Contacts of the helix formed by residues 113 - 145 (chain H) 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 H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4H ASP* 5.7 2.1 + - + +
7H VAL* 3.7 19.6 - - + +
61H ARG* 2.9 25.9 + - - -
65H LEU* 4.0 8.4 - - - +
108H CYS* 2.9 19.7 + - + +
111H VAL* 3.4 13.6 - - + +
112H HIS* 1.3 75.9 - - - +
114H TYR* 1.3 59.0 + - - +
115H VAL 3.6 1.7 + - - -
116H SER* 2.6 29.7 + - - -
117H ARG 3.1 14.0 + - - -
102W ARG* 4.2 4.3 - - - +
128W GLU* 4.7 2.6 - - - +
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Residues in contact with TYR 114 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109H GLU* 3.7 40.0 + - - -
112H HIS* 3.1 59.1 + - + -
113H ASP* 1.3 70.6 - - - +
115H VAL* 1.3 60.8 + - - +
117H ARG* 3.4 9.9 + - + +
118H ASP* 3.0 27.0 + - - +
102W ARG* 4.0 13.9 - - + +
105W ILE* 3.7 39.0 - - + -
106W VAL* 3.1 19.2 + - - +
117W ARG* 3.9 17.6 + - - +
121W LYS* 4.5 14.4 - - + +
124W LEU* 4.1 14.4 - - + -
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Residues in contact with VAL 115 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61H ARG* 3.4 32.3 - - - +
113H ASP* 3.2 1.4 + - - -
114H TYR* 1.3 75.7 - - - +
116H SER* 1.3 63.7 + - - +
118H ASP* 3.4 6.5 + - + +
119H LEU* 3.1 21.7 + - + +
121W LYS* 5.0 4.3 - - + +
124W LEU* 4.0 13.4 - - + +
125W GLU* 3.9 45.1 - - + +
128W GLU* 3.5 25.6 - - + +
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Residues in contact with SER 116 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7H VAL* 4.1 5.8 - - - +
11H LEU* 4.2 10.7 - - - +
61H ARG* 2.9 25.4 + - - +
65H LEU* 3.9 7.3 - - - +
108H CYS* 3.8 14.1 - - - -
113H ASP* 2.6 36.3 + - - -
115H VAL* 1.3 75.5 - - - +
117H ARG* 1.3 63.6 + - - +
119H LEU* 3.2 7.5 + - - +
120H LEU* 3.0 29.3 + - - +
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Residues in contact with ARG 117 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A GLU* 2.5 42.6 + - - -
114A TYR* 3.8 18.2 + - - +
117A ARG* 4.0 16.8 - - - +
105H ILE* 3.9 27.0 - - + +
108H CYS* 3.9 18.3 - - + -
109H GLU* 2.8 40.5 + - - +
113H ASP 3.1 13.4 + - - +
114H TYR* 3.6 13.5 - - - +
115H VAL 3.2 0.2 - - - -
116H SER* 1.3 79.0 - - - +
118H ASP* 1.3 57.6 + - - +
120H LEU* 3.3 5.8 + - - +
121H LYS* 2.8 32.8 + - + +
117W ARG* 4.1 14.6 - - - +
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Residues in contact with ASP 118 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114H TYR 3.0 17.4 + - - +
115H VAL* 3.6 8.5 - - + +
116H SER 3.3 0.2 - - - -
117H ARG* 1.3 74.7 - - - +
119H LEU* 1.3 65.3 + - - +
121H LYS* 3.3 12.9 + - - +
122H ASP* 3.0 38.2 + - - +
121W LYS* 2.6 45.0 + - + +
125W GLU* 4.5 13.6 - - - +
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Residues in contact with LEU 119 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11H LEU* 5.4 1.6 - - + -
57H LYS* 3.8 30.5 - - + +
58H LEU* 4.0 16.2 - - + -
61H ARG* 3.7 37.9 - - + -
115H VAL* 3.1 13.8 + - + +
116H SER* 3.5 7.9 - - - +
118H ASP* 1.3 75.0 + - - +
120H LEU* 1.3 68.1 + - + +
122H ASP* 3.2 8.8 + - - +
123H ILE* 3.1 43.6 + - + +
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Residues in contact with LEU 120 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10H HIS* 5.8 0.4 - - + -
11H LEU* 3.8 27.6 - - + -
14H ILE* 4.3 7.2 - - + -
58H LEU* 4.2 15.0 - - + -
101H LEU* 3.9 23.7 - - + +
104H ALA* 3.6 32.3 - - + -
105H ILE* 3.6 18.9 - - + +
108H CYS* 3.9 20.0 - - - -
116H SER 3.0 19.1 + - - +
117H ARG 3.6 1.1 - - - +
119H LEU* 1.3 78.1 - - + +
121H LYS* 1.3 58.0 + - - +
123H ILE* 3.3 5.3 + - + +
124H LEU* 2.8 30.0 + - - +
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Residues in contact with LYS 121 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A TYR* 4.4 23.6 - - + +
