Contacts of the helix formed by residues 113 - 149 (chain F) in PDB entry 3IZ0
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 LYS 113 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40F PRO* 4.2 1.6 - - - -
105F GLU* 4.9 6.3 + - - +
107F ALA* 4.0 19.4 + - - +
108F ASP* 4.9 5.7 + - - +
111F CYS* 2.7 34.1 + - - +
112F PRO* 1.3 74.4 - - + +
114F ALA* 1.3 60.0 + - - +
115F LYS* 3.5 1.1 - - + +
116F ARG* 4.4 31.3 - - + +
117F THR* 2.7 37.2 + - - +
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Residues in contact with ALA 114 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11F VAL* 5.8 1.0 - - - +
36F LEU 4.5 4.4 - - - +
37F TYR* 4.0 26.9 - - + -
38F PRO* 3.6 23.2 + - + +
40F PRO* 4.1 12.0 - - - +
113F LYS* 1.3 73.2 - - - +
115F LYS* 1.3 62.8 + - + +
117F THR* 3.4 4.8 + - - -
118F SER* 3.0 30.2 + - - -
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Residues in contact with LYS 115 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7F PRO* 5.0 1.9 - - - +
37F TYR* 6.4 1.3 - - + -
113F LYS* 3.5 1.4 - - + +
114F ALA* 1.3 81.0 - - + +
116F ARG* 1.3 67.6 + - + +
118F SER* 3.2 9.3 + - - -
119F ARG* 2.9 23.8 + - - +
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Residues in contact with ARG 116 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4F LEU* 5.9 1.8 - - - +
103F ASP* 2.9 47.0 + - - +
105F GLU* 3.8 17.7 + - - +
108F ASP* 3.1 33.6 + - - +
113F LYS* 3.6 28.5 + - + +
114F ALA 3.5 0.2 - - - -
115F LYS* 1.3 77.3 - - + +
117F THR* 1.3 64.3 + - + +
119F ARG* 3.0 22.0 + - - +
120F PHE* 3.0 38.3 + - + -
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Residues in contact with THR 117 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36F LEU* 4.8 2.8 + - - +
40F PRO* 3.7 14.6 - - - +
45F LEU* 3.7 32.3 - - + +
49F TYR* 3.8 13.5 - - - +
108F ASP* 4.3 9.4 - - + +
112F PRO* 3.8 11.2 - - + -
113F LYS 2.7 29.6 + - - +
114F ALA 3.4 5.2 + - - -
116F ARG* 1.3 78.8 - - + +
118F SER* 1.3 57.9 + - - +
120F PHE* 3.7 12.1 - - + +
121F LEU* 3.0 35.3 + - - +
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Residues in contact with SER 118 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7F PRO* 4.1 13.6 - - - +
9F TYR 4.6 2.0 + - - -
10F ASN* 5.7 0.6 - - - -
11F VAL* 4.7 15.3 - - - -
14F ILE* 3.6 23.3 - - - +
114F ALA 3.0 17.5 + - - -
115F LYS* 3.3 10.2 + - - -
117F THR* 1.3 76.1 - - - +
119F ARG* 1.3 64.4 + - - +
121F LEU* 4.5 3.6 - - - +
122F SER* 3.2 27.0 + - - -
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Residues in contact with ARG 119 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4F LEU* 3.4 42.9 - - - +
5F SER 4.7 8.7 - - - +
7F PRO* 3.9 24.2 - - + -
101F VAL* 4.1 12.7 - - + +
103F ASP* 2.3 45.5 + - - -
115F LYS 2.9 12.9 + - - +
116F ARG* 3.0 29.3 + - - +
118F SER* 1.3 74.8 + - - +
120F PHE* 1.3 89.4 + - + +
122F SER* 3.4 4.0 + - - -
123F GLY* 3.1 18.5 + - - -
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Residues in contact with PHE 120 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49F TYR* 3.5 31.4 - + + +
