Contacts of the helix formed by residues 78 - 89 (chain F) in PDB entry 5UQ9
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 GLY 78 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76F LYS 3.4 1.2 + - - -
77F ALA* 1.3 74.8 - - - +
79F GLN* 1.3 64.8 + - - -
80F ALA 3.2 2.8 + - - -
81F VAL* 3.4 9.5 + - - +
82F ASP* 3.8 1.8 - - - +
104F SER* 5.3 2.8 + - - +
108F ASP* 5.2 6.1 - - - -
112F ARG* 3.0 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 79 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78F GLY* 1.3 70.1 - - - -
80F ALA* 1.3 59.3 + - - +
81F VAL 3.1 0.2 - - - -
82F ASP* 3.1 28.6 + - - +
83F ASP* 2.8 54.6 + - - +
86F GLU* 3.9 9.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 80 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75F VAL* 3.9 11.2 - - + -
76F LYS* 3.2 35.2 - - + +
77F ALA 5.1 0.2 - - - -
78F GLY 3.2 1.2 - - - -
79F GLN* 1.3 78.2 - - - +
81F VAL* 1.3 58.5 + - - +
83F ASP* 3.9 9.6 - - - +
84F PHE* 3.5 29.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 81 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73F LEU* 4.0 13.9 - - + +
75F VAL* 3.8 23.1 - - + +
76F LYS 3.8 11.0 - - - +
77F ALA* 4.7 0.7 - - - -
78F GLY 3.4 8.7 + - - +
79F GLN 3.1 0.6 - - - -
80F ALA* 1.3 75.9 - - - +
82F ASP* 1.3 64.8 + - - +
84F PHE* 3.3 4.9 + - - +
85F ILE* 3.1 38.7 + - + +
100F ASP* 3.6 30.1 - - + +
102F GLY* 6.3 0.7 - - - -
104F SER* 4.3 5.8 - - - +
112F ARG* 3.3 28.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 82 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78F GLY 3.8 3.1 - - - +
79F GLN* 3.1 34.0 + - - +
81F VAL* 1.3 75.6 - - - +
83F ASP* 1.3 57.7 + - - +
85F ILE* 3.2 9.4 + - - +
86F GLU* 2.9 40.1 + - + +
111F ARG* 3.0 29.3 + - - -
112F ARG* 2.7 43.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 83 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79F GLN* 2.8 45.5 + - - +
80F ALA* 3.9 10.0 - - - +
81F VAL 3.2 0.2 - - - -
82F ASP* 1.3 76.8 - - - +
84F PHE* 1.3 62.3 + - + +
86F GLU* 3.3 16.7 + - - +
87F LYS* 3.2 28.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 84 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9F ILE* 3.5 35.0 - - + -
32F PHE* 4.5 7.4 - + - -
34F ARG* 3.5 46.4 - - + -
58F LEU* 4.0 26.7 - - + -
73F LEU* 4.0 20.6 - - + -
75F VAL* 3.5 25.4 - - + -
80F ALA* 3.5 16.7 + - + +
81F VAL 3.3 7.6 + - - +
82F ASP 3.3 0.2 - - - -
83F ASP* 1.3 76.6 - - + +
85F ILE* 1.3 61.0 + - - +
87F LYS* 3.2 8.1 + - + +
88F LEU* 2.8 37.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 85 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73F LEU* 4.1 12.8 - - + -
81F VAL* 3.1 31.8 + - + +
82F ASP* 3.2 10.7 + - - +
84F PHE* 1.3 78.1 - - - +
86F GLU* 1.3 62.8 + - + +
88F LEU* 4.3 4.9 - - - +
89F VAL* 3.0 28.8 + - + +
98F ILE* 4.6 9.2 - - + -
112F ARG* 4.0 22.2 - - + -
116F LEU* 3.7 35.2 - - + -
123F PHE* 4.1 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 86 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79F GLN* 3.9 15.9 - - - +
82F ASP* 2.9 22.5 + - + +
83F ASP* 3.3 15.2 + - - +
85F ILE* 1.3 78.1 - - + +
87F LYS* 1.3 58.9 + - + +
89F VAL* 5.4 1.3 - - - -
90F PRO* 3.3 22.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 87 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34F ARG* 3.9 28.2 - - - +
58F LEU* 3.8 25.1 - - + -
59F LYS* 4.8 10.1 + - - +
83F ASP* 3.2 18.4 + - + +
84F PHE* 3.7 16.8 - - + +
85F ILE 3.2 0.2 - - - -
86F GLU* 1.3 79.7 - - + +
88F LEU* 1.3 59.0 + - - +
90F PRO* 3.7 5.7 - - - +
91F LEU* 3.2 27.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 88 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9F ILE* 4.4 6.1 - - + -
58F LEU* 3.6 30.3 - - + -
61F MET* 4.5 1.6 - - + -
62F VAL* 4.3 8.5 - - + -
71F ILE* 3.6 33.9 - - + -
73F LEU* 4.1 26.2 - - + -
84F PHE* 2.8 30.2 + - + +
85F ILE 3.2 3.1 + - - +
87F LYS* 1.3 75.0 - - - +
89F VAL* 1.3 65.7 + - - +
91F LEU* 3.0 14.3 + - - +
92F LEU* 3.2 21.8 + - + +
98F ILE* 4.1 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 89 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85F ILE* 3.0 19.4 + - + +
86F GLU* 5.0 0.9 - - - +
88F LEU* 1.3 76.2 - - - +
90F PRO* 1.3 72.2 - - + +
91F LEU 3.1 0.9 + - - -
92F LEU* 3.3 22.5 + - - +
98F ILE* 4.9 4.5 - - + -
116F LEU* 3.6 31.0 - - + -
119F LYS* 4.2 29.6 - - + +
121F ILE* 4.0 18.8 - - + +
----------------------------------------------------------
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