Contacts of the helix formed by residues 48 - 77 (chain I) in PDB entry 5JKL
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 LEU 48 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41I PHE* 3.0 33.4 + - + +
46I VAL* 3.8 12.8 - - + +
47I ALA* 1.3 74.5 - - - +
49I LYS* 1.3 63.7 + - - +
51I PHE* 3.3 26.8 + - + -
52I ALA* 3.1 16.3 + - - +
167I GLU* 4.2 23.3 - - + +
168I TYR* 4.0 18.4 - - + +
171I ASP* 3.2 30.3 - - + +
172I LYS* 4.5 3.1 - - - +
154K ASN* 3.9 19.1 - - - +
157K LYS* 6.4 2.5 - - + -
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Residues in contact with LYS 49 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41I PHE 4.9 1.1 - - - -
42I ASP* 6.1 1.8 - - - +
47I ALA* 3.8 8.2 + - - +
48I LEU* 1.3 72.9 - - - +
50I ASN* 1.3 63.3 + - - +
52I ALA* 3.3 9.1 + - - +
53I LYS* 2.9 43.0 + - - +
171I ASP* 3.4 3.8 + - - +
172I LYS* 5.7 0.2 - - - +
147K GLU* 5.3 8.7 + - - +
150K ASP* 4.5 18.1 + - - +
151K HIS* 5.4 9.9 - - - -
174K THR* 6.1 2.0 - - - +
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Residues in contact with ASN 50 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49I LYS* 1.3 77.7 - - - +
51I PHE* 1.3 63.4 + - - -
53I LYS* 3.9 25.6 + - - +
54I TYR* 2.9 24.9 + - - +
171I ASP* 2.8 46.6 + - - +
172I LYS* 4.3 10.7 - - - +
175I LEU* 3.6 20.9 - - + +
176I GLY* 3.6 19.2 - - - -
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Residues in contact with PHE 51 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41I PHE* 3.5 19.1 - + + -
48I LEU* 3.3 22.6 + - + +
50I ASN* 1.3 77.3 - - - +
52I ALA* 1.3 62.1 + - - +
54I TYR* 3.6 1.3 - - - +
55I PHE* 3.1 43.0 + + - -
96I GLY* 3.4 38.4 - - - -
100I MET* 3.8 21.5 - - + -
155I LEU* 4.2 9.6 - - + -
167I GLU* 3.8 21.3 - - + -
170I PHE* 3.6 29.2 - + - -
171I ASP* 2.9 23.0 + - + -
175I LEU* 3.7 13.2 - - + -
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Residues in contact with ALA 52 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38I SER* 2.6 49.5 + - - +
41I PHE* 3.7 6.4 - - + +
42I ASP* 4.1 14.8 - - + +
48I LEU 3.1 10.4 + - - +
49I LYS* 3.5 11.9 - - - +
50I ASN 3.2 0.2 - - - -
51I PHE* 1.3 79.8 - - - +
53I LYS* 1.3 59.8 + - + +
56I LEU* 3.0 16.1 + - - +
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Residues in contact with LYS 53 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49I LYS* 2.9 29.9 + - - +
50I ASN* 3.9 24.6 + - - +
52I ALA* 1.3 77.2 - - + +
54I TYR* 1.3 61.7 + - - +
56I LEU* 3.3 7.1 + - - +
57I HIS* 3.0 25.1 + - - +
175I LEU 6.0 1.1 - - - +
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Residues in contact with TYR 54 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34I TYR* 5.8 0.4 - + - -
50I ASN 2.9 19.0 + - - +
51I PHE 3.6 3.8 - - - +
52I ALA 3.4 0.2 - - - -
53I LYS* 1.3 74.7 - - - +
55I PHE* 1.3 94.0 + + - +
57I HIS* 3.3 9.5 + + - +
58I GLN* 3.1 48.3 + - + +
100I MET* 3.9 20.0 - - + -
147I GLU* 2.6 34.5 + - - +
148I LEU* 3.7 20.8 - - + +
151I HIS* 3.7 15.8 - + - -
175I LEU* 3.9 20.6 - - + +
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Residues in contact with PHE 55 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34I TYR* 3.5 52.3 - + - +
37I MET* 3.9 22.9 - - + -
38I SER* 3.8 8.1 - - - +
