Contacts of the helix formed by residues 89 - 116 (chain B) in PDB entry 1C72
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 89 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B GLU* 1.3 82.7 - - + +
90B GLU* 1.3 60.1 + - - +
91B VAL* 3.6 12.4 + - - +
92B GLU* 3.2 30.4 + - - +
93B LYS* 3.0 30.8 + - - +
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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
----------------------------------------------------------
78A TYR* 3.2 23.8 - - - +
81A ARG* 3.2 41.4 + - + +
82A LYS* 5.0 4.3 - - - +
89B THR* 1.3 72.6 - - - +
91B VAL* 1.3 63.5 + - + +
93B LYS* 3.2 7.2 + - - +
94B GLN* 2.6 65.7 + - - +
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Residues in contact with VAL 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A VAL* 6.4 0.2 - - + -
89B THR* 3.2 9.4 - - - +
90B GLU* 1.3 76.8 - - + +
92B GLU* 1.3 63.2 + - + +
94B GLN* 3.2 23.2 + - - +
95B ARG* 3.0 36.1 + - + +
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Residues in contact with GLU 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B CYS 5.1 0.2 - - - +
87B GLY* 4.0 3.2 - - - -
88B GLU* 2.9 46.9 + - - +
89B THR* 3.2 25.7 + - - +
91B VAL* 1.3 78.4 - - + +
93B LYS* 1.3 61.2 + - - +
95B ARG* 3.2 4.1 + - - +
96B VAL* 3.0 28.4 + - - +
148B VAL* 3.3 38.8 - - + +
149B GLY* 4.9 5.7 - - - -
150B ASP* 4.9 7.1 + - - +
151B LYS* 5.2 7.9 + - - +
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Residues in contact with LYS 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A ARG* 3.8 34.7 - - - +
93A LYS* 6.0 4.5 - - - +
77B ARG* 6.2 2.0 - - - +
86B CYS* 5.5 4.7 - - + -
87B GLY* 3.7 27.6 + - - +
88B GLU 3.8 15.4 + - - -
89B THR 3.0 20.3 + - - +
90B GLU* 3.5 9.1 - - - +
92B GLU* 1.3 76.4 - - - +
94B GLN* 1.3 61.2 + - - +
96B VAL* 3.3 6.2 + - + +
97B ASP* 3.0 35.4 + - - +
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Residues in contact with GLN 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A VAL* 3.4 38.8 - - - +
69A LEU* 4.2 18.0 - - + +
78A TYR* 3.5 14.1 - - + -
81A ARG* 3.9 13.2 - - - +
90B GLU* 2.6 43.9 + - - +
91B VAL* 3.4 26.2 - - - +
93B LYS* 1.3 75.0 - - - +
95B ARG* 1.3 61.5 + - + +
97B ASP* 3.6 3.5 + - - +
98B VAL* 3.0 33.7 + - - +
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Residues in contact with ARG 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A ASP* 5.2 5.7 + - - -
91B VAL* 3.0 25.2 + - + +
92B GLU* 3.2 7.8 + - - +
94B GLN* 1.3 77.3 - - + +
96B VAL* 1.3 64.8 + - - +
98B VAL* 4.1 2.4 - - - +
99B LEU* 3.1 30.8 + - + +
140B PHE* 3.3 52.0 + - + -
144B ARG* 3.0 45.7 - - - +
147B PHE 3.6 10.1 + - - +
148B VAL* 3.9 28.0 - - + -
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Residues in contact with VAL 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B ARG* 4.1 11.2 - - - +
86B CYS* 4.8 1.3 - - + -
87B GLY* 4.0 21.3 - - - +
92B GLU 3.0 15.4 + - - +
93B LYS* 3.6 7.6 - - + +
95B ARG* 1.3 76.4 - - - +
97B ASP* 1.3 60.7 + - - +
100B GLU* 2.9 33.8 + - - +
148B VAL* 3.9 15.3 - - + -
