Contacts of the helix formed by residues 113 - 139 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55E ARG 3.5 8.4 - - - +
56E GLY* 5.1 4.7 - - - -
57E ALA 5.6 0.5 + - - -
112E HIS* 1.3 81.6 - - - +
114E VAL* 1.3 67.0 + - - +
115E GLN* 2.8 46.9 - - - +
116E ASP* 3.1 34.3 + - - +
117E HIS* 3.2 12.8 + - - -
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Residues in contact with VAL 114 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54E MET* 4.3 12.6 - - + -
55E ARG 3.0 37.1 + - - +
56E GLY* 3.8 4.9 - - - +
57E ALA 3.4 28.0 - - - +
58E ASN* 4.5 0.9 - - + +
59E PHE* 4.1 11.0 - - - -
62E VAL* 4.2 24.0 - - + -
112E HIS 4.2 1.3 - - - -
113E ASN* 1.3 74.8 + - - +
115E GLN* 1.3 62.4 + - + +
117E HIS* 3.2 4.3 + - - +
118E LEU* 2.8 46.6 + - + +
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Residues in contact with GLN 115 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A ALA* 5.8 0.4 - - - +
57E ALA* 5.3 4.4 + - + +
58E ASN* 5.9 3.2 - - - +
113E ASN* 2.8 21.5 - - - +
114E VAL* 1.3 80.1 - - + +
116E ASP* 1.3 62.7 - - - +
118E LEU* 3.3 12.7 + - - +
119E LYS* 2.9 41.8 + - - +
165E ASN 3.2 21.6 + - - -
166E ILE* 3.3 13.4 - - - +
167E GLU* 2.8 53.9 + - + +
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Residues in contact with ASP 116 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111E ILE* 4.2 27.8 - - + +
112E HIS 4.9 0.5 + - - -
113E ASN* 3.1 32.1 + - + +
115E GLN* 1.3 77.8 - - - +
117E HIS* 1.3 63.9 + - - +
119E LYS* 3.2 15.4 + - - +
120E GLU* 3.0 26.0 + - + +
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Residues in contact with HIS 117 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49E GLN* 4.5 5.4 - - - -
50E ALA* 3.5 20.8 - - + -
53E ASN* 3.4 14.9 + - + -
54E MET* 3.7 27.1 - - + -
107E TYR* 2.7 34.6 + + - +
108E PRO 4.9 1.6 - - - -
111E ILE* 3.2 42.7 + - + +
112E HIS* 3.4 23.6 - - - -
113E ASN 3.2 8.9 + - - -
114E VAL 3.6 6.5 - - - +
116E ASP* 1.3 74.8 - - - +
118E LEU* 1.3 56.4 + - - +
120E GLU 3.1 0.5 + - - -
121E LEU* 2.7 41.1 + - - +
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Residues in contact with LEU 118 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54E MET* 5.0 1.1 - - + -
58E ASN* 5.8 0.4 - - - +
62E VAL* 3.8 28.0 - - + -
65E MET* 5.1 4.5 - - + -
114E VAL* 2.8 35.4 + - + +
115E GLN* 3.4 15.5 - - - +
117E HIS* 1.3 77.6 - - - +
119E LYS* 1.3 56.0 + - - +
121E LEU* 3.4 10.9 + - + -
122E ALA* 2.8 29.5 + - - +
162E ILE* 3.3 36.5 - - + +
165E ASN* 3.8 33.7 - - + +
166E ILE* 3.9 10.5 - - + +
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Residues in contact with LYS 119 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B ARG* 4.6 9.1 + - - +
115E GLN* 2.9 33.6 + - - +
116E ASP* 3.7 13.2 + - - +
118E LEU* 1.3 74.1 - - - +
120E GLU* 1.3 68.0 + - + +
122E ALA* 3.2 8.1 + - - +
123E ASP* 3.1 29.4 + - - +
166E ILE* 4.0 33.9 - - + -
167E GLU 5.7 0.9 - - - -
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Residues in contact with GLU 120 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107E TYR* 3.5 21.3 - - + +
108E PRO* 3.9 11.7 - - + +
111E ILE* 3.7 21.5 - - + +
116E ASP* 3.0 17.8 + - + +
117E HIS 3.6 4.7 - - - +
119E LYS* 1.3 77.8 - - - +
121E LEU* 1.3 62.3 + - - +
123E ASP* 3.4 13.0 + - - +
124E ARG* 2.9 52.3 + - - +
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Residues in contact with LEU 121 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46E ILE* 3.9 27.8 - - + +
47E THR* 4.2 9.0 - - - -
50E ALA* 3.6 33.2 - - + -
54E MET* 4.7 0.7 - - + -
66E LEU* 3.7 31.9 - - + -
107E TYR* 3.9 2.5 - - + +
117E HIS 2.7 29.8 + - - +
118E LEU* 3.7 12.6 - - + +
120E GLU* 1.3 71.2 - - - +
122E ALA* 1.3 58.0 + - - +
124E ARG* 3.2 3.9 + - - -
125E TYR* 2.8 49.3 + - + -
162E ILE* 4.2 12.1 - - + -
