Contacts of the helix formed by residues 34 - 63 (chain A) in PDB entry 1JI5
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 GLN 34 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A VAL* 5.3 0.7 - - - -
31A LYS 5.3 1.1 - - - -
32A GLY 3.0 1.0 - - - -
33A PRO* 1.3 90.0 - - + +
35A PHE* 1.3 54.3 + - - +
36A PHE 3.5 1.8 - - - -
37A THR* 3.4 22.2 + - - +
38A LEU* 2.7 53.4 + - + +
89A ALA* 5.2 9.2 - - + -
90A GLU* 5.4 9.0 - - - +
143A PHE* 3.6 31.3 - - + -
34C GLN* 3.7 17.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 35 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A HIS 5.0 0.9 - - - -
28A TRP 5.3 0.7 - - - -
30A VAL* 3.4 46.6 - - + +
31A LYS 4.8 0.9 - - - -
32A GLY* 3.1 20.2 + - - +
33A PRO 3.3 1.2 - - - -
34A GLN* 1.3 78.0 - - - +
36A PHE* 1.3 85.1 + + - +
38A LEU* 3.8 0.2 - - - +
39A HIS* 2.5 62.2 + + + +
138C TRP* 4.0 14.4 - + - -
139C MET* 3.5 53.8 - - + -
142C ALA* 3.9 14.1 - - + -
143C PHE* 4.1 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A PRO 5.4 0.4 + - - -
34A GLN 3.5 0.2 - - - -
35A PHE* 1.3 99.1 - + - +
37A THR* 1.3 66.5 + - + +
39A HIS* 3.7 6.6 - + - +
40A GLU* 3.1 27.4 + - - +
37C THR* 4.7 14.6 - - - +
38C LEU* 5.0 7.6 - - + -
41C LYS* 3.5 49.4 - - + -
139C MET* 3.7 24.0 - - + -
140C LEU* 4.0 22.9 - - + -
143C PHE* 4.0 31.2 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A PRO 4.8 3.4 - - - +
34A GLN* 3.9 28.5 + - - +
35A PHE 3.3 0.2 - - - -
36A PHE* 1.3 78.0 - - + +
38A LEU* 1.3 69.6 + - - +
40A GLU* 3.5 7.4 - - - +
41A LYS* 3.0 25.8 + - - +
143A PHE* 5.1 2.4 - - - -
34C GLN* 5.5 0.4 - - - +
37C THR* 4.7 22.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A VAL* 4.0 20.9 - - + -
34A GLN* 2.7 53.7 + - + +
35A PHE 3.8 0.7 - - - +
37A THR* 1.3 77.8 + - - +
39A HIS* 1.3 65.7 + - - +
40A GLU 3.0 2.2 - - - -
41A LYS* 4.2 14.4 - - + +
42A PHE* 3.0 43.2 + - + -
89A ALA* 5.3 4.3 - - + +
93A VAL* 4.0 26.2 - - + -
140A LEU* 6.0 3.1 - - + -
143A PHE* 3.4 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A HIS* 2.7 78.1 + + - -
30A VAL* 4.0 8.6 - - - +
35A PHE* 2.5 49.5 + + + +
36A PHE* 3.7 9.0 - + - +
38A LEU* 1.3 72.3 - - - +
40A GLU* 1.3 65.5 + - + +
42A PHE* 3.8 1.9 + - - +
43A GLU* 3.5 4.5 + - - -
58B GLU* 3.1 22.3 + - - -
151B FE 4.1 0.8 - - - -
135C LYS* 6.3 0.2 - - - -
138C TRP* 3.9 17.1 - + - -
139C MET* 4.9 9.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 40 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A PHE 3.1 16.2 + - - +
37A THR* 3.5 6.7 - - - +
38A LEU 3.0 0.4 - - - -
39A HIS* 1.3 81.8 - - + +
41A LYS* 1.3 68.7 + - - +
43A GLU* 2.9 21.3 + - + +
44A GLU* 3.1 14.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 41 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A THR 3.0 14.4 + - - +
38A LEU* 3.3 18.8 + - + +
40A GLU* 1.3 78.5 - - - +
42A PHE* 1.3 67.7 + - + +
44A GLU* 3.0 45.2 + - - +
45A LEU* 2.9 35.5 + - + +
136A HIS* 4.3 9.3 - - - -
139A MET* 3.3 32.8 - - - +
140A LEU* 5.1 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LEU* 3.7 32.5 - - + +
26A PHE* 3.4 45.5 - + + -
27A HIS* 3.7 9.0 - - - -
30A VAL* 4.1 15.0 - - + -
38A LEU* 3.0 45.3 + - + +
39A HIS 4.1 0.4 - - - +
41A LYS* 1.3 77.8 - - + +
43A GLU* 1.3 58.0 + - - +
45A LEU* 3.1 14.6 + - + +
46A TYR* 2.8 32.4 + - - +
89A ALA 4.8 0.7 - - - -
92A MET* 3.7 22.7 - - + -
93A VAL* 4.4 8.1 - - + -
96A ILE* 4.5 17.7 - - + -
140A LEU* 6.3 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A HIS* 3.7 22.9 - - + -
