Contacts of the helix formed by residues 38 - 74 (chain B) in PDB entry 4O46
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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B PRO 4.1 0.4 + - - -
37B LEU* 1.3 74.1 - - - +
39B ASN* 1.3 60.1 + - - +
40B GLU* 3.6 8.6 + - - +
41B GLU* 2.9 39.2 + - - +
42B ARG* 2.8 29.1 + - - +
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Residues in contact with ASN 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B SER* 1.3 72.7 - - - +
40B GLU* 1.4 59.3 + - - +
42B ARG* 2.9 38.1 + - - +
43B ASN* 2.8 35.5 + - - +
118B GLU* 4.3 13.8 + - - +
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Residues in contact with GLU 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B VAL* 4.4 2.6 - - - +
12B ARG* 2.7 51.2 + - - +
38B SER* 3.6 7.0 + - - +
39B ASN* 1.4 76.1 - - - +
41B GLU* 1.4 57.6 + - - +
43B ASN* 3.2 7.0 + - - +
44B LEU* 2.9 49.7 + - + +
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Residues in contact with GLU 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B ARG* 2.7 42.9 + - - -
8B VAL* 3.5 33.9 - - + +
27B MET* 3.3 22.9 - - + +
30B VAL* 4.7 0.2 - - - -
36B PRO 4.1 0.5 - - - +
37B LEU* 3.5 9.4 - - + -
38B SER* 2.9 36.2 + - - +
40B GLU* 1.4 77.4 - - - +
42B ARG* 1.4 63.0 + - - +
44B LEU* 3.2 4.7 + - - -
45B LEU* 3.1 20.8 + - - +
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Residues in contact with ARG 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B LEU* 3.9 16.4 + - + +
38B SER 2.8 25.9 + - - +
39B ASN* 2.9 46.0 + - - +
41B GLU* 1.4 71.2 - - - +
43B ASN* 1.3 62.2 + - - +
45B LEU* 3.6 3.9 + - - +
46B SER* 3.1 26.7 + - - -
118B GLU* 4.3 5.7 + - - +
119B SER* 3.4 25.6 + - - +
122B PHE* 3.5 39.5 - - + -
123B TYR* 3.2 42.2 - - + +
171B ILE* 3.5 28.3 - - - +
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Residues in contact with ASN 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B ASN* 2.8 31.5 + - - +
40B GLU* 3.7 5.8 - - - +
42B ARG* 1.3 80.8 - - - +
44B LEU* 1.4 59.6 + - - +
46B SER* 3.6 5.2 - - - -
47B VAL* 2.9 41.5 + - + +
122B PHE* 4.0 23.8 - - - -
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Residues in contact with LEU 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B VAL* 3.8 29.6 - - + +
11B ALA* 4.7 0.9 - - + -
12B ARG* 4.2 21.8 - - + +
15B GLU* 3.7 15.5 - - - +
23B MET* 3.3 27.7 - - + +
27B MET* 3.8 19.3 - - + -
40B GLU* 2.9 39.4 + - + +
41B GLU* 3.6 12.3 - - - +
43B ASN* 1.4 75.5 - - - +
45B LEU* 1.4 55.6 + - - +
47B VAL* 4.7 1.1 - - - -
48B ALA* 3.0 30.5 + - - +
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Residues in contact with LEU 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B MET* 3.7 29.5 - - + +
31B THR* 3.9 13.5 - - - +
37B LEU* 4.1 14.1 - - + -
41B GLU 3.1 15.7 + - - +
42B ARG 3.7 5.4 - - - +
44B LEU* 1.4 76.2 - - - +
46B SER* 1.3 60.0 - - - +
48B ALA* 3.4 2.8 - - - +
49B TYR* 3.1 54.4 + - + +
100B VAL* 5.3 1.8 - - + -
103B LEU* 4.4 8.1 - - + -
108B LEU* 3.6 30.1 - - + -
123B TYR* 4.9 3.1 - - + -
126B MET* 4.4 20.0 - - + -
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Residues in contact with SER 46 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B ARG 3.1 18.9 + - - -
43B ASN* 3.3 7.4 + - - -
45B LEU* 1.3 73.0 - - - +
47B VAL* 1.4 56.5 + - - +
49B TYR 3.9 0.2 - - - -
50B LYS* 2.9 40.7 + - - +
122B PHE* 3.9 21.4 - - - -
125B LYS* 5.7 2.8 + - - -
126B MET* 4.2 22.0 - - - +
130B TYR* 4.0 3.6 + - - -
