Contacts of the helix formed by residues 38 - 74 (chain C) in PDB entry 4O46
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 SER 38 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C PRO 4.0 0.6 + - - -
37C LEU* 1.3 74.1 - - - +
39C ASN* 1.4 55.5 + - - +
40C GLU* 3.6 9.3 + - - +
41C GLU* 2.9 39.0 + - - +
42C ARG* 2.8 33.7 + - - +
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Residues in contact with ASN 39 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C SER* 1.4 72.6 - - - +
40C GLU* 1.4 61.2 + - - +
42C ARG* 2.8 38.1 + - - +
43C ASN* 2.8 45.4 + - - +
171C ILE* 5.2 1.4 - - - +
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Residues in contact with GLU 40 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C VAL* 4.6 1.2 - - - +
12C ARG* 2.7 51.2 + - - +
38C SER* 3.2 8.1 + - - +
39C ASN* 1.4 78.8 - - - +
41C GLU* 1.4 58.5 + - - +
43C ASN* 3.2 6.8 + - - +
44C LEU* 2.9 47.8 + - + +
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Residues in contact with GLU 41 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C ARG* 2.7 43.2 + - - -
5C GLU* 5.1 4.3 - - - +
8C VAL* 3.6 33.9 - - + +
27C MET* 3.2 21.6 - - + +
30C VAL* 4.7 0.4 - - - -
36C PRO 4.1 0.2 - - - +
37C LEU* 3.8 8.5 - - + -
38C SER* 2.9 35.2 + - - +
40C GLU* 1.4 73.8 - - + +
42C ARG* 1.3 63.7 + - - +
44C LEU* 3.2 5.3 + - - -
45C LEU* 3.1 21.5 + - - +
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Residues in contact with ARG 42 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C LEU* 4.0 13.6 + - + +
38C SER 2.8 20.8 + - - +
39C ASN* 2.8 44.8 + - - +
41C GLU* 1.3 72.3 - - - +
43C ASN* 1.3 60.6 + - - +
45C LEU* 3.7 4.7 + - - +
46C SER* 3.2 24.9 + - - -
118C GLU* 4.7 6.7 - - - +
119C SER* 3.4 26.7 + - - +
122C PHE* 3.4 50.5 - - + -
123C TYR* 3.4 32.5 - - + +
171C ILE* 3.6 26.2 - - - +
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Residues in contact with ASN 43 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C ASN* 2.8 47.1 + - - +
40C GLU* 3.8 5.2 - - - +
42C ARG* 1.3 78.5 - - - +
44C LEU* 1.4 60.4 + - - +
46C SER* 3.6 5.4 - - - -
47C VAL* 2.9 42.1 + - + +
122C PHE* 4.0 22.4 - - - -
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Residues in contact with LEU 44 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C VAL* 3.8 31.2 - - + +
11C ALA* 4.6 0.7 - - + -
12C ARG* 4.2 22.9 - - + +
15C GLU* 3.7 23.8 - - - +
23C MET* 3.3 23.2 - - + +
27C MET* 3.8 18.6 - - + +
40C GLU* 2.9 39.4 + - + +
41C GLU* 3.2 12.5 + - - +
43C ASN* 1.4 74.8 - - - +
45C LEU* 1.4 55.2 + - - +
47C VAL* 4.8 0.9 - - - -
48C ALA* 3.0 26.7 + - - +
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Residues in contact with LEU 45 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C MET* 3.7 29.1 - - + +
31C THR* 3.9 14.6 - - - +
37C LEU* 4.1 15.9 - - + -
41C GLU 3.1 15.6 + - - +
42C ARG 3.8 5.6 - - - +
44C LEU* 1.4 73.7 - - - +
46C SER* 1.3 64.9 + - - +
48C ALA* 3.5 2.4 + - - +
49C TYR* 3.1 53.7 + - + +
100C VAL* 5.4 2.5 - - + -
103C LEU* 4.4 8.5 - - + -
108C LEU* 3.6 28.7 - - + -
123C TYR* 4.8 3.1 - - + -
126C MET* 4.5 17.3 - - + -
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Residues in contact with SER 46 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C ARG 3.2 15.8 + - - -
43C ASN* 3.3 7.2 + - - -
45C LEU* 1.3 78.9 - - - +
47C VAL* 1.4 53.0 + - - +
49C TYR* 3.9 0.3 - - - -
50C LYS* 2.9 41.1 + - - +
122C PHE* 3.8 24.5 - - - -
125C LYS* 5.8 1.6 + - - -
126C MET* 4.2 22.3 - - - +
130C TYR* 4.1 2.8 + - - -
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Residues in contact with VAL 47 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C GLU* 3.5 25.4 - - + +
20C TYR* 4.4 7.4 - - + +
23C MET* 4.2 8.1 - - + -
43C ASN* 2.9 30.1 + - + +
44C LEU 4.0 2.5 - - - +
