Contacts of the helix formed by residues 113 - 145 (chain J) 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 J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102G ARG* 4.2 4.8 + - - +
128G GLU* 4.5 3.8 - - - +
4J ASP* 5.8 1.6 + - + +
7J VAL* 3.4 17.1 - - + +
61J ARG* 2.8 26.3 + - - -
65J LEU* 4.0 9.4 - - - +
108J CYS* 2.8 29.7 + - + +
111J VAL* 3.4 10.4 + - + -
112J HIS* 1.3 69.8 - - - +
114J TYR* 1.3 63.1 + - - +
115J VAL* 3.8 1.2 + - - +
116J SER* 2.7 29.6 + - - -
117J ARG* 3.1 17.7 + - - +
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Residues in contact with TYR 114 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102G ARG* 4.0 14.9 - - + +
105G ILE* 3.5 43.2 - - + +
106G VAL* 3.2 29.8 + - - +
117G ARG* 3.9 12.4 + - - +
121G LYS* 4.5 16.1 - - + +
124G LEU* 4.1 15.9 - - + -
109J GLU* 3.7 39.4 + - - -
112J HIS* 3.2 46.2 + - + -
113J ASP* 1.3 75.3 + - - +
115J VAL* 1.3 56.6 + - - +
117J ARG* 3.4 8.6 + - - +
118J ASP* 3.0 27.4 + - - +
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Residues in contact with VAL 115 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121G LYS* 4.8 4.5 - - + +
124G LEU* 3.8 14.1 - - + +
125G GLU* 3.7 46.4 - - + +
128G GLU* 3.5 31.4 + - + +
61J ARG* 3.6 22.7 - - - +
113J ASP* 3.3 1.4 + - - -
114J TYR* 1.3 73.7 - - - +
116J SER* 1.3 66.5 + - - +
118J ASP* 3.3 8.2 + - + +
119J LEU* 3.1 22.0 + - + +
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Residues in contact with SER 116 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7J VAL* 4.0 5.4 - - - +
11J LEU* 4.2 7.4 - - - +
61J ARG* 3.0 27.0 + - - +
65J LEU* 3.8 7.6 - - - +
108J CYS* 3.8 15.0 - - - -
113J ASP* 2.7 36.0 + - - -
115J VAL* 1.3 77.7 - - - +
117J ARG* 1.3 60.3 + - - +
119J LEU* 3.3 7.6 + - - +
120J LEU* 3.0 28.8 + - - +
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Residues in contact with ARG 117 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109F GLU* 2.7 39.4 + - - -
114F TYR* 3.9 17.8 + - - +
117F ARG* 4.2 16.6 - - - +
117G ARG* 4.3 12.5 - - - +
105J ILE* 3.8 24.1 - - + +
106J VAL* 5.8 0.2 - - - +
108J CYS* 4.0 17.4 - - + +
109J GLU* 2.9 41.3 + - - +
113J ASP 3.1 13.4 + - - +
114J TYR* 3.5 12.8 - - + +
116J SER* 1.3 76.8 - - - +
118J ASP* 1.3 59.4 + - - +
120J LEU* 3.3 6.0 + - - +
121J LYS* 2.8 33.1 + - + +
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Residues in contact with ASP 118 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118F ASP* 5.6 1.7 - - - +
121G LYS* 2.8 42.8 + - + +
125G GLU* 4.3 10.9 - - - +
114J TYR 3.0 14.2 + - - +
115J VAL* 3.3 12.5 + - + +
117J ARG* 1.3 78.0 - - - +
119J LEU* 1.3 62.3 + - - +
121J LYS* 3.8 11.4 - - - +
122J ASP* 3.1 38.6 + - - +
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Residues in contact with LEU 119 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11J LEU* 5.2 2.0 - - + -
57J LYS* 4.1 24.9 - - + +
58J LEU* 3.7 18.4 - - + -
61J ARG* 3.8 38.6 - - + -
115J VAL* 3.1 12.7 + - + +
116J SER* 3.6 8.3 - - - +
118J ASP* 1.3 76.9 - - - +
120J LEU* 1.3 67.0 + - + +
122J ASP* 3.3 9.1 + - - +
123J ILE* 3.1 47.8 + - + +
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Residues in contact with LEU 120 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11J LEU* 3.8 26.7 - - + -
14J ILE* 4.0 12.3 - - + -
58J LEU* 4.2 13.0 - - + -
101J LEU* 3.6 24.3 - - + +
104J ALA* 3.6 30.1 - - + -
105J ILE* 3.7 16.8 - - + +
108J CYS* 3.9 20.4 - - - -
116J SER 3.0 22.1 + - - +
117J ARG* 3.8 1.1 - - - +
119J LEU* 1.3 76.8 - - + +
121J LYS* 1.3 58.4 + - - +
123J ILE* 3.4 5.4 + - + +
124J LEU* 2.8 30.0 + - - +
