Contacts of the helix formed by residues 82 - 111 (chain B) in PDB entry 3E1J
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 ASP 82 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B TRP* 4.3 4.7 - - - -
81B GLU* 1.3 80.3 - - - +
83B VAL* 1.3 66.1 + - - +
84B GLU* 3.6 8.5 + - - +
85B GLU* 3.0 39.4 + - - +
86B MET* 2.8 26.9 + - - +
146B LEU* 6.4 2.0 - - + -
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Residues in contact with VAL 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B PHE* 4.0 15.9 - - + -
35B TRP* 4.4 6.9 - - + -
37B LEU* 3.9 17.3 - - + -
40B LEU* 4.2 4.9 - - + -
82B ASP* 1.3 72.3 - - - +
84B GLU* 1.3 54.2 + - - +
86B MET* 3.0 11.4 + - - +
87B LEU* 2.7 54.1 + - + +
141B ILE* 4.3 3.4 - - + -
146B LEU* 5.0 7.6 - - + -
149B TYR* 4.0 21.1 - - + -
150B LEU* 3.9 24.2 - - + -
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Residues in contact with GLU 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B ASP* 3.4 6.8 + - - +
83B VAL* 1.3 77.4 - - - +
85B GLU* 1.3 55.6 + - - +
87B LEU* 3.1 2.1 + - - +
88B ARG* 2.6 73.9 + - - +
138B LEU* 3.9 21.9 - - + +
141B ILE* 4.2 20.1 - - + +
142B GLN* 3.9 19.8 + - - -
146B LEU* 5.8 3.5 - - + +
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Residues in contact with GLU 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B GLY* 4.0 11.2 - - - -
81B GLU* 3.7 31.6 + - - +
82B ASP* 3.0 37.1 + - - +
84B GLU* 1.3 76.3 - - - +
86B MET* 1.3 58.6 + - - +
88B ARG* 3.4 8.4 + - - +
89B SER* 3.0 29.3 + - - -
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Residues in contact with MET 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B HIS* 3.2 56.1 - - + +
31B MET* 3.7 44.9 - - + -
32B PHE* 3.4 30.1 - - + -
35B TRP* 3.7 17.3 - - + -
79B ILE 3.3 10.5 - - - +
80B GLY* 4.5 2.7 - - - +
82B ASP 2.8 26.7 + - - +
83B VAL* 3.3 12.6 - - - +
85B GLU* 1.3 74.3 - - - +
87B LEU* 1.3 64.6 + - - +
89B SER* 3.3 1.2 + - - -
90B ASP* 3.1 19.1 + - - +
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Residues in contact with LEU 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B PHE* 3.9 24.5 - - + -
40B LEU* 5.1 3.4 - - + -
44B GLU* 3.8 21.8 - - - +
83B VAL* 2.7 35.8 + - + +
86B MET* 1.3 76.0 - - - +
88B ARG* 1.3 62.2 + - - +
90B ASP* 3.2 8.6 + - - +
91B LEU* 3.0 21.5 + - - +
133B TRP* 4.7 6.7 - - + -
134B LEU* 4.1 16.1 - - + +
137B GLU* 4.1 15.5 - - + -
138B LEU* 3.7 18.8 - - + -
141B ILE* 4.2 11.0 - - + -
149B TYR* 3.9 17.9 - - - +
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Residues in contact with ARG 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B GLU* 2.6 53.7 + - - +
85B GLU* 3.7 7.9 - - - +
87B LEU* 1.3 76.8 - - - +
89B SER* 1.3 58.1 + - - +
91B LEU* 3.3 9.4 + - + +
92B ALA* 2.9 27.9 + - - +
138B LEU* 4.0 37.1 + - + +
142B GLN* 5.1 8.5 - - - +
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Residues in contact with SER 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B GLN* 3.1 10.2 + - - -
28B HIS* 4.7 0.2 - - - -
78B ASN* 2.6 53.9 + - - +
79B ILE 4.7 1.6 - - - -
80B GLY* 5.9 0.2 - - - -
85B GLU 3.0 17.3 + - - -