153B THR* 4.8 2.7 - - - +
154B PHE* 3.4 39.3 - - + -
155B VAL* 3.6 20.5 - - + +
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Residues in contact with ASP 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A LEU* 6.3 0.2 - - + -
74A ALA* 3.6 23.2 - - + +
77A ARG* 3.4 22.7 - - - +
81A ARG* 2.9 32.4 + - - -
77B ARG* 3.2 27.8 + - - +
93B LYS* 3.0 19.5 + - - +
94B GLN* 4.1 4.0 - - - +
95B ARG 3.4 0.2 - - - -
96B VAL* 1.3 78.8 - - - +
98B VAL* 1.3 62.4 + - - +
100B GLU* 3.8 1.1 - - - +
101B ASN* 2.7 30.4 + - - +
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Residues in contact with VAL 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A ASP* 5.9 1.6 - - + -
56A PHE* 3.9 29.6 - - + -
69A LEU* 3.5 26.9 - - + -
70A THR* 3.9 27.4 - - - +
71A GLN* 3.7 8.6 - - + +
74A ALA* 3.9 8.7 - - + -
94B GLN 3.0 20.4 + - - +
95B ARG* 4.1 4.0 - - - +
97B ASP* 1.3 74.7 - - - +
99B LEU* 1.3 59.5 + - - +
101B ASN 3.2 1.7 + - - -
102B HIS* 2.8 31.2 + - + +
140B PHE* 5.8 2.7 - - + -
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Residues in contact with LEU 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A PHE* 4.3 9.6 - - + -
95B ARG* 3.1 16.5 + - + +
96B VAL 3.9 2.0 - - - +
98B VAL* 1.3 76.3 - - - +
100B GLU* 1.3 59.3 + - - +
102B HIS* 4.3 6.5 - - + -
103B LEU* 2.9 57.6 + - + +
137B LEU* 4.0 27.1 - - + -
140B PHE* 3.6 29.4 - - + -
147B PHE* 3.6 32.8 - - + +
148B VAL* 6.3 0.2 - - + -
155B VAL* 4.1 16.6 - - + +
159B ALA* 5.6 0.9 - - + -
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Residues in contact with GLU 100 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A ARG* 4.8 0.5 + - - -
100A GLU* 4.3 13.5 - - - +
101A ASN* 5.1 0.2 + - - -
73B ASN* 3.7 41.9 + - - +
77B ARG* 2.7 50.3 + - - +
96B VAL 2.9 19.1 + - - +
97B ASP* 3.8 3.0 - - - +
99B LEU* 1.3 77.2 - - - +
101B ASN* 1.3 74.8 + - - +
103B LEU* 4.2 2.6 - - - +
104B MET* 3.5 17.2 + - - +
154B PHE* 3.9 9.1 - - + -
155B VAL* 4.0 12.3 - - + +
158B LEU* 4.4 8.5 - - + +
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Residues in contact with ASN 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A GLN* 3.4 30.1 + - + +
73A ASN* 3.3 43.3 - - - +
74A ALA 4.3 2.0 + - - -
100A GLU* 4.9 0.4 - - - +
104A MET* 5.9 3.2 - - - +
220A EPY 5.1 3.9 + - - -
73B ASN* 5.8 0.7 - - - -
97B ASP* 2.7 23.6 - - - +
98B VAL 3.2 0.8 + - - -
99B LEU 3.2 0.4 - - - -
100B GLU* 1.3 92.6 - - - +
102B HIS* 1.3 63.8 + - - +
104B MET* 3.4 7.7 + - - +
105B ASP* 3.2 24.9 + - - +
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Residues in contact with HIS 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A PHE* 3.5 55.8 - + + +
57A PRO 6.2 0.2 - - - -
58A ASN* 5.0 8.4 + - - -
71A GLN* 3.6 19.5 + - + +
98B VAL* 2.8 19.5 + - + +
99B LEU* 4.0 7.4 - - + +
101B ASN* 1.3 75.7 - - - +
103B LEU* 1.3 65.8 + - - +
105B ASP* 3.0 20.8 + - + +
106B LEU* 3.1 46.9 + - + +
133B LYS* 5.4 3.3 + - + +
136B GLN* 4.1 11.4 + - - -
137B LEU* 4.9 8.3 - - + +
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Residues in contact with LEU 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B LEU* 2.9 48.4 + - + +
