Contacts of the helix formed by residues 79 - 86 (chain A) in PDB entry 2FFQ
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 ILE 79 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A LEU* 3.8 25.6 - - + -
48A ILE* 4.8 4.9 - - + -
69A THR* 4.0 24.9 - - + +
70A ALA 3.7 23.1 - - - +
75A PHE* 4.0 4.9 - - + +
76A ARG* 3.1 22.9 + - - +
78A LEU* 1.3 77.6 - - - +
80A PRO* 1.3 70.4 - - + +
81A SER 3.2 2.9 - - - -
82A TYR* 2.9 18.4 + - - +
83A ILE* 3.3 19.2 + - + -
107A TRP* 3.8 30.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A ARG 3.4 13.7 - - - +
77A SER* 3.8 11.0 - - - +
78A LEU 3.8 2.9 - - - -
79A ILE* 1.3 92.3 - - + +
81A SER* 1.3 62.8 + - - +
83A ILE* 3.0 13.9 + - + +
84A ARG* 3.1 10.5 + - - +
114A GLU* 3.1 38.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A LEU* 4.2 11.0 + - - -
79A ILE 3.1 1.4 + - - -
80A PRO* 1.3 79.1 - - - +
82A TYR* 1.3 68.6 + - - +
84A ARG* 4.1 6.9 + - - +
85A ASP* 3.5 19.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A VAL* 4.2 18.4 - - + -
48A ILE* 3.5 47.9 + - + +
67A TRP* 3.7 39.3 - + + -
69A THR* 4.9 3.6 - - + -
78A LEU* 3.2 27.8 - - + -
79A ILE* 2.9 11.6 + - - +
81A SER* 1.3 84.4 - - - +
83A ILE* 1.3 62.8 + - - +
85A ASP* 3.1 14.2 + - - +
86A SER* 2.9 25.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A VAL* 4.6 10.3 - - + -
19A LEU* 3.8 30.5 - - + -
79A ILE* 3.3 27.1 + - + +
80A PRO* 3.0 7.3 + - + +
82A TYR* 1.3 72.6 - - - +
84A ARG* 1.3 68.0 + - - +
85A ASP 3.0 1.3 - - - -
86A SER* 3.0 20.1 + - - +
107A TRP* 5.1 2.9 - - + -
110A ASP* 4.5 14.4 - - + -
111A VAL* 3.9 32.3 - - + -
114A GLU* 3.7 27.4 - - + +
115A ARG* 3.5 9.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A PRO* 3.1 15.2 + - - +
81A SER* 4.1 7.4 - - - +
83A ILE* 1.3 78.1 - - - +
85A ASP* 1.3 54.6 + - + +
113A THR* 4.6 5.1 + - - +
114A GLU* 3.0 57.8 + - + +
115A ARG* 2.8 36.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A LYS* 3.8 29.3 + - - +
65A GLN* 5.1 0.7 + - - -
67A TRP* 4.3 21.4 + - - -
81A SER 3.5 16.8 + - - +
82A TYR* 3.1 10.4 + - - +
83A ILE 3.0 0.4 - - - -
84A ARG* 1.3 82.0 - - + +
86A SER* 1.3 75.3 + - - +
87A THR* 4.1 2.6 + - - +
115A ARG* 4.5 2.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A LYS* 3.4 17.3 + - - -
17A VAL* 3.5 32.6 + - - +
67A TRP* 4.0 8.0 - - - -
82A TYR 2.9 10.8 + - - -
83A ILE 3.0 9.2 + - - +
85A ASP* 1.3 96.0 + - - +
87A THR* 1.3 64.4 + - - +
88A VAL 3.8 3.0 - - - -
115A ARG* 3.3 24.2 + - - +
119A VAL* 4.5 2.9 - - - +
----------------------------------------------------------
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