Contacts of the helix formed by residues 113 - 145 (chain C) 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 C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B ARG* 4.2 5.5 + - - +
128B GLU* 4.7 2.4 - - - +
4C ASP* 5.8 1.3 + - + -
7C VAL* 3.4 29.9 - - + +
61C ARG* 3.0 14.4 + - - -
65C LEU* 3.9 10.1 - - - +
108C CYS* 2.8 25.0 + - + +
111C VAL* 3.4 5.2 - - + -
112C HIS* 1.3 69.0 - - - +
114C TYR* 1.3 57.3 + - - +
115C VAL* 3.7 1.4 + - - +
116C SER* 2.6 40.6 + - - -
117C ARG* 3.0 22.0 + - - +
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Residues in contact with TYR 114 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B ARG* 4.2 14.3 - - + +
105B ILE* 3.6 37.4 - - + +
106B VAL* 3.3 16.5 + - - +
117B ARG* 3.8 22.3 + - - +
121B LYS* 4.6 15.7 - - + +
124B LEU* 4.1 16.2 - - + -
109C GLU* 3.7 34.8 + - - -
112C HIS* 3.2 60.3 + - + -
113C ASP* 1.3 72.0 + - - +
115C VAL* 1.3 60.1 + - - +
117C ARG* 3.4 8.5 - - - +
118C ASP* 2.9 30.5 + - - +
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Residues in contact with VAL 115 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B LYS* 4.8 4.7 - - + +
124B LEU* 3.8 14.1 - - + -
125B GLU* 3.8 47.1 - - + +
128B GLU* 3.4 39.7 - - + +
61C ARG* 3.6 15.5 - - - +
113C ASP* 3.3 1.0 + - - -
114C TYR* 1.3 75.2 - - - +
116C SER* 1.3 66.6 + - - +
118C ASP* 3.2 6.1 + - + +
119C LEU* 3.0 22.6 + - + +
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Residues in contact with SER 116 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C VAL* 3.9 9.6 - - - +
11C LEU* 3.9 8.4 - - - +
61C ARG* 2.9 27.4 + - - +
65C LEU* 3.9 3.3 - - - +
108C CYS* 3.8 15.5 - - - -
113C ASP* 2.6 37.9 + - - -
115C VAL* 1.3 76.5 - - - +
117C ARG* 1.3 65.3 + - - +
119C LEU* 3.3 9.1 + - - +
120C LEU* 3.0 24.1 + - - +
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Residues in contact with ARG 117 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B ARG* 4.0 17.1 - - - +
105C ILE* 3.7 25.6 - - + +
108C CYS* 4.1 14.6 - - + +
109C GLU* 2.6 40.2 + - - +
113C ASP 3.0 16.2 + - - +
114C TYR* 3.4 13.0 - - - +
115C VAL 3.2 0.2 - - - -
116C SER* 1.3 77.2 - - - +
118C ASP* 1.3 68.7 + - - +
120C LEU* 2.9 7.4 + - - +
121C LYS* 2.9 33.5 + - + +
109L GLU* 2.7 39.0 + - - -
114L TYR* 3.9 17.6 - - - +
117L ARG* 4.3 13.3 - - - +
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Residues in contact with ASP 118 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B ASP* 5.1 3.1 - - - +
121B LYS* 3.4 30.8 - - + +
125B GLU* 5.4 5.4 - - - +
114C TYR 2.9 16.6 + - - +
115C VAL* 3.8 6.5 - - + +
116C SER 3.2 0.2 - - - -
117C ARG* 1.3 86.1 - - - +
119C LEU* 1.3 62.2 + - - +
121C LYS* 3.4 8.9 + - - +
122C ASP* 3.2 38.9 + - - +
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Residues in contact with LEU 119 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C LEU* 5.6 2.9 - - + -
57C LYS* 4.0 31.9 - - + +
58C LEU* 4.4 11.9 - - + -
61C ARG* 3.8 37.7 - - + -
115C VAL* 3.0 12.4 + - + +
116C SER* 3.4 10.5 - - - +
118C ASP* 1.3 79.4 - - - +
120C LEU* 1.3 63.0 + - + +
122C ASP* 3.4 8.1 + - + +
123C ILE* 3.2 42.5 + - + +
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Residues in contact with LEU 120 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C LEU* 3.9 25.8 - - + -
14C ILE* 4.1 10.3 - - + -
58C LEU* 4.3 12.6 - - + -
101C LEU* 3.6 27.9 - - + +
104C ALA* 3.7 28.9 - - + -
105C ILE* 3.6 21.1 - - + -
108C CYS* 3.9 21.3 - - - -
116C SER 3.0 15.5 + - - +
117C ARG 2.9 4.4 + - - +
119C LEU* 1.3 80.0 - - + +
121C LYS* 1.3 57.5 + - - +
123C ILE* 3.3 6.3 + - + +
124C LEU* 2.9 28.2 + - - +
