Contacts of the helix formed by residues 37 - 65 (chain A) in PDB entry 3E1J
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 37 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A PHE* 2.8 25.8 + - + +
35A TRP* 3.7 35.4 - - + +
36A GLY* 1.3 76.1 - - - +
38A LYS* 1.3 63.6 + - - +
39A ARG 2.8 5.4 + - - -
40A LEU* 3.0 15.9 + - + +
41A ASN* 3.2 8.3 + - - +
83A VAL* 3.9 28.5 - - + -
150A LEU* 4.0 30.1 - - + +
153A GLN* 3.2 22.0 - - + -
154A ILE* 5.1 1.8 - - + -
140C LEU* 3.8 17.9 - - + -
143C LYS* 6.0 4.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A PHE 5.3 0.2 - - - -
33A LYS* 5.4 4.0 - - + +
36A GLY* 2.9 16.9 + - - +
37A LEU* 1.3 70.8 - - - +
39A ARG* 1.3 55.5 + - - +
41A ASN* 3.3 10.3 + - - +
42A ASP* 3.0 35.9 + - - +
153A GLN 3.0 2.4 + - - +
154A ILE* 3.3 27.6 + - - +
155A ARG* 4.5 0.2 - - - +
156A GLU* 3.9 28.1 + - - +
39C ARG* 5.4 3.0 - - - +
157C GLU* 2.8 41.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A LEU 2.8 0.2 + - - -
38A LYS* 1.3 75.7 - - - +
40A LEU* 1.3 62.0 + - - +
42A ASP* 3.4 9.2 + - + +
43A VAL* 3.1 34.4 + - - +
133A TRP* 4.1 14.6 - - - +
137A GLU* 3.3 34.6 + - - -
140A LEU* 5.5 5.5 - - - +
152A ALA* 4.5 9.8 + - - +
153A GLN* 3.0 40.0 + - - +
155A ARG 3.6 18.6 - - - +
156A GLU* 4.6 0.7 - - - +
157A GLU* 4.1 34.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 40 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A PHE* 3.6 42.0 - - + -
37A LEU* 3.0 15.8 + - + +
39A ARG* 1.3 83.5 - - - +
41A ASN* 1.3 60.4 + - - +
43A VAL* 4.5 2.0 - - - +
44A GLU* 3.0 36.2 + - - +
83A VAL* 4.1 15.9 - - + -
87A LEU* 5.1 2.7 - - + -
133A TRP* 4.2 20.2 - - + -
149A TYR* 3.5 19.5 - - + +
153A GLN* 3.3 42.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 41 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ALA* 3.0 36.6 - - - +
30A ARG* 3.4 27.4 + - - +
32A PHE* 3.9 0.8 - - - +
33A LYS* 3.5 34.9 - - + +
37A LEU 3.2 7.0 + - - +
38A LYS* 3.5 11.3 + - - +
39A ARG 3.2 0.2 - - - -
40A LEU* 1.3 75.1 - - - +
42A ASP* 1.3 81.4 + - - +
45A TYR* 2.9 28.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A LYS* 3.0 18.8 + - - +
39A ARG* 3.7 7.8 - - + +
40A LEU 3.4 0.4 - - - -
41A ASN* 1.3 89.2 + - - +
43A VAL* 1.3 65.8 + - + +
45A TYR* 3.7 3.3 - - - +
46A HIS* 2.8 40.5 + - + +
156A GLU* 3.0 43.8 - - - +
157A GLU 4.7 2.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ARG* 3.1 27.5 + - - +
40A LEU 4.3 0.7 - - - +
41A ASN 3.3 0.4 - - - -
42A ASP* 1.3 76.2 - - + +
44A GLU* 1.3 59.2 + - - +
46A HIS* 3.0 9.9 + - - +
47A GLU* 2.9 37.2 + - - +
133A TRP* 3.5 54.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A TYR* 3.4 31.6 - - + +
28A HIS* 3.1 19.2 - - - +
29A ALA* 3.9 9.9 - - + -
32A PHE* 3.9 17.3 - - + -
40A LEU* 3.0 18.1 + - - +
43A VAL* 1.3 72.1 - - - +
45A TYR* 1.3 66.3 + - - +
47A GLU* 3.1 9.2 + - - +
48A SER* 2.9 22.5 + - - -
87A LEU* 3.8 6.4 - - - +
90A ASP* 2.9 28.0 - - - +
133A TRP* 3.7 26.5 - - + -
134A LEU* 4.0 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A PHE* 3.6 30.5 - + - -
29A ALA* 3.6 11.0 - - + +
30A ARG* 3.3 28.0 - - - +
41A ASN* 2.9 20.9 + - - +
42A ASP* 3.7 3.8 - - - +
44A GLU* 1.3 77.9 - - - +
46A HIS* 1.3 85.1 + + - +
48A SER* 3.0 17.2 + - - -
49A ILE* 3.1 32.3 + - + +
200B HEM 3.2 36.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ASP* 2.8 34.6 + - + +
43A VAL* 3.0 10.5 + - - +
45A TYR* 1.3 98.0 - + - +
47A GLU* 1.3 59.1 + - + +
49A ILE* 3.6 10.8 + - - +
