Contacts of the helix formed by residues 113 - 139 (chain C) in PDB entry 1F33
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 ASN 113 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C ARG* 3.4 8.8 - - - +
56C GLY* 5.1 4.7 - - - -
57C ALA 5.6 0.5 + - - -
112C HIS* 1.3 80.5 - - - +
114C VAL* 1.3 66.5 + - - +
115C GLN* 2.8 46.1 - - - +
116C ASP* 3.1 36.3 + - - +
117C HIS* 3.1 12.5 + - - -
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Residues in contact with VAL 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C MET* 4.3 12.8 - - + -
55C ARG 3.0 31.1 + - - +
56C GLY 3.8 5.4 - - - +
57C ALA 3.4 27.4 - - - +
58C ASN* 4.4 0.9 - - + +
59C PHE* 4.1 10.8 - - - -
62C VAL* 4.2 23.6 - - + -
112C HIS 3.3 1.8 + - - -
113C ASN* 1.3 74.1 - - - +
115C GLN* 1.3 63.9 + - + +
117C HIS* 3.1 4.2 + - - +
118C LEU* 2.8 46.8 + - + +
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Residues in contact with GLN 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C ALA* 5.2 5.1 + - + +
58C ASN* 5.9 2.8 - - - +
113C ASN* 2.8 22.6 - - - +
114C VAL* 1.3 77.4 - - + +
116C ASP* 1.3 61.1 + - - +
118C LEU* 3.3 13.9 + - - +
119C LYS* 3.0 42.6 + - - +
165C ASN 3.2 21.0 + - - -
166C ILE* 3.3 13.9 - - - +
167C GLU* 2.8 53.5 + - + +
57F ALA* 5.8 0.6 - - - +
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Residues in contact with ASP 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C ILE* 4.2 28.5 - - + +
112C HIS 4.8 0.5 + - - -
113C ASN* 3.1 32.8 + - - +
115C GLN* 1.3 77.3 - - - +
117C HIS* 1.3 64.8 + - - +
119C LYS* 3.2 15.4 + - - +
120C GLU* 3.0 26.6 + - + +
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Residues in contact with HIS 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C GLN* 4.6 2.0 - - - -
50C ALA* 3.5 23.5 - - + +
53C ASN* 3.5 19.0 + - + -
54C MET* 3.7 26.9 - - + -
107C TYR* 2.6 33.1 + + - +
108C PRO 4.9 1.3 - - - -
111C ILE* 3.2 40.2 + - + +
112C HIS* 3.4 24.5 - - - -
113C ASN 3.1 9.3 + - - -
114C VAL 3.6 6.1 - - - +
116C ASP* 1.3 78.5 - - - +
118C LEU* 1.3 54.8 + - - +
120C GLU 3.2 0.3 + - - -
121C LEU* 2.7 41.4 + - - +
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Residues in contact with LEU 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C MET* 5.0 0.7 - - + -
58C ASN* 5.8 0.2 - - - +
62C VAL* 3.8 28.3 - - + -
65C MET* 5.1 4.0 - - + -
66C LEU* 5.5 0.2 - - + -
114C VAL* 2.8 34.7 + - + +
115C GLN* 3.4 14.8 - - - +
117C HIS* 1.3 77.4 - - - +
119C LYS* 1.3 57.6 + - - +
121C LEU* 3.4 9.6 + - + -
122C ALA* 2.8 26.3 + - - +
162C ILE* 3.3 38.3 - - + +
165C ASN* 3.7 34.3 - - + +
166C ILE* 3.9 12.1 - - + +
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Residues in contact with LYS 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C GLN* 3.0 34.6 + - - +
116C ASP* 3.2 13.6 + - - +
118C LEU* 1.3 74.4 - - - +
120C GLU* 1.3 66.8 + - + +
122C ALA* 3.3 3.7 + - - +
123C ASP* 3.1 30.0 + - - +
166C ILE* 4.1 37.7 - - + -
167C GLU 5.8 0.4 - - - -
18E ARG* 4.3 9.0 + - - +
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Residues in contact with GLU 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C TYR* 3.5 25.4 - - + +
108C PRO* 3.9 11.1 - - + +
111C ILE* 3.7 20.4 - - + +
116C ASP* 3.0 18.4 + - + +
117C HIS 3.6 1.3 - - - +
119C LYS* 1.3 77.5 - - - +
121C LEU* 1.3 61.9 + - - +
123C ASP* 3.5 11.2 + - - +
124C ARG* 2.9 52.1 + - - +
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Residues in contact with LEU 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C ILE* 3.8 27.6 - - + +
47C THR* 4.2 9.6 - - - -
50C ALA* 3.6 33.0 - - + -
54C MET* 4.6 0.9 - - + -
66C LEU* 3.7 32.8 - - + -
107C TYR* 4.0 2.5 - - + +
117C HIS 2.7 30.0 + - - +
118C LEU* 3.6 12.1 - - + +
120C GLU* 1.3 71.6 - - - +
122C ALA* 1.3 56.8 + - - +
124C ARG* 3.0 4.3 + - + -
