Contacts of the helix formed by residues 127 - 158 (chain G) in PDB entry 3A68
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 GLY 127 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122G ASP* 5.0 0.7 - - - -
123G HIS* 2.9 21.2 + - - -
124G ALA 4.8 0.2 - - - -
125G ASP 3.4 2.0 - - - -
126G LYS* 1.3 84.1 - - - +
128G ASP* 1.3 67.5 + - - -
129G ALA 3.4 3.1 + - - -
130G LEU 3.5 1.2 + - - -
131G HIS* 3.1 19.6 + - - +
193G LYS* 4.0 16.3 - - - +
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Residues in contact with ASP 128 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69G TYR* 4.1 11.0 + - + +
70G PHE* 3.6 17.2 - - + -
75G VAL* 3.6 14.4 - - - +
77G LEU* 3.9 1.5 - - - +
121G PHE 3.6 20.5 - - - +
122G ASP* 3.9 18.1 + - - +
127G GLY* 1.3 73.2 - - - +
129G ALA* 1.3 74.1 + - - +
131G HIS* 3.7 1.2 - - - +
132G ALA* 2.9 32.2 + - - +
197G VAL* 5.0 0.5 - - - +
190H ARG* 3.0 41.0 + - - -
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Residues in contact with ALA 129 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70G PHE* 4.2 0.9 - - - -
77G LEU* 4.1 3.6 - - + -
80G LEU* 3.7 29.0 - - + +
127G GLY 3.4 0.6 - - - -
128G ASP* 1.3 83.8 + - - +
130G LEU* 1.3 63.9 + - - +
132G ALA* 3.4 1.9 + - - +
133G MET* 3.0 28.1 + - - +
188G LEU* 4.0 15.3 - - + -
197G VAL* 3.7 31.6 - - + -
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Residues in contact with LEU 130 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126G LYS* 3.6 37.0 + - + +
127G GLY 3.5 2.0 + - - -
128G ASP 3.4 0.2 - - - -
129G ALA* 1.3 77.8 - - - +
131G HIS* 1.3 58.6 + - - +
133G MET* 3.3 1.0 + - - -
134G GLU* 2.9 51.4 + - - +
185G VAL* 3.9 22.0 - - + +
188G LEU* 4.1 20.3 - - + +
189G ARG* 3.9 33.9 - - + +
197G VAL* 5.8 2.6 - - + +
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Residues in contact with HIS 131 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25F LEU* 4.3 12.2 - - + +
118G LEU* 5.6 3.6 - - - +
120G ASP 5.5 0.6 + - - -
121G PHE* 3.3 30.0 - - - +
122G ASP 3.9 9.2 + - - -
123G HIS* 3.6 32.7 + + + -
126G LYS* 4.2 16.7 - - + +
127G GLY 3.1 18.8 + - - +
128G ASP 3.7 2.7 - - - +
130G LEU* 1.3 78.2 - - - +
132G ALA* 1.3 56.0 + - - +
134G GLU* 3.3 4.2 + - - +
135G LEU* 2.9 66.7 + - + +
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Residues in contact with ALA 132 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66G MET* 4.2 8.7 - - - +
70G PHE* 3.4 41.7 - - + -
80G LEU* 4.9 0.4 - - + -
84G PHE* 4.2 11.9 - - + -
121G PHE* 4.5 9.2 - - + -
128G ASP 2.9 8.2 + - - +
129G ALA 3.8 2.0 - - - +
131G HIS* 1.3 78.8 - - - +
133G MET* 1.3 58.3 + - - +
135G LEU* 3.3 11.6 + - - +
136G ALA* 2.9 28.4 + - - +
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Residues in contact with MET 133 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80G LEU* 4.4 9.9 - - + -
83G PHE* 3.5 36.8 - - + -
84G PHE* 4.2 13.5 - - + -
129G ALA 3.0 14.2 + - - +
130G LEU 3.8 2.5 - - - +
132G ALA* 1.3 73.8 - - - +
134G GLU* 1.3 61.0 + - - +
136G ALA* 3.3 2.0 + - - -
137G LEU* 2.9 24.9 + - - +
181G ILE* 3.5 20.4 - - - +
184G TYR* 3.5 33.9 - - + -
185G VAL* 3.7 17.2 - - + +
188G LEU* 3.6 25.1 - - + -
200G PHE* 4.9 1.1 - - + -
204G LEU* 4.0 15.5 - - + -
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Residues in contact with GLU 134 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25F LEU* 3.9 18.5 - - + +
28F VAL* 4.4 14.3 - - + +
126G LYS* 3.1 35.9 + - - +
130G LEU* 2.9 33.6 + - - +
131G HIS* 3.7 4.0 + - - +
133G MET* 1.3 77.5 - - - +
135G LEU* 1.3 60.7 + - - +
137G LEU* 3.3 5.8 + - - +
138G SER* 3.0 26.3 + - - -
185G VAL* 4.0 21.5 - - + -
189G ARG* 2.8 36.2 + - - +
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Residues in contact with LEU 135 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18F PHE* 4.9 12.1 - - + -