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Residues in contact with LYS 121 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105C ILE* 4.1 10.5 - - + +
117C ARG* 2.9 21.9 + - + +
118C ASP* 3.9 11.7 - - - +
119C LEU 3.2 0.2 - - - -
120C LEU* 1.3 75.9 - - - +
122C ASP* 1.3 61.0 + - - +
124C LEU* 3.3 8.6 + - + +
125C GLU* 2.9 30.2 + - + +
114L TYR* 4.4 26.2 - - + +
115L VAL* 4.8 3.2 - - + +
118L ASP* 4.6 19.7 - - + +
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Residues in contact with ASP 122 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C HIS* 5.0 1.3 + - - -
118C ASP* 3.2 24.8 + - - +
119C LEU* 3.7 9.8 - - + +
121C LYS* 1.3 75.5 - - - +
123C ILE* 1.3 64.6 + - + +
125C GLU* 3.5 14.4 + - - +
126C SER* 3.3 20.8 + - - -
118L ASP* 5.3 3.8 - - - +
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Residues in contact with ILE 123 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C ILE* 4.9 0.2 - - + -
18C GLU* 3.4 22.7 - - - +
54C HIS* 3.9 34.1 - - + +
57C LYS* 5.6 1.8 - - + -
58C LEU* 4.0 28.3 - - + -
101C LEU* 4.0 20.0 - - + -
119C LEU* 3.2 36.9 + - + +
120C LEU* 3.6 11.9 - - + +
122C ASP* 1.3 73.4 - - + +
124C LEU* 1.3 61.5 + - - +
126C SER* 3.1 4.7 + - - -
127C GLU* 2.8 39.2 + - - +
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Residues in contact with LEU 124 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C THR* 3.6 24.7 - - - +
101C LEU* 4.2 24.9 - - + +
102C ARG* 3.8 30.5 - - + +
105C ILE* 4.2 13.5 - - + -
120C LEU 2.9 14.9 + - - +
121C LYS* 3.3 8.7 + - - +
123C ILE* 1.3 77.0 - - - +
125C GLU* 1.3 57.1 + - - +
127C GLU* 3.1 1.4 + - - +
128C GLU* 2.8 40.5 + - + +
114L TYR* 4.0 25.4 - - + -
115L VAL* 3.8 14.8 - - + -
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Residues in contact with GLU 125 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C LYS* 2.9 18.2 + - + +
122C ASP* 3.6 14.7 - - - +
123C ILE 3.3 0.2 - - - -
124C LEU* 1.3 75.1 - - - +
126C SER* 1.3 63.5 + - - +
128C GLU* 3.4 3.7 + - - +
129C GLU* 3.1 44.2 + - + +
115L VAL* 3.8 29.8 - - + +
118L ASP* 4.8 10.7 - - - +
----------------------------------------------------------
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Residues in contact with SER 126 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C ASP* 5.2 6.1 + - - +
51C GLU* 5.1 0.2 + - - -
54C HIS* 3.0 32.7 - - - -
122C ASP 3.3 9.7 + - - -
123C ILE 3.1 7.9 + - - -
125C GLU* 1.3 83.2 - - - +
127C GLU* 1.3 61.9 + - - +
129C GLU* 3.3 15.2 + - - +
130C HIS* 3.1 21.0 + - - +
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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* 3.1 17.6 - - - +
51C GLU* 2.5 30.6 - - - +
54C HIS* 3.6 6.9 + - - -
94C GLU* 2.5 41.0 - - - +
97C ALA* 5.0 6.5 - - + -
98C THR* 4.1 14.8 - - - +
101C LEU* 4.0 13.2 - - + -
123C ILE* 2.8 30.8 + - + +
124C LEU* 3.7 4.3 - - - +
126C SER* 1.3 73.8 + - - +
128C GLU* 1.3 58.5 + - - +
130C HIS* 3.1 7.5 + - - +
131C ILE* 2.9 31.6 + - - +
----------------------------------------------------------
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Residues in contact with GLU 128 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C THR* 4.5 4.7 - - + +
102C ARG* 2.9 35.2 + - - +
124C LEU* 2.8 26.2 + - + +
125C GLU* 3.8 5.6 - - - +
126C SER 3.2 0.2 - - - -
127C GLU* 1.3 78.8 - - - +
129C GLU* 1.3 56.2 + - - +
131C ILE* 3.3 12.6 + - + +
132C ASP* 2.9 24.4 + - - +
61L ARG* 2.9 39.3 + - - +
64L PHE* 3.6 22.2 - - + -
113L ASP* 4.7 0.7 - - - +
115L VAL* 3.3 22.5 - - + +
----------------------------------------------------------
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Residues in contact with GLU 129 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125C GLU* 3.1 41.1 + - + +
