Contacts of the helix formed by residues 112 - 136 (chain F) in PDB entry 5X6E
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 HIS 112 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4F GLN 4.8 2.9 - - - -
7F GLU* 2.7 43.8 + - + +
8F PHE* 3.3 42.8 - + + -
11F TYR* 3.3 34.5 - + + +
106F LEU* 4.8 4.9 - - + -
108F LYS* 5.9 1.6 - - + -
109F ASN* 2.3 44.6 + - - +
110F LEU 3.2 0.2 - - - -
111F THR* 1.3 80.0 - - + +
113F PHE* 1.3 66.8 + - - +
114F PHE 3.3 0.7 - - - -
115F TYR* 3.3 18.8 + - + +
116F VAL* 3.6 11.8 + - - +
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Residues in contact with PHE 113 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110E LEU* 6.0 2.0 - - + -
113E PHE* 3.3 46.7 - + + -
114E PHE* 3.4 31.9 - + - -
117E PHE* 3.4 31.9 - + - -
106F LEU* 2.9 51.2 - - + +
108F LYS* 6.1 0.7 - - + -
109F ASN 4.3 2.0 + - - +
110F LEU* 3.4 28.3 + - + +
112F HIS* 1.3 77.9 - - - +
114F PHE* 1.3 60.7 + - + +
115F TYR 3.0 1.9 + - - -
116F VAL* 3.1 7.6 + - + +
117F PHE* 2.9 27.8 + + + -
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Residues in contact with PHE 114 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74E ILE* 4.6 20.6 - - + -
75E ASP* 4.6 9.5 - - + +
103E LYS* 3.5 59.0 - - + +
106E LEU* 5.4 0.2 - - + -
107E SER* 4.7 7.4 - - - -
113E PHE* 3.2 37.5 - + - -
110F LEU* 3.6 27.8 - - + -
111F THR* 4.3 12.1 - - - +
112F HIS 3.3 0.8 - - - -
113F PHE* 1.3 77.5 - + + +
115F TYR* 1.3 56.9 + - - +
117F PHE* 3.8 11.5 - + + +
118F GLN* 3.0 28.8 + - - +
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Residues in contact with TYR 115 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2F ASN 5.5 1.3 - - - -
4F GLN* 3.8 32.3 - - + +
5F ALA* 3.4 35.2 - - + +
8F PHE* 4.1 20.0 - + + -
40F PHE* 4.0 19.7 - + - -
66F ALA* 3.8 22.2 + - - +
67F PHE* 4.3 0.5 + - - -
68F VAL* 4.2 7.4 - - + -
111F THR 4.1 4.6 + - - +
112F HIS* 3.3 17.9 + - + +
113F PHE 3.0 0.8 + - - -
114F PHE* 1.3 75.1 - - - +
116F VAL* 1.3 68.6 + - + +
118F GLN* 3.2 15.6 + - - +
119F THR* 2.9 52.5 + - + +
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Residues in contact with VAL 116 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117E PHE* 3.7 26.2 - - + -
8F PHE* 3.9 28.3 - - + -
68F VAL* 4.6 16.9 - - + +
102F LEU* 6.2 2.7 - - + -
106F LEU* 3.7 21.8 - - + -
112F HIS 3.7 11.7 - - - +
113F PHE* 3.1 10.4 + - - +
115F TYR* 1.3 82.3 - - + +
117F PHE* 1.3 63.1 + - - +
119F THR* 2.7 21.0 + - - +
120F LEU* 3.4 17.0 + - - +
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Residues in contact with PHE 117 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70E MET* 3.9 9.4 - - - -
74E ILE* 3.7 29.6 - - + -
106E LEU* 5.3 0.7 - - + -
113E PHE* 4.3 12.6 - + - -
116E VAL* 3.5 33.4 - - + -
117E PHE* 3.4 38.8 - + - -
120E LEU* 3.9 12.8 - - + -
113F PHE* 2.9 27.0 + + + +
114F PHE* 3.9 11.7 - + - +
116F VAL* 1.3 77.1 - - - +
118F GLN* 1.3 65.1 + - - +
120F LEU* 3.2 7.8 + - - +
121F GLN* 3.1 44.0 + - + +