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Residues in contact with LYS 121 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114F TYR* 4.8 19.1 - - + +
115F VAL* 4.9 3.2 - - + +
118F ASP* 4.6 23.3 - - + +
105J ILE* 4.1 14.1 - - + +
117J ARG* 2.8 24.0 + - + +
118J ASP* 3.8 13.5 - - - +
119J LEU 3.3 0.2 - - - -
120J LEU* 1.3 77.8 - - - +
122J ASP* 1.3 60.2 + - - +
124J LEU* 3.3 5.8 + - - +
125J GLU* 3.0 29.2 + - + +
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Residues in contact with ASP 122 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118F ASP* 5.5 2.1 - - - +
54J HIS* 5.0 2.0 + - - -
118J ASP* 3.1 25.6 + - - +
119J LEU* 3.6 10.3 - - - +
120J LEU 3.3 0.2 - - - -
121J LYS* 1.3 77.3 - - - +
123J ILE* 1.3 64.8 + - + +
125J GLU* 3.4 8.1 + - - +
126J SER* 3.3 21.1 + - - -
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Residues in contact with ILE 123 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14J ILE* 4.9 0.7 - - + -
18J GLU* 3.4 22.9 - - - +
54J HIS* 3.8 35.2 - - + +
57J LYS* 5.6 3.6 - - + -
58J LEU* 4.0 25.4 - - + -
101J LEU* 4.0 17.7 - - + -
119J LEU* 3.1 38.3 + - + +
120J LEU* 3.6 11.9 - - + +
122J ASP* 1.3 75.7 - - + +
124J LEU* 1.3 57.4 + - - +
126J SER* 3.2 4.3 + - - -
127J GLU* 2.9 38.3 + - - +
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Residues in contact with LEU 124 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114F TYR* 4.1 26.5 - - + -
115F VAL* 3.9 12.8 - - + -
98J THR* 4.1 26.7 - - - +
101J LEU* 4.3 18.3 - - + +
102J ARG* 3.8 33.7 - - + +
105J ILE* 4.1 12.6 - - + -
120J LEU 2.8 20.3 + - - +
121J LYS* 3.3 6.0 + - - +
123J ILE* 1.3 73.2 - - - +
125J GLU* 1.3 58.8 + - - +
127J GLU* 3.3 2.1 + - + +
128J GLU* 2.9 45.6 + - + +
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Residues in contact with GLU 125 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115F VAL* 3.5 35.4 - - + +
118F ASP* 4.8 11.1 - - - +
121J LYS* 3.0 16.1 + - + +
122J ASP* 3.7 7.6 - - - +
123J ILE 3.3 0.4 - - - -
124J LEU* 1.3 79.2 - - - +
126J SER* 1.3 59.2 + - - +
128J GLU* 3.4 3.5 + - - +
129J GLU* 3.0 46.5 + - + +
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Residues in contact with SER 126 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50J ASP* 5.2 4.5 + - - +
54J HIS* 3.1 31.0 - - - -
122J ASP 3.3 9.6 + - - -
123J ILE 3.2 9.1 + - - -
125J GLU* 1.3 79.5 - - - +
127J GLU* 1.3 65.9 + - - +
129J GLU* 3.4 16.0 + - - +
130J HIS* 3.1 20.3 + - - +
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Residues in contact with GLU 127 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18J GLU* 2.9 19.9 - - - +
51J GLU* 2.5 32.2 - - - +
54J HIS* 3.9 6.0 + - - -
94J GLU* 3.0 30.9 - - - +
97J ALA* 4.9 7.5 - - + +
98J THR* 4.1 13.7 - - - +
101J LEU* 4.1 19.7 - - + -
123J ILE* 2.9 22.0 + - + +
124J LEU* 3.3 5.1 + - - +
126J SER* 1.3 79.9 + - - +
128J GLU* 1.3 57.3 + - - +
130J HIS* 3.0 7.9 + - - +
131J ILE* 2.9 31.5 + - - +
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Residues in contact with GLU 128 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61F ARG* 2.9 38.5 + - - +
64F PHE* 3.5 25.0 - - + -
113F ASP* 4.5 0.7 - - - +
115F VAL* 3.4 22.5 - - + +
98J THR* 4.7 4.3 - - - +
102J ARG* 2.8 35.8 + - - +
124J LEU* 2.9 25.8 + - + +
125J GLU* 3.8 4.9 - - - +
126J SER 3.3 0.2 - - - -
127J GLU* 1.3 74.8 - - - +
129J GLU* 1.3 59.6 + - - +
131J ILE* 3.2 10.8 + - + +
132J ASP* 2.9 25.3 + - - +
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Residues in contact with GLU 129 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125J GLU* 3.0 39.5 + - + +
