Contacts of the helix formed by residues 88 - 117 (chain C) in PDB entry 1JI5
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 THR 88 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C GLY 5.0 0.5 + - - -
87C GLU* 1.3 76.9 - - - +
89C ALA* 1.3 67.9 + - + +
90C GLU* 3.4 29.8 - - + +
91C GLY* 3.4 15.3 - - - -
92C MET* 2.7 37.0 + - - +
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Residues in contact with ALA 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C VAL* 4.0 21.1 - - + -
31C LYS 3.5 27.7 + - - +
34C GLN* 5.2 12.1 - - + -
38C LEU* 5.2 4.2 - - + +
42C PHE* 4.9 1.0 - - - -
88C THR* 1.3 77.7 - - + +
90C GLU* 1.3 76.9 + - - +
92C MET* 3.2 5.9 + - - +
93C VAL* 3.1 27.3 + - - +
143C PHE* 5.9 1.6 - - + -
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Residues in contact with GLU 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A PRO* 5.8 3.8 - - - +
34C GLN* 5.5 7.7 - - - +
88C THR* 3.4 19.8 - - + +
89C ALA* 1.3 85.1 - - - +
91C GLY* 1.3 60.4 + - - +
93C VAL* 3.2 7.7 + - - +
94C GLU* 2.8 37.1 + - + +
143C PHE* 5.1 10.6 - - - -
144C LEU* 4.4 16.8 - - + +
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Residues in contact with GLY 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C GLU* 4.7 6.7 - - - -
88C THR* 3.0 22.9 + - - -
90C GLU* 1.3 80.9 - - - +
92C MET* 1.3 50.7 + - - +
94C GLU* 3.2 12.5 + - - +
95C ALA* 2.6 37.5 + - - +
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Residues in contact with MET 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C ASN* 4.4 1.6 - - - +
26C PHE* 3.2 67.3 - - + -
29C TYR* 3.9 17.3 - - + +
30C VAL* 3.8 40.6 - - - +
42C PHE* 3.7 7.6 - - + -
87C GLU* 3.8 25.1 - - + +
88C THR 2.7 24.4 + - - +
89C ALA 3.5 3.8 - - - +
91C GLY* 1.3 73.4 - - - +
93C VAL* 1.3 63.7 + - - +
95C ALA* 3.0 3.3 + - - +
96C ILE* 2.9 26.1 + - - +
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Residues in contact with VAL 93 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C LEU* 4.0 19.7 - - + -
42C PHE* 4.5 7.0 - - + -
89C ALA 3.1 16.4 + - - +
90C GLU* 3.6 5.4 - - - +
92C MET* 1.3 74.3 - - - +
94C GLU* 1.3 60.9 + - - +
96C ILE* 2.7 25.0 - - - +
97C MET* 3.0 14.6 + - - +
140C LEU* 3.6 30.7 - - + +
143C PHE* 3.9 31.2 - - + -
144C LEU* 3.7 22.0 - - + -
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Residues in contact with GLU 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C GLU* 2.8 20.3 + - - +
91C GLY* 3.4 11.1 - - - +
93C VAL* 1.3 77.5 - - - +
95C ALA* 1.3 61.9 + - - +
97C MET* 3.5 11.7 - - + +
98C LYS* 3.1 48.2 + - + +
144C LEU* 4.2 18.7 - - + +
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Residues in contact with ALA 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C LYS* 4.8 8.0 + - - +
26C PHE* 3.9 19.1 - - + -
81C GLN* 5.2 0.3 - - - +
87C GLU* 5.6 3.8 - - + +
91C GLY 2.6 21.1 + - - +
92C MET* 3.0 7.5 + - - +
94C GLU* 1.3 74.0 - - - +
96C ILE* 1.3 62.2 + - - +
98C LYS* 3.3 17.3 + - - +
99C ASP* 3.1 25.4 + - - -
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Residues in contact with ILE 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C LEU* 5.2 4.7 - - + -
22C LYS* 5.1 6.1 - - + -
23C LEU* 4.1 24.7 - - + -
26C PHE* 3.4 30.5 - - + -
42C PHE* 4.5 9.4 - - + -
45C LEU* 5.0 3.4 - - + -
92C MET 2.9 17.9 + - - +
93C VAL* 2.7 37.9 - - - +
95C ALA* 1.3 69.8 - - - +
97C MET* 1.3 63.6 + - - +
99C ASP* 3.3 15.2 - - + +
100C TYR* 2.8 47.7 + - + -
140C LEU* 4.2 19.1 - - + -
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Residues in contact with MET 97 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93C VAL 3.0 20.5 + - - +
94C GLU* 3.5 13.7 - - + +
96C ILE* 1.3 81.6 - - - +
98C LYS* 1.3 69.8 + - + +
100C TYR* 3.3 6.3 + - - +
101C GLU* 3.1 49.3 + - - +
137C ALA* 4.1 9.6 - - - +
140C LEU* 4.1 20.0 - - + -
141C ARG* 3.8 41.7 - - + +
144C LEU* 4.3 13.2 - - + -
145C ASN* 6.3 0.4 - - - +
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Residues in contact with LYS 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C GLU* 3.1 39.1 + - + +