41I PHE* 3.6 29.2 - + - -
51I PHE* 3.1 33.5 + + - +
54I TYR* 1.3 94.9 - + - +
56I LEU* 1.3 61.3 + - - +
58I GLN* 3.3 2.7 + - + -
59I SER* 2.9 24.8 + - - -
99I ALA* 4.0 18.4 - - + -
100I MET* 3.9 26.0 - - + -
103I ALA* 4.3 5.8 - - + -
148I LEU* 5.0 0.2 - - + -
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Residues in contact with LEU 56 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35I LEU* 3.9 28.3 - - + -
38I SER* 3.4 21.2 - - - +
39I TYR* 4.3 17.7 - - + +
52I ALA 3.0 11.9 + - - +
53I LYS* 3.8 7.0 - - + +
54I TYR 3.3 0.2 - - - -
55I PHE* 1.3 77.4 - - - +
57I HIS* 1.3 63.2 + - - +
59I SER* 3.1 8.1 + - - -
60I HIS* 3.1 51.4 + - + +
----------------------------------------------------------
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Residues in contact with HIS 57 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53I LYS 3.0 13.2 + - - +
54I TYR* 3.5 10.8 - + - +
56I LEU* 1.3 76.3 - - - +
58I GLN* 1.3 82.6 + - - +
60I HIS* 3.2 10.4 + - - +
61I GLU* 3.0 37.6 + - + +
----------------------------------------------------------
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Residues in contact with GLN 58 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34I TYR* 3.8 33.5 + - + +
54I TYR* 3.1 54.6 + - + +
55I PHE* 3.3 7.8 + - - +
57I HIS* 1.3 92.1 - - - +
59I SER* 1.3 62.7 + - - +
61I GLU* 2.7 31.0 + - - +
62I GLU* 3.1 29.3 + - - +
107I GLU* 5.4 1.2 - - - +
144I ALA* 5.9 2.4 - - - +
147I GLU* 4.0 6.3 + - - -
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Residues in contact with SER 59 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31I SER* 2.6 53.4 + - - +
34I TYR* 3.7 7.8 - - - +
35I LEU* 3.7 23.8 - - - +
55I PHE 2.9 13.3 + - - -
56I LEU* 3.1 14.3 + - - -
58I GLN* 1.3 77.1 - - - +
60I HIS* 1.3 69.9 + - - +
62I GLU 3.2 1.6 + - - -
63I ARG* 3.1 11.1 + - - +
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Residues in contact with HIS 60 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35I LEU* 5.9 1.0 - - + +
56I LEU* 3.1 42.8 + - + +
57I HIS* 3.8 10.7 - - - +
59I SER* 1.3 86.1 - - - +
61I GLU* 1.3 61.1 + - - +
63I ARG* 3.2 9.3 + - + +
64I GLU* 3.1 27.3 + - + +
----------------------------------------------------------
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Residues in contact with GLU 61 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57I HIS* 3.0 29.0 + - + +
58I GLN* 2.7 35.2 + - - +
60I HIS* 1.3 75.8 - - - +
62I GLU* 1.3 61.5 + - - +
64I GLU* 3.2 9.9 + - + +
65I HIS* 3.0 56.9 + - + +
140I GLU* 4.6 11.1 - - - +
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Residues in contact with GLU 62 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27I GLU* 2.9 13.6 - - - +
30I ALA* 3.9 17.7 - - + +
31I SER* 3.6 24.7 - - - +
34I TYR* 3.8 19.4 - - + -
58I GLN* 3.1 20.1 + - - +
59I SER 3.2 0.4 + - - -
61I GLU* 1.3 78.6 - - - +
63I ARG* 1.3 64.8 + - - +
65I HIS* 3.0 16.9 + - - +
66I ALA* 3.0 22.0 + - - +
107I GLU* 3.4 22.3 - - - +
201I FE 2.1 33.2 - - - -
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Residues in contact with ARG 63 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28I LEU* 4.2 23.2 - - - +
31I SER* 3.9 11.8 + - - +
