4.8 5.4 - - + -
44B PHE* 4.3 12.1 - + - -
47B LEU* 3.8 33.7 - - + -
49B VAL* 3.8 26.9 - - + -
58B ILE* 4.3 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 27 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B LYS* 3.8 27.0 + - + +
8B PHE* 3.5 36.8 - - + -
23B ARG* 2.9 30.2 + - - +
24B ASP* 3.3 18.9 - - - +
26B PHE* 1.3 75.2 - - - +
28B ASP* 1.3 70.5 + - - +
30B GLU* 3.1 18.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 28 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ASP* 2.6 31.2 + - - +
25B ARG* 3.0 11.9 + - - +
27B GLU* 1.3 84.5 - - - +
29B HIS* 1.3 65.8 + - + +
30B GLU* 3.1 9.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 29 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ARG* 3.0 45.7 + - - +
26B PHE 3.4 3.3 + - - +
28B ASP* 1.3 80.1 - - + +
30B GLU* 1.3 71.0 + - - +
31B ILE* 3.4 11.1 + - + +
46B GLU* 4.0 29.4 + - + -
47B LEU* 3.6 31.1 - - + +
----------------------------------------------------------
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