86B MET* 3.6 7.4 - - - -
87B LEU 3.1 0.2 - - - -
88B ARG* 1.3 76.6 - - - +
90B ASP* 1.3 63.7 + - - +
92B ALA* 3.4 7.3 + - - +
93B LEU* 3.1 19.2 + - - +
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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
----------------------------------------------------------
24B GLN* 2.9 32.1 + - - +
25B TYR* 3.5 31.1 - - + +
28B HIS* 2.7 30.1 + - - -
44B GLU* 2.9 21.3 - - - +
86B MET 3.1 8.4 + - - +
87B LEU* 3.2 8.6 + - - +
89B SER* 1.3 74.2 - - - +
91B LEU* 1.3 63.5 + - - +
93B LEU* 3.2 7.5 + - - +
94B GLU* 3.0 26.3 + - - +
134B LEU* 4.3 9.9 - - + -
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Residues in contact with LEU 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B LEU 3.0 12.7 + - - +
88B ARG* 3.5 15.3 - - + +
90B ASP* 1.3 73.6 - - - +
92B ALA* 1.3 66.6 + - - +
93B LEU 3.2 0.2 + - - -
94B GLU* 3.2 2.3 + - - +
95B LEU* 3.0 42.5 + - + +
131B ILE* 4.0 27.1 - - + -
134B LEU* 4.0 20.3 - - + +
135B GLU* 4.1 22.9 - - + +
138B LEU* 3.8 23.6 - - + -
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Residues in contact with ALA 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B ARG 2.9 19.3 + - - +
89B SER* 3.4 7.6 + - - +
91B LEU* 1.3 71.0 - - - +
93B LEU* 1.3 57.3 + - - +
95B LEU* 3.3 11.2 + - - +
96B ASP* 3.0 36.0 + - - +
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Residues in contact with LEU 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B ASN* 5.2 7.7 - - + +
20B VAL* 3.7 34.8 - - + -
21B ALA* 3.8 27.6 - - + +
24B GLN* 4.0 20.4 - - + +
25B TYR* 6.1 1.6 - - + -
76B LYS 5.0 4.9 - - - +
89B SER 3.1 12.5 + - - +
90B ASP* 3.4 11.7 - - - +
91B LEU 3.1 0.6 - - - -
92B ALA* 1.3 74.7 - - - +
94B GLU* 1.3 64.2 + - + +
96B ASP* 3.3 9.2 + - + +
97B GLY* 3.0 19.6 + - - -
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Residues in contact with GLU 94 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B ALA* 6.0 1.6 - - - -
25B TYR* 2.4 37.8 + - + +
51B GLU* 3.6 3.4 - - - +
90B ASP 3.0 18.7 + - - +
91B LEU* 3.2 6.3 + - - +
93B LEU* 1.3 73.3 - - + +
95B LEU* 1.3 60.1 + - - +
97B GLY* 3.2 2.2 + - - +
98B ALA* 2.8 31.2 + - - +
127B GLU* 2.6 38.4 - - - +
130B HIS* 3.0 25.2 + - - -
131B ILE* 3.6 21.1 - - + +
134B LEU* 4.1 9.4 - - + -
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Residues in contact with LEU 95 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B LEU* 3.0 37.5 + - + +
92B ALA* 3.5 9.0 - - - +
94B GLU* 1.3 76.7 - - - +
96B ASP* 1.3 64.1 + - - +
98B ALA* 3.4 6.0 + - + +
99B LYS* 3.2 29.9 + - - +
131B ILE* 3.6 35.0 - - + -
135B GLU* 5.3 2.7 - - - +
1H MET* 4.6 14.8 - - + -
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Residues in contact with ASP 96 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B ASN* 5.5 0.7 - - - +
92B ALA* 3.0 22.6 + - - +
93B LEU* 3.9 10.0 - - + +
94B GLU 3.3 0.2 - - - -
95B LEU* 1.3 76.9 - - - +
97B GLY* 1.3 62.1 + - - +
99B LYS* 3.4 26.7 + - - +
100B ASN* 3.2 30.3 + - - +
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Residues in contact with GLY 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B ASN* 3.6 26.8 + - - -