21F VAL* 4.6 17.3 - - + +
25F LEU* 3.4 34.3 - - + -
66G MET* 3.9 11.9 - - + -
118G LEU* 5.0 5.2 - - + -
121G PHE* 3.9 24.7 - - + -
131G HIS* 2.9 50.1 + - + +
132G ALA* 3.5 4.5 - - - +
134G GLU* 1.3 75.4 - - - +
136G ALA* 1.3 57.3 + - - +
138G SER* 3.2 6.1 + - - -
139G LEU* 2.9 29.6 + - - +
----------------------------------------------------------
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Residues in contact with ALA 136 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63G TYR* 3.8 29.1 + - + +
66G MET* 4.4 4.4 - - - +
83G PHE* 5.4 0.2 - - + -
84G PHE* 4.1 12.6 - - + -
132G ALA 2.9 17.8 + - - +
133G MET* 3.7 9.0 - - - +
134G GLU 3.3 0.2 - - - -
135G LEU* 1.3 73.0 - - - +
137G LEU* 1.3 65.4 + - - +
139G LEU* 3.2 6.4 + - - +
140G GLU* 2.9 28.4 + - - +
181G ILE* 4.2 13.0 - - + -
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Residues in contact with LEU 137 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28F VAL* 4.2 21.3 - - + -
36F LEU* 3.9 23.1 - - + +
133G MET 2.9 17.8 + - - +
134G GLU* 3.5 7.0 - - - +
136G ALA* 1.3 76.7 - - - +
138G SER* 1.3 58.5 + - - +
140G GLU* 3.3 3.5 + - + +
141G LYS* 2.9 41.3 + - + +
178G ILE* 3.9 26.7 - - + +
181G ILE* 3.7 12.7 - - + +
182G SER* 3.4 31.0 - - - +
185G VAL* 4.4 14.1 - - + -
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Residues in contact with SER 138 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21F VAL* 3.5 19.7 - - - +
24F GLU* 3.4 26.3 + - - +
25F LEU* 3.2 28.1 + - - +
28F VAL* 5.1 4.5 - - - +
134G GLU 3.0 14.8 + - - -
135G LEU* 3.5 10.5 - - - -
137G LEU* 1.3 77.2 - - - +
139G LEU* 1.3 57.3 + - - +
141G LYS* 3.3 2.5 + - - -
142G LEU* 2.9 27.2 + - - +
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Residues in contact with LEU 139 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15F PHE* 5.3 1.3 - - + -
17F PRO* 4.1 24.2 - - + -
21F VAL* 3.9 10.1 - - + +
59G VAL* 3.8 41.1 - - + +
62G VAL* 3.7 32.8 - - + -
63G TYR* 4.7 10.8 - - + +
66G MET* 5.3 1.3 - - + -
135G LEU 2.9 16.3 + - - +
136G ALA* 3.2 7.6 + - - +
138G SER* 1.3 74.3 - - - +
140G GLU* 1.3 60.2 + - - +
142G LEU* 3.4 16.9 + - + +
143G THR* 2.9 31.6 + - - +
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Residues in contact with GLU 140 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59G VAL* 4.2 5.9 - - - +
63G TYR* 2.5 35.5 + - - +
91G GLU* 3.8 14.3 - - - +
136G ALA 2.9 20.3 + - - +
137G LEU* 3.7 5.2 - - - +
139G LEU* 1.3 74.1 - - - +
141G LYS* 1.3 61.0 + - - +
143G THR* 3.3 5.6 + - - +
144G ASN* 2.9 25.1 + - - +
174G GLN* 2.7 46.8 + - - +
177G ALA* 4.1 13.2 - - + +
178G ILE* 3.9 13.0 - - + +
181G ILE* 3.5 18.3 - - + +
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Residues in contact with LYS 141 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24F GLU* 3.9 23.8 - - + +
27F LEU* 5.8 2.2 + - - +
28F VAL* 5.6 2.8 - - - +
29F PRO* 5.0 9.9 - - - +
36F LEU 2.7 29.1 + - - -
37F ALA* 3.7 15.0 - - - +
38F ARG 3.4 17.2 + - - -
39F GLN* 3.0 45.3 + - + +
137G LEU* 2.9 36.1 + - + +
138G SER* 3.6 5.2 - - - +
140G GLU* 1.3 73.7 - - - +
142G LEU* 1.3 64.8 + - - +
144G ASN* 3.2 1.0 + - - +
145G GLU* 3.0 13.1 + - - +
178G ILE* 4.1 8.5 - - + -
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Residues in contact with LEU 142 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15F PHE* 3.6 31.2 - - + -
17F PRO 4.1 11.0 - - - +
20F GLU* 3.9 34.5 - - + +
21F VAL* 4.6 4.5 - - + +
23F LYS* 6.0 0.9 - - - +
24F GLU* 4.5 8.0 - - + +
55G VAL* 6.3 0.2 - - + -
138G SER 2.9 18.4 + - - +
139G LEU* 3.6 15.5 - - + +
140G GLU 3.3 0.2 - - - -
141G LYS* 1.3 76.0 - - - +
143G THR* 1.3 62.4 + - - +
145G GLU* 3.1 25.0 + - + +
146G LYS* 3.0 45.5 + - + +
