Contacts of the helix formed by residues 34 - 63 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B VAL* 5.4 1.1 - - - -
31B LYS 5.3 1.1 - - - +
32B GLY 3.0 1.4 - - - -
33B PRO* 1.3 97.5 - - + +
35B PHE* 1.3 54.8 + - - +
36B PHE 3.5 1.6 - - - -
37B THR* 3.4 19.7 + - - +
38B LEU* 2.8 55.1 + - + +
89B ALA* 5.2 8.7 - - + -
90B GLU* 5.5 8.1 - - - +
143B PHE* 3.6 30.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 35 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B HIS 5.0 1.1 - - - -
28B TRP 5.3 3.8 - - - -
30B VAL* 3.4 46.2 - - + -
31B LYS* 4.4 3.3 - - - -
32B GLY* 3.1 22.4 + - - +
33B PRO 3.3 1.4 - - - -
34B GLN* 1.3 77.3 - - - +
36B PHE* 1.3 104.2 + + + +
38B LEU* 3.5 0.3 - - - +
39B HIS* 2.5 64.8 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 36 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B PRO 5.4 0.8 + - - -
35B PHE* 1.3 109.0 - + + +
37B THR* 1.3 67.8 + - + +
39B HIS* 3.7 7.8 - + - +
40B GLU* 3.1 26.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 37 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B PRO 4.8 4.3 - - - +
34B GLN* 3.9 28.4 + - - +
36B PHE* 1.3 79.9 - - + +
38B LEU* 1.3 70.0 + - - +
40B GLU* 3.5 7.0 - - - +
41B LYS* 3.0 26.0 + - - +
143B PHE* 5.2 2.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 38 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B VAL* 3.9 19.3 - - + -
34B GLN* 2.8 53.9 + - + +
35B PHE 3.8 0.9 - - - +
37B THR* 1.3 77.6 + - - +
39B HIS* 1.3 65.5 + - - +
40B GLU 3.0 1.8 - - - -
41B LYS* 3.8 14.5 - - + +
42B PHE* 3.0 44.5 + - + -
89B ALA* 5.2 4.9 - - + +
93B VAL* 3.9 27.4 - - + -
140B LEU* 6.0 2.9 - - + -
143B PHE* 3.5 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 39 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A GLU* 3.3 21.4 + - - -
61A LEU* 6.3 1.3 - - + -
152A FE 4.1 0.6 - - - -
27B HIS* 2.7 78.1 + + - -
28B TRP* 5.4 1.6 - - - -
30B VAL* 4.0 8.4 - - - +
35B PHE* 2.5 55.5 + + + +
36B PHE* 3.7 8.5 - + - +
38B LEU* 1.3 72.9 - - - +
40B GLU* 1.3 65.0 + - + +
42B PHE* 3.8 1.4 + - - +
43B GLU* 3.5 5.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 40 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B PHE 3.1 15.7 + - - +
37B THR* 3.5 8.0 - - - +
38B LEU 3.0 0.4 - - - -
39B HIS* 1.3 83.1 - - + +
41B LYS* 1.3 68.1 + - - +
43B GLU* 2.9 21.3 + - + +
44B GLU* 3.1 14.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 41 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B THR 3.0 14.0 + - - +
38B LEU* 3.3 18.6 + - + +
40B GLU* 1.3 78.2 - - - +
42B PHE* 1.3 64.5 + - + +
44B GLU* 3.0 45.4 + - - +
45B LEU* 2.9 34.2 + - + +
136B HIS* 4.2 10.8 - - - -
139B MET* 3.2 33.9 - - - +
140B LEU* 5.1 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 42 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B LEU* 3.7 31.7 - - + +
26B PHE* 3.5 43.7 - + + -
27B HIS* 3.8 9.4 - - - -
30B VAL* 4.1 14.8 - - + -
38B LEU* 3.0 47.6 + - + +
39B HIS 4.1 0.2 - - - +
41B LYS* 1.3 76.5 - - + +
43B GLU* 1.3 56.7 + - - +
45B LEU* 3.1 15.0 + - + +
46B TYR* 2.8 32.9 + - - +
89B ALA 4.8 0.4 - - - -
92B MET* 3.7 22.9 - - + -
93B VAL* 4.4 7.4 - - + -
96B ILE* 4.5 17.0 - - + -
140B LEU* 6.3 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 43 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A ASP* 4.5 4.9 - - - +
152A FE 4.2 2.1 - - - -
27B HIS* 3.6 25.9 + - + -
39B HIS* 3.5 4.1 + - - +
40B GLU* 2.9 14.0 + - - +
42B PHE* 1.3 79.5 - - - +
44B GLU* 1.3 57.2 + - - +
46B TYR* 3.1 37.8 + - + +
47B THR* 2.6 39.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 44 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B GLU* 3.1 12.7 + - + +
41B LYS* 3.0 55.7 + - - +
43B GLU* 1.3 78.3 - - - +
45B LEU* 1.3 60.4 + - + +
47B THR* 3.3 7.2 + - - -
