Contacts of the helix formed by residues 113 - 145 (chain V) in PDB entry 3IS7
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 V).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102S ARG* 4.2 5.1 + - - +
128S GLU* 4.8 2.3 - - - +
4V ASP* 5.7 1.8 + - + +
7V VAL* 3.3 20.9 - - + +
61V ARG* 2.8 26.7 + - - -
65V LEU* 4.0 7.7 - - - +
108V CYS* 3.0 20.5 + - + +
111V VAL* 3.4 14.7 - - + +
112V HIS* 1.3 73.9 - - - +
114V TYR* 1.3 56.4 + - - +
115V VAL* 3.7 1.6 + - - +
116V SER* 2.5 29.2 + - - -
117V ARG* 3.0 21.7 + - - -
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Residues in contact with TYR 114 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102S ARG* 3.9 15.1 - - + +
105S ILE* 3.5 37.2 - - + +
106S VAL* 3.2 28.2 + - - +
117S ARG* 3.6 24.1 + - - +
121S LYS* 4.5 16.0 - - + +
124S LEU* 4.1 15.5 - - + -
109V GLU* 3.5 40.8 + - - -
112V HIS* 3.2 41.7 + + + -
113V ASP* 1.3 72.6 - - - +
115V VAL* 1.3 60.2 + - - +
117V ARG* 3.5 9.1 - - - +
118V ASP* 3.0 28.1 + - - +
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Residues in contact with VAL 115 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121S LYS* 4.8 4.0 - - + +
124S LEU* 3.9 11.4 - - + +
125S GLU* 3.9 51.4 - - + +
128S GLU* 3.6 26.2 + - + +
61V ARG* 3.7 29.4 - - - +
113V ASP* 3.3 1.4 + - - -
114V TYR* 1.3 73.7 - - - +
116V SER* 1.4 65.0 + - - +
118V ASP* 3.2 6.9 + - - +
119V LEU* 3.1 23.3 + - + +
----------------------------------------------------------
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Residues in contact with SER 116 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7V VAL* 4.3 4.3 - - - -
11V LEU* 4.6 10.3 - - - -
61V ARG* 2.7 28.7 + - - +
65V LEU* 3.9 5.7 - - - +
108V CYS* 3.8 13.7 - - - -
113V ASP* 2.5 35.7 + - - -
115V VAL* 1.4 72.8 - - - +
117V ARG* 1.3 65.0 + - - +
119V LEU* 3.4 6.3 + - - +
120V LEU* 3.0 28.9 + - - +
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Residues in contact with ARG 117 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109R GLU* 2.6 40.4 + - - -
114R TYR* 3.6 21.8 + - - +
117R ARG* 4.2 19.5 - - - +
117S ARG* 4.3 14.1 - - - +
105V ILE* 3.9 22.6 - - + +
108V CYS* 4.0 16.9 - - + +
109V GLU* 2.9 38.2 + - - +
113V ASP 3.0 15.9 + - - +
114V TYR* 3.5 13.5 - - + +
115V VAL 3.3 0.4 - - - -
116V SER* 1.3 76.8 - - - +
118V ASP* 1.3 64.5 + - - +
120V LEU* 3.4 6.2 + - - +
121V LYS* 2.9 35.1 + - + +
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Residues in contact with ASP 118 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118S ASP* 5.5 3.6 - - - +
121S LYS* 4.5 15.9 - - + +
122S ASP* 5.5 3.1 - - - +
125S GLU* 4.5 14.2 - - - +
114V TYR 3.0 16.2 + - - +
115V VAL* 3.6 6.5 - - - +
116V SER 3.2 0.4 - - - -
117V ARG* 1.3 81.9 - - - +
119V LEU* 1.3 66.3 + - - +
121V LYS* 3.1 24.1 + - - +
122V ASP* 3.0 33.2 + - - +
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Residues in contact with LEU 119 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11V LEU* 5.2 3.6 - - + -
57V LYS* 3.9 34.8 - - + +
58V LEU* 4.1 12.1 - - + -
61V ARG* 3.9 24.9 - - + -
115V VAL* 3.1 13.6 + - + +
116V SER* 3.6 8.7 - - - +
118V ASP* 1.3 78.4 - - - +
120V LEU* 1.3 68.3 + - + +
122V ASP* 3.1 9.6 + - - +
123V ILE* 2.9 46.1 + - + +
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Residues in contact with LEU 120 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11V LEU* 3.9 25.6 - - + -
14V ILE* 4.1 10.8 - - + -
58V LEU* 4.3 6.5 - - + -
101V LEU* 4.0 22.4 - - + +
104V ALA* 3.5 33.2 - - + -
105V ILE* 3.7 15.1 - - + +
108V CYS* 3.9 19.7 - - - -
116V SER 3.0 20.6 + - - +
117V ARG 3.6 4.0 - - - +
119V LEU* 1.3 88.3 - - + +
121V LYS* 1.3 58.6 + - - +
123V ILE* 3.4 6.0 + - + +
124V LEU* 2.9 26.7 + - - +
