Contacts of the helix formed by residues 34 - 63 (chain C) 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 C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A PRO* 2.8 45.2 + - + +
34A GLN* 3.7 12.2 + - - +
37A THR* 5.5 1.6 - - - +
30C VAL* 5.4 0.7 - - - -
31C LYS 5.3 0.9 - - - -
32C GLY* 3.0 1.2 - - - -
33C PRO* 1.3 96.9 - - + +
35C PHE* 1.3 55.2 + - - +
36C PHE 3.5 2.0 - - - -
37C THR* 3.4 22.7 + - - +
38C LEU* 2.7 52.4 + - + +
89C ALA* 5.2 9.2 - - + -
90C GLU* 5.5 8.7 - - - +
143C PHE* 3.6 17.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 35 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C HIS 5.0 1.3 - - - -
28C TRP 5.3 3.8 - - - -
30C VAL* 3.4 48.2 - - + +
31C LYS* 4.4 3.1 - - - -
32C GLY 3.1 21.6 + - - +
33C PRO 3.3 1.8 - - - -
34C GLN* 1.3 76.6 - - - +
36C PHE* 1.3 105.2 + + + +
38C LEU* 3.9 0.3 - - - +
39C HIS* 2.5 66.7 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 36 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C PRO 5.4 1.1 + - - -
34C GLN 3.5 0.4 - - - -
35C PHE* 1.3 109.1 - + + +
37C THR* 1.3 66.0 + - + +
39C HIS* 3.7 7.3 - + - +
40C GLU* 3.1 26.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 37 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A PHE* 4.7 18.0 - - - +
37A THR* 4.7 19.3 - - + +
33C PRO 4.8 3.8 - - - +
34C GLN* 3.9 29.0 + - - +
36C PHE* 1.3 78.3 - - + +
38C LEU* 1.3 69.7 + - - +
40C GLU* 3.5 6.8 - - - +
41C LYS* 3.0 26.3 + - - +
143C PHE* 5.1 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 38 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A PHE* 5.0 10.3 - - + -
30C VAL* 4.0 20.4 - - + -
34C GLN* 2.7 54.3 + - + +
35C PHE 3.9 0.7 - - - +
37C THR* 1.3 80.5 + - - +
39C HIS* 1.3 64.9 + - - +
40C GLU 3.0 1.8 - - - -
41C LYS* 3.9 13.8 - - + +
42C PHE* 3.0 42.6 + - + -
89C ALA* 5.2 5.2 - - + +
93C VAL* 4.0 26.7 - - + -
140C LEU* 6.0 2.0 - - + -
143C PHE* 3.5 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 39 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C HIS* 2.7 78.9 + + - -
28C TRP* 5.3 1.6 - - - -
30C VAL* 4.1 8.6 - - - +
35C PHE* 2.5 57.9 + + + +
36C PHE* 3.7 7.9 - + - +
38C LEU* 1.3 72.9 - - - +
40C GLU* 1.3 66.1 + - + +
42C PHE* 3.8 1.4 + - - +
43C GLU* 3.5 4.5 + - - -
58D GLU* 3.2 22.3 + - - -
61D LEU* 6.2 1.3 - - + -
153D FE 4.3 0.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 40 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C PHE 3.1 16.7 + - - +
37C THR* 3.5 7.1 - - - +
39C HIS* 1.3 81.2 - - + +
41C LYS* 1.3 69.3 + - - +
43C GLU* 2.9 22.1 + - - +
44C GLU* 3.1 13.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 41 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A PHE* 3.5 39.9 - - + -
37C THR 3.0 14.6 + - - +
38C LEU* 3.3 15.9 + - + +
40C GLU* 1.3 77.6 - - - +
42C PHE* 1.3 65.0 + - + +
44C GLU* 3.0 44.0 + - - +
45C LEU* 2.9 33.8 + - + +
136C HIS* 4.2 11.7 - - - -
139C MET* 3.1 30.2 - - - +
140C LEU* 5.1 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 42 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C LEU* 3.7 31.6 - - + +
26C PHE* 3.5 44.6 - + + -
27C HIS* 3.8 8.5 - - - -
30C VAL* 4.1 14.8 - - + -
38C LEU* 3.0 37.5 + - + +
39C HIS 4.1 0.7 - - - +
41C LYS* 1.3 77.4 - - + +
43C GLU* 1.3 58.1 + - - +
45C LEU* 3.1 13.4 + - + +
46C TYR* 2.8 32.9 + - - +
89C ALA 4.9 0.4 - - - -
92C MET* 3.7 22.9 - - + -
93C VAL* 4.4 16.4 - - + -
96C ILE* 4.5 17.3 - - + -
140C LEU* 6.3 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 43 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C HIS* 3.7 24.1 + - + -
39C HIS* 3.5 4.0 + - - +
40C GLU* 2.9 14.5 + - + +
42C PHE* 1.3 74.9 - - - +
44C GLU* 1.3 59.8 + - - +
46C TYR* 3.2 35.8 + - + +
47C THR* 2.5 39.3 + - - +
