Contacts of the helix formed by residues 113 - 145 (chain C) in PDB entry 3GVY
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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C ASP* 5.6 3.2 + - + -
7C VAL* 3.4 20.2 - - + +
61C ARG* 3.0 21.3 + - - -
65C LEU* 4.4 7.6 - - - +
108C CYS* 3.1 14.4 + - + +
111C VAL* 3.2 21.1 - - + +
112C ARG* 1.3 74.9 - - - +
114C TYR* 1.3 61.2 + - - +
115C PRO* 3.6 4.2 - - - +
116C SER* 2.7 23.7 + - - -
117C LYS* 3.4 13.2 + - - +
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Residues in contact with TYR 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109C GLU* 3.4 33.1 + - - -
112C ARG* 3.4 47.0 + - + +
113C ASP* 1.3 72.0 - - - +
115C PRO* 1.4 68.5 - - + +
117C LYS* 3.0 28.2 + - + +
118C MET* 2.9 33.7 + - + +
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Residues in contact with PRO 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C ARG* 3.2 26.0 + - - +
113C ASP* 3.6 11.7 - - - +
114C TYR* 1.4 88.1 - - + +
116C SER* 1.3 62.8 + - - +
118C MET* 3.2 18.0 + - + +
119C LEU* 3.0 21.7 + - - +
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Residues in contact with SER 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C VAL* 3.9 10.6 - - - +
11C LEU* 4.6 8.7 - - - +
61C ARG* 2.8 31.8 + - - +
65C LEU* 4.3 1.7 - - - +
108C CYS* 3.7 15.7 - - - -
113C ASP* 2.7 29.0 + - - -
114C TYR 3.3 0.4 - - - -
115C PRO* 1.3 75.7 - - - +
117C LYS* 1.3 61.1 + - - +
119C LEU* 3.1 8.4 + - - +
120C PHE* 3.1 31.6 + - - -
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Residues in contact with LYS 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105C ARG* 2.9 50.6 - - - +
108C CYS* 3.9 10.9 - - + +
109C GLU* 3.1 26.5 - - + +
113C ASP 3.4 8.5 + - - +
114C TYR* 3.0 33.3 + - + +
116C SER* 1.3 78.7 - - - +
118C MET* 1.3 88.1 + - - +
119C LEU 3.3 0.2 + - - -
120C PHE* 3.4 5.2 + - - +
121C GLU* 2.9 39.0 + - - +
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Residues in contact with MET 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C TYR* 2.9 14.2 + - + +
115C PRO* 3.2 21.5 + - + +
117C LYS* 1.3 95.4 - - - +
119C LEU* 1.3 60.6 + - - +
121C GLU* 3.8 10.0 - - - +
122C GLU* 3.1 32.0 + - + +
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Residues in contact with LEU 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C LEU* 4.2 14.4 - - + -
57C LYS* 4.3 39.7 - - + +
58C LEU* 4.0 26.9 - - + -
61C ARG* 4.5 14.8 - - + -
115C PRO 3.0 12.0 + - - +
116C SER* 3.1 10.7 + - - +
118C MET* 1.3 76.3 - - - +
120C PHE* 1.3 56.5 + - + +
122C GLU* 3.0 8.0 + - + +
123C LEU* 2.6 42.7 + - + +
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Residues in contact with PHE 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C TYR* 4.3 2.5 - - + -
11C LEU* 3.5 45.1 - - + -
14C ALA* 3.9 24.2 - - + -
58C LEU* 4.8 0.7 - - + -
100C LEU* 6.2 0.2 - - + -
101C TYR* 4.0 15.9 - + - +
104C ALA* 3.5 27.6 - - + -
105C ARG* 3.6 27.1 - - + -
108C CYS* 3.8 24.0 - - - -
116C SER 3.1 19.0 + - - -
117C LYS 3.8 1.1 - - - +
119C LEU* 1.3 80.3 - - + +
121C GLU* 1.3 59.3 + - - +
123C LEU* 3.5 19.0 - - + +
124C ILE* 2.7 35.4 + - - +
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Residues in contact with GLU 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105C ARG* 2.7 48.2 + - + -
