Contacts of the helix formed by residues 12 - 42 (chain F) in PDB entry 2YW7
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 12 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11F ASP* 1.3 76.7 - - - +
13F LYS* 1.3 68.0 + - + +
14F ALA 3.3 0.2 - - - -
15F SER* 3.0 12.1 + - - -
16F ASP* 3.0 44.7 + - - +
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Residues in contact with LYS 13 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11F ASP 4.1 5.1 - - - +
12F LYS* 1.3 79.1 - - + +
14F ALA* 1.3 58.7 + - - +
16F ASP* 3.1 7.2 + - - +
17F VAL* 2.9 35.9 + - + +
130F LEU* 4.7 20.4 - - + +
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Residues in contact with ALA 14 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11F ASP* 4.0 20.9 - - - +
13F LYS* 1.3 78.7 - - - +
15F SER* 1.3 61.6 + - - +
17F VAL* 3.9 7.9 - - - +
18F ALA* 3.1 25.1 + - - +
75F LEU* 4.1 38.6 - - + +
77F LYS* 4.6 2.4 - - + +
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Residues in contact with SER 15 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11F ASP 2.7 21.8 + - - -
12F LYS* 3.0 21.7 + - - -
14F ALA* 1.3 77.1 - - - +
16F ASP* 1.3 59.8 + - - +
18F ALA* 3.5 3.8 - - - +
19F ASP* 3.2 30.9 + - - +
77F LYS* 2.8 31.6 + - - +
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Residues in contact with ASP 16 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12F LYS* 3.0 45.4 + - - +
13F LYS* 3.1 7.3 + - - +
15F SER* 1.3 78.9 - - - +
17F VAL* 1.3 64.5 + - - +
18F ALA 3.2 0.9 - - - -
19F ASP* 3.3 14.8 + - + +
20F LEU* 3.0 30.3 + - + +
130F LEU* 4.5 14.1 - - + -
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Residues in contact with VAL 17 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13F LYS* 2.9 23.7 + - + +
14F ALA* 3.9 5.8 - - - +
16F ASP* 1.3 74.0 - - - +
18F ALA* 1.3 52.1 + - - +
20F LEU* 3.2 9.8 + - - +
21F LEU* 2.8 38.2 + - + +
75F LEU* 3.5 23.6 - - + -
127F LEU* 4.1 7.6 - - + -
130F LEU* 4.1 21.5 - - + +
131F ASP* 3.7 26.5 - - + +
134F SER* 3.6 22.9 - - - +
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Residues in contact with ALA 18 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14F ALA 3.1 19.4 + - - +
15F SER 3.5 6.3 - - - +
17F VAL* 1.3 74.9 - - - +
19F ASP* 1.3 53.2 + - - +
21F LEU* 2.6 13.1 + - - +
22F GLN* 2.4 39.2 + - - +
72F ILE* 4.2 10.7 - - + +
75F LEU* 4.2 8.4 - - + +
77F LYS* 3.8 31.9 - - + -
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Residues in contact with ASP 19 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15F SER 3.2 16.5 + - - +
16F ASP* 3.3 17.9 + - + +
18F ALA* 1.3 74.2 - - - +
20F LEU* 1.3 59.3 + - + +
22F GLN* 3.2 10.5 + - - +
23F LYS* 2.8 43.1 + - - +
77F LYS* 5.7 2.3 + - - +
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Residues in contact with LEU 20 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16F ASP* 3.0 18.4 + - + +
17F VAL* 3.2 10.3 - - - +
19F ASP* 1.3 77.2 - - + +
21F LEU* 1.3 58.9 + - + +
23F LYS* 3.1 29.7 + - + +
24F GLN* 3.0 26.0 + - - +
123F SER* 4.0 23.0 + - - +
126F LYS* 3.9 40.8 - - + +
127F LEU* 3.8 33.4 - - + -
130F LEU* 5.2 4.7 - - + -
138F LEU* 5.9 0.4 - - + -
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Residues in contact with LEU 21 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17F VAL* 2.8 34.4 + - + +
18F ALA 2.6 11.6 + - - +
20F LEU* 1.3 72.2 - - + +
22F GLN* 1.3 54.5 + - - +
24F GLN* 3.6 4.3 - - - +
25F LEU* 2.8 32.4 + - - +
68F VAL* 4.4 13.9 - - + +
71F ARG* 3.8 30.1 - - + -
