Contacts of the helix formed by residues 113 - 145 (chain R) 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 R).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4R ASP* 5.7 2.7 + - + +
7R VAL* 3.5 20.0 - - + +
61R ARG* 2.9 24.4 + - - -
65R LEU* 3.8 10.0 - - - +
108R CYS* 2.9 19.5 + - - +
111R VAL* 3.1 16.2 + - + +
112R HIS* 1.3 73.3 - - - +
114R TYR* 1.3 57.5 + - - +
115R VAL 3.7 1.0 + - - -
116R SER* 2.7 26.8 + - - -
117R ARG 3.1 16.8 + - - -
102V ARG* 4.1 5.7 + - - +
128V GLU* 4.7 3.1 - - - +
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Residues in contact with TYR 114 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109R GLU* 3.6 20.1 + - - -
112R HIS* 2.9 51.3 + - + -
113R ASP* 1.3 71.1 - - - +
115R VAL* 1.3 59.7 + - - +
117R ARG* 3.4 10.8 + - + +
118R ASP* 3.1 27.7 + - - +
102V ARG* 4.0 19.2 - - + +
105V ILE* 3.6 36.1 - - + -
106V VAL* 3.1 31.7 + - - +
117V ARG* 3.3 35.6 + - - +
121V LYS* 4.6 12.0 - - + +
124V LEU* 4.1 12.3 - - + -
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Residues in contact with VAL 115 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61R ARG* 3.5 17.0 - - - +
113R ASP* 3.3 1.0 + - - -
114R TYR* 1.3 77.7 - - - +
116R SER* 1.3 62.1 + - - +
118R ASP* 3.4 7.3 + - + +
119R LEU* 3.3 20.5 + - + +
121V LYS* 4.8 4.5 - - + +
124V LEU* 3.8 10.9 - - + +
125V GLU* 3.5 51.4 - - + +
128V GLU* 3.2 37.7 + - + +
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Residues in contact with SER 116 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7R VAL* 4.2 5.4 - - - +
11R LEU* 5.0 6.4 - - - +
61R ARG* 2.8 31.5 + - - +
65R LEU* 3.8 5.4 - - - +
108R CYS* 3.9 12.3 - - - -
113R ASP* 2.7 36.0 + - - -
115R VAL* 1.3 74.8 - - - +
117R ARG* 1.3 65.5 + - - +
118R ASP 3.1 0.7 - - - -
119R LEU* 3.5 6.8 + - - +
120R LEU* 3.2 27.2 + - - +
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Residues in contact with ARG 117 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105R ILE* 3.7 28.9 - - + +
108R CYS* 4.0 15.2 - - + -
109R GLU* 3.2 39.5 + - - +
113R ASP 3.1 14.7 + - - +
114R TYR* 3.5 14.6 - - - +
115R VAL 3.3 0.4 - - - -
116R SER* 1.3 75.8 - - - +
118R ASP* 1.3 58.2 + - - +
120R LEU* 3.1 8.2 + - - +
121R LYS* 2.9 39.7 + - + +
109S GLU* 2.8 42.2 + - - -
114S TYR* 3.7 12.8 + - - +
117S ARG* 4.0 17.0 - - - +
117V ARG* 3.8 20.2 - - - +
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Residues in contact with ASP 118 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114R TYR 3.1 12.7 + - - +
115R VAL* 3.6 9.0 - - - +
116R SER 3.1 0.2 - - - -
117R ARG* 1.3 81.7 - - - +
119R LEU* 1.3 64.1 + - - +
121R LYS* 3.4 10.1 + - - +
122R ASP* 3.2 36.0 + - - +
118V ASP* 5.7 0.7 - - - +
121V LYS* 4.0 20.8 - - + +
122V ASP* 5.7 0.7 - - - +
125V GLU* 5.5 2.4 - - - +
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Residues in contact with LEU 119 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11R LEU* 5.2 2.7 - - + -
57R LYS* 4.2 30.3 - - + +
58R LEU* 4.2 18.6 - - + -
61R ARG* 4.0 33.4 - - + -
115R VAL* 3.3 11.4 + - + +
116R SER* 3.7 9.4 - - - +
118R ASP* 1.3 79.0 - - - +
120R LEU* 1.3 63.3 + - + +
122R ASP* 3.2 9.5 + - + +
123R ILE* 3.2 34.2 + - + +
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Residues in contact with LEU 120 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10R HIS* 5.8 0.2 - - + -
11R LEU* 4.0 25.6 - - + -
14R ILE* 4.2 8.3 - - + -
58R LEU* 4.1 15.9 - - + -
101R LEU* 3.8 23.9 - - + +
104R ALA* 3.7 36.1 - - + +
105R ILE* 3.6 20.8 - - + +
108R CYS* 4.1 10.1 - - - -
116R SER 3.2 14.6 + - - +
117R ARG 3.1 6.6 + - - +
119R LEU* 1.3 81.3 - - + +
