Contacts of the helix formed by residues 63 - 91 (chain B) in PDB entry 1N1J
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 63 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B LEU* 5.5 1.4 - - - +
49B LYS* 5.8 3.8 - - - +
61B ILE 3.7 1.4 + - - -
62B SER* 1.3 73.9 - - - +
64B GLU* 1.3 61.6 + - - +
66B PRO* 3.3 14.1 - - - +
67B VAL* 3.8 12.2 - - - +
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Residues in contact with GLU 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A ASN* 3.4 12.8 - - - +
113A GLY* 2.8 34.7 + - - +
114A GLU 4.7 0.3 + - - -
136A LEU* 4.2 16.5 - - + +
140A ARG* 2.9 39.5 + - - +
62B SER* 3.3 10.8 + - - +
63B ALA* 1.3 79.9 - - - +
65B ALA* 1.3 66.5 + - - +
66B PRO 3.4 0.2 - - - -
67B VAL* 3.2 13.4 + - - +
68B LEU* 3.1 23.1 + - - +
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Residues in contact with ALA 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A ILE 4.2 3.4 - - - +
112A ASN 4.9 0.4 - - - +
116A ILE* 4.0 26.2 - - + +
52B MET* 4.2 8.7 - - + -
61B ILE* 3.7 16.6 - - + -
62B SER* 3.2 19.2 + - - +
64B GLU* 1.3 79.0 - - - +
66B PRO* 1.3 71.7 - - + +
68B LEU* 3.2 8.8 + - - +
69B PHE* 3.0 26.0 + - - -
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Residues in contact with PRO 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B LEU* 3.6 28.8 - - + +
48B ILE* 3.7 23.2 - - + +
49B LYS* 4.5 20.0 - - + +
52B MET* 4.5 8.1 - - - -
61B ILE* 4.1 11.0 - - + -
62B SER 3.2 16.6 - - - +
63B ALA 3.3 11.4 - - - +
65B ALA* 1.3 91.6 - - + +
67B VAL* 1.3 55.6 + - - +
69B PHE* 3.2 1.2 + - + -
70B ALA* 2.9 28.6 + - - +
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Residues in contact with VAL 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A TYR* 3.5 27.9 - - + +
136A LEU* 3.9 17.9 - - + -
139A PHE* 3.9 36.6 - - + -
45B LEU* 4.0 24.2 - - + -
63B ALA 3.8 16.6 - - - +
64B GLU* 3.4 10.5 - - - +
65B ALA 3.2 0.4 - - - -
66B PRO* 1.3 73.8 - - - +
68B LEU* 1.3 67.6 + - - +
70B ALA* 3.2 12.4 + - - +
71B LYS 3.4 8.5 + - - -
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Residues in contact with LEU 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A GLY* 3.5 38.4 - - - +
116A ILE* 4.1 18.4 - - + -
117A LEU* 4.4 11.7 - - + -
120A MET* 5.4 0.2 - - - -
132A LEU* 3.5 53.0 - - + +
133A LYS* 4.8 0.7 - - - +
135A TYR* 5.2 1.8 - - + -
136A LEU* 3.9 26.7 - - + -
64B GLU 3.1 12.6 + - - +
65B ALA* 3.2 7.6 + - - +
67B VAL* 1.3 80.5 - - - +
69B PHE* 1.3 56.3 + - - +
71B LYS* 3.3 2.7 + - - -
72B ALA* 2.9 27.9 + - - +
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Residues in contact with PHE 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A PHE* 4.6 4.3 - + - -
92A ILE* 3.6 37.4 - - + +
95A ILE* 3.7 34.8 - - + -
96A THR* 3.4 26.5 - - - -
116A ILE* 3.6 21.5 - - + -
120A MET* 4.0 16.2 - - + -
48B ILE* 3.8 16.4 - - + -
52B MET* 3.8 21.3 - - - -
65B ALA 3.0 20.1 + - - -
66B PRO 3.7 6.5 - - - +
67B VAL 3.2 0.2 - - - -
68B LEU* 1.3 76.5 - - - +
70B ALA* 1.3 56.5 + - - +
72B ALA* 3.7 5.1 - - + +
73B ALA* 2.7 36.7 + - - +
