Contacts of the helix formed by residues 7 - 46 (chain A) in PDB entry 3FRR
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 7 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A GLY 3.9 9.2 - - - +
6A PHE* 1.3 76.2 - - - +
8A ALA* 1.3 66.6 + - - +
9A GLU 3.2 1.8 - - - -
10A ARG* 3.0 39.5 + - + +
11A LEU* 3.1 10.4 + - - +
123A GLN* 2.7 23.1 + - - +
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Residues in contact with ALA 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A PHE* 3.6 34.6 + - + -
7A LYS* 1.3 70.7 - - - +
9A GLU* 1.3 61.5 + - + +
11A LEU* 3.1 2.6 + - - +
12A ARG 2.9 22.9 + - - -
83A PHE* 3.3 18.7 - - + -
87A GLN* 3.6 25.4 - - + +
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Residues in contact with GLU 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A LYS* 3.2 0.8 - - - +
8A ALA* 1.3 78.6 - - + +
10A ARG* 1.3 62.3 + - + +
12A ARG* 3.0 46.3 + - - +
13A VAL* 3.0 38.4 + - + +
87A GLN* 4.3 8.5 + - - +
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Residues in contact with ARG 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A LYS* 3.0 46.4 + - + +
9A GLU* 1.3 78.4 - - + +
11A LEU* 1.3 65.4 + - - +
13A VAL* 3.9 30.8 - - - +
14A ASN* 2.8 56.2 + - - +
17A LEU* 5.5 1.8 - - - +
119A ILE* 5.2 4.7 - - + +
123A GLN* 4.6 11.4 - - + +
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Residues in contact with LEU 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A PHE* 3.7 25.8 - - + -
7A LYS 3.1 8.3 + - - +
8A ALA 3.1 7.4 + - - +
10A ARG* 1.3 77.6 - - - +
12A ARG* 1.3 56.9 + - - +
14A ASN* 3.4 3.1 + - - -
15A LEU* 2.9 43.1 + - + +
83A PHE* 3.7 22.4 - - + -
86A ILE* 4.3 9.2 - - + -
120A VAL* 3.8 43.3 - - + +
123A GLN* 3.9 17.3 - - + +
124A LEU* 3.9 23.6 - - + -
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Residues in contact with ARG 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ALA 2.9 13.3 + - - +
9A GLU* 3.0 41.1 + - - +
11A LEU* 1.3 74.1 - - - +
13A VAL* 1.3 68.2 + - + +
15A LEU 3.5 0.3 + - - -
16A ARG* 3.4 17.0 + - - +
80A LEU* 3.6 30.0 + - + +
83A PHE* 3.4 41.9 - - + +
87A GLN* 3.0 27.3 - - - +
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Residues in contact with VAL 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A GLU* 3.0 24.5 + - + +
10A ARG* 3.9 32.5 - - - +
12A ARG* 1.3 75.0 - - + +
14A ASN* 1.3 63.7 + - - +
16A ARG* 3.1 9.6 + - - +
17A LEU* 3.1 39.9 + - + +
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Residues in contact with ASN 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ARG* 2.8 54.1 + - - +
11A LEU* 4.2 1.1 - - - +
13A VAL* 1.3 74.4 - - - +
15A LEU* 1.3 59.5 + - - +
17A LEU* 3.6 11.7 - - - +
18A VAL* 2.8 35.2 + - - +
116A GLU* 3.3 29.4 - - - +
119A ILE* 3.3 35.4 - - + +
120A VAL* 3.6 16.2 - - + +
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Residues in contact with LEU 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU* 2.9 41.9 + - + +
12A ARG 3.8 4.5 - - - +
13A VAL 3.3 0.2 - - - -
14A ASN* 1.3 76.5 - - - +
16A ARG* 1.3 61.0 + - - +
18A VAL* 3.4 3.4 + - - +
19A ILE* 3.1 26.5 + - - +
76A CYS* 3.9 32.5 - - - +
79A LEU* 3.9 24.7 - - + -
80A LEU* 3.8 26.2 - - + -
83A PHE* 4.1 9.9 - - + -
103A LEU* 4.2 6.7 - - + -
120A VAL* 3.7 26.4 - - + +
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Residues in contact with ARG 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ARG 3.4 8.2 + - - +
13A VAL* 3.1 10.1 + - - +
15A LEU* 1.3 75.4 - - - +
17A LEU* 1.3 67.6 + - + +
19A ILE* 3.2 25.1 + - - +
20A ASN* 3.1 41.2 + - - +
77A ASP* 4.3 14.3 + - - -
80A LEU* 3.9 28.0 - - + +
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Residues in contact with LEU 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ARG* 5.5 2.2 - - - +