96F LEU* 4.9 6.5 - - + +
101F VAL* 3.4 34.5 - - + +
104F PHE* 3.7 20.4 - + - -
108F ASP* 3.4 37.0 - - + -
116F ARG* 3.0 34.0 + - + -
117F THR* 3.7 8.1 - - + +
119F ARG* 1.3 106.3 - - - +
121F LEU* 1.3 63.2 + - - +
123F GLY* 3.0 12.8 + - - -
124F ILE* 3.0 18.6 + - - +
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Residues in contact with LEU 121 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14F ILE* 3.7 31.4 - - + -
18F ILE* 3.9 11.7 - - + -
22F ILE* 6.0 0.7 - - + -
36F LEU* 3.9 26.9 - - + -
45F LEU* 4.2 9.2 - - + -
48F ILE* 3.7 29.6 - - + -
49F TYR* 4.0 20.2 - - + +
117F THR 3.0 23.4 + - - +
118F SER* 4.2 4.0 - - - +
120F PHE* 1.3 75.0 - - - +
122F SER* 1.3 58.1 + - - +
124F ILE* 3.8 8.7 - - + +
125F ILE* 2.8 37.1 + - + +
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Residues in contact with SER 122 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7F PRO* 3.8 6.9 - - - +
8F ARG* 4.0 16.8 - - - -
9F TYR* 3.3 42.9 + - - -
14F ILE* 3.8 4.1 - - - +
118F SER 3.2 19.4 + - - -
119F ARG 3.7 4.5 - - - -
120F PHE 3.2 0.2 - - - -
121F LEU* 1.3 77.2 - - - +
123F GLY* 1.3 51.8 + - - +
125F ILE* 3.2 1.7 + - - +
126F ASN* 2.7 43.8 + - - +
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Residues in contact with GLY 123 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233E TYR* 4.8 0.7 + - - -
99F CYS* 3.3 33.0 - - - +
101F VAL* 5.0 3.6 - - - -
119F ARG 3.1 10.5 + - - -
120F PHE 3.0 7.5 + - - -
122F SER* 1.3 75.4 - - - +
124F ILE* 1.3 56.9 + - - +
126F ASN* 3.7 9.8 - - - +
127F PHE* 3.0 22.5 + - - +
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Residues in contact with ILE 124 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22F ILE* 4.0 25.6 - - + -
48F ILE* 6.1 0.9 - - + -
49F TYR* 3.8 31.4 - - + -
52F ALA* 4.2 12.1 - - + -
92F LEU* 5.3 0.2 - - + -
95F PHE* 3.7 16.6 - - + -
96F LEU* 3.8 22.4 - - + -
99F CYS* 3.7 22.2 - - - +
120F PHE 3.0 14.1 + - - +
121F LEU* 3.8 10.5 - - + +
123F GLY* 1.3 72.9 - - - +
125F ILE* 1.3 58.1 + - - +
127F PHE* 3.1 4.2 + - - +
128F ILE* 2.7 43.3 + - + +
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Residues in contact with ILE 125 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9F TYR* 3.7 20.6 - - + -
14F ILE* 3.8 15.5 - - + +
17F HIS* 3.5 39.0 - - + +
18F ILE* 3.7 28.0 - - + -
21F LYS* 5.9 3.1 - - + -
22F ILE* 4.5 13.0 - - + -
121F LEU* 2.8 29.0 + - + +
122F SER* 3.8 3.1 - - - +
124F ILE* 1.3 74.2 - - - +
126F ASN* 1.3 62.9 + - - +
128F ILE* 3.3 7.6 + - + +
129F HIS* 3.0 43.4 + - + +
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Residues in contact with ASN 126 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233E TYR* 3.8 14.4 - - - +
8F ARG* 3.9 23.9 - - - +
9F TYR* 3.4 24.1 + - - -
122F SER* 2.7 34.0 + - - +
123F GLY* 3.7 8.9 - - - +
125F ILE* 1.3 72.2 - - - +
127F PHE* 1.3 64.9 + - - +
129F HIS* 2.9 18.8 + - - +
130F PHE* 3.1 11.8 + - - +
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Residues in contact with PHE 127 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226E LEU* 4.8 8.5 - - + -