72F ILE* 3.5 19.6 - - + +
75F LEU* 4.0 8.1 - - + -
127F LEU* 5.2 2.0 - - + -
134F SER* 4.0 18.6 - - - +
137F LEU* 5.3 2.2 - - + -
138F LEU* 4.2 34.5 - - + -
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Residues in contact with GLN 22 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18F ALA 2.4 29.3 + - - +
19F ASP* 3.4 12.8 - - - +
21F LEU* 1.3 67.4 - - - +
23F LYS* 1.3 64.0 + - - +
25F LEU* 3.3 10.3 + - - +
26F SER* 3.2 21.3 + - - +
72F ILE* 3.7 10.0 - - + +
78F SER 4.7 0.2 - - - +
79F PRO* 4.2 4.0 - - - +
80F LYS* 3.3 58.4 + - - +
85F ALA* 4.1 8.1 - - - +
89F ASP* 2.8 27.3 + - - +
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Residues in contact with LYS 23 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19F ASP* 2.8 30.3 + - - +
20F LEU* 3.1 28.1 + - + +
22F GLN* 1.3 76.1 - - + +
24F GLN* 1.3 60.0 + - - +
26F SER* 3.5 3.5 + - - -
27F THR* 3.0 29.8 + - - +
89F ASP* 4.5 28.2 - - + +
92F TRP* 4.8 2.3 - - - -
119F ASP* 6.0 2.7 - - - +
123F SER* 5.6 4.3 - - - +
126F LYS* 5.2 9.7 - - - +
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Residues in contact with GLN 24 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20F LEU 3.0 11.5 + - - +
21F LEU* 3.6 11.9 - - - +
22F GLN 3.3 0.2 - - - -
23F LYS* 1.3 77.2 - - - +
25F LEU* 1.3 67.1 + - - +
27F THR* 3.0 15.2 + - - +
28F TYR* 2.9 63.8 + - + -
68F VAL* 4.7 3.6 - - + -
119F ASP* 4.8 4.2 + - - +
120F THR* 3.1 36.1 + - - +
123F SER* 4.2 15.4 + - - -
138F LEU* 3.6 29.8 - - + +
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Residues in contact with LEU 25 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C TRP* 4.0 13.5 - - + -
21F LEU 2.8 14.4 + - - +
22F GLN* 3.3 28.5 - - - +
24F GLN* 1.3 77.3 - - - +
26F SER* 1.3 57.6 + - - +
28F TYR* 3.2 2.9 + - - +
29F ASN* 2.9 54.5 + - - +
65F ALA* 3.4 26.0 - - + +
68F VAL* 3.9 16.1 - - + +
69F ALA* 4.4 1.8 - - + -
72F ILE* 4.0 5.8 - - + -
79F PRO* 3.8 15.5 - - + -
80F LYS 3.7 28.0 - - - +
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Residues in contact with SER 26 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22F GLN* 3.2 13.1 + - - -
23F LYS 3.7 6.3 - - - -
25F LEU* 1.3 76.0 - - - +
27F THR* 1.3 67.9 + - - +
29F ASN* 3.0 3.2 + - - +
30F ASP* 2.9 24.3 + - - +
80F LYS 4.4 2.3 + - - -
85F ALA 3.1 6.4 + - - -
86F ILE* 3.1 38.0 - - - +
89F ASP* 2.8 30.6 + - - -
92F TRP* 4.6 4.7 - - - -
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Residues in contact with THR 27 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23F LYS 3.0 15.8 + - - -
24F GLN* 3.1 23.4 + - - +
26F SER* 1.3 77.0 - - - +
28F TYR* 1.3 79.0 + - + +
30F ASP* 3.4 3.6 + - - +
31F LEU* 3.0 19.8 + - + +
92F TRP* 3.0 34.9 - - + -
116F VAL* 4.1 38.0 - - + +
119F ASP* 4.6 7.5 + - + +
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Residues in contact with TYR 28 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24F GLN* 2.9 49.7 + - + +
25F LEU 3.4 7.0 - - - +
27F THR* 1.3 79.9 - - + +
29F ASN* 1.3 58.9 + - - +
31F LEU* 2.8 25.3 + - + +
32F HIS* 2.9 17.5 + - - -
61F VAL* 3.7 12.4 - - + +
64F TYR* 3.2 30.3 - + + -
65F ALA* 3.3 33.0 - - + -
68F VAL* 4.4 6.1 - - + -
116F VAL* 5.7 0.9 - - + -
138F LEU* 3.8 1.4 - - - +
141F HIS* 2.5 43.9 + + + +
145F LEU* 4.6 14.9 - - + +
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Residues in contact with ASN 29 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C LEU* 4.9 6.6 - - + +
40C TRP* 4.0 8.2 - - - -
25F LEU* 2.9 48.2 + - - +
26F SER* 3.0 3.8 + - - +
