Contacts of the helix formed by residues 82 - 111 (chain E) in PDB entry 3BVI
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 GLY 82 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30E TRP* 3.5 21.4 - - - -
80E PHE 3.5 2.0 - - - -
81E GLU* 1.3 81.4 - - - +
83E LEU* 1.3 60.6 + - - -
84E THR 3.4 2.5 - - - -
85E GLN* 3.3 5.5 + - - +
86E ILE* 3.1 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 83 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30E TRP* 4.3 3.2 - - - -
31E CYS* 4.2 5.8 - - - -
36E LEU* 4.0 21.2 - - + +
39E ALA* 3.6 20.9 - - + -
82E GLY* 1.3 68.4 - - - -
84E THR* 1.3 67.0 + - - +
86E ILE* 3.2 7.1 + - + +
87E PHE* 3.1 53.7 + - + -
141E ILE* 4.1 20.0 - - + -
151E LEU* 3.7 33.9 - - + +
154E ALA* 4.0 24.2 - - + -
155E ASP* 4.7 7.9 - - - +
158E VAL* 5.8 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 84 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82E GLY 3.4 0.6 - - - -
83E LEU* 1.3 78.5 - - - +
85E GLN* 1.3 58.7 + - - +
87E PHE* 3.3 2.0 + - - +
88E GLN* 2.8 31.9 + - + +
138E LEU* 4.2 5.3 - - + +
141E ILE* 3.4 23.3 + - + +
142E GLU* 4.1 31.0 - - + +
151E LEU* 6.1 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 85 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79E LYS 4.4 1.2 + - - +
80E PHE* 3.1 18.4 - - - +
81E GLU* 2.5 63.7 + - + +
82E GLY* 3.3 13.5 + - - +
83E LEU 3.3 0.4 - - - -
84E THR* 1.3 79.4 - - - +
86E ILE* 1.3 56.2 + - - +
88E GLN* 3.3 6.0 + - + +
89E LYS* 2.9 62.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 86 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27E MET* 3.6 35.2 - - + +
30E TRP* 3.4 43.1 - - + -
31E CYS* 3.9 14.4 - - - -
43E LEU* 4.0 15.3 - - + -
80E PHE* 3.6 29.6 - - + -
82E GLY 3.1 16.4 + - - +
83E LEU* 3.2 8.3 + - - +
85E GLN* 1.3 76.0 - - - +
87E PHE* 1.3 67.9 + - + +
89E LYS* 4.7 0.9 - - - -
90E ALA* 2.8 26.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 87 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39E ALA* 4.1 12.1 - - + -
42E PHE* 4.0 27.8 - + - -
43E LEU* 4.1 18.4 - - + -
83E LEU* 3.1 39.3 + - + +
84E THR 4.1 1.8 - - - +
86E ILE* 1.3 84.1 - - + +
88E GLN* 1.3 61.1 + - - +
90E ALA* 3.8 3.7 - - + +
91E TYR* 2.9 29.5 + - - +
134E PHE* 3.9 24.0 - + - +
137E ILE* 3.6 26.2 - - + -
138E LEU* 3.7 16.6 - - + +
141E ILE* 3.4 29.2 - - + -
158E VAL* 4.4 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 88 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84E THR* 2.8 19.5 + - + +
85E GLN* 3.7 7.9 - - + +
87E PHE* 1.3 76.0 - - - +
89E LYS* 1.3 57.6 + - + +
91E TYR* 3.4 5.1 + - - +
92E GLU* 3.0 62.6 + - - +
138E LEU* 3.9 28.7 - - + +
142E GLU* 4.1 15.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 89 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23E LEU* 5.7 0.4 - - - +
27E MET* 4.0 12.6 - - + -
77E GLU* 4.7 19.5 + - + +
79E LYS 5.1 1.2 + - - -
80E PHE* 4.3 21.6 - - + -
85E GLN* 2.9 45.5 + - + +
86E ILE 3.8 3.6 - - - +
88E GLN* 1.3 74.4 - - + +
90E ALA* 1.3 58.0 + - - +
92E GLU* 3.5 15.1 + - - +
93E HIS* 2.9 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 90 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24E TYR* 3.5 16.3 + - + -
27E MET* 3.9 10.7 - - + +
43E LEU* 5.3 0.4 - - + -
86E ILE* 2.8 20.3 + - + +
87E PHE* 3.8 7.6 - - + +
88E GLN 3.3 0.2 - - - -
89E LYS* 1.3 74.3 - - - +
91E TYR* 1.3 59.2 + - - +
93E HIS* 3.3 4.5 + - - +
94E GLU* 2.9 34.8 + - - +
134E PHE* 3.6 29.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 91 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87E PHE 2.9 20.4 + - - +
88E GLN* 3.8 7.2 - - - +