229E THR* 4.0 30.5 - - + -
230E ILE* 5.2 2.2 - - + -
233E TYR* 3.7 43.6 + + + -
56F VAL* 3.7 30.5 - - + -
95F PHE* 3.8 21.3 - + - -
98F ILE* 3.6 22.7 - - + -
99F CYS* 4.0 11.2 - - - -
123F GLY 3.0 14.6 + - - +
124F ILE 3.6 2.9 - - - +
126F ASN* 1.3 78.7 - - - +
128F ILE* 1.3 63.7 + - + +
130F PHE* 3.1 3.3 + - + +
131F ARG* 2.8 39.2 + - + +
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Residues in contact with ILE 128 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21F LYS* 3.9 34.8 - - + +
22F ILE* 3.7 35.0 - - + -
52F ALA* 4.9 5.2 - - + -
55F ILE* 5.0 11.4 - - + -
56F VAL* 4.4 24.0 - - + -
124F ILE* 2.7 30.1 + - + +
125F ILE* 3.7 7.6 - - + +
126F ASN 3.2 0.2 - - - -
127F PHE* 1.3 75.7 - - + +
129F HIS* 1.3 64.6 + - + +
131F ARG* 3.4 14.0 + - + +
132F GLU* 3.3 25.1 + - + +
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Residues in contact with HIS 129 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9F TYR* 4.1 7.7 + - - -
17F HIS* 3.0 40.7 + + - -
21F LYS* 4.1 32.7 - - + +
125F ILE* 3.0 30.8 + - + +
126F ASN* 2.9 10.5 + - - +
128F ILE* 1.3 75.1 - - - +
130F PHE* 1.3 62.3 + - - +
132F GLU* 3.3 24.1 - - - +
133F ALA* 3.3 8.3 + - - +
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Residues in contact with PHE 130 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229E THR* 4.0 6.1 - - + -
232E CYS* 3.6 23.8 - - + -
233E TYR* 3.2 57.0 - + + -
236E PHE* 3.5 39.7 - + + -
243E PHE* 4.0 12.6 - + - -
126F ASN 3.1 7.9 + - - +
127F PHE* 3.1 8.5 + + - +
129F HIS* 1.3 75.3 - - - +
131F ARG* 1.3 66.4 + - - +
133F ALA* 3.0 21.6 + - + +
134F CYS* 3.0 33.2 + - - -
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Residues in contact with ARG 131 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215E THR* 3.8 5.9 + - - +
217E ASP* 3.3 31.3 + - - -
219E ILE* 3.6 18.6 - - - +
222E ASN* 4.2 0.8 + - - -
225E PHE* 3.5 22.3 - - + -
226E LEU* 5.7 1.8 - - - +
229E THR* 3.4 29.8 - - + -
55F ILE* 3.5 30.8 + - - +
56F VAL* 3.6 27.4 + - - +
127F PHE* 2.8 39.4 + - + +
128F ILE* 3.4 19.0 + - + +
130F PHE* 1.3 73.2 - - - +
132F GLU* 1.3 58.3 + - - +
134F CYS* 3.1 2.5 + - - +
135F ARG* 2.6 37.9 + - - +
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Residues in contact with GLU 132 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217E ASP* 5.7 2.0 - - - +
21F LYS* 3.0 45.6 + - - +
128F ILE* 3.3 17.8 + - + +
129F HIS* 3.3 17.2 - - - +
130F PHE 3.1 0.2 - - - -
131F ARG* 1.3 83.3 - - - +
133F ALA* 1.3 61.4 + - - +
135F ARG* 3.2 38.3 + - - +
136F GLU* 3.2 13.2 + - - +
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Residues in contact with ALA 133 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129F HIS 3.3 8.7 + - - +
130F PHE* 3.0 19.3 + - + +
132F GLU* 1.3 78.5 - - - +
134F CYS* 1.3 63.4 + - - +
136F GLU* 3.5 8.3 + - - +
137F THR* 3.5 20.4 + - - -
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Residues in contact with CYS 134 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225E PHE* 3.6 3.4 - - + -
