Contacts of the helix formed by residues 59 - 87 (chain A) in PDB entry 5F0P
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 59 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A MET 3.9 1.0 + - - -
58A LEU* 1.3 76.0 - - - +
60A PRO* 1.3 70.0 - - - +
61A LYS* 3.6 7.1 + - - +
62A SER* 2.9 29.5 + - - -
63A TYR* 2.8 28.7 + - - +
144A LEU* 4.9 1.1 - - - -
212A GLU* 4.8 3.6 - - - -
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Residues in contact with PRO 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A LEU 4.6 0.7 - - - +
59A SER* 1.3 86.2 - - - +
61A LYS* 1.3 56.8 + - - +
63A TYR* 3.9 1.5 - - + +
64A TYR* 3.0 28.4 + - - +
144A LEU* 4.3 22.0 - - + -
148A PHE* 4.6 4.5 - - - -
197A MET* 5.3 3.6 - - + -
212A GLU* 3.2 46.9 - - + +
215A GLU* 3.8 14.6 - - + +
216A LEU* 4.2 27.2 - - + +
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Residues in contact with LYS 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A SER* 3.3 6.9 + - - +
60A PRO* 1.3 76.2 - - - +
62A SER* 1.3 66.7 + - - +
64A TYR* 3.2 13.7 + - + +
65A GLU* 3.1 22.3 + - - +
215A GLU* 4.4 27.1 + - + +
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Residues in contact with SER 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A SER* 5.4 2.6 + - - -
16A LEU* 3.2 39.3 - - - +
58A LEU* 3.9 15.5 - - - -
59A SER* 2.9 26.9 + - - -
61A LYS* 1.3 76.6 - - - +
63A TYR* 1.3 63.1 + - - +
65A GLU* 3.0 12.1 + - - +
66A LEU* 3.1 10.4 + - - +
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Residues in contact with TYR 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A GLU 5.1 0.2 - - - -
53A LEU* 2.8 57.3 + - + +
55A THR* 4.2 17.9 - - + -
58A LEU* 3.8 23.7 - - + +
59A SER 2.8 22.0 + - - +
60A PRO 3.9 2.5 - - - +
62A SER* 1.3 72.7 - - - +
64A TYR* 1.3 56.8 + - - +
66A LEU* 3.2 4.8 + - + +
67A TYR* 2.8 28.4 + - + +
105A ILE* 5.4 1.2 - - - +
109A TYR* 4.7 5.5 + - - -
144A LEU* 3.7 21.8 - - + -
145A ARG* 3.5 23.2 - - + +
148A PHE* 3.6 43.7 - + + -
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Residues in contact with TYR 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A PRO 3.0 20.6 + - - +
61A LYS* 3.4 12.6 - - + +
63A TYR* 1.3 76.4 - - - +
65A GLU* 1.3 77.5 + - - +
67A TYR* 3.4 3.9 + + - +
68A MET* 3.1 59.8 + - + +
148A PHE* 3.8 33.7 - + + -
216A LEU* 5.8 0.9 - - + -
218A ILE* 6.6 0.2 - - + -
219A LEU* 5.5 6.3 - - + -
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Residues in contact with GLU 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A LEU* 4.3 15.3 - - + +
20A ILE* 4.8 12.0 - - + +
61A LYS 3.1 10.2 + - - +
62A SER 3.0 11.0 + - - +
64A TYR* 1.3 93.8 - - - +
66A LEU* 1.3 60.3 + - - +
68A MET* 3.3 7.9 + - - +
69A ALA* 3.1 22.9 + - - +
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Residues in contact with LEU 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A LEU* 4.1 7.2 - - + +
19A ALA* 4.1 21.1 - - + -
20A ILE* 4.4 11.7 - - + -
23A VAL* 3.9 17.0 - - + -
52A GLU* 3.5 29.8 - - + +
53A LEU* 4.1 7.6 - - + -
55A THR* 4.7 2.0 - - + -
58A LEU* 3.5 26.7 - - + -
62A SER 3.1 11.7 + - - +
63A TYR* 3.5 9.4 - - + +
65A GLU* 1.3 76.2 - - - +
67A TYR* 1.3 63.1 + - - +
69A ALA* 3.5 4.8 + - + +
70A ILE* 3.1 43.3 + - + +
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Residues in contact with TYR 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A LEU* 4.0 17.0 - - + +
63A TYR* 2.8 20.2 + - + +
64A TYR* 3.5 6.5 - + - +
65A GLU 3.3 0.2 - - - -
66A LEU* 1.3 73.7 - - - +
68A MET* 1.3 72.5 + - + +
70A ILE* 3.2 3.2 + - - +
71A SER* 2.7 55.0 + - - -
109A TYR* 3.6 28.3 - + - -
148A PHE* 3.5 49.1 - + + -
151A ASN* 3.3 20.8 + - - -
152A TYR* 3.3 31.5 - + + +
155A GLN* 5.1 4.3 - - - +
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Residues in contact with MET 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A TYR* 3.1 52.8 + - + +