90E ALA* 1.3 74.8 - - - +
92E GLU* 1.3 65.4 + - + +
94E GLU* 3.3 2.9 + - + +
95E GLN* 3.0 48.5 + - + +
131E GLU* 3.6 36.9 + - + -
134E PHE* 4.3 14.2 - - + +
135E LYS* 3.6 39.5 - - + +
138E LEU* 4.0 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 92 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88E GLN* 3.0 42.5 + - - +
89E LYS* 3.7 14.5 - - - +
91E TYR* 1.3 79.0 - - + +
93E HIS* 1.3 62.3 + - - +
95E GLN* 3.3 21.4 + - - +
96E HIS* 3.2 20.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 93 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16E LYS 5.3 0.4 - - - -
19E ASN* 4.6 13.0 - - - -
20E SER* 2.7 33.4 + - - -
23E LEU* 3.9 23.9 - - + +
24E TYR* 3.4 28.3 - + - -
89E LYS 2.9 18.2 + - - +
90E ALA* 3.5 6.7 - - - +
92E GLU* 1.3 74.7 - - - +
94E GLU* 1.3 65.2 + - - +
96E HIS* 3.0 19.0 + + - +
97E ILE* 3.0 39.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 94 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24E TYR* 2.4 34.4 + - - +
46E HIS* 3.1 20.7 + - - -
50E GLU* 3.6 1.6 - - - +
90E ALA 2.9 18.2 + - - +
91E TYR* 3.3 6.7 + - - +
93E HIS* 1.3 73.7 - - - +
95E GLN* 1.3 56.2 + - - +
97E ILE* 3.2 4.6 + - - +
98E SER* 2.9 28.1 + - - -
127E GLN* 2.8 31.2 + - - +
130E GLU* 4.1 4.4 - - - +
131E GLU* 4.2 15.7 - - + -
134E PHE* 3.9 23.1 - - + -
1007E FE 2.5 26.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 95 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91E TYR* 3.0 42.9 + - + +
92E GLU* 3.4 29.8 - - - +
93E HIS 3.2 0.2 - - - -
94E GLU* 1.3 75.0 - - - +
96E HIS* 1.3 57.8 + - - +
98E SER* 3.4 3.5 + - - -
99E GLU* 3.0 29.2 + - - +
131E GLU* 3.4 25.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 96 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16E LYS* 3.6 34.2 + - + -
92E GLU 3.2 9.0 + - - +
93E HIS* 3.0 21.4 + + - +
95E GLN* 1.3 80.2 - - - +
97E ILE* 1.3 67.4 + - + +
99E GLU* 3.4 18.1 + - + +
100E SER* 3.0 26.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 97 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13E GLN* 4.2 5.4 - - - +
16E LYS* 4.3 23.3 - - + +
17E GLU* 3.8 9.9 - - - +
20E SER* 3.8 17.7 - - - +
50E GLU* 5.0 1.8 - - - +
93E HIS* 3.0 41.7 + - + +
94E GLU* 3.2 10.1 + - - +
96E HIS* 1.3 84.0 - - + +
98E SER* 1.3 65.3 + - - +
100E SER* 2.7 22.2 + - - +
101E ILE* 3.0 16.5 + - + +
127E GLN* 3.6 24.7 - - - +
1006E FE 3.8 11.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 98 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94E GLU 2.9 14.9 + - - -
95E GLN 3.6 8.3 - - - -
97E ILE* 1.3 75.0 - - - +
99E GLU* 1.3 57.9 + - - +
101E ILE* 3.2 5.7 + - - +
102E ASN* 3.0 37.5 + - - +
127E GLN* 3.3 24.6 + - - +
128E HIS* 5.2 0.3 - - - -
131E GLU* 2.6 32.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 99 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95E GLN 3.0 13.5 + - - +
96E HIS* 3.4 23.7 - - + +
98E SER* 1.3 75.5 - - - +
100E SER* 1.3 61.7 + - - +
102E ASN* 3.3 11.9 + - + +
103E ASN* 3.0 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 100 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13E GLN* 3.2 27.4 + - - -
16E LYS* 3.9 23.3 - - - +
96E HIS* 3.0 14.5 + - - -
97E ILE* 2.7 25.3 + - - -
99E GLU* 1.3 75.0 - - - +
101E ILE* 1.3 60.5 + - - +
103E ASN* 3.5 8.4 + - - +
104E ILE* 3.3 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 101 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13E GLN* 3.7 8.1 - - - +
97E ILE* 3.0 13.3 + - + +
98E SER* 3.2 7.2 + - - +
100E SER* 1.3 76.8 + - - +
102E ASN* 1.3 59.1 + - - +
104E ILE* 3.2 10.6 + - + +
105E VAL* 3.0 30.0 + - + +
120E LEU* 5.2 3.1 - - + +