126J SER* 3.6 15.8 - - - +
128J GLU* 1.3 75.0 - - - +
130J HIS* 1.3 62.6 + - - +
132J ASP* 3.2 9.4 + - - +
133J TYR* 3.0 22.9 + - - +
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Residues in contact with HIS 130 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25J TYR* 3.5 34.4 - + - -
44J GLU* 4.6 4.2 + - - -
47J GLU* 3.2 46.7 + - + +
90J ASP* 4.7 3.1 - - + -
94J GLU* 2.8 24.1 + - - +
126J SER 3.1 12.6 + - - +
127J GLU* 3.0 13.4 + - - +
129J GLU* 1.3 77.7 - - - +
131J ILE* 1.3 62.8 + - - +
133J TYR* 3.2 13.5 + + - -
134J LEU* 3.0 46.6 + - + +
----------------------------------------------------------
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Residues in contact with ILE 131 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64F PHE* 4.1 12.8 - - + -
91J LEU* 4.1 13.0 - - + -
94J GLU* 3.6 26.0 - - + +
95J LEU* 4.2 15.7 - - + -
98J THR* 3.6 26.5 - - + +
127J GLU 2.9 16.3 + - - +
128J GLU* 3.2 15.2 + - + +
130J HIS* 1.3 77.2 - - - +
132J ASP* 1.3 59.1 + - - +
134J LEU* 3.1 7.1 + - - +
135J GLU* 2.9 54.8 + - - +
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Residues in contact with ASP 132 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34E ASP* 4.4 12.8 - - - +
64F PHE* 3.5 35.0 - - + +
128J GLU 2.9 9.5 + - - +
129J GLU* 3.3 13.2 - - - +
131J ILE* 1.3 78.0 - - - +
133J TYR* 1.3 62.5 + - - +
135J GLU* 4.0 3.5 - - - +
136J THR* 2.7 38.8 + - - -
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Residues in contact with TYR 133 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40J LEU* 3.7 25.3 - - - +
43J HIS* 3.3 56.8 - + + +
44J GLU* 5.3 3.8 - - - -
47J GLU* 4.9 0.9 - - - +
87J LEU* 4.7 4.0 - - + +
129J GLU 3.0 13.3 + - - +
130J HIS* 3.6 16.8 - + + +
132J ASP* 1.3 77.9 - - - +
134J LEU* 1.3 78.6 + - + +
136J THR* 3.3 4.1 + - - -
137J GLN* 3.0 72.9 + - + +
153J HIS* 5.3 2.3 + - - -
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Residues in contact with LEU 134 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44J GLU* 5.6 0.4 - - - +
87J LEU* 3.9 35.2 - - + +
90J ASP* 3.9 18.8 - - + +
91J LEU* 3.7 33.0 - - + +
94J GLU* 4.1 7.9 - - + -
130J HIS* 3.0 43.2 + - + +
131J ILE* 3.1 6.9 + - - +
133J TYR* 1.3 93.9 - - + +
135J GLU* 1.3 66.6 + - - +
137J GLN* 3.1 5.3 + - - +
138J LEU* 3.0 30.3 + - + +
----------------------------------------------------------
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Residues in contact with GLU 135 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64F PHE* 4.7 12.8 - - - +
66F GLU* 4.4 18.4 - - - +
91J LEU* 4.1 23.5 - - + +
95J LEU* 5.4 4.5 - - - +
131J ILE* 2.9 36.4 + - - +
132J ASP* 4.1 2.6 - - - +
134J LEU* 1.3 76.3 - - - +
136J THR* 1.3 57.1 + - - +
138J LEU* 3.9 7.3 - - - +
139J GLY* 2.9 26.0 + - - -
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Residues in contact with THR 136 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33E ASN 5.2 0.7 - - - +
34E ASP* 3.3 14.9 + - - +
35E TRP* 3.6 6.3 - - - +
36E GLY* 3.4 37.5 - - - +
132J ASP* 2.7 31.4 + - - -
133J TYR* 3.5 6.9 - - - -
134J LEU 3.2 0.2 - - - -
135J GLU* 1.3 73.9 - - - +
137J GLN* 1.3 69.3 + - - +
139J GLY* 3.4 2.8 + - - -
140J LEU* 2.9 30.5 + - + +
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Residues in contact with GLN 137 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87J LEU* 4.1 15.3 - - + -
133J TYR* 3.0 68.5 + - + +
134J LEU 3.1 5.8 + - - +
136J THR* 1.3 88.2 - - - +
138J LEU* 1.3 62.0 + - - +
140J LEU* 3.2 12.0 + - - +
141J ILE* 3.1 27.6 + - - +
149J TYR* 2.7 43.1 + - + +
153J HIS* 3.9 11.3 + - - -