65A GLU* 3.3 8.5 + - - +
67A TYR* 1.3 93.6 - - + +
69A ALA* 1.3 65.2 + - - +
71A SER* 3.8 4.2 - - - -
72A ASP* 3.1 50.4 + - - +
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Residues in contact with ALA 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ILE* 4.7 20.9 - - + -
23A VAL* 4.8 11.7 - - + -
24A LYS* 6.3 0.9 - - - -
65A GLU 3.1 12.8 + - - +
66A LEU* 3.6 13.0 - - + +
68A MET* 1.3 77.8 - - - +
70A ILE* 1.3 61.4 + - - +
72A ASP* 3.4 6.0 + - - +
73A GLU* 3.3 27.9 + - - +
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Residues in contact with ILE 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A VAL* 3.8 20.2 - - + -
49A MET* 3.7 40.3 - - + +
50A LEU* 3.8 27.8 - - + -
52A GLU* 4.2 2.5 - - + -
53A LEU* 3.6 30.7 - - + -
66A LEU* 3.1 35.4 + - + +
67A TYR 3.8 2.7 - - - +
69A ALA* 1.3 73.7 - - - +
71A SER* 1.3 60.7 + - - +
73A GLU* 3.4 2.3 + - - +
74A LEU* 2.9 31.2 + - + +
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Residues in contact with SER 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A TYR* 2.7 43.4 + - - -
68A MET* 3.8 9.6 - - - -
69A ALA 3.4 0.2 - - - -
70A ILE* 1.3 73.4 - - - +
72A ASP* 1.3 65.4 + - - +
74A LEU* 3.3 12.4 + - - +
75A HIS* 3.2 21.0 + - - +
152A TYR* 4.2 16.6 - - - -
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Residues in contact with ASP 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A MET* 3.1 39.4 + - - +
69A ALA* 3.7 6.2 - - - +
71A SER* 1.3 78.8 + - - +
73A GLU* 1.3 67.0 + - - +
75A HIS* 3.5 18.3 + - - +
76A TYR* 3.6 17.0 - - + -
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Residues in contact with GLU 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A VAL* 4.4 7.0 - - + -
24A LYS* 5.9 2.6 - - + +
27A SER* 3.4 25.1 - - - +
30A MET* 3.6 10.3 - - + +
31A LYS* 3.0 35.8 + - - -
49A MET* 3.6 24.2 - - + -
69A ALA 3.3 15.5 + - - +
70A ILE 3.8 2.0 - - - +
71A SER 3.3 0.4 - - - -
72A ASP* 1.3 78.0 - - - +
74A LEU* 1.3 65.2 + - - +
75A HIS 3.1 1.6 - - - -
76A TYR* 3.0 31.4 + - - +
77A LEU 3.6 3.5 + - - -
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Residues in contact with LEU 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A MET* 5.5 0.2 - - - -
46A ALA* 5.1 0.7 - - + -
49A MET* 3.9 19.0 - - + +
50A LEU* 4.0 35.4 - - + -
70A ILE* 2.9 24.4 + - + +
71A SER* 3.3 8.3 + - - +
73A GLU* 1.3 74.9 - - - +
75A HIS* 1.3 57.9 + - - +
77A LEU* 3.3 24.9 + - + +
78A GLU* 2.9 27.5 + - - +
109A TYR* 4.1 10.3 - - + +
110A LEU* 4.8 2.2 - - + -
113A THR* 4.2 12.1 - - - +
152A TYR* 3.3 38.8 - - + +
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Residues in contact with HIS 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A SER 3.2 12.2 + - - +
72A ASP* 3.6 13.9 - - - +
73A GLU 3.1 1.0 - - - -
74A LEU* 1.3 74.2 - - - +
76A TYR* 1.3 68.1 + + - +
78A GLU* 4.1 17.3 + - - -
79A VAL* 2.8 46.5 + - + +
511A EDO 4.0 20.9 - - - -
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Residues in contact with TYR 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A MET* 4.7 1.6 - - + -
31A LYS* 3.3 44.0 - - + -
34A LEU* 4.4 4.5 - - + +
72A ASP* 3.6 21.5 - - + -
73A GLU* 3.0 27.6 + - - +
75A HIS* 1.3 84.9 - + - +
77A LEU* 1.3 56.5 + - - +
79A VAL* 3.5 12.8 - - + +
80A TYR* 3.2 26.3 + - - +
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Residues in contact with LEU 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A MET* 4.5 16.6 - - + +
34A LEU* 4.0 29.6 - - + -
39A LEU* 4.4 2.9 - - + -
42A ALA* 5.1 1.8 - - + -
43A LEU* 3.8 29.2 - - + -
46A ALA* 4.1 18.6 - - + -
73A GLU 3.6 2.4 + - - -
74A LEU* 3.3 19.7 + - + +
75A HIS 3.2 0.2 - - - -
76A TYR* 1.3 77.0 - - - +
78A GLU* 1.3 64.5 + - - +
80A TYR* 3.3 3.6 + - - +
81A LEU* 3.0 52.1 + - + +
110A LEU* 4.1 11.2 - - + -
113A THR* 4.7 9.4 - - + -
114A VAL* 6.3 1.6 - - + -