115A VAL* 5.0 3.0 - - + +
118A ASP* 3.7 36.1 - - + +
105H ILE* 4.0 12.0 - - + +
117H ARG* 2.8 22.3 + - + +
118H ASP* 3.3 13.9 + - - +
120H LEU* 1.3 78.5 - - - +
122H ASP* 1.3 67.3 + - - +
124H LEU* 3.3 5.3 + - + +
125H GLU* 3.0 31.3 + - + +
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Residues in contact with ASP 122 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A ASP* 5.2 1.6 - - - +
54H HIS* 5.5 0.4 - - - -
118H ASP* 3.0 30.2 + - - +
119H LEU* 3.7 9.7 - - - +
121H LYS* 1.3 84.3 - - - +
123H ILE* 1.3 67.3 + - + +
125H GLU* 3.4 12.4 + - - +
126H SER* 3.3 20.8 + - - -
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Residues in contact with ILE 123 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14H ILE* 4.9 1.1 - - + -
18H GLU* 3.6 22.2 - - - +
54H HIS* 3.8 31.0 - - + +
57H LYS* 5.6 3.4 - - + -
58H LEU* 4.0 26.5 - - + -
101H LEU* 4.0 14.4 - - + -
119H LEU* 3.1 36.0 + - + +
120H LEU* 3.6 11.2 - - + +
122H ASP* 1.3 76.8 - - + +
124H LEU* 1.3 66.2 + - - +
126H SER* 3.1 9.6 + - - -
127H GLU* 2.9 35.6 + - + +
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Residues in contact with LEU 124 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A TYR* 4.0 20.0 - - + -
115A VAL* 3.9 13.2 - - + -
98H THR* 3.6 25.1 - - - +
101H LEU* 4.3 24.4 - - + +
102H ARG* 3.9 27.8 - - + +
105H ILE* 3.9 20.9 - - + -
120H LEU 2.8 18.2 + - - +
121H LYS* 3.3 6.5 + - - +
123H ILE* 1.3 77.4 - - - +
125H GLU* 1.3 56.8 + - - +
127H GLU* 3.7 1.1 - - - +
128H GLU* 2.9 41.5 + - - +
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Residues in contact with GLU 125 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A VAL* 3.8 31.1 - - + +
118A ASP* 4.4 14.0 - - - +
121H LYS* 3.0 18.8 + - + +
122H ASP* 3.8 13.4 - - - +
123H ILE 3.2 0.2 - - - -
124H LEU* 1.3 76.1 - - - +
126H SER* 1.3 59.3 + - - +
128H GLU* 3.4 2.6 + - - +
129H GLU* 3.0 46.1 + - + +
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Residues in contact with SER 126 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50H ASP* 5.2 5.5 + - - +
54H HIS* 2.9 32.5 + - - -
122H ASP 3.3 10.7 + - - -
123H ILE 3.3 9.2 - - - -
125H GLU* 1.3 81.4 - - - +
127H GLU* 1.4 56.3 + - - +
129H GLU* 3.3 16.5 + - - +
130H HIS* 3.0 24.6 + - - +
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Residues in contact with GLU 127 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18H GLU* 2.5 28.0 - - - +
51H GLU* 2.7 24.4 - - - +
54H HIS* 3.6 7.3 + - - -
94H GLU* 2.6 40.4 - - - +
97H ALA* 5.2 6.5 - - + -
98H THR* 4.3 14.1 - - - +
101H LEU* 4.0 13.2 - - + -
123H ILE* 2.9 27.3 + - + +
124H LEU* 3.8 4.5 - - - +
126H SER* 1.4 76.0 - - - +
128H GLU* 1.3 58.3 + - - +
130H HIS* 3.0 7.0 + - - +
131H ILE* 2.8 32.3 + - - +
----------------------------------------------------------
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Residues in contact with GLU 128 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A ARG* 3.0 37.6 + - - +
64A PHE* 3.5 24.8 - - + -
65A LEU* 5.4 0.6 - - - +
113A ASP* 4.9 0.2 - - - +
115A VAL* 3.6 21.0 - - + +
98H THR* 4.4 6.3 - - - +
102H ARG* 2.9 34.9 + - - +
124H LEU* 2.9 25.4 + - + +
125H GLU* 3.7 6.1 - - - +
127H GLU* 1.3 74.7 - - - +
129H GLU* 1.3 60.9 + - - +
131H ILE* 3.3 10.4 + - + +
132H ASP* 2.9 23.9 + - - +
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Residues in contact with GLU 129 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125H GLU* 3.0 36.6 + - + +
126H SER* 3.3 17.2 + - - +
128H GLU* 1.3 75.2 - - - +
130H HIS* 1.3 63.2 + - - +
132H ASP* 3.4 9.1 + - - +
133H TYR* 3.2 22.2 + - - +