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Residues in contact with LEU 138 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84J GLN* 4.1 35.0 + - + +
87J LEU* 4.0 41.5 - - + +
88J GLN* 4.4 13.0 - - + +
91J LEU* 4.0 22.0 - - + -
134J LEU 3.0 29.5 + - - +
135J GLU* 3.9 4.9 - - - +
137J GLN* 1.3 72.2 - - - +
139J GLY* 1.3 64.9 + - - +
141J ILE* 3.3 16.8 + - + +
142J GLN* 3.4 16.3 + - - +
----------------------------------------------------------
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Residues in contact with GLY 139 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35E TRP 5.6 0.7 - - - -
135J GLU 2.9 15.5 + - - -
136J THR* 3.6 4.5 - - - -
138J LEU* 1.3 77.1 - - - +
140J LEU* 1.3 61.0 + - - +
142J GLN* 3.2 10.1 + - - +
143J LYS* 3.1 37.6 + - - +
----------------------------------------------------------
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Residues in contact with LEU 140 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35E TRP 3.3 21.1 - - - +
36E GLY* 4.0 13.5 - - - +
37E LEU* 4.0 15.9 - - + -
154E MET* 3.9 39.0 - - + -
136J THR* 2.9 30.2 + - + +
137J GLN* 3.2 22.6 + - - +
139J GLY* 1.3 71.2 - - - +
141J ILE* 1.3 62.5 + - - +
143J LYS* 3.6 8.5 - - + +
144J VAL* 2.8 42.1 + - + +
149J TYR* 4.0 10.3 - - + -
----------------------------------------------------------
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Residues in contact with ILE 141 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83J THR* 4.8 1.8 - - + -
84J GLN* 4.0 31.6 - - + +
87J LEU* 3.9 24.0 - - + -
137J GLN 3.1 15.6 + - - +
138J LEU* 3.5 17.7 - - + +
139J GLY 3.2 0.2 - - - -
140J LEU* 1.3 76.7 - - - +
142J GLN* 1.3 63.5 + - - +
145J GLY* 3.0 29.3 + - - -
146J LEU* 3.6 27.9 + - + +
149J TYR* 3.5 34.1 - - + -
----------------------------------------------------------
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Residues in contact with GLN 142 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147E GLU* 4.8 3.6 - - - +
84J GLN* 4.1 21.4 + - - +
138J LEU 3.7 12.1 - - - +
139J GLY* 3.2 10.7 + - - +
140J LEU 3.1 0.6 - - - -
141J ILE* 1.3 83.8 - - - +
143J LYS* 1.3 63.1 + - + +
144J VAL 3.5 0.2 + - - -
145J GLY* 3.8 4.3 + - - -
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Residues in contact with LYS 143 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35E TRP* 3.6 56.3 - - + +
37E LEU* 4.7 11.9 - - + -
146E LEU* 5.6 1.4 - - - +
147E GLU* 4.0 12.5 - - - +
150E LEU* 3.6 28.0 - - + +
139J GLY* 3.1 29.6 + - - +
140J LEU* 3.2 10.0 + - + +
142J GLN* 1.3 81.4 - - + +
144J VAL* 1.3 64.3 + - + +
----------------------------------------------------------
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Residues in contact with VAL 144 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147E GLU* 3.5 24.5 - - - +
150E LEU* 3.7 27.6 - - + -
151E GLN* 3.7 13.7 - - + +
154E MET* 4.2 17.7 - - - -
140J LEU* 2.8 28.7 + - + +
143J LYS* 1.3 81.2 - - + +
145J GLY* 1.3 66.7 + - - +
148J ASN* 3.1 31.4 + - + +
149J TYR* 3.8 20.6 - - + +
----------------------------------------------------------
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Residues in contact with GLY 145 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147E GLU* 4.0 15.6 + - - -
141J ILE 3.0 16.0 + - - -
142J GLN 3.8 3.6 + - - -
143J LYS 3.5 1.6 - - - -
144J VAL* 1.3 80.3 - - - +
146J LEU* 1.3 67.1 + - - -
147J GLU* 3.3 3.1 + - - -
148J ASN 3.4 1.0 + - - -
149J TYR* 3.0 22.0 + - - +
----------------------------------------------------------
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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