Contacts of the helix formed by residues 38 - 74 (chain E) in PDB entry 2B05
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 SER 38 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36E PRO 4.1 1.0 + - - -
37E LEU* 1.3 78.8 - - - +
39E ASN* 1.3 61.7 + - - +
40E GLU* 3.3 8.3 - - - +
41E GLU* 3.0 33.7 + - - +
42E ARG* 2.9 24.3 + - - +
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Residues in contact with ASN 39 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37E LEU 4.9 0.9 - - - +
38E SER* 1.3 75.9 - - - +
40E GLU* 1.3 61.9 + - - +
42E ARG* 2.7 44.5 + - - +
43E ASN* 3.2 31.4 + - - +
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Residues in contact with GLU 40 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12E ARG* 5.4 9.0 - - - +
38E SER* 3.3 6.6 - - - +
39E ASN* 1.3 77.2 - - - +
41E GLU* 1.3 60.1 + - + +
43E ASN* 3.3 8.2 + - - +
44E LEU* 2.9 39.0 + - + +
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Residues in contact with GLU 41 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8E VAL* 3.3 42.7 - - + +
12E ARG* 5.4 1.9 + - - +
27E MET* 4.6 7.6 - - + +
30E VAL* 4.5 15.9 - - + +
36E PRO 4.2 4.2 - - - +
37E LEU* 3.7 15.2 - - + +
38E SER* 3.0 37.7 + - - +
40E GLU* 1.3 78.2 - - + +
42E ARG* 1.3 64.9 + - - +
44E LEU* 3.2 7.6 + - + +
45E LEU* 2.9 24.6 + - - +
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Residues in contact with ARG 42 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37E LEU* 4.0 9.8 + - + +
38E SER 2.9 12.7 + - - +
39E ASN* 2.7 45.8 + - - +
41E GLU* 1.3 74.8 - - - +
43E ASN* 1.3 61.6 + - - +
45E LEU* 3.3 10.2 + - - +
46E SER* 2.9 29.6 + - - -
118E GLU* 5.0 5.1 - - - +
119E SER* 3.1 30.5 + - - +
122E PHE* 3.5 47.0 - - + -
123E TYR* 3.2 30.5 - - + +
171E ILE* 3.7 25.0 - - - +
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Residues in contact with ASN 43 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39E ASN* 3.2 17.5 + - - +
40E GLU* 3.6 10.1 - - - +
42E ARG* 1.3 83.1 - - - +
44E LEU* 1.3 57.9 + - + +
46E SER* 3.1 5.5 + - - -
47E VAL* 2.7 47.9 + - + +
122E PHE* 4.2 17.7 - - - -
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Residues in contact with LEU 44 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8E VAL* 3.9 30.7 - - + +
11E ALA* 4.5 10.5 - - + +
12E ARG* 4.2 32.1 - - + +
15E GLU* 4.0 26.7 - - - +
23E MET* 4.0 7.7 - - - +
27E MET* 4.1 14.6 - - + -
40E GLU* 2.9 27.6 + - + +
41E GLU* 3.2 10.1 + - + +
43E ASN* 1.3 76.3 - - + +
45E LEU* 1.3 62.1 + - - +
47E VAL* 4.0 3.1 - - + -
48E ALA* 3.0 25.5 + - - +
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Residues in contact with LEU 45 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27E MET* 4.1 25.9 - - + +
31E THR* 4.0 19.1 - - - +
41E GLU 2.9 13.2 + - - +
42E ARG* 3.4 9.9 - - - +
44E LEU* 1.3 76.3 - - - +
46E SER* 1.3 62.7 + - - +
48E ALA* 3.5 3.6 - - + +
49E TYR* 3.2 49.0 + - + +
103E LEU* 4.3 9.4 - - + -
104E LEU* 5.6 0.2 - - + -
108E LEU* 3.6 32.8 - - + -
122E PHE* 6.3 0.2 - - + -
123E TYR* 4.6 11.7 - - + +
126E MET* 4.8 13.0 - - + -
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Residues in contact with SER 46 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42E ARG 2.9 16.8 + - - -
43E ASN* 3.7 5.9 + - - -
45E LEU* 1.3 74.5 - - - +
47E VAL* 1.3 60.9 + - - +
49E TYR* 3.5 0.9 + - - +
50E LYS* 2.9 37.3 + - - +
122E PHE* 3.7 26.6 - - - -
126E MET* 4.5 20.3 - - - +
130E TYR* 4.4 1.6 + - - -
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Residues in contact with VAL 47 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15E GLU* 3.3 26.9 - - - +
