Contacts of the helix formed by residues 78 - 103 (chain B) in PDB entry 4HYJ
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 PRO 78 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B MET* 3.6 35.8 - - + +
77B PHE* 1.3 83.5 - - - +
79B THR* 1.3 67.5 + - - +
81B ILE* 3.9 1.8 - - + +
82B ARG* 3.0 28.0 + - - +
214B GLU* 5.6 8.4 - - + +
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Residues in contact with THR 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B PHE 3.2 1.0 - - - +
78B PRO* 1.3 81.9 - - - +
80B GLU* 1.3 68.4 + - - +
82B ARG* 3.2 15.8 + - - +
83B TYR* 2.8 51.9 + - + -
127B TYR* 4.4 12.3 - - + -
130B GLU* 3.9 31.7 + - + +
131B SER* 5.1 1.1 - - - +
134B ASN* 5.3 8.3 - - + +
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Residues in contact with GLU 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A ARG* 3.3 28.1 + - - +
112A LEU* 3.9 11.7 - - + -
77B PHE* 3.3 19.5 + - - +
79B THR* 1.3 89.6 - - - +
81B ILE* 1.3 61.4 + - - +
83B TYR* 4.4 0.7 - - - +
84B ILE* 3.0 27.5 + - - +
127B TYR* 2.9 39.2 + - + +
131B SER* 4.5 2.4 + - - -
302B LFA 3.7 42.2 - - + +
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Residues in contact with ILE 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A LFA 3.7 43.4 - - + +
57B HIS* 3.6 32.3 - - + +
60B PHE* 4.8 4.7 - - + -
61B MET* 4.4 10.5 - - + -
77B PHE* 3.0 25.7 - - - +
78B PRO* 3.9 6.7 - - + +
80B GLU* 1.3 72.5 - - - +
82B ARG* 1.3 66.1 + - - +
84B ILE* 3.1 22.7 - - - +
85B ASP* 3.4 8.3 + - - +
302B LFA 4.6 10.8 - - + -
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Residues in contact with ARG 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B HIS* 3.7 24.4 + - + +
61B MET* 5.8 0.2 - - - -
78B PRO 3.0 16.9 + - - +
79B THR* 3.6 16.1 + - - +
81B ILE* 1.3 76.8 - - - +
83B TYR* 1.3 75.9 + - - +
85B ASP* 3.2 6.2 + - - +
86B TRP* 3.0 69.0 + - + +
130B GLU* 2.8 43.0 + - - -
213B ARG* 3.7 9.7 - - - +
214B GLU* 3.4 26.6 + - - +
217B TYR* 3.9 20.4 - - - -
221B ASP* 6.1 0.7 - - - -
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Residues in contact with TYR 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B THR* 2.8 40.9 + - + +
80B GLU 4.1 1.1 - - - +
81B ILE 3.2 0.4 - - - -
82B ARG* 1.3 89.1 - - - +
84B ILE* 1.3 55.9 + - - +
86B TRP* 3.3 21.9 + + - +
87B LEU* 2.8 31.0 + - - +
123B ILE* 3.5 23.6 - - + -
126B GLY* 3.1 21.7 + - - -
127B TYR* 3.3 37.2 - + + -
130B GLU* 2.7 39.9 + - + +
198B TYR* 4.3 0.2 - - - -
301B RET 3.4 16.4 - - + +
302B LFA 3.8 19.8 - - + +
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Residues in contact with ILE 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A LEU 4.3 2.9 - - - +
88A VAL* 4.1 24.0 - - + +
91A PRO* 4.0 31.6 - - + -
92A LEU* 4.8 7.9 - - + -
304A LFA 3.6 30.9 - - + +
80B GLU 3.0 16.7 + - - +
81B ILE* 3.1 20.2 - - - +
83B TYR* 1.3 77.1 - - - +
85B ASP* 1.3 62.9 + - - +
87B LEU* 3.6 18.0 + - + +
88B VAL* 3.4 20.6 + - - +
