Contacts of the helix formed by residues 37 - 65 (chain K) 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 K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140G LEU* 3.8 17.7 - - + -
143G LYS* 6.0 4.0 - - + +
32K PHE* 2.8 25.0 + - + +
35K TRP* 3.7 34.1 - - + +
36K GLY* 1.3 75.8 - - - +
38K LYS* 1.3 65.0 + - - +
39K ARG 2.9 5.0 + - - -
40K LEU* 3.0 17.2 + - + +
41K ASN* 3.2 8.3 + - - +
83K VAL* 3.9 27.8 - - + -
150K LEU* 4.0 31.6 - - + +
153K GLN* 3.2 21.5 - - + -
154K ILE* 5.1 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 38 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39G ARG* 5.5 3.2 - - - +
157G GLU* 2.8 41.2 + - - -
33K LYS* 5.4 4.0 - - + +
36K GLY* 2.9 17.9 + - - +
37K LEU* 1.3 69.6 - - - +
39K ARG* 1.3 57.2 + - - +
41K ASN* 3.3 10.5 + - - +
42K ASP* 3.0 35.6 + - - +
153K GLN 3.0 2.4 + - - +
154K ILE* 3.3 27.8 + - - +
155K ARG* 4.5 0.2 - - - +
156K GLU* 3.9 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 39 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38J LYS* 5.4 3.0 - - - +
154J ILE* 3.1 38.0 + - - +
155J ARG* 3.5 26.0 - - - +
37K LEU 2.9 0.4 + - - -
38K LYS* 1.3 75.0 - - - +
40K LEU* 1.3 62.5 + - - +
42K ASP* 3.4 9.4 + - + +
43K VAL* 3.1 34.0 + - - +
133K TRP* 4.2 14.5 - - - +
137K GLU* 3.3 35.3 + - - -
140K LEU* 5.5 1.4 - - - +
152K ALA 4.5 2.0 + - - -
153K GLN* 3.0 37.5 + - - +
155K ARG 3.6 6.7 - - - +
156K GLU* 4.6 0.7 - - - +
157K GLU* 4.1 27.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 40 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32K PHE* 3.6 42.1 - - + -
37K LEU* 3.0 15.1 + - + +
39K ARG* 1.3 84.3 - - - +
41K ASN* 1.3 61.2 + - - +
43K VAL* 4.1 2.9 - - - +
44K GLU* 3.0 35.8 + - - +
83K VAL* 4.1 17.0 - - + -
87K LEU* 5.1 2.7 - - + -
133K TRP* 4.2 20.0 - - + -
149K TYR* 3.5 19.5 - - + +
153K GLN* 3.3 41.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 41 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29K ALA* 3.0 36.1 - - - +
30K ARG* 3.4 27.3 + - - +
32K PHE* 3.9 1.2 - - - +
33K LYS* 3.5 35.2 - - + +
37K LEU 3.2 7.2 + - - +
38K LYS* 3.5 11.3 + - - +
39K ARG 3.2 0.2 - - - -
40K LEU* 1.3 75.1 - - - +
42K ASP* 1.3 80.0 + - - +
45K TYR* 3.0 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 42 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38K LYS* 3.0 18.4 + - - +
39K ARG* 3.7 7.5 - - + +
40K LEU 3.4 0.2 - - - -
41K ASN* 1.3 87.2 + - - +
43K VAL* 1.3 64.4 + - + +
45K TYR* 3.7 3.3 - - - +
46K HIS* 2.7 42.7 + - + +
156K GLU* 3.0 42.5 - - - +
157K GLU 4.7 2.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 43 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39K ARG* 3.1 26.4 + - - +
40K LEU 4.3 1.1 - - - +
42K ASP* 1.3 77.1 - - + +
44K GLU* 1.3 58.8 + - - +
46K HIS* 3.0 10.1 + - + +
47K GLU* 2.9 36.5 + - - +