13A VAL* 3.1 32.2 + - + +
14A ASN* 3.3 26.2 + - - +
16A ARG* 1.3 74.7 - - + +
18A VAL* 1.3 60.3 + - - +
20A ASN* 3.4 11.5 + - + +
21A ARG* 2.9 30.1 + - - +
116A GLU* 4.0 24.4 - - + +
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Residues in contact with VAL 18 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ASN 2.8 21.6 + - - +
15A LEU 3.6 5.6 - - - +
17A LEU* 1.3 73.4 - - - +
19A ILE* 1.3 65.8 + - - +
21A ARG* 3.1 6.9 + - - +
22A LEU* 2.9 40.1 + - + +
72A LEU* 5.9 0.2 - - + -
76A CYS* 3.6 24.2 - - - -
114A VAL* 4.2 9.6 - - + -
116A GLU* 3.6 10.3 - - + +
117A LEU* 3.5 42.8 - - + +
120A VAL* 3.8 8.1 - - + -
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Residues in contact with ILE 19 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A LEU 3.1 11.8 + - - +
16A ARG* 3.2 30.7 + - - +
18A VAL* 1.3 76.5 - - - +
20A ASN* 1.3 66.0 + - - +
22A LEU* 3.3 3.1 + - - +
23A LYS* 3.0 33.7 + - + +
73A GLU* 4.0 31.8 - - + +
76A CYS* 3.5 15.7 - - + -
77A ASP* 3.7 27.8 - - + +
80A LEU* 3.7 29.8 - - + -
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Residues in contact with ASN 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ARG* 3.1 39.5 + - - +
17A LEU* 3.9 11.1 - - + +
18A VAL 3.2 0.2 - - - -
19A ILE* 1.3 82.4 - - - +
21A ARG* 1.3 63.4 + - - +
23A LYS* 3.4 14.6 + - - +
24A LEU* 3.0 23.9 + - - +
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Residues in contact with ARG 21 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LEU 2.9 18.4 + - - +
18A VAL* 3.6 4.3 - - - +
20A ASN* 1.3 76.9 - - - +
22A LEU* 1.3 58.6 + - - +
24A LEU* 3.4 27.6 + - - +
25A LEU* 2.9 51.4 + - + +
28A LYS* 6.1 1.0 - - - +
113A GLU* 2.8 29.9 + - - +
114A VAL* 3.8 29.6 - - + +
116A GLU* 4.7 10.1 + - - +
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Residues in contact with LEU 22 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A VAL* 2.9 37.9 + - + +
19A ILE 3.7 3.6 - - - +
21A ARG* 1.3 75.2 - - - +
23A LYS* 1.3 59.6 + - - +
25A LEU* 4.1 3.2 - - - +
26A GLU* 2.9 47.7 + - - +
69A MET* 3.6 35.1 - - + +
72A LEU* 3.8 12.3 - - + -
73A GLU* 3.6 37.0 - - + +
110A LEU* 4.7 7.0 - - + -
114A VAL* 4.0 21.1 - - + -
117A LEU* 5.7 1.3 - - + -
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Residues in contact with LYS 23 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A ILE* 3.0 30.9 + - + +
20A ASN* 3.7 15.7 - - - +
22A LEU* 1.3 75.7 - - - +
24A LEU* 1.3 61.5 + - - +
26A GLU* 3.8 11.6 - - - +
27A LYS* 3.4 22.0 + - - +
73A GLU* 3.6 28.4 + - - +
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Residues in contact with LEU 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ASN 3.0 18.0 + - - +
21A ARG* 3.5 33.7 - - - +
22A LEU 3.2 0.2 - - - -
23A LYS* 1.3 77.6 - - - +
25A LEU* 1.3 59.8 + - + +
27A LYS* 3.4 10.4 + - + +
28A LYS* 3.0 37.1 + - + +
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Residues in contact with LEU 25 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ARG* 2.9 49.8 + - - +
22A LEU 4.1 0.2 - - - +
24A LEU* 1.3 74.5 - - + +
26A GLU* 1.3 59.6 + - - +
28A LYS* 4.4 20.0 - - + +
29A LYS* 2.8 47.7 + - + +
69A MET* 3.7 26.5 - - + -
113A GLU* 3.5 36.3 - - + +
114A VAL* 3.7 19.7 - - + -
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Residues in contact with GLU 26 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A LEU 2.9 28.4 + - - +
23A LYS* 3.8 9.4 - - - +
24A LEU 3.3 0.2 - - - -
25A LEU* 1.3 74.7 - - - +
27A LYS* 1.3 58.0 + - - +
30A THR* 2.7 34.5 + - - -
66A VAL* 3.9 26.5 - - + +
69A MET* 3.5 36.4 - - + +
70A GLU* 3.5 22.9 + - + +
73A GLU* 2.7 27.7 - - - +
