Contacts of the helix formed by residues 38 - 64 (chain E) in PDB entry 1BCF
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 LYS 38 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33E LYS* 5.5 4.7 - - + +
36E GLY* 3.2 10.4 + - - +
37E LEU* 1.3 70.8 - - - +
39E ARG* 1.3 56.6 + - - +
41E ASN* 3.4 7.9 + - - +
42E ASP* 3.0 35.6 + - - +
153E GLN 3.1 6.2 + - - +
154E ILE 3.3 17.9 + - - +
155E ARG* 4.5 0.2 - - - -
156E GLU* 3.8 36.8 - - - +
39J ARG* 5.6 8.1 - - - +
157J GLU* 3.4 37.8 + - - +
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Residues in contact with ARG 39 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38E LYS* 1.3 72.5 - - - +
40E LEU* 1.3 67.9 + - - +
42E ASP* 3.5 2.5 + - - +
43E VAL* 3.1 36.2 + - + +
133E TRP* 4.0 14.2 - - - +
137E GLU* 3.1 38.5 + - - -
140E LEU* 5.6 2.2 - - - +
152E ALA 3.6 14.8 - - - -
153E GLN* 2.8 55.6 + - - +
155E ARG 3.7 12.3 - - - +
156E GLU* 4.0 10.0 - - - +
157E GLU* 4.4 23.7 - - + +
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Residues in contact with LEU 40 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32E PHE* 3.7 33.2 - - + -
37E LEU* 3.4 15.7 + - + +
38E LYS 3.4 0.4 - - - -
39E ARG* 1.3 89.6 - - - +
41E ASN* 1.3 65.0 + - - +
43E VAL* 4.2 2.6 - - - +
44E GLU* 3.1 30.7 + - - +
83E VAL* 4.0 26.0 - - + -
87E LEU* 5.0 4.3 - - + -
133E TRP* 4.3 11.4 - - + -
137E GLU* 4.2 1.6 - - - +
149E TYR* 3.6 15.0 - - + +
150E LEU* 5.9 0.7 - - + -
153E GLN* 3.1 42.8 + - + +
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Residues in contact with ASN 41 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29E ALA* 3.2 28.3 - - - +
30E ARG* 3.2 27.5 + - - +
32E PHE* 3.9 1.5 - - - +
33E LYS* 3.3 38.0 - - + +
37E LEU 3.1 11.5 + - - +
38E LYS* 3.7 6.3 + - - +
40E LEU* 1.3 75.3 - - - +
42E ASP* 1.3 82.7 + - - +
45E TYR* 2.9 29.2 + - - +
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Residues in contact with ASP 42 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38E LYS* 3.0 21.3 + - - +
39E ARG 3.7 5.4 - - - +
41E ASN* 1.3 91.1 + - - +
43E VAL* 1.3 64.6 + - + +
45E TYR* 3.8 6.6 - - - +
46E HIS* 3.4 19.1 + - - +
156E GLU* 3.2 38.7 - - + +
157E GLU 5.3 0.3 - - - +
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Residues in contact with VAL 43 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39E ARG* 3.1 26.0 + - + +
40E LEU 4.2 0.9 - - - +
42E ASP* 1.3 76.4 - - + +
44E GLU* 1.3 65.7 + - - +
46E HIS* 3.2 7.5 + - - +
47E GLU* 3.2 27.3 + - + +
133E TRP* 3.3 56.8 - - + +
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Residues in contact with GLU 44 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25E TYR* 3.2 37.2 - - - +
28E HIS* 3.2 20.1 - - - +
29E ALA* 3.9 18.2 - - + -
32E PHE* 3.6 19.7 - - + -
40E LEU 3.1 21.9 + - - +
43E VAL* 1.3 75.1 - - - +
45E TYR* 1.3 61.0 + - - +
47E GLU* 3.3 13.7 + - - +
48E SER* 3.3 17.0 + - - -
87E LEU* 5.0 2.2 - - - +
