Contacts of the helix formed by residues 4 - 42 (chain F) in PDB entry 5JRE
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 ASN 4 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100E SER* 4.4 9.2 - - - -
102E GLU* 4.0 17.7 - - - +
2F LEU 3.8 0.2 + - - -
3F PRO* 1.3 78.2 - - - +
5F LEU* 1.3 60.2 + - - +
6F ASP 3.4 2.5 - - - -
7F ASN* 3.2 24.5 + - + +
8F LEU* 2.9 26.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 5 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151E ASP* 3.7 41.1 - - + +
154E TYR* 3.6 26.9 - - + -
155E ILE* 3.5 29.2 - - + -
0F SER* 4.1 8.3 - - - +
2F LEU* 3.8 24.2 - - + +
3F PRO 3.2 4.5 - - - -
4F ASN* 1.3 75.9 - - - +
6F ASP* 1.3 59.2 + - - +
8F LEU* 3.2 6.8 + - + +
9F LYS* 2.9 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 6 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154E TYR* 2.7 33.3 + - - -
4F ASN 3.4 0.4 - - - -
5F LEU* 1.3 77.8 - - - +
7F ASN* 1.3 66.3 + - - +
9F LYS* 3.5 6.9 + - - +
10F GLU* 3.1 29.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 7 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4F ASN* 3.2 27.0 + - + +
6F ASP* 1.3 77.6 - - - +
8F LEU* 1.3 60.8 + - - +
10F GLU* 3.8 7.1 - - - +
11F GLU* 2.9 45.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 8 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101E LYS* 4.3 14.4 - - + +
108E THR* 3.8 25.4 - - + -
111E TYR* 3.9 31.9 - - + -
112E LEU* 4.0 15.5 - - + -
155E ILE* 5.0 4.7 - - + -
2F LEU* 3.9 33.7 - - + -
3F PRO 4.8 5.4 - - - +
4F ASN* 2.9 17.6 + - + +
5F LEU* 3.5 11.4 - - + +
7F ASN* 1.3 76.1 - - - +
9F LYS* 1.3 59.4 + - - +
11F GLU* 3.7 5.9 - - - +
12F TYR* 2.8 32.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 9 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154E TYR* 3.0 54.6 + - + +
155E ILE* 3.9 29.1 - - + +
156E GLU* 3.2 29.1 + - - +
5F LEU 2.9 16.5 + - - +
6F ASP* 3.6 7.0 - - - +
8F LEU* 1.3 76.7 - - - +
10F GLU* 1.3 60.2 + - + +
12F TYR* 3.3 3.7 + - - +
13F GLN* 2.9 39.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 10 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6F ASP* 3.1 17.6 + - + +
7F ASN* 3.8 8.5 - - - +
9F LYS* 1.3 80.2 - - + +
11F GLU* 1.3 57.7 + - + +
13F GLN* 3.4 6.5 + - - +
14F LYS* 3.0 29.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 11 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101E LYS* 3.1 38.7 + - - -
102E GLU* 4.4 3.0 - - - +
108E THR* 3.9 13.5 - - - +
7F ASN* 2.9 34.0 + - - +
8F LEU* 3.8 5.7 - - - +
10F GLU* 1.3 78.9 - - + +
12F TYR* 1.3 62.4 + - - +
14F LYS* 3.3 17.4 + - - +
15F LEU* 3.0 28.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 12 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108E THR* 4.1 8.0 - - + +
109E TRP* 3.7 17.9 - + - -
112E LEU* 3.4 27.6 - - + -
155E ILE* 4.3 9.4 - - + -
157E LEU* 3.7 28.9 - - + -
158E LYS* 2.8 21.0 + - + -
159E ASN* 3.0 6.9 + - - +
162E LEU* 3.6 21.0 - - + +
8F LEU 2.8 19.1 + - - +
9F LYS* 3.7 3.8 - - - +
11F GLU* 1.3 76.3 - - - +
13F GLN* 1.3 84.8 + - - +
15F LEU* 3.1 6.7 + - - +
16F GLU* 2.6 56.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 13 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155E ILE 2.9 26.1 + - - +
156E GLU* 3.0 24.8 + - - +
158E LYS* 4.1 20.2 - - - +
9F LYS* 2.9 31.0 + - + +
10F GLU* 3.9 6.1 - - - +
12F TYR* 1.3 85.5 - - - +
14F LYS* 1.3 62.7 + - - +