100B GLU 4.2 2.5 - - - +
102B HIS* 1.3 77.3 - - + +
104B MET* 1.3 57.6 + - - +
106B LEU* 3.7 12.7 - - + +
107B ARG* 2.9 31.8 + - - +
137B LEU* 4.7 11.2 - - + -
155B VAL* 3.9 7.0 - - + +
158B LEU* 3.6 19.7 - - + -
159B ALA* 3.6 39.7 - - + +
162B VAL* 3.7 29.6 - - + +
163B LEU* 6.3 0.2 - - + -
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Residues in contact with MET 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A ASN* 5.1 3.4 - - - +
108A MET* 6.2 3.1 - - + -
12B LEU* 5.1 8.3 - - + -
72B SER* 4.2 17.3 - - - +
73B ASN* 4.1 21.1 - - - +
100B GLU 3.5 13.1 + - - +
101B ASN* 3.4 12.9 + - - +
102B HIS 3.1 0.4 - - - -
103B LEU* 1.3 74.9 - - - +
105B ASP* 1.3 62.2 + - - +
107B ARG* 3.1 33.2 - - - +
108B MET* 2.9 49.5 + - + +
221B EPY 4.4 16.6 - - - +
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Residues in contact with ASP 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ASN* 4.2 9.9 + - - -
71A GLN* 3.2 23.2 + - - +
104A MET* 5.4 2.1 - - - +
220A EPY 3.5 25.0 + - - +
101B ASN 3.2 11.4 + - - +
102B HIS* 3.0 15.0 + - + +
104B MET* 1.3 80.1 - - - +
106B LEU* 1.3 60.9 + - + +
108B MET* 3.3 5.7 + - - +
109B ALA* 2.9 30.5 + - - +
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Residues in contact with LEU 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B HIS* 3.1 53.6 + - + +
103B LEU* 3.7 20.9 - - + +
104B MET 3.3 0.2 - - - -
105B ASP* 1.3 76.6 - - + +
107B ARG* 1.3 66.3 + - - +
109B ALA* 3.3 8.1 + - + +
110B PHE* 3.1 23.9 + - - +
126B TYR* 4.9 2.1 + - - -
133B LYS* 4.0 35.7 - - + +
137B LEU* 4.5 14.6 - - + -
162B VAL* 4.4 13.5 - - + -
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Residues in contact with ARG 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B GLY 5.0 1.2 + - - -
12B LEU* 3.5 31.7 + - + +
15B ALA* 5.2 0.6 - - - +
72B SER* 5.8 0.8 + - - -
73B ASN* 5.9 1.2 - - - +
103B LEU* 2.9 26.8 + - - +
104B MET* 3.1 35.9 - - - +
106B LEU* 1.3 73.8 - - - +
108B MET* 1.3 58.2 + - - +
110B PHE* 3.4 5.4 + - - +
111B ALA* 3.1 21.0 + - - +
158B LEU* 4.2 28.1 + - - +
161B ASP* 2.7 34.8 + - - +
162B VAL* 4.2 21.3 - - + +
165B GLN* 4.6 4.5 - - - +
221B EPY 2.4 53.9 + - + +
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Residues in contact with MET 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A MET* 4.6 20.0 - - + -
112A ARG* 4.7 14.6 - - - +
12B LEU* 6.2 1.3 - - - -
104B MET* 2.9 36.2 + - + +
105B ASP* 3.7 6.3 - - - +
107B ARG* 1.3 75.6 - - - +
109B ALA* 1.3 60.1 + - - +
111B ALA* 3.5 15.9 + - + +
112B ARG* 3.1 44.1 + - + +
115B TYR* 6.4 0.7 - - + -
221B EPY 4.4 19.3 - - + -
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Residues in contact with ALA 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B ASP 2.9 18.2 + - - +
106B LEU* 3.7 8.5 - - + +
108B MET* 1.3 76.4 - - - +
110B PHE* 1.3 60.8 + - - +
112B ARG* 3.1 32.2 + - - +
113B LEU* 3.5 12.0 + - - +
126B TYR* 4.3 13.7 - - + -
133B LYS* 6.0 6.1 - - - -
