Contacts of the helix formed by residues 4 - 30 (chain D) 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 4 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D VAL* 1.3 92.5 + - - +
6D ILE* 3.8 33.1 - - + +
7D GLU* 3.5 24.5 + - + +
8D VAL* 3.7 9.7 + - - +
63D ILE* 5.9 2.0 + - - +
113D ILE* 4.1 8.9 - - - +
117D SER* 4.5 8.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 5 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D GLN* 1.3 87.7 + - - +
6D ILE* 1.3 61.6 + - - +
7D GLU 3.0 2.2 - - - -
8D VAL* 2.8 21.3 + - + +
9D LEU* 3.0 19.7 + - + +
63D ILE* 4.7 6.5 - - + -
110D GLY 5.5 0.4 - - - +
113D ILE* 3.4 27.8 - - + -
114D ALA* 4.2 9.2 - - + -
117D SER* 3.8 21.3 - - - +
119D ASP* 4.2 12.3 - - + +
122D THR* 3.7 33.9 - - + -
126D LEU* 6.1 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 6 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D GLN* 3.2 26.4 - - + +
5D VAL* 1.3 78.8 - - - +
7D GLU* 1.3 60.3 + - - +
9D LEU* 3.7 9.3 - - - +
10D ASN* 2.8 58.1 + - - +
60D ILE* 4.2 11.9 - - + -
63D ILE* 4.0 22.9 - - + +
64D GLY 4.6 2.5 - - - +
65D GLY* 3.4 30.1 - - - +
66D LYS 4.4 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 7 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D GLN* 3.5 21.2 + - + +
5D VAL 3.0 0.8 - - - -
6D ILE* 1.3 85.5 - - - +
8D VAL* 1.3 66.0 + - + +
10D ASN* 3.9 17.0 + - - +
11D LYS* 3.1 23.6 + - - +
68D VAL* 5.6 1.6 - - - +
77D ILE* 4.3 12.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 8 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D GLN 3.8 7.6 - - - +
5D VAL* 2.8 7.5 + - + +
7D GLU* 1.3 79.0 - - + +
9D LEU* 1.3 66.6 + - + +
11D LYS* 3.1 9.4 + - - +
12D GLN* 3.1 25.3 + - + +
106D GLU 4.8 5.6 - - - +
107D LEU* 6.1 0.4 - - + -
110D GLY* 3.7 23.1 - - - -
113D ILE* 3.7 38.4 - - + -
126D LEU* 4.3 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 9 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D VAL* 3.0 17.2 + - + +
6D ILE 3.7 1.8 - - - +
8D VAL* 1.3 80.6 - - + +
10D ASN* 1.3 57.5 + - - +
12D GLN* 2.9 9.7 + - + +
13D VAL* 2.8 30.6 + - - +
56D ILE* 3.4 16.0 - - + +
59D ARG* 4.0 16.8 - - + -
60D ILE* 3.2 33.7 - - + -
63D ILE* 4.0 17.3 - - + -
122D THR* 3.6 33.4 - - + -
125D LEU* 5.7 0.4 - - + -
126D LEU* 3.8 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 10 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D ILE* 2.8 48.6 + - - +
7D GLU* 3.9 18.6 + - - +
9D LEU* 1.3 73.9 - - - +
11D LYS* 1.3 61.5 + - - +
13D VAL* 3.4 7.8 + - - +
14D ALA 3.1 16.1 + - - -
60D ILE* 3.5 10.5 - - - +
66D LYS 3.6 7.5 + - - -
67D PRO* 3.2 6.8 - - - +
68D VAL* 2.7 52.9 + - + +
77D ILE* 3.6 7.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 11 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D GLU 3.1 13.3 + - - +
8D VAL* 3.5 10.3 - - - +