39A HIS* 3.5 4.9 + - - +
40A GLU* 2.9 12.7 + - - +
42A PHE* 1.3 78.3 - - - +
44A GLU* 1.3 57.8 + - - +
46A TYR* 3.2 39.7 + - + +
47A THR* 2.6 40.1 + - - +
54B ASP* 4.6 4.9 - - - +
151B FE 4.6 0.7 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
40A GLU* 3.1 11.6 + - + +
41A LYS* 3.0 53.6 + - - +
43A GLU* 1.3 77.2 - - - +
45A LEU* 1.3 61.9 + - + +
47A THR* 3.3 7.5 + - - -
48A GLU* 3.1 37.6 + - + +
136A HIS* 4.2 8.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A TRP* 5.5 0.5 - - - -
23A LEU* 3.5 15.8 - - + +
41A LYS* 2.9 36.0 + - + +
42A PHE* 3.1 21.5 + - + +
44A GLU* 1.3 81.3 - - + +
46A TYR* 1.3 59.3 + - - +
48A GLU* 3.2 9.7 + - - +
49A SER* 2.8 26.0 + - - -
96A ILE* 4.9 7.2 - - + -
100A TYR* 3.1 29.9 + - + +
136A HIS* 3.5 38.1 - - + +
140A LEU* 5.1 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A PHE* 3.6 18.1 - + + +
23A LEU* 3.4 29.6 - - + +
24A HIS* 3.4 37.6 + + + +
27A HIS* 3.7 30.6 + + + -
42A PHE 2.8 25.1 + - - -
43A GLU* 3.2 48.3 + - + -
45A LEU* 1.3 69.3 - - - +
47A THR* 1.3 74.1 + - - +
49A SER* 2.6 24.1 + - - +
50A ALA* 3.0 10.9 + - - +
54B ASP* 3.9 12.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A GLU* 2.6 28.1 + - - +
44A GLU* 3.4 8.4 - - - +
46A TYR* 1.3 87.9 - - - +
48A GLU* 1.3 64.1 - - + +
50A ALA* 3.2 8.7 + - - +
51A THR* 3.1 22.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A TRP* 6.2 0.7 - - + -
44A GLU* 3.1 25.4 + - + +
45A LEU* 3.4 14.7 - - - +
47A THR* 1.3 74.7 - - + +
49A SER* 1.3 66.5 + - - +
51A THR* 2.9 21.3 + - - -
52A HIS* 3.1 19.4 + - + +
100A TYR* 5.1 1.4 + - - +
132A GLU* 3.4 31.4 - - - +
136A HIS* 2.7 37.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A TRP* 3.7 39.5 - - - +
20A PHE* 3.5 18.4 - - - +
23A LEU* 4.2 8.1 - - - -
45A LEU 2.8 15.1 + - - -
46A TYR* 2.6 25.0 + - - -
48A GLU* 1.3 75.0 - - - +
50A ALA* 1.3 65.8 + - - +
52A HIS* 3.0 16.6 + - - +
53A ILE* 3.0 18.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A PHE* 4.0 17.3 - - + -
46A TYR 3.0 9.1 + - - +
47A THR* 3.4 11.2 - - - +
48A GLU 3.2 0.2 - - - -
49A SER* 1.3 81.3 + - - +
51A THR* 1.3 64.0 + - - +
53A ILE* 3.3 22.4 + - - +
54A ASP* 3.3 13.0 + - - +
20B PHE* 4.7 9.0 - - + -
24B HIS* 5.1 3.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A THR* 3.1 15.9 + - - +
48A GLU* 2.9 14.5 + - - -
50A ALA* 1.3 76.7 - - - +
52A HIS* 1.3 66.9 + - + +
54A ASP* 3.1 7.6 + - - +
55A GLU* 3.0 51.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A TRP* 3.6 47.7 - + + +
48A GLU* 3.2 24.2 + - + -
49A SER* 3.0 6.7 + - - +
51A THR* 1.3 79.4 - - + +
53A ILE* 1.3 64.3 + - - +
54A ASP 3.1 0.3 + - - -
55A GLU* 3.2 18.1 + - - -
56A ILE* 2.9 35.9 + - + +
129A ILE* 3.9 26.5 - - + +
132A GLU* 2.7 41.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A VAL* 4.4 11.5 - - + +
16A TRP* 3.7 22.2 - - + +
17A SER* 3.7 22.0 - - - +
20A PHE* 4.3 9.4 - - + -
49A SER 3.0 19.1 + - - +
50A ALA* 3.5 17.3 - - - +
51A THR 3.3 0.2 - - - -
52A HIS* 1.3 76.2 - - - +
54A ASP* 1.3 59.3 + - - +
56A ILE* 4.4 2.9 - - - +
57A ALA* 3.2 24.8 + - - +
20B PHE* 4.7 3.6 - - + -
24B HIS* 4.2 10.8 - - + +
28B TRP* 3.7 23.8 - - + -
2001B MPD 3.4 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 54 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ALA 3.3 7.0 + - - +
51A THR* 3.1 7.7 + - - +
52A HIS 3.1 0.6 - - - -
53A ILE* 1.3 78.3 - - - +
55A GLU* 1.3 60.8 + - + +