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Residues in contact with HIS 130 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25H TYR* 3.4 35.5 - + - -
44H GLU* 4.6 2.4 + - - -
47H GLU* 3.2 46.1 + - + +
51H GLU* 5.6 0.4 - - - -
90H ASP* 4.5 4.9 + - + -
94H GLU* 2.7 25.7 + - - +
126H SER 3.0 11.5 + - - +
127H GLU* 3.0 13.0 + - - +
129H GLU* 1.3 77.7 - - - +
131H ILE* 1.3 62.4 + - - +
133H TYR* 3.2 8.5 + + - +
134H LEU* 3.0 51.2 + - + +
----------------------------------------------------------
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Residues in contact with ILE 131 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A PHE* 4.2 12.1 - - + -
91H LEU* 3.9 11.7 - - + -
94H GLU* 3.7 31.9 - - + +
95H LEU* 4.2 14.4 - - + -
98H THR* 3.9 22.9 - - + +
127H GLU 2.8 17.8 + - - +
128H GLU* 3.5 15.0 - - + +
130H HIS* 1.3 77.2 - - - +
132H ASP* 1.3 56.9 + - - +
134H LEU* 3.3 6.3 + - - +
135H GLU* 2.9 52.7 + - - +
----------------------------------------------------------
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Residues in contact with ASP 132 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A PHE* 3.4 35.6 - - + +
34B ASP* 4.6 10.9 - - - +
128H GLU 2.9 12.1 + - - +
129H GLU* 3.6 10.7 - - - +
130H HIS 3.3 0.2 - - - -
131H ILE* 1.3 73.7 - - - +
133H TYR* 1.3 63.5 + - - +
135H GLU* 4.1 3.2 - - - +
136H THR* 2.6 44.6 + - - -
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Residues in contact with TYR 133 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40H LEU* 3.8 21.7 - - - +
43H HIS* 3.4 56.5 - + + +
44H GLU* 5.3 4.0 - - - -
47H GLU* 4.8 1.1 - - - +
87H LEU* 4.6 4.4 - - + +
129H GLU 3.2 10.2 + - - +
130H HIS* 3.2 16.8 + + + +
132H ASP* 1.3 81.0 - - - +
134H LEU* 1.3 79.1 + - + +
136H THR* 3.3 4.2 + - - -
137H GLN* 2.8 75.8 + - + +
153H HIS* 5.3 3.1 + - - -
----------------------------------------------------------
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Residues in contact with LEU 134 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44H GLU* 5.5 0.4 - - - +
87H LEU* 3.9 31.1 - - + +
90H ASP* 4.1 13.0 - - + +
91H LEU* 3.9 30.3 - - + +
94H GLU* 4.1 6.5 - - + -
130H HIS* 3.0 58.2 + - + +
131H ILE* 3.6 6.5 - - - +
133H TYR* 1.3 91.6 - - + +
135H GLU* 1.3 65.6 + - - +
137H GLN* 3.2 5.5 + - - +
138H LEU* 3.1 31.5 + - + +
----------------------------------------------------------
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Residues in contact with GLU 135 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A PHE* 4.8 9.8 - - + +
66A GLU* 2.9 26.7 - - - +
91H LEU* 4.1 24.5 - - + +
95H LEU* 5.4 4.7 - - - +
131H ILE* 2.9 40.5 + - - +
132H ASP* 4.1 4.3 - - - +
134H LEU* 1.3 72.0 - - - +
136H THR* 1.3 58.8 + - - +
138H LEU* 3.5 7.7 + - - +
139H GLY* 3.0 25.5 + - - -
----------------------------------------------------------
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Residues in contact with THR 136 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ASN 4.9 0.9 - - - +
34B ASP* 3.2 15.9 + - - +
35B TRP* 3.6 6.5 - - - +
36B GLY* 3.6 36.6 - - - +
132H ASP* 2.6 31.9 + - - -
133H TYR* 3.4 6.3 - - - -
135H GLU* 1.3 74.3 - - - +
137H GLN* 1.3 75.9 + - - +
139H GLY* 3.3 1.9 + - - +
140H LEU* 2.8 24.2 + - + +
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Residues in contact with GLN 137 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B MET* 5.4 0.2 - - - +
87H LEU* 4.0 15.5 - - + -
133H TYR* 2.8 73.9 + - + +
134H LEU 3.2 4.7 + - - +
136H THR* 1.3 83.7 - - - +
138H LEU* 1.3 63.6 + - - +
140H LEU* 3.0 13.7 + - - +
141H ILE* 3.0 28.1 + - - +
149H TYR* 2.7 43.0 + - + +
153H HIS* 3.9 11.3 + - - -
----------------------------------------------------------