----------------------------------------------------------
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Residues in contact with THR 143 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15F PHE* 6.1 0.2 - - - -
52G GLN* 4.0 7.4 - - - +
55G VAL* 4.2 8.9 - - + +
56G GLU* 3.6 26.9 - - - +
59G VAL* 3.4 23.2 - - + +
91G GLU* 5.3 0.2 + - - -
139G LEU* 2.9 18.9 + - - +
140G GLU* 3.6 9.7 + - - -
141G LYS 3.2 0.2 - - - -
142G LEU* 1.3 75.9 - - - +
144G ASN* 1.3 58.3 + - - +
146G LYS* 3.1 8.4 + - - +
147G LEU* 2.8 29.6 + - + +
174G GLN* 3.6 18.4 - - - +
214G CA 4.2 5.8 - - - -
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Residues in contact with ASN 144 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39F GLN* 3.0 31.5 + - - +
40F LYS* 6.1 0.2 - - - +
105F ARG* 6.2 0.2 - - - +
140G GLU 2.9 13.0 + - - +
141G LYS 3.2 8.9 + - - +
143G THR* 1.3 75.7 - - - +
145G GLU* 1.3 63.5 + - - +
147G LEU* 3.2 3.8 + - - +
148G LEU* 2.9 44.8 + - - +
171G LEU* 4.4 13.2 - - - +
174G GLN* 3.3 30.5 - - + +
175G VAL* 5.2 10.0 - - - +
178G ILE* 3.9 7.3 - - + +
----------------------------------------------------------
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Residues in contact with GLU 145 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23F LYS* 3.5 19.0 + - - -
24F GLU* 3.0 29.0 - - - +
39F GLN* 3.4 21.5 + - - +
40F LYS* 3.8 26.9 + - - +
141G LYS 3.0 10.0 + - - +
142G LEU* 3.2 21.8 - - + +
144G ASN* 1.3 76.1 - - - +
146G LYS* 1.3 58.2 + - + +
148G LEU* 3.3 4.5 + - - +
149G ASN* 2.9 38.0 + - - +
----------------------------------------------------------
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Residues in contact with LYS 146 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15F PHE* 3.1 30.7 - - + -
20F GLU* 2.8 31.1 + - - -
51G GLU* 5.1 7.2 - - + +
52G GLN* 3.5 20.7 - - - +
55G VAL* 3.2 31.9 - - + -
142G LEU* 3.0 29.5 + - + +
143G THR 3.1 7.6 + - - +
145G GLU* 1.3 78.3 - - + +
147G LEU* 1.3 56.1 + - - +
149G ASN* 3.2 15.6 + - - +
150G LEU* 2.9 25.5 + - - +
----------------------------------------------------------
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Residues in contact with LEU 147 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52G GLN* 3.5 30.5 - - + +
56G GLU* 4.0 7.6 - - - +
98G LEU* 5.5 0.9 - - + -
143G THR* 2.8 19.8 + - + +
144G ASN* 3.6 6.3 - - - +
146G LYS* 1.3 76.9 - - - +
148G LEU* 1.3 58.6 + - - +
150G LEU* 3.3 9.5 + - + +
151G HIS* 2.9 27.0 + - - +
166G VAL* 3.9 13.1 - - + +
170G TYR* 3.8 37.7 - - + +
171G LEU* 3.8 15.3 - - + -
174G GLN* 3.8 37.2 - - + +
----------------------------------------------------------
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Residues in contact with LEU 148 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40F LYS* 3.7 35.7 - - + -
158F GLY 5.5 1.6 - - - +
160F VAL* 4.1 33.0 - - + +
161F GLN* 5.3 3.4 - - + +
144G ASN* 2.9 38.1 + - - +
145G GLU* 3.7 4.5 - - - +
147G LEU* 1.3 73.4 - - - +
149G ASN* 1.3 63.3 + - - +
151G HIS* 3.2 5.9 + - + +
152G SER* 2.8 30.1 + - - -
171G LEU* 4.2 18.2 - - + -
----------------------------------------------------------
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Residues in contact with ASN 149 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145G GLU* 2.9 26.0 + - - +
146G LYS* 3.2 17.6 + - - +
148G LEU* 1.3 75.0 - - - +
150G LEU* 1.3 64.9 + - - +
152G SER* 3.1 10.3 + - - -
153G VAL* 3.0 26.4 + - - +
----------------------------------------------------------
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Residues in contact with LEU 150 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48G ALA* 3.5 38.1 - - + +
49G VAL* 4.0 13.7 - - + +
52G GLN* 3.9 30.3 - - + +
98G LEU* 4.5 12.6 - - + -