16F GLU* 3.4 5.6 + - - +
17F GLU* 3.1 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 14 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10F GLU 3.0 17.2 + - - +
11F GLU* 3.5 15.7 - - - +
12F TYR 3.2 0.2 - - - -
13F GLN* 1.3 76.8 - - - +
15F LEU* 1.3 60.3 + - - +
17F GLU* 3.2 8.4 + - + +
18F LYS* 2.9 43.0 + - + +
69F TYR* 2.8 38.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 15 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108E THR* 3.8 31.2 - - + +
109E TRP* 4.0 33.0 - - + +
11F GLU* 3.0 16.5 + - + +
12F TYR* 3.1 8.3 + - - +
14F LYS* 1.3 80.5 - - - +
16F GLU* 1.3 57.8 + - - +
18F LYS* 3.2 3.0 + - - +
19F LYS* 2.9 25.3 + - - +
69F TYR* 3.6 35.4 - - + -
71F MET* 4.3 12.3 - - + -
72F PHE* 3.3 24.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 16 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109E TRP* 3.5 15.8 - - + -
158E LYS* 4.0 20.4 - - + -
159E ASN* 3.1 23.4 + - - +
12F TYR* 2.6 55.9 + - + +
13F GLN* 3.9 9.9 - - - +
15F LEU* 1.3 75.7 - - - +
17F GLU* 1.3 61.5 + - - +
19F LYS* 3.5 17.6 + - - +
20F GLN* 3.2 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 17 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13F GLN 3.1 14.2 + - - +
14F LYS* 3.4 11.9 - - + +
16F GLU* 1.3 77.8 - - - +
18F LYS* 1.3 59.6 + - + +
20F GLN* 3.4 6.6 + - - +
21F GLU* 3.0 46.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 18 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14F LYS* 2.9 30.5 + - + +
15F LEU* 3.7 6.3 - - - +
17F GLU* 1.3 77.2 - - + +
19F LYS* 1.3 59.8 + - - +
21F GLU* 3.2 27.1 + - + +
22F ILE* 2.8 37.4 + - + +
65F GLU* 3.3 28.7 - - - +
69F TYR* 3.5 47.8 - - + +
72F PHE* 4.8 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 19 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109E TRP* 4.8 4.3 - - + -
159E ASN* 4.2 20.0 - - - +
15F LEU 2.9 16.9 + - - +
16F GLU* 3.6 20.7 + - - +
18F LYS* 1.3 76.5 - - - +
20F GLN* 1.3 57.6 + - - +
22F ILE* 3.2 5.3 + - - +
23F VAL* 2.9 35.6 + - + +
72F PHE* 3.8 38.2 - - + -
75F ASN* 3.7 29.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 20 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16F GLU 3.2 13.4 + - - +
17F GLU* 3.7 6.5 - - - +
19F LYS* 1.3 79.4 - - - +
21F GLU* 1.3 58.0 + - + +
23F VAL* 3.4 13.8 + - - +
24F ASP* 2.9 70.0 + - - +
20G GLN* 5.1 18.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 21 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17F GLU* 3.0 31.8 + - + +
18F LYS* 3.2 39.7 + - + +
20F GLN* 1.3 77.0 - - + +
22F ILE* 1.3 58.5 + - + +
24F ASP* 3.4 8.1 + - - +
25F ARG* 2.9 49.1 + - - +
28F ARG* 5.2 0.9 + - - -
65F GLU* 4.4 4.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 22 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18F LYS* 2.8 27.5 + - + +
19F LYS* 3.5 4.5 - - - +
21F GLU* 1.3 73.5 - - + +
23F VAL* 1.3 58.0 + - - +
25F ARG* 3.4 6.0 + - - +
26F SER* 2.9 25.6 + - - -
62F GLN* 3.1 35.7 + - - +
65F GLU* 4.4 14.1 - - + +
66F LEU* 3.8 27.1 - - + -
69F TYR* 4.4 14.6 - - + -
72F PHE* 3.9 29.2 - - + +
75F ASN* 4.0 5.6 - - + -
76F GLY 3.8 15.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 23 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19F LYS* 2.9 28.1 + - + +
20F GLN* 3.8 18.2 - - - +
22F ILE* 1.3 75.8 - - - +
24F ASP* 1.3 64.0 + - - +
26F SER* 3.2 4.4 + - - -
27F ILE* 3.1 38.3 + - + +