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Residues in contact with GLU 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A LEU 2.9 17.5 + - - +
75A HIS* 3.2 23.8 + - - +
77A LEU* 1.3 75.4 - - - +
79A VAL* 1.3 54.0 + - - +
81A LEU* 3.5 4.9 + - - +
82A THR* 2.5 58.5 + - - -
113A THR* 3.8 25.5 - - + +
116A VAL* 4.0 23.3 - - + +
117A VAL* 3.9 3.4 - - + +
120A LYS* 3.1 23.3 + - - -
152A TYR* 5.6 1.6 - - - +
156A CYS* 5.9 3.8 - - - -
511A EDO 4.1 9.7 + - - -
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Residues in contact with VAL 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A HIS* 2.8 40.5 + - + +
76A TYR* 3.5 17.9 - - + +
78A GLU* 1.3 72.6 - - - +
80A TYR* 1.3 68.5 + - - +
82A THR* 4.0 6.2 - - - -
83A ASP* 3.0 46.6 + - - +
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Residues in contact with TYR 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A LEU* 3.3 55.9 - - + -
37A ASN* 3.5 25.8 + - - +
39A LEU* 4.1 20.4 - - + +
76A TYR 3.2 15.8 + - - +
77A LEU* 3.3 6.5 + - - +
79A VAL* 1.3 84.6 - - - +
81A LEU* 1.3 77.0 + - + +
83A ASP* 3.9 3.8 - - - +
84A GLU* 2.8 63.5 + - + +
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Residues in contact with LEU 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LEU* 4.0 22.0 - - + -
43A LEU* 5.3 2.9 - - + -
77A LEU* 3.0 56.4 + - + +
78A GLU* 3.8 1.3 - - - +
80A TYR* 1.3 85.3 - - + +
82A THR* 1.3 60.4 + - - +
84A GLU* 3.4 3.2 + - + -
85A PHE* 2.8 47.9 + - + -
91A VAL* 4.9 1.8 - - + -
94A LEU* 3.5 32.1 - - + -
113A THR* 5.5 2.7 - - + -
114A VAL* 5.3 8.1 - - + -
117A VAL* 3.8 22.2 - - + -
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Residues in contact with THR 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A GLU* 2.5 40.8 + - - -
79A VAL* 4.0 7.7 - - - -
80A TYR 3.4 0.4 - - - -
81A LEU* 1.3 75.3 - - - +
83A ASP* 1.3 60.3 + - - +
85A PHE* 3.8 2.1 - - - +
86A ALA* 2.9 31.5 + - + +
117A VAL* 3.6 15.2 - - + +
120A LYS* 3.7 35.7 - - + +
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Residues in contact with ASP 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A VAL* 3.0 37.8 + - - +
80A TYR* 3.9 3.6 - - - +
82A THR* 1.3 74.5 - - - +
84A GLU* 1.3 56.6 + - - +
86A ALA* 3.0 8.5 + - - +
87A LYS* 2.8 56.8 + - - +
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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
----------------------------------------------------------
37A ASN* 3.0 17.2 + - - -
80A TYR* 2.8 64.4 + - + +
81A LEU* 3.5 8.5 - - + +
83A ASP* 1.3 78.4 - - + +
85A PHE* 1.3 64.9 + - + +
87A LYS* 3.5 12.1 + - - +
89A ARG* 3.0 73.7 + - - +
91A VAL* 5.9 2.7 - - + -
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Residues in contact with PHE 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A LEU* 2.8 52.1 + - + +
82A THR 3.8 3.8 - - - +
84A GLU* 1.3 75.5 - - + +
86A ALA* 1.3 63.3 + - - +
88A GLY 3.4 8.5 + - - -
90A LYS* 3.4 46.3 - - + +
91A VAL* 3.6 35.4 - - + -
94A LEU* 4.2 8.7 - - + -
117A VAL* 3.8 17.3 - - + -
118A TYR* 4.1 20.0 - + - -
121A SER* 3.6 32.5 + - - +
122A PHE* 3.9 18.4 - + - -
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Residues in contact with ALA 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A THR* 2.9 20.4 + - + +
83A ASP* 3.0 9.4 + - - +
85A PHE* 1.3 76.7 - - - +
87A LYS* 1.3 58.6 + - + +
88A GLY 3.3 3.4 + - - -
----------------------------------------------------------
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Residues in contact with LYS 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A ASP* 2.8 37.9 + - - +
84A GLU* 3.5 7.2 + - - +
85A PHE 3.3 0.4 - - - -
86A ALA* 1.3 77.0 - - + +
88A GLY* 1.3 54.5 + - - +
89A ARG* 3.3 38.1 + - - +
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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