Contacts of the helix formed by residues 59 - 88 (chain A) in PDB entry 3ARG
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).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A LYS 4.2 0.8 + - - -
58A LEU* 1.3 75.2 - - - +
60A ASN* 1.3 61.9 + - - +
61A GLN* 3.9 8.2 + - - +
62A GLN* 2.8 35.1 + - - +
63A TRP* 2.8 27.1 + - - +
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Residues in contact with ASN 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A GLN* 4.1 15.1 - - - -
59A SER* 1.3 73.0 - - - +
61A GLN* 1.3 53.2 + - - +
63A TRP* 3.3 9.0 + - - +
64A GLU* 2.7 38.2 + - - +
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Residues in contact with GLN 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A SER* 3.1 8.2 + - - +
60A ASN* 1.3 74.6 - - - +
62A GLN* 1.3 66.0 + - + +
64A GLU* 4.3 3.9 - - - +
65A LYS* 3.3 25.6 + - - +
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Residues in contact with GLN 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A LYS 4.8 2.8 - - - +
58A LEU* 3.4 35.6 - - + +
59A SER* 2.8 34.2 + - - +
61A GLN* 1.3 77.0 - - + +
63A TRP* 1.3 60.7 + - - +
65A LYS* 4.2 4.3 - - - +
66A LEU* 3.5 25.3 + - - +
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Residues in contact with TRP 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A HIS* 4.1 23.6 - + - -
47A ILE* 4.3 22.4 + - + -
48A SER 6.3 0.2 - - - -
49A PHE* 6.3 0.4 - - + -
54A SER 5.4 1.1 - - - -
55A GLN* 4.5 28.5 - - + -
58A LEU* 4.6 16.6 - - + -
59A SER 2.8 13.4 + - - +
60A ASN* 3.7 8.7 - - - +
62A GLN* 1.3 76.2 - - - +
64A GLU* 1.3 65.1 + - + +
65A LYS 3.2 1.6 - - - -
66A LEU* 3.0 14.8 + - + -
67A GLN* 2.8 63.2 + - + +
70A PHE* 6.3 2.0 - + - -
171A PHE* 4.6 20.4 - + - -
650A DB6 5.0 16.2 - - + -
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Residues in contact with GLU 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A ASN 2.7 21.9 + - - +
61A GLN* 4.3 3.8 - - - +
63A TRP* 1.3 77.6 - - + +
65A LYS* 1.3 55.9 + - - +
67A GLN* 3.8 9.4 - - - +
68A HIS* 3.0 29.6 + - - +
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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 GLN 3.3 16.7 + - - +
62A GLN* 4.2 4.5 - - - +
63A TRP 3.2 0.4 - - - -
64A GLU* 1.3 79.8 - - - +
66A LEU* 1.3 58.0 + - - +
68A HIS* 3.5 8.4 + - - +
69A MET* 3.0 24.6 + - - +
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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
----------------------------------------------------------
58A LEU* 4.2 24.2 - - + -
62A GLN 3.5 9.8 + - - +
63A TRP* 3.0 20.0 + - + +
65A LYS* 1.3 76.0 - - - +
67A GLN* 1.3 65.7 + - - +
69A MET* 3.1 23.6 + - + +
70A PHE* 3.0 48.5 + - + -
163A LEU* 6.1 4.5 - - + -
167A THR* 4.5 23.3 - - + -
171A PHE* 5.7 2.9 - - + -
650A DB6 4.7 17.3 - - + -
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Residues in contact with GLN 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A TRP* 5.4 0.5 - - - -
46A THR* 3.6 14.6 - - - +
47A ILE* 3.2 54.9 + - + +
