Contacts of the helix formed by residues 53 - 65 (chain F) in PDB entry 2W8B
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 ASP 53 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41F PRO* 4.9 5.0 - - - +
42F PHE 5.3 0.9 + - - -
52F GLU* 1.3 83.3 + - - +
54F ILE* 1.3 62.9 + - - +
55F GLY* 3.6 3.1 + - - -
56F GLY* 2.9 22.4 + - - -
57F ILE* 3.0 23.0 + - - +
73F ARG* 3.2 31.3 + - - -
1431F SO4 4.5 3.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 54 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42F PHE* 3.4 35.7 - - + +
52F GLU* 3.4 25.2 + - + +
53F ASP* 1.3 70.9 + - - +
55F GLY* 1.3 63.0 + - - +
57F ILE* 3.2 8.2 + - + +
58F VAL* 3.0 24.1 + - + +
104F VAL* 3.7 24.9 - - + +
114F VAL* 3.9 22.4 - - + -
141F LEU* 3.5 28.7 - - + +
145F GLY* 4.0 17.9 - - - +
148F ALA* 5.5 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 55 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39F VAL* 3.4 13.8 - - - +
40F VAL 4.0 9.2 - - - -
41F PRO* 4.7 1.1 - - - -
42F PHE* 3.8 29.7 - - - +
53F ASP* 3.4 5.0 + - - -
54F ILE* 1.3 76.2 - - - +
56F GLY* 1.3 56.6 + - - +
58F VAL* 3.2 1.7 + - - -
59F ALA* 2.9 28.0 + - - +
73F ARG* 3.9 7.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 56 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53F ASP* 2.9 26.1 + - - -
55F GLY* 1.3 72.8 - - - +
57F ILE* 1.3 58.9 + - - +
59F ALA* 3.7 5.7 - - - +
60F ALA* 2.9 29.3 + - - +
73F ARG* 3.4 11.9 - - - +
1431F SO4 3.5 9.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 57 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52F GLU* 3.6 25.8 - - + +
53F ASP 3.0 10.3 + - - +
54F ILE* 3.2 14.1 + - + +
56F GLY* 1.3 72.9 - - - +
58F VAL* 1.3 55.6 + - - +
60F ALA* 3.2 1.6 + - - +
61F ASP* 2.7 37.8 + - - +
142F ARG* 3.5 46.0 - - - +
145F GLY* 4.2 2.7 - - - -
146F HIS* 3.6 43.3 - - + +
1431F SO4 3.6 18.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 58 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39F VAL* 4.1 14.8 - - + -
42F PHE* 4.4 13.7 - - + -
54F ILE* 3.0 23.3 + - + +
55F GLY 3.7 5.8 - - - +
57F ILE* 1.3 72.0 - - - +
59F ALA* 1.3 69.3 + - - +
61F ASP* 3.2 1.2 + - - +
62F LEU* 2.9 43.8 + - + +
100F VAL* 4.4 13.9 - - + -
145F GLY 3.9 11.7 - - - +
148F ALA* 4.3 14.1 - - + -
149F SER* 3.2 25.6 - - - +
152F VAL* 5.1 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 59 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39F VAL* 3.9 19.4 - - + +
55F GLY 2.9 20.9 + - - +
56F GLY* 3.7 7.2 - - - +
58F VAL* 1.3 74.6 - - - +
60F ALA* 1.3 63.7 + - - +
62F LEU* 4.9 0.2 - - - -
63F ARG* 2.9 34.5 + - - +
70F PRO* 3.5 23.2 - - + +
73F ARG* 6.0 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 60 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56F GLY 2.9 18.6 + - - +
57F ILE 3.2 3.1 + - - +
59F ALA* 1.3 77.1 - - - +
61F ASP* 1.3 58.0 + - - +
63F ARG* 3.4 15.9 + - - +
64F ASN* 2.8 46.1 + - - +
1431F SO4 3.8 23.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 61 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57F ILE* 2.7 20.8 + - - +
58F VAL 3.7 0.2 - - - +
60F ALA* 1.3 76.6 - - - +
62F LEU* 1.3 63.4 + - - +
64F ASN* 3.2 2.3 + - - +
65F SER 3.2 10.6 + - - -
146F HIS* 2.6 41.3 + - - -
149F SER* 2.7 33.8 + - - +
163F PHE* 2.9 34.4 - - + +
187F TYR* 2.7 26.9 + - - -
188F ASP* 4.2 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 62 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37F ILE* 3.9 28.9 - - + -
39F VAL* 4.2 11.2 - - + -
58F VAL* 2.9 36.8 + - + +
59F ALA 3.9 2.7 - - - +
61F ASP* 1.3 76.5 - - - +
63F ARG* 1.3 62.0 + - - +
65F SER* 2.7 24.0 + - - -
68F PHE* 3.6 37.1 + - + +
70F PRO* 4.6 2.5 - - + -
100F VAL* 4.8 0.4 - - + -
149F SER* 4.1 11.0 - - - +
152F VAL* 4.0 8.7 - - + -
153F PHE* 3.9 32.3 - - + +
163F PHE* 4.1 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 63 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27F ILE* 3.7 23.6 - - + -
31F VAL* 3.7 29.6 - - + +
59F ALA* 2.9 23.7 + - - +
60F ALA* 3.7 23.4 - - - +
62F LEU* 1.3 76.6 - - - +
64F ASN* 1.3 61.8 + - - +
65F SER 3.1 1.0 + - - -
66F GLY* 3.1 11.8 + - - -
68F PHE 3.6 9.9 - - - +
69F ASN* 5.3 0.6 + - - -
70F PRO* 3.9 40.8 + - + +
71F LEU 5.2 2.2 + - - -
72F ASP* 5.7 2.6 - - - +
410F PHE* 3.5 10.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 64 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25F ILE* 3.7 30.0 - - + +
27F ILE* 3.6 17.2 - - - +
60F ALA* 2.8 36.0 + - - +
61F ASP* 3.6 2.2 + - - +
63F ARG* 1.3 72.7 - - - +
65F SER* 1.3 60.9 + - - +
66F GLY 3.1 0.9 + - - -
163F PHE* 5.1 0.9 - - + -
187F TYR* 2.9 42.4 + - + +
188F ASP* 4.4 6.1 + - - +
388F MET* 3.5 6.9 - - - +
403F LEU* 6.1 0.3 - - - +
410F PHE* 3.4 25.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 65 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61F ASP 3.2 3.8 + - - -
62F LEU 2.7 17.7 + - - -
63F ARG 3.1 0.8 - - - -
64F ASN* 1.3 77.7 - - - +
66F GLY* 1.3 56.4 + - - +
67F LYS* 2.9 30.8 + - - +
68F PHE* 3.9 1.9 - - - -
153F PHE* 3.6 25.3 - - - -
163F PHE* 3.7 19.5 - - - -
387F THR* 5.0 6.1 + - - +
388F MET* 3.3 19.8 - - - +
405F SER* 5.2 2.1 - - - -
----------------------------------------------------------
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