123E TYR* 3.5 48.2 - - + +
124E VAL* 3.8 30.5 - - + -
127E GLN* 3.5 39.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 102 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98E SER* 3.0 25.4 + - - +
99E GLU* 3.3 11.8 + - - +
101E ILE* 1.3 77.5 - - - +
103E ASN* 1.3 57.0 + - - +
105E VAL* 3.4 6.5 + - - +
106E ASP* 2.8 33.0 + - - +
124E VAL* 5.1 10.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 103 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9E LEU* 3.6 26.3 - - - +
99E GLU 3.0 12.9 + - - +
100E SER* 3.6 12.8 - - - +
102E ASN* 1.3 73.0 - - - +
104E ILE* 1.3 59.7 + - - +
106E ASP* 3.6 9.1 + - - +
107E HIS* 3.0 28.2 + - - +
110E LYS* 6.2 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 104 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6E ILE* 4.4 9.8 - - + +
9E LEU* 4.0 39.0 - - + +
10E LEU* 4.0 20.2 - - + -
13E GLN* 3.5 45.1 - - + +
100E SER 3.3 12.1 - - - +
101E ILE* 3.2 9.7 + - - +
103E ASN* 1.3 74.2 - - - +
105E VAL* 1.3 62.9 + - - +
107E HIS* 3.0 3.6 + - - +
108E ALA* 2.9 27.2 + - - +
116E THR* 5.1 1.1 - - + -
120E LEU* 3.7 25.1 - - + -
123E TYR* 5.5 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 105 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101E ILE* 3.0 22.3 + - + +
102E ASN* 3.8 7.2 - - - +
104E ILE* 1.3 75.1 - - - +
106E ASP* 1.3 62.8 + - - +
108E ALA* 3.2 6.9 + - - +
109E ILE* 3.1 25.7 + - + +
117E PHE* 3.6 31.2 - - + -
120E LEU* 3.9 25.6 - - + -
121E GLN* 4.5 5.2 - - - +
124E VAL* 3.8 27.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 106 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102E ASN 2.8 19.5 + - - +
103E ASN* 3.8 9.1 + - - +
105E VAL* 1.3 76.9 - - - +
107E HIS* 1.3 57.8 + - - +
109E ILE* 3.3 16.9 + - - +
110E LYS* 2.9 61.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 107 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3E SER* 5.2 0.6 + - - -
5E ASP* 3.1 42.3 + - + +
6E ILE* 3.5 21.3 - - + +
9E LEU* 3.8 17.8 - - + +
103E ASN* 3.0 20.0 + - - +
104E ILE 3.0 4.9 + - - +
106E ASP* 1.3 73.8 + - - +
108E ALA* 1.3 63.7 + - - +
110E LYS* 3.4 18.1 + - + +
111E SER* 2.9 42.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 108 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6E ILE* 4.1 10.9 - - + +
104E ILE 2.9 12.7 + - - +
105E VAL* 3.2 11.9 + - - +
107E HIS* 1.3 77.7 - - - +
109E ILE* 1.3 60.3 + - - +
111E SER* 4.1 4.3 - - - -
112E LYS* 3.1 3.5 + - - -
113E ASP* 2.8 50.5 + - + +
114E HIS* 5.0 0.5 - - - -
116E THR* 4.6 6.7 - - + -
117E PHE* 4.0 19.7 - - + +
120E LEU* 5.1 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 109 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106D ASP* 4.4 9.2 - - - +
109D ILE* 4.1 35.0 - - + -
105E VAL* 3.1 16.3 + - + +
106E ASP* 3.5 19.7 - - - +
107E HIS 3.3 0.2 - - - -
108E ALA* 1.3 76.0 - - - +
110E LYS* 1.3 66.0 + - + +
112E LYS* 3.2 16.3 + - - +
114E HIS* 4.5 8.5 + - + -
117E PHE* 3.7 30.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 110 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103E ASN* 6.2 0.2 - - - +
106E ASP* 2.9 43.7 + - - +
107E HIS* 3.4 20.4 + - + +
109E ILE* 1.3 81.5 - - + +
111E SER* 1.3 57.9 + - - +
112E LYS* 3.3 5.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 111 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3E SER* 4.7 9.5 + - - -
6E ILE* 4.3 4.7 - - - +
107E HIS* 2.9 35.2 + - - -
108E ALA* 3.8 4.0 + - - -
110E LYS* 1.3 75.3 - - - +
112E LYS* 1.3 69.3 + - - +
113E ASP* 3.3 13.2 + - - +
----------------------------------------------------------
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