Contacts of the helix formed by residues 113 - 145 (chain F) in PDB entry 3ISE
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 113 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4F ASP* 6.3 0.2 - - + -
7F VAL* 4.0 14.6 - - + +
61F ARG* 3.0 22.2 + - - -
65F LEU* 4.1 9.1 - - - +
108F CYS* 2.7 29.4 + - + +
111F VAL* 3.2 15.3 + - + +
112F HIS* 1.3 71.7 - - - +
114F TYR* 1.3 57.7 + - - +
115F VAL* 3.6 1.7 + - - +
116F SER* 2.7 28.0 + - - -
117F ARG* 3.2 17.3 + - - +
102J ARG* 4.1 9.2 + - - +
128J GLU* 4.5 1.0 - - - +
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Residues in contact with TYR 114 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109F GLU* 3.3 40.4 + - - -
112F HIS* 3.2 37.9 + - + -
113F ASP* 1.3 73.8 + - - +
115F VAL* 1.3 60.9 + - - +
117F ARG* 3.3 8.6 + - - +
118F ASP* 2.9 27.7 + - - +
102J ARG* 3.9 16.0 - - - +
105J ILE* 3.3 45.9 - - + +
106J VAL* 3.1 29.3 + - - +
117J ARG* 3.7 16.4 + - - +
121J LYS* 5.1 11.2 - - + +
124J LEU* 4.0 16.2 - - + -
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Residues in contact with VAL 115 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61F ARG* 3.5 24.0 - - - +
113F ASP* 3.5 1.2 + - - -
114F TYR* 1.3 77.0 - - - +
116F SER* 1.3 57.7 + - - +
118F ASP* 3.3 7.5 + - + +
119F LEU* 3.0 26.0 + - + +
121J LYS* 4.9 2.5 - - + +
124J LEU* 4.1 10.3 - - + -
125J GLU* 3.9 44.9 - - + +
128J GLU* 3.4 31.6 - - + +
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Residues in contact with SER 116 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7F VAL* 4.6 4.5 - - - -
11F LEU* 4.2 9.9 - - - +
61F ARG* 2.8 27.7 + - - +
65F LEU* 4.1 4.9 - - - +
108F CYS* 3.9 15.5 - - - -
113F ASP* 2.7 30.8 + - - -
114F TYR 3.3 0.4 - - - -
115F VAL* 1.3 74.6 - - - +
117F ARG* 1.3 68.5 + - - +
119F LEU* 3.3 6.8 + - - +
120F LEU* 3.2 25.8 + - - +
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Residues in contact with ARG 117 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105F ILE* 3.8 32.1 - - + +
108F CYS* 4.0 14.9 - - + +
109F GLU* 3.0 37.8 + - - +
113F ASP 3.2 15.8 + - - +
114F TYR* 3.3 11.9 + - - +
116F SER* 1.3 78.4 - - - +
118F ASP* 1.3 60.3 + - - +
120F LEU* 3.2 1.7 + - - +
121F LYS* 2.8 38.0 + - + +
109G GLU* 2.6 44.9 + - - -
114G TYR* 3.7 17.6 + - - +
117G ARG* 3.9 21.4 - - - +
117J ARG* 4.2 12.4 - - - +
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Residues in contact with ASP 118 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114F TYR 2.9 17.5 + - - +
115F VAL* 3.6 9.0 - - + +
116F SER 3.2 0.2 - - - -
117F ARG* 1.3 78.2 - - - +
119F LEU* 1.3 63.8 + - - +
121F LYS* 3.4 10.7 - - - +
122F ASP* 3.1 37.7 + - - +
118G ASP* 5.8 0.5 - - - +
121J LYS* 5.0 12.5 - - + +
122J ASP* 5.7 1.9 - - - +
125J GLU* 5.3 5.4 - - - +
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Residues in contact with LEU 119 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11F LEU* 5.4 2.7 - - + -
57F LYS* 4.0 34.5 - - + +
58F LEU* 4.0 23.8 - - + -
61F ARG* 4.0 22.9 - - + +
115F VAL* 3.0 15.0 + - + +
116F SER* 3.5 10.5 - - - +
118F ASP* 1.3 76.9 - - - +
120F LEU* 1.3 59.0 + - + +
122F ASP* 3.0 22.2 + - + +
123F ILE* 3.2 27.4 + - + +
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Residues in contact with LEU 120 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11F LEU* 4.0 28.3 - - + -
14F ILE* 4.1 15.3 - - + -
58F LEU* 4.3 10.8 - - + -
101F LEU* 3.8 25.1 - - + +
104F ALA* 3.5 32.3 - - + -
105F ILE* 3.7 15.7 - - + +
108F CYS* 4.1 14.6 - - - -
116F SER 3.2 16.5 + - - +
117F ARG 3.7 2.7 - - - +
119F LEU* 1.3 77.5 - - + +
121F LYS* 1.3 55.3 + - - +
123F ILE* 3.2 8.8 + - + +
124F LEU* 2.7 35.5 + - - +
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Residues in contact with LYS 121 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105F ILE* 4.0 11.3 - - + +
