Contacts of the helix formed by residues 39 - 67 (chain C) in PDB entry 1QGH
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 PHE 39 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C HIS 4.6 0.9 - - - -
32C TRP 5.4 0.2 - - - -
34C MET* 3.4 42.0 - - + -
36C GLY 2.9 17.2 + - - +
37C HIS 3.2 1.8 - - - -
38C ASN* 1.3 77.6 - - - +
40C PHE* 1.3 79.8 + + - +
43C HIS* 2.8 58.4 + + + +
95C MET* 3.7 10.4 - - + +
144E TRP* 4.0 15.7 - + - -
145E MET* 3.5 49.8 - - + -
148E ALA* 3.6 15.3 - - + -
149E PHE* 4.1 11.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 40 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C HIS 4.8 0.8 + - - -
38C ASN 3.3 1.0 - - - -
39C PHE* 1.3 88.3 - + - +
41C THR* 1.3 63.6 + - + +
43C HIS* 3.6 3.9 - + - +
44C GLU* 3.2 37.6 + - - +
41E THR* 4.0 14.6 - - - +
42E LEU* 3.8 21.8 - - + -
45E LYS* 3.4 37.2 - - + -
145E MET* 3.7 31.9 - - + -
146E PHE* 3.4 45.5 - + - -
149E PHE* 3.8 24.2 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 41 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C HIS 5.1 1.1 - - - +
38C ASN* 3.4 35.0 - - + +
40C PHE* 1.3 73.8 - - + +
42C LEU* 1.3 62.4 + - + +
44C GLU* 3.3 9.5 + - - +
45C LYS* 2.9 27.5 + - - +
149C PHE* 6.4 0.4 - - + -
38E ASN* 6.3 0.4 - - - +
41E THR* 4.7 17.7 + - + +
37L HIS 5.7 1.1 - - - +
40L PHE* 4.0 22.0 - - - +
41L THR* 4.8 19.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 42 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C MET* 3.7 18.6 - - + -
38C ASN* 3.0 29.6 + - + +
41C THR* 1.3 76.7 - - + +
43C HIS* 1.3 67.6 + - - +
45C LYS* 3.6 10.2 - - + +
46C MET* 2.9 29.4 + - + +
95C MET* 3.6 14.8 - - + -
99C MET* 4.1 14.1 - - - -
146C PHE* 4.6 4.3 - - + -
149C PHE* 3.3 35.9 - - + -
40L PHE* 3.8 34.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 43 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A GLU* 3.7 7.3 + - - -
31C HIS* 3.0 80.1 + + - -
34C MET* 3.4 12.4 - - - -
39C PHE* 2.8 41.9 + + + +
40C PHE* 3.6 4.3 - + - +
42C LEU* 1.3 78.4 - - - +
44C GLU* 1.3 71.1 + - + +
46C MET 3.5 0.3 + - - -
47C ASP* 3.5 7.1 + - - +
157C FE 4.0 2.2 - - - -
141E LYS* 5.4 1.4 + - - -
144E TRP* 3.6 28.4 - + - -
145E MET* 4.6 9.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 44 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C PHE* 3.2 31.2 + - - +
41C THR* 3.8 6.7 - - - +
42C LEU 3.1 0.6 - - - -
43C HIS* 1.3 83.6 - - + +
45C LYS* 1.3 65.4 + - - +
47C ASP* 3.0 18.8 + - - +
48C ASP* 3.2 18.8 + - - +
45E LYS* 5.2 8.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 45 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C THR* 2.9 18.5 + - - +
42C LEU* 3.1 13.7 + - + +
44C GLU* 1.3 76.5 - - - +
46C MET* 1.3 67.1 + - + +
48C ASP* 3.1 23.3 + - - +
49C LEU* 3.0 24.8 + - + +
142C HIS* 4.4 9.0 + - - -
145C MET* 3.9 19.8 - - - +
146C PHE* 3.8 26.8 - - + -
40L PHE* 3.5 37.7 - - + -