54D ASP* 4.5 5.0 - - - +
153D FE 4.5 0.7 - - - -
----------------------------------------------------------
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 GLU* 3.1 11.9 + - + +
41C LYS* 3.0 52.1 + - - +
43C GLU* 1.3 78.4 - - - +
45C LEU* 1.3 66.5 + - + +
47C THR* 3.4 7.1 + - - -
48C GLU* 3.1 33.5 + - + +
136C HIS* 4.1 9.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 45 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C TRP* 5.5 0.7 - - - -
23C LEU* 3.5 14.6 - - + +
41C LYS* 2.9 37.0 + - + +
42C PHE* 3.1 22.9 + - + +
44C GLU* 1.3 81.2 - - + +
46C TYR* 1.3 59.4 + - - +
48C GLU* 3.2 8.8 + - - +
49C SER* 2.8 26.0 + - - -
96C ILE* 5.0 6.5 - - + -
100C TYR* 3.1 31.4 + - + +
136C HIS* 3.4 39.5 - - + +
140C LEU* 5.1 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 46 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C PHE* 3.6 18.6 - + + +
23C LEU* 3.4 33.8 - - + +
24C HIS* 3.4 35.9 - + + +
27C HIS* 3.6 30.5 + + + -
42C PHE 2.8 25.1 + - - -
43C GLU* 3.2 47.8 + - + -
45C LEU* 1.3 69.8 - - - +
47C THR* 1.3 72.9 + - - +
49C SER* 2.8 19.6 + - - +
50C ALA* 3.0 11.1 + - - +
54D ASP* 3.7 12.2 + - + +
153D FE 3.8 0.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 47 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C GLU* 2.5 29.1 + - - +
44C GLU* 3.4 7.7 - - - -
46C TYR* 1.3 87.1 - - - +
48C GLU* 1.3 64.0 + - + +
50C ALA* 3.1 9.3 + - - +
51C THR* 3.1 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 48 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C TRP* 6.2 0.4 - - + -
44C GLU* 3.1 21.5 + - + +
45C LEU* 3.4 12.7 - - - +
47C THR* 1.3 78.6 - - + +
49C SER* 1.3 66.8 + - - +
51C THR* 2.9 20.5 + - - -
52C HIS* 3.1 26.7 + - + +
100C TYR* 5.1 1.9 + - - -
132C GLU* 3.7 21.6 - - - +
136C HIS* 2.7 38.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 49 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C TRP* 3.6 39.4 - - - +
20C PHE* 3.4 23.5 - - - +
23C LEU* 4.2 8.1 - - - -
45C LEU 2.8 17.2 + - - -
46C TYR* 2.8 12.9 + - - -
48C GLU* 1.3 76.7 - - - +
50C ALA* 1.3 65.6 + - - +
52C HIS* 3.0 16.7 + - - +
53C ILE* 3.0 16.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 50 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C PHE* 3.9 18.2 - - + -
46C TYR 3.0 9.3 + - - +
47C THR* 3.1 11.0 + - - +
49C SER* 1.3 82.0 + - - +
51C THR* 1.3 65.2 + - - +
53C ILE* 3.3 21.6 + - - +
54C ASP* 3.4 12.3 + - - +
20D PHE* 4.7 8.7 - - + -
24D HIS* 5.1 3.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 51 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C THR* 3.1 15.1 + - - +
48C GLU* 2.9 15.1 + - - -
50C ALA* 1.3 77.0 - - - +
52C HIS* 1.3 65.8 + - + +
54C ASP* 3.2 6.1 + - - +
55C GLU* 3.0 52.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 52 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C TRP* 3.5 49.4 - + + +
48C GLU* 3.1 25.3 + - + -
49C SER* 3.0 4.0 + - - +
51C THR* 1.3 80.3 - - + +
53C ILE* 1.3 64.3 + - - +
55C GLU* 3.2 18.6 + - - -
56C ILE* 2.9 36.2 + - + +
129C ILE* 4.0 23.9 - - + +
132C GLU* 2.5 42.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 53 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C VAL* 4.4 11.4 - - + +
16C TRP* 3.7 22.6 - - + +
17C SER* 3.8 34.5 - - - +
20C PHE* 4.3 10.8 - - + -
49C SER 3.0 13.8 + - - +
50C ALA* 3.5 17.9 - - - +
51C THR 3.3 0.2 - - - -
52C HIS* 1.3 76.1 - - - +
54C ASP* 1.3 58.2 + - - +
56C ILE* 4.3 3.1 - - - +
57C ALA* 3.1 26.0 + - - +
74C TYR* 5.2 0.4 - - - +
20D PHE* 4.6 14.8 - - + -
24D HIS* 4.1 11.0 - - + +
28D TRP* 3.7 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 54 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C ALA 3.4 6.7 + - - +
51C THR* 3.2 7.9 + - - +