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Residues in contact with ALA 70 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A TYR* 4.7 11.7 - - - +
43B LEU* 3.6 25.4 - - + +
45B LEU* 4.0 12.8 - - + -
48B ILE* 3.8 16.8 - - + +
66B PRO 2.9 12.9 + - - +
67B VAL* 3.2 10.1 + - - +
69B PHE* 1.3 77.1 - - - +
71B LYS* 1.3 62.1 + - - +
73B ALA 3.6 0.2 + - - -
74B GLN* 3.4 16.8 + - - +
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Residues in contact with LYS 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A PRO* 4.7 9.4 - - - +
132A LEU* 3.4 23.6 - - + -
135A TYR* 3.5 53.1 - - + -
67B VAL 3.4 1.6 + - - -
68B LEU 3.3 2.3 + - - +
69B PHE 3.2 0.2 - - - -
70B ALA* 1.3 76.2 - - - +
72B ALA* 1.3 67.1 + - - +
74B GLN* 2.8 42.2 + - - +
75B ILE* 3.0 36.8 + - + +
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Residues in contact with ALA 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A PHE* 3.9 13.0 - - + -
120A MET* 3.6 28.5 - - + -
128A TYR* 3.5 16.1 - - + -
132A LEU* 3.6 8.9 - - + +
68B LEU 2.9 17.9 + - - +
69B PHE* 3.7 6.7 - - - +
71B LYS* 1.3 76.5 - - - +
73B ALA* 1.3 57.9 + - - +
75B ILE* 3.2 1.8 + - - -
76B PHE* 2.8 31.9 + - - +
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Residues in contact with ALA 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A LEU* 4.1 16.2 - - + -
88A VAL* 4.3 12.8 - - + -
91A PHE* 4.6 4.4 - - - -
92A ILE* 5.4 4.9 - - + -
43B LEU* 3.9 17.5 - - + -
48B ILE* 5.8 0.2 - - + -
69B PHE 2.7 22.0 + - - +
70B ALA 3.7 5.6 - - - +
72B ALA* 1.3 74.9 - - - +
74B GLN* 1.3 56.8 + - - +
76B PHE* 3.8 5.3 - - - +
77B ILE* 2.9 39.9 + - + +
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Residues in contact with GLN 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ILE* 3.9 33.4 - - + +
43B LEU* 5.1 1.1 - - + +
70B ALA 3.4 10.2 + - - +
71B LYS* 2.8 45.6 + - + +
73B ALA* 1.3 79.3 - - - +
75B ILE* 1.3 70.7 + - - +
78B THR* 2.9 33.7 + - - +
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Residues in contact with ILE 75 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A TYR* 3.6 40.4 - - + +
131A PRO* 4.2 22.2 - - + -
132A LEU* 4.4 5.4 - - + -
71B LYS* 3.0 32.9 + - + +
72B ALA 3.6 5.6 - - - +
74B GLN* 1.3 88.4 - - - +
76B PHE* 1.3 63.4 + - - +
78B THR* 3.6 5.0 - - - -
79B GLU* 3.0 25.0 + - + +
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Residues in contact with PHE 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A CYS 3.7 27.6 - - - -
88A VAL* 3.9 20.2 - - + -
91A PHE* 4.0 26.0 - + + -
125A PHE* 5.1 1.6 - + - -
128A TYR* 3.2 22.0 - - - +
72B ALA 2.8 18.0 + - - +
73B ALA 3.8 2.7 - - - +
75B ILE* 1.3 75.4 - - - +
77B ILE* 1.3 69.0 + - - +
79B GLU* 3.3 2.9 + - - +
80B LEU* 2.9 44.7 + - + +
111B PHE* 3.8 26.5 - + - -
113B PHE* 3.9 18.8 - + - -
114B LEU* 3.8 22.2 - - + -
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Residues in contact with ILE 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A LEU* 4.8 4.0 - - + -
62A VAL* 4.0 21.3 - - + +
65A ILE* 3.6 41.3 - - + -
66A MET* 3.7 27.8 - - + +
