Contacts of the helix formed by residues 59 - 86 (chain C) in PDB entry 1DPS
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 PHE 59 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C HIS 4.4 1.3 - - - -
54C MET* 3.2 43.2 - - + +
56C GLY 3.2 9.4 + - - +
57C ALA 3.2 0.2 - - - -
58C ASN* 1.3 76.7 - - - +
60C ILE* 1.3 80.4 + - + +
62C VAL* 3.9 0.5 - - - +
63C HIS* 2.8 68.2 + + + +
114C VAL* 4.0 8.3 - - + -
160E TRP* 4.3 6.7 - + - -
161E PHE* 3.6 31.4 - + - -
164E CYS* 3.3 45.8 - - + +
165E ASN* 3.5 17.5 + - - +
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Residues in contact with ILE 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C ASN 3.6 0.2 - - - -
59C PHE* 1.3 84.5 - - + +
61C ALA* 1.3 60.1 + - - +
63C HIS* 3.5 4.0 - - + +
64C GLU* 3.0 59.7 + - + +
58E ASN* 4.8 2.7 - - - +
61E ALA* 3.8 34.1 - - + +
62E VAL* 4.5 1.8 - - + +
65E MET* 4.1 19.1 - - + -
161E PHE* 3.5 45.1 - - + -
165E ASN* 3.2 24.7 + - - +
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Residues in contact with ALA 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C ASN* 3.6 19.5 + - - +
59C PHE 3.4 0.6 - - - -
60C ILE* 1.3 81.3 - - - +
62C VAL* 1.3 57.6 + - - +
64C GLU* 3.9 6.9 - - - +
65C MET* 2.9 30.0 + - - +
61E ALA* 4.1 10.1 - - + +
60L ILE* 3.8 19.2 - - + +
61L ALA* 4.1 19.1 - - + -
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Residues in contact with VAL 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C MET* 3.8 27.6 - - + -
58C ASN* 3.2 41.0 + - + +
59C PHE 3.4 1.7 + - - +
60C ILE 3.3 0.4 - - - -
61C ALA* 1.3 74.8 - - - +
63C HIS* 1.3 65.4 + - - +
65C MET* 3.2 11.6 + - + +
66C LEU* 3.0 28.8 + - + +
114C VAL* 4.4 11.4 - - + -
118C LEU* 4.0 19.7 - - + -
165C ASN* 4.2 20.4 - - + +
60L ILE* 4.8 0.9 - - + -
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Residues in contact with HIS 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A GLU* 4.8 5.9 + - - -
51C HIS* 2.8 81.2 + + - -
52C TRP* 4.7 2.0 - + - -
54C MET* 4.1 8.2 - - - -
59C PHE* 2.8 40.0 + + + +
60C ILE* 3.5 8.5 - - + +
62C VAL* 1.3 78.9 - - - +
64C GLU* 1.3 68.1 + - + +
66C LEU* 3.6 1.0 + - - +
67C ASP 3.3 7.3 + - - -
160E TRP* 3.9 22.7 - + - -
161E PHE* 3.9 26.5 - + - -
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Residues in contact with GLU 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C ILE* 3.0 47.3 + - + +
61C ALA* 4.1 5.3 - - - +
63C HIS* 1.3 79.0 - - + +
65C MET* 1.3 66.7 + - - +
67C ASP* 3.1 16.6 + - - +
68C GLY* 3.2 10.0 + - - -
161E PHE* 5.1 3.6 - - + -
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Residues in contact with MET 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C ALA 2.9 20.2 + - - +
62C VAL* 3.4 22.7 - - + +
64C GLU* 1.3 76.0 - - - +
66C LEU* 1.3 71.1 + - + +
68C GLY* 3.2 11.8 + - - -
69C PHE* 3.2 50.2 + - + -
118C LEU* 4.7 2.0 - - + -
161C PHE* 4.0 12.3 - - + +
162C ILE* 4.5 11.2 - - + -
165C ASN* 3.7 28.7 - - - +
60L ILE* 4.0 25.1 - - + -
