Contacts of the strand formed by residues 106 - 110 (chain A) in PDB entry 2JFF
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 106 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A PHE* 3.9 20.4 - - + -
99A CYS* 4.2 13.2 - - + +
102A ALA* 4.1 11.4 - - + -
104A ALA 3.9 7.2 - - - +
105A PRO* 1.3 78.7 - - - +
107A VAL* 1.3 73.3 + - - +
108A ALA* 4.4 2.9 - - + +
154A TYR* 3.4 15.5 - - + +
156A LEU* 3.9 23.3 - - + -
169A LEU* 4.0 29.4 - - + -
170A GLN 5.3 5.6 + - - +
171A ALA* 3.3 9.1 - - - +
172A VAL* 2.9 35.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A ILE* 1.3 74.2 - - - +
108A ALA* 1.3 60.9 + - - +
109A ILE* 3.8 20.9 - - + -
122A VAL* 4.2 16.6 - - + -
153A LEU* 4.3 10.3 - - + -
154A TYR 2.8 9.9 + - - +
155A VAL* 4.4 7.2 - - + +
156A LEU 2.8 27.9 + - - +
172A VAL* 4.0 9.9 - - + -
173A ALA* 3.3 10.3 - - + +
278A LEU* 3.9 29.8 - - + +
282A ALA* 3.9 28.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A ILE* 3.9 3.3 + - + -
107A VAL* 1.3 73.5 - - - +
109A ILE* 1.3 63.9 + - - +
156A LEU 3.5 3.8 - - - -
158A LEU* 3.8 17.7 - - + -
169A LEU* 3.8 15.7 - - + -
171A ALA* 4.0 11.4 - - + -
173A ALA 2.9 7.7 + - - +
174A ALA* 3.2 3.5 - - + -
175A THR* 3.0 24.6 + - - +
201A ILE* 3.6 22.6 - - + +
278A LEU* 4.8 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A VAL* 3.8 12.1 - - + -
108A ALA* 1.3 77.1 - - - +
110A THR* 1.3 66.0 + - - +
115A LYS* 3.7 32.3 - - + +
118A VAL* 4.2 6.3 - - + +
119A THR* 3.4 33.9 - - - +
122A VAL* 4.6 0.7 - - + -
155A VAL* 3.8 20.0 - - + -
156A LEU 3.0 9.9 + - - +
157A GLU* 3.5 5.5 - - - +
158A LEU 3.0 24.1 + - - +
175A THR* 3.7 12.8 - - + -
177A LEU* 4.1 7.2 - - + -
201A ILE* 3.8 2.4 - - - +
278A LEU* 3.5 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A ILE* 1.3 72.6 - - - +
111A GLY* 1.3 64.2 + - - +
115A LYS* 4.1 9.2 - - - -
158A LEU 2.7 23.6 + - - -
160A SER 4.1 0.5 + - - -
163A LEU* 4.0 10.3 - - + +
175A THR 2.9 18.6 + - - +
176A ILE* 3.7 21.8 - - + -
177A LEU* 2.9 30.1 + - - +
198A KCX 3.0 32.5 + - + +
201A ILE* 3.7 15.0 - - + +
----------------------------------------------------------
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