20E TYR* 4.8 2.0 - - + -
23E MET* 4.5 8.5 - - + -
43E ASN* 2.7 33.3 + - + +
44E LEU* 4.0 4.3 - - - +
46E SER* 1.3 71.4 + - - +
48E ALA* 1.3 63.3 + - - +
50E LYS* 3.6 5.6 - - - +
51E ASN* 2.7 45.2 + - - +
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Residues in contact with ALA 48 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20E TYR* 4.1 2.9 - - - +
23E MET* 3.6 26.0 - - + +
24E ALA* 3.7 29.6 - - - +
27E MET* 5.5 0.2 - - + -
44E LEU 3.0 19.9 + - - +
45E LEU* 3.5 6.5 - - - +
46E SER 3.3 0.2 - - - -
47E VAL* 1.3 79.7 - - - +
49E TYR* 1.3 59.1 + - + +
51E ASN* 3.1 3.5 + - - +
52E VAL* 3.0 31.0 + - - +
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Residues in contact with TYR 49 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24E ALA* 3.5 36.6 + - + +
28E LYS* 3.6 20.3 - - - +
45E LEU* 3.2 36.0 + - + +
46E SER 4.3 0.7 - - - +
48E ALA* 1.3 77.2 - - - +
50E LYS* 1.3 60.2 + - - +
52E VAL* 3.9 6.5 - - + +
53E VAL* 2.8 34.5 + - - +
96E VAL* 4.0 16.2 - - + -
99E ASP* 2.8 33.6 + - + -
100E VAL* 3.1 31.6 - - + -
103E LEU* 4.2 10.2 - - + +
126E MET* 4.9 5.4 - - + -
130E TYR* 3.1 13.6 + - + +
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Residues in contact with LYS 50 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46E SER* 2.9 25.0 + - - +
47E VAL* 3.6 7.4 - - - +
49E TYR* 1.3 77.6 - - - +
51E ASN* 1.3 58.2 + - - +
53E VAL* 3.4 5.7 - - + +
54E GLY* 2.8 27.0 + - - -
130E TYR* 3.1 11.5 + - + +
133E TYR* 5.2 9.2 - - + +
505K SEP 6.0 1.8 - - - +
506K LEU 5.5 3.4 - - - +
507K PRO 4.4 16.8 - - - +
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Residues in contact with ASN 51 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20E TYR* 3.4 55.2 + - + -
47E VAL* 2.7 38.7 + - - +
48E ALA 3.1 1.3 + - - +
50E LYS* 1.3 77.4 - - - +
52E VAL* 1.3 64.6 + - - +
54E GLY* 4.3 1.3 - - - +
55E ALA* 3.1 24.6 + - - +
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Residues in contact with VAL 52 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20E TYR* 3.6 26.2 - - + +
21E ASP* 3.5 27.1 - - - +
24E ALA* 4.2 10.5 - - + -
48E ALA 3.0 16.2 + - - +
49E TYR* 3.9 7.6 - - + +
51E ASN* 1.3 77.9 - - - +
53E VAL* 1.3 62.7 + - - +
55E ALA 3.5 2.4 + - - -
56E ARG* 3.2 39.6 + - - +
96E VAL* 3.7 27.8 - - + -
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Residues in contact with VAL 53 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49E TYR 2.8 25.1 + - - +
50E LYS* 3.4 8.5 - - + +
52E VAL* 1.3 73.6 - - - +
54E GLY* 1.3 63.2 + - - +
56E ARG* 3.0 9.0 + - - +
57E ARG* 2.9 35.0 + - - +
93E LEU* 4.4 15.7 - - + +
96E VAL* 3.9 17.4 - - + +
97E CYS* 3.9 28.0 - - - -
130E TYR* 3.9 16.8 - - + +
133E TYR* 4.0 21.8 - - + -
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Residues in contact with GLY 54 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50E LYS 2.8 22.0 + - - -
51E ASN* 3.8 2.0 - - - -
52E VAL 3.2 0.4 - - - -
53E VAL* 1.3 79.7 - - - +
55E ALA* 1.3 55.2 + - - +
57E ARG* 3.4 14.2 + - - +
58E SER* 3.0 30.7 + - - -
61E ARG* 4.8 1.7 + - - -
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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
----------------------------------------------------------
51E ASN 3.1 16.9 + - - +
53E VAL 3.3 0.2 - - - -
54E GLY* 1.3 75.2 - - - +
56E ARG* 1.3 78.8 + - - +
58E SER* 3.6 5.5 + - - -
59E SER* 3.0 31.4 + - - -
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Residues in contact with ARG 56 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21E ASP* 3.7 22.0 + - - -