90E ASP* 2.7 28.4 - - - +
133E TRP* 3.6 18.9 - - + -
134E LEU* 4.3 1.7 - - - +
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Residues in contact with TYR 45 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26E PHE* 3.5 28.9 - + - -
29E ALA* 3.7 10.4 - - + +
30E ARG* 3.4 33.4 - - - +
41E ASN* 2.9 22.2 + - - +
42E ASP* 3.8 7.4 - - - +
44E GLU* 1.3 76.8 - - - +
46E HIS* 1.3 68.2 + - + +
48E SER* 3.2 9.1 + - - -
49E ILE* 3.2 41.2 + - + +
202E HEM 3.5 28.4 - - + +
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Residues in contact with HIS 46 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42E ASP 3.4 10.3 + - - +
43E VAL* 3.2 8.9 + - - +
45E TYR* 1.3 80.2 - - + +
47E GLU* 1.3 63.6 + - + +
49E ILE* 3.2 18.9 + - + +
50E ASP* 2.9 57.4 + - - -
53E LYS* 5.4 6.5 - - - -
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Residues in contact with GLU 47 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25E TYR* 3.3 31.5 + - + -
43E VAL* 3.2 19.8 + - + +
44E GLU* 3.3 30.1 - - - +
45E TYR 3.3 0.2 - - - -
46E HIS* 1.3 75.4 - - + +
48E SER* 1.3 60.5 + - - +
50E ASP* 3.1 11.2 + - - +
51E GLU* 2.9 34.4 + - - +
130E HIS* 3.3 42.1 - - + +
133E TRP* 3.6 23.6 - - - +
134E LEU* 4.8 0.2 - - - +
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Residues in contact with SER 48 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22E ILE* 3.0 22.3 + - - +
25E TYR* 3.8 16.1 - - - +
26E PHE* 3.5 15.7 - - - -
44E GLU 3.3 10.1 + - - -
45E TYR 3.2 12.7 + - - -
47E GLU* 1.3 79.5 - - - +
49E ILE* 1.3 56.2 + - - +
51E GLU* 3.4 7.2 + - - +
52E MET* 3.0 51.6 + - - +
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Residues in contact with ILE 49 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45E TYR* 3.2 50.4 + - + +
46E HIS* 3.2 20.2 + - + +
48E SER* 1.3 72.8 - - - +
50E ASP* 1.3 66.0 + - - +
52E MET* 3.3 27.2 - - + +
53E LYS* 3.1 43.1 + - - +
202E HEM 3.8 34.8 - - + +
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Residues in contact with ASP 50 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46E HIS* 2.9 53.5 + - - +
47E GLU* 3.1 12.5 + - - +
49E ILE* 1.3 77.2 - - - +
51E GLU* 1.3 58.1 + - - +
53E LYS* 3.0 16.4 + - - +
54E HIS* 2.9 37.3 + - + +
126E ASP* 6.0 1.1 - - + +
130E HIS* 3.8 25.3 + - + +
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Residues in contact with GLU 51 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18E GLU* 2.8 13.0 - - - +
21E ALA* 4.0 10.1 - - + -
22E ILE* 3.9 19.1 - - + +
25E TYR* 3.3 22.9 - - + -
47E GLU 2.9 16.9 + - - +
48E SER* 3.6 6.3 - - - +
50E ASP* 1.3 75.8 - - - +
52E MET* 1.3 53.5 + - - +
54E HIS* 3.0 5.9 + - - +
55E ALA* 2.9 33.6 + - - +
94E GLU* 3.1 4.5 - - - +
130E HIS* 2.9 9.3 + - - -
600E MN 2.1 31.8 + - - -
601E MN 2.0 37.3 + - - -
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Residues in contact with MET 52 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22E ILE* 4.0 15.3 - - + -