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Residues in contact with LEU 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C THR* 3.3 27.7 - - + +
51C HIS* 4.0 21.3 - - + +
54C MET* 3.5 32.1 - - + -
62C VAL* 3.0 24.6 + - + +
63C HIS 3.9 4.3 - - - +
65C MET* 1.3 80.9 - - + +
67C ASP* 1.3 65.2 + - - +
69C PHE* 3.2 27.7 + - + +
70C ARG* 3.1 18.2 + - - +
118C LEU* 5.8 0.4 - - + -
121C LEU* 3.6 27.8 - - + -
125C TYR* 4.7 2.5 - - - +
162C ILE* 4.6 6.7 - - + -
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Residues in contact with ASP 67 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A ASP* 4.7 0.2 - - - +
48C LYS* 2.8 31.9 + - - +
51C HIS* 3.9 21.0 + - + -
63C HIS 3.3 4.3 + - - +
64C GLU* 3.1 14.5 + - - +
66C LEU* 1.3 77.2 - - - +
68C GLY* 1.3 63.6 + - - +
70C ARG* 3.3 19.4 + - - +
71C THR* 3.3 17.9 + - - -
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Residues in contact with GLY 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C GLU 3.2 7.6 + - - -
65C MET* 3.2 9.0 + - - -
67C ASP* 1.3 77.6 + - - +
69C PHE* 1.3 64.0 + - - +
71C THR* 3.4 8.8 + - - -
72C ALA* 3.3 21.1 + - - +
158C PHE* 5.1 0.6 - - - -
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Residues in contact with PHE 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C MET* 3.2 32.2 + - + -
66C LEU* 3.2 25.3 + - + +
68C GLY* 1.3 79.0 - - - +
70C ARG* 1.3 62.3 + - - +
72C ALA* 3.2 3.5 + - - +
73C LEU* 2.9 28.4 + - - +
125C TYR* 3.5 31.6 - + - +
158C PHE* 3.4 65.6 - + + -
161C PHE* 3.8 22.2 - + + -
162C ILE* 3.9 15.0 - - + -
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Residues in contact with ARG 70 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ILE* 4.3 32.0 - - - +
75A ASP* 5.4 2.0 + - - -
77A LEU* 5.8 2.2 - - - +
78A ASP* 2.9 30.5 + - - -
44C SER* 3.8 27.1 + - - +
47C THR* 4.4 6.9 - - + +
48C LYS* 3.3 40.0 - - + +
66C LEU 3.1 12.4 + - - +
67C ASP* 3.3 13.9 + - - +
69C PHE* 1.3 74.8 - - - +
71C THR* 1.3 67.1 + - - +
73C LEU* 3.4 10.5 + - - +
74C ILE* 3.0 50.7 + - - +
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Residues in contact with THR 71 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C ASP* 3.3 15.6 + - - -
68C GLY* 3.7 10.3 - - - -
69C PHE 3.3 0.6 - - - -
70C ARG* 1.3 83.3 + - - +
72C ALA* 1.3 62.6 + - - +
74C ILE* 3.2 17.0 - - + +
75C ASP* 3.1 35.7 + - - +
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Residues in contact with ALA 72 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C GLY 3.3 8.0 + - - +
69C PHE 3.2 4.5 + - - +
71C THR* 1.3 76.2 - - - +
73C LEU* 1.3 65.1 + - - +
75C ASP* 3.2 8.1 + - - +
76C HIS* 3.0 30.3 + - + -
154C ASP* 4.2 11.2 - - - +
158C PHE* 3.6 31.6 - - + -
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Residues in contact with LEU 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C PHE* 4.0 20.0 - - + +
43C LEU* 4.1 18.4 - - + -
44C SER* 3.8 36.6 - - - +
47C THR* 4.0 4.0 - - - +
69C PHE 2.9 19.6 + - - +
70C ARG* 3.7 7.2 - - - +
72C ALA* 1.3 75.6 - - - +
74C ILE* 1.3 58.5 - - - +
76C HIS* 3.3 3.6 + - + +
77C LEU* 3.0 32.6 + - - +
