Contacts of the helix formed by residues 59 - 86 (chain A) in PDB entry 6O0Z
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 ALA 59 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A THR* 1.3 71.2 - - - +
60A GLU* 1.3 62.1 + - - +
61A ALA 3.5 1.8 - - - +
62A THR* 4.3 7.0 - - - -
63A ARG* 3.5 19.9 + - - +
66A ARG* 5.6 0.2 + - - -
13B U 3.0 22.3 + - - +
14B G 3.7 22.9 + - - +
64B U 3.7 32.1 + - - +
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Residues in contact with GLU 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A THR* 3.3 20.1 + - - +
59A ALA* 1.3 77.9 - - - +
61A ALA* 1.3 64.9 + - + +
63A ARG* 3.1 25.2 + - - +
64A LEU* 2.9 39.1 + - + +
12B A 5.9 1.8 - - - +
13B U 4.6 5.3 + - - +
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Residues in contact with ALA 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A THR 4.8 3.6 + - - +
59A ALA 3.5 0.4 - - - -
60A GLU* 1.3 83.1 - - + +
62A THR* 1.3 59.4 + - - +
64A LEU* 3.3 9.5 + - - +
65A LYS* 3.0 52.0 + - - +
63B U 5.1 4.0 - - - +
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Residues in contact with THR 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ALA* 4.1 9.5 + - - -
60A GLU 3.3 0.2 - - - -
61A ALA* 1.3 78.4 - - - +
63A ARG* 1.3 57.0 + - - +
65A LYS* 3.4 5.1 + - - +
66A ARG* 2.9 43.2 + - - +
69A ARG* 4.7 1.9 + - - +
63B U 3.1 59.5 + - + +
64B U 3.7 27.6 + - + +
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Residues in contact with ARG 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ALA 3.5 12.6 + - - +
60A GLU* 3.1 32.8 + - - +
62A THR* 1.3 79.2 - - - +
64A LEU* 1.3 66.2 + - + +
66A ARG* 3.3 14.5 + - - +
67A THR* 2.7 37.4 + - - +
13B U 4.4 25.0 + - - -
14B G 3.2 61.5 + - - +
15B A 3.5 31.7 + - - +
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Residues in contact with LEU 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A GLU* 2.9 26.2 + - + +
61A ALA* 3.8 8.1 - - - +
63A ARG* 1.3 89.4 - - + +
65A LYS* 1.3 60.8 + - + +
67A THR* 3.4 8.1 + - - +
68A ALA* 3.0 27.4 + - - +
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Residues in contact with LYS 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A ALA* 3.0 37.8 + - - +
62A THR* 4.0 5.6 - - + +
64A LEU* 1.3 75.7 - - + +
66A ARG* 1.3 60.1 + - - +
68A ALA* 3.3 8.3 + - - +
69A ARG* 3.0 45.4 + - - +
1108A GLU* 4.0 20.0 - - - -
51B A 4.9 0.5 + - - -
63B U 3.3 45.4 + - + +
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Residues in contact with ARG 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ALA 5.6 0.2 + - - -
62A THR* 2.9 42.4 + - - +
63A ARG* 3.6 17.8 - - - +
65A LYS* 1.3 76.4 - - - +
67A THR* 1.3 62.2 + - - +
69A ARG* 3.2 21.5 + - - +
70A ARG* 3.1 40.2 + - + +
462A PHE* 4.0 29.3 - - - -
14B G 3.8 21.4 + - - -
15B A 2.8 41.4 + - - -
61B C 5.7 0.2 - - - +
62B G 3.5 29.9 + - - +
63B U 5.6 0.4 - - - -
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Residues in contact with THR 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A ARG* 2.7 24.2 + - - +
64A LEU* 3.8 9.0 - - - +
66A ARG* 1.3 76.9 - - - +
68A ALA* 1.3 61.5 + - - +
70A ARG* 3.3 10.5 + - + +
71A ARG* 3.0 39.5 + - + +
15B A 4.8 6.2 + - - -
16B G 4.2 38.9 + - + +
17B A 4.9 8.5 - - + +
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Residues in contact with ALA 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A LEU 3.0 17.4 + - - +
65A LYS* 3.6 8.7 - - - +
66A ARG 3.3 0.2 - - - -
67A THR* 1.3 76.2 - - - +
69A ARG* 1.3 62.5 + - - +
71A ARG* 3.3 17.9 + - - +
72A TYR* 3.0 42.0 + - + -
51B A 4.9 4.3 - - - +
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Residues in contact with ARG 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A THR* 4.7 3.6 + - - +
65A LYS* 3.0 26.8 + - - +
66A ARG* 3.2 35.8 + - - +
68A ALA* 1.3 75.9 - - - +
