Contacts of the strand formed by residues 84 - 89 (chain A) in PDB entry 1BAR
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 LEU 84 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A GLU* 3.8 11.4 - - + +
53A GLU* 3.2 30.3 - - + +
54A VAL 3.8 5.2 - - - +
55A TYR* 2.6 52.5 - - + +
80A ASN 3.9 2.9 + - - +
81A GLU* 4.4 10.6 - - - +
82A GLU 3.3 3.1 - - - -
83A CYS* 1.3 80.8 - - - +
85A PHE* 1.3 64.1 + - - +
99A SER* 4.3 0.2 - - - -
100A LYS* 3.0 45.8 + - + +
101A LYS 4.6 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A GLU* 3.5 4.7 - - - +
54A VAL* 3.0 37.0 + - - +
56A ILE* 4.2 16.8 - - + -
65A LEU* 3.8 38.8 - - + -
66A ALA* 4.3 7.4 - - - -
67A MET* 3.8 19.7 - - + -
73A LEU* 4.6 0.9 - - + -
82A GLU 4.6 2.2 - - - -
83A CYS 4.0 10.1 - - - -
84A LEU* 1.3 78.0 - - - +
86A LEU* 1.3 63.2 + - - +
97A TYR* 4.0 20.2 - - + -
98A ILE 3.3 3.8 - - - +
99A SER* 3.2 37.2 - - - -
100A LYS* 5.0 1.1 - - - -
109A VAL* 3.2 29.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A GLY 3.5 9.9 - - - +
53A GLU* 4.2 16.4 - - + +
84A LEU 4.3 0.6 + - - -
85A PHE* 1.3 75.8 - - - +
87A GLU* 1.3 66.8 + - - +
88A ARG* 4.2 3.1 - - + -
96A THR 3.5 0.5 - - - +
97A TYR* 3.0 7.8 - - - +
98A ILE* 2.6 56.5 + - + +
100A LYS* 3.8 24.8 - - + +
103A ALA* 5.6 1.6 - - + -
92B ASN 4.4 16.6 - - - +
93B GLY* 4.5 13.2 - - - +
94B TYR* 4.9 6.7 - - + -
133B LEU* 3.4 33.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A LEU* 4.9 3.8 - - - +
52A GLY* 2.9 22.1 + - - +
54A VAL* 3.7 25.9 - - + +
86A LEU* 1.3 79.4 - - - +
88A ARG* 1.3 61.8 + - - +
89A LEU 4.0 1.0 + - - -
95A ASN* 3.6 17.4 - - - +
96A THR 3.4 3.4 - - - +
97A TYR* 3.0 43.2 + - + -
134A PRO* 5.4 1.6 - - - +
133B LEU* 4.4 2.7 - - - +
135B LEU* 4.1 18.4 - - - +
136B PRO* 5.4 11.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A LEU* 4.7 1.6 - - + +
87A GLU* 1.3 78.3 - - - +
89A LEU* 1.3 63.3 + - - +
90A GLU* 2.6 45.2 + - - +
95A ASN* 3.4 11.0 - - - +
96A THR* 2.8 50.4 + - + +
98A ILE* 3.3 16.8 - - + -
108A PHE* 4.3 1.1 - - - -
125A PHE* 3.6 11.7 - - - -
89B LEU* 3.4 20.8 - - - +
93B GLY 3.1 24.4 + - - +
94B TYR* 3.8 4.0 - - - +
95B ASN* 2.4 36.5 + - - +
133B LEU* 4.6 7.0 - - + -
134B PRO* 4.2 18.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A GLU 4.0 0.4 + - - -
88A ARG* 1.3 75.1 - - - +
90A GLU* 1.3 80.1 + - - +
93A GLY* 3.5 26.7 - - - +
94A TYR 3.8 2.5 - - - +
95A ASN* 4.3 10.5 - - - +
10B LYS* 5.4 5.6 - - + +
11B PRO 4.7 1.8 - - - +
12B LYS* 3.6 21.4 + - + +
134B PRO* 3.2 36.6 + - - +
135B LEU 3.3 22.0 - - - +
136B PRO* 3.4 35.0 - - + -
----------------------------------------------------------
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