Contacts of the helix formed by residues 112 - 136 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4E GLN* 4.6 7.6 - - + -
7E GLU* 3.2 36.3 - - + +
8E PHE* 3.1 45.5 + + + -
11E TYR* 3.2 37.8 - - + -
106E LEU* 4.4 3.6 - - + +
109E ASN* 4.0 10.0 + - - +
110E LEU 3.1 0.2 - - - -
111E THR* 1.3 92.3 + - - +
113E PHE* 1.3 66.1 + - - +
114E PHE 3.3 2.2 - - - -
115E TYR* 3.2 22.1 + - + +
116E VAL* 3.6 9.5 + - - +
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Residues in contact with PHE 113 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74E ILE* 5.7 0.2 - - + -
106E LEU* 3.4 59.7 - - + -
107E SER* 4.0 5.4 - - - -
109E ASN 3.6 3.7 + - - +
110E LEU* 3.2 33.2 + - + +
112E HIS* 1.3 77.7 - - - +
114E PHE* 1.3 65.5 + - + +
116E VAL* 3.2 9.4 + - - +
117E PHE* 3.2 13.6 + - + -
110F LEU* 5.4 3.8 - - + -
113F PHE* 3.3 45.1 - + + -
114F PHE* 3.2 37.7 - + - -
117F PHE* 4.3 12.3 - + - -
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Residues in contact with PHE 114 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110E LEU* 3.2 34.0 + - + +
111E THR* 4.3 5.6 + - - +
112E HIS 3.3 0.4 - - - -
113E PHE* 1.3 73.4 - - + +
115E TYR* 1.3 56.0 + - - +
116E VAL 3.3 0.2 - - - -
117E PHE* 3.4 11.3 - + + +
118E GLN* 2.6 36.9 + - - +
74F ILE* 4.2 20.6 - - + +
75F ASP* 3.9 20.9 - - - +
103F LYS* 3.7 24.2 - - + -
106F LEU* 3.4 32.5 - - + -
107F SER* 4.6 7.4 - - - -
113F PHE* 3.4 29.6 - + - -
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Residues in contact with TYR 115 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2E ASN 5.4 1.1 - - - -
4E GLN* 3.1 56.3 - - + +
5E ALA* 3.3 23.3 - - + +
8E PHE* 3.5 34.5 - + - -
40E PHE* 3.5 13.8 - + - -
66E ALA* 3.8 17.0 + - - +
67E PHE* 4.1 3.3 + - - -
68E VAL* 4.0 13.0 - - + -
111E THR 4.4 3.9 + - - +
112E HIS* 3.2 19.8 + - + +
113E PHE 3.1 0.2 - - - -
114E PHE* 1.3 78.9 - - - +
116E VAL* 1.3 66.0 - - - +
118E GLN* 3.9 7.7 - - - +
119E THR* 3.0 44.6 + - + +
75F ASP* 4.9 1.1 + - - -
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Residues in contact with VAL 116 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8E PHE* 4.1 21.8 - - + -
68E VAL* 4.4 18.1 - - + +
70E MET* 4.7 8.7 - - - -
102E LEU* 5.7 4.3 - - + -
106E LEU* 4.0 29.6 - - + -
112E HIS 4.1 4.9 - - - +
113E PHE 3.2 7.8 + - - +
115E TYR* 1.3 79.7 - - + +
117E PHE* 1.3 60.9 + - - +
119E THR* 2.6 21.8 + - - -
120E LEU* 3.0 12.2 + - + +
117F PHE* 3.5 30.1 - - + -
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Residues in contact with PHE 117 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113E PHE 3.2 4.3 + - - +
114E PHE* 3.1 24.1 + + - +
116E VAL* 1.3 80.8 - - - +
118E GLN* 1.3 61.1 + - - +
120E LEU* 3.3 9.4 + - - +
121E GLN* 3.1 48.1 + - - +
70F MET* 5.1 4.9 - - + -
74F ILE* 3.4 31.0 - - + -
102F LEU* 5.9 0.7 - - + -
106F LEU* 4.1 7.4 - - + -
113F PHE* 3.4 18.8 - + + -
116F VAL* 3.7 32.8 - - + -
117F PHE* 3.4 32.1 - + + -
120F LEU* 3.8 18.2 - - + -
