Contacts of the helix formed by residues 13 - 42 (chain A) in PDB entry 6WYG
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 HIS 13 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ARG* 3.5 3.4 + - - -
11A ASN 4.0 3.0 + - - -
12A TYR* 1.3 76.9 - - - +
14A GLN* 1.3 73.7 + - + +
15A ASP* 2.9 51.8 + - - +
16A SER* 3.1 22.9 + - - +
17A GLU 3.1 10.2 + - - -
124A LYS* 3.0 48.1 + - + -
126A ASP* 4.8 1.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 14 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ARG* 3.3 36.9 - - - +
12A TYR 3.8 0.2 + - - -
13A HIS* 1.3 78.3 + - + +
15A ASP* 1.3 63.2 + - - +
17A GLU* 3.3 10.3 + - - +
18A ALA* 3.0 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 15 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A HIS* 2.9 23.5 + - - +
14A GLN* 1.3 78.5 - - - +
16A SER* 1.3 58.6 + - - +
18A ALA* 3.4 6.6 + - - +
19A ALA* 2.9 30.0 + - - +
22A ARG* 4.2 4.3 + - - +
120A LEU* 3.5 24.8 - - + +
124A LYS* 3.4 18.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 16 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A TYR* 4.1 10.3 - - - -
13A HIS* 3.1 24.9 + - - +
15A ASP* 1.3 75.7 - - - +
17A GLU* 1.3 59.6 + - - +
19A ALA* 3.3 3.0 + - - +
20A ILE* 2.8 35.9 + - - +
117A LEU* 5.1 0.2 - - - +
120A LEU* 4.1 18.2 - - - +
121A ALA* 4.7 2.4 - - - -
124A LYS* 4.5 7.6 - - - +
126A ASP* 4.4 4.1 + - - -
129A LEU* 3.8 26.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 17 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ARG* 2.9 30.5 + - - -
12A TYR* 3.6 22.0 + - + -
13A HIS 3.1 10.2 + - - +
14A GLN* 3.3 16.9 + - - +
16A SER* 1.3 74.1 - - - +
18A ALA* 1.3 63.0 + - - +
20A ILE 3.2 1.4 + - - -
21A ASN* 3.0 23.0 + - - +
73A GLN* 3.1 31.2 + - - +
78A GLY* 4.0 0.7 - - - -
79A ARG* 3.1 35.5 + - - +
81A PHE* 5.0 4.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 18 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A GLN 3.0 16.8 + - - +
15A ASP* 3.7 6.1 - - - +
17A GLU* 1.3 77.5 - - - +
19A ALA* 1.3 63.8 + - - +
21A ASN* 3.2 12.1 + - - +
22A ARG* 3.0 40.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 19 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ASP 2.9 17.9 + - - +
16A SER 3.7 3.6 - - - +
18A ALA* 1.3 75.3 - - - +
20A ILE* 1.3 57.8 + - - +
22A ARG* 3.2 28.3 + - - +
23A GLN* 2.9 30.0 + - - +
117A LEU* 3.9 22.0 - - + +
120A LEU* 3.9 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 20 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A TYR* 3.4 16.6 - - - +
16A SER 2.8 21.9 + - - +
17A GLU 3.5 4.9 - - - +
18A ALA 3.2 0.2 - - - -
19A ALA* 1.3 75.9 - - - +
21A ASN* 1.3 57.2 + - - +
23A GLN* 3.2 2.8 + - - +
24A ILE* 2.9 31.7 + - + +
69A LEU* 3.9 32.5 - - + +
72A LEU* 4.1 10.5 - - + -
73A GLN* 3.8 22.2 - - + +
117A LEU* 3.5 26.2 - - + -