52E VAL* 3.2 43.4 + - - +
53E VAL* 3.0 8.7 + - - +
55E ALA* 1.3 88.2 - - - +
57E ARG* 1.3 56.6 + - - +
59E SER* 3.2 3.1 + - - -
60E TRP* 2.8 36.6 + - - +
89E ILE* 3.7 11.1 - - + +
92E GLU* 3.1 33.4 + - - +
93E LEU* 3.9 34.5 - - + +
96E VAL* 5.0 6.9 - - + +
19F ARG* 4.3 11.6 - - - +
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Residues in contact with ARG 57 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50E LYS* 6.4 0.2 - - - +
53E VAL* 2.9 28.6 + - + +
54E GLY* 3.6 13.4 - - - +
56E ARG* 1.3 75.4 - - - +
58E SER* 1.3 63.4 + - - +
60E TRP* 3.3 4.4 + - - +
61E ARG* 3.0 56.0 + - - +
93E LEU* 3.8 18.8 - - + +
133E TYR* 3.4 35.3 + - + +
136E GLU* 2.9 36.8 + - - +
505K SEP 2.6 44.8 + - - -
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Residues in contact with SER 58 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54E GLY 3.0 17.9 + - - -
55E ALA* 3.8 7.4 - - - -
56E ARG 3.2 0.2 - - - -
57E ARG* 1.3 77.6 - - - +
59E SER* 1.3 61.0 + - - +
61E ARG* 3.4 22.3 + - - +
62E VAL* 3.2 29.7 + - - +
18F GLU* 5.4 3.8 + - - -
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Residues in contact with SER 59 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55E ALA 3.0 19.0 + - - -
56E ARG* 3.2 4.9 + - - -
58E SER* 1.3 75.4 + - - +
60E TRP* 1.3 57.4 + - - +
62E VAL* 3.3 5.9 + - - +
63E ILE* 2.9 35.6 + - - +
89E ILE* 4.3 12.1 - - - -
17F ALA* 3.1 29.8 + - - +
19F ARG* 3.8 24.5 + - - +
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Residues in contact with TRP 60 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56E ARG 2.8 21.2 + - - +
57E ARG* 3.3 7.4 + - - +
59E SER* 1.3 72.3 - - - +
61E ARG* 1.3 69.8 + - + +
63E ILE* 3.4 4.1 + - - +
64E SER* 2.7 58.8 + - - -
86E ARG* 4.0 24.9 - - + +
89E ILE* 4.2 8.7 - - + +
90E GLU* 3.1 47.5 + - + +
93E LEU* 4.3 4.9 - - + -
136E GLU* 3.5 24.2 - - + -
137E VAL* 3.4 30.5 - - + -
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Residues in contact with ARG 61 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54E GLY 4.8 1.4 + - - -
57E ARG* 3.0 57.5 + - - +
58E SER* 3.7 28.3 - - - +
59E SER 3.3 0.2 - - - -
60E TRP* 1.3 93.4 - - + +
62E VAL* 1.3 58.3 + - + +
64E SER* 3.8 3.0 - - - -
65E SER* 2.9 32.3 + - - -
136E GLU* 4.5 4.9 + - - -
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Residues in contact with VAL 62 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58E SER* 3.2 18.3 + - - +
59E SER* 3.6 8.7 - - - +
61E ARG* 1.3 77.0 - - + +
63E ILE* 1.3 63.9 + - + +
65E SER* 3.4 5.7 + - - -
66E ILE* 3.2 35.2 + - + +
16F GLN* 3.4 43.1 - - + +
17F ALA* 4.0 7.2 - - - +
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Residues in contact with ILE 63 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59E SER 2.9 20.7 + - - +
60E TRP* 4.0 3.4 - - - +
62E VAL* 1.3 79.5 - - + +
64E SER* 1.3 54.4 + - - +
66E ILE* 3.3 10.1 + - + +
67E GLU* 2.8 34.7 + - - +
82E VAL* 3.9 15.6 - - + +
85E TYR* 4.0 15.5 - - + -
86E ARG* 3.8 36.3 - - + +
89E ILE* 3.9 17.5 - - + -
13F LEU* 3.9 21.8 - - + +
17F ALA* 3.8 23.1 - - + -
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Residues in contact with SER 64 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60E TRP* 2.7 59.3 + - - -
61E ARG* 3.8 4.0 - - - -
63E ILE* 1.3 71.4 - - - +
65E SER* 1.3 62.1 + - - +
67E GLU* 3.2 13.3 + - - +
68E GLN* 2.9 31.5 + - - +
86E ARG* 3.6 11.9 - - - +
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Residues in contact with SER 65 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61E ARG 2.9 18.6 + - - -