125C TYR* 2.7 49.4 + - + -
162C ILE* 4.1 12.1 - - + -
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Residues in contact with ALA 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C LEU 2.8 21.7 + - - +
119C LYS* 3.5 4.3 - - - +
121C LEU* 1.3 72.0 - - - +
123C ASP* 1.3 57.9 + - - +
125C TYR* 4.5 0.9 - - - -
126C ALA* 2.8 32.6 + - - +
159C LEU* 3.5 9.4 - - - +
162C ILE* 3.8 15.6 - - + +
163C GLU* 4.3 8.5 - - + -
166C ILE* 4.3 2.7 - - + -
18E ARG* 3.4 34.5 - - - +
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Residues in contact with ASP 123 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C LYS* 3.1 15.4 + - - +
120C GLU* 3.6 15.8 - - - +
121C LEU 3.1 0.2 - - - -
122C ALA* 1.3 77.9 - - - +
124C ARG* 1.3 68.7 + - - +
126C ALA* 3.3 2.8 + - - +
127C ILE* 3.1 30.2 + - + +
18E ARG* 2.8 30.4 + - - +
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Residues in contact with ARG 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C LEU* 3.8 17.7 - - + -
46C ILE* 4.2 10.3 - - + +
104C LEU* 3.7 18.0 - - + +
105C LYS* 2.9 51.5 + - - +
106C SER 3.7 6.5 + - - -
107C TYR* 2.9 37.1 - - + +
108C PRO* 3.5 15.8 - - - +
120C GLU* 2.9 42.9 + - - +
121C LEU* 3.0 7.9 + - - +
123C ASP* 1.3 77.2 - - - +
125C TYR* 1.3 66.0 + - - +
127C ILE* 3.3 8.6 + - - +
128C VAL* 3.1 26.2 + - - +
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Residues in contact with TYR 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C LEU* 3.5 36.6 - - + -
47C THR* 2.6 37.3 + - + +
66C LEU* 5.5 0.2 - - + -
69C PHE* 3.6 11.4 - + - +
73C LEU* 3.5 12.2 - - + +
121C LEU* 2.7 41.1 + - + +
122C ALA 3.8 2.9 - - - +
124C ARG* 1.3 69.8 - - - +
126C ALA* 1.3 54.7 + - - +
128C VAL* 3.2 1.2 + - - +
129C ALA* 2.6 40.4 + - - +
155C LEU* 4.2 8.9 - - + +
158C PHE* 3.7 35.9 - + + -
159C LEU* 4.2 13.2 - - + -
162C ILE* 3.5 29.4 - - + -
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Residues in contact with ALA 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122C ALA 2.8 18.4 + - - +
123C ASP* 3.4 6.1 - - - +
125C TYR* 1.3 76.7 - - - +
127C ILE* 1.3 58.1 + - + +
130C ASN* 2.7 44.9 + - - +
159C LEU* 3.9 14.7 - - + +
18E ARG* 3.4 33.7 - - + -
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Residues in contact with ILE 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C GLN* 4.3 10.1 - - - +
103C PRO* 4.5 17.7 - - + +
104C LEU* 3.9 23.8 - - + -
105C LYS* 5.5 3.4 - - + +
123C ASP* 3.1 19.6 + - + +
124C ARG* 3.6 11.4 - - - +
125C TYR 3.2 0.2 - - - -
126C ALA* 1.3 76.1 - - + +
128C VAL* 1.3 56.9 + - - +
130C ASN* 4.1 3.7 - - - +
131C ASP* 3.0 32.4 + - + +
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Residues in contact with VAL 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C GLN* 3.3 35.6 - - + +
40C PHE* 3.6 28.9 - - + -
43C LEU* 4.0 17.9 - - + -
104C LEU* 3.9 17.9 - - + -
124C ARG 3.1 14.6 + - - +
125C TYR 3.8 4.9 - - - +
127C ILE* 1.3 72.8 - - - +
129C ALA* 1.3 61.1 + - - +
131C ASP* 3.4 0.5 + - - +
132C VAL* 2.9 33.1 + - - +
155C LEU* 3.5 22.0 - - + -
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Residues in contact with ALA 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125C TYR 2.6 24.8 + - - +
126C ALA* 3.7 6.1 - - - +
128C VAL* 1.3 73.5 - - - +
130C ASN* 1.3 62.8 + - - +
132C VAL* 3.2 9.5 - - - +
133C ARG* 3.0 30.4 + - - +
155C LEU* 3.9 22.8 - - + +
156C ASP* 3.7 18.3 - - - +
159C LEU* 4.4 10.3 - - + -
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Residues in contact with ASN 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126C ALA* 2.7 32.3 + - - +
127C ILE* 4.2 3.9 - - - +
129C ALA* 1.3 73.3 - - - +
131C ASP* 1.3 64.1 + - - +
133C ARG* 2.4 36.0 + - - +
134C LYS* 3.3 30.4 + - - +
18E ARG 2.9 21.2 + - - -
19E ASN* 3.5 3.8 - - - -
20E ASP* 2.7 37.4 + - - +