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Residues in contact with GLN 118 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4E GLN* 3.5 28.8 + - - +
114E PHE 2.6 18.7 + - - +
115E TYR* 3.9 6.8 - - - +
117E PHE* 1.3 72.6 - - - +
119E THR* 1.3 68.2 + - + +
121E GLN* 3.3 13.8 + - - +
122E LYS* 3.2 37.4 + - + +
73F PHE* 4.6 12.6 - - + +
74F ILE* 5.5 2.2 - - + +
75F ASP* 2.8 45.0 - - + +
76F THR* 5.9 4.4 - - - -
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Residues in contact with THR 119 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66E ALA 5.7 0.2 - - - +
67E PHE* 3.2 48.7 - - + -
68E VAL* 3.3 20.6 - - + +
115E TYR* 3.0 43.2 + - + +
116E VAL* 2.6 23.2 + - - -
118E GLN* 1.3 79.5 - - + +
120E LEU* 1.3 61.5 + - - +
122E LYS* 3.3 10.6 + - + +
123E GLN* 3.2 10.6 + - - +
301E GSH 5.9 1.1 - - - +
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Residues in contact with LEU 120 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67E PHE* 5.4 0.9 - - - -
68E VAL* 5.8 7.4 - - + +
70E MET* 5.6 9.4 - - + +
116E VAL* 3.0 13.8 + - + +
117E PHE 3.6 7.6 - - - +
118E GLN 3.2 0.2 - - - -
119E THR* 1.3 82.6 + - - +
121E GLN* 1.3 59.7 + - - +
123E GLN* 3.3 10.9 - - + +
124E VAL* 3.2 24.7 + - - +
117F PHE* 3.9 24.5 - - + +
120F LEU* 3.7 28.0 - - + -
121F GLN* 3.9 28.3 - - + +
124F VAL* 3.9 24.9 - - + +
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Residues in contact with GLN 121 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117E PHE* 3.1 48.5 - - - +
118E GLN* 3.3 5.5 + - - +
119E THR 3.3 0.4 - - - -
120E LEU* 1.3 72.4 - - - +
122E LYS* 1.3 61.5 + - - +
123E GLN 3.1 1.6 - - - -
124E VAL* 3.1 11.1 + - + +
125E SER* 2.9 31.7 + - - -
70F MET* 3.9 30.4 - - + +
72F GLY 4.7 1.8 - - - -
73F PHE* 3.0 46.7 - - + +
74F ILE* 3.4 4.4 + - - +
80F VAL* 5.2 3.8 - - + +
120F LEU* 3.7 14.8 - - + +
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Residues in contact with LYS 122 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67E PHE* 4.4 10.7 - - + -
118E GLN* 3.2 32.5 + - + +
119E THR* 3.3 19.1 - - + +
121E GLN* 1.3 76.3 - - - +
123E GLN* 1.3 57.7 + - - +
125E SER* 2.8 20.4 + - - -
126E TYR* 2.9 13.9 + - - +
224E TRP* 3.0 25.6 + - + -
228E ALA* 3.9 26.2 - - + -
229E CYS* 4.5 9.5 - - - +
301E GSH 2.4 43.4 + - - -
73F PHE* 3.8 9.2 - - + -
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Residues in contact with GLN 123 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61E GLN* 2.5 31.5 + - - +
63E TYR* 3.1 28.7 + - - -
67E PHE* 3.9 6.5 - - + -
68E VAL 5.2 0.5 - - - +
119E THR 3.2 7.4 + - - +
120E LEU* 3.3 16.4 - - + +
121E GLN 3.1 0.2 - - - -
122E LYS* 1.3 79.9 - - - +
124E VAL* 1.3 56.1 + - - +
126E TYR* 3.3 2.3 + - - +
127E SER* 2.9 47.4 + - - +
301E GSH 3.8 14.6 - - - -
124F VAL* 3.6 31.9 - - + +
128F LEU* 4.4 11.7 - - - +
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Residues in contact with VAL 124 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120E LEU 3.2 15.9 - - - +
121E GLN* 3.1 12.9 + - + +
123E GLN* 1.3 75.7 - - - +
125E SER* 1.3 64.3 + - - +