121R LYS* 1.3 56.2 + - - +
123R ILE* 3.3 5.8 + - + +
124R LEU* 2.8 31.4 + - - +
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Residues in contact with LYS 121 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105R ILE* 4.0 8.5 - - + +
117R ARG* 2.9 26.9 + - + +
118R ASP* 3.7 12.6 - - - +
119R LEU 3.3 0.2 - - - -
120R LEU* 1.3 75.6 - - - +
122R ASP* 1.3 60.0 + - - +
124R LEU* 3.4 8.7 - - + +
125R GLU* 3.1 25.3 + - - +
114S TYR* 4.2 26.5 - - + +
115S VAL* 4.9 3.0 - - + +
118S ASP* 3.8 25.4 - - + +
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Residues in contact with ASP 122 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54R HIS* 5.2 0.7 - - - -
118R ASP* 3.2 21.5 + - - +
119R LEU* 3.2 11.8 + - + +
120R LEU 3.2 0.6 - - - -
121R LYS* 1.3 78.2 - - - +
123R ILE* 1.3 66.3 + - + +
125R GLU* 3.2 15.0 + - - +
126R SER* 3.1 22.2 + - - -
118S ASP* 5.3 4.3 - - - +
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Residues in contact with ILE 123 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14R ILE* 4.7 3.6 - - + -
18R GLU* 3.4 20.9 - - - +
54R HIS* 3.6 42.5 - - + +
58R LEU* 3.9 35.0 - - + -
101R LEU* 3.7 18.8 - - + -
119R LEU* 3.2 23.1 + - + +
120R LEU* 3.6 10.5 - - + +
122R ASP* 1.3 76.3 - - - +
124R LEU* 1.3 64.0 + - - +
126R SER* 2.9 5.2 + - - -
127R GLU* 2.9 26.6 + - - +
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Residues in contact with LEU 124 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98R THR* 4.3 16.6 - - - +
101R LEU* 3.8 31.2 - - + +
102R ARG* 4.0 35.4 - - + +
105R ILE* 4.3 12.6 - - + -
120R LEU 2.8 21.4 + - - +
121R LYS* 3.4 7.2 - - - +
123R ILE* 1.3 73.9 - - - +
125R GLU* 1.3 65.7 + - - +
127R GLU* 3.2 2.4 + - + -
128R GLU* 2.9 23.0 + - + +
114S TYR* 4.1 20.4 - - + -
115S VAL* 3.9 20.0 - - + -
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Residues in contact with GLU 125 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121R LYS 3.1 12.2 + - - +
122R ASP* 3.2 18.2 + - - +
124R LEU* 1.3 80.0 - - - +
126R SER* 1.3 59.0 + - - +
128R GLU* 3.1 5.6 + - - +
129R GLU* 3.0 45.2 + - + +
115S VAL* 3.8 29.9 - - + +
118S ASP* 5.1 9.4 - - - +
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Residues in contact with SER 126 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50R ASP* 4.9 8.3 + - - +
54R HIS* 2.9 32.2 - - - -
122R ASP 3.1 7.8 + - - -
123R ILE 2.9 8.8 + - - -
125R GLU* 1.3 83.5 - - - +
127R GLU* 1.3 61.9 + - - +
129R GLU* 3.1 17.3 + - - +
130R HIS* 3.1 20.3 + - - +
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Residues in contact with GLU 127 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18R GLU* 2.6 16.3 - - - +
51R GLU* 2.2 47.0 - - - +
54R HIS* 3.3 8.5 + - - -
94R GLU* 2.8 37.2 - - - +
97R ALA* 5.1 8.5 - - + -
98R THR* 4.8 11.4 - - - +
101R LEU* 4.1 12.8 - - + -
123R ILE* 2.9 24.6 + - + +
124R LEU* 3.2 6.7 + - + +
126R SER* 1.3 74.6 + - - +
128R GLU* 1.3 66.3 + - - +
130R HIS* 3.3 4.5 + - - +
131R ILE* 3.0 24.2 + - - +
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Residues in contact with GLU 128 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98R THR* 4.7 5.4 - - - +
102R ARG* 2.8 35.5 + - - +
124R LEU* 2.9 20.7 + - + +
125R GLU* 3.1 9.8 + - - +
127R GLU* 1.3 76.7 - - - +
129R GLU* 1.4 57.8 + - - +
131R ILE* 3.4 10.2 + - + -
132R ASP* 3.0 23.0 + - - +
61S ARG* 2.7 41.1 + - - +
64S PHE* 3.5 23.9 - - + -
65S LEU* 5.3 0.6 - - - +
113S ASP* 4.7 0.9 - - - +
115S VAL* 3.3 25.2 - - + +
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Residues in contact with GLU 129 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125R GLU* 3.0 42.6 + - + +