26E PHE* 4.0 7.9 - - + -
48E SER* 3.0 38.2 + - - +
49E ILE* 3.3 19.7 - - + +
51E GLU* 1.3 76.1 - - - +
53E LYS* 1.3 61.4 + - - +
55E ALA* 3.6 1.2 - - - +
56E ASP* 3.3 17.8 + - - +
202E HEM 2.7 115.1 - - + +
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Residues in contact with LYS 53 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46E HIS* 5.4 5.1 - - - -
49E ILE* 3.1 22.1 + - - +
50E ASP* 3.0 17.6 + - - +
52E MET* 1.3 75.0 - - - +
54E HIS* 1.3 68.9 + - + +
55E ALA 3.2 0.2 - - - -
56E ASP* 3.4 6.8 + - - +
57E ARG* 3.2 25.4 + - - +
202E HEM 3.8 43.5 + - + -
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Residues in contact with HIS 54 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18E GLU* 3.0 16.6 - - - +
50E ASP* 2.9 18.0 + - + +
51E GLU* 3.0 11.7 + - - +
53E LYS* 1.3 77.8 - - + +
55E ALA* 1.3 63.0 + - - +
57E ARG* 3.0 27.5 + - - +
58E TYR* 3.2 15.1 + - + -
123E ILE* 3.7 26.9 - - + +
126E ASP* 2.9 41.8 + - + +
127E GLU* 3.1 12.3 - - - -
130E HIS* 4.3 7.2 - + - -
601E MN 1.8 32.8 + - - -
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Residues in contact with ALA 55 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15E LEU* 3.7 22.9 - - + -
18E GLU* 4.2 10.0 - - + +
19E LEU* 4.8 6.7 - - + -
22E ILE* 5.3 2.5 - - + -
51E GLU 2.9 15.3 + - - +
52E MET* 3.6 8.3 - - - +
53E LYS 3.2 0.2 - - - -
54E HIS* 1.3 73.6 - - - +
56E ASP* 1.3 66.3 + - - +
58E TYR* 3.1 8.1 + - - +
59E ILE* 3.0 27.7 + - - +
202E HEM 3.7 16.2 - - + -
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Residues in contact with ASP 56 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52E MET 3.3 12.0 + - - +
53E LYS* 3.9 10.1 - - - +
54E HIS 3.4 0.2 - - - -
55E ALA* 1.3 77.6 - - - +
57E ARG* 1.3 62.1 + - - +
59E ILE* 3.4 8.9 + - - +
60E GLU* 3.1 32.9 + - - +
202E HEM 4.1 7.3 - - + +
26F PHE* 3.2 27.6 - - + -
30F ARG* 2.9 40.7 + - - +
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Residues in contact with ARG 57 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125D ARG* 3.9 15.0 - - - +
53E LYS* 3.2 15.2 + - - +
54E HIS* 3.0 19.2 + - - +
56E ASP* 1.3 77.2 - - - +
58E TYR* 1.3 59.6 + - - +
60E GLU* 3.8 4.9 - - - +
61E ARG* 3.1 23.2 + - - +
119E MET* 3.1 45.3 + - - +
122E GLU* 2.7 36.9 + - - +
123E ILE* 3.8 21.1 - - + +
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Residues in contact with TYR 58 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11E LEU* 4.1 29.2 - - + +
14E LEU* 3.8 23.5 - - + +
15E LEU* 4.0 27.6 - - + -
18E GLU* 3.7 28.4 + - + -
54E HIS 3.2 17.5 + - - -
55E ALA* 3.1 6.4 + - - +
57E ARG* 1.3 75.6 - - - +
59E ILE* 1.3 56.2 + - - +
61E ARG* 3.1 4.1 + - - +
62E ILE* 2.8 42.6 + - + +
101E LEU* 3.8 19.2 - - - +
119E MET* 3.7 26.5 - - + -
120E MET* 4.4 2.8 - - + +
123E ILE* 3.7 28.9 - - + +
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Residues in contact with ILE 59 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15E LEU* 4.0 17.9 - - + -