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Residues in contact with LYS 121 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114R TYR* 4.2 24.7 - - + +
115R VAL* 5.1 3.5 - - + +
117R ARG* 6.4 1.8 - - - -
118R ASP* 2.9 47.6 + - + +
105V ILE* 4.1 11.2 - - + +
117V ARG* 2.9 25.7 + - + +
118V ASP* 3.1 25.0 + - - +
120V LEU* 1.3 77.5 - - - +
122V ASP* 1.3 83.0 + - - +
124V LEU* 3.2 8.6 + - + +
125V GLU* 2.9 31.8 + - + +
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Residues in contact with ASP 122 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54V HIS* 5.3 1.6 - - - -
118V ASP* 3.0 23.2 + - - +
119V LEU* 3.4 10.5 - - - +
121V LYS* 1.3 92.8 + - - +
123V ILE* 1.3 66.8 + - + +
125V GLU* 3.2 12.1 + - - +
126V SER* 3.1 22.7 + - - -
----------------------------------------------------------
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Residues in contact with ILE 123 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14V ILE* 4.9 0.9 - - + -
18V GLU* 3.6 23.3 - - - +
54V HIS* 3.7 35.2 - - + +
57V LYS* 5.7 2.9 - - + -
58V LEU* 4.1 23.6 - - + -
101V LEU* 4.1 17.7 - - + -
119V LEU* 2.9 36.4 + - + +
120V LEU* 3.5 11.0 - - + +
122V ASP* 1.3 76.6 - - + +
124V LEU* 1.3 58.0 + - - +
126V SER* 3.2 3.5 + - - -
127V GLU* 2.8 38.9 + - - +
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Residues in contact with LEU 124 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114R TYR* 4.0 20.0 - - + -
115R VAL* 3.9 14.6 - - + -
98V THR* 3.8 30.3 - - - +
101V LEU* 4.2 15.7 - - + +
102V ARG* 3.7 31.2 - - + +
105V ILE* 4.0 20.6 - - + -
120V LEU 2.9 14.4 + - - +
121V LYS* 3.2 9.8 + - - +
123V ILE* 1.3 74.8 - - - +
125V GLU* 1.3 64.7 + - - +
127V GLU* 3.2 2.2 + - - +
128V GLU* 2.9 34.9 + - + +
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Residues in contact with GLU 125 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115R VAL* 3.9 32.0 - - + +
118R ASP* 4.8 11.4 - - - +
121V LYS* 2.9 18.1 + - + +
122V ASP* 3.2 13.5 + - - +
124V LEU* 1.3 77.6 - - - +
126V SER* 1.3 57.4 + - - +
128V GLU* 3.4 2.4 + - - +
129V GLU* 3.0 46.6 + - + +
----------------------------------------------------------
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Residues in contact with SER 126 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50V ASP* 5.2 3.8 + - - +
54V HIS* 2.7 35.5 - - - -
122V ASP 3.1 12.1 + - - -
123V ILE 3.5 7.2 - - - -
125V GLU* 1.3 78.8 - - - +
127V GLU* 1.3 62.2 + - - +
129V GLU* 3.3 17.5 + - - +
130V HIS* 3.1 19.4 + - - +
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Residues in contact with GLU 127 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18V GLU* 2.9 16.5 - - - +
51V GLU* 2.8 31.2 - - - +
54V HIS* 3.8 1.6 + - - -
94V GLU* 2.6 38.1 - - - +
97V ALA* 5.1 5.8 - - + -
98V THR* 3.8 14.8 - - - +
101V LEU* 3.9 21.3 - - + -
123V ILE* 2.8 28.6 + - + +
124V LEU* 3.2 4.5 + - - +
126V SER* 1.3 76.4 + - - +
128V GLU* 1.3 57.0 + - - +
130V HIS* 3.0 10.1 + - - +
131V ILE* 2.9 31.6 + - - +
----------------------------------------------------------
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Residues in contact with GLU 128 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61R ARG* 2.7 43.2 + - - +
64R PHE* 3.6 21.0 - - + -
65R LEU* 6.1 0.4 - - - -
113R ASP* 4.7 0.7 - - - +
115R VAL* 3.3 24.4 - - + +
98V THR* 4.7 3.8 - - + +
102V ARG* 3.0 32.9 + - - +
124V LEU* 2.9 28.0 + - + +
125V GLU* 3.7 6.3 - - - +
127V GLU* 1.3 72.5 - - - +
129V GLU* 1.3 62.0 + - + +
131V ILE* 3.2 13.6 + - + +
132V ASP* 3.0 18.4 + - - +
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Residues in contact with GLU 129 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125V GLU* 3.0 34.7 + - + +
126V SER* 3.6 20.2 - - - +
127V GLU 3.3 0.2 - - - -
128V GLU* 1.3 75.8 - - + +
130V HIS* 1.3 64.4 + - - +
132V ASP* 3.1 10.1 + - - +