10D ASN* 1.3 74.9 - - - +
12D GLN* 1.3 56.7 + - - +
14D ALA* 3.3 1.2 + - - +
15D ASP* 2.7 47.0 + - - +
77D ILE* 2.9 42.4 + - + +
79D SER* 2.9 36.8 + - - +
106D GLU* 2.8 44.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 12 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D VAL* 3.1 20.7 + - + +
9D LEU* 2.9 17.5 + - + +
11D LYS* 1.3 74.0 - - - +
13D VAL* 1.3 56.5 + - - +
15D ASP* 3.1 8.2 + - - +
16D TRP* 2.7 63.5 + - - -
56D ILE* 3.6 20.4 - - + +
103D MET* 2.9 38.1 + - - +
106D GLU* 5.4 6.1 - - - +
107D LEU* 3.9 18.2 - - + +
126D LEU* 5.3 3.6 - - + -
129D ILE* 3.9 9.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 13 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C TRP* 4.4 5.2 - - + -
9D LEU 2.8 19.1 + - - +
10D ASN* 3.5 17.0 - - - +
11D LYS 3.2 0.2 - - - -
12D GLN* 1.3 75.9 - - - +
14D ALA* 1.3 57.1 + - - +
16D TRP* 3.8 5.4 - - - +
17D SER* 2.8 35.9 + - - +
53D ILE* 4.4 17.3 - - + +
56D ILE* 3.7 19.0 - - + +
57D ALA* 4.1 17.5 - - + +
60D ILE* 5.3 1.1 - - + -
67D PRO* 5.3 1.8 - - + -
68D VAL* 4.0 9.2 - - + +
74D TYR* 3.5 30.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 14 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D ASN 3.1 10.9 + - - +
11D LYS 3.6 6.3 - - - +
13D VAL* 1.3 81.1 - - - +
15D ASP* 1.3 64.0 + - - +
17D SER* 3.1 3.5 + - - -
18D VAL* 3.0 26.0 + - - +
68D VAL* 5.0 0.2 - - + -
74D TYR* 3.4 44.7 - - + +
77D ILE* 3.9 9.4 - - + -
78D SER* 3.9 13.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 15 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D LYS* 2.7 46.4 + - - +
12D GLN* 3.6 13.1 + - - +
14D ALA* 1.3 71.7 - - - +
16D TRP* 1.3 65.0 + - - +
18D VAL* 2.9 6.4 + - - +
19D LEU* 2.9 26.2 + - - +
78D SER* 3.1 10.5 + - - -
79D SER* 3.0 31.0 + - - -
80D ILE* 3.6 16.6 - - + +
103D MET* 4.5 16.4 - - - +
106D GLU* 3.5 7.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 16 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D GLN* 2.7 50.0 + - - +
13D VAL 3.9 1.1 - - - +
15D ASP* 1.3 72.8 - - - +
17D SER* 1.3 57.3 + - - +
19D LEU* 3.2 16.7 + - + +
20D PHE* 2.8 29.6 + - - +
23D LEU* 5.7 0.4 - - + -
45D LEU 5.5 0.9 - - - -
48D GLU* 6.2 0.4 - - + -
49D SER* 3.6 30.5 + - - +
52D HIS* 3.6 29.3 - + + +
53D ILE* 3.6 23.0 - - + +
56D ILE* 3.5 22.3 - - + +
100D TYR* 4.3 19.5 - + - -
103D MET* 3.3 25.4 - - + +
129D ILE* 3.6 19.1 - - + +
132D GLU* 4.6 0.2 - - - -
133D LEU* 3.6 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 17 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C MET* 4.2 6.9 - - - +
13D VAL* 2.8 25.8 + - - +
14D ALA 3.4 5.2 - - - -
16D TRP* 1.3 76.2 - - - +
18D VAL* 1.3 63.1 + - - +
20D PHE* 3.2 16.5 - - - +
21D THR* 3.4 10.6 + - - -
53D ILE* 3.7 21.3 - - - +
74D TYR* 3.4 40.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 18 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C MET* 4.2 17.5 - - - -