133K TRP* 3.5 54.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 44 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25K TYR* 3.4 31.0 - - - +
28K HIS* 3.1 19.4 - - - +
29K ALA* 3.9 10.1 - - + -
32K PHE* 3.9 17.3 - - + -
40K LEU 3.0 18.3 + - - +
43K VAL* 1.3 73.3 - - - +
45K TYR* 1.3 66.2 + - - +
47K GLU* 3.1 10.1 + - - +
48K SER* 2.9 22.3 + - - -
87K LEU* 3.8 6.7 - - - +
90K ASP* 2.9 27.6 - - - +
133K TRP* 3.7 26.2 - - + -
134K LEU* 4.0 2.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 45 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26K PHE* 3.6 31.0 - + - -
29K ALA* 3.6 11.3 - - + +
30K ARG* 3.3 29.2 - - - +
41K ASN* 3.0 21.7 + - - +
42K ASP* 3.7 4.0 - - - +
44K GLU* 1.3 76.1 - - - +
46K HIS* 1.3 85.6 + + - +
48K SER* 3.0 16.7 + - - -
49K ILE* 3.1 32.4 + - + +
200L HEM 3.4 35.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 46 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42K ASP* 2.7 34.2 + - + +
43K VAL* 3.0 10.9 + - + +
45K TYR* 1.3 99.7 - + - +
47K GLU* 1.3 57.2 + - + +
49K ILE* 3.6 10.4 + - - +
50K ASP* 3.1 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 47 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25K TYR* 3.6 32.7 + - + -
43K VAL* 2.9 31.7 + - + +
44K GLU* 3.6 16.2 - - - +
45K TYR 3.1 0.4 - - - -
46K HIS* 1.3 76.6 - - + +
48K SER* 1.3 63.5 + - - +
50K ASP* 3.1 5.4 + - - +
51K GLU* 3.0 27.2 + - - +
130K HIS* 3.2 48.7 - - + +
133K TRP* 4.1 16.2 - - - +
134K LEU* 5.0 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 48 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22K ILE* 2.8 28.9 + - - +
25K TYR* 3.9 13.3 - - - +
26K PHE* 3.6 22.0 - - - +
44K GLU 2.9 13.0 + - - -
45K TYR* 3.3 9.6 - - - -
47K GLU* 1.3 73.2 - - - +
49K ILE* 1.3 65.5 + - - +
51K GLU* 3.2 4.0 + - - +
52K MET* 3.0 39.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 49 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45K TYR* 3.1 49.3 + - + +
46K HIS* 3.8 13.7 - - - +
47K GLU 3.3 0.2 - - - -
48K SER* 1.3 74.8 - - - +
50K ASP* 1.3 63.2 + - - +
52K MET* 3.2 26.8 + - + +
53K LYS* 3.1 36.1 + - - +
200L HEM 3.8 51.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 50 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46K HIS 3.1 15.6 + - - +
47K GLU 3.2 11.0 - - - +
48K SER 3.1 0.2 - - - -
49K ILE* 1.3 77.2 - - - +
51K GLU* 1.3 63.5 + - - +
53K LYS* 3.1 29.7 + - - +
54K HIS* 3.1 34.9 + - - -
126K ASP* 3.8 11.1 - - - +
130K HIS* 3.3 31.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 51 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18K GLU* 2.9 23.6 - - - +
21K ALA* 3.9 20.3 - - + +
22K ILE* 3.6 22.5 - - + +
25K TYR* 3.9 10.8 - - + -
47K GLU 3.0 18.6 + - - +
48K SER 3.2 1.3 + - - +
50K ASP* 1.3 77.0 - - - +
52K MET* 1.3 57.6 + - - +
54K HIS* 2.8 35.9 + - - +
55K ALA* 3.0 27.0 + - - +
94K GLU* 3.6 8.8 - - - +