129A LEU* 3.8 25.6 - - + -
133A ILE* 5.4 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 21 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A GLU* 3.0 19.8 + - - +
18A ALA* 3.5 9.8 - - - +
20A ILE* 1.3 73.2 - - - +
22A ARG* 1.3 65.5 + - + +
24A ILE* 3.3 13.9 + - - +
25A ASN* 3.0 21.8 + - - +
73A GLN* 2.9 25.1 + - - +
79A ARG 3.5 12.7 + - - -
80A ILE* 3.5 4.0 - - - +
81A PHE* 3.1 48.5 + - + +
83A GLN* 6.0 1.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 22 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ASP* 4.2 5.5 + - - +
18A ALA* 3.0 25.6 + - - +
19A ALA* 3.2 46.9 + - - +
21A ASN* 1.3 76.7 - - + +
23A GLN* 1.3 57.2 + - - +
25A ASN* 3.3 7.7 + - - +
26A LEU* 2.9 27.5 + - - +
113A SER* 5.9 0.4 - - - +
120A LEU* 5.5 3.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 23 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ALA 2.9 16.7 + - - +
20A ILE* 3.7 4.3 - - - +
21A ASN 3.2 0.2 - - - -
22A ARG* 1.3 73.2 - - - +
24A ILE* 1.3 62.4 + - - +
26A LEU* 3.1 8.9 + - - +
27A GLU* 2.9 55.6 + - - +
69A LEU* 3.5 22.4 - - + -
110A VAL* 3.4 21.0 + - - +
113A SER* 2.5 34.3 + - - +
114A LEU* 3.5 26.6 - - + +
117A LEU* 4.1 15.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 24 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ILE* 2.9 24.6 + - + +
21A ASN* 3.4 25.4 - - - +
23A GLN* 1.3 76.0 - - - +
25A ASN* 1.3 63.5 + - - +
27A GLU* 3.2 3.0 + - - +
28A LEU* 3.0 41.0 + - + +
66A ALA* 4.2 3.1 - - - +
69A LEU* 3.6 30.5 - - + +
70A MET* 3.7 42.2 - - + +
73A GLN* 4.6 2.7 - - + -
80A ILE* 4.6 6.7 - - + -
81A PHE 5.9 1.1 - - - +
82A LEU* 4.0 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 25 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ASN 3.0 12.4 + - - +
22A ARG* 3.6 9.9 - - - +
24A ILE* 1.3 79.0 - - + +
26A LEU* 1.3 58.7 + - - +
28A LEU* 3.3 8.3 + - - +
29A TYR* 2.9 31.7 + - - +
83A GLN* 3.3 35.2 + - + +
84A ASP 2.9 29.8 + - - +
85A ILE* 4.2 8.3 - - - +
86A GLN* 5.4 4.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 26 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ARG 2.9 14.5 + - - +
23A GLN* 3.1 20.2 + - - +
25A ASN* 1.3 78.4 - - - +
27A GLU* 1.3 57.6 + - - +
29A TYR* 3.2 20.5 + - + +
30A ALA* 2.9 27.3 + - - +
106A LEU* 5.8 1.3 - - + -
109A ASN* 4.6 4.5 - - + +
110A VAL* 3.9 28.7 - - + +
113A SER* 3.6 34.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 27 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A GLN* 2.9 42.7 + - - +
24A ILE 3.8 3.8 - - - +
26A LEU* 1.3 72.8 - - - +
28A LEU* 1.3 57.8 + - - +
30A ALA* 3.3 4.4 + - - +
31A SER* 2.9 27.7 + - - -
62A GLU* 2.8 23.5 - - - +
65A HIS* 4.0 8.4 - - - +
66A ALA* 3.9 22.4 - - + +
69A LEU* 3.6 19.3 - - + -
110A VAL* 3.3 10.9 - - - +
114A LEU* 4.3 0.9 - - - +
137A TYR* 4.2 10.9 - - - -