62E VAL* 3.5 8.1 - - - -
64E SER* 1.3 75.3 - - - +
66E ILE* 1.3 62.2 + - - +
68E GLN* 3.4 8.0 + - - +
69E LYS* 3.3 28.2 + - - +
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Residues in contact with ILE 66 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62E VAL* 3.2 25.7 + - + +
63E ILE* 3.6 12.8 - - + +
64E SER 3.2 0.2 - - - -
65E SER* 1.3 76.9 - - - +
67E GLU* 1.3 59.4 + - - +
68E GLN 3.2 0.4 - - - -
69E LYS* 3.3 8.2 + - + +
70E THR* 2.9 51.0 + - + +
82E VAL* 4.3 13.9 - - + -
13F LEU* 5.0 11.9 - - + +
16F GLN* 3.6 44.0 - - + +
----------------------------------------------------------
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Residues in contact with GLU 67 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63E ILE 2.8 15.9 + - - +
64E SER* 3.4 8.0 - - - +
66E ILE* 1.3 77.3 - - - +
68E GLN* 1.3 66.2 + - + +
70E THR* 3.9 3.5 + - - -
71E SER* 2.9 33.5 + - - -
79E ILE* 5.3 4.0 - - + +
82E VAL* 4.1 13.4 - - + +
83E ARG* 2.9 59.9 + - + +
86E ARG* 2.8 44.8 + - - +
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Residues in contact with GLN 68 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64E SER* 2.9 22.1 + - - +
65E SER* 3.7 7.9 - - - +
66E ILE 3.2 0.4 - - - -
67E GLU* 1.3 88.1 - - - +
69E LYS* 1.3 63.2 + - + +
71E SER* 3.7 10.2 + - - -
72E ALA* 3.1 24.1 + - - +
83E ARG* 5.6 2.4 + - - -
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Residues in contact with LYS 69 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65E SER* 3.3 19.7 + - - +
66E ILE* 3.5 11.0 - - + +
68E GLN* 1.3 77.1 - - + +
70E THR* 1.3 61.6 + - + +
72E ALA* 3.4 9.3 + - - +
73E ASP* 3.2 20.6 + - - +
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Residues in contact with THR 70 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66E ILE* 2.9 36.0 + - + +
67E GLU* 3.9 3.8 + - - -
69E LYS* 1.3 78.6 - - + +
71E SER* 1.3 62.9 + - - +
73E ASP* 3.2 13.1 + - - +
74E GLY* 2.9 22.3 + - - -
75E ASN 4.3 1.7 + - - +
78E LYS* 4.9 9.5 - - + -
79E ILE* 3.9 16.1 + - - +
82E VAL* 4.1 18.9 - - + +
----------------------------------------------------------
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Residues in contact with SER 71 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67E GLU* 2.9 21.3 + - - -
68E GLN* 3.7 13.9 + - - -
69E LYS 3.3 0.2 - - - -
70E THR* 1.3 75.3 + - - +
72E ALA* 1.3 59.6 + - - +
74E GLY* 3.0 19.9 + - - -
79E ILE* 3.9 21.6 - - - +
83E ARG* 4.4 15.0 + - - -
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Residues in contact with ALA 72 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68E GLN 3.1 13.7 + - - +
69E LYS* 3.4 12.1 - - - +
71E SER* 1.3 73.9 - - - +
73E ASP* 1.3 65.4 + - - +
74E GLY* 4.5 0.2 - - - -
----------------------------------------------------------
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Residues in contact with ASP 73 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69E LYS 3.2 7.8 + - - +
70E THR* 3.2 21.3 + - - +
71E SER 3.1 0.4 - - - -
72E ALA* 1.3 79.1 - - - +
74E GLY* 1.3 58.7 + - - +
75E ASN* 3.7 10.6 + - - +
----------------------------------------------------------
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Residues in contact with GLY 74 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70E THR 2.9 9.7 + - - -
71E SER 3.0 14.9 + - - -
72E ALA 4.4 0.4 - - - -
73E ASP* 1.3 76.7 - - - +
75E ASN* 1.3 65.4 + - - +
76E GLU* 3.3 12.6 + - - +
79E ILE* 3.6 11.7 - - - +
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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