63A TRP* 2.8 44.3 + - + +
64A GLU* 3.8 8.4 - - - +
66A LEU* 1.3 75.8 - - - +
68A HIS* 1.3 52.5 + - - +
70A PHE* 3.2 8.0 + - - +
71A GLN* 2.7 63.3 + - - +
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Residues in contact with HIS 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A GLU 3.0 19.2 + - - +
65A LYS* 3.6 8.2 + - - +
67A GLN* 1.3 73.9 - - - +
69A MET* 1.3 65.2 + - - +
71A GLN* 3.6 20.2 - - + +
72A VAL* 3.1 31.5 + - + +
27C THR* 5.4 11.2 - - + +
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Residues in contact with MET 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A LYS 3.0 14.1 + - - +
66A LEU* 3.1 24.9 + - + +
68A HIS* 1.3 80.5 + - - +
70A PHE* 1.3 73.8 + - - +
72A VAL* 3.8 4.4 + - - +
73A TYR* 3.3 16.9 + - - +
159A THR* 5.5 15.0 - - + +
650A DB6 3.9 35.6 - - - +
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Residues in contact with PHE 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A CYS* 6.1 0.2 - - - -
40A TRP* 3.6 22.7 - - + -
47A ILE* 5.3 4.0 - - + -
63A TRP* 6.3 1.8 - + - -
66A LEU* 3.0 48.4 + - + -
67A GLN* 3.8 7.0 - - - +
69A MET* 1.3 82.3 - - + +
71A GLN* 1.3 61.5 + - - +
72A VAL 3.2 0.4 - - - -
73A TYR* 3.0 8.1 + + - +
74A ARG 2.9 27.0 + - - -
163A LEU* 5.9 7.0 - - + -
650A DB6 3.7 99.6 - - + -
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Residues in contact with GLN 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A TRP* 3.9 15.9 - - + -
45A ALA 3.6 25.6 + - - +
46A THR* 3.8 8.3 - - - +
67A GLN* 2.7 57.9 + - + +
68A HIS* 3.3 22.2 + - + +
70A PHE* 1.3 74.1 - - - +
72A VAL* 1.3 60.7 + - - +
74A ARG* 3.7 12.5 + - - +
75A VAL* 4.0 12.0 + - - +
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Residues in contact with VAL 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A HIS* 3.1 23.5 + - + +
69A MET* 4.0 5.2 - - - +
71A GLN* 1.3 75.0 - - - +
73A TYR* 1.3 61.6 + - - +
74A ARG 3.4 0.2 + - - -
75A VAL* 3.6 5.6 + - - +
76A SER* 2.7 33.4 + - - +
650A DB6 4.8 4.5 - - - +
27C THR* 4.9 17.3 - - + -
28C PRO* 5.5 7.2 - - + -
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Residues in contact with TYR 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A GLN* 3.3 34.8 + - - -
40A TRP* 5.6 2.2 - + - -
69A MET 3.3 12.2 + - - +
70A PHE* 3.0 19.4 + + + +
72A VAL* 1.3 76.7 - - - +
74A ARG* 1.3 62.9 + - + +
76A SER* 3.2 1.5 + - - -
77A PHE* 2.7 66.1 + + + +
100A LEU* 4.3 4.0 - - - +
650A DB6 3.5 108.2 + - + +
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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
----------------------------------------------------------
14A GLN* 5.9 0.4 - - - +
26A THR* 4.5 31.5 + - + -
40A TRP* 3.4 54.4 - - + -
41A SER 2.7 31.5 + - - -
42A ASN* 4.0 14.1 + - - +
44A SER 2.5 23.8 + - - -
45A ALA* 3.9 10.1 + - - +
70A PHE 2.9 7.0 + - - +
71A GLN* 3.9 5.5 + - - +
72A VAL 3.3 0.2 - - - -
73A TYR* 1.3 84.7 - - - +
75A VAL* 1.3 59.9 + - + +
77A PHE* 3.8 3.9 - - - +
78A THR* 2.8 33.5 + - - +
314A NAG 5.0 8.2 + - - -