228E TYR* 3.9 10.8 - - + -
229E THR* 3.9 24.7 - - - +
232E CYS* 4.1 16.6 - - - -
243E PHE* 6.5 0.2 - - - -
130F PHE* 3.0 49.1 + - - -
131F ARG* 3.4 7.6 - - - +
133F ALA* 1.3 75.7 - - - +
135F ARG* 1.3 58.4 + - - +
137F THR* 3.2 6.6 + - - +
138F TYR* 2.8 30.7 + - - +
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Residues in contact with ARG 135 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217E ASP* 3.5 33.0 + - - +
219E ILE* 3.5 39.7 - - + -
225E PHE* 3.5 9.8 - - + -
131F ARG* 2.6 19.7 + - - +
132F GLU* 3.2 34.5 + - - +
134F CYS* 1.3 71.3 - - - +
136F GLU* 1.3 66.2 + - - +
138F TYR* 3.1 0.6 + - + -
139F MET* 2.8 57.7 + - + +
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Residues in contact with GLU 136 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132F GLU 3.2 8.4 + - - +
133F ALA* 3.7 10.1 - - - +
134F CYS 3.3 0.2 - - - -
135F ARG* 1.3 82.3 - - - +
137F THR* 1.3 66.3 + - - +
139F MET* 4.0 4.3 - - - +
140F GLU* 3.1 29.4 + - + +
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Residues in contact with THR 137 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228E TYR* 3.1 26.5 - - - +
247E ASN* 3.8 8.7 - - - +
133F ALA 3.5 11.5 + - - -
134F CYS* 3.2 7.3 + - - -
136F GLU* 1.3 80.3 - - - +
138F TYR* 1.3 62.9 + - - +
140F GLU* 3.3 12.8 + - - +
141F PHE* 3.2 41.7 + - + -
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Residues in contact with TYR 138 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219E ILE* 4.5 7.6 - - + -
220E MET 2.9 28.8 + - - -
221E HIS* 3.4 17.0 + - - +
224E LEU* 3.9 9.3 - - + +
225E PHE* 3.5 47.8 - + + -
228E TYR* 4.3 6.1 - + + -
250E LEU* 3.7 43.3 - - + -
254E LEU* 5.3 2.7 - - + -
134F CYS 2.8 21.3 + - - +
135F ARG 3.6 2.5 - - - +
137F THR* 1.3 74.4 - - - +
139F MET* 1.3 62.3 + - + +
141F PHE* 3.1 5.5 + - - +
142F LEU* 2.8 56.9 + - + +
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Residues in contact with MET 139 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217E ASP 4.8 1.3 - - - +
218E GLY* 3.5 29.2 - - - +
219E ILE* 4.5 5.8 - - - -
135F ARG* 2.8 63.1 + - + +
136F GLU* 4.1 4.5 - - - +
138F TYR* 1.3 79.2 - - + +
140F GLU* 1.3 56.9 + - - +
142F LEU* 3.8 15.3 - - - +
143F TRP* 2.9 30.3 + - - +
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Residues in contact with GLU 140 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136F GLU* 3.1 26.0 + - + +
137F THR* 3.5 12.0 - - - +
139F MET* 1.3 78.5 - - - +
141F PHE* 1.3 62.8 + - + +
143F TRP* 3.7 6.8 + - + +
144F GLN* 3.2 39.2 + - + +
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Residues in contact with PHE 141 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247E ASN* 3.7 35.2 - - + -
250E LEU* 3.6 20.9 - - + -
251E GLN* 3.5 42.6 - - + -
254E LEU* 3.7 18.4 - - + -
137F THR* 3.2 29.7 + - + -
138F TYR 3.1 7.2 + - - +
140F GLU* 1.3 76.9 - - + +
142F LEU* 1.3 62.9 + - - +
144F GLN* 3.0 16.4 + - - +
145F TYR* 3.0 35.2 + + - -
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Residues in contact with LEU 142 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218E GLY 5.9 0.4 - - - +