117C LYS* 2.9 32.3 + - - +
118C MET* 4.3 8.7 - - - +
119C LEU 3.1 0.2 - - - -
120C PHE* 1.3 79.2 - - - +
122C GLU* 1.3 63.9 + - + +
123C LEU 3.1 0.6 + - - -
124C ILE* 3.5 16.8 + - + +
125C ALA* 3.5 12.6 + - - +
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Residues in contact with GLU 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C MET* 3.1 22.1 + - + +
119C LEU* 3.0 9.8 + - + +
121C GLU* 1.3 78.7 - - + +
123C LEU* 1.3 59.4 + - - +
125C ALA* 4.0 10.7 + - - +
126C ASP* 3.4 25.7 + - - +
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Residues in contact with LEU 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C GLU* 3.6 13.0 - - - +
54C HIS* 3.7 17.0 - - + +
58C LEU* 4.3 22.2 - - + -
101C TYR* 3.0 52.3 - - + +
119C LEU* 2.6 27.4 + - + +
120C PHE* 3.5 24.7 - - + +
121C GLU 3.1 0.2 - - - -
122C GLU* 1.3 72.3 - - - +
124C ILE* 1.3 65.6 + - - +
126C ASP* 3.1 20.4 - - - +
127C GLU* 3.2 20.1 + - - +
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Residues in contact with ILE 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C ARG* 4.1 17.5 - - + +
101C TYR* 3.8 17.9 - - + +
102C ILE* 3.7 33.9 - - + +
105C ARG* 4.8 8.1 - - + -
120C PHE 2.7 25.7 + - - +
121C GLU* 3.9 11.4 - - + +
122C GLU 3.5 0.2 - - - -
123C LEU* 1.3 73.6 - - - +
125C ALA* 1.3 65.7 + - - +
127C GLU* 3.2 5.9 + - - +
128C GLU* 2.9 45.2 + - - +
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Residues in contact with ALA 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C GLU 3.5 12.2 + - - +
122C GLU* 4.1 13.5 - - - +
123C LEU 3.4 0.2 - - - -
124C ILE* 1.3 74.1 - - - +
126C ASP* 1.3 67.7 + - - +
127C GLU 3.2 0.2 + - - -
128C GLU* 3.2 8.6 + - - +
129C GLY* 2.9 22.3 + - - -
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Residues in contact with ASP 126 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C GLU* 3.1 30.7 - - - +
54C HIS* 2.5 36.3 + - + -
122C GLU 3.4 15.8 + - - +
123C LEU* 3.1 12.9 + - - +
125C ALA* 1.3 80.9 - - - +
127C GLU* 1.3 72.3 + - - +
129C GLY* 3.3 1.4 + - - -
130C HIS* 3.3 17.7 + - - +
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Residues in contact with GLU 127 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C GLU* 3.2 9.6 - - - +
50C GLU* 4.9 1.2 - - - +
51C GLU* 3.1 10.3 - - - +
54C HIS* 3.6 3.3 + - - -
94C GLU* 3.0 27.1 - - - +
97C ALA* 4.4 7.6 - - + +
98C ARG* 4.7 14.1 - - + +
101C TYR* 3.6 23.1 - - + -
123C LEU* 3.3 13.1 - - - +
124C ILE* 3.2 5.5 + - - +
126C ASP* 1.3 92.3 - - - +
128C GLU* 1.3 54.7 + - - +
130C HIS* 2.9 7.5 - - - +
131C ILE* 2.8 39.5 + - + +
162C FE 2.4 30.7 - - - -
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Residues in contact with GLU 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C ARG* 2.6 48.4 + - - +
124C ILE* 2.9 30.5 + - + +
125C ALA* 3.7 7.3 - - - +
127C GLU* 1.3 76.8 - - - +
129C GLY* 1.3 60.0 + - - +
131C ILE* 3.4 9.2 + - + +
132C ASP* 2.8 26.9 + - - +
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Residues in contact with GLY 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125C ALA 2.9 15.2 + - - -
126C ASP 3.9 1.3 - - - -
128C GLU* 1.3 73.9 - - - +
130C HIS* 1.3 64.9 + - - +
132C ASP* 3.4 10.3 - - - +
