Contacts of the helix formed by residues 36 - 64 (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 LEU 36 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1005B HIS* 5.4 2.7 - - + -
30E TRP* 4.0 25.8 - - + -
31E CYS* 2.8 25.3 + - + +
32E TYR 4.8 0.2 + - - -
34E HIS* 3.5 12.6 - - + +
35E SER* 1.3 83.0 - - - +
37E ASP* 1.3 58.5 + - - +
38E GLY 3.2 3.5 + - - -
39E ALA* 4.5 2.0 - - + -
40E GLY* 2.8 23.9 + - - -
83E LEU* 4.0 31.0 - - + +
151E LEU* 4.3 32.5 - - + +
152E TYR* 5.9 0.7 - - - -
155E ASP* 3.3 29.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 37 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31E CYS 4.2 0.2 + - - -
32E TYR* 4.0 30.6 - - + +
35E SER 3.6 5.4 - - - +
36E LEU* 1.3 73.2 - - - +
38E GLY* 1.3 64.8 + - - +
40E GLY 3.6 0.7 - - - -
41E LEU* 2.9 29.6 + - - +
155E ASP* 3.3 8.5 - - - +
156E GLN* 4.7 5.2 + - - -
159E LYS* 2.8 29.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 38 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37E ASP* 1.3 79.4 + - - +
39E ALA* 1.3 63.6 + - - +
41E LEU* 3.5 3.2 + - - +
42E PHE* 3.1 22.3 + - - +
155E ASP* 3.0 21.0 + - - -
158E VAL* 3.9 1.7 - - - +
159E LYS* 3.6 38.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 39 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31E CYS* 3.8 13.7 - - - -
36E LEU* 3.8 2.0 - - + +
38E GLY* 1.3 69.8 - - - -
40E GLY* 1.3 60.1 + - - +
42E PHE* 3.2 1.2 + - - +
43E LEU* 2.9 35.5 + - - +
83E LEU* 3.6 30.1 - - + -
87E PHE* 4.1 10.3 - - + -
155E ASP* 2.7 19.0 + - - +
158E VAL* 3.7 17.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 40 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28E SER* 2.5 33.0 + - - -
31E CYS* 3.6 3.3 - - - +
32E TYR* 3.2 26.6 - - - -
36E LEU 2.8 17.4 + - - -
37E ASP 3.8 1.6 - - - -
38E GLY 3.2 0.2 - - - -
39E ALA* 1.3 76.2 - - - +
41E LEU* 1.3 55.1 + - - +
44E PHE* 2.9 15.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 41 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32E TYR* 3.3 16.4 + - - +
37E ASP 2.9 18.3 + - - +
38E GLY 3.8 2.5 - - - +
40E GLY* 1.3 72.5 - - - +
42E PHE* 1.3 65.5 + - - +
44E PHE* 3.3 6.6 + - + +
45E ASP* 2.9 32.8 + - - +
159E LYS* 4.7 16.8 - - + -
162E ALA* 3.8 21.8 - - + -
163E LYS* 4.5 18.8 - - + +
166E LYS* 3.5 30.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 42 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38E GLY 3.1 6.3 + - - +
39E ALA 3.7 1.6 - - - +
41E LEU* 1.3 79.1 - - - +
43E LEU* 1.3 64.2 + - + +
46E HIS* 3.0 24.2 + - + +
87E PHE* 4.0 14.1 - + - -
133E LEU* 3.6 28.3 - - + -
134E PHE* 3.6 33.9 - + - -
137E ILE* 3.2 30.7 - - + -
158E VAL* 3.4 25.8 - - + -
161E ILE* 3.8 19.1 - - + -
162E ALA* 3.8 16.6 - - + +
1010E GOL 3.1 37.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 43 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24E TYR* 3.6 34.6 - - + +
27E MET* 3.8 32.5 - - + -
28E SER* 3.7 15.3 - - - +