93B LEU 3.0 14.4 + - - -
94B GLU* 3.7 3.1 - - - -
96B ASP* 1.3 74.7 - - - +
98B ALA* 1.3 61.2 + - - +
100B ASN* 3.3 2.6 + - - +
101B LEU* 2.9 36.2 + - - +
127B GLU* 6.1 1.1 - - - -
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Residues in contact with ALA 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B GLU 2.8 17.3 + - - +
95B LEU* 3.8 7.0 - - + +
96B ASP 3.3 0.2 - - - -
97B GLY* 1.3 75.8 - - - +
99B LYS* 1.3 57.7 + - - +
101B LEU* 3.2 4.7 + - - +
102B ARG* 2.9 57.6 + - - +
124B LEU* 3.9 17.5 - - + -
127B GLU* 5.4 4.1 - - + +
131B ILE* 4.2 16.8 - - + -
1H MET* 5.8 0.2 - - - -
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Residues in contact with LYS 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B LEU* 3.2 16.3 + - - +
96B ASP* 3.4 32.1 + - - +
98B ALA* 1.3 78.6 - - - +
100B ASN* 1.3 66.6 + - - +
102B ARG* 3.2 12.1 + - - +
103B GLU* 3.1 22.0 + - - +
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Residues in contact with ASN 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B TYR* 4.8 4.7 - - + -
13B LYS* 3.5 34.1 + - - +
14B LEU* 3.7 18.3 - - + +
17B ASN* 2.9 25.7 + - - +
96B ASP* 3.2 15.3 + - - +
97B GLY 3.3 6.9 + - - +
99B LYS* 1.3 80.5 - - - +
101B LEU* 1.3 55.5 + - - +
103B GLU* 3.3 15.8 + - - +
104B ALA* 2.9 30.3 + - - +
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Residues in contact with LEU 101 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B LEU* 3.8 20.0 - - + -
18B GLU* 5.2 2.0 - - - +
58B TYR* 3.5 21.5 - - - +
97B GLY 2.9 22.4 + - - +
98B ALA 3.2 4.9 + - - +
100B ASN* 1.3 72.5 - - - +
102B ARG* 1.3 60.5 + - - +
104B ALA* 3.3 1.9 + - - +
105B ILE* 2.9 40.2 + - + +
120B MET* 3.7 32.1 - - + +
123B ILE* 4.1 7.0 - - + -
124B LEU* 3.9 32.8 - - + -
127B GLU* 3.9 19.7 - - + +
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Residues in contact with ARG 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B ALA* 2.9 45.8 + - - +
99B LYS* 3.5 9.1 - - - +
101B LEU* 1.3 75.2 - - - +
103B GLU* 1.4 61.6 + - - +
105B ILE* 3.5 0.4 + - - -
106B GLY 3.3 17.0 + - - -
124B LEU* 4.1 17.4 - - + +
128B GLU* 2.7 36.3 + - - -
1H MET* 3.8 18.8 - - - +
111H VAL 5.5 0.4 - - - -
112H HIS* 3.1 49.9 + - + +
113H ASP* 4.7 7.9 + - - +
114H TYR* 3.5 17.0 - - - -
115H VAL* 4.7 1.2 - - - +
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Residues in contact with GLU 103 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B LYS* 5.2 1.7 + - - -
10B TYR* 2.8 34.5 + - + +
13B LYS* 5.4 3.5 - - - -
99B LYS* 3.1 12.1 + - - +
100B ASN* 3.5 22.1 + - - +
102B ARG* 1.4 78.6 - - - +
104B ALA* 1.3 60.6 + - - +
106B GLY* 3.4 1.7 + - - -
107B TYR* 3.2 20.6 + - - +
112H HIS* 5.5 2.0 - - - -
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Residues in contact with ALA 104 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B TYR* 3.7 33.9 - - + -
14B LEU* 3.9 11.7 - - + -
100B ASN 2.9 16.6 + - - +
101B LEU 3.8 2.2 - - - +
103B GLU* 1.3 72.3 - - - +
105B ILE* 1.3 60.0 + - - +
107B TYR* 3.2 3.3 + - - +
108B ALA* 2.9 31.0 + - - +