46C SER* 1.4 68.7 - - - +
48C ALA* 1.3 66.3 + - - +
50C LYS* 3.4 5.6 + - - +
51C ASN* 2.9 45.1 + - - +
----------------------------------------------------------
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Residues in contact with ALA 48 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C TYR* 3.9 4.8 - - - +
23C MET* 3.7 20.8 - - + +
24C ALA* 3.5 33.0 - - - +
44C LEU 3.0 19.7 + - - +
45C LEU* 3.5 8.1 - - - +
47C VAL* 1.3 79.1 - - - +
49C TYR* 1.4 60.9 + - - +
51C ASN* 3.3 3.1 + - - +
52C VAL* 3.1 27.2 + - - +
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Residues in contact with TYR 49 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C ALA* 3.8 32.2 + - + +
25C ALA* 5.4 0.2 - - - -
28C LYS* 3.6 21.2 - - + +
45C LEU* 3.1 45.3 + - + +
46C SER 4.3 0.2 - - - +
48C ALA* 1.4 74.9 - - - +
50C LYS* 1.4 58.1 + - - +
52C VAL* 3.8 5.7 - - + +
53C VAL* 2.9 34.0 + - - +
96C VAL* 4.0 21.3 - - + -
99C ASP* 2.7 36.2 + - + -
100C VAL* 4.0 22.4 - - + -
103C LEU* 3.8 13.1 - - + +
126C MET* 5.2 0.9 - - + -
130C TYR* 3.3 18.1 - - + +
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Residues in contact with LYS 50 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C SER* 2.9 28.6 + - - +
47C VAL* 3.7 7.0 - - - +
48C ALA 3.3 0.4 - - - -
49C TYR* 1.4 71.2 - - - +
51C ASN* 1.4 56.3 + - - +
53C VAL* 3.6 4.3 - - - +
54C GLY* 2.8 32.7 + - - -
57C ARG* 4.2 15.2 - - - +
130C TYR* 3.2 11.5 + - + +
133C TYR* 3.3 28.7 - - + +
178C ASN* 6.3 0.7 - - - +
----------------------------------------------------------
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Residues in contact with ASN 51 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C TYR* 3.4 55.1 + - + -
47C VAL* 2.9 36.5 + - - +
48C ALA 3.7 0.4 - - - +
50C LYS* 1.4 76.3 - - - +
52C VAL* 1.4 64.9 + - - +
54C GLY* 3.8 1.5 - - - -
55C ALA* 3.1 24.1 + - - +
----------------------------------------------------------
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Residues in contact with VAL 52 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C TYR* 3.5 26.9 - - + +
21C ASP* 3.5 20.4 - - - +
24C ALA* 4.2 7.6 - - + -
48C ALA 3.1 18.4 + - - +
49C TYR* 3.4 10.5 + - + +
51C ASN* 1.4 77.3 - - - +
53C VAL* 1.4 62.0 + - - +
55C ALA* 3.4 4.2 + - - -
56C ARG* 3.1 41.5 + - - +
96C VAL* 3.8 26.9 - - + -
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Residues in contact with VAL 53 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C TYR 2.9 19.5 + - - +
50C LYS* 3.6 7.9 - - + +
52C VAL* 1.4 73.8 - - - +
54C GLY* 1.3 62.6 + - - +
56C ARG* 3.0 9.0 + - - +
57C ARG* 2.9 36.2 + - + +
93C LEU* 4.0 18.8 - - + +
96C VAL* 3.9 18.8 - - + -
97C CYS* 3.8 28.9 - - - -
130C TYR* 3.7 17.3 - - + -
133C TYR* 3.9 19.5 - - + -
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Residues in contact with GLY 54 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C LYS* 2.8 21.1 + - - -
51C ASN* 3.8 2.7 - - - -
52C VAL 3.3 0.4 - - - -
53C VAL* 1.3 78.0 - - - +
55C ALA* 1.3 56.0 + - - +
57C ARG* 3.3 14.8 + - - +
58C SER* 2.9 31.5 + - - -
61C ARG* 5.0 1.4 + - - -
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Residues in contact with ALA 55 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ARG* 6.0 0.9 - - - -
51C ASN 3.1 12.6 + - - +
52C VAL* 3.5 11.7 - - - +
53C VAL 3.3 0.4 - - - -
54C GLY* 1.3 74.0 - - - +
56C ARG* 1.3 68.6 + - - +
58C SER* 3.6 4.5 + - - -
59C SER* 2.9 32.8 + - - -
----------------------------------------------------------
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Residues in contact with ARG 56 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ARG* 4.4 7.8 - - - +
21C ASP* 4.1 16.8 + - - -
52C VAL* 3.1 41.3 + - - +
53C VAL* 3.0 7.7 + - - +
55C ALA* 1.3 90.2 - - - +
57C ARG* 1.4 53.7 + - - +
