Contacts of the helix formed by residues 39 - 65 (chain C) in PDB entry 2B5F
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 ARG 39 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C TRP* 3.0 82.3 - - - +
36C SER* 5.1 2.0 - - - +
37C PHE 2.4 14.5 + - - +
38C TRP* 1.3 68.9 - - - +
40C ALA* 1.3 58.1 + - - +
41C ALA 3.1 0.9 - - - -
42C ILE* 2.5 31.4 + - - +
43C ALA* 2.7 12.7 + - - +
95C ILE* 6.1 5.6 - - + -
262D TYR* 3.4 49.2 + - - -
263D VAL* 3.2 36.6 - - + +
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Residues in contact with ALA 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C SER 5.2 0.9 - - - +
37C PHE* 2.5 19.7 + - + +
39C ARG* 1.3 75.1 - - - +
41C ALA* 1.3 56.9 + - - +
43C ALA* 2.9 25.1 + - - +
44C GLU* 3.1 16.5 + - - +
95C ILE* 4.5 7.1 - - - +
96C SER* 4.1 11.4 - - - -
118C ARG* 3.8 14.8 - - - +
122C TYR* 3.6 24.9 - - + +
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Residues in contact with ALA 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C PHE* 3.0 12.6 + - + +
38C TRP* 4.7 10.3 - - + +
40C ALA* 1.3 75.7 - - - +
42C ILE* 1.3 61.9 + - + +
44C GLU* 4.1 6.3 - - - -
45C PHE* 3.5 6.9 + - - +
121C VAL* 3.2 35.0 - - + +
122C TYR* 4.4 4.9 - - + -
125C ALA* 3.0 32.4 - - + +
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Residues in contact with ILE 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C TRP 3.7 15.9 - - - +
39C ARG* 2.5 24.5 + - - +
41C ALA* 1.3 75.8 - - + +
43C ALA* 1.3 62.4 + - - +
44C GLU 3.2 1.1 - - - -
45C PHE* 3.6 13.4 - - + +
46C ILE* 3.3 21.4 + - + +
259D TYR* 3.3 23.7 + - + -
262D TYR* 4.7 29.4 - - + +
263D VAL* 5.0 9.4 - - + -
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Residues in contact with ALA 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C ARG 2.7 8.2 + - - +
40C ALA* 3.3 11.9 - - - +
42C ILE* 1.3 80.0 - - - +
44C GLU* 1.3 61.5 + - - +
47C ALA* 3.2 22.9 + - - +
92C THR* 4.1 12.8 - - + +
95C ILE* 4.7 8.5 - - + -
96C SER* 3.5 26.7 - - - +
177D TYR* 5.0 0.8 + - - +
259D TYR* 3.2 16.8 + - - +
263D VAL* 6.2 3.1 - - + -
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Residues in contact with GLU 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C ALA 3.5 13.2 - - - +
41C ALA* 4.0 6.1 - - - +
43C ALA* 1.3 75.6 - - - +
45C PHE* 1.3 71.2 + - - +
47C ALA* 2.8 6.4 + - - +
48C THR* 2.8 24.0 + - - -
92C THR* 4.8 1.0 + - - -
96C SER* 3.9 21.3 + - - +
98C GLY* 4.1 1.7 + - - -
99C HIS* 3.5 19.0 + - - -
100C ILE* 3.0 31.2 + - - +
122C TYR* 4.2 24.7 - - + -
125C ALA* 4.2 9.9 - - + -
126C GLN* 3.0 23.2 + - + +
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Residues in contact with PHE 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C ALA 3.5 13.9 + - - +
42C ILE* 3.6 18.2 - - + +
44C GLU* 1.3 84.0 - - - +
46C ILE* 1.3 86.6 + - + +
47C ALA 2.8 3.3 + - - -
48C THR* 3.1 2.4 + - - -
49C LEU* 3.0 27.2 + - + +
125C ALA* 3.5 25.3 - - + +
128C LEU* 3.7 17.3 - - + -
129C GLY* 3.4 27.2 - - - -
132C CYS* 4.0 21.8 - - + -