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Residues in contact with LYS 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A LYS 3.4 10.7 + - - +
24A LEU* 3.8 13.7 - - + +
25A LEU 3.3 0.2 - - - -
26A GLU* 1.3 77.3 - - - +
28A LYS* 1.3 65.7 + - - +
30A THR* 3.2 6.5 + - - -
31A GLU* 3.1 50.6 + - + +
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Residues in contact with LYS 28 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ARG* 6.1 1.4 - - - +
24A LEU* 3.0 27.7 + - + +
25A LEU* 4.1 20.4 - - + +
27A LYS* 1.3 75.9 - - - +
29A LYS* 1.3 60.5 + - + +
31A GLU* 3.3 14.0 + - - +
32A LEU* 2.9 36.6 + - + +
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Residues in contact with LYS 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LEU* 2.8 35.0 + - + +
28A LYS* 1.3 72.5 - - + +
30A THR* 1.3 60.0 + - - +
32A LEU* 3.7 10.4 - - + +
33A ALA* 2.9 29.5 + - - +
62A GLU* 2.8 38.2 + - + +
65A LEU* 3.4 21.2 - - + +
66A VAL* 3.6 23.3 - - + -
69A MET* 3.9 13.7 - - + -
113A GLU* 2.8 41.0 + - - -
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Residues in contact with THR 30 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A GLU 2.7 23.0 + - - -
27A LYS* 3.2 6.3 + - - -
29A LYS* 1.3 75.6 - - - +
31A GLU* 1.3 63.3 + - + +
33A ALA* 3.2 20.7 + - + +
34A GLN* 3.4 8.0 + - - +
63A ASP* 6.1 0.2 - - - -
66A VAL* 4.0 17.1 - - - +
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Residues in contact with GLU 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A LYS* 3.1 51.3 + - + +
28A LYS* 3.7 12.7 - - - +
30A THR* 1.3 75.7 - - + +
32A LEU* 1.3 64.9 + - - +
34A GLN* 3.3 17.0 + - - +
35A LYS* 3.6 11.4 + - - +
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Residues in contact with LEU 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A LYS* 2.9 25.8 + - + +
29A LYS* 3.7 12.3 - - + +
31A GLU* 1.3 75.8 - - - +
33A ALA* 1.3 56.9 + - - +
35A LYS* 3.2 14.7 + - + +
36A ALA* 3.0 26.6 + - + +
58A HIS* 5.4 12.1 - - + -
62A GLU* 5.5 7.2 - - + +
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Residues in contact with ALA 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A LYS 2.9 14.6 + - - +
30A THR* 3.3 14.4 - - + +
31A GLU 3.2 0.4 - - - -
32A LEU* 1.3 74.7 - - - +
34A GLN* 1.3 58.6 + - - +
36A ALA* 3.3 7.6 + - - +
37A ARG* 3.0 43.2 + - - +
59A ILE* 4.9 6.2 - - + +
62A GLU* 5.6 6.7 - - + -
63A ASP* 4.1 20.2 - - - +
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Residues in contact with GLN 34 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A THR 3.4 7.0 + - - +
31A GLU* 3.3 12.1 + - - +
33A ALA* 1.3 77.9 - - - +
35A LYS* 1.3 60.6 + - - +
37A ARG* 3.3 17.3 + - - +
38A LYS* 3.1 19.2 + - - +
173A TYR* 2.7 31.5 + - - +
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Residues in contact with LYS 35 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A GLU 3.6 6.3 + - - +
32A LEU* 3.2 19.1 + - + +
34A GLN* 1.3 77.6 - - - +
36A ALA* 1.3 58.4 + - - +
38A LYS* 3.3 12.0 + - + +
39A GLU* 3.1 25.5 + - - +
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Residues in contact with ALA 36 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A LEU* 3.0 16.8 + - + +
33A ALA* 3.7 7.0 - - - +
34A GLN 3.3 0.2 - - - -
35A LYS* 1.3 76.7 - - - +
37A ARG* 1.3 58.8 + - - +
39A GLU* 3.3 14.4 + - - +
40A ILE* 3.1 30.7 + - - +
58A HIS* 5.6 5.8 - - - +
59A ILE* 3.5 23.7 - - + +
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Residues in contact with ARG 37 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ALA* 3.0 29.3 + - - +
34A GLN* 3.3 25.1 + - - +
36A ALA* 1.3 72.1 - - - +
38A LYS* 1.3 61.0 + - - +
40A ILE* 3.2 4.9 + - - +
41A ALA* 2.9 24.1 + - - +
59A ILE* 3.9 20.7 - - + +
63A ASP* 2.9 28.5 + - - -