31E CYS* 3.9 17.0 - - - -
39E ALA 2.9 21.0 + - - +
42E PHE* 1.3 79.8 - - + +
44E PHE* 1.3 60.2 + - - +
46E HIS* 3.9 1.7 - - - -
47E ALA* 2.9 28.4 + - - +
86E ILE* 4.0 9.9 - - + -
87E PHE* 4.1 15.7 - - + -
90E ALA* 5.3 0.4 - - + -
134E PHE* 4.1 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 44 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B LYS* 3.9 29.4 - - + -
58B ILE* 3.9 15.9 - - + -
59B ILE* 3.5 41.1 - - + -
62B ASN* 4.2 9.0 - - - -
25E MET* 3.6 31.0 - - + +
28E SER* 3.5 10.9 + - - +
32E TYR* 4.6 5.2 - + + +
40E GLY 2.9 18.3 + - - +
41E LEU* 3.3 9.6 + - + +
43E LEU* 1.3 74.1 - - - +
45E ASP* 1.3 78.5 - - - +
47E ALA* 3.3 7.6 + - - +
48E ALA* 3.0 22.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 45 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41E LEU* 2.9 26.8 + - - +
44E PHE* 1.3 90.7 - - - +
46E HIS* 1.3 62.2 + - - +
48E ALA* 3.3 8.5 + - - +
49E GLU* 3.2 21.0 + - - +
162E ALA* 4.5 6.6 - - - +
166E LYS* 2.5 43.1 + - - +
1010E GOL 3.6 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 46 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24E TYR* 3.5 29.8 - + - -
42E PHE* 3.0 19.3 + - + +
43E LEU* 3.9 6.7 - - - +
44E PHE 3.3 0.2 - - - -
45E ASP* 1.3 73.8 - - - +
47E ALA* 1.3 64.4 + - - +
49E GLU* 3.1 4.4 + - + +
50E GLU* 3.0 34.2 + - - +
94E GLU* 3.1 20.4 + - - -
130E GLU* 3.4 34.3 - - + -
134E PHE* 3.5 32.4 - + + -
1007E FE 3.9 1.1 - - - -
1010E GOL 2.8 32.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 47 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B TYR* 4.4 0.4 - - - -
21E SER* 3.0 45.9 + - - +
24E TYR* 3.6 14.2 - - + +
25E MET* 3.8 20.9 - - + +
43E LEU 2.9 15.8 + - - +
44E PHE 3.3 10.1 - - - +
46E HIS* 1.3 75.4 - - - +
48E ALA* 1.3 61.4 + - - +
50E GLU* 3.3 3.3 + - - +
51E TYR 3.2 12.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 48 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B TYR* 4.3 10.1 + - - -
55B LYS* 3.8 31.4 + - + +
25E MET* 5.2 0.4 - - - +
44E PHE* 3.0 16.0 + - + +
45E ASP* 3.6 12.3 - - - +
46E HIS 3.3 0.2 - - - -
47E ALA* 1.3 76.4 - - - +
49E GLU* 1.3 57.5 + - - +
51E TYR* 3.4 5.3 + - - +
52E GLU* 3.1 31.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 49 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45E ASP 3.2 12.1 + - - +
46E HIS* 3.1 13.3 + - - +
48E ALA* 1.3 76.0 - - - +
50E GLU* 1.3 64.4 + - - +
52E GLU* 3.2 18.5 + - - +
53E HIS* 3.1 42.3 + - - -
56E LYS* 5.4 3.1 + - - -
126E GLU* 4.1 6.3 - - - +
130E GLU* 3.9 20.0 - - - +
1010E GOL 4.4 15.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 50 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17E GLU* 3.4 35.4 - - - +
20E SER* 3.7 14.0 + - - -
21E SER 4.0 5.2 - - - +
24E TYR* 3.9 15.2 - - + -
46E HIS* 3.0 34.1 + - - +
47E ALA 3.3 6.0 + - - +
49E GLU* 1.3 74.4 - - - +
51E TYR* 1.3 62.3 + - - +
53E HIS* 3.2 7.7 + - - -
54E ALA 3.2 16.5 + - - -