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Residues in contact with ILE 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C ILE* 3.3 13.1 + - + +
45C PHE* 1.3 97.7 - - + +
47C ALA* 1.3 63.6 + - - +
49C LEU* 3.4 20.4 - - + +
50C LEU* 3.4 22.4 + - + +
173D PHE* 4.2 20.0 - - + -
177D TYR* 4.8 5.1 - - + -
259D TYR* 3.3 52.3 - - + +
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Residues in contact with ALA 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C ALA 3.2 16.5 + - - +
44C GLU* 2.8 11.1 + - - +
45C PHE 2.8 1.8 + - - -
46C ILE* 1.3 73.9 - - - +
48C THR* 1.3 63.7 + - - +
49C LEU 2.9 5.1 + - - -
50C LEU* 3.2 3.6 + - - -
51C PHE 3.1 17.2 + - - -
88C LEU* 3.4 27.3 - - + +
92C THR* 4.6 8.1 - - + -
100C ILE* 3.7 27.1 - - + -
177D TYR* 5.7 3.6 - - + +
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Residues in contact with THR 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C GLU 2.8 17.8 + - - -
45C PHE 3.8 2.9 - - - -
47C ALA* 1.3 72.4 - - - +
49C LEU* 1.3 63.3 + - - +
51C PHE* 3.4 10.1 - - + +
52C LEU* 3.2 25.2 + - + +
100C ILE* 3.7 19.6 - - + +
126C GLN* 3.0 53.0 - - + +
129C GLY 4.1 1.6 - - - +
130C ALA* 3.4 17.7 - - + +
222C ASN* 6.2 0.4 - - - +
224C ALA* 4.6 5.2 - - + -
225C ARG 5.6 0.2 - - - +
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Residues in contact with LEU 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C PHE* 3.0 21.0 + - + +
46C ILE* 3.4 31.9 - - + +
47C ALA 2.9 1.2 - - - -
48C THR* 1.3 73.0 - - - +
50C LEU* 1.3 79.4 + - + +
51C PHE 2.9 9.3 + - - -
52C LEU* 3.1 3.8 + - - -
53C TYR* 2.9 22.0 + - + +
129C GLY* 3.5 20.1 + - - +
132C CYS* 4.4 13.0 - - + -
133C GLY* 3.8 13.0 - - - +
136C LEU* 4.3 20.4 - - + -
170D ILE* 4.4 5.8 - - + -
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Residues in contact with LEU 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C ILE* 3.4 15.7 + - + +
47C ALA 3.2 4.5 + - - +
49C LEU* 1.3 88.5 - - + +
51C PHE* 1.3 55.1 + - - +
53C TYR* 3.8 5.4 - - - -
54C ILE* 2.9 35.7 + - - +
84C MET* 3.2 9.2 - - + +
88C LEU* 4.8 6.3 - - + -
170D ILE* 2.9 34.1 - - + -
173D PHE* 3.2 40.8 - - + -
174D VAL* 3.4 27.4 - - + -
177D TYR* 4.9 7.2 - - + -
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Residues in contact with PHE 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C ALA 3.1 13.2 + - - +
48C THR* 3.4 14.8 - - + +
49C LEU 2.9 0.6 + - - -
50C LEU* 1.3 75.4 - - - +
52C LEU* 1.3 71.3 + - + +
54C ILE* 4.2 0.5 - - - +
55C THR* 2.5 37.2 + - + +
81C PHE* 3.8 35.4 - + - -
84C MET* 4.0 16.8 - - + -
85C ILE* 3.2 42.0 - - + -
88C LEU* 3.5 12.8 - - + +
100C ILE* 4.4 7.0 - - + -
206C VAL* 5.7 2.0 - - + -
222C ASN* 3.9 24.0 - - + -
225C ARG* 4.0 20.0 - - + -
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Residues in contact with LEU 52 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C THR* 3.2 11.7 + - + +
49C LEU 3.1 4.4 + - - +
51C PHE* 1.3 89.3 - - + +
53C TYR* 1.3 68.5 + - - +
55C THR* 3.5 3.8 - - - +
56C VAL* 3.2 48.1 + - + +
130C ALA* 3.6 36.3 - - + +
133C GLY* 4.0 0.2 - - - -
134C VAL* 3.5 30.3 - - + +
137C VAL* 3.7 4.0 - - - +