127K GLU* 2.7 27.5 - - - +
130K HIS* 3.5 11.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 52 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22K ILE* 3.6 14.1 - - + +
26K PHE* 4.6 0.4 - - + -
48K SER* 3.0 37.1 + - - +
49K ILE* 3.4 20.4 - - + +
51K GLU* 1.3 74.5 - - - +
53K LYS* 1.3 64.9 + - - +
55K ALA* 3.2 2.8 + - - +
56K ASP* 2.9 24.9 + - - +
200L HEM 2.1 118.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 53 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49K ILE* 3.1 33.6 + - + +
50K ASP* 3.1 21.1 + - - +
52K MET* 1.3 75.2 - - - +
54K HIS* 1.3 67.2 + - + +
56K ASP* 3.4 9.2 + - - +
57K ARG* 3.1 30.1 + - - +
200L HEM 5.2 19.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 54 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18K GLU* 3.3 19.4 + - + +
50K ASP* 3.1 24.8 + - - -
51K GLU* 2.8 33.2 + - - +
52K MET 3.2 0.2 - - - -
53K LYS* 1.3 77.9 - - + +
55K ALA* 1.3 65.6 + - - +
57K ARG* 3.0 12.8 + - - +
58K TYR* 3.0 29.1 + - - -
123K ILE* 3.7 34.0 - - + +
126K ASP* 2.9 36.7 + - + +
127K GLU* 3.4 13.9 + - - -
130K HIS* 4.7 0.2 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 55 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15K LEU* 3.6 23.1 - - + +
18K GLU* 4.3 6.9 - - + +
19K LEU* 4.7 2.5 - - + -
22K ILE* 4.1 11.2 - - + -
51K GLU 3.0 13.8 + - - +
52K MET 3.2 3.3 + - - +
54K HIS* 1.3 75.5 - - - +
56K ASP* 1.3 58.2 + - - +
58K TYR* 3.2 6.6 + - - +
59K ILE* 2.8 36.6 + - - +
200L HEM 3.3 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 56 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52K MET 2.9 12.2 + - - +
53K LYS* 3.4 13.6 - - - +
55K ALA* 1.3 76.4 - - - +
57K ARG* 1.3 66.1 + - + +
59K ILE* 3.2 2.2 + - - +
60K GLU* 2.9 29.5 + - - +
26L PHE* 3.3 23.0 - - + -
30L ARG* 2.7 47.7 + - - -
200L HEM 3.8 10.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 57 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125F ARG* 5.2 12.7 - - - +
53K LYS* 3.1 19.9 + - - +
54K HIS* 3.0 17.0 + - - +
56K ASP* 1.3 78.6 - - + +
58K TYR* 1.3 60.7 - - - +
60K GLU* 3.4 9.5 + - - +
61K ARG* 3.0 25.3 + - - +
119K MET* 3.6 56.0 + - + +
122K GLU* 4.2 19.2 - - - +
123K ILE* 3.8 21.7 - - + +
126K ASP* 5.0 4.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 58 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11K LEU* 4.1 30.3 - - + +
14K LEU* 3.6 29.7 - - + +
15K LEU* 3.8 29.2 - - + -
18K GLU* 3.7 25.0 + - + -
54K HIS 3.0 25.0 + - - -
55K ALA* 3.6 5.6 - - - +
57K ARG* 1.3 73.2 - - - +
59K ILE* 1.3 55.6 + - - +
61K ARG* 3.1 4.2 + - - +
62K ILE* 2.7 42.2 + - + +
101K LEU* 3.5 27.4 - - - +
119K MET* 4.4 7.4 - - - -
120K MET* 4.4 6.9 - - + +
123K ILE* 3.6 30.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 59 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15K LEU* 3.9 23.1 - - + -
55K ALA 2.8 23.8 + - - +