117F ARG* 2.8 29.6 + - + +
118F ASP* 3.4 13.5 - - - +
120F LEU* 1.3 76.7 - - - +
122F ASP* 1.3 65.1 + - - +
124F LEU* 3.2 4.8 + - + +
125F GLU* 3.1 22.7 + - - +
114G TYR* 4.2 27.8 - - + +
115G VAL* 5.0 2.1 - - + +
117G ARG* 6.5 0.4 - - - -
118G ASP* 4.0 22.7 - - - +
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Residues in contact with ASP 122 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54F HIS* 5.0 0.6 + - - -
118F ASP* 3.1 23.4 + - - +
119F LEU* 3.0 12.9 + - + +
121F LYS* 1.3 80.6 - - - +
123F ILE* 1.3 63.8 + - + +
125F GLU* 3.6 12.2 + - - +
126F SER* 3.2 22.5 + - - -
118G ASP* 5.6 2.6 - - - +
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Residues in contact with ILE 123 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14F ILE* 5.1 1.3 - - + -
18F GLU* 3.5 21.3 - - - +
54F HIS* 3.9 39.9 - - + +
57F LYS* 5.6 0.7 - - + -
58F LEU* 4.2 27.4 - - + -
101F LEU* 4.1 15.0 - - + -
119F LEU* 3.2 31.0 + - + +
120F LEU* 3.5 14.6 - - + +
122F ASP* 1.3 73.3 - - + +
124F LEU* 1.3 61.2 + - - +
126F SER* 3.4 1.0 + - - -
127F GLU* 2.9 42.3 + - + +
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Residues in contact with LEU 124 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98F THR* 3.5 30.1 - - - +
101F LEU* 4.0 28.5 - - + -
102F ARG* 3.9 24.7 - - + +
105F ILE* 4.4 6.7 - - + -
120F LEU 2.7 17.2 + - - +
121F LYS* 3.4 7.6 - - - +
122F ASP 3.2 0.2 - - - -
123F ILE* 1.3 75.7 - - - +
125F GLU* 1.3 66.8 + - - +
127F GLU* 3.1 3.0 + - - -
128F GLU* 2.9 26.2 + - + +
114G TYR* 4.1 26.7 - - + -
115G VAL* 3.9 20.0 - - + +
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Residues in contact with GLU 125 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121F LYS 3.1 12.5 + - - +
122F ASP* 3.9 12.0 - - - +
124F LEU* 1.3 79.0 - - - +
126F SER* 1.3 62.9 + - - +
128F GLU* 3.1 4.8 + - + +
129F GLU* 3.0 42.2 + - + +
115G VAL* 3.7 32.0 - - + +
118G ASP* 5.1 8.7 - - - +
----------------------------------------------------------
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Residues in contact with SER 126 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50F ASP* 4.6 8.7 + - - +
54F HIS* 2.8 35.7 + - - -
122F ASP 3.2 14.9 + - - -
123F ILE 3.9 0.7 - - - -
124F LEU 3.1 0.8 - - - -
125F GLU* 1.3 79.8 - - - +
127F GLU* 1.3 60.4 + - - +
129F GLU* 3.4 19.7 + - - +
130F HIS* 3.1 19.8 + - - +
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Residues in contact with GLU 127 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18F GLU* 2.2 21.7 - - - +
51F GLU* 2.2 34.1 - - - +
54F HIS* 3.3 5.7 + - - -
94F GLU* 2.5 45.6 - - - +
97F ALA* 5.2 7.6 - - + -
98F THR* 4.4 11.7 - - - +
101F LEU* 4.1 11.9 - - + -
123F ILE* 2.9 34.3 + - + +
124F LEU* 3.1 3.8 + - - +
126F SER* 1.3 76.2 - - - +
128F GLU* 1.3 56.7 + - - +
130F HIS* 3.2 6.5 + - - +
131F ILE* 3.1 31.4 + - - +
----------------------------------------------------------
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Residues in contact with GLU 128 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98F THR* 4.5 11.2 - - - +
102F ARG* 3.4 28.2 + - - +
124F LEU* 2.9 17.8 + - + +
125F GLU* 3.1 8.7 + - + +
127F GLU* 1.3 73.7 - - - +
129F GLU* 1.3 60.4 - - - +
131F ILE* 3.1 12.1 + - + +
132F ASP* 2.9 28.5 + - - +
61G ARG* 2.9 39.9 + - - +
64G PHE* 3.5 19.0 - - + -
65G LEU* 5.2 0.4 - - - +
113G ASP* 4.5 1.4 - - - +
115G VAL* 3.4 26.1 - - + +
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Residues in contact with GLU 129 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125F GLU* 3.0 36.2 + - + +
126F SER* 3.5 19.4 - - - +
127F GLU 3.3 0.2 - - - -
128F GLU* 1.3 72.4 - - - +
130F HIS* 1.3 64.9 + - - +
132F ASP* 3.2 10.4 + - - +
133F TYR* 3.0 22.2 + - - +