75F ASN* 3.8 38.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 24 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20F GLN* 2.9 46.5 + - - +
21F GLU* 3.7 7.3 - - - +
23F VAL* 1.3 77.0 - - - +
25F ARG* 1.3 63.3 + - - +
27F ILE* 3.3 12.3 + - - +
28F ARG* 3.0 40.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 25 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21F GLU* 2.9 45.0 + - - +
22F ILE* 3.7 8.4 - - - +
24F ASP* 1.3 77.0 - - - +
26F SER* 1.3 57.8 + - - +
28F ARG* 3.2 29.7 + - - +
29F MET* 2.8 40.4 + - - +
58F LEU* 3.7 33.5 - - + +
61F THR* 3.8 25.4 - - - +
62F GLN* 2.8 43.5 + - - +
65F GLU* 3.8 22.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 26 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22F ILE 2.9 18.1 + - - -
23F VAL 3.2 6.0 + - - -
25F ARG* 1.3 76.1 - - - +
27F ILE* 1.3 58.0 + - - +
29F MET* 3.3 3.7 + - - +
30F SER* 2.9 28.8 + - - -
62F GLN* 3.5 10.9 - - - +
75F ASN 3.7 18.6 + - - -
76F GLY* 3.9 3.0 + - - -
78F ILE* 4.4 4.7 + - - +
79F GLY* 3.0 32.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 27 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23F VAL* 3.1 31.9 + - + +
24F ASP* 3.6 13.7 - - - +
25F ARG 3.2 0.2 - - - -
26F SER* 1.3 76.9 - - - +
28F ARG* 1.3 64.6 + - + +
30F SER* 3.3 8.7 + - - -
31F LYS* 3.0 23.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 28 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21F GLU 5.2 0.6 + - - -
24F ASP* 3.0 32.3 + - - +
25F ARG* 3.2 42.3 + - - +
27F ILE* 1.3 79.5 - - + +
29F MET* 1.3 55.8 + - - +
31F LYS* 3.3 7.1 + - - +
32F LEU* 2.9 34.2 + - + +
58F LEU* 3.9 29.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 29 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25F ARG* 2.8 25.1 + - - +
26F SER* 3.6 5.4 - - - +
28F ARG* 1.3 72.5 - - - +
30F SER* 1.3 57.6 + - - +
33F SER* 2.8 32.5 + - - -
55F LEU* 3.6 14.7 - - + +
58F LEU* 3.8 24.0 - - + +
59F ALA* 3.7 24.7 - - + -
62F GLN* 3.9 31.2 - - - -
79F GLY* 3.4 31.6 - - - +
80F LEU* 3.8 9.0 - - + -
83F TYR* 3.7 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 30 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26F SER 2.9 13.6 + - - -
27F ILE* 3.5 11.9 - - - -
28F ARG 3.3 0.2 - - - -
29F MET* 1.3 77.0 - - - +
31F LYS* 1.3 62.5 + - - +
33F SER* 3.4 3.6 + - - -
34F LYS* 2.9 49.3 + - - +
78F ILE* 5.7 3.8 - - - -
79F GLY* 4.7 3.5 - - - -
82F GLU* 3.3 21.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 31 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27F ILE* 3.0 14.2 + - + +
28F ARG* 3.6 10.1 - - + +
30F SER* 1.3 77.0 + - - +
32F LEU* 1.3 74.4 + - + +
34F LYS* 3.2 11.5 + - - +
35F SER* 3.0 47.9 + - - +
51F TYR* 4.3 15.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 32 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28F ARG* 2.9 17.2 + - + +
29F MET 3.9 3.1 - - - +
31F LYS* 1.3 89.4 - - + +
33F SER* 1.3 56.5 + - - +
35F SER* 3.3 3.5 + - - -
36F LEU* 2.9 31.2 + - - +
51F TYR* 3.8 34.0 - - + +
54F GLU* 4.0 37.5 - - + +
55F LEU* 4.1 21.0 - - + +
58F LEU* 3.7 29.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 33 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29F MET 2.8 18.8 + - - -
30F SER 3.5 4.0 - - - -
32F LEU* 1.3 76.2 - - - +
34F LYS* 1.3 55.9 + - - +
36F LEU* 3.4 3.5 + - - +
37F ILE* 3.0 39.5 + - - +
55F LEU* 3.9 14.7 - - - +
82F GLU* 3.0 49.6 + - - +
