Contacts of the helix formed by residues 88 - 117 (chain B) in PDB entry 1JI5
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 THR 88 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B GLY 5.1 0.3 + - - -
87B GLU* 1.3 76.6 - - - +
89B ALA* 1.3 67.2 + - + +
90B GLU* 3.4 29.4 - - + +
91B GLY* 3.5 14.5 - - - -
92B MET* 2.7 36.2 + - - +
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Residues in contact with ALA 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B VAL* 4.0 20.9 - - + -
31B LYS 3.5 27.1 + - - +
34B GLN* 5.2 11.7 - - + -
38B LEU* 5.2 3.7 - - + +
42B PHE* 4.8 1.0 - - - -
88B THR* 1.3 77.1 - - + +
90B GLU* 1.3 77.5 + - - +
92B MET* 3.2 5.9 + - - +
93B VAL* 3.1 27.4 + - - +
143B PHE* 5.9 1.3 - - + -
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Residues in contact with GLU 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B GLN* 5.5 6.4 - - - +
88B THR* 3.4 19.5 - - + +
89B ALA* 1.3 85.4 - - - +
91B GLY* 1.3 60.5 + - - +
93B VAL* 3.2 8.9 + - - +
94B GLU* 2.8 36.9 + - - +
143B PHE* 4.9 11.8 - - - -
144B LEU* 4.4 15.2 - - + +
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Residues in contact with GLY 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B GLU* 4.8 6.3 - - - -
88B THR* 3.1 23.3 + - - -
90B GLU* 1.3 79.9 - - - +
92B MET* 1.3 50.3 + - - +
94B GLU* 3.3 14.1 + - - +
95B ALA* 2.6 37.2 + - - +
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Residues in contact with MET 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ASN* 4.4 2.2 - - - +
26B PHE* 3.3 62.7 - - + -
29B TYR* 3.9 17.3 - - + +
30B VAL* 3.8 39.7 - - - +
42B PHE* 3.7 7.9 - - + -
87B GLU* 3.8 27.6 - - + +
88B THR 2.7 25.0 + - - +
89B ALA 3.5 4.0 - - - +
91B GLY* 1.3 70.1 - - - +
93B VAL* 1.3 61.4 - - - +
95B ALA* 3.1 2.9 + - - +
96B ILE* 2.9 30.6 + - - +
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Residues in contact with VAL 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B LEU* 3.9 20.4 - - + -
42B PHE* 4.5 5.6 - - + -
89B ALA 3.1 16.3 + - - +
90B GLU* 3.6 5.2 - - - +
92B MET* 1.3 75.6 - - - +
94B GLU* 1.3 61.0 + - - +
96B ILE* 2.7 24.0 - - - +
97B MET* 3.1 14.0 + - - +
140B LEU* 3.6 29.8 - - + +
143B PHE* 3.8 31.2 - - + -
144B LEU* 3.6 23.3 - - + -
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Residues in contact with GLU 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B GLU* 2.8 18.2 + - - +
91B GLY* 3.3 14.4 - - - +
93B VAL* 1.3 76.5 - - - +
95B ALA* 1.3 61.7 + - - +
97B MET* 3.5 10.6 - - + +
98B LYS* 3.1 49.3 + - + +
144B LEU* 4.2 17.6 - - + +
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Residues in contact with ALA 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B LYS* 4.8 8.4 + - - +
26B PHE* 3.8 19.5 - - + -
87B GLU* 5.6 4.0 - - + -
91B GLY 2.6 20.9 + - - +
92B MET* 3.1 7.6 + - - +
94B GLU* 1.3 74.3 - - - +
96B ILE* 1.3 62.8 + - + +
98B LYS* 3.3 17.7 + - - +
99B ASP* 3.1 25.7 + - - +
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Residues in contact with ILE 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B LEU* 5.2 4.9 - - + -
22B LYS* 5.1 5.2 - - + -
23B LEU* 4.1 23.8 - - + -
26B PHE* 3.4 31.0 - - + -
42B PHE* 4.5 7.9 - - + -
45B LEU* 4.9 5.8 - - + -
92B MET 2.9 17.9 + - - +
93B VAL* 2.7 39.3 - - - +
95B ALA* 1.3 70.0 - - - +
97B MET* 1.3 62.1 + - - +
99B ASP* 3.3 15.3 - - + +
100B TYR* 2.8 46.9 + - + -
140B LEU* 4.1 19.3 - - + -
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Residues in contact with MET 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B VAL 3.1 21.6 + - - +
94B GLU* 3.5 17.3 - - + +
95B ALA 3.2 0.2 - - - -
96B ILE* 1.3 81.9 - - - +
98B LYS* 1.3 71.1 + - + +
100B TYR* 3.2 6.1 + - - +
101B GLU* 3.1 49.5 + - - +
137B ALA* 4.2 9.2 - - - +
140B LEU* 4.1 20.6 - - + -
141B ARG* 3.8 39.7 - - + +
144B LEU* 4.3 10.1 - - + -
