Contacts of the helix formed by residues 83 - 111 (chain R) in PDB entry 1BFR
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 VAL 83 (chain R).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32R PHE* 4.1 13.0 - - + -
35R TRP* 4.1 14.3 - - + -
37R LEU* 4.0 17.3 - - + -
40R LEU* 4.2 6.7 - - + -
82R ASP* 1.3 73.3 - - - +
84R GLU* 1.3 63.9 + - - +
86R MET* 3.3 8.8 + - - +
87R LEU* 3.0 32.0 + - + +
141R ILE* 4.6 2.9 - - + -
146R LEU* 5.0 7.2 - - + -
149R TYR* 4.1 26.2 - - + -
150R LEU* 3.9 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 84 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82R ASP* 3.3 8.1 + - - +
83R VAL* 1.3 78.8 - - - +
85R GLU* 1.3 58.5 + - - +
87R LEU* 3.3 2.6 + - - +
88R ARG* 2.9 66.0 + - - +
138R LEU* 4.0 11.2 - - + -
141R ILE* 4.2 27.5 - - + +
142R GLN* 3.2 20.1 + - - +
146R LEU* 5.5 6.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 85 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78R ASN* 5.5 2.1 - - - +
80R GLY* 3.6 13.7 - - - -
81R GLU* 3.1 36.0 + - - +
82R ASP* 2.9 26.5 + - - +
84R GLU* 1.3 75.3 - - - +
86R MET* 1.3 62.6 + - - +
88R ARG* 3.4 9.5 + - - +
89R SER* 3.0 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 86 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28R HIS* 3.3 40.8 + - + +
31R MET* 3.6 38.1 - - + -
32R PHE* 3.7 26.2 - - + -
35R TRP* 3.4 29.6 - - + -
79R ILE 3.3 20.4 - - - +
80R GLY 4.0 7.4 - - - +
82R ASP* 2.9 23.0 + - - +
83R VAL 3.6 3.6 - - - +
85R GLU* 1.3 77.5 - - - +
87R LEU* 1.3 62.9 + - - +
89R SER* 3.3 0.9 + - - -
90R ASP* 3.2 18.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 87 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32R PHE* 3.7 29.6 - - + -
40R LEU* 5.0 3.6 - - + -
44R GLU* 4.4 9.4 - - - +
83R VAL* 3.0 24.0 + - + +
84R GLU 3.9 0.2 - - - +
86R MET* 1.3 75.1 - - - +
88R ARG* 1.3 57.9 + - - +
90R ASP* 3.4 4.8 + - - +
91R LEU* 3.0 26.3 + - - +
133R TRP* 4.8 7.4 - - + -
134R LEU* 3.8 24.8 - - + +
137R GLU* 4.2 13.7 - - + -
138R LEU* 3.8 18.8 - - + +
141R ILE* 4.1 18.2 - - + -
149R TYR* 3.8 21.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 88 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84R GLU* 2.9 55.7 + - - +
85R GLU* 3.9 6.7 - - + +
87R LEU* 1.3 69.5 - - - +
89R SER* 1.3 64.4 + - - +
91R LEU* 3.2 6.9 + - + +
92R ALA* 2.9 24.3 + - - +
138R LEU* 3.9 30.1 - - + +
142R GLN* 3.4 18.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 89 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24R GLN* 3.4 10.0 - - - +
28R HIS* 4.6 0.7 - - - -
78R ASN* 3.0 51.5 + - - +
79R ILE 4.3 4.0 + - - -
80R GLY* 4.6 1.0 + - - -
85R GLU* 3.0 21.0 + - - +
86R MET 3.3 5.3 + - - -
88R ARG* 1.3 70.4 - - - +
90R ASP* 1.3 58.7 + - - +
92R ALA* 3.4 5.8 + - - +
93R LEU* 2.9 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 90 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24R GLN* 3.0 23.9 - - - +
25R TYR* 4.0 17.8 - - + -
28R HIS* 3.0 23.4 + - - -
44R GLU* 2.8 32.8 - - - +
86R MET 3.2 6.6 + - - +
87R LEU* 3.5 8.6 - - - +
89R SER* 1.3 76.5 - - - +
91R LEU* 1.3 65.5 + - - +
93R LEU* 3.2 7.3 + - - +
94R GLU* 3.0 26.3 + - - +
134R LEU* 3.9 19.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 91 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87R LEU 3.0 15.0 + - - +
88R ARG* 3.2 11.8 + - + +
90R ASP* 1.3 73.4 - - - +
92R ALA* 1.3 58.9 + - - +
94R GLU* 3.3 1.5 + - - +
95R LEU* 2.9 45.5 + - + +
131R ILE* 3.8 36.1 - - + +
134R LEU* 3.8 15.5 - - + +
135R GLU* 4.1 23.1 - - + +
138R LEU* 3.6 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 92 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78R ASN* 6.1 1.3 - - - +