70A ARG* 1.3 60.3 + - + +
72A TYR* 3.3 5.9 + - - +
73A THR* 2.8 29.9 + - - +
51B A 3.6 33.3 + - - +
62B G 3.3 54.8 + - - +
63B U 3.0 54.4 + - - -
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Residues in contact with ARG 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ARG* 3.1 35.1 + - + +
67A THR* 3.7 10.1 + - + +
68A ALA 3.3 0.2 - - - -
69A ARG* 1.3 76.9 - - + +
71A ARG* 1.3 58.2 + - + +
73A THR* 3.4 7.1 + - - -
74A ARG* 3.0 53.5 + - - +
454A PRO* 3.8 18.4 - - - +
462A PHE* 3.8 10.7 - - - -
15B A 2.7 35.6 + - - -
16B G 3.4 32.2 + - - +
60B C 5.3 6.5 - - - +
61B C 2.8 44.4 + - - +
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Residues in contact with ARG 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A THR* 3.0 28.0 + - + +
68A ALA* 3.8 15.9 - - - +
69A ARG 3.3 0.2 - - - -
70A ARG* 1.3 76.8 - - + +
72A TYR* 1.3 71.6 + - + +
74A ARG* 3.4 7.5 + - - +
75A ARG* 3.0 29.1 + - - +
78A ARG* 5.6 0.5 + - - -
17B A 3.8 46.9 + - - +
18B C 3.3 61.3 + - - +
19B G 4.8 8.9 + - - -
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Residues in contact with TYR 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ALA* 3.0 31.7 + - + +
69A ARG* 3.8 4.9 - - - +
71A ARG* 1.3 89.1 + - + +
73A THR* 1.3 64.4 + - - +
75A ARG* 3.3 30.2 + - - +
76A LYS* 3.1 24.1 + - - +
20B C 4.4 13.7 + - - -
50B U 3.8 70.4 + + + +
51B A 4.0 19.7 - - - +
11C G 5.0 2.4 + - - -
12C C 5.9 0.5 + - - -
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Residues in contact with THR 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A ARG 2.8 19.8 + - - -
70A ARG* 3.7 6.8 - - - -
71A ARG 3.3 0.2 - - - -
72A TYR* 1.3 76.3 - - - +
74A ARG* 1.3 58.2 + - - +
76A LYS* 3.4 7.2 + - + +
77A ASN* 3.0 44.4 + - - +
59B U 4.4 9.2 - - - +
60B C 5.1 17.7 - - + +
61B C 5.6 4.8 + - - +
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Residues in contact with ARG 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ARG* 3.0 41.3 + - - +
71A ARG* 3.4 5.6 + - - +
72A TYR 3.3 0.2 - - - -
73A THR* 1.3 78.2 - - - +
75A ARG* 1.3 58.8 + - - +
77A ASN* 3.2 2.6 + - - +
78A ARG* 3.0 38.5 + - + +
448A ILE* 4.3 19.2 - - - +
453A GLY 4.9 0.2 + - - -
454A PRO* 4.1 13.1 - - - +
16B G 3.0 31.9 + - - -
17B A 3.4 32.8 + - - +
59B U 3.4 33.0 + - + +
60B C 2.7 34.8 + - - +
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Residues in contact with ARG 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ARG 3.0 17.0 + - - +
72A TYR* 3.7 26.2 + - - +
73A THR 3.3 0.2 - - - -
74A ARG* 1.3 74.5 - - - +
76A LYS* 1.3 64.5 + - - +
78A ARG* 3.2 30.1 + - + +
79A ILE* 3.1 29.0 + - + +
163A LYS* 3.8 50.9 + - + +
164A PHE* 4.5 15.5 - - - -
49B A 5.5 3.8 + - - -
50B U 2.9 34.8 + - - -
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Residues in contact with LYS 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A TYR 3.1 16.7 + - - +
73A THR* 3.7 7.0 - - + +
74A ARG 3.4 0.2 - - - -
75A ARG* 1.3 76.8 - - - +
77A ASN* 1.3 60.6 + - - +
79A ILE* 3.4 18.1 + - + +
80A CYS* 3.0 51.1 + - - -
83A GLN* 5.1 5.3 + - - +
102A GLU* 4.2 16.2 + - - -
48B A 5.0 8.9 + - - -
49B A 3.7 31.6 + - - +
50B U 6.0 1.6 - - - +
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Residues in contact with ASN 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A THR* 3.0 26.4 + - - +
74A ARG 3.6 1.3 - - - +
75A ARG 3.2 0.6 - - - -
76A LYS* 1.3 78.0 - - - +
78A ARG* 1.3 58.0 + - - +
80A CYS* 3.3 11.5 + - - +
81A TYR* 2.9 44.3 + - + -
59B U 3.0 54.6 + - + +
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Residues in contact with ARG 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ARG 5.6 0.4 + - - -
74A ARG* 3.0 23.5 + - + +
75A ARG* 3.2 32.7 + - - +
77A ASN* 1.3 76.2 - - - +
79A ILE* 1.3 65.0 + - + +
81A TYR* 3.2 15.3 + - + +