58A GLU* 2.8 43.5 + - - +
152A FE 2.1 28.9 - - - -
24B HIS* 4.4 5.1 - - + +
27B HIS* 3.3 5.4 - - - -
28B TRP* 2.7 35.3 + - + -
43B GLU* 4.5 3.8 - - - +
46B TYR* 3.9 12.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 55 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A THR* 3.0 34.9 + - + +
52A HIS* 3.8 23.6 + - - +
54A ASP* 1.3 76.5 - - + +
56A ILE* 1.3 55.3 + - + +
58A GLU* 3.2 7.3 + - - +
59A ARG* 2.7 36.5 + - - +
125A LEU* 4.2 24.4 - - + +
129A ILE* 5.5 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 56 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LEU* 3.4 45.5 - - + +
12A GLN* 3.6 20.0 - - + +
13A VAL* 3.7 8.7 - - + +
16A TRP* 3.6 31.2 - - + +
52A HIS* 2.9 20.3 + - + +
53A ILE* 5.1 0.7 - - - -
55A GLU* 1.3 76.8 - - + +
57A ALA* 1.3 56.2 + - - +
59A ARG* 2.7 27.1 + - - +
60A ILE* 2.9 16.9 + - - +
125A LEU* 4.3 10.8 - - + -
126A LEU* 5.8 1.8 - - + -
129A ILE* 4.1 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 57 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A VAL* 4.2 9.1 - - + +
53A ILE 3.2 19.8 + - - +
54A ASP 3.7 0.4 - - - +
56A ILE* 1.3 78.6 - - - +
58A GLU* 1.3 59.0 + - - +
60A ILE* 3.2 7.1 + - - +
61A LEU* 2.8 30.2 + - - +
67A PRO* 4.1 17.0 - - + +
28B TRP* 3.3 38.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A ASP* 2.8 37.1 + - - +
55A GLU* 3.4 5.9 - - - +
57A ALA* 1.3 75.2 - - - +
59A ARG* 1.3 57.2 + - - +
61A LEU* 3.6 16.4 - - + +
62A ALA* 3.0 25.8 + - - +
152A FE 2.4 27.7 - - - -
27B HIS* 3.3 1.6 + - - -
28B TRP* 4.0 8.9 - - + +
39B HIS* 3.3 24.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LEU* 3.9 16.2 - - + -
55A GLU 2.7 16.5 + - - +
56A ILE* 2.7 13.0 + - - +
58A GLU* 1.3 72.5 - - - +
60A ILE* 1.3 59.0 + - - +
61A LEU 3.0 0.9 - - - -
62A ALA* 2.8 35.3 + - - +
63A ILE* 3.0 34.3 + - + +
119A ASP* 3.2 13.5 + - - -
121A MET* 2.9 37.7 - - - +
122A THR* 3.1 18.8 + - + +
125A LEU* 3.7 26.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ILE* 4.3 9.2 - - + +
9A LEU* 3.2 36.6 - - + -
10A ASN* 3.5 19.5 - - - +
13A VAL* 5.3 0.9 - - + -
56A ILE* 3.0 17.9 - - + +
57A ALA* 3.3 7.6 - - - +
59A ARG* 1.3 75.5 - - - +
61A LEU* 1.3 59.9 + - - +
63A ILE* 3.1 22.2 + - + +
65A GLY 2.7 33.1 + - - -
66A LYS 3.6 4.9 - - - +
67A PRO* 3.0 48.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 61 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A ALA 2.8 14.5 + - - +
58A GLU* 3.6 19.3 - - + +
60A ILE* 1.3 80.8 - - - +
62A ALA* 1.3 58.2 + - - +
63A ILE 3.6 0.2 + - - -
64A GLY* 3.7 8.7 + - - -
65A GLY 3.8 9.7 - - - +
66A LYS* 6.0 0.7 - - - -
67A PRO* 3.4 25.4 - - + -
28B TRP* 3.4 49.8 - - + +
29B TYR* 4.8 8.5 - - + -
31B LYS* 5.8 4.3 - - - +
39B HIS* 6.3 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 62 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A GLU 3.0 14.6 + - - +
59A ARG* 2.8 27.9 + - - +
61A LEU* 1.3 77.7 - - - +
63A ILE* 1.3 58.8 + - - +
64A GLY 3.3 2.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 63 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A GLN* 5.8 2.5 + - - +
5A VAL* 4.8 5.4 - - + -
6A ILE* 4.1 25.3 - - + +
9A LEU* 4.0 17.5 - - + -
59A ARG* 3.4 41.1 - - - +
60A ILE* 3.1 28.7 - - + +
62A ALA* 1.3 79.8 - - - +
64A GLY* 1.3 58.5 + - - +
65A GLY* 3.3 1.9 + - - +
119A ASP* 4.5 9.4 - - - +
122A THR* 4.5 6.5 - - - +
----------------------------------------------------------
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