146G LYS 2.9 14.0 + - - +
147G LEU* 3.4 12.1 - - + +
149G ASN* 1.3 74.9 - - - +
151G HIS* 1.3 63.6 + - - +
153G VAL* 3.1 8.1 + - + +
154G ALA* 3.1 19.1 + - - +
162G LEU* 4.6 9.0 - - + -
166G VAL* 3.7 29.2 - - + -
170G TYR* 6.6 0.2 - - + -
----------------------------------------------------------
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Residues in contact with HIS 151 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160F VAL* 3.5 32.0 - - + +
147G LEU 2.9 14.4 + - - +
148G LEU* 3.4 15.5 - - + +
149G ASN 3.2 0.2 - - - -
150G LEU* 1.3 78.1 - - - +
152G SER* 1.3 57.3 + - - +
154G ALA* 3.2 8.2 + - - +
155G THR* 3.0 48.9 + - + +
163G ALA* 3.5 28.3 - - + +
166G VAL* 4.3 15.2 - - + +
167G GLU* 2.6 35.9 + - + +
171G LEU* 4.5 0.9 - - + -
----------------------------------------------------------
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Residues in contact with SER 152 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148G LEU 2.8 16.7 + - - -
149G ASN* 3.1 13.4 + - - -
151G HIS* 1.3 75.5 + - - +
153G VAL* 1.3 59.4 + - - +
155G THR* 3.2 10.1 + - - -
156G LYS* 2.8 32.4 + - - +
----------------------------------------------------------
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Residues in contact with VAL 153 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44G GLU* 3.7 40.8 - - + +
45G SER* 4.1 7.2 - - - +
48G ALA* 3.9 20.6 - - + -
149G ASN* 3.0 18.6 + - + +
150G LEU* 3.1 8.0 + - + +
152G SER* 1.3 75.5 - - - +
154G ALA* 1.3 63.3 + - - +
156G LYS* 3.4 7.5 + - + +
157G ASN* 3.0 44.8 + - - +
162G LEU* 5.5 0.4 - - + -
----------------------------------------------------------
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Residues in contact with ALA 154 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45G SER* 4.8 1.1 - - - -
150G LEU 3.1 8.9 + - - +
151G HIS* 3.2 10.3 + - - +
153G VAL* 1.3 78.0 - - - +
155G THR* 1.3 56.8 + - - +
157G ASN* 3.3 1.1 + - - -
158G GLY 2.9 8.0 + - - -
159G ASP* 2.8 38.6 + - - +
162G LEU* 3.7 25.5 - - + +
163G ALA* 3.7 31.0 - - - +
166G VAL* 6.0 0.2 - - + -
----------------------------------------------------------
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Residues in contact with THR 155 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151G HIS* 3.0 43.8 + - + +
152G SER* 3.2 17.3 + - - -
154G ALA* 1.3 73.3 - - - +
156G LYS* 1.3 65.7 + - - +
158G GLY* 3.3 11.6 + - - +
163G ALA* 4.5 8.3 - - + -
----------------------------------------------------------
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Residues in contact with LYS 156 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44G GLU* 3.6 31.9 - - - +
152G SER 2.8 23.0 + - - +
153G VAL* 3.6 7.2 - - + +
155G THR* 1.3 74.4 + - - +
157G ASN* 1.3 64.8 + - - +
158G GLY 3.7 0.2 + - - -
----------------------------------------------------------
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Residues in contact with ASN 157 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42G VAL* 3.8 31.8 - - + +
44G GLU* 2.8 37.6 + - - +
45G SER* 4.2 6.5 + - - +
153G VAL* 3.0 32.2 + - - +
154G ALA 4.2 1.8 - - - +
156G LYS* 1.3 85.3 - - - +
158G GLY* 1.3 63.2 + - - +
159G ASP* 3.3 3.5 + - + +
----------------------------------------------------------
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Residues in contact with GLY 158 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154G ALA 2.9 5.2 + - - -
155G THR* 3.3 11.9 + - - -
156G LYS 3.4 0.8 + - - -
157G ASN* 1.3 78.3 - - - +
159G ASP* 1.3 59.5 + - - +
160G VAL* 3.3 16.5 + - - +
----------------------------------------------------------
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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