Contacts of the helix formed by residues 26 - 57 (chain F) in PDB entry 6BAA
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 CYS 26 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B PHE* 4.5 16.2 - - + -
6F CYS* 2.0 51.8 - - + -
12F SER* 5.7 3.8 - - - -
25F GLY* 1.3 72.5 - - - +
27F PHE* 1.3 64.6 + - - +
28F VAL 3.3 0.4 - - - -
29F ASP* 3.2 24.4 + - - +
30F ALA* 3.4 5.9 + - - +
105F HIS* 3.7 20.6 - - - +
106F LEU* 5.3 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 27 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B LEU* 3.5 43.3 - - + -
95B PHE* 4.3 33.7 - + + -
96B ALA* 4.5 15.9 - - + -
15F TYR* 5.9 1.8 - - + -
24F ASN* 3.5 32.7 - - + +
25F GLY 3.2 0.6 - - - -
26F CYS* 1.3 79.9 - - - +
28F VAL* 1.3 57.2 + - + +
30F ALA* 3.0 10.9 + - + +
31F LEU* 2.9 57.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 28 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23F ASN 4.3 8.7 - - - +
24F ASN* 3.2 17.2 + - + +
25F GLY* 3.3 20.4 - - - +
27F PHE* 1.3 74.9 - - - +
29F ASP* 1.3 66.8 + - - +
31F LEU* 3.2 17.4 + - + +
32F ASN* 2.8 34.0 + - - +
149F THR 5.3 1.3 - - - +
152F ILE* 4.1 23.8 - - + -
153F LYS* 4.4 25.4 - - + +
156F LYS* 4.8 9.2 - - + -
157F PHE* 5.6 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 29 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25F GLY 4.0 10.6 - - - +
26F CYS* 3.2 14.6 + - - +
27F PHE 3.2 0.4 - - - -
28F VAL* 1.3 81.1 - - - +
30F ALA* 1.3 56.2 + - - +
32F ASN* 3.1 9.7 + - - +
33F VAL* 3.0 28.8 + - - +
105F HIS* 3.4 31.7 - - + +
106F LEU* 3.4 19.0 - - - +
109F PRO* 4.1 10.9 - - + +
153F LYS* 3.6 27.8 + - - +
157F PHE* 5.3 2.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 30 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B MET* 5.2 1.4 - - - +
91B TRP* 3.9 29.8 - - + -
92B LEU* 4.2 13.7 - - + +
95B PHE* 5.1 6.1 - - + -
26F CYS 3.4 5.7 + - - +
27F PHE* 3.0 17.6 + - + +
29F ASP* 1.3 75.5 - - - +
31F LEU* 1.3 64.9 + - - +
33F VAL* 3.2 24.9 + - - +
34F VAL* 3.3 12.4 - - - +
105F HIS* 5.3 3.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 31 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B LEU* 3.8 14.8 - - + -
27F PHE* 2.9 51.0 + - + +
28F VAL* 3.2 26.9 + - + +
30F ALA* 1.3 77.5 - - - +
32F ASN* 1.3 57.3 + - - +
34F VAL* 3.1 11.2 + - + +
35F PRO* 3.0 24.9 - - - +
149F THR* 3.7 23.0 - - + +
152F ILE* 4.8 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 32 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28F VAL 2.8 22.0 + - - +
29F ASP* 3.1 9.6 + - - +
31F LEU* 1.3 73.3 - - - +
33F VAL* 1.3 67.8 + - - +
35F PRO* 3.9 4.1 - - - +
36F HIS* 3.2 28.9 + - - +
109F PRO* 4.9 9.4 - - + -
149F THR* 3.1 27.3 + - - +
150F LYS* 3.2 29.9 - - - +
153F LYS* 3.2 35.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 33 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B MET* 3.6 26.2 - - + -
91B TRP* 5.3 4.0 - - + -
29F ASP 3.0 16.3 + - - +
30F ALA* 3.2 18.2 - - + +
31F LEU 3.1 0.8 - - - -
32F ASN* 1.3 79.4 - - - +