133C TYR* 3.1 21.8 + - - +
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Residues in contact with HIS 130 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C TYR* 2.3 48.1 + + - -
47C GLU* 2.9 38.5 + - + +
50C GLU* 3.4 16.8 + - - -
51C GLU* 4.1 7.5 + - - -
94C GLU* 3.0 18.8 + - - -
126C ASP 3.3 7.3 + - - +
127C GLU* 2.9 19.0 + - - +
129C GLY* 1.3 75.6 - - - +
131C ILE* 1.3 63.9 + - - +
133C TYR* 2.9 20.2 + + - +
134C LEU* 2.9 28.5 + - + +
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Residues in contact with ILE 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C LEU* 3.8 16.6 - - + -
94C GLU* 3.5 29.2 - - + +
95C HIS* 3.9 32.5 - - + +
98C ARG* 4.2 20.9 - - + -
127C GLU 2.8 26.3 + - - +
128C GLU* 3.4 10.5 - - + +
130C HIS* 1.3 74.1 - - - +
132C ASP* 1.3 64.5 + - - +
133C TYR 2.8 1.4 + - - -
134C LEU* 3.0 3.7 + - - +
135C GLU* 2.9 51.0 + - - +
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Residues in contact with ASP 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128C GLU 2.8 17.0 + - - +
129C GLY* 3.4 14.0 - - - +
131C ILE* 1.3 73.0 - - - +
133C TYR* 1.3 55.8 + - - +
135C GLU* 3.5 11.8 + - - +
136C THR* 2.9 36.6 + - - -
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Residues in contact with TYR 133 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C TYR* 6.4 0.2 - + - -
40C ILE* 3.4 22.3 - - + +
43C LYS* 3.2 50.6 - - + +
47C GLU* 5.3 4.3 - - + -
129C GLY 3.1 8.9 + - - +
130C HIS* 2.9 19.2 + + - +
131C ILE 2.8 0.8 + - - -
132C ASP* 1.3 77.8 - - - +
134C LEU* 1.3 96.8 + - + +
136C THR* 2.8 28.1 + - - -
137C GLN* 3.1 34.1 + - + +
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Residues in contact with LEU 134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C TYR* 3.9 12.8 - - + +
87C LEU* 4.1 22.7 - - + +
90C ASP* 3.8 21.5 - - + +
91C LEU* 3.6 47.3 - - + +
94C GLU* 4.1 9.2 - - + -
130C HIS* 2.9 20.9 + - + +
131C ILE 3.7 3.6 - - - +
133C TYR* 1.3 101.6 - - + +
135C GLU* 1.3 63.6 + - - +
136C THR 2.9 1.4 + - - -
137C GLN* 3.1 14.2 + - - +
138C ILE* 3.2 19.6 + - + +
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Residues in contact with GLU 135 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C LEU* 3.8 24.4 - - + +
95C HIS* 4.3 11.3 + - - -
131C ILE* 2.9 44.1 + - + +
132C ASP* 3.8 9.3 + - - +
134C LEU* 1.3 75.2 - - - +
136C THR* 1.3 57.9 + - - +
138C ILE* 4.5 5.3 - - - +
139C ASP* 3.0 27.1 + - - +
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Residues in contact with THR 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C ASP* 2.9 24.4 + - - -
133C TYR* 2.8 14.2 + - - -
135C GLU* 1.3 79.2 - - - +
137C GLN* 1.3 62.0 + - - +
138C ILE 3.2 0.9 - - - -
139C ASP* 3.3 9.0 + - + +
140C LEU* 2.7 38.9 + - + +
----------------------------------------------------------
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Residues in contact with GLN 137 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C ILE* 5.8 0.2 - - - -
87C LEU* 3.8 19.1 - - + -
133C TYR* 3.1 50.7 - - + +
134C LEU* 3.1 7.5 + - - +
136C THR* 1.3 80.5 - - - +
138C ILE* 1.3 56.6 - - - +
140C LEU* 3.0 10.7 + - - +
141C MET* 2.6 39.7 + - - +
149C TYR* 2.5 47.0 + - + +
153C ASN* 4.9 1.8 + - - +