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Residues in contact with VAL 47 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B GLU* 3.5 24.7 - - - +
20B TYR* 4.4 3.6 - - + -
23B MET* 4.0 12.6 - - + -
43B ASN* 2.9 29.0 + - + +
44B LEU* 4.0 2.9 - - - +
46B SER* 1.4 69.4 - - - +
48B ALA* 1.4 65.9 + - - +
50B LYS* 3.4 5.5 + - - +
51B ASN* 2.9 46.5 + - - +
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Residues in contact with ALA 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B TYR* 3.9 4.1 - - - +
23B MET* 3.7 22.0 - - + +
24B ALA* 3.5 32.3 - - - +
44B LEU 3.0 18.7 + - - +
45B LEU* 3.4 8.3 - - - +
47B VAL* 1.4 79.0 - - - +
49B TYR* 1.3 62.1 + - - +
51B ASN* 3.4 3.5 + - - +
52B VAL* 3.2 27.1 + - - +
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Residues in contact with TYR 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ALA* 3.8 31.5 + - + +
25B ALA* 5.4 0.3 - - - -
28B LYS* 3.6 20.1 - - - +
45B LEU* 3.1 44.3 + - + +
46B SER 4.3 0.2 - - - +
48B ALA* 1.3 76.0 - - - +
50B LYS* 1.4 59.4 + - - +
52B VAL* 3.8 5.3 - - + +
53B VAL* 3.0 33.8 + - - +
96B VAL* 3.9 24.2 - - + -
99B ASP* 2.7 33.9 + - + -
100B VAL* 4.0 21.5 - - + -
103B LEU* 3.7 12.4 - - + +
126B MET* 5.2 0.7 - - + -
130B TYR* 3.3 19.0 - - + +
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Residues in contact with LYS 50 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B SER* 2.9 24.2 + - - +
47B VAL* 3.7 7.2 - - - +
49B TYR* 1.4 74.4 - - - +
51B ASN* 1.3 55.9 + - - +
53B VAL* 3.5 4.9 - - - +
54B GLY* 2.8 31.9 + - - -
57B ARG* 4.1 15.5 - - - +
130B TYR* 3.2 10.0 + - + +
133B TYR* 3.3 29.6 - - + +
178B ASN* 6.2 0.9 - - - +
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Residues in contact with ASN 51 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B TYR* 3.4 56.6 + - + -
47B VAL* 2.9 36.8 + - - +
48B ALA 3.8 0.2 - - - +
50B LYS* 1.3 77.8 - - - +
52B VAL* 1.4 62.9 + - - +
54B GLY* 3.8 1.3 - - - -
55B ALA* 3.1 23.7 + - - +
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Residues in contact with VAL 52 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B TYR* 3.4 26.5 - - + +
21B ASP* 3.5 21.5 - - - +
24B ALA* 4.2 8.7 - - + -
48B ALA 3.2 18.3 + - - +
49B TYR* 3.3 9.6 + - + +
51B ASN* 1.4 76.8 - - - +
53B VAL* 1.3 61.4 + - - +
55B ALA* 3.4 5.0 + - - +
56B ARG* 3.1 41.0 + - - +
96B VAL* 3.8 27.1 - - + -
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Residues in contact with VAL 53 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B TYR 3.0 19.4 + - - +
50B LYS* 3.5 8.3 - - + +
52B VAL* 1.3 73.6 - - - +
54B GLY* 1.3 63.6 + - - +
56B ARG* 3.0 9.5 + - - +
57B ARG* 2.9 35.8 + - + +
93B LEU* 4.0 22.4 - - + +
96B VAL* 3.9 15.5 - - + +
97B CYS* 3.8 28.5 - - - -
130B TYR* 3.7 18.2 - - + -
133B TYR* 3.9 20.4 - - + -
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Residues in contact with GLY 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B LYS* 2.8 21.1 + - - -
51B ASN* 3.8 2.9 - - - -
52B VAL 3.3 0.4 - - - -
53B VAL* 1.3 77.5 - - - +
55B ALA* 1.3 54.7 + - - +
57B ARG* 3.6 16.2 - - - +
58B SER* 2.9 32.8 + - - -
61B ARG* 4.9 1.2 + - - -
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Residues in contact with ALA 55 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B ASN 3.1 12.3 + - - +
52B VAL* 3.5 11.7 - - - +
53B VAL 3.3 0.4 - - - -
54B GLY* 1.3 74.9 - - - +
56B ARG* 1.4 68.9 + - - +
58B SER* 3.6 5.4 + - - -
59B SER* 2.9 32.6 + - - -
19D ARG* 6.2 0.2 - - - -
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Residues in contact with ARG 56 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B ASP* 4.1 16.4 + - - -
