Contacts of the helix formed by residues 44 - 69 (chain D) in PDB entry 5JRE
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 ASP 44 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D SER* 2.9 10.9 + - - +
42D ARG* 3.1 37.9 + - + +
43D GLU* 1.3 73.6 - - - +
45D TYR* 1.3 58.2 + - - +
46D LYS* 3.6 8.7 + - - +
47D SER* 2.7 34.2 + - - -
48D ALA* 3.0 24.4 + - - +
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Residues in contact with TYR 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D MET* 3.6 42.3 + - + -
43D GLU* 3.3 51.3 + - + +
44D ASP* 1.3 70.4 + - - +
46D LYS* 1.3 60.5 + - - +
48D ALA* 3.7 3.8 - - + +
49D ASP* 3.0 42.8 + - - +
90D TYR* 6.5 0.2 - - + -
93D ILE* 3.8 18.3 - - + +
94D LYS* 6.3 2.0 - - + -
125D LYS* 4.8 1.4 + - - -
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Residues in contact with LYS 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44D ASP* 3.6 7.6 + - - +
45D TYR* 1.3 78.3 - - - +
47D SER* 1.3 61.9 + - - +
49D ASP* 3.5 5.9 + - - +
50D LYS* 3.3 24.2 + - + +
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Residues in contact with SER 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D SER* 3.6 14.8 - - - -
42D ARG* 4.0 4.3 + - - -
44D ASP* 2.7 32.2 + - - -
46D LYS* 1.3 75.4 - - - +
48D ALA* 1.3 67.0 + - - +
50D LYS* 3.2 9.5 + - - +
51D TYR* 3.0 37.8 + - - -
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Residues in contact with ALA 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36D LEU* 3.2 21.0 - - + +
39D SER* 3.8 10.7 - - - -
40D MET* 3.5 35.0 - - + +
44D ASP 3.0 17.0 + - - +
45D TYR* 3.7 6.7 - - - +
47D SER* 1.3 76.7 - - - +
49D ASP* 1.3 56.4 + - - +
51D TYR* 3.3 2.6 + - - -
52D LYS* 2.8 27.3 + - - +
90D TYR* 4.6 2.9 - - + -
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Residues in contact with ASP 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D TYR* 3.0 28.2 + - - +
46D LYS* 3.9 5.9 - - - +
47D SER 3.3 0.2 - - - -
48D ALA* 1.3 74.3 - - - +
50D LYS* 1.3 63.4 + - - +
52D LYS* 3.8 5.8 - - - +
53D GLU* 3.1 24.3 + - - +
90D TYR* 2.7 33.4 + - - -
94D LYS* 5.4 1.7 + - - -
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Residues in contact with LYS 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46D LYS* 3.3 14.4 + - + +
47D SER* 3.2 13.1 + - - +
49D ASP* 1.3 77.7 - - - +
51D TYR* 1.3 66.1 + - + +
53D GLU* 3.3 6.9 + - - +
54D GLU* 3.1 33.3 + - - +
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Residues in contact with TYR 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32D LEU* 3.8 26.0 - - + +
35D SER* 3.7 32.8 + - - -
36D LEU* 3.9 18.6 - - + +
39D SER* 3.3 24.9 - - - -
42D ARG* 5.4 3.4 + - - -
47D SER* 3.0 32.2 + - - +
48D ALA 3.8 3.1 - - - +
50D LYS* 1.3 78.7 - - + +
52D LYS* 1.3 58.4 + - - +
54D GLU* 3.3 15.9 + - - +
55D LEU* 2.8 33.2 + - - +
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Residues in contact with LYS 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36D LEU* 3.9 18.8 - - + +
48D ALA 2.8 18.6 + - - +
49D ASP* 3.8 6.7 - - - +
51D TYR* 1.3 75.4 - - - +
53D GLU* 1.3 58.0 + - - +
55D LEU* 3.8 1.6 - - - +
56D THR* 2.7 47.3 + - - +
87D LEU* 3.7 22.7 - - + -
90D TYR* 3.4 40.1 + - + +
91D TYR* 3.4 26.4 + - - -