84A VAL* 4.1 10.3 - - + -
88A VAL* 3.4 31.9 - - + -
43B LEU* 5.9 0.9 - - + -
73B ALA* 2.9 31.1 + - + +
76B PHE* 1.3 73.4 - - - +
78B THR* 1.3 57.9 + - - +
80B LEU* 3.9 3.3 - - - +
81B THR* 2.8 35.8 + - - +
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Residues in contact with THR 78 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ILE* 3.4 17.2 + - - +
69A ALA* 4.0 21.1 - - + +
74B GLN* 2.9 23.0 + - - +
75B ILE* 3.6 6.2 - - - -
77B ILE* 1.3 77.2 - - - +
79B GLU* 1.3 60.2 + - - +
81B THR* 3.8 1.0 - - - -
82B LEU* 2.9 35.6 + - + +
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Residues in contact with GLU 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A TYR* 5.2 3.6 - - - +
75B ILE* 3.0 19.8 + - + +
76B PHE* 4.0 3.8 - - - +
78B THR* 1.3 78.9 - - - +
80B LEU* 1.3 57.5 + - - +
82B LEU* 3.7 18.7 - - - +
83B ARG* 2.8 73.1 + - - +
108B PHE* 4.0 17.4 - - + -
110B GLN* 5.1 3.4 - - - +
111B PHE* 4.2 5.2 - - + -
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Residues in contact with LEU 80 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A VAL* 4.2 24.2 - - + -
87A CYS* 3.8 33.4 - - + -
76B PHE* 2.9 32.7 + - + +
77B ILE 3.9 2.7 - - - +
79B GLU* 1.3 77.1 - - - +
81B THR* 1.3 58.1 + - - +
83B ARG* 3.4 1.7 + - - +
84B ALA* 3.0 27.9 + - - +
101B ILE* 4.1 23.3 - - + +
104B ALA* 4.9 3.4 - - + -
105B ILE* 4.4 9.4 - - + -
111B PHE* 3.6 37.3 - - + -
114B LEU* 4.8 2.0 - - + -
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Residues in contact with THR 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A MET* 3.3 55.7 - - + +
69A ALA* 4.0 7.2 - - + -
70A ILE* 3.7 17.5 - - + -
76A ILE* 5.5 0.2 - - + -
84A VAL* 4.7 4.1 - - - +
77B ILE* 2.8 22.0 + - - +
78B THR 3.8 2.5 - - - -
80B LEU* 1.3 74.8 - - - +
82B LEU* 1.3 66.5 + - - +
84B ALA* 3.2 6.7 + - - +
85B TRP* 2.9 23.2 + - - +
96B LEU* 3.7 14.9 - - + +
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Residues in contact with LEU 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A ALA* 4.4 17.2 - - + +
78B THR* 2.9 24.8 + - + +
79B GLU* 3.7 18.8 - - - +
81B THR* 1.3 75.5 - - - +
83B ARG* 1.3 77.1 + - + +
85B TRP* 3.3 16.0 + - - +
86B ILE* 3.3 24.1 + - + +
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Residues in contact with ARG 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B GLU* 2.8 42.7 + - - +
80B LEU 3.8 3.4 - - - +
82B LEU* 1.3 82.9 - - + +
84B ALA* 1.3 64.0 + - - +
86B ILE* 3.3 32.9 + - + +
87B HIS* 3.4 12.5 + - - -
104B ALA* 3.6 15.7 + - + -
107B LYS* 4.1 12.5 + - - +
108B PHE* 3.4 61.4 - - - +
111B PHE* 3.7 12.3 - - + -
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Residues in contact with ALA 84 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B LEU 3.0 17.8 + - - +
81B THR* 3.2 6.0 + - - +
83B ARG* 1.3 76.3 - - - +
85B TRP* 1.3 58.1 + - - +
87B HIS* 3.0 18.7 + - - +
88B THR* 3.2 12.9 + - - -
96B LEU* 4.1 12.8 - - + -
100B ASP* 3.4 18.9 - - - +
101B ILE* 3.7 35.9 - - + +
104B ALA* 3.7 2.0 - - + +