127E SER* 3.3 6.3 + - - -
128E LEU* 3.1 38.2 + - + +
80F VAL* 6.4 1.3 - - + -
120F LEU* 4.3 17.9 - - + -
123F GLN* 3.6 30.7 - - + +
124F VAL* 3.6 21.8 - - + +
127F SER* 5.1 1.9 + - - +
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Residues in contact with SER 125 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121E GLN 2.9 14.2 + - - -
122E LYS* 2.8 11.8 + - - -
124E VAL* 1.3 74.9 - - - +
126E TYR* 1.3 54.7 + - - +
128E LEU* 3.7 10.5 + - - +
129E ALA* 3.0 29.5 + - - +
224E TRP* 2.6 24.9 + - - -
73F PHE* 3.6 5.9 - - - -
80F VAL* 3.2 43.7 - - - +
83F TYR* 3.9 4.5 + - - -
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Residues in contact with TYR 126 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61E GLN* 3.2 26.2 - - + -
122E LYS 2.9 15.1 + - - +
123E GLN* 3.3 7.4 - - - +
125E SER* 1.3 76.4 - - - +
127E SER* 1.3 62.0 + - - +
129E ALA* 3.2 4.1 + - - +
130E LYS* 2.7 74.3 + - + +
149E ILE* 3.3 20.9 - - + +
221E LEU* 4.3 7.4 - - + +
224E TRP* 2.9 37.7 - + + +
225E PHE* 5.4 2.2 - + - -
301E GSH 2.3 55.8 + - + -
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Residues in contact with SER 127 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123E GLN* 2.9 33.3 + - - +
124E VAL* 3.8 4.6 - - - -
126E TYR* 1.3 80.1 - - - +
128E LEU* 1.3 57.3 + - - +
130E LYS* 3.3 5.3 + - - +
131E PHE* 2.7 37.2 + - - +
124F VAL* 5.4 1.8 + - - +
127F SER* 3.6 31.3 - - - -
128F LEU* 5.0 6.7 - - - +
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Residues in contact with LEU 128 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124E VAL* 3.1 30.6 + - + +
125E SER* 3.9 7.0 - - - +
127E SER* 1.3 75.1 - - - +
129E ALA* 1.3 57.1 + - - +
131E PHE* 3.3 8.1 + - + +
132E ASN* 2.9 31.2 + - - +
48F LEU* 4.0 21.8 - - + -
60F LEU* 4.2 29.2 - - + +
61F GLN* 4.1 10.5 - - + +
63F TYR* 5.4 1.3 - - - +
80F VAL* 5.6 4.3 - - + -
83F TYR* 3.9 21.8 - - + +
123F GLN* 3.9 21.8 - - - +
127F SER* 4.8 4.3 - - - +
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Residues in contact with ALA 129 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125E SER 3.0 20.4 + - - +
126E TYR* 3.2 7.6 - - - +
128E LEU* 1.3 76.3 - - - +
130E LYS* 1.3 61.9 + - - +
132E ASN* 3.3 13.8 + - - +
133E ASP* 3.4 20.8 + - - +
220E LYS* 3.0 26.0 - - - +
221E LEU* 3.6 11.7 - - + -
223E GLU* 4.4 0.4 - - - +
224E TRP* 4.2 9.4 - - + -
83F TYR* 3.5 10.4 + - - +
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Residues in contact with LYS 130 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60E LEU 2.7 25.6 + - - +
61E GLN* 4.1 1.0 - - - +
126E TYR* 2.7 57.2 + - + +
127E SER* 3.6 6.5 - - - +
129E ALA* 1.3 72.0 - - - +
131E PHE* 1.3 63.0 + - - +
132E ASN 3.3 0.2 + - - -
133E ASP 3.4 0.7 + - - -
134E PHE* 3.0 57.4 + - + +
146E GLN* 3.6 18.7 + - - -
149E ILE* 4.1 6.7 - - + -
177E SER 4.8 1.2 + - - -
221E LEU* 3.5 13.8 - - + +
301E GSH 4.0 4.0 + - - -
131F PHE* 3.6 33.0 - - + -
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Residues in contact with PHE 131 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127E SER 2.7 22.8 + - - +
