Contacts of the helix formed by residues 54 - 65 (chain F) in PDB entry 2BWJ
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 SER 54 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137C ARG 5.3 0.2 - - - -
138C SER* 5.1 7.0 - - - +
139C SER 5.9 0.2 - - - +
140C LEU* 5.9 7.2 - - - -
49F GLU* 2.9 27.5 + - - -
52F SER* 3.1 17.1 + - - -
53F GLU* 1.3 79.1 - - - +
55F GLU* 1.3 65.8 + - - +
56F ARG* 3.6 7.1 + - - +
57F SER* 2.7 28.3 + - - -
58F LYS* 3.2 6.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 55 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C LEU 4.6 2.5 - - - +
136C SER* 2.9 32.4 + - - +
137C ARG 4.1 1.4 + - - -
138C SER* 4.3 9.0 + - - +
140C LEU* 6.3 1.2 - - - +
145C THR* 3.3 37.5 - - + +
148C THR* 3.5 26.3 - - + +
149C ILE* 3.4 14.4 - - + +
152C ARG* 2.9 31.4 + - - -
53F GLU 3.8 0.8 + - - -
54F SER* 1.3 74.4 - - - +
56F ARG* 1.3 62.1 + - - +
58F LYS* 3.1 18.6 + - - +
59F LEU 3.1 16.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 56 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148C THR* 3.7 15.7 + - + +
49F GLU* 3.0 26.6 + - - +
54F SER* 3.1 6.7 + - - +
55F GLU* 1.3 76.3 - - - +
57F SER* 1.3 64.8 + - - +
59F LEU* 3.2 12.4 + - + +
60F ILE* 3.0 34.1 + - + +
74F ILE* 4.7 13.9 + - + +
77F GLU* 4.2 14.9 - - - +
78F LEU* 3.4 20.0 - - - +
81F GLU* 2.9 42.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 57 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49F GLU* 3.0 41.4 + - - -
50F LEU* 3.5 14.8 + - - +
52F SER* 3.8 0.4 - - - -
53F GLU* 3.6 8.8 + - - -
54F SER* 2.7 38.6 + - - -
56F ARG* 1.3 75.3 - - - +
58F LYS* 1.3 60.1 + - - +
60F ILE* 4.4 2.2 - - - -
61F ARG* 2.9 31.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 58 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135C MET* 3.4 24.7 + - - +
136C SER* 4.1 0.4 - - - +
137C ARG* 3.8 17.0 - - - +
152C ARG* 3.6 28.9 - - - +
53F GLU* 4.1 17.0 + - - +
54F SER 3.2 6.3 + - - +
55F GLU* 3.1 31.5 + - - +
56F ARG 3.1 1.0 - - - -
57F SER* 1.3 81.7 + - - +
59F LEU* 1.3 58.3 + - - +
61F ARG* 3.7 14.5 - - - +
62F ASP* 2.9 34.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 59 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148C THR* 4.5 7.2 - - + -
151C LYS* 3.8 34.5 - - + +
152C ARG* 3.7 43.2 - - + +
155C ALA* 4.4 7.0 - - + -
55F GLU 3.1 9.8 + - - +
56F ARG* 3.4 14.8 - - + +
58F LYS* 1.3 74.7 - - - +
60F ILE* 1.3 66.9 + - + +
62F ASP* 3.3 6.6 + - + +
63F ILE* 3.1 44.0 + - + +
74F ILE* 5.1 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 60 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46F LEU* 4.0 14.8 - - + -
49F GLU* 3.6 30.1 - - + -
50F LEU* 4.2 10.5 - - + -
56F ARG* 3.0 26.2 + - + +
57F SER* 3.8 4.5 - - - +
59F LEU* 1.3 76.4 - - + +
61F ARG* 1.3 59.1 + - - +
63F ILE* 3.3 10.3 + - + +
64F MET* 2.9 55.3 + - - +
70F VAL* 4.2 11.0 - - + -
74F ILE* 3.6 34.3 - - + -
78F LEU* 4.3 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 61 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50F LEU* 2.7 56.4 + - + +
57F SER* 2.9 21.0 + - - +
58F LYS* 3.7 14.4 - - - +
59F LEU 3.2 0.2 - - - -
60F ILE* 1.3 74.2 - - - +
62F ASP* 1.3 57.6 + - - +
64F MET* 4.0 3.9 - - - +
65F GLU* 2.8 64.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 62 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C PRO* 4.0 14.1 - - - +
152C ARG* 2.8 52.6 + - - +
58F LYS 2.9 24.0 + - - +
59F LEU* 3.3 9.4 + - + +
61F ARG* 1.3 72.9 - - - +
63F ILE* 1.3 63.3 + - - +
65F GLU* 3.6 14.7 + - - +
66F ARG* 3.5 43.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 63 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155C ALA* 4.8 5.4 - - + -
59F LEU* 3.1 36.9 + - + +
60F ILE* 3.5 10.5 - - + +
62F ASP* 1.3 80.9 - - - +
64F MET* 1.3 60.3 + - - +
66F ARG* 3.1 29.4 + - - +
68F ASP* 3.0 42.7 + - + +
69F LEU 3.3 25.1 - - - +
70F VAL* 3.8 8.3 - - + +
71F PRO* 3.9 25.8 - - + -
74F ILE* 6.2 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 64 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C GLY* 5.1 0.2 - - - -
46C LEU* 4.1 12.0 - - - +
64C MET* 3.1 58.9 - - + +
67C GLY* 4.4 5.8 - - - -
68C ASP 6.0 0.4 - - - +
46F LEU* 4.8 9.2 - - + -
50F LEU* 4.2 20.2 - - + -
60F ILE* 2.9 37.0 + - - +
61F ARG* 4.0 3.8 - - - +
63F ILE* 1.3 71.4 - - - +
65F GLU* 1.3 61.8 + - + +
66F ARG 3.1 2.2 - - - -
67F GLY* 3.0 19.2 + - - +
68F ASP 4.5 5.6 - - - +
70F VAL* 3.5 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 65 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C THR* 3.5 8.5 + - - -
43C GLY* 3.2 38.7 + - - -
1199C AMP 4.2 20.7 + - - -
61F ARG* 2.8 48.4 + - + +
62F ASP* 3.8 16.6 + - - +
63F ILE 3.3 0.2 - - - -
64F MET* 1.3 76.2 - - - +
66F ARG* 1.3 59.0 + - + +
67F GLY 3.4 0.4 - - - -
----------------------------------------------------------
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