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Residues in contact with ASP 131 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C ARG* 2.8 41.0 + - - -
36C GLN* 3.7 2.3 - - - +
39C GLN* 3.1 26.6 + - - +
103C PRO* 5.9 0.2 - - - +
127C ILE* 3.0 20.9 + - + +
128C VAL 3.8 2.7 - - - +
130C ASN* 1.3 78.1 - - - +
132C VAL* 1.3 64.7 + - - +
134C LYS* 3.0 12.2 + - - +
135C ALA* 3.0 16.6 + - - +
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Residues in contact with VAL 132 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C GLN* 3.6 28.0 - - - +
40C PHE* 4.3 19.5 - - + -
128C VAL 2.9 22.0 + - - +
129C ALA* 3.2 12.3 - - - +
131C ASP* 1.3 77.2 + - - +
133C ARG* 1.3 66.2 + - - +
135C ALA* 3.2 10.4 + - + +
136C ILE* 3.3 13.6 + - - +
148C LEU* 3.9 35.7 - - + +
151C ALA* 4.6 0.7 - - + -
152C SER* 4.0 20.9 - - - +
155C LEU* 4.7 2.7 - - + -
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Residues in contact with ARG 133 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129C ALA* 3.0 28.5 + - - +
130C ASN* 2.4 33.5 + - - +
131C ASP 3.1 0.4 - - - -
132C VAL* 1.3 76.1 - - - +
134C LYS* 1.3 63.3 + - + +
136C ILE* 3.4 23.0 - - + +
137C GLY 4.3 1.2 + - - -
152C SER* 3.6 17.3 - - - +
156C ASP* 2.6 43.2 + - - -
19E ASN* 2.9 24.1 + - - +
20E ASP* 3.1 13.5 + - - +
21E VAL* 3.3 23.0 - - - +
83E ARG* 4.0 6.3 - - - +
141E ASP* 4.3 6.3 - - - +
142E ASP* 4.4 7.4 - - + +
143E ASP* 4.0 7.2 - - - +
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Residues in contact with LYS 134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130C ASN* 3.3 19.1 + - - +
131C ASP* 3.0 10.1 + - - +
133C ARG* 1.3 76.8 - - + +
135C ALA* 1.3 67.3 + - - +
136C ILE 3.0 2.9 + - - -
137C GLY* 3.2 11.3 + - - -
138C GLU* 3.2 14.8 + - - +
20E ASP* 2.3 45.9 + - - -
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Residues in contact with ALA 135 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C LEU* 3.9 20.0 - - + +
35C ARG* 4.4 4.0 - - - +
36C GLN* 3.6 23.3 - - - +
131C ASP 3.0 8.3 + - - +
132C VAL* 3.2 10.7 + - - +
134C LYS* 1.3 77.2 - - - +
136C ILE* 1.3 56.4 + - - +
138C GLU* 3.1 14.5 + - - +
139C ALA* 2.8 31.4 + - - +
148C LEU* 3.8 12.8 - - + +
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Residues in contact with ILE 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C VAL 3.5 8.7 - - - +
133C ARG* 3.4 18.6 - - + +
134C LYS 3.0 0.2 - - - -
135C ALA* 1.3 78.0 - - - +
137C GLY* 1.3 62.6 + - - +
139C ALA* 3.2 20.7 + - - +
145C ALA* 4.0 14.0 - - + +
148C LEU* 3.9 22.4 - - + +
149C THR* 3.4 30.1 - - - +
152C SER* 3.7 11.9 - - - +
142E ASP* 3.8 29.2 - - + +
143E ASP* 3.4 25.8 - - - +
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Residues in contact with GLY 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133C ARG 4.3 0.6 + - - -
134C LYS* 3.2 7.4 + - - +
136C ILE* 1.3 81.8 - - - +
138C GLU* 1.3 59.7 + - - +
139C ALA 3.2 5.1 + - - +
142E ASP* 4.3 10.5 + - - -
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Residues in contact with GLU 138 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C LEU* 3.6 29.3 - - + +
35C ARG* 3.8 15.2 + - - -
134C LYS* 3.2 14.1 + - - +
135C ALA* 3.1 12.3 + - - +
137C GLY* 1.3 75.5 - - - +
139C ALA* 1.3 61.1 + - - +
140C LYS* 3.4 12.0 + - - +
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Residues in contact with ALA 139 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C LEU* 4.0 11.2 - - + -
135C ALA 2.8 10.8 + - - +
136C ILE 3.4 16.4 - - - +
137C GLY 3.2 5.4 - - - +
138C GLU* 1.3 76.8 - - - +
140C LYS* 1.3 64.3 + - - +
141C ASP 4.4 2.0 - - - +
144C THR* 4.4 5.2 - - + -
145C ALA* 3.9 31.5 - - + +
148C LEU* 4.1 10.8 - - + -
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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