Contacts of the helix formed by residues 54 - 81 (chain F) in PDB entry 5K58
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 54 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49F TYR* 4.0 10.3 - - - -
52F PHE* 3.1 22.0 + - - +
53F PRO* 1.3 82.3 - - - +
55F LYS* 1.3 64.6 + - - +
56F THR* 3.4 22.1 + - - -
57F ARG* 3.9 9.9 + - - +
58F MET* 3.5 8.7 + - - +
118F GLN* 4.9 1.7 + - - -
13R C 3.7 27.4 - - - -
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Residues in contact with LYS 55 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31F ARG* 3.4 19.7 - - - +
32F ILE* 3.3 18.9 + - - -
34F THR* 3.5 26.0 - - + -
54F SER* 1.3 74.0 - - - +
56F THR* 1.3 67.7 + - - +
57F ARG 3.2 0.4 - - - -
58F MET* 2.9 30.1 + - + +
59F PHE* 2.9 38.3 + - + -
116F PHE* 5.0 7.2 + - - +
117F GLU* 5.8 5.8 - - + +
12R A 2.9 45.2 + - - +
13R C 3.3 13.0 + - - +
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Residues in contact with THR 56 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54F SER* 3.6 10.3 + - - -
55F LYS* 1.3 78.3 - - - +
57F ARG* 1.3 57.9 + - - +
59F PHE* 3.3 1.7 + - - +
60F ASP* 2.8 34.4 + - - +
117F GLU* 4.5 5.3 - - - +
118F GLN* 2.4 37.9 + - - +
120F ARG* 3.4 41.5 - - + +
121F LEU* 3.6 22.4 - - + +
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Residues in contact with ARG 57 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12F ARG* 5.1 12.9 - - - +
52F PHE* 4.0 11.4 - - + -
53F PRO* 3.6 44.1 - - + +
54F SER* 3.9 10.6 + - - +
55F LYS 3.2 0.6 - - - -
56F THR* 1.3 76.3 - - + +
58F MET* 1.3 59.0 - - - +
60F ASP* 3.7 7.3 - - - +
61F SER* 2.9 36.7 + - - +
120F ARG* 4.5 14.8 - - - +
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Residues in contact with MET 58 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15F ILE* 4.3 11.7 - - - -
16F LEU* 3.4 22.1 - - + +
19F LEU* 4.4 14.1 - - + +
34F THR* 4.3 5.6 - - + -
37F LEU* 3.5 34.1 - - + -
48F LEU* 4.3 12.3 - - - +
49F TYR* 6.0 1.8 - - + -
52F PHE* 3.5 36.1 - - + -
54F SER 3.5 10.8 - - - +
55F LYS* 2.9 38.4 + - + +
57F ARG* 1.3 78.3 - - - +
59F PHE* 1.3 67.6 + - + +
62F LEU* 3.7 10.2 + - - +
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Residues in contact with PHE 59 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19F LEU* 4.1 34.1 - - + -
23F LEU* 4.8 7.9 - - + -
32F ILE* 5.3 9.2 - - + -
55F LYS* 2.9 50.6 + - + +
56F THR 3.9 0.2 - - - +
58F MET* 1.3 78.8 - - + +
60F ASP* 1.3 57.0 + - - +
61F SER 3.2 1.3 - - - -
62F LEU* 3.0 7.1 + - + +
63F ILE* 2.8 36.1 + - + +
108F ILE* 4.1 24.2 - - + +
113F ALA* 4.5 11.4 - - + -
116F PHE* 6.4 2.2 - - + -
117F GLU* 3.0 48.0 - - + +
121F LEU* 3.6 6.5 - - + -
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Residues in contact with ASP 60 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56F THR 2.8 17.5 + - - +
57F ARG* 3.3 11.9 + - - +
59F PHE* 1.3 78.4 - - - +
61F SER* 1.3 59.8 + - - +
62F LEU 3.0 0.2 - - - -
63F ILE* 3.2 10.4 + - - +
64F GLU* 3.1 30.9 + - - +
120F ARG* 2.3 35.3 + - - -
121F LEU* 3.2 26.0 - - - +
124F ARG* 2.8 29.1 + - - +
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Residues in contact with SER 61 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12F ARG* 3.4 23.7 + - - -
16F LEU* 4.0 22.0 - - - +
52F PHE* 4.8 0.7 - - - -
57F ARG* 2.9 22.0 + - - +
58F MET 3.9 5.8 - - - -
60F ASP* 1.3 76.1 - - - +
62F LEU* 1.3 62.5 + - - +
64F GLU* 4.1 24.5 + - - +
65F PHE* 4.2 6.4 + - - +
375M PHE* 5.5 1.9 - - - -
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Residues in contact with LEU 62 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16F LEU* 3.6 31.2 - - + +
19F LEU* 4.0 27.8 - - + -
20F ALA* 4.6 7.2 - - - +
23F LEU* 4.6 6.5 - - + -
58F MET 3.7 3.8 + - - +
59F PHE* 3.0 11.6 + - + +
61F SER* 1.3 79.7 - - - +
63F ILE* 1.3 64.8 + - - +