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Residues in contact with VAL 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A GLN 4.0 11.9 + - - +
72A VAL* 3.6 6.1 + - - +
73A TYR 3.3 0.2 - - - -
74A ARG* 1.3 80.0 - - + +
76A SER* 1.3 66.7 + - - +
77A PHE 3.1 0.5 + - - -
78A THR* 3.1 9.2 + - - -
79A ARG* 3.0 28.9 + - + +
314A NAG 6.1 4.7 - - - -
95C ARG* 6.3 0.2 - - - +
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Residues in contact with SER 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A VAL* 2.7 23.7 + - - -
73A TYR 3.6 3.4 - - - -
75A VAL* 1.3 78.7 - - - +
77A PHE* 1.3 57.8 + - - +
79A ARG* 3.5 0.7 + - - +
80A ASP* 2.9 35.6 + - - +
650A DB6 3.4 40.6 - - - -
28C PRO* 3.9 11.8 - - - +
95C ARG* 3.8 18.9 + - - +
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Residues in contact with PHE 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A GLN* 4.0 13.7 - - - -
16A SER* 3.5 31.0 - - - -
18A PHE* 4.1 4.5 - + - -
26A THR* 4.9 3.6 - - + -
73A TYR* 2.7 50.4 + + + +
74A ARG* 3.8 4.7 - - - +
76A SER* 1.3 70.7 - - - +
78A THR* 1.3 73.8 + - - +
80A ASP* 3.1 6.1 + - + +
81A ILE* 3.1 48.8 + - + +
98A ILE* 3.9 16.6 - - + -
100A LEU* 4.9 5.4 - - + -
650A DB6 3.6 46.8 - - + +
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Residues in contact with THR 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A PHE* 3.7 26.1 - - + -
24A SER* 4.0 15.9 - - - +
25A ARG* 6.4 0.2 - - - -
26A THR* 4.4 13.4 + - - +
74A ARG* 2.8 18.5 + - - +
75A VAL* 3.1 9.6 + - - -
77A PHE* 1.3 82.8 - - - +
79A ARG* 1.3 62.6 + - - +
81A ILE* 3.4 2.8 + - - +
82A GLN* 3.2 38.0 + - - +
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Residues in contact with ARG 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A VAL* 3.0 21.3 + - + +
76A SER 4.0 3.1 - - - +
78A THR* 1.3 77.1 - - - +
80A ASP* 1.3 58.9 + - - +
82A GLN* 3.5 24.6 - - + +
83A GLU* 3.2 38.4 - - + +
94C ASP* 2.9 20.8 + - - -
95C ARG* 3.2 31.0 - - - +
100C GLY* 3.5 33.3 - - - +
103C ARG* 3.7 15.2 - - - +
105C HIS* 5.6 2.8 - - - -
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Residues in contact with ASP 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A SER 2.9 23.2 + - - +
77A PHE* 3.1 6.9 + - + +
79A ARG* 1.3 76.0 + - - +
81A ILE* 1.3 68.3 + - + +
83A GLU* 3.0 9.4 + - - +
84A LEU* 3.0 32.0 + - + +
650A DB6 2.9 37.4 + - + +
95C ARG* 2.6 37.2 + - - -
97C SER* 5.2 2.3 + - - -
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Residues in contact with ILE 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A PHE* 3.5 37.2 - - + -
77A PHE* 3.1 49.7 + - + +
78A THR 3.8 0.2 - - - +
80A ASP* 1.3 74.8 - - + +
82A GLN* 1.3 56.9 + - - +
84A LEU* 2.8 31.4 + - + +
85A VAL* 2.9 27.4 + - + +
96A ILE* 5.4 6.5 - - + -
98A ILE* 5.3 4.0 - - + -
120A PHE* 6.4 0.2 - - + -
650A DB6 3.8 39.7 - - + -
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Residues in contact with GLN 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A PHE* 4.4 11.3 - - + -
20A ASN 6.0 0.2 - - - +
