Contacts of the helix formed by residues 41 - 51 (chain F) in PDB entry 2BWJ
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 SER 41 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39F HIS* 4.4 0.8 + - - -
40F LEU* 1.3 75.9 - - - +
42F THR* 1.3 64.1 + - - +
43F GLY* 3.7 3.8 + - - -
44F GLU* 3.3 27.0 + - - +
45F LEU* 3.0 29.4 + - - +
79F LEU* 5.8 0.7 - - - -
95F ILE* 5.8 1.6 - - - -
96F ASP* 3.8 26.9 - - - -
98F TYR* 6.2 0.4 - - - -
1202F AMP 3.8 18.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 42 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C GLU* 2.9 23.1 + - - +
66C ARG* 3.8 14.0 - - + +
41F SER* 1.3 74.3 - - - +
43F GLY* 1.3 58.1 + - - +
45F LEU* 3.7 10.6 - - + +
46F LEU* 2.8 35.6 + - - +
75F VAL* 3.5 31.0 - - + -
79F LEU* 5.6 3.8 - - + +
96F ASP 4.8 2.4 + - - -
97F GLY 5.6 1.8 + - - +
98F TYR* 3.6 30.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 43 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C GLU* 3.2 44.2 + - - +
41F SER* 3.2 5.1 + - - -
42F THR* 1.3 78.3 + - - +
44F GLU* 1.3 57.6 + - - +
46F LEU* 3.5 3.4 + - - +
47F ARG* 3.0 28.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 44 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39F HIS 5.9 2.7 - - - +
40F LEU* 6.4 0.2 - - - -
41F SER* 3.3 24.2 + - - +
42F THR 3.3 0.2 - - - -
43F GLY* 1.3 75.7 - - - +
45F LEU* 1.3 61.2 + - + +
47F ARG* 3.1 42.4 + - - -
48F GLU* 3.0 34.1 + - + +
1202F AMP 4.0 45.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 45 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40F LEU* 4.4 8.7 - - + -
41F SER 3.0 28.5 + - - +
42F THR* 3.7 9.6 - - + +
44F GLU* 1.3 74.5 - - + +
46F LEU* 1.3 65.2 - - + +
48F GLU* 3.5 16.3 + - - +
49F GLU* 3.0 24.8 + - - +
75F VAL* 4.9 3.6 - - + +
78F LEU* 3.9 22.7 - - + +
79F LEU* 3.6 43.3 - - + +
82F ALA* 3.4 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 46 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C MET 3.8 8.3 - - - +
65C GLU* 3.5 24.2 - - - +
66C ARG 3.9 2.9 - - - +
67C GLY* 3.5 25.4 - - - +
42F THR* 2.8 15.7 + - - +
43F GLY* 3.8 3.8 - - - +
45F LEU* 1.3 74.5 - - + +
47F ARG* 1.3 58.7 + - - +
49F GLU* 3.3 3.1 + - - +
50F LEU* 2.9 42.8 + - + +
60F ILE* 4.0 28.7 - - + -
64F MET* 4.8 5.6 - - + -
70F VAL* 4.8 4.7 - - + -
75F VAL* 4.6 16.8 - - + -
78F LEU* 3.9 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 47 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43F GLY 3.0 17.7 + - - +
44F GLU* 3.1 38.7 + - - +
45F LEU 3.3 0.2 - - - -
46F LEU* 1.3 76.4 - - - +
48F GLU* 1.3 81.7 + - - +
50F LEU* 3.4 9.8 + - - +
51F ALA* 3.1 36.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 48 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44F GLU* 3.0 20.7 + - - +
45F LEU* 3.9 19.3 - - - +
47F ARG* 1.3 97.7 - - - +
49F GLU* 1.3 64.1 + - - +
51F ALA* 3.2 12.9 + - - +
52F SER* 3.4 11.6 + - - -
82F ALA* 5.6 1.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 49 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45F LEU 3.0 18.9 + - - +
46F LEU* 3.6 4.0 - - - +
48F GLU* 1.3 78.2 - - - +
50F LEU* 1.3 57.1 + - + +
52F SER* 2.7 38.0 + - - -
54F SER* 2.9 22.9 + - - -
56F ARG* 3.0 39.2 + - - +
57F SER* 3.0 20.2 + - - -
60F ILE* 3.6 24.0 - - + -
78F LEU* 3.9 15.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 50 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46F LEU* 2.9 26.2 + - + +
47F ARG* 3.8 8.1 - - - +
48F GLU 3.3 0.4 - - - -
49F GLU* 1.3 77.9 - - + +
51F ALA* 1.3 57.6 + - - +
52F SER 3.3 1.0 + - - -
53F GLU* 4.4 4.0 + - - -
57F SER* 3.5 28.3 + - - +
60F ILE* 4.2 11.9 - - + -
61F ARG* 2.7 62.7 + - + +
64F MET* 4.2 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 51 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47F ARG* 3.1 28.5 + - - +
48F GLU* 3.7 6.5 - - - +
49F GLU 3.1 1.0 - - - -
50F LEU* 1.3 77.4 - - - +
52F SER* 1.3 58.5 + - - +
53F GLU* 3.5 8.8 + - - +
----------------------------------------------------------
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