125C TYR* 3.8 21.1 - - + +
155C LEU* 3.8 31.2 - - + -
158C PHE* 4.6 10.3 - - + -
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Residues in contact with ILE 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ARG* 4.3 28.0 - - - +
74A ILE* 4.2 21.1 - - + -
44C SER* 4.2 17.0 - - - +
70C ARG* 3.0 44.1 + - - +
71C THR* 3.2 24.2 - - + +
73C LEU* 1.3 77.5 - - - +
75C ASP* 1.3 65.6 + - - +
77C LEU* 3.7 12.7 - - + +
78C ASP* 3.1 29.9 + - - +
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Residues in contact with ASP 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ARG* 5.4 1.9 + - - -
71C THR* 3.1 30.3 + - - +
72C ALA* 3.2 7.4 + - - +
74C ILE* 1.3 79.0 - - - +
76C HIS* 1.3 64.0 + - + +
78C ASP* 3.4 9.0 + - - +
79C THR* 3.0 29.2 + - - -
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Residues in contact with HIS 76 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C PHE* 3.9 18.2 - + + -
72C ALA* 3.0 29.0 + - + +
73C LEU* 3.8 5.6 - - - +
75C ASP* 1.3 78.6 - - + +
77C LEU* 1.3 62.3 + - - +
79C THR* 3.1 10.2 + - - -
80C MET* 3.0 27.4 + - + +
147C ILE* 4.8 4.5 + - + +
150C ALA* 3.5 31.6 + - + +
151C ALA* 3.5 24.6 + - + +
154C ASP* 2.6 37.3 + - + +
155C LEU* 5.2 2.0 - - + -
158C PHE* 5.7 0.2 - + - -
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Residues in contact with LEU 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A TRP* 3.8 18.2 - - + -
70A ARG* 5.8 2.0 - - - +
37C VAL* 3.9 9.3 - - + +
40C PHE* 3.8 20.4 - - + +
41C ILE* 3.5 49.8 - - + +
44C SER* 4.8 0.4 - - - +
73C LEU 3.0 20.5 + - - +
74C ILE* 3.7 22.7 - - + +
76C HIS* 1.3 77.0 - - - +
78C ASP* 1.3 71.9 + - - +
80C MET* 3.3 13.4 + - + +
81C ALA* 2.9 30.3 + - - +
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Residues in contact with ASP 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A LYS* 2.8 32.9 + - - +
52A TRP* 3.4 26.9 - - - +
67A ASP* 4.4 0.3 - - - +
70A ARG* 3.2 17.3 + - - -
74C ILE 3.1 22.4 + - - +
75C ASP* 3.8 9.6 - - - +
77C LEU* 1.3 82.7 - - - +
79C THR* 1.3 57.9 + - - +
81C ALA* 3.4 1.6 + - - +
82C GLU* 3.0 45.3 + - - +
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Residues in contact with THR 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C ASP 3.0 15.5 + - - -
76C HIS* 3.1 13.8 + - - -
78C ASP* 1.3 78.0 - - - +
80C MET* 1.3 55.8 + - - +
82C GLU* 3.5 9.8 + - - +
83C ARG* 3.1 26.5 + - - +
147C ILE* 3.9 20.6 - - + +
153H ARG* 3.5 28.7 - - - +
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Residues in contact with MET 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C LEU* 3.7 21.4 - - + +
36C GLN* 3.7 35.2 - - + -
37C VAL* 3.9 10.1 - - + +
40C PHE* 3.9 29.2 - - + -
76C HIS* 3.0 9.9 + - + +
77C LEU* 3.5 28.0 - - + +
78C ASP 3.2 0.2 - - - -
79C THR* 1.3 74.7 - - - +
81C ALA* 1.3 62.9 + - - +
83C ARG* 3.3 5.6 + - - +
84C ALA* 3.1 22.5 + - - +
147C ILE* 3.6 21.3 - - + -
148C LEU* 4.1 15.7 - - - -
151C ALA* 4.9 6.3 - - - -
