Contacts of the strand formed by residues 84 - 90 (chain F) in PDB entry 2EFW
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 GLU 84 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74F LYS* 2.4 61.6 + - + +
75F VAL* 2.6 25.4 + - - +
76F LYS* 3.7 21.5 + - + +
82F LEU 4.4 0.6 + - - -
83F GLN* 1.3 80.1 - - - +
85F VAL* 1.3 60.9 + - - +
86F VAL* 5.4 0.9 - - + -
21I C 3.6 12.2 + - - +
3J C 5.2 2.9 - - - +
4J T 5.3 2.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 85 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33F TYR* 2.9 44.0 - - + -
75F VAL* 2.6 42.4 + - + +
76F LYS 4.8 0.4 - - - -
77F LYS* 3.9 37.9 - - + +
83F GLN* 5.8 2.0 - - + -
84F GLU* 1.3 74.1 - - - +
86F VAL* 1.3 63.0 + - - +
87F LEU* 3.6 3.9 + - + +
3J C 3.6 9.4 - - - +
4J T 1.8 37.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 86 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33F TYR* 3.4 19.4 - - - +
34F GLY 4.0 1.2 + - - -
72F GLN* 3.7 40.8 - - + +
73F ILE 3.3 5.6 - - - +
74F LYS* 3.5 40.6 - - + +
84F GLU* 5.4 1.1 - - + -
85F VAL* 1.3 78.4 - - - +
87F LEU* 1.3 67.1 + - - +
88F TYR* 3.7 19.0 - - + +
4J T 3.4 24.3 + - - +
5J G 5.1 2.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 87 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31F ARG* 2.8 40.4 - - + +
32F LEU* 3.7 1.8 - - + -
33F TYR* 3.5 25.4 - - + +
72F GLN* 3.7 4.2 - - - -
73F ILE* 2.8 50.6 + - + +
75F VAL* 3.0 36.6 - - + -
85F VAL* 3.6 4.0 + - + +
86F VAL* 1.3 78.5 - - - +
88F TYR* 1.3 60.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 88 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27F THR* 3.8 18.6 - - - +
31F ARG* 3.8 17.3 - - - +
32F LEU 4.0 18.6 + - - +
34F GLY* 4.2 13.7 - - - -
37F LEU* 5.5 0.7 - - + -
58F TYR* 4.8 4.5 - - - -
61F LEU* 3.4 49.9 - - + +
62F HIS* 4.0 17.2 + - - -
65F LEU* 4.0 17.7 - - + +
70F LEU* 4.3 17.7 - - + -
71F LYS 3.3 12.6 - - - -
72F GLN* 4.0 24.1 + - + -
73F ILE* 4.7 0.4 - - - -
86F VAL* 3.7 24.1 - - + +
87F LEU* 1.3 78.4 - - - +
89F GLN* 1.3 65.7 + - - +
4J T 4.5 4.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 89 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27F THR* 4.1 6.3 - - + -
31F ARG* 2.3 47.0 + - - +
70F LEU* 4.6 1.5 - - - +
71F LYS* 2.7 68.0 + - + +
73F ILE* 3.3 28.5 - - + +
88F TYR* 1.3 76.4 - - - +
90F PHE* 1.3 74.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 90 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24F ILE* 3.2 45.3 - - + -
27F THR* 3.3 26.3 - - + +
28F GLU* 3.6 22.7 - - + -
69F ILE* 3.5 14.6 - - + -
70F LEU* 4.5 5.3 - - + +
71F LYS* 4.1 9.2 - - - +
89F GLN* 1.3 84.8 + - + +
91F LYS* 1.3 59.3 + - - +
92F ASP 4.8 2.7 - - - +
93F TYR* 3.5 44.0 - + + -
96F ALA* 4.6 5.8 - - + -
----------------------------------------------------------
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