21A ARG 4.7 14.0 - - - +
22A SER 5.6 1.2 - - - +
24A SER* 4.6 3.8 - - - -
78A THR* 3.2 33.6 + - - +
79A ARG* 3.5 33.7 - - - +
81A ILE* 1.3 78.2 - - - +
83A GLU* 1.3 63.9 + - - +
85A VAL* 3.9 5.3 - - - +
86A LYS* 3.3 29.6 + - - +
94A TYR* 3.8 22.8 + - - +
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Residues in contact with GLU 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A ARG* 3.2 33.1 + - - +
80A ASP* 3.0 10.8 + - - +
82A GLN* 1.3 82.1 - - - +
84A LEU* 1.3 58.9 + - - +
85A VAL 3.2 1.1 - - - -
86A LYS* 3.0 23.5 + - - +
87A MET* 3.0 32.1 + - - +
100C GLY 5.6 2.9 - - - +
48D TYR* 3.1 26.9 + - - -
50D TYR* 2.7 35.9 + - + +
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Residues in contact with LEU 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ASP* 3.0 33.5 + - + +
81A ILE* 2.8 18.9 + - + +
83A GLU* 1.3 75.6 - - - +
85A VAL* 1.3 62.5 + - - +
87A MET* 3.3 30.5 - - + +
88A MET* 3.3 23.9 - - + +
146A PRO* 3.7 38.4 - - + +
149A VAL* 4.9 8.3 - - + -
150A LEU* 5.9 1.8 - - + -
650A DB6 3.8 29.8 - - + -
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Residues in contact with VAL 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A ILE* 2.9 30.8 + - + +
82A GLN* 3.9 2.7 - - - +
84A LEU* 1.3 75.4 - - + +
86A LYS* 1.3 61.7 + - + +
88A MET* 2.9 31.3 + - - +
92A GLU* 4.4 17.5 - - + +
93A ASP* 5.3 0.7 - - - -
94A TYR* 3.7 42.4 - - + +
96A ILE* 3.7 29.6 - - + -
650A DB6 5.5 3.1 - - + -
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Residues in contact with LYS 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ARG* 6.5 1.3 - - - -
82A GLN* 3.3 14.7 + - - +
83A GLU* 3.0 32.6 + - - +
85A VAL* 1.3 80.3 - - + +
87A MET* 1.3 63.1 + - - +
88A MET 4.2 2.8 - - - +
94A TYR* 6.0 0.4 - - - +
48D TYR* 3.2 23.1 + - - +
50D TYR* 4.6 7.8 - - + -
54D SER* 4.7 8.1 + - - -
56D GLU* 3.3 46.1 + - + +
57D LYS* 4.5 10.3 + - - +
----------------------------------------------------------
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Residues in contact with MET 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A GLU 3.0 20.5 + - - +
84A LEU* 3.3 34.8 - - + +
85A VAL 3.1 0.2 - - - -
86A LYS* 1.3 80.5 - - - +
88A MET* 1.3 87.1 + - + +
90A PRO* 5.5 0.9 - - - +
145A LEU* 4.9 1.3 - - + -
146A PRO* 4.4 4.0 - - + -
149A VAL* 3.9 30.7 - - + -
98C ALA* 6.0 1.6 - - - -
50D TYR* 3.9 45.5 - - + +
54D SER* 5.8 3.1 + - - -
----------------------------------------------------------
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Residues in contact with MET 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A LEU 3.3 12.1 - - - +
85A VAL* 2.9 20.3 + - - +
86A LYS 4.2 2.5 - - - +
87A MET* 1.3 119.2 - - + +
90A PRO* 3.1 36.6 - - - +
91A LYS* 3.2 32.2 + - + -
92A GLU* 3.8 18.2 - - + +
142A TRP* 4.1 35.7 - - + +
145A LEU* 4.4 9.4 - - + -
146A PRO* 3.7 23.3 - - + -
----------------------------------------------------------
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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