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Residues in contact with LYS 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B GLU* 3.1 39.7 + - + +
95B ALA* 3.5 13.9 - - - +
97B MET* 1.3 85.1 - - + +
99B ASP* 1.3 59.0 + - - +
101B GLU* 3.2 16.2 + - - +
102B MET* 2.8 50.8 + - + +
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Residues in contact with ASP 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B LEU* 4.1 11.8 - - + +
22B LYS* 2.9 35.8 + - - +
80B ILE* 3.9 34.3 - - + +
81B GLN* 4.6 5.5 + - - +
95B ALA 3.1 15.6 + - - +
96B ILE* 3.1 15.3 + - - +
98B LYS* 1.3 77.6 - - - +
100B TYR* 1.3 62.6 + - + +
102B MET* 3.4 22.7 + - - +
103B MET* 3.1 24.8 + - - +
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Residues in contact with TYR 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B TRP* 4.3 18.4 - + - -
19B LEU* 4.7 13.2 - - + -
23B LEU* 4.5 7.7 - - + +
45B LEU* 3.0 35.9 + - + +
48B GLU* 5.1 1.2 + - - -
96B ILE* 2.8 29.0 + - + -
97B MET* 3.5 8.7 - - - +
98B LYS 3.2 0.2 - - - -
99B ASP* 1.3 77.0 - - + +
101B GLU* 1.3 57.5 + - + +
103B MET* 2.9 22.3 + - - +
104B LEU* 2.9 18.6 + - + +
133B LEU* 4.0 39.9 - - + +
136B HIS* 3.7 37.9 - + + -
137B ALA* 4.7 5.4 - - + -
140B LEU* 4.2 16.8 - - + -
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Residues in contact with GLU 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B MET* 3.1 32.1 + - - +
98B LYS* 3.6 19.2 - - - +
100B TYR* 1.3 70.7 - - - +
102B MET* 1.3 64.4 + - + +
103B MET 3.0 4.7 - - - -
104B LEU* 3.1 32.3 + - + +
105B VAL* 3.5 10.9 + - - +
137B ALA* 4.5 10.5 - - + -
141B ARG* 2.4 36.9 + - - +
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Residues in contact with MET 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B ILE* 6.0 2.9 - - + -
81B GLN* 6.6 0.2 - - + -
98B LYS* 2.8 40.5 + - + +
99B ASP* 3.4 30.5 - - - +
101B GLU* 1.3 76.8 - - + +
103B MET* 1.3 56.4 + - - +
105B VAL* 3.0 29.2 - - + +
106B GLU* 3.7 8.0 + - - +
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Residues in contact with MET 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B GLN* 2.9 44.0 - - - +
15B ASP* 4.5 15.9 - - + +
16B TRP* 3.3 37.2 - - + +
19B LEU* 4.4 16.6 - - - -
80B ILE* 5.2 4.9 - - + -
99B ASP 3.1 12.3 + - - +
100B TYR* 2.9 13.9 + - - +
102B MET* 1.3 77.6 - - - +
104B LEU* 1.3 63.7 + - - +
105B VAL 3.2 2.0 - - - -
106B GLU* 3.3 9.6 + - + +
107B LEU* 2.9 43.8 + - + +
129B ILE* 4.4 0.7 - - + -
133B LEU* 4.1 7.6 - - + -
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Residues in contact with LEU 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B TYR 2.9 16.2 + - - +
101B GLU* 3.1 23.8 + - + +
103B MET* 1.3 77.5 - - - +
105B VAL* 1.3 64.2 + - + +
107B LEU* 3.0 7.9 + - + +
108B LYS* 2.9 27.1 + - + +
130B TYR* 3.3 58.6 - - + +
133B LEU* 4.0 14.1 - - + -
134B GLU* 3.8 27.1 - - + +
137B ALA* 5.5 3.8 - - + -
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Residues in contact with VAL 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B GLU 3.8 11.9 - - - +
102B MET* 3.0 22.0 - - - +
104B LEU* 1.3 78.4 - - + +
106B GLU* 1.3 82.3 + - + +
107B LEU 3.1 0.2 + - - -
108B LYS* 3.1 12.6 + - + +
109B LYS* 3.0 38.6 + - + +
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Residues in contact with GLU 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B VAL* 4.7 5.5 - - - +
11B LYS* 2.8 46.2 - - - +
12B GLN* 5.3 6.0 + - - +
15B ASP* 3.5 10.0 - - - +
79B SER* 3.6 8.2 + - - -
102B MET 3.7 12.0 + - - +
103B MET* 3.3 15.2 + - + +
105B VAL* 1.3 87.6 - - + +
107B LEU* 1.3 56.7 + - - +
109B LYS* 3.6 14.1 - - + +
110B GLY* 2.9 22.9 + - - -
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Residues in contact with LEU 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B VAL* 6.1 1.3 - - + -
12B GLN* 3.9 23.6 - - + +
103B MET* 2.9 41.0 + - + +
104B LEU* 3.3 10.1 - - - +
106B GLU* 1.3 77.3 - - - +