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Residues in contact with PHE 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B LEU 3.1 11.7 + - - +
107B ARG* 3.6 8.7 - - - +
109B ALA* 1.3 75.6 - - - +
111B ALA* 1.3 63.9 + - - +
113B LEU* 3.2 7.4 + - + +
114B CYS* 3.1 41.4 + - - -
126B TYR* 3.3 33.8 - + - +
165B GLN* 3.7 34.5 - - + +
166B GLN* 3.3 22.7 - - - +
169B PHE* 3.5 31.6 - + - -
207B ILE* 5.1 0.4 - - + -
208B PHE* 3.4 29.8 - + - -
214B TRP* 3.9 11.2 - + - -
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Residues in contact with ALA 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B ARG 3.1 11.5 + - - +
108B MET* 3.8 12.8 - - + +
109B ALA 3.4 0.2 - - - -
110B PHE* 1.3 72.9 - - - +
112B ARG* 1.3 66.9 + - - +
114B CYS 3.2 1.7 + - - -
115B TYR* 2.9 37.0 + - + -
208B PHE* 3.6 18.3 - - + -
221B EPY 3.5 37.5 - - + -
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Residues in contact with ARG 112 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B MET* 3.1 35.0 + - + +
109B ALA* 3.1 27.5 + - - +
111B ALA* 1.3 75.3 - - - +
113B LEU* 1.3 66.7 + - - +
115B TYR* 3.9 4.6 - - - +
116B SER* 3.1 25.2 + - - -
122B LEU* 5.4 11.1 - - - +
126B TYR* 6.1 1.0 - - - -
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Residues in contact with LEU 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B ALA 3.5 8.4 + - - +
110B PHE* 3.2 24.5 + - + +
111B ALA 3.2 0.4 - - - -
112B ARG* 1.3 83.6 - - - +
114B CYS* 1.3 60.0 + - - +
116B SER* 2.7 22.2 + - - -
119B PHE* 3.0 35.5 - - + +
122B LEU* 3.5 47.3 - - + +
123B LYS* 3.8 7.4 - - - +
126B TYR* 3.7 37.5 - - + -
169B PHE* 4.5 7.9 - - + -
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Residues in contact with CYS 114 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B PHE* 3.1 48.5 + - - +
111B ALA 3.7 1.8 - - - +
113B LEU* 1.3 80.6 - - - +
115B TYR* 1.3 59.7 + - - +
119B PHE* 3.6 24.2 - - + -
169B PHE* 4.6 0.2 - - - -
208B PHE* 3.7 28.5 - - + -
212B ALA* 3.6 2.9 - - - -
213B LEU* 2.9 30.9 + - - +
214B TRP* 4.0 15.3 - - + +
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Residues in contact with TYR 115 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B MET* 6.4 0.4 - - + -
111B ALA* 2.9 27.5 + - + +
112B ARG* 4.0 4.5 - - - +
114B CYS* 1.3 78.8 - - - +
116B SER* 1.3 61.1 + - - +
117B PRO* 3.6 6.2 - - - +
208B PHE* 3.6 14.8 - + + +
209B TRP* 2.9 33.4 + + + -
211B THR* 4.4 13.1 - - - +
212B ALA* 3.5 36.1 - - + +
213B LEU* 4.6 7.8 - - - +
221B EPY 3.0 45.0 + + - -
----------------------------------------------------------
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Residues in contact with SER 116 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B ARG 3.1 13.9 + - - -
113B LEU 2.7 20.6 + - - +
115B TYR* 1.3 76.5 - - - +
117B PRO* 1.3 68.0 - - - +
118B ASP* 4.2 6.1 - - - -
119B PHE* 3.0 30.3 + - - +
122B LEU* 3.4 26.7 - - - +
213B LEU* 3.5 5.7 - - - +
----------------------------------------------------------
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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