201A FE 2.5 29.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 28 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ILE* 3.0 38.0 + - + +
25A ASN* 3.7 9.0 - - - +
27A GLU* 1.3 76.5 - - - +
29A TYR* 1.3 62.7 + - - +
31A SER* 3.3 8.7 + - - -
32A TYR* 3.0 18.0 + - - +
63A ARG* 5.1 15.3 - - + -
66A ALA* 3.5 21.5 - - + -
67A GLU* 6.2 1.1 - - + -
70A MET* 5.3 5.2 - - - -
82A LEU* 4.5 12.6 - - + -
83A GLN 5.8 0.9 - - - +
85A ILE* 3.6 40.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 29 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ASN* 2.9 21.9 + - - +
26A LEU* 3.2 20.8 + - + +
28A LEU* 1.3 76.7 - - - +
30A ALA* 1.3 60.1 + - - +
32A TYR* 2.9 4.7 + - + +
33A VAL* 2.9 45.8 + - + +
85A ILE* 3.8 11.6 - - + +
86A GLN* 3.3 41.5 - - + +
87A LYS 3.9 12.3 - - - -
89A ASP* 3.4 31.0 + - - -
106A LEU* 3.8 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 30 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A LEU 2.9 13.9 + - - +
27A GLU* 3.6 9.0 - - - +
29A TYR* 1.3 77.3 - - - +
31A SER* 1.3 62.3 + - - +
33A VAL* 3.3 2.9 + - - +
34A TYR* 3.0 31.5 + - + -
62A GLU* 3.8 22.9 - - + +
106A LEU* 3.8 28.5 - - + -
107A GLU* 4.9 0.4 - - - +
110A VAL* 4.6 8.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 31 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A GLU 2.9 14.0 + - - -
28A LEU* 3.3 15.7 - - - -
29A TYR 3.3 0.2 - - - -
30A ALA* 1.3 75.4 - - - +
32A TYR* 1.3 57.9 + - - +
34A TYR 3.3 0.3 + - - -
35A LEU* 3.0 24.5 + - - +
59A SER* 3.0 43.0 + - - +
62A GLU* 3.7 8.1 - - - +
63A ARG* 3.8 21.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 32 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A LEU 3.0 12.0 + - - +
29A TYR* 2.9 10.1 + - - +
31A SER* 1.3 73.9 - - - +
33A VAL* 1.3 66.3 + - - +
35A LEU* 3.1 24.1 + - + +
36A SER* 2.9 24.1 + - - -
85A ILE* 3.8 23.1 - - + -
86A GLN 3.3 20.9 - - - +
87A LYS* 3.7 25.4 - - + +
88A PRO* 4.0 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 33 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A TYR* 2.9 47.9 + - + +
30A ALA 3.3 6.7 + - - +
32A TYR* 1.3 75.6 - - - +
34A TYR* 1.3 63.6 + - + +
36A SER* 3.1 4.7 + - - -
37A MET* 2.9 46.0 + - + +
88A PRO* 3.9 22.0 - - + +
89A ASP 5.5 0.2 - - - +
93A TRP* 4.3 13.2 - - + -
102A ALA* 6.1 2.5 - - + +
103A ALA* 6.0 0.9 - - - -
106A LEU* 4.0 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 34 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ALA 3.0 25.0 + - - +
33A VAL* 1.3 76.4 - - + +
35A LEU* 1.3 57.8 + - - +
37A MET* 3.3 8.8 + - - -
38A SER* 2.9 28.9 + - - -
55A PHE* 3.5 44.2 - + - +
58A GLN* 3.7 29.4 + - + -
59A SER* 3.6 9.4 - - - -
62A GLU* 3.7 27.4 - - + -
103A ALA* 3.8 28.7 + - + +
106A LEU* 4.2 15.7 - - + -
107A GLU* 3.1 36.9 + - - +