108B LYS* 1.3 66.8 + - - +
110B GLY* 2.8 4.4 + - - +
111B MET* 2.8 30.9 + - + +
126B LEU* 3.7 37.9 - - + +
129B ILE* 4.4 5.2 - - + -
130B TYR* 3.9 35.4 - - + +
133B LEU* 4.3 8.1 - - + -
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Residues in contact with LYS 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B LEU 2.9 12.8 + - - +
105B VAL* 3.1 12.8 + - + +
107B LEU* 1.3 72.5 - - - +
109B LYS* 1.3 65.3 + - + +
111B MET* 3.0 17.4 + - + +
112B GLU* 3.0 24.3 + - - +
130B TYR* 3.2 40.1 + - + +
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Residues in contact with LYS 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B VAL* 3.0 30.0 + - - +
106B GLU* 3.6 15.7 - - + +
108B LYS* 1.3 77.5 - - + +
110B GLY* 1.3 59.7 + - - +
112B GLU* 3.1 19.2 + - - +
113B ILE* 2.9 22.6 - - + +
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Residues in contact with GLY 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B VAL* 5.4 0.3 - - - +
8B VAL* 3.6 24.7 - - - +
106B GLU 2.9 14.2 + - - -
107B LEU 2.8 9.6 + - - -
109B LYS* 1.3 77.8 - - - +
111B MET* 1.3 55.1 + - - -
113B ILE* 3.4 8.5 - - - +
114B ALA* 3.1 27.2 + - - +
126B LEU* 3.8 11.3 - - - +
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Residues in contact with MET 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B LEU* 2.8 16.8 + - + +
108B LYS* 3.0 34.3 + - + +
110B GLY* 1.3 71.3 - - - +
112B GLU* 1.3 66.2 + - - +
114B ALA* 3.5 4.3 - - - +
115B GLN* 2.9 37.6 + - - +
123B SER* 3.4 28.9 - - - +
126B LEU* 3.9 10.8 - - + +
127B LEU* 3.9 28.0 - - + +
130B TYR* 3.7 28.9 - - + -
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Residues in contact with GLU 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B LYS 3.0 12.6 + - - +
109B LYS* 3.1 15.3 - - - +
111B MET* 1.3 78.2 - - - +
113B ILE* 1.3 58.5 + - + +
115B GLN* 3.1 14.5 + - - +
116B ASN* 2.8 54.1 + - - +
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Residues in contact with ILE 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B GLN* 4.5 7.0 - - - +
5B VAL* 3.4 41.5 - - + +
8B VAL* 3.7 17.0 - - + -
109B LYS* 2.9 20.6 - - + +
110B GLY* 3.4 13.7 - - - +
112B GLU* 1.3 72.2 - - - +
114B ALA* 1.3 62.1 + - - +
116B ASN* 3.6 11.0 + - + +
117B SER* 2.8 43.0 + - - +
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Residues in contact with ALA 114 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B VAL* 4.2 11.4 - - + -
110B GLY 3.1 20.4 + - - +
111B MET* 3.5 5.2 - - - +
112B GLU 3.2 0.2 - - - -
113B ILE* 1.3 82.4 - - - +
115B GLN* 1.3 57.1 + - - +
117B SER 3.2 6.2 + - - -
119B ASP* 2.8 48.6 + - - +
122B THR* 4.5 10.1 - - + -
123B SER* 4.0 17.9 - - - +
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Residues in contact with GLN 115 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B MET* 2.9 32.0 + - - +
112B GLU* 3.4 14.9 + - - +
114B ALA* 1.3 77.6 - - - +
116B ASN* 1.3 61.9 + - - +
118B ASP* 2.9 19.4 + - - -
119B ASP 4.4 4.7 - - - +
120B GLU* 4.9 10.0 - - + +
123B SER* 3.9 19.1 - - - +
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Residues in contact with ASN 116 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B GLU* 2.8 42.4 + - - +
113B ILE* 3.6 10.4 + - - +
115B GLN* 1.3 81.2 - - - +
117B SER* 1.3 60.1 + - - +
118B ASP* 3.1 3.4 + - - +
----------------------------------------------------------
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Residues in contact with SER 117 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B GLN* 4.6 7.1 + - - -
5B VAL* 3.8 25.0 - - - +
113B ILE* 2.8 24.3 + - - +
114B ALA 3.8 1.3 - - - -
115B GLN 3.2 0.6 - - - -
116B ASN* 1.3 75.7 - - - +
118B ASP* 1.3 71.5 + - - +
119B ASP* 3.4 3.8 + - - +
----------------------------------------------------------
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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