59I SER 3.1 12.3 + - - +
60I HIS* 3.5 13.2 - - + +
61I GLU 3.2 0.4 - - - -
62I GLU* 1.3 78.4 - - - +
64I GLU* 1.3 61.4 + - - +
66I ALA* 3.2 4.9 + - - +
67I GLU* 3.0 64.2 + - - +
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Residues in contact with GLU 64 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60I HIS* 3.1 16.4 + - + +
61I GLU* 3.2 9.6 + - - +
63I ARG* 1.3 81.6 - - - +
65I HIS* 1.3 63.5 + - + +
67I GLU* 2.9 32.7 + - - +
68I LYS* 3.1 24.3 + - - +
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Residues in contact with HIS 65 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27I GLU* 3.3 17.0 - - - +
61I GLU* 3.0 46.9 + - + +
62I GLU* 3.0 19.6 + - - +
64I GLU* 1.3 77.1 - - + +
66I ALA* 1.3 62.0 + - - +
68I LYS* 4.7 1.6 - - + -
69I LEU* 3.3 10.6 + - - +
136I HIS 5.4 3.8 - - - -
137I TYR* 2.6 44.3 + + + -
140I GLU* 4.9 20.0 + - + +
141I GLN* 4.8 7.4 - - - -
201I FE 2.1 28.9 - - - -
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Residues in contact with ALA 66 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24I ILE* 4.1 7.9 - - + +
27I GLU* 3.8 21.9 - - + +
28I LEU* 3.7 34.1 - - + +
62I GLU 3.0 9.5 + - - +
63I ARG* 3.2 8.7 + - - +
65I HIS* 1.3 73.9 - - - +
67I GLU* 1.3 58.9 + - + +
69I LEU* 3.2 8.5 + - - +
70I MET* 3.0 32.5 + - - +
----------------------------------------------------------
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Residues in contact with GLU 67 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63I ARG* 3.0 55.3 + - - +
64I GLU* 2.9 32.0 - - - +
66I ALA* 1.3 76.8 - - + +
68I LYS* 1.3 55.8 + - - +
70I MET* 3.2 16.1 + - - +
71I LYS* 2.9 28.9 + - - +
----------------------------------------------------------
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Residues in contact with LYS 68 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64I GLU 3.1 16.7 + - - +
65I HIS* 4.7 1.3 - - + -
67I GLU* 1.3 76.0 - - - +
69I LEU* 1.3 57.1 + - - +
71I LYS* 3.3 15.0 + - + +
72I LEU* 3.0 25.1 + - - +
132I PHE* 3.9 13.1 - - + -
136I HIS* 3.2 51.9 + - + +
137I TYR* 3.4 18.2 - - + +
----------------------------------------------------------
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Residues in contact with LEU 69 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20I ILE* 3.8 30.8 - - + +
23I GLN* 3.7 28.3 - - + +
24I ILE* 3.6 14.8 - - + +
27I GLU* 3.6 31.4 - - + -
65I HIS 3.3 7.5 + - - +
66I ALA* 3.2 7.7 + - - +
68I LYS* 1.3 73.6 - - - +
70I MET* 1.3 60.6 + - - +
72I LEU* 3.3 5.4 + - - +
73I GLN* 2.9 28.4 + - - +
114I LEU* 5.9 0.9 - - + -
117I LEU* 5.2 2.5 - - + -
132I PHE* 3.7 22.2 - - + -
137I TYR* 3.3 18.6 - - + +
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Residues in contact with MET 70 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24I ILE* 3.9 32.5 - - + -
28I LEU* 5.5 4.7 - - - -
66I ALA* 3.0 23.3 + - - +
67I GLU* 3.6 17.7 - - - +
69I LEU* 1.3 71.7 - - - +
71I LYS* 1.3 67.0 + - - +
73I GLN* 3.3 4.2 + - - +
74I ASN* 3.2 20.1 + - - -
80I ILE* 3.7 31.5 - - + +
82I LEU* 4.1 26.2 - - + -
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Residues in contact with LYS 71 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67I GLU 2.9 15.8 + - - +