94E GLU* 3.6 9.2 - - - +
97E ILE* 5.0 1.9 - - - +
130E GLU* 2.9 10.6 - - - +
1006E FE 3.0 13.7 - - - -
1007E FE 2.7 29.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 51 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B SER* 3.2 20.6 + - - -
25B MET* 3.7 19.1 - - + +
47B ALA 4.1 2.6 + - - -
48B ALA* 4.2 3.7 - - - -
51B TYR* 3.3 52.4 - + + +
52B GLU* 5.8 0.2 - - - -
55B LYS* 5.7 0.9 - - - -
17E GLU 5.0 0.7 - - - -
18E MET* 4.5 17.7 - - + +
21E SER* 3.9 5.5 - - - +
47E ALA 3.2 5.1 + - - +
48E ALA 3.5 8.5 - - - +
50E GLU* 1.3 76.5 - - - +
52E GLU* 1.3 67.1 + - - +
54E ALA* 3.2 7.1 + - + +
55E LYS* 3.0 54.5 + - + +
1009E GOL 3.5 41.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 52 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B GLU* 4.7 6.2 - - - +
55B LYS* 4.9 4.7 + - - -
48E ALA* 3.1 21.9 + - + +
49E GLU* 3.2 30.0 + - - +
51E TYR* 1.3 79.2 - - - +
53E HIS* 1.3 62.4 + - + +
55E LYS* 2.9 37.6 + - - +
56E LYS* 3.0 37.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 53 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17E GLU* 3.8 13.9 + - + -
49E GLU* 3.1 30.0 + - - -
50E GLU* 3.2 14.5 + - - +
52E GLU* 1.3 74.2 - - + +
54E ALA* 1.3 65.1 + - - +
56E LYS* 3.2 5.0 + - + +
57E LEU* 3.0 28.2 + - - +
122E TRP* 3.6 25.9 - + + -
123E TYR* 4.0 16.6 - + + -
126E GLU* 3.2 19.4 + - + -
127E GLN* 5.1 0.9 - - - -
130E GLU* 2.9 36.5 + - - -
1006E FE 3.2 18.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 54 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14E VAL* 4.2 10.4 - - + +
17E GLU* 3.8 24.1 - - + +
18E MET* 4.0 26.7 - - + -
50E GLU 3.2 4.5 + - - +
51E TYR* 3.2 14.1 + - + +
53E HIS* 1.3 77.6 - - - +
55E LYS* 1.3 58.7 + - - +
57E LEU* 3.2 9.5 + - - +
58E ILE* 2.9 34.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 55 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B MET* 4.1 7.9 - - + -
44B PHE* 3.9 23.0 - - + -
48B ALA* 4.0 27.5 - - + +
52B GLU* 4.7 8.3 + - - -
51E TYR* 3.0 45.7 + - + +
52E GLU* 2.9 46.4 + - - +
53E HIS 3.3 0.2 - - - -
54E ALA* 1.3 77.4 - - + +
56E LYS* 1.3 56.6 + - + +
58E ILE* 3.2 8.8 + - + +
59E ILE* 2.9 36.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 56 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49E GLU* 5.4 2.6 + - - -
52E GLU* 3.0 29.1 + - - +
53E HIS* 3.2 6.5 + - - +
55E LYS* 1.3 75.7 - - + +
57E LEU* 1.3 62.6 + - - +
59E ILE* 3.6 15.6 + - + +
60E PHE 3.2 15.8 + - - -
119E PHE* 3.7 14.5 - - + -
122E TRP* 3.5 42.5 - - + -
126E GLU* 4.1 18.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 57 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10E LEU* 4.7 14.1 - - + +
13E GLN* 3.8 41.5 - - + +
14E VAL* 3.8 13.0 - - + +
17E GLU* 4.3 5.6 - - + -
53E HIS 3.0 19.0 + - - +
54E ALA* 3.5 6.5 - - - +
56E LYS* 1.3 73.3 - - - +
58E ILE* 1.3 64.5 + - - +
60E PHE* 3.3 7.7 + - + +
61E LEU* 3.0 28.1 + - + +