59C SER* 3.3 2.5 + - - -
60C TRP* 2.8 35.9 + - - +
89C ILE* 3.3 15.2 - - + +
92C GLU* 3.1 46.3 + - + +
93C LEU* 3.8 26.0 - - + +
96C VAL* 4.7 11.3 - - - +
----------------------------------------------------------
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Residues in contact with ARG 57 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C LYS* 4.2 13.1 - - - +
53C VAL* 2.9 27.7 + - + +
54C GLY* 3.5 12.7 - - - +
56C ARG* 1.4 75.1 - - - +
58C SER* 1.3 61.3 + - - +
60C TRP* 3.4 4.7 + - - +
61C ARG* 3.0 53.6 + - - +
93C LEU* 3.8 18.8 - - + -
132C ARG* 4.3 5.5 - - - +
133C TYR* 3.3 50.4 + - + +
136C GLU* 3.1 39.6 + - - +
----------------------------------------------------------
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Residues in contact with SER 58 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ALA 5.5 0.2 - - - -
18A GLU* 5.2 5.5 + - - -
54C GLY 2.9 17.4 + - - -
55C ALA* 3.8 5.8 - - - -
57C ARG* 1.3 76.1 - - - +
59C SER* 1.4 61.7 + - - +
61C ARG* 3.4 22.9 + - - +
62C VAL* 3.2 30.1 + - - +
----------------------------------------------------------
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Residues in contact with SER 59 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ALA* 2.8 36.2 + - - +
19A ARG* 3.7 26.0 + - - +
55C ALA 2.9 19.9 + - - -
56C ARG* 3.7 5.1 - - - -
58C SER* 1.4 74.1 - - - +
60C TRP* 1.4 58.2 + - - +
62C VAL* 3.1 4.6 + - - +
63C ILE* 2.9 34.6 + - - +
89C ILE* 4.2 9.2 - - - -
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Residues in contact with TRP 60 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C ARG 2.8 22.2 + - - +
57C ARG* 3.6 7.0 - - - +
59C SER* 1.4 71.8 - - - +
61C ARG* 1.3 72.6 + - + +
63C ILE* 3.4 5.0 + - - +
64C SER* 2.8 57.3 + - - -
86C ARG* 3.4 23.6 - - + +
89C ILE* 3.8 8.9 - - + +
90C GLU* 2.9 48.0 + - + +
93C LEU* 4.7 3.6 - - + -
136C GLU* 3.5 22.7 - - + -
137C VAL* 3.4 29.6 - - + -
----------------------------------------------------------
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Residues in contact with ARG 61 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C GLY 5.0 1.0 + - - -
57C ARG* 3.0 56.4 + - - +
58C SER* 3.6 26.8 + - - +
60C TRP* 1.3 93.8 - - + +
62C VAL* 1.3 57.1 + - + +
64C SER* 3.8 3.4 - - - -
65C SER* 3.0 29.7 + - - -
136C GLU* 4.6 4.8 + - - -
----------------------------------------------------------
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Residues in contact with VAL 62 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A GLN* 3.4 39.7 - - + +
17A ALA* 4.0 4.9 - - - +
58C SER* 3.2 19.7 + - - +
59C SER* 3.1 9.3 + - - +
61C ARG* 1.3 76.3 - - + +
63C ILE* 1.4 62.9 + - + +
65C SER* 3.4 7.2 + - - -
66C ILE* 3.1 39.0 + - + +
----------------------------------------------------------
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Residues in contact with ILE 63 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A LEU* 3.7 25.6 - - + +
17A ALA* 3.7 18.4 - - + -
59C SER 2.9 19.9 + - - +
60C TRP* 4.0 3.1 - - - +
62C VAL* 1.4 70.9 - - + +
64C SER* 1.4 55.4 + - - +
66C ILE* 3.1 9.2 + - + +
67C GLU* 2.8 32.7 + - - +
82C VAL* 3.5 32.7 - - + +
85C TYR* 3.6 21.5 - - + -
86C ARG* 3.8 24.0 - - + +
89C ILE* 3.8 21.5 - - + -
----------------------------------------------------------
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Residues in contact with SER 64 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C TRP* 2.8 60.8 + - - -
61C ARG* 3.8 4.9 - - - -
63C ILE* 1.4 71.1 - - - +
65C SER* 1.3 56.5 + - - +
67C GLU* 3.3 14.6 + - - +
68C GLN* 3.0 44.8 + - - -
86C ARG* 3.8 9.6 - - - +
----------------------------------------------------------
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Residues in contact with SER 65 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C ARG 3.0 18.6 + - - -