44L GLU* 5.4 7.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 46 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C ILE* 3.3 16.4 - - + +
30C ILE* 4.2 17.7 - - + -
31C HIS* 3.7 28.3 - - + +
34C MET* 3.8 17.0 - - + -
42C LEU* 2.9 21.2 + - + +
43C HIS 3.7 2.5 - - - +
45C LYS* 1.3 79.9 - - + +
47C ASP* 1.3 67.8 + - - +
49C LEU* 3.8 16.8 - - + -
50C TYR* 2.8 25.8 + - - +
99C MET* 4.4 8.5 - - + -
102C LEU* 4.0 9.4 - - + -
146C PHE* 3.5 38.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 47 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ASP* 4.7 2.0 - - - +
28C HIS* 4.8 8.7 + - - -
31C HIS* 3.4 27.8 + - - -
43C HIS* 3.5 5.9 + - - +
44C GLU* 3.0 14.5 + - - +
46C MET* 1.3 79.3 - - - +
48C ASP* 1.3 66.2 + - - +
50C TYR* 3.3 6.8 + - - +
51C SER* 3.1 27.1 + - - -
157C FE 3.6 13.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 48 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C GLU* 3.2 14.1 + - - +
45C LYS* 3.1 28.1 + - - +
46C MET 3.1 0.4 - - - -
47C ASP* 1.3 79.3 - - - +
49C LEU* 1.3 67.1 + - + +
51C SER* 3.3 7.0 + - - -
52C GLU* 3.0 24.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 49 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C PHE* 5.1 0.7 - - + -
27C ILE* 4.0 13.2 - - + -
45C LYS* 3.0 20.1 + - + +
46C MET* 3.2 22.4 + - + +
48C ASP* 1.3 77.1 - - + +
50C TYR* 1.3 58.8 + - - +
52C GLU* 3.1 3.2 + - - +
53C PHE* 2.8 53.5 + - + +
102C LEU* 3.7 38.4 - - + -
106C LEU* 5.4 2.9 - - + -
142C HIS* 3.6 35.4 - - + +
146C PHE* 4.0 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 50 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ASN* 5.4 0.9 + - - -
24A THR* 5.9 2.6 - - - +
50A TYR* 4.8 15.9 + + - -
54A GLY* 5.7 4.1 - - - -
57A MET* 4.2 8.7 - - - +
24C THR* 3.4 46.3 + - + +
25C VAL* 6.1 0.2 - - + -
27C ILE* 3.9 11.4 - - + +
28C HIS* 2.9 57.0 + + + +
46C MET 2.8 17.1 + - - +
47C ASP* 3.4 10.5 - - - +
49C LEU* 1.3 78.2 - - - +
51C SER* 1.3 70.1 + - - +
53C PHE* 4.3 0.2 - - - -
54C GLY* 3.0 22.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 51 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C ASP 3.1 14.4 + - - -
48C ASP* 3.7 5.8 - - - -
49C LEU 3.2 0.2 - - - -
50C TYR* 1.3 85.4 - - - +
52C GLU* 1.3 64.2 + - - +
54C GLY* 3.3 1.9 + - - -
55C GLU* 2.9 32.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 52 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C ASP 3.0 16.7 + - - +
49C LEU* 3.1 6.0 + - - +
51C SER* 1.3 78.5 - - - +
53C PHE* 1.3 75.9 + - + +
55C GLU* 3.0 20.1 + - - +
56C GLN* 3.0 23.1 + - + +
138C SER* 2.6 29.2 + - - -
142C HIS* 2.8 28.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 53 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C LEU* 4.2 15.6 - - + +
23C PHE* 3.8 33.7 - + + -
24C THR* 4.8 7.4 - - - +
27C ILE* 4.4 6.1 - - + -
49C LEU* 2.8 45.9 + - + +
50C TYR 4.7 0.7 - - - +
52C GLU* 1.3 83.9 - - + +