55E ALA 3.0 18.4 + - - +
56E ASP* 3.7 6.3 - - - +
58E TYR* 1.3 75.2 - - - +
60E GLU* 1.3 57.7 + - - +
62E ILE* 4.6 0.7 - - - -
63E LEU* 3.1 29.5 + - + +
69E PRO* 3.7 24.6 - - + +
71E LEU* 4.2 19.5 - - + -
202E HEM 3.4 33.2 - - + -
26F PHE* 3.8 14.4 - - + -
27F LEU* 4.0 17.7 - - + -
30F ARG* 4.2 19.7 - - + -
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Residues in contact with GLU 60 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56E ASP* 3.1 30.5 + - - +
57E ARG* 3.8 5.3 - - - +
59E ILE* 1.3 77.0 - - - +
61E ARG* 1.3 62.9 + - - +
63E LEU* 3.4 6.5 + - - +
64E PHE* 3.0 22.9 + - - +
30F ARG* 3.1 29.1 + - + +
33F LYS* 2.7 37.0 + - - +
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Residues in contact with ARG 61 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128D GLU* 3.1 30.3 + - - +
1E MET* 5.1 0.6 - - - +
11E LEU* 4.0 8.1 - - + -
57E ARG 3.1 17.5 + - - +
58E TYR* 3.1 5.1 + - - +
60E GLU* 1.3 75.0 - - - +
62E ILE* 1.3 64.4 + - - +
64E PHE* 3.2 21.8 + - - +
65E LEU* 3.0 56.0 + - + +
113E ASP* 3.3 23.4 + - - -
115E VAL* 3.9 16.5 - - - +
116E SER* 2.9 18.4 + - - +
119E MET* 3.8 32.1 - - + -
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Residues in contact with ILE 62 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8E ILE* 3.9 15.9 - - + -
11E LEU* 4.0 22.9 - - + +
12E ASN* 3.5 38.1 - - - +
15E LEU* 4.2 7.4 - - + -
58E TYR 2.8 25.0 + - - +
61E ARG* 1.3 76.0 - - - +
63E LEU* 1.3 60.5 + - - +
65E LEU* 3.5 8.4 + - - +
66E GLU 3.2 5.0 + - - -
67E GLY 2.8 48.4 + - - -
68E LEU 3.7 2.9 - - - +
69E PRO* 3.7 28.7 - - + -
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Residues in contact with LEU 63 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59E ILE* 3.1 25.3 + - + +
60E GLU* 3.7 6.1 - - - +
61E ARG 3.2 0.2 - - - -
62E ILE* 1.3 77.3 - - - +
64E PHE* 1.3 66.2 + - - +
66E GLU* 3.2 13.2 + - - +
67E GLY 3.6 10.3 - - - +
68E LEU* 4.8 2.9 - - + -
69E PRO* 3.3 27.1 - - + -
27F LEU* 4.3 5.6 - - + -
30F ARG* 3.7 38.8 - - + +
31F MET* 4.1 14.4 - - + +
34F ASN* 3.9 33.5 + - + +
----------------------------------------------------------
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Residues in contact with PHE 64 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128D GLU* 3.5 37.0 - - + -
131D ILE* 4.3 3.1 - - + -
132D ASP* 3.5 46.2 - - + -
135D GLU* 3.9 10.8 - - - -
1E MET* 2.9 67.4 + - + -
60E GLU 3.0 14.0 + - - +
61E ARG* 3.2 28.2 + - - +
63E LEU* 1.3 72.6 - - - +
65E LEU* 1.3 62.1 + - + +
66E GLU* 3.0 11.2 + - - +
34F ASN* 4.5 7.1 + - - -
----------------------------------------------------------
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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) + - + + + + + -
------------------------------------------------------------
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