133V TYR* 3.0 22.9 + - - +
----------------------------------------------------------
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Residues in contact with HIS 130 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25V TYR* 3.3 39.5 - + - -
44V GLU* 4.6 5.0 + - - -
47V GLU* 3.3 42.6 + - + +
51V GLU* 5.1 0.6 + - - -
90V ASP* 4.5 2.0 - - + -
94V GLU* 3.4 20.7 + - + +
126V SER 3.1 11.5 + - - +
127V GLU* 3.0 16.1 + - - +
129V GLU* 1.3 77.4 - - - +
131V ILE* 1.3 62.3 + - - +
133V TYR* 3.3 10.6 + + - +
134V LEU* 2.9 51.4 + - + +
----------------------------------------------------------
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Residues in contact with ILE 131 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64R PHE* 4.2 13.0 - - + -
91V LEU* 4.0 12.6 - - + -
94V GLU* 3.7 29.2 - - + +
95V LEU* 4.1 18.4 - - + -
98V THR* 3.9 25.4 - - + +
127V GLU 2.9 15.4 + - - +
128V GLU* 3.2 14.6 + - + +
130V HIS* 1.3 77.0 - - - +
132V ASP* 1.3 62.5 + - - +
134V LEU* 3.1 6.8 + - - +
135V GLU* 2.9 49.6 + - - +
----------------------------------------------------------
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Residues in contact with ASP 132 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34Q ASP* 4.6 12.5 - - - +
64R PHE* 3.6 34.5 - - + +
128V GLU 3.0 9.1 + - - +
129V GLU* 3.1 13.9 + - - +
131V ILE* 1.3 76.6 - - - +
133V TYR* 1.3 62.6 + - - +
135V GLU* 4.1 3.7 - - - +
136V THR* 2.8 40.4 + - - -
----------------------------------------------------------
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Residues in contact with TYR 133 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40V LEU* 3.8 24.4 + - - +
43V HIS* 3.4 56.9 - + + +
44V GLU* 5.5 3.4 - - - -
47V GLU* 5.0 1.1 - - - +
87V LEU* 4.6 4.5 - - + +
129V GLU 3.0 13.1 + - - +
130V HIS* 3.7 15.0 - + + +
132V ASP* 1.3 78.5 - - - +
134V LEU* 1.3 76.6 + - + +
136V THR* 3.3 4.6 + - - -
137V GLN* 2.9 71.6 + - + +
153V HIS* 5.3 2.2 + - - -
----------------------------------------------------------
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Residues in contact with LEU 134 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44V GLU* 5.6 0.7 - - - +
87V LEU* 3.8 36.7 - - + +
90V ASP* 4.0 14.4 - - + +
91V LEU* 4.1 30.7 - - + +
94V GLU* 4.1 6.5 - - + -
130V HIS* 2.9 61.2 + - + +
131V ILE* 3.6 6.5 - - - +
133V TYR* 1.3 83.6 - - + +
135V GLU* 1.3 65.9 + - - +
137V GLN* 3.2 5.5 + - - +
138V LEU* 3.1 29.4 + - + +
----------------------------------------------------------
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Residues in contact with GLU 135 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64R PHE* 4.7 16.4 - - - +
66R GLU* 4.2 15.1 - - - +
91V LEU* 4.2 19.9 - - + +
95V LEU* 5.3 4.0 - - - +
131V ILE* 2.9 43.2 + - + +
132V ASP* 4.1 2.6 - - - +
134V LEU* 1.3 72.3 - - - +
136V THR* 1.3 53.5 + - - +
138V LEU* 3.3 9.6 + - - +
139V GLY* 2.7 33.8 + - - -
----------------------------------------------------------
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Residues in contact with THR 136 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33Q ASN 5.0 1.4 + - - +
34Q ASP* 3.2 16.9 + - - +
35Q TRP* 3.7 5.4 - - - +
36Q GLY* 3.6 36.3 - - - +
132V ASP* 2.8 31.4 + - - -
133V TYR* 3.5 6.1 - - - -
135V GLU* 1.3 76.8 - - - +
137V GLN* 1.3 67.8 + - - +
139V GLY* 3.2 3.7 + - - -
140V LEU* 2.9 30.2 + - + +
----------------------------------------------------------
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Residues in contact with GLN 137 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154Q MET* 5.3 0.4 - - - +
87V LEU* 4.1 15.7 - - + -
133V TYR* 2.9 72.1 + - + +
134V LEU 3.2 4.7 + - - +
136V THR* 1.3 88.0 - - - +
138V LEU* 1.3 64.4 + - - +
140V LEU* 3.1 13.7 + - - +