126R SER* 3.1 16.7 + - - +
128R GLU* 1.4 73.3 - - - +
130R HIS* 1.3 60.5 - - - +
132R ASP* 3.1 25.4 - - - +
133R TYR* 3.1 9.4 + - - +
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Residues in contact with HIS 130 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25R TYR* 3.6 32.3 - + - -
44R GLU* 4.3 4.1 + - - -
47R GLU* 3.1 52.0 + - + +
51R GLU* 4.5 1.6 + - - -
90R ASP* 5.0 0.4 - - + -
94R GLU* 3.6 22.0 + - - +
126R SER 3.1 11.7 + - - +
127R GLU* 3.5 10.8 - - - +
128R GLU 3.2 0.2 - - - -
129R GLU* 1.3 75.3 - - - +
131R ILE* 1.3 64.5 + - - +
133R TYR* 3.0 19.0 + + - +
134R LEU* 3.0 45.2 + - + +
----------------------------------------------------------
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Residues in contact with ILE 131 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91R LEU* 4.2 13.2 - - + -
94R GLU* 3.6 30.5 - - + +
95R LEU* 4.4 14.4 - - + -
98R THR* 3.4 26.7 - - + +
127R GLU 3.0 18.7 + - - +
128R GLU* 3.4 15.5 + - + +
130R HIS* 1.3 74.1 - - - +
132R ASP* 1.3 63.9 + - - +
134R LEU* 4.2 7.6 - - - -
135R GLU* 3.0 52.5 + - + +
64S PHE* 4.2 13.2 - - + -
----------------------------------------------------------
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Residues in contact with ASP 132 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128R GLU 3.0 14.7 + - - +
129R GLU* 3.1 17.8 - - - +
130R HIS 3.1 0.2 - - - -
131R ILE* 1.3 78.7 - - - +
133R TYR* 1.3 58.5 + - - +
135R GLU* 4.0 3.5 - - - +
136R THR* 2.8 38.3 + - - -
64S PHE* 3.7 30.9 - - + +
34T ASP* 4.8 9.2 - - - +
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Residues in contact with TYR 133 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32R TRP* 5.9 1.0 - - - -
40R LEU* 3.5 26.7 + - - +
43R HIS* 3.4 55.4 - + + +
44R GLU* 5.0 6.8 + - - +
47R GLU* 5.1 0.9 - - - +
87R LEU* 4.7 3.2 - - + +
129R GLU 3.1 7.9 + - - +
130R HIS* 3.0 30.3 + + + +
132R ASP* 1.3 75.5 - - - +
134R LEU* 1.3 79.5 + - + +
136R THR* 3.2 5.8 + - - -
137R GLN* 2.9 69.0 + - + +
153R HIS* 5.8 1.0 - - - -
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Residues in contact with LEU 134 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44R GLU* 5.7 0.4 - - - +
87R LEU* 3.9 38.0 - - + +
90R ASP* 4.2 15.9 - - + +
91R LEU* 4.2 24.0 - - + +
94R GLU* 4.4 3.6 - - + -
130R HIS* 3.0 55.3 + - + +
131R ILE* 3.8 8.7 - - - +
133R TYR* 1.3 97.2 - - + +
135R GLU* 1.3 63.5 + - - +
137R GLN* 3.0 15.0 + - - +
138R LEU* 3.0 19.5 + - + +
----------------------------------------------------------
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Residues in contact with GLU 135 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91R LEU* 4.4 17.0 - - + +
95R LEU* 5.9 2.3 - - - +
131R ILE* 3.0 33.0 + - + +
132R ASP* 4.0 3.3 - - - +
134R LEU* 1.3 76.4 - - - +
136R THR* 1.3 56.8 + - - +
138R LEU* 3.7 9.0 - - - +
139R GLY* 2.9 25.5 + - - -
64S PHE* 4.2 19.9 - - - +
66S GLU* 3.5 22.7 - - - +
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Residues in contact with THR 136 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132R ASP* 2.8 29.3 + - - -
133R TYR* 3.4 7.0 - - - -
134R LEU 3.2 0.2 - - - -
135R GLU* 1.3 75.8 - - - +
137R GLN* 1.3 75.5 + - - +
139R GLY* 3.5 1.5 + - - -
140R LEU* 2.9 25.6 + - + +
33T ASN 5.2 0.8 + - - +
34T ASP 3.2 15.8 + - - +
35T TRP* 3.7 4.4 - - - +
36T GLY* 3.3 37.5 - - - +
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Residues in contact with GLN 137 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87R LEU* 4.1 15.9 - - + -
133R TYR* 2.9 65.3 + - + +
134R LEU 3.0 6.5 + - - +