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Residues in contact with GLN 118 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73E PHE* 4.4 11.2 - - + -
75E ASP* 3.3 34.7 + - - +
76E THR* 4.8 2.8 + - - -
4F GLN* 5.2 10.9 - - - +
114F PHE 3.0 19.3 + - - +
115F TYR* 3.7 21.2 - - - +
117F PHE* 1.3 74.0 - - - +
119F THR* 1.3 55.2 + - - +
120F LEU 3.1 1.8 - - - -
121F GLN* 2.9 12.1 + - - +
122F LYS* 2.6 55.2 + - + +
228F ALA* 6.2 0.6 - - - +
229F CYS 5.9 2.2 - - - +
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Residues in contact with THR 119 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67F PHE* 3.1 44.8 - - + -
68F VAL* 4.1 16.7 + - + +
115F TYR* 2.9 49.1 + - + +
116F VAL* 2.7 29.3 + - - -
118F GLN* 1.3 77.8 - - - +
120F LEU* 1.3 58.3 + - - +
122F LYS* 3.4 5.9 + - + -
123F GLN* 2.9 23.4 + - - +
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Residues in contact with LEU 120 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117E PHE* 3.8 30.3 - - + +
120E LEU* 3.7 21.5 - - + -
121E GLN* 3.7 30.3 - - + +
124E VAL* 4.3 19.5 - - + -
67F PHE* 6.5 0.2 - - + -
68F VAL* 5.7 6.7 - - + +
70F MET* 4.9 15.5 - - + -
116F VAL 3.4 10.8 - - - +
117F PHE 3.2 8.7 + - - +
118F GLN 3.1 0.4 - - - -
119F THR* 1.3 81.2 + - - +
121F GLN* 1.3 55.0 + - - +
123F GLN* 2.9 8.5 + - + +
124F VAL* 2.6 41.1 + - - +
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Residues in contact with GLN 121 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70E MET* 3.4 42.6 + - - +
72E GLY 3.6 6.3 + - - -
73E PHE* 3.3 25.0 - - + +
74E ILE* 3.3 23.7 + - - +
75E ASP* 5.1 0.2 - - - +
80E VAL* 4.7 6.9 - - + +
120E LEU* 3.9 15.0 - - + +
117F PHE* 3.1 29.9 + - + +
118F GLN* 2.9 12.4 + - - +
120F LEU* 1.3 76.3 - - - +
122F LYS* 1.3 57.3 + - - +
124F VAL* 4.0 7.7 - - - +
125F SER* 2.9 31.7 + - - -
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Residues in contact with LYS 122 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73E PHE* 3.8 8.7 - - + -
67F PHE* 4.3 15.0 - - + -
118F GLN* 2.6 38.0 + - + +
119F THR* 3.4 13.5 - - + +
121F GLN* 1.3 73.6 - - - +
123F GLN* 1.3 55.9 + - - +
125F SER* 3.7 1.5 - - - -
126F TYR* 2.8 30.1 + - - +
224F TRP* 3.3 21.6 - - - -
228F ALA* 4.2 16.2 - - + -
229F CYS* 3.3 31.8 - - + +
301F GSH 2.6 49.0 + - - +
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Residues in contact with GLN 123 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124E VAL* 3.6 29.5 - - + +
128E LEU* 3.9 13.1 - - - +
61F GLN* 2.8 44.1 + - - -
63F TYR* 3.5 15.5 + - - -
67F PHE* 4.2 4.4 - - + -
119F THR 2.9 15.1 + - - +
120F LEU* 2.9 13.7 + - + +
122F LYS* 1.3 73.4 - - - +
124F VAL* 1.3 60.2 + - - +
126F TYR* 3.1 4.4 + - - +
127F SER* 2.9 51.5 + - - +
301F GSH 3.2 14.8 - - - -
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Residues in contact with VAL 124 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120E LEU* 3.9 28.0 - - + +
123E GLN* 3.6 30.5 - - + +
124E VAL* 3.6 25.8 - - + +
127E SER* 5.7 1.1 - - - +