52B VAL* 3.1 41.7 + - - +
53B VAL* 3.0 7.7 + - - +
55B ALA* 1.4 85.9 - - - +
57B ARG* 1.4 57.1 + - - +
59B SER* 3.3 2.6 + - - -
60B TRP* 2.8 36.0 + - - +
89B ILE* 3.4 15.7 - - + +
92B GLU* 3.2 46.7 + - + +
93B LEU* 3.8 25.8 - - + +
96B VAL* 4.7 11.9 - - - +
19D ARG* 4.5 6.7 - - - +
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Residues in contact with ARG 57 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B LYS* 4.1 13.7 - - - +
53B VAL* 2.9 30.1 + - + +
54B GLY* 3.6 13.4 - - - +
56B ARG* 1.4 74.9 - - - +
58B SER* 1.3 62.4 + - - +
60B TRP* 3.4 5.1 + - - +
61B ARG* 3.0 53.4 + - - +
93B LEU* 3.8 18.6 - - + -
132B ARG* 4.4 5.1 - - - +
133B TYR* 3.3 49.7 + - + +
136B GLU* 3.1 39.6 + - - +
185B GLU* 5.7 0.4 + - - -
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Residues in contact with SER 58 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B GLY 2.9 17.2 + - - -
55B ALA* 3.8 6.3 - - - -
57B ARG* 1.3 75.9 - - - +
59B SER* 1.4 62.3 + - - +
61B ARG* 3.4 23.3 + - - +
62B VAL* 3.2 29.8 + - - +
18D GLU* 5.2 6.4 + - - -
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Residues in contact with SER 59 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B ALA 2.9 20.5 + - - -
56B ARG* 3.7 4.7 - - - -
58B SER* 1.4 71.6 - - - +
60B TRP* 1.4 59.6 + - - +
62B VAL* 3.1 5.2 + - - +
63B ILE* 2.9 34.0 + - - +
89B ILE* 4.2 9.2 - - - -
17D ALA* 2.7 40.2 + - - +
18D GLU 5.1 0.3 + - - -
19D ARG* 3.8 19.0 + - - +
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Residues in contact with TRP 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B ARG 2.8 22.8 + - - +
57B ARG* 3.6 7.2 - - - +
59B SER* 1.4 72.3 - - - +
61B ARG* 1.4 69.1 + - + +
63B ILE* 3.4 5.0 + - - +
64B SER* 2.8 60.6 + - - -
86B ARG* 3.4 23.8 - - + +
89B ILE* 3.8 9.3 - - + +
90B GLU* 2.9 46.5 + - + +
93B LEU* 4.7 3.4 - - + -
136B GLU* 3.5 23.6 - - + -
137B VAL* 3.5 30.3 - - + -
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Residues in contact with ARG 61 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B GLY 4.9 1.0 + - - -
57B ARG* 3.0 52.9 + - - +
58B SER* 3.6 29.7 + - - +
59B SER 3.3 0.2 - - - -
60B TRP* 1.4 93.1 - - + +
62B VAL* 1.3 56.7 + - + +
64B SER* 3.7 3.1 - - - -
65B SER* 3.0 30.0 + - - -
136B GLU* 4.6 4.9 + - - -
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Residues in contact with VAL 62 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B SER* 3.2 19.8 + - - +
59B SER* 3.1 10.1 + - - +
61B ARG* 1.3 73.9 - - + +
63B ILE* 1.4 62.4 + - + +
65B SER* 3.4 7.6 + - - -
66B ILE* 3.1 39.3 + - + +
16D GLN* 3.3 38.8 - - + +
17D ALA* 4.0 4.7 - - - +
18D GLU* 6.1 1.3 - - - +
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Residues in contact with ILE 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B SER 2.9 19.7 + - - +
60B TRP* 4.0 3.4 - - - +
62B VAL* 1.4 71.3 - - - +
64B SER* 1.4 55.0 + - - +
66B ILE* 3.1 11.2 + - + +
67B GLU* 2.8 32.4 + - + +
82B VAL* 3.5 33.7 - - + +
85B TYR* 3.6 21.1 - - + -
86B ARG* 3.8 22.0 - - + +
89B ILE* 3.7 21.1 - - + -
13D LEU* 3.8 25.6 - - + +
17D ALA* 3.6 19.5 - - + -
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Residues in contact with SER 64 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B TRP* 2.8 58.3 + - - -
61B ARG* 3.7 5.2 - - - -
63B ILE* 1.4 70.5 - - - +
65B SER* 1.3 61.7 + - - +
67B GLU* 3.3 11.1 + - - +
68B GLN* 3.1 36.9 + - - -
86B ARG* 3.8 10.4 + - - +
----------------------------------------------------------