28F TYR* 1.3 72.4 - - - +
30F ASP* 1.3 61.9 + - - +
32F HIS* 3.6 18.4 + - - +
33F LEU* 3.3 30.0 + - - +
65F ALA* 3.5 17.8 - - - +
80F LYS 4.7 0.4 + - - -
81F GLY* 3.8 22.9 - - - -
86F ILE* 3.5 22.6 - - + +
----------------------------------------------------------
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Residues in contact with ASP 30 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C THR* 5.6 0.2 - - - +
83C PRO* 3.1 27.9 - - + +
26F SER 2.9 15.0 + - - +
27F THR 3.7 3.7 - - - +
29F ASN* 1.3 76.4 - - - +
31F LEU* 1.3 59.3 + - - +
33F LEU* 3.3 3.3 + - - +
34F THR* 3.0 40.5 + - - -
86F ILE* 4.0 7.7 - - + +
90F ARG* 2.7 26.4 + - + +
92F TRP* 3.3 32.7 + - + +
93F ASP 4.8 1.1 - - - +
94F ASP* 4.1 4.2 - - - +
112F VAL* 5.8 3.5 - - - +
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Residues in contact with LEU 31 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27F THR* 3.0 14.5 + - + +
28F TYR* 2.8 16.1 + - + +
30F ASP* 1.3 80.2 + - - +
32F HIS* 1.3 54.5 + - - -
34F THR* 3.2 6.0 + - - -
35F LEU* 3.1 42.8 + - + +
61F VAL* 3.3 37.2 - - + -
112F VAL* 3.7 30.7 - - + -
113F TYR* 3.7 31.6 - - + +
116F VAL* 4.6 17.9 - - + -
145F LEU* 6.2 2.0 - - + -
----------------------------------------------------------
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Residues in contact with HIS 32 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C HIS* 4.4 8.1 - + - -
33C LEU* 4.4 10.6 - - + +
62C ARG* 4.6 4.0 + - - -
28F TYR 2.9 12.7 + - - -
29F ASN* 3.6 45.3 + - - +
31F LEU* 1.3 72.6 - - - +
33F LEU* 1.3 78.1 + - + +
35F LEU* 3.8 12.2 + - + +
36F LYS* 3.7 19.6 + - - +
58F VAL* 4.2 6.9 - - - +
61F VAL* 3.7 19.7 - - + -
62F ARG* 3.2 53.3 + - + +
65F ALA* 4.6 4.0 - - + +
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Residues in contact with LEU 33 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C ASN* 4.1 13.7 - - - +
32C HIS* 4.0 25.4 - - + +
33C LEU* 3.6 30.7 - - + -
81C GLY 3.3 26.1 - - - +
82C THR* 5.3 0.4 - - - -
83C PRO* 3.8 28.3 - - + -
86C ILE* 3.9 9.0 - - + -
29F ASN 3.3 17.9 + - - +
30F ASP 3.5 5.4 - - - +
31F LEU 3.2 0.2 - - - -
32F HIS* 1.3 89.5 + - + +
34F THR* 1.3 63.8 + - - +
36F LYS* 3.8 6.4 + - + +
37F HIS* 3.4 13.5 + - - +
40F TRP* 5.4 1.4 - - + -
86F ILE* 4.4 2.5 - - + -
----------------------------------------------------------
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Residues in contact with THR 34 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C THR* 4.1 14.1 - - - +
30F ASP* 3.0 23.9 + - - -
31F LEU* 3.2 12.8 + - - -
33F LEU* 1.3 75.1 - - - +
35F LEU* 1.3 63.1 + - + +
37F HIS* 2.6 28.2 + - - +
38F VAL* 2.8 25.4 + - + +
94F ASP 5.2 2.1 + - - -
95F TYR* 3.8 37.1 - - + +
109F LEU* 5.0 4.0 - - + -
112F VAL* 5.1 9.1 - - + +
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Residues in contact with LEU 35 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31F LEU* 3.1 52.0 + - + +
32F HIS* 4.0 5.4 - - - +
33F LEU 3.5 0.2 - - - -
34F THR* 1.3 78.9 - - - +
36F LYS* 1.3 58.6 + - - +
38F VAL* 3.4 8.6 + - - +
39F HIS* 2.8 27.9 + - - +
54F ILE* 3.3 21.5 - - + +
57F GLN* 3.6 28.0 - - + -
58F VAL* 3.5 33.7 - - + +
61F VAL* 4.1 2.2 - - + -
109F LEU* 4.0 21.1 - - + -
113F TYR* 4.1 5.4 - - - +
148F PHE* 5.6 0.7 - - + -
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Residues in contact with LYS 36 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C ARG* 5.1 3.6 + - - +
66C ASP* 3.1 30.9 + - - +
32F HIS 3.7 9.1 + - - +
33F LEU* 4.0 10.3 - - + +