220E MET* 4.1 27.8 - - + +
221E HIS* 4.0 18.6 - - + +
254E LEU* 3.9 27.1 - - + +
258E PHE* 4.4 12.6 - - + -
138F TYR* 2.8 40.1 + - + +
139F MET* 3.8 15.0 - - - +
141F PHE* 1.3 77.6 - - - +
143F TRP* 1.3 56.8 + - - +
145F TYR* 3.2 2.6 + - - +
146F LYS* 3.0 44.8 + - + +
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Residues in contact with TRP 143 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139F MET 2.9 19.1 + - - +
140F GLU* 3.9 8.5 - - + +
141F PHE 3.3 0.2 - - - -
142F LEU* 1.3 74.8 - - - +
144F GLN* 1.3 67.0 + - + +
146F LYS* 4.1 21.6 - - + +
147F SER* 2.9 45.8 + - - -
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Residues in contact with GLN 144 (chain F).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251E GLN* 5.7 2.6 - - - +
140F GLU* 3.2 29.4 + - + +
141F PHE* 3.0 28.4 + - - +
143F TRP* 1.3 86.1 - - + +
145F TYR* 1.3 67.8 + - + +
147F SER* 4.1 2.7 - - - -
148F SER* 3.0 28.9 + - - -
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Residues in contact with TYR 145 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251E GLN* 3.4 42.7 + - + +
254E LEU* 3.7 31.6 - - + +
255E LYS* 3.3 46.0 + - + -
258E PHE* 3.6 25.9 - - + +
260E VAL* 3.8 20.6 - - + +
261E ASP* 5.9 0.7 - - - -
141F PHE* 3.0 32.8 + + - +
142F LEU 3.2 0.9 + - - +
144F GLN* 1.3 87.2 - - + +
146F LYS* 1.3 59.6 + - - +
147F SER 3.2 2.0 - - - -
148F SER* 3.4 4.3 + - - -
149F ALA* 3.0 27.0 + - - +
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Residues in contact with LYS 146 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258E PHE* 4.2 21.4 - - + -
142F LEU* 3.0 31.7 + - + +
143F TRP* 4.1 24.3 - - + +
145F TYR* 1.3 75.7 - - - +
147F SER* 1.3 60.5 + - - +
149F ALA* 3.9 9.2 - - - +
150F ASP* 2.8 48.6 + - - +
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Residues in contact with SER 147 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143F TRP* 2.9 41.0 + - - -
144F GLN* 4.1 4.3 - - - -
145F TYR 3.2 0.6 - - - -
146F LYS* 1.3 79.8 - - - +
148F SER* 1.3 59.0 + - - +
149F ALA 3.3 0.4 - - - -
150F ASP* 3.5 9.5 + - - +
151F LYS* 3.1 28.6 + - - +
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Residues in contact with SER 148 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260E VAL* 3.4 27.8 - - - +
265E LEU* 3.7 18.6 - - - +
144F GLN 3.0 18.4 + - - -
145F TYR* 3.4 5.8 + - - -
147F SER* 1.3 74.1 - - - +
149F ALA* 1.3 62.6 + - - +
150F ASP 3.2 2.0 - - - -
151F LYS* 3.9 6.5 - - - +
152F MET* 3.4 24.3 + - - +
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Residues in contact with ALA 149 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258E PHE* 3.8 27.6 - - + -
259E ASN 5.7 0.9 - - - +
260E VAL* 4.6 2.4 - - - +
145F TYR 3.0 16.5 + - - +
146F LYS* 4.1 8.7 - - - +
147F SER 3.3 0.4 - - - -
148F SER* 1.3 77.6 - - - +
150F ASP* 1.3 63.6 + - - +
152F MET* 3.4 19.7 - - - +
153F GLN* 3.6 13.2 + - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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