14D ALA 3.0 15.7 - - - +
15D ASP 2.9 6.0 + - - +
17D SER* 1.3 75.5 - - - +
19D LEU* 1.3 67.3 + - - +
21D THR* 3.0 6.1 + - - -
22D LYS* 2.8 22.6 + - + +
74D TYR* 4.7 4.9 - - + +
75D LEU* 4.9 5.6 - - + -
78D SER* 3.1 27.4 - - - +
80D ILE* 3.9 27.8 - - + +
82D GLU* 3.9 32.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 19 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D ASP 2.9 28.3 + - - +
16D TRP* 3.4 36.1 - - + +
18D VAL* 1.3 76.6 - - - +
20D PHE* 1.3 52.7 + - - +
22D LYS* 3.1 9.1 + - + -
23D LEU* 2.7 54.7 + - + +
49D SER* 4.6 0.2 - - - -
80D ILE* 3.9 34.5 - - + -
96D ILE* 5.3 6.3 - - + -
99D ASP* 4.1 19.3 - - + +
100D TYR* 4.7 12.6 - - + -
103D MET* 4.4 11.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 20 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C PHE* 3.4 52.5 - + - -
50C ALA* 4.7 8.7 - - + -
53C ILE* 4.6 11.2 - - + -
16D TRP 2.8 11.1 + - - +
17D SER 3.2 12.3 - - - +
19D LEU* 1.3 77.4 - - - +
21D THR* 1.3 66.3 + - - +
23D LEU* 3.5 2.6 + - - +
24D HIS* 2.7 64.3 + + - -
46D TYR* 3.6 18.2 - + - -
49D SER* 3.5 24.6 + - - +
50D ALA* 4.0 13.5 - - + -
53D ILE* 4.2 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 21 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C ALA* 3.9 19.5 - - - +
70C THR* 4.1 6.5 - - - +
71C MET* 3.5 20.4 - - - +
74C TYR* 3.5 35.5 - - + +
17D SER 3.4 9.9 + - - -
18D VAL 3.0 6.7 + - - -
20D PHE* 1.3 84.4 - - - +
22D LYS* 1.3 66.4 + - - +
24D HIS* 2.9 11.4 + - + +
25D ASN* 2.9 21.7 + - - +
71D MET* 5.2 0.7 - - - +
82D GLU* 4.7 2.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 22 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C ALA 5.2 1.3 - - - -
18D VAL* 2.8 18.2 + - + +
19D LEU* 3.6 11.0 - - + +
21D THR* 1.3 78.3 - - - +
23D LEU* 1.3 56.9 + - + +
25D ASN* 3.3 8.6 - - - +
26D PHE* 3.1 62.4 + - + -
80D ILE* 4.1 10.9 - - + +
81D GLN* 2.8 31.5 + - - +
82D GLU* 4.2 3.6 - - + -
83D ALA* 4.1 21.1 - - + +
87D GLU* 5.9 0.2 - - - -
95D ALA* 4.8 9.3 + - - +
96D ILE* 5.1 3.1 - - + -
99D ASP* 2.8 33.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 23 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D TRP* 5.7 0.4 - - + -
19D LEU* 2.7 37.7 + - + +
22D LYS* 1.3 70.5 - - + +
24D HIS* 1.3 60.2 + - - +
26D PHE* 3.8 2.6 - - - +
27D HIS* 2.8 28.4 + - - +
42D PHE* 3.7 24.4 - - + +
45D LEU* 3.5 29.6 - - + +
46D TYR* 3.4 44.8 - - + +
49D SER* 4.2 6.1 - - - -
96D ILE* 4.1 25.8 - - + -
100D TYR* 4.5 7.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 24 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C ALA* 5.1 5.3 + - - +
53C ILE* 4.1 14.6 - - + +
54C ASP* 4.5 6.7 - - + +
20D PHE* 2.7 66.6 + + - -
21D THR* 2.9 12.9 + - + +
23D LEU* 1.3 74.0 - - - +
25D ASN* 1.3 56.2 + - - +