148A LEU* 4.2 5.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 35 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A SER 3.0 14.9 + - - +
32A TYR* 3.1 29.1 + - + +
34A TYR* 1.3 72.3 - - - +
36A SER* 1.3 66.0 + - - +
38A SER* 3.3 3.0 + - - -
39A TYR* 3.1 58.3 + - + +
56A LEU* 3.9 14.1 - - + -
59A SER* 3.7 13.4 - - - +
60A HIS* 6.2 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A TYR* 2.9 9.4 + - - -
33A VAL 3.1 8.5 + - - -
35A LEU* 1.3 78.2 - - - +
37A MET* 1.3 57.7 + - - +
39A TYR* 3.4 2.9 + - - +
40A TYR* 2.9 27.2 + - - +
88A PRO* 3.6 25.6 - - - +
90A GLU 3.9 7.3 + - - -
91A ASP* 4.7 5.4 + - - -
93A TRP* 2.9 19.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A VAL* 2.9 32.1 + - - +
34A TYR* 3.8 23.3 - - - +
36A SER* 1.3 71.5 - - - +
38A SER* 1.3 67.3 + - - +
40A TYR* 3.1 1.9 + - - +
41A PHE* 3.0 31.7 + - + -
55A PHE* 3.4 22.9 - - + -
93A TRP* 3.6 37.0 - - + +
99A ALA* 3.0 50.3 - - + +
102A ALA* 4.9 0.4 - - + -
103A ALA* 4.2 6.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A TYR 2.9 18.2 + - - -
35A LEU* 3.6 6.3 - - - -
36A SER 3.2 0.2 - - - -
37A MET* 1.3 76.1 - - - +
39A TYR* 1.3 66.8 + - - +
41A PHE 2.9 17.0 + - - -
42A ASP* 3.3 7.7 + - - +
52A ALA* 2.7 41.4 + - - +
55A PHE* 3.8 7.6 - - - +
56A LEU* 3.5 28.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A LEU* 3.1 42.6 + - + +
36A SER* 4.3 2.5 - - - +
38A SER* 1.3 82.3 - - - +
40A TYR* 1.3 65.5 + - - +
42A ASP* 3.1 38.5 + - + +
43A ARG* 3.5 12.4 + - - +
56A LEU* 4.0 23.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 40 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A SER 2.9 8.3 + - - +
37A MET 3.1 7.1 + - - +
39A TYR* 1.3 77.3 - - - +
41A PHE* 1.3 94.8 + + - +
42A ASP 3.2 1.3 + - - -
43A ARG* 3.3 53.1 + - - +
46A VAL* 3.7 27.3 - - + +
91A ASP 4.2 4.9 - - - +
92A ASP* 3.2 22.2 + - - -
93A TRP* 3.5 38.8 - + + -
94A GLU* 3.0 40.2 + - - -
95A SER* 4.2 2.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 41 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A MET* 3.0 24.8 + - + -
38A SER 2.9 9.7 + - - +
40A TYR* 1.3 95.8 - + - +
42A ASP* 1.3 56.5 + - - +
43A ARG 3.4 0.4 - - - -
46A VAL* 3.6 17.9 - - + -
47A ALA* 3.3 7.1 + - - -
48A LEU* 3.0 40.4 + - + +
49A LYS* 5.1 0.5 - - - -
51A PHE* 3.6 16.4 - + + -
52A ALA* 3.7 19.2 - - - +
55A PHE* 3.5 24.7 - + - -
95A SER* 3.4 9.2 - - - -
96A GLY* 3.6 25.1 - - - -
99A ALA* 3.4 34.3 - - + -
----------------------------------------------------------
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 SER 3.3 8.3 + - - +
39A TYR* 3.1 38.1 + - + +
41A PHE* 1.3 73.8 - - - +
43A ARG* 1.3 66.5 + - - +
47A ALA* 4.8 1.3 - - - +
49A LYS* 6.3 0.7 - - - +
52A ALA* 4.6 8.5 - - + -
146C LYS* 2.9 29.4 + - - -
150C ASP* 5.4 0.2 - - - +
----------------------------------------------------------
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