120B MET* 3.6 23.0 - - + +
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Residues in contact with ILE 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B LEU* 2.9 25.1 + - + +
103B GLU 3.4 0.2 - - - -
104B ALA* 1.3 75.6 - - - +
106B GLY* 1.3 62.0 + - - +
108B ALA* 3.5 1.2 + - - +
109B ASP 3.2 17.8 + - - -
117B ARG* 3.3 34.8 + - + +
120B MET* 3.6 39.9 - - + +
121B ILE* 4.0 16.6 - - + -
124B LEU* 3.9 28.5 - - + -
114H TYR* 3.5 31.2 - - + -
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Residues in contact with GLY 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B ARG 3.3 10.1 + - - -
103B GLU 3.4 3.1 + - - -
104B ALA 3.3 0.2 - - - -
105B ILE* 1.3 78.4 - - - +
107B TYR* 1.3 60.9 + - - +
109B ASP* 3.5 5.5 + - - +
110B SER* 3.3 20.1 + - - -
117B ARG* 4.3 4.0 - - - -
112H HIS* 4.8 6.1 - - - -
114H TYR* 3.5 18.4 - - - -
----------------------------------------------------------
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Residues in contact with TYR 107 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B ASP* 2.9 36.6 + - - -
6B LYS* 3.4 32.1 - - + +
7B VAL* 3.7 15.3 - - + -
10B TYR* 3.8 33.2 - + + +
103B GLU 3.2 8.7 + - - +
104B ALA 3.2 7.0 + - - +
106B GLY* 1.3 73.8 - - - +
108B ALA* 1.3 66.5 + - + +
110B SER* 2.8 27.1 + - - -
111B VAL* 3.1 27.8 + - + +
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Residues in contact with ALA 108 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B VAL* 4.4 7.9 - - + -
104B ALA 2.9 17.6 + - - +
105B ILE 3.5 3.6 + - - +
107B TYR* 1.3 78.8 - - - +
109B ASP* 1.3 61.0 + - - +
111B VAL* 3.4 9.1 + - - +
112B HIS 3.0 3.8 + - - -
113B ASP* 2.8 51.1 + - + +
116B SER* 4.7 1.8 - - - -
117B ARG* 4.1 4.9 - - + +
120B MET* 3.6 21.5 - - + -
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Residues in contact with ASP 109 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B ILE 3.2 4.9 + - - -
106B GLY* 3.5 9.0 - - - +
107B TYR 3.2 0.2 - - - -
108B ALA* 1.3 75.8 - - - +
110B SER* 1.3 64.7 + - - +
112B HIS* 3.2 13.9 + - - -
114B TYR* 3.3 22.5 + - - -
117B ARG* 3.2 35.5 + - - +
109C ASP* 5.5 3.7 - - - +
117C ARG* 2.8 33.7 + - - -
109H ASP* 5.5 4.0 - - - +
----------------------------------------------------------
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Residues in contact with SER 110 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B GLY 3.3 6.8 + - - -
107B TYR* 2.8 36.0 + - - -
109B ASP* 1.3 82.9 - - - +
111B VAL* 1.3 61.0 + - - +
112B HIS* 3.4 14.6 + - - -
----------------------------------------------------------
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Residues in contact with VAL 111 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B ASP* 3.8 18.6 - - + +
7B VAL* 3.7 27.8 - - + -
107B TYR* 3.1 45.5 + - + +
108B ALA 3.6 7.2 - - - +
110B SER* 1.3 76.0 - - - +
112B HIS* 1.3 72.6 + - - +
113B ASP* 3.3 5.6 + - + +
102C ARG* 5.5 0.3 - - - -
----------------------------------------------------------
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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