120F LEU 2.6 25.0 + - - +
121F GLN* 4.0 5.6 - - - +
123F GLN* 1.3 71.8 - - - +
125F SER* 1.3 63.0 + - - +
127F SER* 3.3 7.6 + - - -
128F LEU* 3.2 33.4 + - + +
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Residues in contact with SER 125 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73E PHE* 4.4 6.1 - - - -
80E VAL* 2.3 46.5 + - - -
83E TYR* 4.8 3.0 + - - -
121F GLN 2.9 20.6 + - - -
122F LYS 3.9 0.9 - - - -
124F VAL* 1.3 77.4 - - - +
126F TYR* 1.3 61.0 + - - +
128F LEU* 4.1 8.4 - - - +
129F ALA* 3.3 15.6 + - - +
224F TRP* 3.0 31.5 + - - -
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Residues in contact with TYR 126 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61F GLN* 3.5 34.3 - - + -
122F LYS 2.8 20.1 + - - +
123F GLN* 3.1 11.2 + - - +
125F SER* 1.3 73.9 - - - +
127F SER* 1.3 69.4 + - - +
129F ALA* 3.4 3.3 + - - +
130F LYS* 3.1 50.9 + - + +
149F ILE* 3.7 21.0 - - + +
221F LEU* 4.5 6.0 - - + +
224F TRP* 3.1 31.4 - + + +
225F PHE* 5.3 0.9 - + - -
301F GSH 2.3 58.7 + - + -
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Residues in contact with SER 127 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124E VAL* 5.1 2.6 + - - +
127E SER* 3.6 32.5 - - - -
128E LEU* 4.8 5.4 - - - +
123F GLN* 2.9 32.2 + - - +
124F VAL* 3.3 6.7 + - - -
126F TYR* 1.3 81.6 - - - +
128F LEU* 1.3 52.2 + - - +
130F LYS* 3.2 5.8 + - - +
131F PHE* 2.8 37.3 + - - +
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Residues in contact with LEU 128 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48E LEU* 3.8 24.2 - - + -
60E LEU* 3.9 30.1 - - + +
61E GLN* 4.9 3.8 - - + +
63E TYR* 5.1 0.7 - - - +
80E VAL* 6.1 2.9 - - + -
83E TYR* 3.5 31.2 + - + +
123E GLN* 4.4 16.8 - - - +
127E SER* 5.0 6.3 - - - +
124F VAL* 3.2 31.0 + - + +
125F SER* 4.1 6.1 - - - +
127F SER* 1.3 79.7 - - - +
129F ALA* 1.3 60.8 - - - +
131F PHE* 3.5 10.0 + - + +
132F ASN* 3.2 23.6 + - - +
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Residues in contact with ALA 129 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83E TYR* 3.6 9.8 + - - +
125F SER 3.3 15.8 + - - +
126F TYR 3.8 2.5 - - - +
127F SER 3.3 0.6 - - - -
128F LEU* 1.3 79.2 - - - +
130F LYS* 1.3 61.6 + - - +
133F ASP* 3.4 29.6 + - - +
220F LYS* 3.2 30.2 - - - +
221F LEU* 3.5 16.0 - - + +
224F TRP* 4.0 12.1 - - + -
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Residues in contact with LYS 130 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131E PHE* 3.8 20.7 - - + -
59F ASN 4.8 0.2 + - - -
60F LEU 2.7 30.0 + - - +
61F GLN* 4.2 3.6 - - - +
126F TYR* 3.1 43.2 + - + +
127F SER* 3.7 4.9 - - - +
129F ALA* 1.3 73.7 - - - +
131F PHE* 1.3 65.4 + - - +
133F ASP 3.5 0.2 + - - -
134F PHE* 3.1 70.9 + - + +
146F GLN* 3.4 17.2 + - - +
149F ILE* 4.0 7.4 - - + -
177F SER* 4.2 2.6 + - - -
221F LEU* 3.6 16.7 - - + +
301F GSH 4.5 0.4 + - - -
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Residues in contact with PHE 131 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58E MET* 4.3 12.5 - - + +