54C GLY* 1.3 55.6 + - - +
56C GLN* 3.1 37.0 + - - +
57C MET* 2.9 29.7 + - - +
106C LEU* 3.9 20.0 - - + -
109C LEU* 4.7 3.4 - - + -
139C ILE* 4.0 17.9 - - + -
142C HIS* 4.0 21.5 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 54 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A HIS* 5.4 1.0 + - - -
50A TYR* 5.7 4.3 - - - -
24C THR* 4.3 9.5 + - - -
50C TYR* 3.0 20.4 + - - -
51C SER 3.7 1.8 - - - -
52C GLU 3.2 0.2 - - - -
53C PHE* 1.3 77.2 - - - +
55C GLU* 1.3 60.9 + - - +
57C MET* 3.5 16.2 + - - +
58C ASP* 3.1 21.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 55 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C SER* 2.9 21.3 + - - +
52C GLU* 3.0 10.4 + - - +
54C GLY* 1.3 76.2 - - - +
56C GLN* 1.3 64.6 + - - +
58C ASP* 3.2 5.9 + - - +
59C GLU* 3.0 39.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 56 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C LEU* 4.2 6.4 - - + +
52C GLU* 3.0 30.9 + - + +
53C PHE* 3.1 40.1 + - - +
55C GLU* 1.3 74.1 - - - +
57C MET* 1.3 59.4 + - - +
59C GLU* 3.2 3.5 + - - +
60C VAL* 2.8 35.2 + - - +
113C TYR* 3.0 25.5 + - - -
135C PHE* 3.4 60.8 + - + +
138C SER* 4.7 1.2 + - - -
139C ILE* 4.6 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 57 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A HIS* 3.5 35.0 - - + +
32A TRP* 3.8 19.5 - - + -
50A TYR* 4.2 7.6 - - - +
17C VAL* 4.2 8.5 - - - +
20C LEU* 3.5 30.0 - - + +
21C ASN* 3.3 41.5 - - - +
24C THR* 6.1 3.6 - - + -
53C PHE 2.9 15.8 + - - +
54C GLY* 3.5 12.1 - - - +
55C GLU 3.1 0.2 - - - -
56C GLN* 1.3 77.4 - - - +
58C ASP* 1.3 64.3 + - - +
60C VAL* 3.2 3.0 + - - +
61C ALA* 3.0 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 58 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A HIS* 3.8 13.9 - - + -
31A HIS* 3.7 5.6 - - - -
32A TRP* 2.6 39.6 + - - -
47A ASP* 4.5 1.8 - - - +
54C GLY 3.1 16.1 + - - +
55C GLU* 3.2 6.0 + - - +
57C MET* 1.3 76.3 - - - +
59C GLU* 1.3 57.6 + - + +
61C ALA* 3.4 0.9 + - - +
62C GLU* 2.8 42.5 + - - +
157D FE 1.8 33.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 59 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C GLU* 3.0 28.8 + - + +
56C GLN 3.4 7.4 - - - +
58C ASP* 1.3 75.9 - - + +
60C VAL* 1.3 61.1 + - - +
62C GLU* 3.6 5.2 - - - +
63C ARG* 2.7 32.8 + - - +
131C MET* 4.1 10.8 - - - +
135C PHE* 3.7 29.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 60 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C LEU* 3.5 39.1 - - + +
16C GLN* 4.3 8.1 - - + -
17C VAL* 3.7 15.0 - - + +
20C LEU* 4.1 13.2 - - + -
56C GLN 2.8 22.9 + - - +
57C MET* 3.6 5.6 - - - +
59C GLU* 1.3 72.9 - - - +
61C ALA* 1.3 66.2 + - - +
63C ARG* 3.1 4.2 + - - +
64C LEU* 2.9 21.8 + - - +
113C TYR* 4.9 2.5 - - + +
131C MET* 4.1 15.5 - - + -
132C LEU* 5.1 3.8 - - + -