128E LEU* 3.6 7.9 - - + +
130E LYS* 1.3 73.3 - - - +
132E ASN* 1.3 60.2 + - - +
134E PHE* 4.7 4.0 - - + -
135E SER* 2.3 54.3 + - - -
58F MET* 3.7 19.7 - - + -
60F LEU* 3.4 41.1 - - + -
130F LYS* 3.8 17.9 - - + -
131F PHE* 5.1 21.9 - + + -
134F PHE* 3.5 45.1 - + + -
177F SER 4.0 1.6 - - - -
178F SER* 5.4 0.2 - - - -
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Residues in contact with ASN 132 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128E LEU 2.9 17.2 + - - +
129E ALA* 3.5 7.4 - - - +
130E LYS 3.2 0.2 - - - -
131E PHE* 1.3 79.0 - - - +
133E ASP* 1.3 75.5 + - - +
135E SER* 4.3 0.7 - - - -
136E ILE* 3.2 35.7 + - - +
219E PRO* 4.9 1.4 - - - +
220E LYS* 3.7 17.9 + - + +
50F SER* 3.6 30.1 + - - -
58F MET* 3.8 16.4 - - - +
60F LEU* 3.8 19.6 - - + +
83F TYR* 5.0 2.0 - - + -
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Residues in contact with ASP 133 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129E ALA 3.4 9.8 + - - +
130E LYS 4.3 2.0 - - - +
132E ASN* 1.3 91.8 - - - +
134E PHE* 1.3 64.9 + - + +
135E SER 3.5 0.2 - - - -
136E ILE* 3.6 17.8 - - - +
137E ASN* 3.7 12.1 + - - -
141E GLY 4.2 5.1 - - - +
217E TYR 4.0 5.8 - - - +
218E ALA* 3.1 21.7 - - + -
219E PRO* 3.2 10.9 - - + +
220E LYS* 2.9 18.8 + - - +
221E LEU* 2.9 42.6 + - + +
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Residues in contact with PHE 134 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130E LYS* 3.0 50.5 + - + +
131E PHE* 4.3 3.8 - - + +
133E ASP* 1.3 85.6 - - + +
135E SER* 1.3 63.3 + - - +
136E ILE 3.3 5.0 - - - +
138E GLY* 3.9 8.8 + - - +
141E GLY 4.6 0.4 - - - -
142E SER* 3.4 57.8 + - - +
145E GLY* 4.0 15.9 - - - -
146E GLN* 4.1 11.0 - - - -
149E ILE* 5.3 0.2 - - + -
177E SER 4.0 12.1 - - - -
178E SER* 4.3 6.5 - - - -
179E GLY 5.6 0.4 - - - -
221E LEU* 4.5 4.5 - - + -
131F PHE* 3.5 35.7 - + + -
135F SER* 5.1 3.1 - - - +
139F LYS* 4.9 1.0 + - - -
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Residues in contact with SER 135 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131E PHE* 2.3 51.5 + - - -
132E ASN 4.3 0.2 - - - -
133E ASP 3.5 0.2 - - - -
134E PHE* 1.3 74.4 - - - +
136E ILE* 1.3 67.9 + - - +
137E ASN 3.8 0.2 + - - -
138E GLY 4.2 0.7 + - - -
58F MET* 3.5 24.2 - - - +
134F PHE* 5.9 0.2 - - - -
139F LYS* 2.4 32.0 + - - +
178F SER 4.5 3.1 - - - -
179F GLY* 3.7 10.7 - - - +
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Residues in contact with ILE 136 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132E ASN* 3.2 33.6 + - - +
133E ASP* 3.6 7.6 - - - +
134E PHE 3.3 8.3 - - - +
135E SER* 1.3 80.5 - - - +
137E ASN* 1.3 68.7 + - + +
138E GLY 2.8 10.7 + - - -
217E TYR 5.2 1.1 - - - +
219E PRO* 4.2 25.4 - - + -
52F SER* 5.9 4.7 - - - -
56F THR* 4.3 26.7 - - + +
57F ILE 5.0 1.6 - - - +
58F MET* 4.3 24.5 - - + -
179F GLY 4.0 11.2 - - - +
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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