27D HIS* 3.0 8.3 + - - +
28D TRP* 2.6 79.2 + + + -
46D TYR* 3.5 33.9 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 25 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C ALA* 2.9 46.0 + - + +
21D THR 2.9 9.0 + - - +
22D LYS* 3.3 11.4 - - - +
24D HIS* 1.3 75.7 - - - +
26D PHE* 1.3 64.8 + - + +
28D TRP* 2.9 6.1 + - - -
29D TYR* 2.7 49.4 + - - +
83D ALA* 3.5 23.6 - - + +
85D TYR* 3.9 20.4 - - - -
87D GLU* 4.5 3.8 - - - +
92D MET* 4.5 1.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 26 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D LYS* 3.1 37.7 + - + +
23D LEU* 3.9 3.8 - - - +
25D ASN* 1.3 80.4 - - - +
27D HIS* 1.3 66.2 + - - +
30D VAL* 3.1 30.3 + - - +
42D PHE* 3.6 24.2 - + + -
83D ALA* 4.0 20.9 - - + -
87D GLU* 4.1 15.9 - - + -
92D MET* 3.2 50.5 - - + -
95D ALA* 3.8 10.3 - - + -
96D ILE* 3.4 34.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 27 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C ASP* 3.2 13.9 - - - -
58C GLU* 3.3 2.3 + - - -
154C FE 2.1 31.4 - - - -
23D LEU 2.8 17.2 + - - +
24D HIS* 3.1 12.6 - - - +
26D PHE* 1.3 79.0 - - - +
28D TRP* 1.3 71.0 + + - +
30D VAL* 3.7 6.6 - - - +
35D PHE* 5.0 0.9 - - - -
39D HIS* 2.7 75.7 + + - -
42D PHE* 3.9 11.6 - - + -
43D GLU* 3.7 22.3 + - + +
46D TYR* 3.5 20.0 + + + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 28 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C VAL* 4.4 2.9 - - + -
53C ILE* 3.4 28.0 - - + -
54C ASP* 2.6 25.8 + - - -
57C ALA* 3.2 32.6 - - + +
58C GLU* 3.9 17.4 - - + +
61C LEU* 3.2 36.8 - - + +
67C PRO* 4.2 16.4 - - + -
68C VAL 3.8 9.9 - - - -
69C ALA* 4.1 9.9 - - + -
74C TYR* 3.8 20.9 - - - -
24D HIS* 2.6 54.9 + + + +
25D ASN* 2.9 8.0 + - - +
27D HIS* 1.3 86.0 - + - +
29D TYR* 1.3 62.6 + + + +
30D VAL 3.6 3.3 + - - +
31D LYS* 4.9 3.6 + - - -
35D PHE* 5.4 3.5 - - - -
39D HIS* 5.4 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 29 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C LEU* 4.8 6.3 - - + -
66C LYS* 3.0 33.5 - - + +
67C PRO* 2.6 56.3 + - + -
69C ALA* 4.3 2.9 - - + -
25D ASN* 2.7 44.6 + - - +
28D TRP* 1.3 75.5 - - + +
30D VAL* 1.3 68.1 + - - +
31D LYS* 3.3 29.0 + - - +
85D TYR* 3.6 31.4 - + - -
86D GLY 6.3 1.6 - - - +
87D GLU 5.3 2.1 - - - +
92D MET* 3.8 16.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 30 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26D PHE 3.1 20.1 + - - +
27D HIS 3.7 11.9 - - - +
28D TRP 3.6 1.6 - - - +
29D TYR* 1.3 78.9 - - - +
31D LYS* 1.3 73.1 + - - +
34D GLN 5.4 0.2 - - - -
35D PHE* 3.4 36.2 - - + +
38D LEU* 4.0 22.0 - - + -
39D HIS* 4.1 17.0 - - - +
42D PHE* 4.2 4.5 - - + -
89D ALA* 4.0 21.8 - - + +
92D MET* 3.8 17.6 - - - +
----------------------------------------------------------
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