88R ARG 2.9 16.9 + - - +
89R SER* 3.6 7.9 - - - +
91R LEU* 1.3 76.6 - - - +
93R LEU* 1.3 61.7 + - - +
95R LEU* 3.4 11.1 + - - +
96R ASP* 3.1 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 93 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17R ASN* 4.9 13.5 - - + +
20R VAL* 3.7 28.0 - - + -
21R ALA* 4.0 21.3 - - + -
24R GLN* 3.6 33.7 - - + +
25R TYR* 5.9 3.6 - - + -
89R SER 2.9 14.9 + - - +
90R ASP* 3.6 9.6 - - - +
92R ALA* 1.3 71.0 - - - +
94R GLU* 1.3 65.6 + - + +
96R ASP* 3.3 9.6 + - + +
97R GLY* 3.0 20.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 94 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21R ALA* 4.9 4.0 - - - +
25R TYR* 3.0 27.6 + - + +
51R GLU* 3.2 5.0 - - - +
90R ASP 3.0 17.4 + - - +
91R LEU* 3.6 6.5 - - - +
93R LEU* 1.3 76.8 - - + +
95R LEU* 1.3 57.8 + - - +
97R GLY* 3.2 2.9 + - - +
98R ALA* 2.9 31.2 + - - +
127R GLU* 2.8 21.3 - - + +
130R HIS* 3.2 13.2 - - + +
131R ILE* 3.6 21.1 - - + +
134R LEU* 4.1 9.9 - - + -
201R MN 2.4 35.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 95 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91R LEU* 2.9 38.0 + - + +
92R ALA* 3.6 8.3 - - - +
93R LEU 3.4 0.2 - - - -
94R GLU* 1.3 76.4 - - - +
96R ASP* 1.3 60.1 + - - +
98R ALA* 3.5 5.7 + - + +
99R LYS* 3.1 22.0 + - - +
131R ILE* 3.7 34.1 - - + -
135R GLU* 5.5 2.2 - - - +
1S MET* 4.5 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 96 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17R ASN* 6.5 0.4 - - - -
92R ALA* 3.1 18.2 + - - +
93R LEU* 3.6 13.2 - - + +
95R LEU* 1.3 73.5 - - - +
97R GLY* 1.3 65.3 + - - +
99R LYS* 3.3 29.9 + - - +
100R ASN* 2.9 32.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 97 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14R LEU* 5.2 0.3 - - - +
17R ASN* 4.1 22.1 - - - +
93R LEU* 3.0 15.2 + - - +
94R GLU* 3.7 2.9 - - - -
96R ASP* 1.3 74.7 - - - +
98R ALA* 1.3 57.1 + - - +
100R ASN* 3.1 3.8 + - - +
101R LEU* 2.8 38.3 + - - +
127R GLU* 5.8 3.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 98 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94R GLU 2.9 17.6 + - - +
95R LEU* 3.8 6.5 - - + +
97R GLY* 1.3 72.3 - - - +
99R LYS* 1.3 57.3 + - - +
101R LEU* 3.2 6.2 + - - +
102R ARG* 2.9 55.6 + - - +
124R LEU* 4.1 17.4 - - + +
127R GLU* 5.2 5.2 - - + +
128R GLU* 5.6 0.2 - - + -
131R ILE* 4.3 17.3 - - + -
1S MET* 5.9 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 99 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95R LEU 3.1 10.8 + - - +
96R ASP* 3.3 30.4 + - - +
98R ALA* 1.3 79.4 - - - +
100R ASN* 1.3 79.9 + - - +
102R ARG* 3.4 17.7 + - - +
103R GLU* 3.4 15.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 100 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13R LYS* 3.3 35.1 + - - +
14R LEU* 3.7 17.3 - - + +
17R ASN* 2.9 30.5 + - - +
96R ASP* 2.9 25.6 + - - +
97R GLY 3.7 3.8 - - - +
99R LYS* 1.3 86.7 + - - +
101R LEU* 1.3 57.9 + - - +
103R GLU* 3.3 9.4 + - - +
104R ALA* 2.9 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 101 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14R LEU* 4.2 14.6 - - + +
18R GLU* 5.9 0.9 - - - +
58R TYR* 3.7 22.4 - - - +
97R GLY 2.8 21.9 + - - +
98R ALA* 3.4 7.9 - - - +
100R ASN* 1.3 73.4 - - - +
102R ARG* 1.3 58.0 + - - +
104R ALA* 3.2 2.5 + - - +
105R ILE* 2.8 37.7 + - + +
120R MET* 4.0 33.2 - - + +
123R ILE* 4.6 4.7 - - + -
124R LEU* 3.9 36.8 - - + +
127R GLU* 4.1 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 102 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98R ALA* 2.9 43.9 + - - +