48B GLU* 3.1 37.7 + - + +
136B HIS* 4.1 9.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 45 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B TRP* 5.5 0.7 - - - -
23B LEU* 3.6 16.4 - - + +
41B LYS* 2.9 35.7 + - + +
42B PHE* 3.4 21.3 - - + +
44B GLU* 1.3 81.1 - - + +
46B TYR* 1.3 59.3 + - - +
48B GLU* 3.2 10.3 + - - +
49B SER* 2.8 26.0 + - - -
96B ILE* 4.9 7.9 - - + -
100B TYR* 3.0 30.2 + - + +
136B HIS* 3.5 37.9 - - + +
140B LEU* 5.1 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 46 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A ASP* 3.9 11.3 + - - +
152A FE 3.9 0.2 - - - -
20B PHE* 3.7 15.3 - + - +
23B LEU* 3.5 30.2 - - + +
24B HIS* 3.5 36.3 - + + +
27B HIS* 3.6 31.0 + + + -
42B PHE 2.8 25.0 + - - -
43B GLU* 3.1 50.5 + - + -
45B LEU* 1.3 70.3 - - - +
47B THR* 1.3 73.4 + - - +
49B SER* 2.6 23.4 + - - +
50B ALA* 3.0 10.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 47 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B PHE* 5.9 0.2 - - - -
43B GLU* 2.6 26.8 + - - +
44B GLU* 3.5 8.0 - - - -
45B LEU 3.1 0.2 - - - -
46B TYR* 1.3 90.4 - - - +
48B GLU* 1.3 63.3 + - + +
50B ALA* 3.2 9.3 + - - +
51B THR* 3.1 22.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 48 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B TRP* 6.2 0.4 - - + -
44B GLU* 3.1 25.5 + - + +
45B LEU* 3.2 14.4 + - - +
47B THR* 1.3 74.5 - - + +
49B SER* 1.3 67.0 + - - +
51B THR* 2.9 20.5 + - - -
52B HIS* 3.1 26.3 + - - +
100B TYR* 5.1 1.6 + - - +
132B GLU* 3.6 21.1 - - - +
136B HIS* 2.7 38.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 49 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B TRP* 3.7 39.9 - - - +
19B LEU* 4.6 0.2 - - - -
20B PHE* 3.5 18.2 - - - +
23B LEU* 4.2 8.5 - - - -
45B LEU 2.8 14.7 + - - -
46B TYR* 2.6 26.5 + - - -
48B GLU* 1.3 75.8 - - - +
50B ALA* 1.3 65.0 + - - +
52B HIS* 3.0 16.1 + - - +
53B ILE* 3.0 17.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 50 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A PHE* 4.7 8.1 - - + -
24A HIS* 5.1 4.4 + - - +
20B PHE* 4.0 17.7 - - + -
46B TYR 3.0 8.8 + - - +
47B THR* 3.4 12.3 - - + +
49B SER* 1.3 81.7 + - - +
51B THR* 1.3 64.6 + - - +
53B ILE* 3.4 14.9 + - - +
54B ASP* 3.3 19.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 51 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B THR* 3.1 15.1 + - - +
48B GLU* 2.9 14.7 + - - -
50B ALA* 1.3 76.7 - - - +
52B HIS* 1.3 67.2 + - + +
54B ASP* 3.1 7.1 + - - +
55B GLU* 3.0 51.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 52 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B TRP* 3.6 49.6 - + + +
48B GLU* 3.1 25.7 + - + +
49B SER* 3.0 4.6 + - - +
51B THR* 1.3 80.1 - - + +
53B ILE* 1.3 63.7 + - - +
54B ASP 3.1 0.2 + - - -
55B GLU* 3.2 18.1 + - - -
56B ILE* 2.9 35.7 + - + +
129B ILE* 4.0 23.6 - - + +
132B GLU* 2.6 42.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 53 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A PHE* 4.7 5.8 - - + -
24A HIS* 4.2 10.3 - - + +
28A TRP* 3.4 24.6 - - + -
13B VAL* 4.4 11.0 - - + +
16B TRP* 3.6 23.8 - - + +
17B SER* 3.7 36.8 - - - +
20B PHE* 4.2 11.7 - - + -
49B SER 3.0 18.3 + - - +
50B ALA* 3.5 17.3 - - - +
52B HIS* 1.3 75.9 - - - +
54B ASP* 1.3 57.3 + - - +
56B ILE* 4.4 3.4 - - - +
57B ALA* 3.1 26.3 + - - +
74B TYR* 5.2 0.7 - - - +
2001B MPD 4.3 8.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 54 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A HIS* 4.5 5.1 - - + +
27A HIS* 3.3 5.2 - - - -
28A TRP* 2.6 34.5 + - + -
43A GLU* 4.6 3.5 - - - +
46A TYR* 3.9 14.4 + - - +
50B ALA 3.3 7.5 + - - +
51B THR* 3.1 7.4 + - - +
52B HIS 3.1 0.4 - - - -
53B ILE* 1.3 79.6 - - - +
55B GLU* 1.3 61.4 + - + +
57B ALA* 3.8 0.2 - - - +