95C ALA* 3.6 13.5 - - - +
96C ILE 3.2 0.2 - - - -
97C MET* 1.3 82.1 - - + +
99C ASP* 1.3 60.5 + - - +
101C GLU* 3.1 17.7 + - - +
102C MET* 2.8 52.1 + - + +
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Residues in contact with ASP 99 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C LEU* 4.1 11.7 - - + +
22C LYS* 2.7 31.9 + - - +
80C ILE* 3.9 24.9 - - + +
81C GLN* 2.5 30.9 + - - +
95C ALA 3.1 15.9 + - - +
96C ILE* 3.1 14.6 + - + +
98C LYS* 1.3 77.9 - - - +
100C TYR* 1.3 63.4 + - + +
102C MET* 3.4 13.3 + - - +
103C MET* 3.1 24.5 + - - +
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Residues in contact with TYR 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C TRP* 4.3 24.0 - + - -
19C LEU* 4.7 13.2 - - + -
23C LEU* 4.5 8.4 - - + +
45C LEU* 3.1 33.4 + - + +
48C GLU* 5.1 1.0 + - - -
96C ILE* 2.8 27.8 + - + -
97C MET* 3.5 8.3 - - - +
98C LYS 3.2 0.2 - - - -
99C ASP* 1.3 77.0 - - + +
101C GLU* 1.3 57.3 + - - +
103C MET* 3.0 23.3 + - - +
104C LEU* 3.0 18.0 + - - +
133C LEU* 4.0 34.8 - - + +
136C HIS* 3.8 39.2 - + + -
137C ALA* 4.7 6.7 - - + -
140C LEU* 4.3 17.3 - - + -
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Residues in contact with GLU 101 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97C MET* 3.1 32.6 + - - +
98C LYS* 3.5 19.9 - - - +
100C TYR* 1.3 71.9 - - - +
102C MET* 1.3 63.1 + - + +
103C MET 3.0 4.5 - - - -
104C LEU* 3.0 30.0 + - + +
105C VAL* 3.6 11.0 + - - +
137C ALA* 4.5 9.9 - - + -
141C ARG* 2.4 35.1 + - - +
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Residues in contact with MET 102 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C ILE* 6.1 2.5 - - + -
81C GLN* 3.8 20.4 - - - +
95C ALA 5.3 0.2 - - - +
98C LYS* 2.8 43.9 + - + +
99C ASP* 3.4 28.9 - - - +
101C GLU* 1.3 72.1 - - + +
103C MET* 1.3 56.7 + - - +
105C VAL* 3.0 29.4 - - + +
106C GLU* 3.7 8.5 + - - +
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Residues in contact with MET 103 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C GLN* 2.9 44.9 - - - +
15C ASP* 4.5 14.8 - - + +
16C TRP* 3.4 36.8 - - + +
19C LEU* 4.4 16.8 - - - -
80C ILE* 5.2 4.7 - - + -
99C ASP 3.1 11.8 + - - +
100C TYR* 3.0 14.4 + - - +
102C MET* 1.3 77.3 - - - +
104C LEU* 1.3 64.7 + - - +
105C VAL 3.2 1.8 - - - -
106C GLU* 3.2 10.2 + - + +
107C LEU* 2.9 44.5 + - + +
129C ILE* 4.4 0.9 - - + -
133C LEU* 4.1 7.2 - - + -
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Residues in contact with LEU 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100C TYR 3.0 16.7 + - - +
101C GLU* 3.0 23.0 + - + +
103C MET* 1.3 76.8 - - - +
105C VAL* 1.3 63.7 + - + +
107C LEU* 3.1 8.6 + - + +
108C LYS* 2.9 26.2 + - - +
130C TYR* 3.4 57.3 - - + +
133C LEU* 4.0 15.5 - - + -
134C GLU* 3.8 27.8 - - + +
137C ALA* 5.5 3.4 - - + -
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Residues in contact with VAL 105 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101C GLU 3.8 10.8 - - - +
102C MET* 3.0 22.2 - - - +
104C LEU* 1.3 78.5 - - + +
106C GLU* 1.3 81.3 + - + +
108C LYS* 3.1 13.6 + - + +
109C LYS* 3.0 38.7 + - - +
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Residues in contact with GLU 106 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C VAL* 4.8 5.0 - - - +
11C LYS* 2.8 44.4 - - - +
12C GLN* 5.4 6.4 + - - +
15C ASP* 3.4 9.0 - - - +
79C SER* 3.6 7.8 + - - -
102C MET 4.1 11.8 - - - +
103C MET* 3.2 15.2 + - + +
105C VAL* 1.3 85.9 - - + +
107C LEU* 1.3 57.9 + - - +
109C LYS* 3.6 13.9 + - + +
110C GLY* 2.9 23.4 + - - -
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Residues in contact with LEU 107 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C VAL* 6.1 0.9 - - + -
12C GLN* 3.9 22.9 - - + +
103C MET* 2.9 40.9 + - + +
104C LEU* 3.3 11.7 - - - +
105C VAL 3.0 0.2 - - - -
106C GLU* 1.3 76.4 - - - +
108C LYS* 1.3 67.4 + - - +
110C GLY* 2.8 13.2 + - - -
111C MET* 2.8 21.1 + - + +
126C LEU* 3.7 39.9 - - + +
129C ILE* 4.3 8.5 - - + -
130C TYR* 3.9 34.8 - - + +