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Residues in contact with TRP 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A ALA 5.3 1.8 - - - +
70A ILE* 3.8 29.2 - - + -
71A PRO* 3.4 30.2 - - + +
74A GLY* 3.8 11.4 - - - -
75A LYS 3.9 13.0 - - - -
81B THR 2.9 16.8 + - - +
82B LEU* 3.6 9.0 - - - +
83B ARG 3.2 0.2 - - - -
84B ALA* 1.3 74.0 - - - +
86B ILE* 1.3 64.6 + - + +
87B HIS 3.1 0.2 - - - -
88B THR* 3.5 33.2 - - + -
89B GLU* 2.8 56.9 + - + +
93B ARG 4.5 2.2 - - - -
94B ARG* 3.4 48.5 - - - -
96B LEU* 4.0 10.3 - - + +
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Residues in contact with ILE 86 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B LEU* 3.3 22.5 + - + +
83B ARG* 3.3 32.7 + - + +
84B ALA 3.1 0.6 - - - -
85B TRP* 1.3 78.4 - - - +
87B HIS* 1.3 72.8 + - + +
89B GLU* 3.5 5.0 + - - +
90B ASP* 3.0 27.5 + - + +
----------------------------------------------------------
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Residues in contact with HIS 87 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B ARG 3.4 23.2 + - - -
84B ALA 3.0 6.7 + - - +
86B ILE* 1.3 88.8 - - + +
88B THR* 1.3 65.4 + - - +
90B ASP* 3.7 10.9 + - - +
91B ASN* 2.8 35.4 + - - +
100B ASP* 3.7 20.6 - - + +
103B MET* 3.3 44.9 + - + +
104B ALA* 3.6 22.0 - - - -
107B LYS* 4.2 16.4 - - + +
----------------------------------------------------------
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Residues in contact with THR 88 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B ALA 3.2 9.2 + - - -
85B TRP* 3.1 35.9 + - + -
87B HIS* 1.3 76.5 - - - +
89B GLU* 1.3 61.5 + - - +
91B ASN* 3.2 8.7 + - - +
93B ARG* 3.0 49.4 + - - +
95B THR 3.4 24.2 - - - +
96B LEU* 3.6 9.0 - - - +
100B ASP* 2.8 24.4 + - - +
----------------------------------------------------------
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Residues in contact with GLU 89 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A PRO* 4.2 9.5 - - - +
85B TRP* 2.8 55.4 + - + +
86B ILE* 3.9 5.2 - - - +
88B THR* 1.3 74.6 - - - +
90B ASP* 1.3 59.8 + - - +
91B ASN 3.0 2.2 - - - -
92B LYS* 2.8 30.5 + - - +
93B ARG 4.5 4.5 - - - +
94B ARG* 4.8 8.7 + - - +
----------------------------------------------------------
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Residues in contact with ASP 90 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B ILE* 3.0 20.3 + - + +
87B HIS* 3.7 15.5 + - - +
88B THR 3.3 0.6 - - - -
89B GLU* 1.3 76.2 - - - +
91B ASN* 1.3 63.2 + - - +
92B LYS* 3.2 11.5 + - - +
----------------------------------------------------------
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Residues in contact with ASN 91 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B HIS* 2.8 29.0 + - - +
88B THR 3.7 4.3 - - - +
89B GLU 3.0 0.8 - - - -
90B ASP* 1.3 82.8 + - - +
92B LYS* 1.3 72.9 + - - +
93B ARG* 3.1 37.7 + - - +
99B ASN* 5.4 2.4 - - - +
100B ASP* 4.2 2.0 + - - -
----------------------------------------------------------
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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