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Residues in contact with ALA 81 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A TRP* 3.3 45.3 - - + +
34C ASN* 5.9 0.2 - - - -
37C VAL* 3.9 10.4 - - + +
77C LEU 2.9 15.6 + - - +
78C ASP 3.7 0.7 - - - +
80C MET* 1.3 72.5 - - - +
82C GLU* 1.3 66.9 + - - +
84C ALA* 3.2 6.7 + - - +
85C VAL* 3.1 27.4 + - - +
91C ALA* 3.8 14.0 - - + +
----------------------------------------------------------
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Residues in contact with GLU 82 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A LYS* 5.7 0.5 + - - -
51A HIS* 4.8 10.4 + - - -
52A TRP* 4.4 11.8 + - + -
63A HIS* 4.9 5.1 + - + -
78C ASP* 3.0 32.0 + - - +
79C THR* 3.8 8.7 - - - +
81C ALA* 1.3 76.8 - - - +
83C ARG* 1.3 61.8 + - - +
85C VAL* 3.2 9.6 - - - +
86C GLN* 2.9 42.6 + - - +
157H LYS* 3.9 23.1 + - - +
160H TRP* 3.9 21.1 - - + -
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Residues in contact with ARG 83 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C ASN* 4.6 2.2 - - - +
33C LEU* 3.7 10.1 - - + -
79C THR 3.1 15.1 + - - +
80C MET* 3.6 8.3 - - - +
81C ALA 3.3 0.2 - - - -
82C GLU* 1.3 76.5 - - - +
84C ALA* 1.3 64.2 + - - +
86C GLN* 3.2 18.6 + - - +
87C LEU* 3.2 42.3 + - + +
141C ASP* 2.9 37.4 + - - -
143C ASP* 3.2 27.2 + - - +
144C THR* 3.6 16.9 + - - +
147C ILE* 3.7 23.6 - - + -
133H ARG* 4.3 4.6 - - - +
152H SER 5.0 0.4 + - - -
153H ARG* 5.1 3.7 - - - +
156H ASP* 2.8 41.8 + - - +
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Residues in contact with ALA 84 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C VAL* 3.5 26.5 - - + +
33C LEU* 3.7 21.7 - - + +
34C ASN* 5.0 4.3 - - - +
80C MET 3.1 12.8 + - - +
81C ALA* 3.2 12.3 + - - +
83C ARG* 1.3 77.2 - - - +
85C VAL* 1.3 61.0 + - + +
87C LEU* 3.3 7.1 + - - -
88C GLY 3.5 0.2 + - - -
89C GLY* 3.0 23.1 + - - -
90C VAL 5.4 0.2 - - - -
91C ALA* 4.8 12.6 - - + +
----------------------------------------------------------
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Residues in contact with VAL 85 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A TRP* 3.7 16.6 - - + +
53A ASN* 3.4 26.7 - - - +
55A ARG* 4.2 10.1 + - - +
81C ALA 3.1 13.8 + - - +
82C GLU* 3.2 17.9 - - - +
84C ALA* 1.3 72.1 - - - +
86C GLN* 1.3 65.4 + - - +
87C LEU 3.1 2.0 - - - -
88C GLY* 3.0 13.3 + - - -
89C GLY 3.5 15.7 - - - +
91C ALA* 3.7 13.5 - - + +
160H TRP* 3.4 41.2 - - + +
----------------------------------------------------------
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Residues in contact with GLN 86 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C THR* 3.9 19.8 + - - +
19C ASN* 4.3 8.5 + - - +
82C GLU* 2.9 41.3 + - - +
83C ARG* 3.2 37.3 + - - +
85C VAL* 1.3 76.4 - - - +
87C LEU* 1.3 59.0 + - - +
88C GLY 3.2 3.2 + - - -
153H ARG* 4.6 3.1 - - - +
156H ASP* 3.9 8.0 - - + +
157H LYS* 3.7 26.9 + - - +
160H TRP* 3.5 51.6 - - + +
----------------------------------------------------------
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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