50A ASP* 3.1 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A TYR* 3.6 32.1 - - + -
43A VAL* 2.9 29.8 + - - +
44A GLU* 3.6 16.9 - - - +
45A TYR 3.1 0.4 - - - -
46A HIS* 1.3 77.0 - - - +
48A SER* 1.3 63.8 + - - +
50A ASP* 3.1 6.5 + - + +
51A GLU* 3.0 26.0 + - - +
130A HIS* 3.2 49.3 - - + +
133A TRP* 4.1 19.1 - - - +
134A LEU* 5.0 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ILE* 2.8 29.2 + - - +
25A TYR* 3.8 13.5 - - - +
26A PHE* 3.6 22.3 - - - +
44A GLU 2.9 11.4 + - - -
45A TYR 3.3 9.9 - - - -
47A GLU* 1.3 75.9 - - - +
49A ILE* 1.3 63.0 + - - +
51A GLU* 3.2 3.8 + - - +
52A MET* 3.0 40.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A TYR* 3.1 47.4 + - + +
46A HIS* 3.8 12.8 - - - +
47A GLU 3.3 0.2 - - - -
48A SER* 1.3 74.8 - - - +
50A ASP* 1.3 63.9 + - - +
52A MET* 3.2 26.4 + - + +
53A LYS* 3.1 37.8 + - - +
200B HEM 3.7 53.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A HIS 3.1 14.8 + - - +
47A GLU* 3.2 10.5 - - - +
48A SER 3.1 0.2 - - - -
49A ILE* 1.3 79.0 - - - +
51A GLU* 1.3 64.7 + - - +
53A LYS* 3.1 29.2 + - - +
54A HIS* 3.1 35.0 + - - -
126A ASP* 3.8 11.1 - - - +
130A HIS* 3.3 30.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A GLU* 2.9 23.0 - - - +
21A ALA* 3.8 20.8 - - + +
22A ILE* 3.6 22.1 - - + +
25A TYR* 3.9 10.1 - - + -
47A GLU 3.0 18.5 + - - +
48A SER 3.9 0.9 - - - +
50A ASP* 1.3 76.2 - - - +
52A MET* 1.3 57.0 + - - +
54A HIS* 2.8 34.4 + - - +
55A ALA* 2.9 27.7 + - - +
94A GLU* 3.6 9.4 - - - +
127A GLU* 2.8 25.9 - - - +
130A HIS* 3.5 13.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ILE* 3.6 14.1 - - + +
26A PHE* 4.6 0.4 - - + -
48A SER* 3.0 36.8 + - - +
49A ILE* 3.4 21.1 - - + +
50A ASP 3.1 0.4 - - - -
51A GLU* 1.3 74.9 - - - +
53A LYS* 1.3 64.4 + - - +
55A ALA* 3.2 3.2 + - - +
56A ASP* 2.9 24.5 + - - +
200B HEM 2.1 117.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ILE* 3.1 32.1 + - + +
50A ASP* 3.1 20.6 + - - +
52A MET* 1.3 75.6 - - + +
54A HIS* 1.3 67.5 + - + +
56A ASP* 3.4 8.7 + - - +
57A ARG* 3.1 29.8 + - - +
200B HEM 5.3 18.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 54 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A GLU* 3.2 18.9 + - + +
50A ASP* 3.1 23.6 + - - -
51A GLU* 2.8 33.5 + - - +
52A MET 3.2 0.2 - - - -
53A LYS* 1.3 79.1 - - + +
55A ALA* 1.3 65.3 + - - +
57A ARG* 3.0 12.9 + - - +
58A TYR* 3.0 27.8 + - - -
123A ILE* 3.7 33.5 - - + +
126A ASP* 2.9 36.8 + - + +
127A GLU* 3.4 13.9 + - - -
130A HIS* 4.7 0.2 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 55 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A LEU* 3.6 23.8 - - + -
18A GLU* 4.3 6.9 - - + +
19A LEU* 4.7 3.6 - - + -
22A ILE* 4.1 11.2 - - + -
51A GLU 2.9 13.2 + - - +
52A MET 3.2 2.7 + - - +
54A HIS* 1.3 75.0 - - - +
56A ASP* 1.3 58.5 + - - +
58A TYR* 3.2 7.5 + - - +
59A ILE* 2.8 36.2 + - - +
200B HEM 3.3 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 56 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A MET 2.9 13.1 + - - +
53A LYS* 3.4 13.5 - - - +
55A ALA* 1.3 76.9 - - - +
57A ARG* 1.3 64.5 + - + +
59A ILE* 3.2 2.2 + - - +
60A GLU* 2.9 29.5 + - - +
26B PHE* 3.3 23.7 - - + -
30B ARG* 2.7 47.0 + - - -
200B HEM 3.7 9.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 57 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A LYS* 3.1 21.0 + - - +
54A HIS* 3.0 17.8 + - - +
56A ASP* 1.3 77.1 - - + +
58A TYR* 1.3 62.1 + - - +