34F VAL* 1.3 65.6 + - - +
36F HIS* 3.1 17.3 + - - +
37F VAL* 3.1 32.9 + - + -
105F HIS* 5.5 6.5 - - + -
109F PRO* 4.4 19.1 - - + -
112F MET* 4.1 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 34 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B LEU* 6.3 1.3 - - + -
88B MET* 4.8 11.2 - - + -
89B VAL* 6.1 5.8 - - + -
92B LEU* 4.1 17.3 - - + -
30F ALA 3.3 17.5 - - - +
31F LEU* 3.1 12.2 + - + +
33F VAL* 1.3 76.5 - - - +
35F PRO* 1.3 69.2 - - + +
37F VAL* 3.1 10.7 - - + +
38F PHE* 2.8 38.4 + - + +
145F LEU* 4.7 10.8 - - + -
149F THR* 5.6 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 35 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31F LEU 3.0 13.7 - - - +
32F ASN* 3.9 3.8 - - - +
33F VAL 3.9 1.1 - - - -
34F VAL* 1.3 97.0 - - + +
36F HIS* 1.3 68.4 + - + +
38F PHE* 3.6 5.4 - - + +
39F LEU 2.9 20.1 + - - -
142F TYR* 3.2 20.9 - - + +
145F LEU* 3.7 23.6 - - + -
146F ALA* 3.7 26.0 - - + +
149F THR* 3.7 22.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 36 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32F ASN* 3.2 29.1 + - + +
33F VAL* 3.1 3.8 + - - +
35F PRO* 1.3 85.7 - - + +
37F VAL* 1.3 62.2 + - - +
39F LEU* 3.2 4.5 + - - +
40F LEU* 3.2 25.1 + - - +
109F PRO 3.7 10.2 + - - -
112F MET* 3.7 15.7 - - + +
113F ALA* 3.2 41.1 - - + +
116F ALA* 3.5 17.5 - - + -
142F TYR* 3.2 22.2 + - - -
146F ALA* 4.6 7.6 - - + -
150F LYS* 6.1 4.9 - - + +
179F TYR* 4.2 11.9 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 37 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B LEU* 4.7 6.7 - - + -
88B MET* 4.1 26.0 - - + -
33F VAL* 3.1 32.7 + - + +
34F VAL* 3.1 22.9 - - + +
36F HIS* 1.3 75.3 - - - +
38F PHE* 1.3 64.2 + - - +
40F LEU* 3.6 6.3 + - + +
41F PHE* 3.2 47.6 + - + -
112F MET* 3.7 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 38 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B LEU* 3.4 33.2 - - + -
34F VAL* 2.8 23.8 + - + +
35F PRO* 3.6 7.2 - - + +
37F VAL* 1.3 77.2 - - - +
39F LEU* 1.3 69.4 + - + +
41F PHE* 3.2 3.3 + - - +
42F ILE* 2.9 62.3 + - + +
138F ALA* 5.0 2.7 - - + -
141F ILE* 4.0 28.3 - - + -
142F TYR* 4.8 13.2 - + + -
145F LEU* 6.5 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 39 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35F PRO 2.9 17.4 + - - +
36F HIS* 3.2 5.1 + - - +
38F PHE* 1.3 84.6 - - - +
40F LEU* 1.3 66.0 + - + +
42F ILE* 3.2 3.9 - - + +
43F THR* 3.1 43.3 + - + +
116F ALA* 4.0 8.5 - - + +
119F THR* 4.2 14.1 - - - +
120F SER* 3.6 25.8 - - - +
123F TYR* 5.6 3.6 - - + -
139F LEU* 6.4 0.7 - - - -
142F TYR* 3.4 48.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 40 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36F HIS 3.2 17.2 + - - +
37F VAL* 3.9 9.0 - - + +
39F LEU* 1.3 80.1 - - + +
41F PHE* 1.3 75.8 + - + +
43F THR* 3.4 5.9 + - - -
44F PHE* 2.9 48.7 + - + -
112F MET* 5.3 7.4 - - + +
115F MET* 4.6 17.5 - - + -
116F ALA* 3.4 20.0 - - + -
119F THR* 3.4 35.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 41 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B MET* 6.1 0.2 - - + -