225C ARG* 3.7 39.3 - - + +
229C ALA* 5.1 0.2 - - + -
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Residues in contact with TYR 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C LEU* 2.9 19.8 + - + +
50C LEU* 3.9 9.0 - - - +
51C PHE 3.2 0.2 - - - -
52C LEU* 1.3 75.9 - - - +
54C ILE* 1.3 99.7 + - + +
57C ALA* 2.6 42.0 + - + +
133C GLY* 4.3 4.4 - - - +
136C LEU* 4.4 20.2 - - + -
137C VAL* 4.1 14.3 - - + +
140C PHE* 4.2 23.1 - + - -
141C MET* 6.5 0.2 - - - -
167D ALA* 3.5 29.0 + - - +
170D ILE* 3.2 42.2 - - + -
171D GLY* 5.1 1.3 - - - -
212D ALA* 4.6 6.0 + - + +
213D THR* 4.6 7.9 + - - -
216D ILE* 5.2 4.9 - - - +
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Residues in contact with ILE 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C LEU 2.9 20.1 + - - +
53C TYR* 1.3 100.7 - - + +
55C THR* 1.3 64.2 + - - +
57C ALA* 3.0 5.3 + - - +
58C THR* 2.9 22.0 + - - +
80C ALA* 4.8 8.3 - - + -
84C MET* 3.5 37.7 - - + -
171D GLY* 5.6 0.9 - - - -
174D VAL* 4.2 10.5 - - + -
208D MET* 3.7 20.9 - - + +
209D VAL* 4.1 31.9 - - + -
212D ALA* 3.5 6.2 - - + +
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Residues in contact with THR 55 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C PHE* 2.5 29.5 + - + +
52C LEU* 3.4 8.5 + - - +
53C TYR 3.1 0.2 + - - -
54C ILE* 1.3 76.6 - - - +
56C VAL* 1.3 56.1 + - - +
58C THR* 2.5 26.2 + - - -
59C VAL* 2.6 20.2 + - - +
80C ALA* 3.6 29.6 - - - +
81C PHE* 3.4 53.8 - - + -
84C MET* 4.8 1.6 - - + -
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Residues in contact with VAL 56 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C LEU* 3.2 40.8 + - + +
55C THR* 1.3 83.8 + - - +
57C ALA* 1.3 59.0 + - - +
58C THR 3.0 0.9 - - - -
59C VAL* 3.5 9.0 - - + +
60C ILE* 3.2 31.8 + - + +
81C PHE* 5.2 1.6 - - + -
134C VAL* 5.2 4.7 - - + -
137C VAL* 3.6 23.9 - - + +
145C TYR* 4.6 2.7 - - + -
150C GLY 3.7 25.4 - - - +
151C GLY* 4.5 14.1 - - - +
225C ARG* 4.9 8.1 - - - +
229C ALA* 5.4 0.9 - - + -
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Residues in contact with ALA 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C TYR* 2.6 47.8 + - + +
54C ILE* 3.0 8.1 - - - +
56C VAL* 1.3 72.8 - - - +
58C THR* 1.3 59.1 + - - +
61C GLY* 3.7 6.7 + - - -
137C VAL* 4.0 10.0 - - + +
141C MET* 3.7 21.5 - - + +
212D ALA* 3.3 29.1 - - + +
216D ILE* 6.4 0.4 - - + -
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Residues in contact with THR 58 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C ILE 2.9 6.1 + - - -
55C THR 2.5 16.2 + - - +
57C ALA* 1.3 72.2 - - - +
59C VAL* 1.3 57.7 + - - +
60C ILE 3.4 1.8 - - - -
61C GLY* 3.8 3.8 - - - +
62C HIS* 3.1 23.7 + - - +
72C VAL* 3.9 17.6 - - + +
76C GLY 4.4 0.4 - - - +
77C ILE* 3.9 14.9 - - + +
80C ALA* 4.0 21.0 - - + +
208D MET 4.7 0.2 + - - -
211D LEU* 2.4 44.3 + - + +
212D ALA* 2.6 8.1 + - - +
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Residues in contact with VAL 59 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C THR 2.6 21.3 + - - +
56C VAL* 3.4 11.4 + - + -