133C LEU* 4.4 4.9 - - + -
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Residues in contact with LYS 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B ASP* 2.6 39.3 + - - -
121B MET* 6.1 2.9 - - - -
104C LEU 2.9 12.4 + - - +
105C VAL* 3.6 12.6 - - + +
107C LEU* 1.3 73.6 - - - +
109C LYS* 1.3 65.2 + - + +
111C MET* 3.1 18.0 + - + +
112C GLU* 3.0 23.6 + - - +
130C TYR* 3.2 39.5 + - + +
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Residues in contact with LYS 109 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105C VAL* 3.0 31.3 + - - +
106C GLU* 3.6 15.5 - - + +
108C LYS* 1.3 76.2 - - + +
110C GLY* 1.3 62.0 + - - +
112C GLU* 3.1 19.7 + - - +
113C ILE* 2.8 23.1 - - + +
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Residues in contact with GLY 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C VAL* 5.4 0.2 - - - +
8C VAL* 3.7 24.4 - - - +
106C GLU 2.9 13.3 + - - -
107C LEU 2.8 9.5 + - - -
109C LYS* 1.3 77.2 - - - +
111C MET* 1.3 55.0 + - - -
113C ILE* 3.4 9.9 - - - +
114C ALA* 3.1 27.4 + - - +
126C LEU* 3.8 10.4 - - - +
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Residues in contact with MET 111 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B GLU* 3.9 13.2 - - + +
121B MET* 3.7 27.4 - - + -
107C LEU* 2.8 16.6 + - + +
108C LYS* 3.1 21.9 + - + +
110C GLY* 1.3 71.6 - - - +
112C GLU* 1.3 66.4 + - - +
114C ALA* 3.5 3.8 - - - +
115C GLN* 2.8 38.4 + - - +
123C SER* 3.3 29.4 - - - +
126C LEU* 3.9 9.9 - - + -
127C LEU* 3.9 15.3 - - - +
130C TYR* 3.7 34.5 - - + -
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Residues in contact with GLU 112 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C LYS 3.0 13.1 + - - +
109C LYS* 3.1 15.5 - - - +
111C MET* 1.3 80.8 - - - +
113C ILE* 1.3 57.2 + - + +
115C GLN* 3.1 13.9 + - - +
116C ASN* 2.8 53.6 + - - +
----------------------------------------------------------
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Residues in contact with ILE 113 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C GLN* 4.1 7.6 - - - +
5C VAL* 3.3 40.8 - - + -
8C VAL* 3.7 18.2 - - + -
109C LYS* 2.8 20.4 - - + +
110C GLY* 3.4 13.0 - - - +
112C GLU* 1.3 72.3 - - - +
114C ALA* 1.3 63.2 + - - +
116C ASN* 3.2 10.5 + - - +
117C SER* 2.8 42.8 + - - +
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Residues in contact with ALA 114 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C VAL* 4.2 18.4 - - + -
110C GLY 3.1 21.0 + - - +
111C MET* 3.5 6.1 - - - +
113C ILE* 1.3 81.6 - - - +
115C GLN* 1.3 62.7 + - - +
117C SER 3.2 7.3 + - - -
118C ASP 3.4 0.2 + - - -
119C ASP* 2.8 43.2 + - - +
122C THR* 4.6 2.7 - - + -
123C SER* 4.0 17.5 - - - +
126C LEU* 5.1 0.4 - - + -
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Residues in contact with GLN 115 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B GLU* 3.7 29.0 + - - +
111C MET* 2.8 29.5 + - - +
112C GLU* 3.3 15.6 + - - +
114C ALA* 1.3 77.8 - - - +
116C ASN* 1.3 62.4 + - - +
118C ASP* 3.0 18.5 + - - -
119C ASP 4.4 5.4 - - - +
120C GLU* 4.9 10.6 - - + +
123C SER* 3.9 16.8 + - - +
----------------------------------------------------------
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Residues in contact with ASN 116 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C GLU* 2.8 42.3 + - - +
113C ILE* 3.6 10.4 - - - +
115C GLN* 1.3 82.6 - - - +
117C SER* 1.3 58.2 + - - +
118C ASP* 3.1 3.6 + - - +
----------------------------------------------------------
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Residues in contact with SER 117 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C GLN* 4.6 7.3 + - - -
5C VAL* 3.8 21.6 - - - +
113C ILE* 2.8 24.2 + - - +
114C ALA 3.8 3.8 - - - -
115C GLN 3.2 0.6 - - - -
116C ASN* 1.3 77.2 - - - +
118C ASP* 1.3 71.3 + - - +
119C ASP* 3.4 3.8 + - - +
----------------------------------------------------------
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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