302B LFA 3.7 23.5 - - + +
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Residues in contact with ASP 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A LFA 4.1 1.6 - - + -
53B VAL* 3.9 16.4 - - + -
54B ALA* 3.6 17.1 - - - +
57B HIS* 2.7 38.9 + - + +
81B ILE 3.7 4.7 - - - +
82B ARG 3.2 8.9 + - - +
84B ILE* 1.3 79.3 - - - +
86B TRP* 1.3 64.9 + - - +
88B VAL* 3.0 6.4 + - - +
89B THR* 2.7 60.0 + - - +
221B ASP* 5.1 2.4 - - - +
225B LYS* 3.6 7.9 + - - -
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Residues in contact with TRP 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B HIS* 5.2 0.8 - - - -
82B ARG* 3.0 65.3 + - + +
83B TYR* 3.6 26.7 - + - +
85B ASP* 1.3 86.2 + - - +
87B LEU* 1.3 64.8 + - - +
88B VAL 3.0 0.5 + - - -
89B THR* 3.8 4.7 - - - -
90B THR* 2.9 32.1 + - + -
123B ILE* 3.9 15.9 - - + -
130B GLU* 4.8 0.2 - - - -
194B TYR* 3.5 30.1 - + + -
217B TYR* 3.7 14.1 - + + -
221B ASP* 4.4 8.9 + - - -
301B RET 3.5 72.8 - - + +
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Residues in contact with LEU 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A LEU* 3.7 45.0 - - + +
91A PRO* 4.6 2.2 - - + -
120A VAL* 3.8 39.9 - - + -
83B TYR 2.8 20.2 + - - +
84B ILE* 3.7 20.9 - - + +
85B ASP 3.2 0.2 - - - -
86B TRP* 1.3 71.7 - - - +
88B VAL* 1.3 60.2 + - + +
91B PRO* 3.2 22.5 - - - +
119B ASP* 5.0 0.3 - - - +
120B VAL* 4.8 14.3 - - + +
123B ILE* 4.1 14.5 - - + +
124B VAL* 5.0 1.1 - - + -
302B LFA 4.3 19.3 - - + -
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Residues in contact with VAL 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A ILE* 4.1 21.5 - - + -
87A LEU* 4.2 16.6 - - + -
88A VAL* 4.2 20.6 - - + -
304A LFA 5.5 0.2 - - + -
49B LEU* 5.7 0.2 - - + -
53B VAL* 3.5 34.3 - - + -
84B ILE 3.4 9.4 + - - +
85B ASP 3.0 14.4 + - - +
87B LEU* 1.3 81.7 - - + +
89B THR* 1.3 63.7 + - - +
90B THR 3.4 0.4 - - - -
91B PRO* 3.5 8.1 - - - +
92B LEU* 3.3 34.8 - - + +
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Residues in contact with THR 89 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B VAL* 3.6 31.2 - - - +
53B VAL* 3.6 29.4 - - + -
85B ASP* 2.7 45.1 + - - +
86B TRP* 3.8 3.5 - - - -
88B VAL* 1.3 75.7 - - + +
90B THR* 1.3 59.1 + - - +
92B LEU* 3.3 1.4 + - + -
93B LEU* 2.8 35.4 + - - +
225B LYS* 3.2 22.7 + - - -
301B RET 3.8 1.2 - - - +
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Residues in contact with THR 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B TRP* 2.9 22.7 + - + +
89B THR* 1.3 75.5 - - - +
91B PRO* 1.4 65.7 - - - +
93B LEU* 3.5 2.4 + - - -
94B LEU* 3.1 27.4 + - - +
119B ASP* 2.6 33.8 + - - -
122B MET* 4.8 0.4 - - - -
123B ILE* 3.6 7.3 - - + +
191B TRP* 3.6 12.1 - - + -
301B RET 3.5 54.3 - - + -
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Residues in contact with PRO 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A LEU* 5.1 6.1 - - + -
87B LEU 3.2 25.6 - - - +
88B VAL* 3.5 9.4 - - - +