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Residues in contact with SER 65 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B ARG 3.0 18.2 + - - -
62B VAL* 3.4 8.7 - - - -
64B SER* 1.3 73.0 - - - +
66B ILE* 1.4 63.5 + - - +
68B GLN* 3.5 6.9 + - - +
69B LYS* 3.4 29.2 + - - +
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Residues in contact with ILE 66 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B VAL* 3.1 31.8 + - + +
63B ILE* 3.5 9.0 - - + +
65B SER* 1.4 72.4 - - - +
67B GLU* 1.4 54.1 + - - +
69B LYS* 3.2 7.6 + - - +
70B THR* 2.7 40.8 + - - -
82B VAL* 4.2 11.7 - - + -
13D LEU* 3.8 29.6 - - + -
16D GLN* 3.5 40.4 - - + +
----------------------------------------------------------
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Residues in contact with GLU 67 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B ILE 2.8 17.0 + - - +
64B SER* 3.4 13.0 + - - +
66B ILE* 1.4 72.4 - - - +
68B GLN* 1.3 64.1 + - - +
70B THR* 4.0 4.0 - - - -
71B SER* 3.1 30.4 + - - -
79B ILE* 5.2 6.3 - - + +
82B VAL* 3.8 19.3 - - + +
83B ARG* 3.4 24.9 - - - +
86B ARG* 2.9 46.8 + - - +
----------------------------------------------------------
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Residues in contact with GLN 68 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B SER* 3.1 33.6 + - - +
65B SER* 3.8 6.5 - - - +
66B ILE 3.3 0.2 - - - -
67B GLU* 1.3 86.1 - - - +
69B LYS* 1.3 62.9 + - + +
71B SER* 3.9 10.4 + - - -
72B ALA* 3.9 10.2 + - - +
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Residues in contact with LYS 69 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B SER* 3.4 17.7 + - - +
66B ILE* 3.2 8.9 + - - +
68B GLN* 1.3 77.1 - - + +
70B THR* 1.4 62.8 + - - +
72B ALA* 3.4 20.4 + - - +
73B ASP* 3.7 6.4 + - - +
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Residues in contact with THR 70 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B ILE* 2.7 30.4 + - - -
67B GLU* 4.0 6.3 - - - -
69B LYS* 1.4 69.2 - - - +
71B SER* 1.4 64.1 + - - +
72B ALA 3.4 0.3 + - - -
73B ASP* 3.4 14.9 + - - +
74B GLY 3.5 8.7 + - - -
75B ASN* 4.3 5.0 + - - +
78B LYS* 5.7 5.2 - - - -
79B ILE* 3.8 19.7 - - - +
82B VAL* 4.8 11.4 - - - -
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Residues in contact with SER 71 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B GLU* 3.1 18.9 + - - -
68B GLN* 3.9 8.3 - - - -
69B LYS 3.3 0.2 - - - -
70B THR* 1.4 75.4 - - - +
72B ALA* 1.3 60.7 + - - +
74B GLY* 3.6 11.8 + - - -
79B ILE* 3.9 14.3 - - - +
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Residues in contact with ALA 72 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B GLN 3.9 8.5 + - - +
69B LYS* 3.4 13.8 + - - +
70B THR 3.3 0.2 - - - -
71B SER* 1.3 78.3 - - - +
73B ASP* 1.4 61.3 + - - +
74B GLY* 3.5 0.7 + - - -
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Residues in contact with ASP 73 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B LYS 3.7 6.3 + - - +
70B THR* 3.4 11.3 + - - +
72B ALA* 1.4 77.0 - - - +
74B GLY* 1.3 63.9 + - - +
75B ASN* 5.0 5.8 - - + +
----------------------------------------------------------
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Residues in contact with GLY 74 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B THR 3.5 5.0 + - - -
71B SER* 3.6 9.6 + - - -
72B ALA 3.3 3.9 - - - -
73B ASP* 1.3 80.8 - - - +
75B ASN* 1.3 60.2 + - - +
76B GLU 3.8 2.6 + - - -
79B ILE* 5.7 1.3 - - - -
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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