135C PHE* 3.5 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 61 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A TRP* 3.4 40.2 - - + -
17C VAL* 3.9 20.0 - - + -
57C MET 3.0 12.5 + - - +
58C ASP 3.8 1.1 - - - +
60C VAL* 1.3 79.0 - - - +
62C GLU* 1.3 58.4 + - - +
64C LEU* 3.3 6.5 + - - +
65C LEU* 3.0 31.7 + - - +
71C PRO* 4.1 9.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 62 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A HIS* 2.9 12.6 + - - -
32A TRP* 3.9 13.5 - - + -
43A HIS* 3.6 7.4 - - - -
58C ASP* 2.8 26.1 + - - +
59C GLU* 4.1 4.4 - - - +
61C ALA* 1.3 73.7 - - - +
63C ARG* 1.3 60.6 + - - +
65C LEU* 3.4 7.1 - - + +
66C ALA* 2.9 27.7 + - - +
157D FE 2.2 31.9 - - - -
141H LYS* 3.1 27.1 + - + +
144H TRP* 3.8 30.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 63 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C LEU* 4.1 6.3 - - + -
59C GLU 2.7 20.4 + - - +
60C VAL 3.5 4.5 - - - +
62C GLU* 1.3 71.6 - - - +
64C LEU* 1.3 65.7 + - - +
66C ALA* 3.1 10.2 + - - +
67C ILE* 3.0 44.3 + - - +
125C ASP* 2.8 27.1 + - - -
127C VAL* 3.2 30.9 - - - +
128C THR* 2.8 20.8 + - - +
131C MET* 3.8 26.2 - - + -
136H LYS* 4.5 4.8 - - - +
137H ALA 5.1 1.0 + - - -
140H ASP* 2.9 37.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 64 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C LYS* 3.7 37.5 - - + +
13C LEU* 4.2 13.4 - - + +
14C ASN* 3.6 27.8 - - + +
17C VAL* 4.9 2.5 - - + -
60C VAL 2.9 12.5 + - - +
61C ALA* 3.4 8.5 - - - +
62C GLU 3.3 0.2 - - - -
63C ARG* 1.3 75.6 - - - +
65C LEU* 1.3 58.2 + - - +
67C ILE* 3.0 15.1 + - + +
69C GLY* 2.6 51.4 + - - -
70C SER 3.8 3.8 - - - +
71C PRO* 3.5 36.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 65 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A TRP* 3.7 41.7 - - + +
33A TYR* 4.7 9.0 - - + -
61C ALA 3.0 17.4 + - - +
62C GLU* 3.4 11.0 - - - +
64C LEU* 1.3 75.7 - - - +
66C ALA* 1.3 58.9 + - - +
68C GLY* 3.0 20.1 + - - -
69C GLY 3.6 13.9 + - - +
70C SER* 4.6 0.7 - - - -
71C PRO* 3.4 26.2 - - + -
144H TRP* 3.8 34.1 - - + +
154H PRO* 3.5 15.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 66 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C GLU 2.9 14.8 + - - +
63C ARG* 3.1 26.7 + - - +
65C LEU* 1.3 79.5 - - - +
67C ILE* 1.3 56.3 + - - +
68C GLY 3.1 3.4 + - - -
140H ASP* 4.2 26.6 - - + +
141H LYS* 4.9 3.8 - - - +
144H TRP* 4.2 16.4 - - + +
154H PRO* 4.3 10.5 - - - +
155H LEU* 4.3 9.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 67 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C THR* 3.9 26.0 - - + -
10C LYS* 3.4 41.5 + - + -
13C LEU* 3.9 16.6 - - + -
63C ARG* 3.0 49.7 + - - +
64C LEU* 3.0 14.5 + - + +
66C ALA* 1.3 76.8 - - - +
68C GLY* 1.3 55.3 + - - +
125C ASP* 3.9 8.5 - - - +
128C THR* 4.8 0.2 - - - +
155H LEU* 3.7 16.9 - - - +
----------------------------------------------------------
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