59E ASN 4.6 1.1 - - - -
60E LEU* 3.4 42.4 - - + -
130E LYS* 3.6 24.2 - - + -
131E PHE* 5.1 21.0 - + + -
134E PHE* 3.5 46.0 - + + -
177E SER 4.5 2.0 - - - -
127F SER 2.8 20.9 + - - +
128F LEU* 3.7 12.8 - - + +
129F ALA 3.4 0.2 - - - -
130F LYS* 1.3 74.0 - - - +
132F ASN* 1.3 57.1 + - - +
134F PHE* 4.2 3.2 - - + +
135F SER* 2.6 44.9 + - - -
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Residues in contact with ASN 132 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50E SER* 3.6 14.9 + - - +
52E SER* 6.3 1.2 - - - -
56E THR 5.7 0.2 - - - +
58E MET* 3.2 35.5 - - - +
60E LEU* 4.0 13.0 - - + +
83E TYR* 5.4 0.9 - - - +
128F LEU 3.2 15.1 + - - +
129F ALA 3.7 2.7 + - - +
130F LYS 3.3 0.2 - - - -
131F PHE* 1.3 80.3 - - - +
133F ASP* 1.3 84.0 + - - +
135F SER* 4.2 0.3 - - - -
136F ILE* 3.3 39.2 + - - +
219F PRO* 4.8 3.0 - - - +
220F LYS* 3.4 20.3 - - + +
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Residues in contact with ASP 133 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129F ALA 3.4 13.4 + - - +
130F LYS 4.3 0.2 - - - +
132F ASN* 1.3 105.0 + - - +
134F PHE* 1.3 63.2 + - + +
136F ILE* 4.1 12.8 - - - +
137F ASN 4.5 0.5 + - - -
141F GLY* 3.8 14.4 - - - -
217F TYR 3.8 11.6 - - - +
218F ALA* 3.1 26.9 - - + -
219F PRO* 3.5 5.6 - - - +
220F LYS 3.1 13.6 + - - -
221F LEU* 2.5 47.1 + - + +
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Residues in contact with PHE 134 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131E PHE* 3.5 30.3 - + + -
135E SER* 5.3 0.7 - - - -
130F LYS* 3.1 45.1 + - + +
131F PHE* 4.2 3.1 - - + +
133F ASP* 1.3 82.5 - - - +
135F SER* 1.3 60.8 + - - +
138F GLY* 3.1 24.3 + - - +
142F SER* 3.1 53.2 + - - +
145F GLY* 3.7 17.9 - - - -
146F GLN* 3.7 12.3 - - + -
177F SER 3.6 20.6 - - - -
178F SER* 4.0 4.9 - - - -
221F LEU* 4.0 6.5 - - + -
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Residues in contact with SER 135 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58E MET* 3.6 20.4 - - - -
134E PHE* 5.1 2.5 - - - +
139E LYS* 3.7 13.9 + - - +
179E GLY* 3.5 26.3 - - - +
131F PHE* 2.6 43.3 + - - -
132F ASN 4.2 1.3 - - - -
133F ASP 3.4 0.2 - - - -
134F PHE* 1.3 79.2 - - - +
136F ILE* 1.3 64.1 + - - +
137F ASN 3.4 1.3 + - - -
138F GLY* 3.6 7.2 + - - -
----------------------------------------------------------
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Residues in contact with ILE 136 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52E SER* 5.9 4.0 - - - -
56E THR* 4.6 30.3 - - + +
57E ILE 5.7 0.7 - - - +
58E MET* 4.4 18.4 - - + -
139E LYS* 5.8 0.2 + - - -
179E GLY* 4.5 9.8 - - - +
132F ASN* 3.3 40.8 - - - +
133F ASP* 4.1 13.5 - - - +
135F SER* 1.3 76.2 - - - +
137F ASN* 1.3 84.7 + - - +
138F GLY 3.5 0.4 + - - -
217F TYR 5.1 0.2 - - - +
219F PRO* 4.6 14.4 - - + -
18G G 6.1 1.0 - - - +
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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