81B CYS* 3.4 40.1 - - + +
84B LEU* 3.8 39.0 - - + -
85B LEU* 3.7 39.5 - - + -
88B MET* 6.4 0.7 - - + -
37F VAL* 3.2 34.3 - - + +
38F PHE 3.2 3.2 + - - +
39F LEU 3.2 0.4 - - - -
40F LEU* 1.3 90.9 - - + +
42F ILE* 1.3 64.0 + - - +
44F PHE* 4.3 7.0 - + - -
45F PRO* 3.2 20.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 42 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B LEU* 5.4 3.7 - - + +
38F PHE* 2.9 56.3 + - + +
39F LEU* 3.2 13.9 - - + +
41F PHE* 1.3 74.8 - - - +
43F THR* 1.3 73.1 + - + +
44F PHE 3.8 0.2 + - - -
45F PRO* 3.9 10.0 - - - +
46F ILE* 4.3 10.6 - - + +
138F ALA* 4.1 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 43 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39F LEU* 3.1 38.4 + - + +
40F LEU* 3.4 5.2 + - - -
42F ILE* 1.3 85.5 - - + +
44F PHE* 1.3 60.0 + - - +
45F PRO 3.3 2.7 - - - -
46F ILE* 3.2 7.9 + - - +
47F LEU* 2.8 44.2 + - - +
119F THR* 5.0 2.1 - - - +
123F TYR* 3.7 39.9 - - + +
138F ALA* 5.6 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 44 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B MET* 4.0 21.3 - - + -
81B CYS* 4.0 15.5 - - - -
40F LEU* 2.9 46.6 + - + +
41F PHE* 4.3 4.9 - + - -
43F THR* 1.3 76.0 - - - +
45F PRO* 1.3 69.3 - - + +
47F LEU* 4.0 13.2 - - + +
48F PHE* 2.9 68.5 + + + -
119F THR* 5.4 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 45 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B ILE* 5.0 11.1 - - + +
77B MET* 5.7 3.4 - - + -
78B SER* 4.3 26.9 - - - +
81B CYS* 4.8 4.7 - - + -
41F PHE 3.2 16.8 - - - +
42F ILE* 3.9 7.9 - - - +
43F THR 3.7 0.9 - - - -
44F PHE* 1.3 98.9 - - + +
46F ILE* 1.3 67.7 + - + +
48F PHE* 3.7 5.3 + - + +
49F ILE* 3.4 30.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 46 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B LEU* 5.2 11.8 - - + +
59B VAL* 6.0 7.4 - - + -
42F ILE 4.3 13.9 - - - +
43F THR* 3.2 8.6 + - - +
45F PRO* 1.3 80.6 - - + +
47F LEU* 1.3 67.6 + - + +
49F ILE* 3.2 19.6 + - + +
50F GLY* 3.4 9.0 + - - -
123F TYR* 4.7 15.7 - - + +
135F LEU* 4.2 26.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 47 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43F THR* 2.8 42.1 + - - +
44F PHE* 4.0 15.0 - - + +
46F ILE* 1.3 74.0 - - + +
48F PHE* 1.3 57.8 + - + +
50F GLY* 3.2 4.5 + - - -
51F TRP* 3.0 27.4 + - - +
119F THR* 4.9 19.1 - - + +
122F VAL* 4.6 7.0 - - + -
123F TYR* 3.8 39.3 - - + +
126F ASN* 3.9 22.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 48 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B LEU* 5.2 18.2 - - + -
74B ILE* 4.4 18.8 - - + +
77B MET* 3.8 34.3 - - + -
44F PHE* 2.9 57.6 + + - +
45F PRO* 4.0 4.7 - - + +
47F LEU* 1.3 78.4 - - + +
49F ILE* 1.3 63.0 + - - +
51F TRP* 3.2 29.6 + + + +
52F GLY* 2.9 20.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 49 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B LEU* 4.6 13.7 - - + -
59B VAL* 4.2 17.9 - - + +