56K ASP* 3.6 4.3 - - - +
58K TYR* 1.3 72.3 - - - +
60K GLU* 1.3 64.0 + - - +
62K ILE* 3.8 2.6 - - - +
63K LEU* 3.1 41.4 + - + +
69K PRO* 4.0 14.5 - - + +
71K LEU* 4.1 23.3 - - + -
26L PHE* 3.9 14.1 - - + -
27L LEU* 4.4 8.7 - - + +
30L ARG* 4.1 16.8 - - + -
200L HEM 3.9 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 60 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56K ASP* 2.9 24.8 + - - +
57K ARG* 3.9 8.9 - - - +
59K ILE* 1.3 76.4 - - - +
61K ARG* 1.3 58.4 + - - +
63K LEU* 3.5 7.8 + - + +
64K PHE* 3.0 27.0 + - - +
30L ARG* 2.9 48.4 + - + +
33L LYS* 3.4 21.8 - - + -
34L ASN* 5.2 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 61 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128F GLU* 2.7 27.1 + - - +
1K MET* 5.0 0.4 - - - +
11K LEU* 3.8 20.9 - - + -
57K ARG 3.0 18.3 + - - +
58K TYR 3.6 3.4 - - - +
60K GLU* 1.3 75.8 - - - +
62K ILE* 1.4 60.5 + - - +
64K PHE* 3.0 24.9 + - - +
65K LEU* 2.8 52.2 + - + +
113K ASP* 2.8 28.3 + - - -
115K VAL* 3.2 24.7 - - - +
116K SER* 2.9 18.3 + - - +
119K MET* 3.6 29.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 62 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8K ILE* 4.0 11.9 - - + +
11K LEU* 3.6 26.0 - - + +
12K ASN* 3.2 43.3 - - - +
15K LEU* 4.3 8.7 - - + -
58K TYR 2.7 25.2 + - - +
59K ILE 3.8 3.8 - - - +
61K ARG* 1.4 71.8 - - - +
63K LEU* 1.3 60.8 + - - +
65K LEU* 3.2 7.6 + - - +
66K GLU 3.0 5.4 + - - -
67K GLY* 2.8 52.2 + - - +
68K LEU 3.8 2.7 - - - +
69K PRO* 3.7 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 63 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59K ILE* 3.1 37.3 + - + +
60K GLU* 3.7 6.5 - - - +
61K ARG 3.1 0.2 - - - -
62K ILE* 1.3 73.3 - - - +
64K PHE* 1.3 68.6 + - - +
66K GLU* 3.0 16.5 + - - +
67K GLY 3.8 7.4 - - - +
68K LEU* 6.0 1.3 - - + -
69K PRO* 3.4 29.2 - - + -
27L LEU* 4.2 4.0 - - + -
30L ARG* 3.7 33.4 - - + +
31L MET* 3.9 20.2 - - + +
34L ASN* 4.1 24.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 64 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128F GLU* 3.4 43.3 - - + -
131F ILE* 4.4 1.8 - - + -
132F ASP* 3.6 46.7 - - + +
135F GLU* 4.0 13.2 - - - -
1K MET* 3.3 50.7 + - + +
60K GLU 3.0 18.6 + - - +
61K ARG* 3.0 24.8 + - - +
63K LEU* 1.3 77.8 - - - +
65K LEU* 1.3 64.4 + - + +
66K GLU* 3.1 7.1 + - - +
34L ASN* 3.9 11.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 65 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1K MET* 3.3 18.4 - - + +
2K LYS* 3.8 0.7 - - - +
3K GLY* 3.0 39.0 + - - -
7K VAL* 4.2 6.1 - - + -
8K ILE* 3.6 17.9 - - + +
11K LEU* 3.9 20.9 - - + -
61K ARG* 2.8 33.3 + - - +
62K ILE 3.7 4.7 - - - +
63K LEU 3.2 0.2 - - - -
64K PHE* 1.3 92.6 - - + +
66K GLU* 1.3 66.3 + - - +
67K GLY 3.4 1.0 + - - -
113K ASP* 3.7 21.8 - - - +
116K 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