90B THR* 1.4 97.0 - - - +
92B LEU* 1.3 58.8 + - + +
94B LEU* 3.1 6.0 + - + +
95B VAL* 2.8 34.4 + - - +
116B VAL* 4.5 28.8 - - + +
119B ASP* 3.2 17.3 - - + +
120B VAL* 5.1 8.7 - - + -
309B LFA 4.9 11.4 - - + -
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Residues in contact with LEU 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A ILE* 4.0 13.7 - - + -
305A LFA 6.4 0.2 - - + -
46B VAL* 3.3 34.3 - - + +
49B LEU* 3.5 35.7 - - + -
50B VAL* 3.5 21.5 - - + -
53B VAL* 5.8 0.4 - - + -
88B VAL* 3.3 32.2 + - + +
89B THR* 3.3 3.5 + - + +
90B THR 3.3 0.2 - - - -
91B PRO* 1.3 77.0 - - + +
93B LEU* 1.3 62.6 + - - +
95B VAL* 3.3 13.9 + - + +
96B LYS 3.6 2.1 + - - -
309B LFA 3.9 34.5 - - + -
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Residues in contact with LEU 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B VAL* 4.0 19.1 - - + -
89B THR 2.8 26.5 + - - +
90B THR 3.7 4.9 - - - +
91B PRO 3.2 0.2 - - - -
92B LEU* 1.3 76.6 - - - +
94B LEU* 1.3 63.7 + - - +
96B LYS* 3.2 33.3 + - - +
187B ILE* 6.0 0.2 - - - -
191B TRP* 3.9 15.9 - - + +
224B ASN 3.5 26.2 - - - +
225B LYS* 4.2 6.5 - - + -
228B PHE* 3.5 32.9 - - + -
301B RET 3.9 33.9 - - + -
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Residues in contact with LEU 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B THR 3.1 15.2 + - - +
91B PRO* 3.1 5.1 + - + +
93B LEU* 1.3 76.3 - - - +
95B VAL* 1.3 62.7 + - + +
97B PHE* 3.0 34.3 + - + +
98B PRO* 3.4 7.3 - - - +
115B LEU* 3.9 27.4 - - + +
116B VAL* 6.4 0.4 - - + -
119B ASP* 3.3 37.9 - - + +
157B ILE* 3.7 32.8 - - + -
161B LEU* 4.5 1.1 - - + -
187B ILE* 3.6 31.4 - - + -
191B TRP* 3.8 8.7 - - + -
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Residues in contact with VAL 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B VAL* 4.7 5.6 - - + -
91B PRO 2.8 20.9 + - - +
92B LEU* 3.5 10.5 - - - +
93B LEU 3.2 0.2 - - - -
94B LEU* 1.3 76.9 - - - +
96B LYS* 1.3 56.9 + - - +
97B PHE 3.1 0.2 - - - -
98B PRO* 3.1 11.2 - - - +
99B LEU* 2.9 42.3 + - + +
112B LEU* 4.2 19.5 - - + -
115B LEU* 5.4 1.6 - - + -
116B VAL* 4.5 8.7 - - + -
309B LFA 3.6 51.6 - - + -
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Residues in contact with LYS 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B THR* 3.9 26.2 - - + +
46B VAL* 4.1 11.8 - - + +
47B ALA* 3.5 32.3 - - - +
50B VAL* 5.2 1.2 - - - +
92B LEU 3.6 6.7 + - - +
93B LEU* 3.2 35.2 + - - +
94B LEU 3.1 0.4 + - - -
95B VAL* 1.3 78.5 - - - +
97B PHE* 1.3 62.6 + - - +
99B LEU* 3.5 11.8 - - + +
100B LEU* 3.0 31.5 + - + +
183B MET* 5.1 4.9 - - - -
225B LYS 5.2 1.2 + - - -
228B PHE* 3.6 24.0 - - + -
229B GLY* 4.4 7.4 - - - -
232B ALA* 4.1 24.2 - - + -
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Residues in contact with PHE 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B LEU 4.5 0.7 - - - -
94B LEU* 3.0 30.3 + - + +
96B LYS* 1.3 79.8 - - - +
98B PRO* 1.3 70.8 - - + +
100B LEU* 3.2 2.3 + - - +