62B THR* 3.5 30.5 - - + -
63B LEU* 3.3 28.0 - - + -
66B LEU* 4.7 7.4 - - + +
74B ILE* 3.4 27.4 - - + -
45F PRO* 3.4 14.3 + - + +
46F ILE* 3.2 13.8 + - + +
48F PHE* 1.3 75.8 - - - +
50F GLY* 1.3 57.9 + - - +
52F GLY 3.2 1.8 + - - +
53F SER* 2.8 28.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 50 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B LEU* 5.1 11.7 - - - +
46F ILE 3.4 6.9 + - - -
47F LEU* 3.2 7.4 + - - -
49F ILE* 1.3 78.0 - - - +
51F TRP* 1.3 56.6 + - - +
53F SER* 2.6 23.2 + - - -
54F GLN* 2.9 25.3 + - - +
126F ASN* 5.8 7.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 51 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B HIS* 4.0 27.8 - + - -
73B LEU* 5.2 7.4 - - + -
47F LEU 3.0 12.8 + - - +
48F PHE* 3.2 31.8 + + + +
50F GLY* 1.3 78.2 - - - +
52F GLY* 1.3 65.0 + - - +
54F GLN* 3.5 16.0 + - - +
55F SER* 3.2 24.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 52 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B LEU* 4.3 13.4 - - - +
70B HIS* 3.9 20.3 + - - -
48F PHE 2.9 13.6 + - - -
49F ILE* 3.2 4.2 + - - -
51F TRP* 1.3 79.1 - - - +
53F SER* 1.3 58.1 + - - +
55F SER* 2.5 23.2 + - - -
56F SER* 3.0 15.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 53 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B PHE* 3.8 33.8 - - - -
56B LEU* 5.2 0.2 - - - +
62B THR* 5.4 4.7 - - - -
66B LEU* 4.6 2.6 - - - +
49F ILE* 2.8 17.1 + - - -
50F GLY* 2.6 29.0 + - - -
52F GLY* 1.3 75.4 - - - +
54F GLN* 1.3 58.5 + - - +
56F SER* 3.0 8.7 + - - -
57F LYS 2.8 38.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 54 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50F GLY 2.9 22.4 + - - +
51F TRP* 3.8 15.2 - - + +
53F SER* 1.3 78.2 + - - +
55F SER* 1.3 61.3 + - - +
57F LYS 4.5 0.7 - - - -
58F VAL* 3.3 32.6 + - + +
61F HIS* 5.4 7.6 - - + -
125F HIS* 6.3 1.4 - - - -
126F ASN* 4.0 20.8 - - - +
129F THR* 5.3 9.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 55 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B LYS* 5.1 10.2 + - - -
70B HIS* 3.3 23.6 - - - -
51F TRP* 3.2 17.5 + - - -
52F GLY* 2.5 24.3 + - - -
54F GLN* 1.3 79.0 - - - +
56F SER* 1.3 61.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 56 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B PHE* 6.0 0.5 - - - -
65B ASP 6.0 1.3 - - - -
66B LEU* 5.1 8.2 - - - +
67B LYS* 5.3 14.8 - - - +
207C LYS* 4.0 15.2 + - - -
52F GLY 3.0 11.4 + - - -
53F SER* 3.0 18.4 + - - -
54F GLN 4.6 0.2 - - - -
55F SER* 1.3 81.1 + - - +
57F LYS* 1.3 72.3 + - - +
58F VAL 4.1 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 57 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B PHE* 5.0 15.3 - - + -
207C LYS* 4.0 31.0 - - + +
53F SER 2.8 17.8 + - - +
54F GLN* 4.5 0.3 - - - -
56F SER* 1.3 84.3 + - - +
58F VAL* 1.3 58.0 + - - +
59F HIS* 3.7 2.7 - - + +
60F ILE* 4.9 9.1 + - + +
61F HIS* 5.0 3.3 + - - +
----------------------------------------------------------
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