----------------------------------------------------------
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Residues in contact with HIS 130 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25F TYR* 3.4 35.1 - + - -
44F GLU* 4.3 5.9 + - - -
47F GLU* 3.2 45.9 + - + +
51F GLU* 5.7 0.4 - - - -
90F ASP* 4.6 2.2 - - + +
94F GLU* 2.8 26.8 + - - +
126F SER 3.1 14.0 + - - +
127F GLU* 3.2 10.0 + - - +
129F GLU* 1.3 75.9 - - - +
131F ILE* 1.3 61.1 + - - +
133F TYR* 3.4 12.7 + + - -
134F LEU* 3.1 44.3 + - + +
----------------------------------------------------------
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Residues in contact with ILE 131 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91F LEU* 4.0 15.3 - - + -
94F GLU* 3.8 25.4 - - + +
95F LEU* 4.4 20.2 - - + -
98F THR* 4.1 20.9 - - + +
127F GLU 3.1 19.9 + - - +
128F GLU* 3.1 15.2 + - + +
130F HIS* 1.3 73.2 - - - +
132F ASP* 1.3 63.3 + - - +
134F LEU* 3.2 7.6 + - - +
135F GLU* 2.8 58.5 + - + +
64G PHE* 4.3 9.9 - - + -
----------------------------------------------------------
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Residues in contact with ASP 132 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128F GLU 2.9 9.8 + - - +
129F GLU* 3.4 12.5 - - - +
131F ILE* 1.3 77.9 - - - +
133F TYR* 1.3 60.0 + - - +
135F GLU* 4.2 3.6 - - - +
136F THR* 2.8 40.1 + - - -
64G PHE* 3.4 37.2 - - + +
34H ASP* 4.1 13.5 - - - +
----------------------------------------------------------
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Residues in contact with TYR 133 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32F TRP* 6.0 0.5 - - - -
40F LEU* 3.7 25.1 + - - +
43F HIS* 3.1 57.8 - + + +
44F GLU* 5.1 4.5 + - - +
47F GLU* 5.0 1.1 - - - +
87F LEU* 4.6 4.0 - - + +
129F GLU 3.0 12.9 + - - +
130F HIS* 3.7 19.5 - + + +
131F ILE 3.2 0.2 - - - -
132F ASP* 1.3 75.8 - - - +
134F LEU* 1.3 80.7 + - + +
136F THR* 3.3 4.4 + - - -
137F GLN* 2.9 68.7 + - + +
153F HIS* 5.6 2.0 + - - -
----------------------------------------------------------
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Residues in contact with LEU 134 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44F GLU* 5.6 0.4 - - - +
87F LEU* 3.6 44.5 - - + +
90F ASP* 3.9 10.3 - - + +
91F LEU* 3.7 33.2 - - + +
94F GLU* 4.3 3.8 - - + -
130F HIS* 3.1 50.5 + - + +
131F ILE* 3.5 6.5 - - - +
133F TYR* 1.3 89.0 - - + +
135F GLU* 1.3 67.0 + - - +
137F GLN* 3.0 13.0 + - - +
138F LEU* 3.0 20.4 + - + +
----------------------------------------------------------
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Residues in contact with GLU 135 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91F LEU* 4.2 16.7 - - + +
131F ILE* 2.8 41.6 + - + +
132F ASP* 4.2 4.9 - - - +
134F LEU* 1.3 72.4 - - - +
136F THR* 1.3 63.8 + - - +
138F LEU* 3.6 10.1 - - - +
139F GLY* 2.8 21.8 + - - -
64G PHE* 4.2 17.0 - - + +
66G GLU* 4.8 11.8 - - - +
----------------------------------------------------------
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Residues in contact with THR 136 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132F ASP* 2.8 28.8 + - - -
133F TYR* 3.5 6.1 - - - -
135F GLU* 1.3 79.9 - - - +
137F GLN* 1.3 61.9 + - - +
139F GLY* 3.1 4.0 + - - -
140F LEU* 2.6 37.5 + - + +
33H ASN 5.1 0.6 + - - +
34H ASP 3.2 17.4 + - - -
35H TRP* 3.6 23.8 - - - +
36H GLY* 3.7 16.4 - - - -
----------------------------------------------------------
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Residues in contact with GLN 137 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87F LEU* 3.9 17.0 - - + -
133F TYR* 2.9 63.5 + - + +
134F LEU 3.0 5.6 + - - +
136F THR* 1.3 81.4 - - - +
138F LEU* 1.3 65.3 + - - +
140F LEU* 2.9 17.8 + - - +
141F ILE* 2.8 27.3 + - - +