64F GLU 3.2 2.0 + - - -
65F PHE* 3.4 13.3 + - - +
66F ILE* 3.6 13.3 - - - +
105F LEU* 3.6 30.6 - - + +
108F ILE* 3.8 20.0 - - + -
375M PHE* 3.7 28.9 - - + -
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Residues in contact with ILE 63 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59F PHE* 2.8 15.8 + - + +
60F ASP* 3.2 10.1 + - - +
62F LEU* 1.3 75.7 - - - +
64F GLU* 1.3 64.9 + - - +
66F ILE* 3.0 23.0 + - - +
67F GLU* 3.2 33.0 + - + +
108F ILE* 4.4 10.0 - - + +
114F LEU* 5.1 0.9 - - + -
121F LEU* 3.7 45.1 - - + +
124F ARG* 3.7 26.5 - - + +
125F ILE* 3.8 25.6 - - + -
128F LEU* 4.5 2.0 - - + -
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Residues in contact with GLU 64 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60F ASP* 3.1 20.8 + - - +
61F SER* 4.1 17.6 + - - +
62F LEU 3.2 0.2 - - - -
63F ILE* 1.3 76.8 - - - +
65F PHE* 1.3 53.8 + - - +
67F GLU* 2.8 18.0 + - - +
68F ASP* 2.8 47.9 + - - +
124F ARG* 3.8 19.4 + - - +
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Residues in contact with PHE 65 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61F SER 4.2 5.7 + - - +
62F LEU 3.4 10.8 + - - +
63F ILE 3.3 1.0 + - - -
64F GLU* 1.3 76.9 - - - +
66F ILE* 1.3 56.9 + - - +
68F ASP* 3.7 8.7 - - + -
69F SER* 2.7 55.4 + - - -
98F PHE* 3.9 16.8 - + - -
105F LEU* 3.5 19.7 - - + -
373M PRO* 4.8 4.5 - - + -
374M ALA 3.9 24.5 - - - -
375M PHE* 3.5 45.1 - + + -
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Residues in contact with ILE 66 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62F LEU 3.6 12.6 - - - +
63F ILE* 3.0 14.3 + - - +
65F PHE* 1.3 77.0 - - - +
67F GLU* 1.3 67.9 + - - +
70F LEU* 2.8 54.0 + - + +
98F PHE* 3.8 15.0 - - + -
105F LEU* 3.9 31.0 - - + +
108F ILE* 4.3 15.3 - - + -
109F LEU* 4.0 35.4 - - + -
125F ILE* 5.0 0.9 - - + -
128F LEU* 4.1 11.7 - - + -
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Residues in contact with GLU 67 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63F ILE* 3.4 21.8 - - - +
64F GLU* 2.8 20.7 + - - +
66F ILE* 1.3 72.5 - - - +
68F ASP* 1.3 62.6 + - - +
71F ILE* 2.9 39.7 + - + +
124F ARG* 3.4 38.1 + - - +
128F LEU* 3.7 29.6 - - + +
131F ARG* 4.7 11.5 + - - +
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Residues in contact with ASP 68 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64F GLU* 2.8 36.8 + - - +
65F PHE* 3.6 7.1 + - + +
67F GLU* 1.3 78.6 - - - +
69F SER* 1.3 60.0 + - - +
70F LEU 2.9 10.7 + - - -
72F THR* 3.5 31.0 + - - +
73F ARG* 4.0 1.7 + - - +
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Residues in contact with SER 69 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65F PHE* 2.7 45.0 + - - -
66F ILE 3.6 1.1 - - - -
68F ASP* 1.3 74.9 - - - +
70F LEU* 1.3 69.4 + - - +
73F ARG* 3.6 18.0 - - - +
98F PHE* 3.7 11.9 - - - -
373M PRO* 3.7 31.9 - - - +
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Residues in contact with LEU 70 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66F ILE* 2.8 37.0 + - + +
67F GLU 4.9 0.2 - - - -
68F ASP 2.9 2.0 + - - -
69F SER* 1.3 88.3 - - - +
71F ILE* 1.3 59.9 + - - +
72F THR 3.4 0.7 - - - -
73F ARG* 3.1 4.4 + - - +
74F ILE* 2.8 39.3 + - + +
94F LEU* 3.8 25.7 - - + +
95F LEU* 4.5 17.9 - - + -
98F PHE* 3.7 35.7 - - + -
109F LEU* 4.9 8.5 - - + -
128F LEU* 5.0 9.4 - - + -
132F ILE* 5.4 4.9 - - + -
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Residues in contact with ILE 71 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67F GLU* 2.9 26.4 + - + +
70F LEU* 1.3 75.9 - - - +
72F THR* 1.3 65.8 + - - +
73F ARG 3.1 1.0 + - - -
74F ILE* 3.2 6.0 + - + +
75F ASN* 3.1 42.0 + - - +
128F LEU* 4.3 15.3 - - + +
131F ARG* 3.7 35.2 - - + +
132F ILE* 3.6 26.2 - - + -
135F GLN* 3.9 11.9 - - - +