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Residues in contact with GLU 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D ASP 3.1 14.1 + - - +
50D LYS* 3.6 10.1 - - - +
51D TYR 3.3 0.2 - - - -
52D LYS* 1.3 79.3 - - - +
54D GLU* 1.3 63.4 + - + +
56D THR* 3.5 5.0 + - - -
57D ASN* 3.1 42.0 + - - +
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Residues in contact with GLU 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D ARG* 4.5 12.9 + - - +
32D LEU* 4.0 26.4 - - + +
50D LYS* 3.1 19.3 + - - +
51D TYR* 3.8 20.9 - - - +
53D GLU* 1.3 79.5 - - + +
55D LEU* 1.3 63.6 + - - +
57D ASN* 3.3 9.3 + - - +
58D LEU* 3.0 26.9 + - + +
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Residues in contact with LEU 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D MET* 3.6 42.2 - - + +
32D LEU* 4.1 15.7 - - + +
33D SER* 3.5 29.8 - - - +
36D LEU* 4.0 10.3 - - + -
51D TYR 2.8 18.8 + - - +
52D LYS 3.8 3.4 - - - +
54D GLU* 1.3 73.7 - - - +
56D THR* 1.3 61.8 + - - +
58D LEU* 3.3 2.8 + - - +
59D ALA* 2.9 29.7 + - - +
83D TYR* 3.8 18.2 - - + -
86D ALA* 4.1 3.6 - - + -
87D LEU* 3.7 23.6 - - + -
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Residues in contact with THR 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D LYS* 2.7 34.9 + - - +
53D GLU* 3.7 6.3 - - - -
55D LEU* 1.3 77.6 - - - +
57D ASN* 1.3 59.6 + - - +
59D ALA* 3.3 0.7 + - - +
60D LYS* 3.0 55.0 + - + +
83D TYR* 4.1 19.9 - - - +
87D LEU* 4.5 6.8 - - - +
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Residues in contact with ASN 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53D GLU* 3.1 34.2 + - - +
54D GLU* 3.6 11.3 - - - +
55D LEU 3.2 0.2 - - - -
56D THR* 1.3 76.9 - - - +
58D LEU* 1.3 64.9 + - + +
60D LYS* 3.3 10.1 + - - +
61D THR* 3.1 25.7 + - - -
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Residues in contact with LEU 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D ARG* 3.7 21.1 - - + +
28D ARG* 3.5 51.1 - - + +
29D MET* 3.8 25.6 - - + +
32D LEU* 3.7 20.4 - - + -
54D GLU 3.0 15.3 + - - +
55D LEU* 3.7 7.2 - - - +
57D ASN* 1.3 75.1 - - - +
59D ALA* 1.3 58.6 + - - +
61D THR* 3.2 8.9 + - - +
62D GLN* 2.8 30.3 + - - +
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Residues in contact with ALA 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D MET* 3.7 19.7 - - + +
55D LEU 2.9 17.2 + - - +
56D THR 3.5 5.2 - - - +
57D ASN 3.2 0.2 - - - -
58D LEU* 1.3 77.4 - - - +
60D LYS* 1.3 57.3 + - - +
62D GLN* 3.3 0.9 + - - +
63D ILE* 2.8 40.1 + - + +
80D LEU* 4.3 2.0 - - + -
83D TYR* 3.7 39.0 - - + +
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Residues in contact with LYS 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56D THR* 3.0 44.8 + - + +
57D ASN* 3.5 12.8 - - - +
58D LEU 3.3 0.2 - - - -
59D ALA* 1.3 78.6 - - - +
61D THR* 1.3 62.1 + - - +
63D ILE* 3.5 9.7 + - + +
64D GLU* 3.2 29.7 + - - +
83D TYR* 3.5 9.5 + - - -
103D GLU 4.8 4.2 + - - -
104D LEU 3.4 27.2 + - - -
105D GLY* 4.7 3.8 - - - -
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Residues in contact with THR 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25D ARG* 3.8 29.8 - - - +
57D ASN 3.1 12.2 + - - -
58D LEU* 3.5 11.9 - - + +
60D LYS* 1.3 78.9 - - - +
62D GLN* 1.3 56.0 + - - +
64D GLU* 3.3 6.0 + - - +
65D GLU* 2.9 33.8 + - + +