126C SER* 3.6 14.8 - - - +
128C GLU* 1.3 76.9 - - + +
130C HIS* 1.3 63.4 + - - +
132C ASP* 3.3 9.1 + - - +
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* 3.6 34.2 - + - -
44C GLU* 4.6 3.0 + - - -
47C GLU* 3.3 44.5 + - + +
51C GLU* 6.0 0.4 - - - -
90C ASP* 4.5 2.9 - - + -
94C GLU* 3.0 23.6 + - - +
126C SER 3.1 12.9 + - - +
127C GLU* 3.5 11.4 - - - +
129C GLU* 1.3 74.7 - - - +
131C ILE* 1.3 64.4 + - - +
133C TYR* 3.3 14.4 + + - -
134C LEU* 3.0 49.2 + - + +
----------------------------------------------------------
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Residues in contact with ILE 131 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C LEU* 4.0 14.1 - - + -
94C GLU* 3.6 32.3 - - + +
95C LEU* 4.4 13.7 - - + -
98C THR* 3.7 25.8 - - + +
127C GLU 2.9 19.1 + - - +
128C GLU* 3.5 15.3 - - + +
130C HIS* 1.3 74.4 - - - +
132C ASP* 1.3 63.1 + - - +
134C LEU* 3.3 6.6 + - - +
135C GLU* 3.0 47.5 + - - +
64L PHE* 4.3 11.7 - - + -
----------------------------------------------------------
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Residues in contact with ASP 132 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128C GLU 2.9 9.7 + - - +
129C GLU* 3.4 12.7 - - - +
130C HIS 3.2 0.2 - - - -
131C ILE* 1.3 76.4 - - - +
133C TYR* 1.4 53.7 + - - +
135C GLU* 3.9 4.0 - - - +
136C THR* 2.6 46.7 + - - -
34K ASP* 4.3 13.7 - - - +
64L PHE* 3.6 34.3 - - + +
----------------------------------------------------------
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Residues in contact with TYR 133 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C LEU* 3.8 21.8 - - - +
43C HIS* 3.3 56.9 - + + +
44C GLU* 5.3 4.0 - - - -
47C GLU* 5.0 0.9 - - - +
87C LEU* 4.8 3.8 - - + -
129C GLU 3.1 13.6 + - - +
130C HIS* 3.6 15.9 - + - +
132C ASP* 1.4 76.0 - - - +
134C LEU* 1.3 79.6 + - + +
136C THR* 3.3 4.7 + - - -
137C GLN* 2.8 76.4 + - + +
153C HIS* 5.1 3.5 + - - -
----------------------------------------------------------
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Residues in contact with LEU 134 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C GLU* 5.5 0.4 - - - +
87C LEU* 3.9 29.3 - - + +
90C ASP* 3.9 19.5 - - + +
91C LEU* 3.7 39.7 - - + +
94C GLU* 4.2 4.3 - - + -
130C HIS* 3.0 53.5 + - + +
131C ILE* 3.6 6.7 - - - +
133C TYR* 1.3 85.9 - - + +
135C GLU* 1.3 64.6 + - - +
137C GLN* 3.2 6.3 + - - +
138C LEU* 3.1 29.5 + - + +
----------------------------------------------------------
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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* 4.1 22.2 - - + +
95C LEU* 5.4 3.1 - - - +
131C ILE* 3.0 37.5 + - - +
132C ASP* 4.1 3.2 - - - +
134C LEU* 1.3 72.8 - - - +
136C THR* 1.4 58.1 - - - +
138C LEU* 3.4 8.3 + - - +
139C GLY* 3.0 26.2 + - - -
64L PHE* 4.4 14.6 - - - +
66L GLU* 4.0 19.9 - - - +
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Residues in contact with THR 136 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C ASP* 2.6 32.5 + - - -
133C TYR* 3.4 7.6 - - - -
135C GLU* 1.4 77.8 - - - +
137C GLN* 1.3 70.8 + - - +
139C GLY* 3.3 2.9 + - - -
140C LEU* 2.9 24.2 + - + +
33K ASN 5.0 0.8 + - - +
34K ASP* 3.4 14.6 + - - +
35K TRP* 3.6 6.0 - - - +
36K GLY* 3.5 37.5 - - - +
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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
----------------------------------------------------------
87C LEU* 3.9 16.6 - - + -
133C TYR* 2.8 71.3 + - + +
134C LEU* 3.2 6.0 + - - +
136C THR* 1.3 83.8 - - - +
138C LEU* 1.3 58.1 + - - +
140C LEU* 3.1 12.9 + - - +
141C ILE* 2.9 33.3 + - - +
149C TYR* 2.7 42.6 + - - +
153C HIS* 3.9 11.3 + - - -
154K MET* 5.4 0.2 - - - +