----------------------------------------------------------
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Residues in contact with ILE 138 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C ARG* 5.5 2.5 - - + +
87C LEU* 3.9 20.9 - - + -
88C ASP* 3.9 35.2 - - - +
91C LEU* 4.1 24.2 - - + -
134C LEU* 3.2 16.4 + - + +
135C GLU* 4.5 4.0 - - - +
137C GLN* 1.3 76.2 - - - +
139C ASP* 1.3 63.3 + - - +
141C MET* 3.1 22.1 + - + +
142C GLY* 3.2 12.1 + - - -
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Residues in contact with ASP 139 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135C GLU 3.0 23.7 + - - +
136C THR* 3.3 12.8 + - + +
137C GLN 3.1 0.2 - - - -
138C ILE* 1.3 79.7 - - - +
140C LEU* 1.3 58.6 + - - +
142C GLY* 3.6 6.9 + - - -
143C SER* 3.6 15.8 + - - -
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Residues in contact with LEU 140 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136C THR* 2.7 23.3 + - + +
137C GLN* 3.5 10.3 - - - +
139C ASP* 1.3 71.5 - - - +
141C MET* 1.3 67.3 + - - +
143C SER* 3.2 15.4 + - - +
144C ILE* 3.2 47.2 + - + +
149C TYR* 3.9 22.0 - - + -
152C LEU* 4.5 12.1 - - + -
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Residues in contact with MET 141 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C LEU* 5.4 1.1 - - + -
84C ARG* 2.8 46.7 - - + -
87C LEU* 4.1 19.3 - - - -
137C GLN 2.6 20.5 + - - +
138C ILE* 3.1 15.7 + - + +
140C LEU* 1.3 73.8 - - - +
142C GLY* 1.3 62.6 + - - +
143C SER 3.0 1.2 + - - -
145C GLY* 3.2 30.9 + - - -
146C GLU* 3.5 44.3 + - + +
149C TYR* 3.7 31.0 - - + -
----------------------------------------------------------
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Residues in contact with GLY 142 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138C ILE 3.2 9.3 + - - -
139C ASP 3.6 4.5 + - - -
140C LEU 3.4 0.2 - - - -
141C MET* 1.3 77.9 - - - +
143C SER* 1.3 60.9 + - - +
145C GLY* 4.5 1.9 + - - -
146C GLU* 4.2 7.5 + - - -
----------------------------------------------------------
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Residues in contact with SER 143 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139C ASP* 3.6 13.4 + - - -
140C LEU* 3.2 13.8 + - - -
141C MET 3.0 3.2 - - - -
142C GLY* 1.3 80.1 - - - +
144C ILE* 1.3 66.0 + - - +
145C GLY 3.4 0.4 + - - -
----------------------------------------------------------
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Residues in contact with ILE 144 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140C LEU* 3.2 46.2 - - + +
143C SER* 1.3 78.6 - - - +
145C GLY* 1.3 56.6 + - - +
148C ASN* 2.7 40.4 + - + +
149C TYR* 3.7 32.1 - - + +
152C LEU* 4.5 9.9 - - + -
----------------------------------------------------------
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Residues in contact with GLY 145 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141C MET 3.2 13.2 + - - +
142C GLY 4.5 1.5 + - - -
143C SER 3.4 2.6 + - - -
144C ILE* 1.3 81.1 - - - +
146C GLU* 1.3 60.6 + - - -
147C GLN* 2.9 13.2 + - - -
148C ASN* 4.1 3.6 - - - -
149C TYR* 3.2 23.9 + - - +
----------------------------------------------------------
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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