68I LYS* 3.5 13.5 - - + +
70I MET* 1.3 78.2 - - - +
72I LEU* 1.3 57.2 + - - +
74I ASN* 3.2 8.8 + - - +
75I GLN* 2.9 58.9 + - + +
----------------------------------------------------------
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Residues in contact with LEU 72 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12I TYR* 4.0 19.1 - - + +
20I ILE* 4.2 12.3 - - + -
68I LYS 3.0 13.7 + - - +
69I LEU* 3.5 8.1 - - - +
71I LYS* 1.3 74.0 - - - +
73I GLN* 1.3 65.9 + - - +
75I GLN* 3.1 17.0 + - + +
76I ARG* 2.9 32.5 + - + +
128I HIS* 3.7 30.7 - - + +
129I LEU* 4.1 19.5 - - + -
132I PHE* 3.8 38.8 - - + -
----------------------------------------------------------
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Residues in contact with GLN 73 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12I TYR* 2.6 39.6 + - - -
17I GLU* 3.0 27.2 + - - +
20I ILE* 3.6 11.2 - - + +
21I ASN* 3.1 25.0 + - - +
24I ILE* 4.7 0.9 - - + -
69I LEU 2.9 13.7 + - - +
70I MET* 3.5 9.0 - - - +
71I LYS 3.3 0.4 - - - -
72I LEU* 1.3 81.6 - - - +
74I ASN* 1.3 60.5 + - - +
76I ARG* 3.4 1.7 + - - +
77I GLY 3.2 2.4 + - - -
78I GLY* 3.0 48.9 + - - -
79I ARG 3.8 2.2 + - - +
80I ILE* 3.7 22.9 - - + +
----------------------------------------------------------
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Residues in contact with ASN 74 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8I VAL* 4.2 5.2 - - - +
70I MET 3.2 10.2 + - - -
71I LYS* 3.8 7.9 - - - +
73I GLN* 1.3 75.1 - - - +
75I GLN* 1.3 67.1 + - - +
77I GLY* 3.1 11.6 + - - -
78I GLY 3.8 6.3 - - - +
79I ARG* 3.7 20.1 + - - +
80I ILE* 3.8 26.4 + - - +
----------------------------------------------------------
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Residues in contact with GLN 75 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8I VAL* 3.7 13.7 - - - +
68I LYS 5.4 0.2 - - - +
71I LYS* 2.9 43.6 + - + +
72I LEU* 3.1 32.1 + - + +
74I ASN* 1.3 77.2 - - - +
76I ARG* 1.3 67.2 + - + +
77I GLY 3.5 0.2 + - - -
128I HIS* 5.4 4.3 - - + -
132I PHE* 5.4 2.9 - - - -
----------------------------------------------------------
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Residues in contact with ARG 76 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8I VAL* 4.0 4.0 - - - +
9I ARG* 3.4 27.3 - - - +
10I GLN 3.0 29.2 + - - +
11I ASN* 3.1 22.6 + - - +
12I TYR* 3.7 40.0 - - + +
72I LEU* 2.9 31.7 + - + +
73I GLN 4.0 0.4 - - - +
75I GLN* 1.3 80.8 - - + +
77I GLY* 1.3 60.8 + - - +
78I GLY 3.3 0.4 - - - -
126I ASP* 2.9 32.0 + - - -
128I HIS* 3.1 39.2 + - - +
129I LEU* 3.8 6.7 - - - +
----------------------------------------------------------
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Residues in contact with GLY 77 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6I SER* 3.5 24.8 + - - -
8I VAL* 3.5 18.5 - - - +
9I ARG* 3.9 14.7 + - - +
73I GLN 3.2 0.2 + - - -
74I ASN 3.1 13.1 + - - -
75I GLN 3.3 1.4 + - - -
76I ARG* 1.3 78.8 - - - +
78I GLY* 1.3 63.8 + - - +
79I ARG* 4.1 11.5 + - - +
----------------------------------------------------------
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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