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Residues in contact with THR 72 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68F ASP* 3.5 22.2 + - - +
70F LEU 3.4 0.2 - - - -
71F ILE* 1.3 83.4 - - - +
73F ARG* 1.3 61.8 + - - +
75F ASN* 3.7 11.9 + - + +
76F LEU* 3.1 27.3 + - + +
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Residues in contact with ARG 73 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68F ASP 4.0 1.4 + - - +
69F SER* 3.6 22.4 - - - +
70F LEU 3.1 8.2 + - - +
71F ILE 3.0 0.8 - - - -
72F THR* 1.3 83.1 + - - +
74F ILE* 1.3 63.8 + - - +
76F LEU* 3.5 28.9 - - - +
77F ILE* 3.2 19.7 + - - +
94F LEU* 3.5 31.6 - - + -
370M LEU* 4.7 14.3 - - + +
371M ASP* 4.0 24.6 + - - -
373M PRO* 4.5 20.4 - - + +
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Residues in contact with ILE 74 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70F LEU* 2.8 25.5 + - + +
71F ILE* 3.6 7.9 - - + +
73F ARG* 1.3 73.1 - - - +
75F ASN* 1.3 68.7 + - - +
77F ILE* 2.9 21.9 + - - +
78F LEU* 3.1 19.4 + - + +
91F ILE* 3.7 41.5 - - + -
94F LEU* 3.5 17.0 - - + -
95F LEU* 5.6 2.5 - - + -
132F ILE* 3.4 39.0 - - + +
135F GLN* 4.5 20.9 - - + +
136F LEU* 5.9 0.4 - - + -
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Residues in contact with ASN 75 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71F ILE* 3.2 24.3 + - - +
72F THR* 3.7 13.0 + - + +
74F ILE* 1.3 76.6 - - - +
76F LEU* 1.3 60.5 + - - +
78F LEU* 3.4 12.3 + - - +
79F LYS* 3.3 29.2 + - + +
135F GLN* 2.9 34.7 + - - +
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Residues in contact with LEU 76 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72F THR* 3.1 15.9 + - + +
73F ARG* 3.5 35.0 - - - +
74F ILE 3.1 0.4 - - - -
75F ASN* 1.3 74.9 - - - +
77F ILE* 1.3 65.6 + - - +
79F LYS* 3.6 14.4 + - + +
80F ASP* 3.2 43.9 + - - +
----------------------------------------------------------
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Residues in contact with ILE 77 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73F ARG* 3.2 13.6 + - - +
74F ILE* 2.9 13.1 + - + +
76F LEU* 1.3 78.0 - - - +
78F LEU* 1.3 59.2 + - + +
80F ASP* 3.1 2.9 + - - -
81F GLU* 2.3 49.1 + - + +
87F ARG* 3.8 28.5 - - + +
90F LEU* 3.6 25.8 - - + -
91F ILE* 4.0 20.6 - - + +
94F LEU* 4.8 4.0 - - + -
370M LEU* 3.5 33.7 - - + -
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Residues in contact with LEU 78 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74F ILE* 3.1 20.3 + - + +
75F ASN* 3.6 13.2 - - - +
76F LEU 3.2 0.4 - - - -
77F ILE* 1.3 79.3 - - + +
79F LYS* 1.3 66.5 + - + +
81F GLU 2.8 15.5 - - - +
82F LYS* 3.6 9.4 + - - +
87F ARG* 3.2 53.7 + - + +
91F ILE* 4.9 1.1 - - + -
135F GLN* 5.3 10.3 - - + -
138F GLN* 4.0 30.3 - - + +
139F VAL* 3.7 15.0 - - + -
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Residues in contact with LYS 79 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75F ASN* 3.3 14.0 + - - +
76F LEU* 3.7 19.5 - - + +
78F LEU* 1.3 79.7 - - + +
80F ASP* 1.3 67.4 + - - +
82F LYS* 4.1 10.4 + - - +
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Residues in contact with ASP 80 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76F LEU* 3.2 34.4 + - - +
77F ILE* 3.1 3.9 + - - +
79F LYS* 1.3 87.7 - - - +
81F GLU* 1.3 63.1 + - + +
82F LYS* 3.8 8.8 + - - +
----------------------------------------------------------
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Residues in contact with GLU 81 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77F ILE* 2.3 38.1 + - + +
78F LEU 2.8 9.7 - - - +
80F ASP* 1.3 69.7 - - + +
82F LYS* 1.3 68.7 + - - +
83F ASP* 2.9 19.4 + - - +
86F ALA* 3.8 19.1 - - + +
87F ARG* 2.7 45.9 + - + -
90F LEU* 3.9 21.1 - - + +
----------------------------------------------------------
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il