83F TYR 4.4 0.4 - - - -
85F GLU* 5.4 0.7 + - - -
86F ALA* 3.8 6.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 34 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30F SER* 2.9 24.9 + - - +
31F LYS* 3.2 8.9 + - - +
33F SER* 1.3 76.4 - - - +
35F SER* 1.3 58.0 + - - +
37F ILE* 3.4 9.8 + - + +
38F TYR* 2.9 31.6 + - - +
82F GLU* 2.8 37.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 35 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31F LYS* 3.0 36.9 + - - -
32F LEU 3.6 8.3 - - - -
34F LYS* 1.3 77.5 - - - +
36F LEU* 1.3 62.3 + - - +
38F TYR* 3.9 4.8 - - - +
39F SER* 3.0 29.1 + - - -
51F TYR* 3.7 31.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 36 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32F LEU 2.9 17.4 + - - +
33F SER 3.6 4.3 - - - +
35F SER* 1.3 76.4 - - - +
37F ILE* 1.3 62.7 + - - +
39F SER* 3.4 1.7 + - - -
40F MET* 2.9 31.0 + - + +
48F ALA* 3.2 39.3 - - + +
51F TYR* 3.9 12.5 - - + -
52F LYS* 3.9 22.4 - - + +
55F LEU* 4.0 9.2 - - + -
86F ALA* 4.0 17.3 - - + +
87F LEU* 4.0 23.3 - - + -
90F TYR* 4.1 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 37 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33F SER* 3.0 30.6 + - - +
34F LYS* 3.8 8.7 - - + +
35F SER 3.4 0.2 - - - -
36F LEU* 1.3 74.8 - - - +
38F TYR* 1.3 65.6 + - - +
40F MET* 3.2 3.9 + - - +
41F ILE* 3.0 31.7 + - + +
85F GLU* 3.9 23.1 - - + +
86F ALA* 3.9 26.9 - - + +
89F LEU* 3.7 26.0 - - + +
121F GLU* 3.2 32.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 38 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34F LYS 2.9 17.6 + - - +
35F SER* 3.9 4.5 - - - +
37F ILE* 1.3 78.2 - - - +
39F SER* 1.3 68.1 + - - +
41F ILE* 3.3 8.8 + - + +
42F ARG* 3.1 68.5 + - + +
124F ARG* 3.9 29.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 39 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35F SER 3.0 19.7 + - - -
36F LEU 3.6 3.6 - - - -
38F TYR* 1.3 80.2 - - - +
40F MET* 1.3 60.7 + - - +
42F ARG* 3.5 15.1 + - - +
43F GLU 3.1 3.5 + - - -
44F ASP* 2.9 33.8 + - - +
47F SER* 3.6 7.7 - - - -
48F ALA* 3.8 24.9 - - - -
51F TYR* 3.3 18.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 40 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36F LEU* 2.9 24.1 + - + +
37F ILE* 3.2 7.4 + - - +
39F SER* 1.3 76.0 - - - +
41F ILE* 1.3 63.1 + - - +
43F GLU* 3.1 15.6 + - - +
45F TYR* 3.6 35.9 + - + -
48F ALA* 3.5 24.2 - - + -
86F ALA 5.9 0.2 - - - +
89F LEU* 4.7 3.6 - - + -
90F TYR* 3.6 55.0 - - + +
93F ILE* 3.8 36.8 - - + +
94F LYS* 4.3 7.6 - - + +
125F LYS* 4.6 1.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 41 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37F ILE* 3.0 37.7 + - + +
38F TYR* 3.8 8.1 - - + +
40F MET* 1.3 77.4 - - - +
42F ARG* 1.3 58.3 + - + +
43F GLU* 3.1 13.6 + - - +
89F LEU* 4.4 7.9 - - + -
93F ILE* 5.0 0.4 - - + -
121F GLU* 4.3 7.4 - - - +
124F ARG* 3.2 45.8 - - + +
125F LYS* 3.9 29.2 + - + -
128F GLU* 3.8 40.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 42 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38F TYR* 3.1 56.2 + - + +
39F SER* 3.6 17.3 + - - +
41F ILE* 1.3 76.0 - - + +
43F GLU* 1.3 69.0 + - - +
44F ASP* 3.1 34.3 + - + +
47F SER* 4.4 4.6 + - - -
128F GLU* 5.6 2.7 - - - -
----------------------------------------------------------
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