82A LEU* 3.1 22.2 + - - +
162A ILE* 3.2 38.9 + - + +
163A LYS* 3.6 15.6 + - - +
165A ARG* 3.7 36.1 - - - +
443A ILE* 4.0 30.3 - - + +
444A LEU* 5.7 0.8 - - - +
446A PHE 5.7 0.4 - - - -
18B C 3.9 14.3 + - - -
59B U 5.8 4.0 - - - +
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Residues in contact with ILE 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A ARG* 3.1 16.2 + - + +
76A LYS* 3.8 19.3 - - + +
78A ARG* 1.3 76.1 - - + +
80A CYS* 1.3 58.1 + - - +
82A LEU* 3.4 7.7 + - + +
83A GLN* 3.0 40.5 + - - +
155A TYR* 4.3 10.5 + - + +
159A ALA* 4.3 17.7 - - + +
162A ILE* 4.3 13.5 - - + -
163A LYS* 4.1 38.4 - - + -
48B A 4.2 19.3 - - - +
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Residues in contact with CYS 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A LYS* 3.0 48.6 + - - +
77A ASN* 3.6 12.6 - - - +
78A ARG 3.2 0.4 - - - -
79A ILE* 1.3 78.1 - - - +
81A TYR* 1.3 58.3 + - + +
83A GLN* 3.3 9.0 + - - +
84A GLU* 3.0 33.2 + - - +
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Residues in contact with TYR 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A ASN* 2.9 33.1 + - + +
78A ARG* 3.2 13.4 + - + +
80A CYS* 1.3 78.2 - - + +
82A LEU* 1.3 61.9 + - - +
84A GLU* 3.1 24.8 - - + +
85A ILE* 3.0 22.5 + - - +
443A ILE* 3.8 22.5 - - + +
473A ILE 4.1 8.0 + - - -
474A THR* 4.2 12.5 - - + +
475A PRO* 3.7 31.4 - - + +
476A TRP* 4.7 9.0 - + + -
59B U 4.1 32.9 + - - -
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Residues in contact with LEU 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A ARG 3.1 9.6 + - - +
79A ILE* 3.9 10.1 - - + +
81A TYR* 1.3 78.7 - - - +
83A GLN* 1.3 57.9 + - - +
85A ILE* 3.2 19.9 - - + +
86A PHE* 3.0 33.1 + - + +
155A TYR* 3.8 27.6 - - + -
158A LEU* 4.2 11.0 - - + -
159A ALA* 4.0 22.7 - - + +
162A ILE* 3.8 32.3 - - + -
440A ILE* 4.4 22.2 - - + -
443A ILE* 4.3 6.8 - - + +
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Residues in contact with GLN 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A LYS* 5.1 5.2 + - - -
79A ILE* 3.0 27.5 + - - +
80A CYS* 3.6 9.1 - - - +
81A TYR 3.2 0.2 - - - -
82A LEU* 1.3 78.1 - - - +
84A GLU* 1.3 57.1 + - - +
86A PHE* 3.3 4.5 + - - +
87A SER* 2.9 27.4 + - - -
98A PHE* 3.4 56.4 + - + +
101A LEU* 5.9 1.2 - - - +
102A GLU* 5.9 2.6 + - - +
155A TYR* 3.5 20.4 + - - +
48B A 5.4 1.6 + - - -
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Residues in contact with GLU 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A CYS 3.0 22.2 + - - +
81A TYR* 3.1 30.6 - - + +
83A GLN* 1.3 74.2 - - - +
85A ILE* 1.3 66.6 + - - +
87A SER* 3.1 25.5 + - - +
88A ASN* 3.8 5.9 - - - +
476A TRP* 4.1 15.1 - - - -
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Residues in contact with ILE 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A TYR 3.0 15.8 + - - +
82A LEU* 3.2 32.1 - - + +
84A GLU* 1.3 85.5 - - - +
86A PHE* 1.3 69.8 + - + +
87A SER 3.4 0.4 + - - -
88A ASN* 5.3 0.7 + - - -
89A GLU* 6.1 0.2 - - - +
432A PHE* 4.3 10.8 - - + -
436A ASN* 4.0 29.7 - - + +
439A LYS* 3.8 35.7 - - + -
440A ILE* 4.5 13.7 - - + -
443A ILE* 5.3 3.1 - - + -
476A TRP* 5.0 6.1 - - + -
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Residues in contact with PHE 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A LEU* 3.0 19.5 + - + +
83A GLN* 3.5 3.6 - - - +
84A GLU 3.3 0.2 - - - -
85A ILE* 1.3 84.7 - - + +
87A SER* 1.3 63.5 + - - +
88A ASN 3.6 0.9 - - - -
89A GLU* 3.8 4.4 + - - +
90A MET* 3.4 23.3 + - + +
98A PHE* 4.4 12.6 - + + -
151A LEU* 4.8 17.6 - - + +
154A ILE* 4.9 4.7 - - + -
155A TYR* 3.6 51.1 - + + -
158A LEU* 4.2 22.0 - - + -
432A PHE* 3.5 33.6 - + - -
433A LEU* 4.1 22.0 - - + -
440A ILE* 4.8 9.4 - - + -
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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