149F TYR* 2.7 46.7 + - - +
153F HIS* 3.9 10.7 + - - -
159F FE 4.2 3.8 - - - -
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Residues in contact with LEU 138 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84F GLN* 4.3 28.9 + - + +
87F LEU* 3.7 35.2 - - + -
88F GLN* 4.1 20.2 - - + +
91F LEU* 3.8 29.4 - - + -
134F LEU 3.0 12.5 + - - +
135F GLU* 3.6 8.3 - - - +
137F GLN* 1.3 76.7 - - - +
139F GLY* 1.3 62.9 + - - +
141F ILE* 3.2 19.8 + - + +
142F GLN* 3.4 18.3 + - - +
----------------------------------------------------------
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Residues in contact with GLY 139 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135F GLU 2.8 18.7 + - - -
136F THR* 3.4 4.0 - - - -
138F LEU* 1.3 72.7 - - - +
140F LEU* 1.3 61.3 + - - +
142F GLN* 3.1 19.4 + - - +
143F LYS* 3.2 29.3 + - - +
35H TRP 5.6 0.4 - - - -
----------------------------------------------------------
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Residues in contact with LEU 140 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136F THR* 2.6 21.5 + - + +
137F GLN* 2.9 35.4 + - - +
139F GLY* 1.3 70.9 - - - -
141F ILE* 1.3 63.3 + - - +
143F LYS* 3.1 9.1 + - + +
144F VAL* 3.0 33.8 + - + +
149F TYR* 4.0 9.4 - - + -
35H TRP 3.0 24.0 + - - +
36H GLY* 3.9 18.2 - - - +
37H LEU* 4.3 11.4 - - + -
154H MET* 3.9 34.5 - - + -
----------------------------------------------------------
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Residues in contact with ILE 141 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83F THR* 4.9 1.6 - - + -
84F GLN* 4.4 20.2 - - + +
87F LEU* 4.0 24.2 - - + -
137F GLN 2.8 15.6 + - - +
138F LEU* 3.2 19.2 + - + +
140F LEU* 1.3 72.1 - - - +
142F GLN* 1.3 73.2 + - - +
145F GLY* 3.2 21.3 + - - -
146F LEU* 3.6 36.2 + - + +
149F TYR* 3.6 39.3 - - + -
----------------------------------------------------------
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Residues in contact with GLN 142 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84F GLN* 4.2 16.4 + - - +
138F LEU 3.4 13.9 + - - +
139F GLY* 3.1 12.3 + - - +
141F ILE* 1.3 90.2 - - - +
143F LYS* 1.3 65.2 + - + +
144F VAL 3.6 0.3 + - - -
145F GLY 4.2 2.9 + - - -
147H GLU* 4.4 5.5 - - - +
----------------------------------------------------------
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Residues in contact with LYS 143 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139F GLY* 3.3 25.6 + - - +
140F LEU* 3.1 11.9 + - + +
142F GLN* 1.3 81.9 - - + +
144F VAL* 1.3 62.4 + - + +
35H TRP* 3.8 49.8 + - + +
37H LEU* 4.5 18.4 - - + -
146H LEU* 5.6 2.1 - - - +
147H GLU* 4.1 12.1 - - - +
150H LEU* 3.7 26.7 - - + +
----------------------------------------------------------
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Residues in contact with VAL 144 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140F LEU* 3.0 21.5 + - + +
143F LYS* 1.3 83.8 - - + +
145F GLY* 1.3 71.2 + - - +
148F ASN* 2.9 29.8 + - + +
149F TYR* 3.8 20.0 - - + +
37H LEU* 5.1 2.7 - - + -
147H GLU* 2.8 32.3 - - - +
150H LEU* 3.7 27.1 - - + +
151H GLN* 3.8 14.6 - - + +
154H MET* 4.6 16.6 - - + -
----------------------------------------------------------
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Residues in contact with GLY 145 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141F ILE 3.2 14.5 + - - -
142F GLN 4.2 1.9 + - - -
143F LYS 3.7 1.0 - - - -
144F VAL* 1.3 81.8 - - - +
146F LEU* 1.3 66.9 + - - -
147F GLU 3.2 3.6 - - - -
148F ASN 3.2 2.9 + - - -
149F TYR* 2.9 20.3 + - - +
147H GLU* 3.7 12.5 + - - -
----------------------------------------------------------
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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