119E PHE* 3.8 23.6 - - + -
120E LEU* 4.5 6.5 - - + -
122E TRP* 5.0 3.1 - - + -
123E TYR* 4.1 31.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 58 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B MET* 4.1 30.3 - - + +
28B SER* 6.5 0.2 - - - -
44B PHE* 3.8 14.6 - - + -
14E VAL* 3.8 29.4 - - + -
18E MET* 3.9 17.7 - - + -
54E ALA 2.9 22.4 + - - +
55E LYS* 3.6 7.0 - - - +
57E LEU* 1.3 73.5 - - - +
59E ILE* 1.3 59.2 + - - +
61E LEU* 3.1 9.4 + - - +
62E ASN* 2.9 43.9 + - - +
68E VAL* 4.1 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 59 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B PHE* 3.6 30.1 - - + -
55E LYS* 2.9 25.3 + - + +
56E LYS* 3.6 14.8 - - + +
57E LEU 3.4 0.2 - - - -
58E ILE* 1.3 73.4 - - - +
60E PHE* 1.3 58.3 + - - +
62E ASN* 3.3 9.4 + - - +
63E GLU* 2.9 55.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 60 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128D HIS* 3.9 18.2 - + - -
2E LEU* 4.0 6.7 - - + -
10E LEU* 3.9 29.4 - - + -
56E LYS 3.2 2.8 + - - +
57E LEU* 3.5 9.0 - - + +
58E ILE 3.2 0.4 - - - -
59E ILE* 1.3 80.1 - - - +
61E LEU* 1.3 62.1 + - + +
63E GLU* 3.6 15.8 + - - +
64E ASN* 2.7 56.1 + - - -
115E ALA 4.8 0.9 - - - -
116E THR* 3.7 26.5 - - + -
119E PHE* 3.5 69.8 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 61 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2E LEU* 4.4 4.7 - - + -
7E ILE* 5.4 0.9 - - - +
10E LEU* 3.6 40.6 - - + +
11E ASN* 4.2 20.2 - - - +
14E VAL* 4.0 22.2 - - + -
57E LEU* 3.0 20.9 + - + +
58E ILE* 3.1 5.4 + - - +
60E PHE* 1.3 73.9 - - + +
62E ASN* 1.3 64.5 + - - +
64E ASN* 3.1 9.0 + - - -
66E VAL* 3.0 56.3 + - + +
68E VAL* 3.9 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 62 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B SER* 4.4 2.6 + - - -
29B SER* 4.0 13.2 + - - -
32B TYR* 3.4 61.4 - - + +
33B THR* 6.0 0.7 - - - -
44B PHE* 4.2 8.9 - - - -
135D LYS* 4.2 1.2 + - - -
58E ILE* 2.9 35.5 + - - +
59E ILE* 3.6 10.6 - - - +
61E LEU* 1.3 74.3 - - - +
63E GLU* 1.3 63.5 + - + +
65E ASN* 3.1 19.1 + - - +
66E VAL 4.7 3.6 - - - +
68E VAL* 3.9 15.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 63 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B TYR* 5.7 1.1 - - - -
128D HIS* 5.3 4.2 + - - -
132D VAL* 3.6 23.0 - - + +
135D LYS* 2.5 31.9 + - - +
59E ILE* 2.9 36.9 + - + +
60E PHE* 3.7 23.5 - - - +
62E ASN* 1.3 75.9 - - - +
64E ASN* 1.3 59.8 + - - +
119E PHE* 6.0 0.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 64 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128D HIS* 3.1 28.7 + - - -
132D VAL* 4.9 0.2 - - - -
1E MET* 3.0 48.8 + - + +
2E LEU* 3.9 19.3 - - + +
60E PHE* 2.7 53.7 + - - +
61E LEU 3.1 6.2 + - - +
63E GLU* 1.3 79.6 - - - +
65E ASN* 1.3 64.0 + - - +
66E VAL* 3.2 13.8 + - + +
----------------------------------------------------------
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