165A TYR* 3.4 20.3 + - - -
168A GLU* 5.5 4.8 - - - +
169A ILE* 3.5 43.7 - - + +
172A ASN* 5.4 6.7 - - - +
173A TYR* 4.2 8.5 - - + +
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Residues in contact with LYS 38 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A GLN 3.1 9.9 + - - +
35A LYS* 3.5 14.8 - - + +
37A ARG* 1.3 78.4 - - - +
39A GLU* 1.3 56.0 + - - +
41A ALA* 3.1 3.9 + - + +
42A ASP* 2.9 51.7 + - - +
173A TYR* 3.6 40.1 + - + +
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Residues in contact with GLU 39 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A LYS 3.1 12.8 + - - +
36A ALA* 3.5 16.1 - - - +
37A ARG 3.3 0.2 - - - -
38A LYS* 1.3 73.4 - - - +
40A ILE* 1.3 64.6 + - - +
42A ASP* 3.2 13.3 + - + +
43A TYR* 3.0 44.6 + - + -
55A ARG* 3.5 34.5 + - - +
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Residues in contact with ILE 40 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A ALA 3.1 18.9 + - - +
37A ARG 3.2 7.8 + - - +
39A GLU* 1.3 76.1 - - - +
41A ALA* 1.3 63.6 + - - +
43A TYR* 3.2 7.3 + - + +
44A LEU* 3.0 27.9 + - + +
52A ALA* 4.0 13.0 - - + +
55A ARG* 3.8 40.4 - - + +
56A VAL* 3.9 14.8 - - + +
59A ILE* 3.6 17.9 - - + -
166A LEU* 3.6 28.0 - - + -
169A ILE* 3.9 17.3 - - + -
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Residues in contact with ALA 41 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A ARG 2.9 11.2 + - - +
38A LYS* 3.1 10.3 + - + +
40A ILE* 1.3 78.7 - - - +
42A ASP* 1.3 56.1 + - - +
44A LEU* 3.2 3.6 + - - +
45A ALA* 2.9 30.9 + - - +
169A ILE* 4.2 6.1 - - + -
173A TYR* 3.5 44.6 - - + -
175A VAL* 3.9 15.7 - - + +
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Residues in contact with ASP 42 (chain A).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A LYS* 2.9 46.1 + - - +
39A GLU* 3.3 16.4 - - + +
41A ALA* 1.3 72.5 - - - +
43A TYR* 1.3 68.4 + - + +
45A ALA* 3.5 7.8 + - - +
46A ALA* 3.3 21.7 + - - +
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Residues in contact with TYR 43 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A GLU* 3.0 41.7 + - + +
40A ILE* 3.3 12.3 - - + +
42A ASP* 1.3 76.7 - - + +
44A LEU* 1.3 54.6 + - - +
46A ALA* 3.0 14.6 + - - +
48A LYS* 2.8 46.5 + - + +
51A ARG* 3.4 53.0 + - + -
52A ALA* 3.7 32.1 - - + -
55A ARG* 2.9 39.8 + - - -
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Residues in contact with LEU 44 (chain A).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A ILE* 3.0 29.1 + - + +
41A ALA* 3.6 7.9 - - - +
43A TYR* 1.3 70.9 - - - +
45A ALA* 1.3 57.4 + - - +
46A ALA 3.0 5.2 - - - -
47A GLY* 3.0 20.9 - - - -
48A LYS 4.5 0.2 - - - +
49A ASP* 4.1 12.2 - - - +
52A ALA* 3.6 26.2 - - + -
166A LEU* 4.2 12.3 - - + +
170A ALA* 3.9 30.1 - - + +
175A VAL* 3.9 11.2 - - + -
176A PRO* 3.9 22.3 - - - +
177A TYR* 3.8 30.5 - - + -
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Residues in contact with ALA 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A ALA 2.9 16.1 + - - +
42A ASP* 3.8 9.9 - - - +
43A TYR 3.3 0.2 - - - -
44A LEU* 1.3 75.6 - - - +
46A ALA* 1.3 57.8 + - + +
47A GLY* 4.0 0.6 - - - -
175A VAL* 3.9 20.3 - - + +
176A PRO* 4.8 5.6 - - - -
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Residues in contact with ALA 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ASP 3.3 15.0 + - - +
43A TYR 3.0 9.0 + - - +
44A LEU 3.0 1.0 - - - -
45A ALA* 1.3 79.8 - - - +
47A GLY* 1.3 46.0 + - - -
48A LYS* 3.5 28.7 + - + +
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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) + - + + + + + -
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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