99R LYS* 3.4 11.2 + - - +
101R LEU* 1.3 70.6 - - - +
103R GLU* 1.3 62.4 + - - +
105R ILE* 3.6 0.4 + - - -
106R GLY 3.3 16.8 + - - -
124R LEU* 3.8 23.4 - - + +
128R GLU* 2.7 28.7 + - - -
1S MET* 4.6 15.4 - - - +
111S VAL 5.5 0.2 + - - -
112S HIS* 3.2 53.8 + - + +
113S ASP* 4.5 12.3 + - - +
114S TYR* 3.7 10.2 - - - +
115S VAL 5.1 0.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 103 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10R TYR* 2.8 33.8 + - - +
13R LYS* 3.9 14.2 + - - -
99R LYS* 3.4 10.4 + - - +
100R ASN* 3.3 12.9 + - - +
101R LEU 3.2 0.6 - - - -
102R ARG* 1.3 79.5 - - - +
104R ALA* 1.3 62.0 + - - +
106R GLY* 3.4 1.4 + - - -
107R TYR* 3.1 21.0 + - - +
112S HIS* 5.4 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 104 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10R TYR* 3.8 32.2 - - + +
14R LEU* 3.7 15.3 - - + -
100R ASN 2.9 19.1 + - - +
101R LEU 3.7 2.7 - - - +
103R GLU* 1.3 72.6 - - - +
105R ILE* 1.3 57.5 + - - +
107R TYR* 3.2 3.2 + - - +
108R ALA* 2.9 31.0 + - - +
120R MET* 3.7 23.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 105 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101R LEU* 2.8 28.3 + - + +
104R ALA* 1.3 69.2 - - - +
106R GLY* 1.3 63.4 + - - +
108R ALA* 3.3 2.3 + - - +
109R ASP* 3.0 24.1 + - + +
117R ARG* 3.6 22.5 - - + +
120R MET* 3.6 30.7 - - + +
121R ILE* 3.7 33.7 - - + +
124R LEU* 3.8 27.8 - - + -
114S TYR* 3.7 31.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 106 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102R ARG 3.3 10.1 + - - -
103R GLU* 3.8 3.1 - - - -
105R ILE* 1.3 78.7 - - - +
107R TYR* 1.3 60.1 + - - +
109R ASP* 3.4 7.1 - - - +
110R SER* 3.1 22.9 + - - -
112S HIS* 4.8 6.3 - - - -
114S TYR* 3.7 17.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 107 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4R ASP* 2.9 31.4 + - - -
6R LYS* 3.3 37.2 - - + +
7R VAL* 3.6 16.6 - - + -
10R TYR* 3.6 33.0 - + + +
103R GLU 3.1 11.4 + - - +
104R ALA 3.2 5.8 + - - +
106R GLY* 1.3 72.8 - - - +
108R ALA* 1.3 67.8 + - - +
110R SER* 2.9 27.8 + - - -
111R VAL* 3.1 29.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 108 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7R VAL* 4.1 10.8 - - + -
104R ALA 2.9 10.7 + - - +
105R ILE 3.6 3.4 - - - +
107R TYR* 1.3 73.4 - - - +
109R ASP* 1.3 62.1 + - - +
111R VAL* 3.4 10.3 + - - +
112R HIS 3.2 3.6 + - - -
113R ASP* 2.9 39.7 + - + +
116R SER* 4.7 1.1 - - - -
117R ARG* 3.9 13.5 - - + +
120R MET* 3.6 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 109 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105R ILE 3.0 17.7 + - - +
106R GLY* 3.4 9.2 - - - +
108R ALA* 1.3 76.7 - - - +
110R SER* 1.3 59.2 + - - +
112R HIS* 2.9 21.4 + - - +
114R TYR* 4.0 22.0 + - - -
117R ARG* 3.2 39.1 + - - +
109S ASP* 5.4 3.9 - - - +
114S TYR* 5.9 2.8 - - + +
109V ASP* 5.3 4.4 - - - +
117V ARG* 4.9 2.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 110 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106R GLY 3.1 8.5 + - - -
107R TYR* 2.9 31.3 + - - -
109R ASP* 1.3 80.5 + - - +
111R VAL* 1.3 60.5 + - - +
112R HIS* 3.5 16.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 111 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4R ASP* 3.9 18.4 - - + +
7R VAL* 3.5 29.4 - - + -
107R TYR* 3.1 37.4 + - + +
108R ALA 3.5 11.7 - - - +
110R SER* 1.3 77.0 + - - +
112R HIS* 1.3 68.3 + - - +
113R ASP* 3.3 6.6 + - + +
102V ARG* 5.9 0.2 - - - -
----------------------------------------------------------
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