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Residues in contact with GLN 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D ILE* 3.1 45.3 + - - +
25D ARG* 2.8 39.2 + - - +
26D SER* 3.5 16.8 - - - +
29D MET* 3.9 14.2 - - - -
58D LEU 2.8 19.9 + - - +
59D ALA* 3.7 4.0 - - - +
61D THR* 1.3 69.9 - - - +
63D ILE* 1.3 67.4 + - - +
65D GLU* 3.2 1.1 + - - +
66D LEU* 2.9 34.5 + - + +
76D GLY* 3.8 12.2 + - - +
80D LEU* 4.3 18.4 - - + -
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Residues in contact with ILE 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59D ALA* 2.8 31.7 + - + +
60D LYS* 3.8 13.0 - - + +
62D GLN* 1.3 77.2 - - - +
64D GLU* 1.3 74.8 + - - +
66D LEU* 3.5 5.2 + - - +
67D LYS* 3.3 19.4 + - - +
80D LEU* 3.8 22.7 - - + -
104D LEU 4.5 4.9 - - - +
105D GLY* 3.5 28.7 - - - +
106D VAL* 4.0 17.0 - - + -
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Residues in contact with GLU 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60D LYS* 3.2 18.9 + - - +
61D THR* 3.9 4.7 - - - +
63D ILE* 1.3 92.8 - - - +
65D GLU* 1.3 62.6 + - + +
67D LYS* 3.4 29.9 - - - +
68D LYS* 3.3 34.0 + - - +
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Residues in contact with GLU 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D LYS* 3.3 35.3 - - - +
21D GLU* 4.4 4.7 - - - +
22D ILE* 4.4 13.2 - - + +
25D ARG* 3.8 25.6 + - - +
61D THR* 2.9 30.5 + - + +
62D GLN* 3.2 3.6 + - - +
64D GLU* 1.3 74.6 - - - +
66D LEU* 1.3 61.6 + - - +
68D LYS* 3.2 21.8 + - - +
69D TYR* 2.9 38.4 + - + +
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Residues in contact with LEU 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C PRO* 5.4 3.6 - - - +
22D ILE* 3.8 27.1 - - + -
62D GLN* 2.9 21.6 + - + +
63D ILE* 4.0 4.3 - - - +
65D GLU* 1.3 76.3 - - - +
67D LYS* 1.3 62.8 + - - +
69D TYR 3.3 2.4 - - - -
70D PRO* 3.2 26.5 - - - +
72D PHE 3.4 26.7 - - - +
73D TYR* 3.8 39.4 - - + +
76D GLY* 4.3 8.7 - - - -
77D PHE* 4.9 0.4 - - - +
80D LEU* 3.6 30.7 - - + -
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Residues in contact with LYS 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70C PRO* 6.3 2.9 - - - -
63D ILE* 3.3 11.9 + - + +
64D GLU* 3.4 34.8 - - - +
65D GLU 3.2 0.4 - - - -
66D LEU* 1.3 79.4 - - - +
68D LYS* 1.3 70.7 + - + +
69D TYR 3.5 0.2 + - - -
70D PRO* 3.6 10.6 - - - +
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Residues in contact with LYS 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64D GLU* 3.3 20.4 + - - +
65D GLU* 3.2 26.0 + - - +
67D LYS* 1.3 86.0 - - + +
69D TYR* 1.3 87.3 + - + +
70D PRO* 3.4 7.0 - - - +
71D MET* 5.2 1.2 - - - +
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Residues in contact with TYR 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14D LYS* 2.8 33.3 + - - +
15D LEU* 3.6 27.1 - - + -
18D LYS* 3.5 48.5 - - + -
22D ILE* 4.4 6.5 - - + +
65D GLU* 2.9 32.7 + - - +
66D LEU* 3.3 8.5 - - - +
67D LYS 3.3 0.2 - - - -
68D LYS* 1.3 103.5 - - + +
70D PRO* 1.4 60.1 - - - +
71D MET* 3.2 9.2 - - + -
72D PHE* 2.9 40.3 + - + +
73D TYR 3.9 1.9 + - - -
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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) + - + + + + + -
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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