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Residues in contact with ALA 122 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B ARG* 3.5 32.1 - - - +
118E LEU 2.8 18.3 + - - +
119E LYS* 3.2 8.0 + - - +
121E LEU* 1.3 75.4 - - - +
123E ASP* 1.3 56.6 + - - +
125E TYR* 4.6 0.4 - - - -
126E ALA* 2.8 32.1 + - - +
159E LEU* 3.5 10.0 - - - +
162E ILE* 3.9 15.0 - - + +
163E GLU* 4.3 5.2 - - + -
166E ILE* 4.3 4.7 - - + -
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Residues in contact with ASP 123 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B ARG* 2.9 29.3 + - - +
119E LYS* 3.1 13.5 + - - +
120E GLU* 3.6 16.6 - - - +
121E LEU 3.2 0.2 - - - -
122E ALA* 1.3 76.7 - - - +
124E ARG* 1.3 69.8 + - - +
126E ALA* 3.3 4.5 + - - +
127E ILE* 3.1 30.3 + - + +
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Residues in contact with ARG 124 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43E LEU* 3.8 19.1 - - + -
46E ILE* 4.1 13.6 - - + +
104E LEU* 3.8 17.8 - - + +
105E LYS* 2.9 51.5 + - - +
106E SER 3.6 6.5 + - - -
107E TYR* 2.9 35.1 - - - +
108E PRO* 3.6 15.0 - - - +
120E GLU* 2.9 41.9 + - - +
121E LEU* 3.2 7.0 + - - +
123E ASP* 1.3 76.5 - - - +
125E TYR* 1.3 65.8 + - - +
127E ILE* 3.2 9.8 + - - +
128E VAL* 3.1 26.3 + - - +
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Residues in contact with TYR 125 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43E LEU* 3.5 35.2 - - + -
47E THR* 2.6 31.5 + - + +
66E LEU* 5.4 0.7 - - + -
69E PHE* 3.6 21.7 - + - +
73E LEU* 3.5 12.7 - - + +
121E LEU* 2.8 41.6 + - + +
122E ALA 3.9 2.9 - - - +
124E ARG* 1.3 73.1 - - - +
126E ALA* 1.3 53.5 + - - +
128E VAL* 3.3 1.4 + - - +
129E ALA* 2.6 39.9 + - + +
155E LEU* 4.2 9.1 - - + +
158E PHE* 3.8 35.2 - + + -
159E LEU* 4.2 13.9 - - + -
162E ILE* 3.5 25.8 - - + -
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Residues in contact with ALA 126 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B ARG* 3.6 31.0 - - + -
122E ALA 2.8 20.3 + - - +
123E ASP* 3.4 5.8 - - - +
124E ARG 3.2 0.2 - - - -
125E TYR* 1.3 77.2 - - - +
127E ILE* 1.3 57.1 + - + +
129E ALA* 4.2 0.2 - - - -
130E ASN* 2.8 44.3 + - - +
159E LEU* 3.9 15.0 - - + +
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Residues in contact with ILE 127 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39E GLN* 4.3 11.0 - - - +
103E PRO* 4.5 17.5 - - + +
104E LEU* 3.8 24.7 - - + -
105E LYS* 5.5 3.8 - - + +
123E ASP* 3.1 18.8 + - + +
124E ARG* 3.2 11.6 + - - +
126E ALA* 1.3 76.8 - - + +
128E VAL* 1.3 61.3 + - - +
130E ASN* 4.2 3.7 - - - +
131E ASP* 3.0 28.7 + - + +
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Residues in contact with VAL 128 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39E GLN* 3.4 36.3 - - + +
40E PHE* 3.6 27.8 - - + -
43E LEU* 4.0 18.2 - - + -
104E LEU* 3.9 17.9 - - + -
124E ARG 3.1 13.3 + - - +
125E TYR 3.8 2.5 - - - +
127E ILE* 1.3 73.2 - - - +
129E ALA* 1.3 66.4 + - - +
131E ASP* 3.9 0.2 - - - +
132E VAL* 2.9 27.4 + - - +
155E LEU* 3.5 22.7 - - + -
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Residues in contact with ALA 129 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125E TYR 2.6 23.9 + - - +
126E ALA* 3.7 5.6 - - - +
128E VAL* 1.3 74.0 - - - +
130E ASN* 1.3 62.9 + - - +
132E VAL* 3.2 10.0 - - - +
133E ARG* 3.1 30.8 + - - +
155E LEU* 3.8 23.1 - - + +
156E ASP* 3.7 17.6 - - - +
159E LEU* 4.4 10.5 - - + -
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Residues in contact with ASN 130 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B ARG 3.2 19.2 + - - -
19B ASN* 3.6 3.9 - - - -
20B ASP* 2.8 36.8 + - - +
126E ALA* 2.8 32.2 + - - +
127E ILE* 4.2 3.7 - - - +
129E ALA* 1.3 75.8 - - - +
131E ASP* 1.3 61.7 + - - +
133E ARG* 2.4 35.9 + - - +
134E LYS* 3.3 32.2 + - - +