58C THR* 1.3 74.5 - - - +
60C ILE* 1.3 65.7 + - + +
62C HIS* 3.7 2.1 + - - +
63C SER* 3.3 24.4 + - - +
77C ILE* 3.6 38.0 - - + +
81C PHE* 3.8 16.8 - - + -
148C PHE 6.0 0.4 - - - +
151C GLY* 4.2 23.6 - - - +
225C ARG* 5.5 2.5 - - - +
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Residues in contact with ILE 60 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C VAL* 3.2 24.0 + - + +
59C VAL* 1.3 73.9 - - + +
61C GLY* 1.3 57.6 + - - +
62C HIS 2.7 15.1 + - - -
63C SER* 2.8 5.8 + - - -
64C LYS* 2.8 29.4 + - + +
141C MET* 4.0 25.6 - - + +
144C PRO* 4.2 27.6 - - + +
145C TYR* 3.6 50.3 - - + +
148C PHE* 4.1 18.6 - - + +
150C GLY* 4.6 4.9 - - - -
151C GLY 4.8 0.9 - - - +
159D TYR* 5.8 0.2 - - - +
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Residues in contact with GLY 61 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C ALA 3.7 16.4 + - - -
58C THR* 3.8 5.6 - - - -
59C VAL 3.4 0.4 - - - -
60C ILE* 1.3 81.0 - - - +
62C HIS* 1.3 60.6 + - - +
64C LYS* 4.2 5.0 - - - +
65C GLU* 3.9 10.4 + - - +
71C SER* 3.5 11.2 - - - -
72C VAL* 5.4 2.5 - - - -
141C MET* 4.5 5.1 - - - +
159D TYR* 5.7 1.1 - - - -
211D LEU 5.8 0.2 - - - -
215D PRO* 4.1 28.7 - - - +
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Residues in contact with HIS 62 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C THR 3.1 16.8 + - - +
59C VAL 4.0 1.1 - - - +
60C ILE 2.7 4.8 + - - -
61C GLY* 1.3 76.9 - - - +
63C SER* 1.3 74.8 + - - +
64C LYS 3.2 1.4 + - - -
65C GLU* 3.3 12.3 + - - +
71C SER* 2.2 48.3 + - - +
72C VAL* 4.5 4.0 - - + -
73C GLY* 4.1 14.9 + - - -
74C LEU* 3.6 26.3 - - + +
77C ILE* 3.7 31.2 - - + -
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Residues in contact with SER 63 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C VAL* 3.3 19.8 + - - +
60C ILE 2.8 6.9 + - - -
62C HIS* 1.3 88.2 - - - +
64C LYS* 1.3 60.0 + - - +
65C GLU 4.3 3.7 - - - +
77C ILE* 5.8 0.2 - - - +
148C PHE* 3.1 44.8 - - - +
----------------------------------------------------------
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Residues in contact with LYS 64 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C ILE* 2.8 22.5 + - + +
61C GLY* 4.6 4.5 - - - +
63C SER* 1.3 73.0 - - - +
65C GLU* 1.3 69.4 + - - +
66C THR* 3.2 4.5 + - - -
144C PRO* 3.8 33.9 - - + +
148C PHE* 3.3 17.7 - - + -
157D LEU 3.9 17.6 + - - -
158D GLY* 4.6 7.3 - - - -
159D TYR* 3.5 40.3 + - - +
215D PRO* 6.1 2.7 - - + -
----------------------------------------------------------
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Residues in contact with GLU 65 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C GLY 3.9 5.3 + - - +
62C HIS 3.3 16.8 + - - +
63C SER 4.3 2.9 - - - +
64C LYS* 1.3 80.2 - - - +
66C THR* 1.3 96.0 + - - +
67C VAL* 3.2 18.4 - - - +
70C GLY* 3.8 11.2 - - - -
71C SER* 3.5 33.0 + - - +
74D LEU* 5.7 3.6 - - - +
215D PRO* 6.1 1.6 - - - +
----------------------------------------------------------
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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