Contacts of the helix formed by residues 74 - 82 (chain F) in PDB entry 2BK6
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 THR 74 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25E VAL* 3.7 3.1 - - - +
29E GLN* 3.8 1.6 - - - +
86E GLU* 3.4 26.2 - - + -
87E ALA* 3.4 38.1 - - - +
88E PRO* 3.7 5.3 - - + +
73F SER* 1.3 82.4 - - - +
75F LEU* 1.3 62.8 + - - +
76F LYS* 4.2 3.2 - - - +
77F GLU* 2.6 39.2 + - - +
78F PHE* 3.1 29.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 75 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21E ASN* 3.6 23.6 - - + +
22E VAL* 3.6 18.4 - - + -
25E VAL* 3.8 15.9 - - + -
75E LEU* 3.6 27.9 - - + +
78E PHE* 3.6 40.4 - - + -
79E LEU* 3.8 15.5 - - + -
86E GLU* 2.8 27.7 + - - +
74F THR* 1.3 69.0 - - - +
76F LYS* 1.3 56.4 + - - +
78F PHE* 3.2 9.5 + - + +
79F LEU* 2.9 37.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 76 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79E LEU* 3.7 20.1 - - + +
86E GLU* 3.1 15.9 + - - +
88E PRO* 5.9 7.4 - - + -
74F THR* 4.2 4.0 - - - +
75F LEU* 1.3 77.4 - - - +
77F GLU* 1.3 58.8 + - + +
79F LEU* 3.4 2.9 + - - +
80F GLU* 3.0 63.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 77 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88E PRO* 3.8 22.9 - - + +
89E TYR 4.9 0.9 + - - -
71F PRO 5.1 1.1 - - - +
72F PHE* 3.5 36.8 - - + -
73F SER* 3.3 18.2 + - - -
74F THR* 2.6 36.5 + - - +
76F LYS* 1.3 78.4 - - + +
78F PHE* 1.3 64.4 + - - +
80F GLU* 3.4 3.6 + - - +
81F ASN* 3.0 32.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 78 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25E VAL* 3.5 34.1 - - + -
32E TRP* 4.9 5.4 - + - -
75E LEU* 3.7 17.3 - - + -
17F VAL* 3.6 10.5 - - + -
18F ALA* 3.5 29.8 - - - +
21F ASN* 3.4 36.6 - - + -
22F VAL* 4.6 1.1 - - - -
57F MET* 6.0 0.2 - - + -
72F PHE* 3.2 40.6 - - + -
73F SER* 3.9 2.2 - - - -
74F THR 3.1 19.4 + - - -
75F LEU* 3.2 10.1 + - + +
77F GLU* 1.3 74.7 - - - +
79F LEU* 1.3 58.2 + - - +
81F ASN 3.3 0.2 + - - -
82F ALA* 2.9 35.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 79 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75E LEU* 3.8 13.2 - - + +
76E LYS* 3.9 25.4 - - + +
79E LEU* 3.8 28.3 - - + -
22F VAL* 5.1 5.8 - - + -
75F LEU 2.9 14.3 + - - +
76F LYS* 3.7 4.3 - - - +
78F PHE* 1.3 77.1 - - - +
80F GLU* 1.3 64.0 + - + +
81F ASN 3.4 0.9 + - - -
82F ALA* 4.0 10.7 + - - +
86F GLU* 3.2 36.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 80 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76F LYS* 3.0 50.6 + - + +
77F GLU* 4.1 5.2 - - - +
78F PHE 3.4 0.2 - - - -
79F LEU* 1.3 78.3 - - + +
81F ASN* 1.3 66.1 + - - +
82F ALA 5.4 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 81 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15F HIS* 2.9 34.6 + - + -
18F ALA* 4.0 6.3 - - + -
72F PHE* 3.2 45.0 - - + -
77F GLU* 3.0 25.4 + - - +
80F GLU* 1.3 86.3 + - - +
82F ALA* 1.3 60.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 82 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15F HIS* 4.4 0.2 - - - -
18F ALA* 3.8 11.2 - - - +
19F ASN* 3.3 14.6 - - - +
22F VAL* 3.7 24.0 - - + -
78F PHE 2.9 17.3 + - - +
79F LEU* 4.0 8.3 + - - +
80F GLU 3.9 0.7 - - - +
81F ASN* 1.3 77.6 - - - +
83F SER* 1.3 61.1 + - - +
84F VAL 3.7 12.3 - - - +
----------------------------------------------------------
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