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Residues in contact with LEU 138 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84H GLN* 3.9 28.1 + - + +
87H LEU* 3.7 33.2 - - + +
88H GLN* 4.0 27.4 - - + +
91H LEU* 3.9 27.4 - - + -
134H LEU 3.1 21.7 + - - +
135H GLU* 3.8 5.2 - - - +
137H GLN* 1.3 79.9 - - - +
139H GLY* 1.3 58.9 + - - +
141H ILE* 3.4 8.7 + - + +
142H GLN* 3.4 27.5 + - - +
----------------------------------------------------------
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Residues in contact with GLY 139 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B TRP 5.3 0.9 - - - -
135H GLU 3.0 14.6 + - - -
136H THR* 3.7 2.9 - - - -
138H LEU* 1.3 75.0 - - - +
140H LEU* 1.3 58.6 + - - +
142H GLN* 3.2 13.4 + - - +
143H LYS* 2.9 47.3 + - - +
----------------------------------------------------------
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Residues in contact with LEU 140 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B TRP 3.2 24.4 + - - +
36B GLY* 3.9 19.3 - - - +
37B LEU* 4.1 13.9 - - + -
38B LYS* 6.5 0.2 - - - -
154B MET* 3.8 44.4 - - + -
136H THR* 2.8 15.1 + - + +
137H GLN* 3.0 27.8 + - - +
139H GLY* 1.3 75.0 - - - +
141H ILE* 1.3 59.0 + - - +
143H LYS* 4.2 6.3 - - + +
144H VAL* 2.7 45.1 + - + +
149H TYR* 3.9 9.4 - - + -
----------------------------------------------------------
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Residues in contact with ILE 141 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83H THR* 4.9 0.9 - - + -
84H GLN* 3.4 37.2 - - - +
87H LEU* 4.1 22.0 - - + -
137H GLN 3.0 15.4 + - - +
138H LEU* 3.6 14.4 - - + +
139H GLY 3.4 0.2 - - - -
140H LEU* 1.3 74.7 - - - +
142H GLN* 1.3 60.1 + - + +
145H GLY* 2.9 30.0 + - - -
146H LEU* 3.8 31.4 + - + +
149H TYR* 3.6 38.1 - - + -
----------------------------------------------------------
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Residues in contact with GLN 142 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B GLU* 4.7 4.9 - - - +
84H GLN* 5.8 2.9 - - - +
138H LEU* 3.4 17.7 + - - +
139H GLY* 3.2 13.0 + - - +
140H LEU 3.1 0.4 - - - -
141H ILE* 1.3 83.1 - - + +
143H LYS* 1.3 63.2 + - + +
145H GLY* 4.3 2.1 + - - -
----------------------------------------------------------
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Residues in contact with LYS 143 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B TRP* 3.6 57.2 - - + +
37B LEU* 4.7 12.6 - - + -
146B LEU* 5.6 1.2 - - - +
147B GLU* 3.6 13.9 - - - +
150B LEU* 3.7 25.6 - - + +
139H GLY* 2.9 33.5 + - - +
140H LEU* 3.2 4.9 + - + +
142H GLN* 1.3 81.3 - - + +
144H VAL* 1.3 66.0 + - + +
----------------------------------------------------------
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Residues in contact with VAL 144 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B LEU* 5.0 0.2 - - + -
147B GLU* 3.3 35.1 - - - +
150B LEU* 3.6 16.8 - - + +
151B GLN* 3.6 26.0 - - + +
154B MET* 4.2 18.6 - - + -
140H LEU* 2.7 29.7 + - + +
143H LYS* 1.3 78.1 - - + +
145H GLY* 1.3 69.6 - - - +
148H ASN* 3.4 19.5 + - + +
149H TYR* 3.7 21.5 - - + +
----------------------------------------------------------
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Residues in contact with GLY 145 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B GLU* 3.9 15.1 + - - -
141H ILE 2.9 17.6 + - - -
142H GLN 4.3 1.3 + - - -
143H LYS 3.5 1.4 - - - -
144H VAL* 1.3 81.2 - - - +
146H LEU* 1.3 66.5 + - - -
147H GLU 3.4 2.4 + - - -
148H ASN 3.5 1.3 + - - -
149H TYR* 3.0 23.4 + - - +
----------------------------------------------------------
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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