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Residues in contact with ASP 131 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35E ARG* 2.8 41.9 + - - -
36E GLN* 3.7 2.7 - - - +
39E GLN* 3.0 26.9 + - - +
103E PRO* 5.4 0.2 - - - +
127E ILE* 3.0 22.0 + - + +
128E VAL 3.9 2.5 - - - +
130E ASN* 1.3 74.8 - - - +
132E VAL* 1.3 67.6 + - - +
134E LYS* 3.0 11.4 + - - +
135E ALA* 3.0 16.1 + - - +
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Residues in contact with VAL 132 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36E GLN* 3.6 27.8 + - - +
40E PHE* 4.3 19.7 - - + -
128E VAL 2.9 22.1 + - - +
129E ALA* 3.2 11.9 - - - +
131E ASP* 1.3 77.5 - - - +
133E ARG* 1.3 65.5 + - - +
135E ALA* 3.1 9.4 + - - +
136E ILE* 3.3 13.9 + - - +
148E LEU* 3.9 36.1 - - + +
151E ALA* 4.7 0.7 - - + -
152E SER* 4.0 20.0 - - - +
155E LEU* 4.7 2.7 - - + -
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Residues in contact with ARG 133 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B ASN* 3.1 21.6 + - - +
20B ASP* 3.1 14.5 + - - -
21B VAL* 3.4 17.6 - - - +
83B ARG* 4.0 10.3 - - - +
141B ASP* 4.3 6.7 - - - +
142B ASP* 4.3 7.9 - - + +
143B ASP* 3.9 8.7 - - - +
129E ALA* 3.1 25.6 + - - +
130E ASN* 2.4 34.5 + - - +
131E ASP 3.1 0.2 - - - -
132E VAL* 1.3 78.3 - - - +
134E LYS* 1.3 64.2 + - + +
136E ILE* 3.4 24.1 - - + +
137E GLY 4.4 0.5 + - - -
152E SER* 3.7 14.8 - - - +
156E ASP* 2.6 44.2 + - - -
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Residues in contact with LYS 134 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B ASP* 2.4 41.8 + - - -
130E ASN* 3.3 22.0 + - - +
131E ASP* 3.0 10.3 + - - +
133E ARG* 1.3 76.9 - - + +
135E ALA* 1.3 65.9 + - - +
136E ILE 3.0 3.3 + - - -
137E GLY* 3.2 11.3 + - - -
138E GLU* 3.3 13.8 + - - +
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Residues in contact with ALA 135 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32E LEU* 3.9 15.8 - - + +
35E ARG* 4.4 3.6 - - - +
36E GLN* 3.6 23.3 - - - +
131E ASP 3.0 8.7 + - - +
132E VAL* 3.1 10.9 + - - +
134E LYS* 1.3 76.8 - - - +
136E ILE* 1.3 56.8 + - - +
138E GLU* 3.0 13.3 + - - +
139E ALA* 2.8 31.5 + - - +
148E LEU* 3.9 17.1 - - + +
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Residues in contact with ILE 136 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B ASP* 3.8 28.3 - - + +
143B ASP* 3.4 26.2 - - - +
132E VAL 3.5 8.3 - - - +
133E ARG* 3.4 18.2 - - + +
134E LYS 3.0 0.2 - - - -
135E ALA* 1.3 77.8 - - - +
137E GLY* 1.3 62.0 + - - +
139E ALA* 3.2 20.3 + - - +
145E ALA* 4.0 14.9 - - + +
148E LEU* 3.9 21.7 - - + +
149E THR* 3.4 30.1 - - - +
152E SER* 3.7 11.9 - - - +
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Residues in contact with GLY 137 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B ASP* 4.3 10.2 + - - -
133E ARG 4.4 0.4 + - - -
134E LYS 3.2 6.6 + - - -
136E ILE* 1.3 81.8 - - - +
138E GLU* 1.3 59.7 + - - +
139E ALA 3.2 5.3 + - - +
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Residues in contact with GLU 138 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32E LEU* 3.6 31.4 - - + +
35E ARG* 3.8 11.9 + - - -
134E LYS* 3.3 13.7 + - - +
135E ALA* 3.0 13.6 + - - +
137E GLY* 1.3 76.3 - - - +
139E ALA* 1.3 61.3 + - - +
140E LYS* 3.4 12.1 + - - +
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Residues in contact with ALA 139 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32E LEU* 4.0 16.4 - - + -
135E ALA 2.8 11.2 + - - +
136E ILE 3.4 16.5 - - - +
137E GLY 3.2 4.7 - - - +
138E GLU* 1.3 76.6 - - - +
140E LYS* 1.3 65.2 + - - +
141E ASP 4.4 1.3 - - - +
144E THR* 4.3 6.7 - - + -
145E ALA* 4.0 30.8 - - - +
148E LEU* 4.1 6.1 - - + -
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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