----------------------------------------------------------
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Residues in contact with LEU 138 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C GLN* 3.4 35.9 + - - +
87C LEU* 3.7 40.8 - - + +
88C GLN* 4.1 11.7 - - - +
91C LEU* 4.0 25.4 - - + -
134C LEU 3.1 23.2 + - - +
135C GLU* 3.7 5.8 - - - +
137C GLN* 1.3 74.7 - - - +
139C GLY* 1.3 61.7 + - - +
141C ILE* 3.3 15.1 + - + +
142C GLN* 3.4 19.7 + - - +
----------------------------------------------------------
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Residues in contact with GLY 139 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135C GLU 3.0 14.5 + - - -
136C THR* 3.6 4.9 - - - -
137C GLN 3.2 0.2 - - - -
138C LEU* 1.3 74.8 - - - +
140C LEU* 1.3 62.7 + - - +
142C GLN* 3.3 8.7 + - - +
143C LYS* 3.1 39.7 + - - +
35K TRP 5.5 0.4 - - - -
----------------------------------------------------------
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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* 2.9 22.3 + - + +
137C GLN* 3.1 26.6 + - - +
139C GLY* 1.3 77.5 - - - +
141C ILE* 1.3 63.9 + - - +
143C LYS* 4.3 7.6 - - + +
144C VAL* 2.9 35.9 + - + +
149C TYR* 3.8 10.3 - - + -
35K TRP 3.4 22.4 - - - +
36K GLY* 4.2 15.3 - - - +
37K LEU* 4.0 15.7 - - + -
154K MET* 3.9 35.9 - - + -
----------------------------------------------------------
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Residues in contact with ILE 141 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C THR* 4.8 1.6 - - + -
84C GLN* 4.3 18.4 - - - +
87C LEU* 3.9 24.5 - - + -
137C GLN 2.9 18.7 + - - +
138C LEU* 3.5 17.7 - - + +
139C GLY 3.2 0.2 - - - -
140C LEU* 1.3 76.7 - - - +
142C GLN* 1.3 71.8 + - - +
145C GLY* 3.0 28.9 + - - -
146C LEU* 4.2 32.1 - - + +
149C TYR* 3.5 35.7 - - + -
----------------------------------------------------------
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Residues in contact with GLN 142 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C GLN* 4.5 10.1 - - - +
138C LEU 3.6 13.8 + - - +
139C GLY* 3.3 9.1 + - - +
140C LEU 3.2 0.2 - - - -
141C ILE* 1.3 92.1 - - - +
143C LYS* 1.3 63.4 + - + +
145C GLY* 4.1 3.6 + - - -
147K GLU* 4.9 3.3 - - - +
----------------------------------------------------------
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Residues in contact with LYS 143 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139C GLY* 3.1 27.3 + - - +
140C LEU* 3.2 7.6 + - + +
142C GLN* 1.3 78.2 - - + +
144C VAL* 1.3 66.0 + - + +
35K TRP* 3.7 57.3 + - + +
37K LEU* 4.6 12.3 - - + -
146K LEU* 5.4 1.9 - - - +
147K GLU* 3.9 13.9 - - - +
150K LEU* 3.6 28.9 - - + +
----------------------------------------------------------
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Residues in contact with VAL 144 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140C LEU* 2.9 28.4 + - + +
143C LYS* 1.3 83.2 - - + +
145C GLY* 1.3 66.8 + - - +
148C ASN* 3.1 31.0 + - + +
149C TYR* 3.8 22.4 - - + +
147K GLU* 3.5 23.3 - - - +
150K LEU* 3.7 15.3 - - + +
151K GLN* 3.6 26.9 - - + +
154K MET* 4.3 16.8 - - - -
----------------------------------------------------------
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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 ILE 3.0 16.9 + - - -
142C GLN 4.1 2.4 + - - -
143C LYS 3.5 1.4 - - - -
144C VAL* 1.3 80.0 - - - +
146C LEU* 1.3 59.3 + - - -
147C GLU 3.3 2.2 - - - -
148C ASN 3.4 1.0 + - - -
149C TYR* 3.0 28.8 + - - +
147K GLU* 3.8 14.9 + - - -
----------------------------------------------------------
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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