52C HIS 3.1 0.6 - - - -
53C ILE* 1.3 78.8 - - - +
55C GLU* 1.3 61.3 + - + +
58C GLU* 2.8 41.2 + - - +
154C FE 2.0 30.6 - - - -
24D HIS* 4.5 5.8 - - + +
27D HIS* 3.2 5.4 - - - -
28D TRP* 2.6 34.3 + - + -
43D GLU* 4.6 3.6 - - - +
46D TYR* 3.9 13.4 + - - +
----------------------------------------------------------
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 THR* 3.0 35.2 + - + +
52C HIS* 3.7 24.9 + - - +
54C ASP* 1.3 78.0 - - + +
56C ILE* 1.3 53.7 + - + +
58C GLU* 3.2 5.7 + - - +
59C ARG* 2.7 35.7 + - - +
125C LEU* 4.4 25.5 - - + +
129C ILE* 5.5 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 56 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C LEU* 3.4 45.3 - - + +
12C GLN* 3.7 17.5 - - + +
13C VAL* 3.6 10.3 - - + +
16C TRP* 3.4 34.8 - - + +
52C HIS* 2.9 22.5 + - + +
53C ILE* 4.3 0.7 - - - +
55C GLU* 1.3 76.4 - - + +
57C ALA* 1.3 55.7 + - - +
59C ARG* 2.7 28.0 + - - +
60C ILE* 2.9 15.9 + - - +
125C LEU* 4.3 9.9 - - + -
126C LEU* 5.8 1.1 - - + -
129C ILE* 4.1 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 57 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C VAL* 4.1 8.2 - - + +
53C ILE 3.1 20.2 + - - +
54C ASP 3.7 0.2 - - - +
56C ILE* 1.3 79.1 - - - +
58C GLU* 1.3 58.2 + - - +
60C ILE* 3.3 7.1 - - - +
61C LEU* 2.8 30.6 + - - +
67C PRO* 4.1 16.4 - - + +
28D TRP* 3.2 39.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 58 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C ASP* 2.8 36.3 + - - +
55C GLU* 3.4 5.0 - - - +
57C ALA* 1.3 75.5 - - - +
59C ARG* 1.3 56.0 + - - +
61C LEU* 3.5 14.1 - - + +
62C ALA* 3.0 26.0 + - - +
154C FE 2.4 27.7 - - - -
27D HIS* 3.3 2.4 + - - -
28D TRP* 3.9 9.0 - - + +
39D HIS* 3.2 26.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 59 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C LEU* 4.0 10.3 - - + -
55C GLU 2.7 12.5 + - - +
56C ILE* 2.7 14.7 + - - +
58C GLU* 1.3 75.3 - - - +
60C ILE* 1.3 56.2 + - - +
61C LEU 3.0 1.1 - - - -
62C ALA* 2.7 39.0 + - - +
63C ILE* 3.0 33.4 + - + +
119C ASP* 3.3 12.7 + - - -
121C MET* 3.0 37.8 - - - +
122C THR* 3.0 24.2 + - + +
125C LEU* 3.7 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 60 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C ILE* 4.3 8.7 - - + +
9C LEU* 3.2 36.6 - - + -
10C ASN* 3.5 19.1 - - - +
13C VAL* 5.3 0.7 - - + -
56C ILE* 2.9 18.1 + - + +
57C ALA* 3.3 7.4 - - - +
59C ARG* 1.3 75.3 - - - +
61C LEU* 1.3 60.4 - - - +
63C ILE* 3.1 22.1 + - + +
65C GLY 2.7 33.7 + - - -
66C LYS 3.5 5.4 - - - +
67C PRO* 3.0 49.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 61 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C ALA 2.8 15.8 + - - +
58C GLU* 3.5 14.1 - - + +
60C ILE* 1.3 80.1 - - - +
62C ALA* 1.3 58.8 + - - +
63C ILE 3.6 0.3 + - - -
64C GLY* 3.6 9.0 + - - -
65C GLY 3.8 10.0 - - - +
66C LYS* 6.0 1.1 - - - -
67C PRO* 3.4 25.4 - - + -
28D TRP* 3.2 53.8 - - + +
29D TYR* 4.8 7.9 - - + -
31D LYS* 5.7 4.7 - - - +
39D HIS* 6.2 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 62 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C GLU 3.0 14.3 + - - +
59C ARG* 2.7 28.2 + - - +
61C LEU* 1.3 78.5 - - - +
63C ILE* 1.3 58.3 + - - +
64C GLY 3.3 2.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 63 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C GLN* 5.8 2.3 + - - +
5C VAL* 4.7 8.7 - - + -
6C ILE* 4.0 23.1 - - + +
9C LEU* 4.0 16.4 - - + -
59C ARG* 3.4 40.4 - - - +
60C ILE* 3.2 26.7 - - - +
62C ALA* 1.3 81.1 - - - +
64C GLY* 1.3 57.6 + - - +
65C GLY* 3.4 1.9 + - - +
119C ASP* 4.4 8.5 - - - +
122C THR* 4.4 7.2 - - - +
----------------------------------------------------------
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