34F THR 3.1 0.6 - - - -
35F LEU* 1.3 78.4 - - - +
37F HIS* 1.3 57.6 + - - +
39F HIS* 3.0 19.8 + - + +
40F TRP* 2.9 66.2 + - + +
55F ASP* 5.2 6.3 - - - -
58F VAL* 3.9 29.2 - - + -
62F ARG* 3.9 21.3 - - - +
----------------------------------------------------------
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Residues in contact with HIS 37 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C PRO 3.8 12.9 + - - -
80C LYS* 3.9 16.2 - - + -
81C GLY 3.1 23.2 + - - +
82C THR* 3.8 20.5 - - + +
33F LEU 3.4 12.0 + - - +
34F THR* 2.6 19.9 + - - +
36F LYS* 1.3 74.6 - - - +
38F VAL* 1.3 62.5 + - - -
39F HIS 3.2 0.3 + - - -
40F TRP* 3.3 14.8 + - - +
41F ASN* 3.2 30.3 + - + +
95F TYR* 3.4 29.5 - + - -
97F VAL 2.7 24.2 + - - -
98F GLU* 5.2 2.0 - - + -
----------------------------------------------------------
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Residues in contact with VAL 38 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34F THR* 2.8 35.0 + - + +
35F LEU* 3.6 9.9 - - - +
37F HIS* 1.3 78.4 - - - +
39F HIS* 1.3 57.5 + - - +
41F ASN 3.8 0.2 - - - -
42F VAL* 3.0 30.0 + - - +
50F VAL* 4.1 9.6 - - + -
54F ILE* 3.8 13.5 - - + -
95F TYR* 4.0 11.0 - - + +
105F HIS* 3.7 30.2 - - + +
109F LEU* 3.6 29.8 - - + -
----------------------------------------------------------
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Residues in contact with HIS 39 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C ASP* 5.7 3.4 - - - -
70C GLU* 6.0 2.0 - - - -
35F LEU 2.8 15.7 + - - +
36F LYS* 3.0 26.8 - - + +
38F VAL* 1.3 81.4 - - - +
40F TRP* 1.3 72.7 + + + +
41F ASN 3.3 0.7 + - - -
42F VAL* 3.9 2.4 + - - -
51F HIS* 2.9 78.4 + + - +
54F ILE* 3.9 21.5 - - + -
55F ASP* 3.9 21.2 + - - -
----------------------------------------------------------
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Residues in contact with TRP 40 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C LEU* 3.8 26.5 - - + -
29C ASN* 4.3 11.4 - - - -
65C ALA* 3.9 9.0 - - + -
66C ASP* 3.4 33.6 + - - -
69C ALA* 3.4 27.7 - - + +
70C GLU* 5.1 11.7 - - + +
73C ALA* 4.1 16.4 - - + +
79C PRO* 3.9 17.5 - - + -
81C GLY* 3.7 27.1 - - - -
33F LEU* 5.4 1.1 - - + -
36F LYS* 2.9 47.8 + - + +
37F HIS* 3.3 12.3 + - - +
39F HIS* 1.3 87.1 + + - +
41F ASN* 1.3 71.8 + - - +
42F VAL 3.7 0.4 - - - -
51F HIS* 6.0 0.2 - - - -
99F ARG* 5.5 0.9 - - - +
150J TRP* 4.4 11.8 - - - -
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Residues in contact with ASN 41 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C ALA* 5.2 0.2 - - - +
78C SER* 3.5 19.5 - - - +
79C PRO* 2.9 52.7 + - - +
37F HIS* 3.2 21.8 + - + +
38F VAL 3.8 0.9 - - - -
39F HIS 3.2 0.4 - - - -
40F TRP* 1.3 91.1 + - - +
42F VAL* 1.3 59.5 + - - +
43F VAL* 3.3 7.7 + - - -
98F GLU* 3.5 21.1 - - - +
99F ARG* 3.4 12.3 - - - +
100F ASP 3.2 22.0 + - - -
105F HIS* 3.5 7.6 + - + -
----------------------------------------------------------
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Residues in contact with VAL 42 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38F VAL 3.0 17.1 + - - +
40F TRP 3.7 1.2 - - - -
41F ASN* 1.3 73.6 - - - +
43F VAL* 1.3 64.6 + - - +
47F PHE* 2.8 33.2 - - + +
50F VAL* 3.9 25.1 - - + -
51F HIS* 3.6 30.2 + - + -
102F VAL* 4.0 25.4 - - - +
105F HIS* 3.6 23.1 - - + -
150J TRP* 4.6 3.5 - - - -
----------------------------------------------------------
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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