58B GLU* 2.8 40.7 + - - +
151B FE 2.0 29.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 55 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B THR* 3.0 32.7 + - + +
52B HIS* 3.6 25.0 + - - +
54B ASP* 1.3 78.7 - - + +
56B ILE* 1.3 53.5 + - + +
58B GLU* 3.2 7.3 + - - +
59B ARG* 2.7 35.4 + - - +
125B LEU* 4.3 25.1 - - + +
129B ILE* 5.5 1.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 56 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B LEU* 3.4 45.8 - - + +
12B GLN* 3.6 17.9 - - + +
13B VAL* 3.7 10.1 - - + -
16B TRP* 3.5 36.8 - - + +
52B HIS* 2.9 17.6 + - - +
55B GLU* 1.3 74.8 - - + +
57B ALA* 1.3 55.8 + - - +
59B ARG* 2.7 27.1 + - - +
60B ILE* 2.9 16.8 + - - +
125B LEU* 4.3 9.9 - - + -
126B LEU* 5.7 1.1 - - + -
129B ILE* 4.0 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 57 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A TRP* 3.2 38.1 - - + +
13B VAL* 4.2 9.4 - - + +
53B ILE 3.1 20.4 + - - +
54B ASP 3.8 0.2 - - - +
56B ILE* 1.3 78.4 - - - +
58B GLU* 1.3 58.0 + - - +
60B ILE* 3.3 7.1 + - - +
61B LEU* 2.8 31.0 + - - +
67B PRO* 4.0 16.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 58 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A HIS* 3.2 2.4 + - - -
28A TRP* 3.9 8.7 - - + +
39A HIS* 3.1 25.3 + - - -
54B ASP* 2.8 36.6 + - - +
55B GLU* 3.4 6.0 - - - +
57B ALA* 1.3 74.8 - - - +
59B ARG* 1.3 57.0 + - - +
61B LEU* 3.5 11.3 - - - +
62B ALA* 3.0 26.3 + - - +
151B FE 2.4 28.9 - - - -
135C LYS* 3.4 29.9 + - - +
138C TRP* 3.4 21.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 59 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B LEU* 3.9 17.0 - - + -
55B GLU 2.7 16.6 + - - +
56B ILE* 2.7 16.4 + - - +
58B GLU* 1.3 67.3 - - - +
60B ILE* 1.3 59.2 + - - +
61B LEU 3.0 1.1 - - - -
62B ALA* 2.8 23.9 + - - +
63B ILE* 3.0 28.1 + - + +
119B ASP* 3.3 12.7 + - - -
121B MET* 3.0 30.1 - - - +
122B THR* 3.1 18.6 + - + +
125B LEU* 3.7 28.5 - - + -
130C TYR* 5.1 0.4 - - - -
131C THR* 4.9 14.6 + - - +
134C GLU* 2.4 43.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 60 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B ILE* 4.3 8.7 - - + +
9B LEU* 3.1 37.5 - - + -
10B ASN* 3.5 18.6 - - - +
13B VAL* 5.3 1.1 - - + -
56B ILE* 2.9 17.4 + - + +
57B ALA* 3.3 6.3 - - - +
59B ARG* 1.3 74.3 - - - +
61B LEU* 1.3 60.7 + - - +
63B ILE* 3.1 20.9 + - + +
65B GLY 2.7 34.0 + - - -
66B LYS 3.5 5.4 - - - +
67B PRO* 3.0 48.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 61 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A TRP* 3.3 40.6 - - + +
29A TYR* 4.8 7.4 - - + -
31A LYS* 5.8 3.6 - - - +
57B ALA 2.8 14.7 + - - +
58B GLU* 3.5 14.1 - - - +
60B ILE* 1.3 80.2 - - - +
62B ALA* 1.3 59.4 + - - +
63B ILE 3.5 0.2 + - - -
64B GLY* 3.6 8.8 + - - -
65B GLY 3.8 9.4 + - - +
66B LYS* 6.1 0.4 - - - -
67B PRO* 3.4 26.0 - - + -
138C TRP* 3.3 57.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 62 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B GLU 3.0 13.9 + - - +
59B ARG* 2.8 28.5 + - - +
61B LEU* 1.3 78.3 - - - +
63B ILE* 1.3 57.8 + - - +
64B GLY 3.3 3.0 + - - -
134C GLU* 3.8 34.3 - - - +
135C LYS* 4.1 10.3 - - + +
138C TRP* 4.0 12.7 - - + +
141C ARG* 5.6 2.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 63 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B GLN* 5.8 2.4 + - - +
5B VAL* 4.8 8.5 - - + -
6B ILE* 4.0 23.5 - - + +
9B LEU* 4.1 15.5 - - + -
59B ARG* 3.4 42.0 - - - +
60B ILE* 3.2 26.7 - - - +
62B ALA* 1.3 79.1 - - - +
64B GLY* 1.3 56.5 - - - +
65B GLY 3.3 2.5 + - - +
119B ASP* 4.4 15.5 - - - +
122B THR* 4.5 0.7 - - - +
134C GLU* 4.2 7.6 - - - +
----------------------------------------------------------
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