136R THR* 1.3 86.3 - - - +
138R LEU* 1.3 59.4 + - - +
140R LEU* 2.9 29.9 + - - +
141R ILE* 2.9 19.8 + - - +
149R TYR* 2.8 43.8 + - + +
153R HIS* 3.9 12.1 + - - -
159T FE 4.0 5.9 - - - -
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Residues in contact with LEU 138 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84R GLN* 3.7 33.2 - - + +
87R LEU* 3.9 22.7 - - + +
88R GLN* 4.2 26.0 - - + +
91R LEU* 3.9 26.5 - - + -
134R LEU 3.0 19.2 + - - +
135R GLU* 3.7 6.1 - - - +
137R GLN* 1.3 75.6 - - - +
139R GLY* 1.3 64.0 + - - +
141R ILE* 3.0 29.3 + - + +
142R GLN* 3.4 12.4 + - - +
----------------------------------------------------------
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Residues in contact with GLY 139 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135R GLU 2.9 17.9 + - - -
136R THR 3.7 2.2 - - - -
138R LEU* 1.3 75.1 - - - +
140R LEU* 1.3 62.2 + - - +
142R GLN* 3.3 10.2 + - - +
143R LYS* 3.1 41.3 + - - +
35T TRP 5.5 0.9 - - - -
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Residues in contact with LEU 140 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136R THR* 2.9 31.8 + - + +
137R GLN* 2.9 31.1 + - - +
139R GLY* 1.3 76.5 - - - +
141R ILE* 1.3 65.0 - - - +
143R LYS* 3.0 8.2 + - + +
144R VAL* 2.9 36.8 + - + +
149R TYR* 4.1 10.1 - - + -
35T TRP 3.3 19.7 - - - +
36T GLY* 4.0 9.9 - - - +
37T LEU* 3.8 26.5 - - + -
154T MET* 3.8 25.8 - - + -
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Residues in contact with ILE 141 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83R THR* 5.2 1.3 - - + -
84R GLN* 3.9 23.6 - - + +
87R LEU* 4.0 27.4 - - + -
137R GLN 2.9 16.6 + - - +
138R LEU* 3.0 21.7 + - + +
140R LEU* 1.3 76.9 - - - +
142R GLN* 1.3 69.2 + - - +
145R GLY* 3.0 26.5 + - - -
146R LEU* 3.6 29.5 + - + +
149R TYR* 3.9 30.5 - - + -
----------------------------------------------------------
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Residues in contact with GLN 142 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84R GLN* 3.3 29.1 + - - +
138R LEU 3.4 11.3 + - - +
139R GLY* 3.3 10.6 + - - +
140R LEU 3.2 0.6 - - - -
141R ILE* 1.3 83.3 - - - +
143R LYS* 1.3 63.8 + - + +
145R GLY* 4.3 2.6 + - - -
147T GLU* 5.3 3.5 - - - +
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Residues in contact with LYS 143 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139R GLY* 3.1 27.4 + - - +
140R LEU* 3.0 10.2 + - + +
142R GLN* 1.3 82.6 - - + +
144R VAL* 1.3 63.4 + - + +
35T TRP* 3.9 53.0 + - + +
37T LEU* 5.0 7.6 - - + -
146T LEU* 5.5 1.6 - - - +
147T GLU* 4.1 13.2 - - - +
150T LEU* 3.5 31.0 - - + +
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Residues in contact with VAL 144 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140R LEU* 2.9 25.7 + - + +
143R LYS* 1.3 81.4 - - + +
145R GLY* 1.3 68.6 + - - +
148R ASN* 3.2 26.8 + - + +
149R TYR* 3.9 21.5 - - + +
147T GLU* 3.3 24.8 - - - +
150T LEU* 3.7 13.2 - - + +
151T GLN* 3.4 33.9 - - + +
154T MET* 4.5 16.6 - - + -
----------------------------------------------------------
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Residues in contact with GLY 145 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141R ILE 3.0 18.0 + - - -
142R GLN 4.3 2.3 + - - -
143R LYS 3.6 1.0 - - - -
144R VAL* 1.3 82.2 - - - +
146R LEU* 1.3 66.9 + - - -
147R GLU 3.3 3.3 + - - -
148R ASN 3.5 0.8 + - - -
149R TYR* 3.1 21.8 + - - +
147T GLU* 4.1 8.0 + - - -
----------------------------------------------------------
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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