101B LEU* 3.0 27.9 + - - +
115B LEU* 4.8 1.3 - - + -
161B LEU* 3.7 38.6 - - + -
165B VAL* 3.8 26.7 - - + -
180B LEU* 3.8 26.8 - - + +
183B MET* 3.6 45.5 - - + -
184B ARG* 3.8 10.3 - - + -
187B ILE* 4.2 7.6 - - + -
228B PHE* 4.0 17.3 - + - -
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Residues in contact with PRO 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B LEU 3.4 8.1 - - - +
95B VAL* 3.1 23.1 - - - +
97B PHE* 1.3 90.1 - - + +
99B LEU* 1.3 62.5 + - - +
101B LEU* 3.2 12.1 + - + +
102B GLY 3.1 16.5 + - - -
103B LEU* 3.3 22.5 + - + +
108B GLY* 4.3 19.5 - - - +
111B LEU* 4.3 9.0 - - + -
112B LEU* 4.1 28.0 - - + +
115B LEU* 3.9 10.5 - - + -
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Residues in contact with LEU 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B SER* 3.8 36.6 - - - +
43B THR* 4.2 12.6 - - + +
46B VAL* 3.7 30.1 - - + -
95B VAL* 2.9 31.2 + - + +
96B LYS* 3.5 12.3 - - + +
98B PRO* 1.3 78.9 - - - +
100B LEU* 1.3 64.2 + - + +
102B GLY* 3.1 11.3 + - - -
103B LEU* 4.1 24.3 + - + -
309B LFA 4.8 9.9 - - + -
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Residues in contact with LEU 100 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B TYR* 5.2 5.3 - - + -
43B THR* 3.9 15.7 - - + +
96B LYS* 3.0 19.6 + - + +
97B PHE 3.8 2.5 - - - +
99B LEU* 1.3 78.5 - - + +
101B LEU* 1.3 62.7 + - - +
102B GLY* 3.2 1.0 + - - -
172B LYS* 3.3 16.5 + - - -
176B ILE* 3.7 26.0 - - + +
179B ALA* 4.9 4.7 - - + -
180B LEU* 3.9 12.6 - - + -
183B MET* 3.1 40.6 - - + -
232B ALA* 4.2 13.5 - - + +
235B ALA* 5.6 0.4 - - + -
236B VAL* 3.5 32.1 - - + -
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Residues in contact with LEU 101 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B PHE 3.0 21.9 + - - +
98B PRO* 3.2 7.4 + - + +
100B LEU* 1.3 76.3 - - - +
102B GLY* 1.3 63.0 + - - +
108B GLY* 6.6 0.2 - - - -
111B LEU* 3.7 29.6 - - + -
164B ASN* 5.2 0.4 - - - +
165B VAL* 4.3 13.5 - - + +
168B ALA* 3.7 45.1 - - + +
169B ALA* 3.8 2.0 - - - +
172B LYS* 2.8 28.1 + - + +
180B LEU* 3.6 25.1 - - + -
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Residues in contact with GLY 102 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B PRO 3.1 3.0 + - - -
99B LEU 3.1 5.7 + - - -
100B LEU 3.1 4.6 - - - -
101B LEU* 1.3 83.2 - - - +
103B LEU* 1.3 63.2 + - - +
104B LYS* 3.5 5.2 + - - +
107B LEU* 4.1 12.6 - - - +
108B GLY* 5.3 1.4 - - - -
172B LYS* 4.2 5.4 - - - -
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Residues in contact with LEU 103 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B PRO* 3.3 21.4 + - + +
99B LEU* 4.1 22.1 + - + +
102B GLY* 1.3 73.2 - - - +
104B LYS* 1.3 59.5 + - - +
105B GLY 4.5 6.5 - - - +
107B LEU 3.6 12.8 - - - +
108B GLY* 3.6 27.8 - - - +
109B ARG* 4.1 8.7 - - - +
112B LEU* 3.5 22.0 - - + -
309B LFA 3.5 43.5 - - + +
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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