60A GLU* 3.4 9.7 + - - +
61A ARG* 3.0 24.8 + - - +
119A MET* 3.5 55.6 + - + +
122A GLU* 4.2 19.6 - - - +
123A ILE* 3.9 20.7 - - + +
126A ASP* 5.0 4.8 + - - -
125J ARG* 5.2 13.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU* 4.1 30.1 - - + +
14A LEU* 3.6 29.3 - - + +
15A LEU* 3.8 29.2 - - + -
18A GLU* 3.7 26.3 + - + -
54A HIS 3.0 25.4 + - - -
55A ALA* 3.2 5.4 + - - +
57A ARG* 1.3 71.9 - - - +
59A ILE* 1.3 57.7 + - - +
61A ARG* 3.1 3.8 + - - +
62A ILE* 2.7 42.0 + - + +
101A LEU* 3.5 26.9 - - - +
119A MET* 4.4 7.4 - - - -
120A MET* 4.4 7.0 - - + -
123A ILE* 3.6 29.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A LEU* 3.9 23.6 - - + -
55A ALA 2.8 29.1 + - - +
56A ASP* 3.6 3.8 - - - +
58A TYR* 1.3 72.9 - - - +
60A GLU* 1.3 63.7 + - - +
62A ILE* 3.5 2.3 + - - +
63A LEU* 3.1 40.8 + - + +
69A PRO* 4.0 15.9 - - + +
71A LEU* 4.1 23.8 - - + -
26B PHE* 3.9 24.2 - - + -
27B LEU* 4.4 8.7 - - + +
30B ARG* 4.1 16.2 - - + -
200B HEM 4.0 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A ASP* 2.9 25.6 + - - +
57A ARG* 3.9 8.3 - - - +
59A ILE* 1.3 76.3 - - - +
61A ARG* 1.3 59.1 + - - +
63A LEU* 3.5 7.2 + - - +
64A PHE* 3.0 26.9 + - - +
30B ARG* 2.9 48.8 + - + +
33B LYS* 3.4 22.4 - - + -
34B ASN* 5.2 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 61 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 5.0 0.4 - - - +
11A LEU* 3.8 20.2 - - + -
57A ARG 3.0 18.0 + - - +
58A TYR* 3.1 3.6 + - - +
60A GLU* 1.3 75.6 - - - +
62A ILE* 1.3 66.2 + - - +
64A PHE* 3.0 29.7 + - - +
65A LEU* 2.9 40.1 + - + +
113A ASP* 2.8 28.5 + - - -
115A VAL* 3.2 19.9 - - - +
116A SER* 2.9 18.7 + - - +
119A MET* 3.6 29.1 - - + +
128J GLU* 2.7 31.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 62 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ILE* 4.0 12.6 - - + +
11A LEU* 3.6 26.7 - - + +
12A ASN* 3.2 43.7 - - - +
15A LEU* 4.3 8.7 - - + -
58A TYR 2.7 24.9 + - - +
59A ILE 3.8 4.0 - - - +
61A ARG* 1.3 70.6 - - - +
63A LEU* 1.3 61.2 + - - +
65A LEU* 3.2 6.9 + - - +
66A GLU 3.0 5.0 + - - -
67A GLY* 2.8 52.8 + - - +
68A LEU 3.8 1.8 - - - +
69A PRO* 3.7 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 63 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ILE* 3.1 37.3 + - + +
60A GLU* 3.7 6.1 - - - +
62A ILE* 1.3 76.2 - - - +
64A PHE* 1.3 65.3 + - - +
66A GLU* 2.9 15.9 + - - +
67A GLY 3.8 7.6 - - - +
68A LEU* 6.0 1.6 - - + -
69A PRO* 3.4 28.5 - - + -
27B LEU* 4.3 4.0 - - + -
30B ARG* 3.7 33.4 - - + +
31B MET* 3.9 18.8 - - + +
34B ASN* 4.1 25.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 3.3 47.8 + - + -
60A GLU 3.0 16.2 + - - +
61A ARG* 3.0 28.0 + - - +
63A LEU* 1.3 78.6 - - - +
65A LEU* 1.3 63.5 + - + +
66A GLU* 3.1 6.6 + - - +
34B ASN* 3.9 11.4 - - - +
128J GLU* 3.3 43.3 - - + -
131J ILE* 4.4 1.3 - - + -
132J ASP* 3.6 47.8 - - + +
135J GLU* 4.0 12.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 65 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 3.3 18.4 - - + +
2A LYS* 3.8 0.7 - - - +
3A GLY* 3.0 39.2 + - - -
7A VAL* 4.2 6.7 - - + -
8A ILE* 3.7 17.4 - - + +
11A LEU* 3.9 21.3 - - + -
61A ARG* 2.9 34.2 + - - +
62A ILE 3.8 4.5 - - - +
63A LEU 3.2 0.2 - - - -
64A PHE* 1.3 91.4 - - + +
66A GLU* 1.3 67.1 + - - +
67A GLY 3.4 0.6 + - - -
113A ASP* 3.7 21.1 - - - +
116A SER* 3.8 10.3 - - - +
----------------------------------------------------------
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