62C VAL* 3.4 7.6 - - - -
64C SER* 1.3 75.3 - - - +
66C ILE* 1.4 63.3 + - - +
68C GLN* 3.5 12.7 + - - +
69C LYS* 3.3 27.9 + - - +
----------------------------------------------------------
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Residues in contact with ILE 66 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A LEU* 3.8 30.3 - - + -
16A GLN* 3.6 38.6 - - + +
62C VAL* 3.1 31.8 + - + +
63C ILE* 3.1 8.7 + - + +
65C SER* 1.4 72.4 - - - +
67C GLU* 1.4 54.6 + - - +
69C LYS* 3.2 7.2 + - - +
70C THR* 2.7 41.2 + - - -
82C VAL* 4.3 12.1 - - + -
----------------------------------------------------------
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Residues in contact with GLU 67 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C ILE 2.8 16.9 + - - +
64C SER* 3.3 13.0 + - - +
66C ILE* 1.4 72.9 - - - +
68C GLN* 1.4 58.0 + - + +
70C THR* 4.0 3.8 - - - -
71C SER* 3.1 30.0 + - - -
79C ILE* 5.2 5.4 - - + +
82C VAL* 3.8 19.0 - - + +
83C ARG* 3.4 25.4 - - + +
86C ARG* 2.9 46.9 + - - +
----------------------------------------------------------
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Residues in contact with GLN 68 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C SER* 3.0 31.8 + - - -
65C SER* 3.7 12.0 - - - +
66C ILE 3.3 0.2 - - - -
67C GLU* 1.4 79.6 + - + +
69C LYS* 1.3 63.3 + - + +
71C SER* 3.6 14.2 + - - -
72C ALA* 3.8 7.1 + - - +
----------------------------------------------------------
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Residues in contact with LYS 69 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C SER* 3.3 18.1 + - - +
66C ILE* 3.2 9.9 + - - +
68C GLN* 1.3 76.2 - - + +
70C THR* 1.4 62.2 + - - +
72C ALA* 3.4 20.9 + - - +
73C ASP* 3.6 8.1 + - - +
----------------------------------------------------------
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Residues in contact with THR 70 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C ILE* 2.7 29.4 + - - -
67C GLU* 4.0 5.8 - - - -
69C LYS* 1.4 70.5 - - - +
71C SER* 1.4 64.1 + - - +
73C ASP* 3.0 32.7 + - - +
74C GLY 3.5 4.0 + - - -
75C ASN* 6.3 0.2 - - - -
78C LYS* 5.2 9.9 - - - -
79C ILE* 3.7 18.2 - - - +
82C VAL* 4.9 11.9 - - - -
----------------------------------------------------------
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Residues in contact with SER 71 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C GLU* 3.1 19.7 + - - -
68C GLN* 3.7 8.5 - - - -
70C THR* 1.4 75.2 - - - +
72C ALA* 1.3 61.0 + - - +
74C GLY* 3.6 11.6 + - - -
79C ILE* 4.2 12.1 - - - +
----------------------------------------------------------
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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 GLN 3.8 7.0 + - - +
69C LYS* 3.4 14.1 + - - +
70C THR 3.3 0.2 - - - -
71C SER* 1.3 79.0 - - - +
73C ASP* 1.4 60.7 + - - +
74C GLY* 3.6 0.5 + - - -
----------------------------------------------------------
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Residues in contact with ASP 73 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C LYS 3.6 4.6 + - - +
70C THR* 3.0 35.2 - - - +
72C ALA* 1.4 77.7 - - - +
74C GLY* 1.3 61.6 + - - +
75C ASN* 3.3 21.7 + - - +
----------------------------------------------------------
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Residues in contact with GLY 74 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C THR 3.5 4.6 + - - -
71C SER 3.6 9.3 + - - -
72C ALA 3.4 3.6 - - - -
73C ASP* 1.3 80.2 + - - +
75C ASN* 1.3 60.8 + - - +
76C GLU 3.8 2.8 + - - -
79C ILE* 5.3 2.5 - - - -
----------------------------------------------------------
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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