141V ILE* 3.0 28.4 + - - +
149V TYR* 2.5 45.2 + - + +
153V HIS* 3.9 11.7 + - - -
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Residues in contact with LEU 138 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84V GLN* 4.4 23.1 + - + +
87V LEU* 3.8 35.9 - - + +
88V GLN* 4.1 25.4 - - + +
91V LEU* 4.1 17.0 - - + -
134V LEU 3.1 20.2 + - - +
135V GLU* 3.5 9.0 - - - +
137V GLN* 1.3 78.0 - - - +
139V GLY* 1.3 64.4 + - - +
141V ILE* 3.2 21.0 + - + +
142V GLN* 3.4 17.8 + - - +
----------------------------------------------------------
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Residues in contact with GLY 139 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35Q TRP 5.5 0.9 - - - -
135V GLU 2.7 19.0 + - - -
136V THR* 3.5 4.5 - - - -
138V LEU* 1.3 74.5 - - - +
140V LEU* 1.3 60.3 + - - +
142V GLN* 3.2 10.3 + - - +
143V LYS* 3.1 39.7 + - - +
----------------------------------------------------------
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Residues in contact with LEU 140 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35Q TRP 3.3 20.6 - - - +
36Q GLY* 3.9 14.8 - - - +
37Q LEU* 3.9 24.9 - - + -
154Q MET* 4.0 27.4 - - + -
136V THR* 2.9 32.9 + - + +
137V GLN* 3.1 24.4 + - - +
139V GLY* 1.3 70.3 - - - +
141V ILE* 1.3 62.0 + - - +
143V LYS* 4.3 7.6 - - + +
144V VAL* 2.8 41.3 + - + +
149V TYR* 4.0 10.3 - - + -
----------------------------------------------------------
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Residues in contact with ILE 141 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83V THR* 4.8 1.6 - - + -
84V GLN* 4.1 34.1 - - + +
87V LEU* 4.1 20.4 - - + -
137V GLN 3.0 17.2 + - - +
138V LEU* 3.2 18.4 + - + +
140V LEU* 1.3 77.5 - - - +
142V GLN* 1.3 62.6 + - - +
145V GLY* 3.0 29.3 + - - -
146V LEU* 3.6 28.8 + - + +
149V TYR* 3.6 37.9 - - + -
----------------------------------------------------------
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Residues in contact with GLN 142 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147Q GLU* 5.2 1.7 - - - +
84V GLN* 3.8 23.4 - - - +
138V LEU 3.5 13.5 - - - +
139V GLY* 3.3 10.5 - - - +
140V LEU 3.1 0.2 - - - -
141V ILE* 1.3 84.1 - - - +
143V LYS* 1.3 63.0 + - + +
144V VAL 3.7 0.2 + - - -
145V GLY* 4.0 3.6 + - - -
----------------------------------------------------------
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Residues in contact with LYS 143 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35Q TRP* 3.8 52.6 + - + +
37Q LEU* 4.5 19.7 - - + -
146Q LEU* 5.5 1.4 - - - +
147Q GLU* 3.8 12.3 - - - +
150Q LEU* 3.7 27.7 - - + +
139V GLY* 3.1 26.5 + - - +
140V LEU* 3.9 6.7 - - + +
142V GLN* 1.3 80.1 - - + +
144V VAL* 1.3 64.0 + - + +
----------------------------------------------------------
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Residues in contact with VAL 144 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37Q LEU* 5.0 0.2 - - + -
147Q GLU* 3.5 24.6 - - - +
150Q LEU* 3.9 11.7 - - + +
151Q GLN* 3.6 28.7 - - + +
154Q MET* 4.2 17.0 - - + -
140V LEU* 2.8 29.7 + - + +
143V LYS* 1.3 77.9 - - + +
145V GLY* 1.3 69.1 + - - +
148V ASN* 3.1 30.4 + - + +
149V TYR* 3.7 23.6 - - + +
----------------------------------------------------------
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Residues in contact with GLY 145 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147Q GLU* 3.7 14.5 + - - -
141V ILE 3.0 17.4 + - - -
142V GLN 4.0 2.8 + - - -
143V LYS 3.5 2.2 - - - -
144V VAL* 1.3 83.0 - - - +
146V LEU* 1.3 66.3 - - - -
147V GLU 3.3 3.0 + - - -
148V ASN 3.4 0.8 + - - -
149V TYR* 3.0 19.2 + - - +
----------------------------------------------------------
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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