Contacts of the helix formed by residues 98 - 122 (chain E) in PDB entry 2PGW
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 ILE 98 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55D PRO* 4.7 8.1 - - + -
100D ARG* 3.6 18.2 - - + +
101D ALA* 3.4 33.2 - - + +
104D GLN* 3.8 22.0 - - + +
228D TRP* 4.6 0.2 - - - -
251D PHE* 5.0 4.9 - - + -
87E PHE* 4.5 2.6 - - - -
91E TYR* 3.6 27.6 - - + -
96E ALA* 2.8 28.3 + - + +
97E ASN* 1.3 71.2 - - - +
99E MSE 1.3 64.4 + - - +
100E ARG 3.4 2.7 - - - -
101E ALA* 3.3 20.9 + - + +
102E ALA* 3.0 18.5 + - - +
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Residues in contact with MSE 99 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100D ARG* 5.2 2.2 - - - +
228D TRP* 3.3 61.0 - - + +
87E PHE* 3.9 24.8 - - + -
97E ASN 3.5 4.9 + - - -
98E ILE* 1.3 73.3 - - - +
100E ARG* 1.3 58.4 + - - +
102E ALA* 3.2 2.1 + - - +
103E ASN* 2.8 46.3 + - - +
252E THR* 3.6 34.3 - - + -
253E LEU* 5.2 1.3 - - - -
254E TYR* 3.9 20.2 - - + -
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Residues in contact with ARG 100 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97D ASN* 2.9 33.1 + - - +
98D ILE* 3.6 20.8 - - + +
99D MSE 5.4 0.9 - - - +
98E ILE 3.4 0.8 - - - -
99E MSE 1.3 77.9 - - + +
101E ALA* 1.3 63.9 + - - +
103E ASN* 3.2 10.9 + - - +
104E GLN* 3.2 19.1 + - - +
227E SER* 5.3 3.0 + - - -
228E TRP* 3.5 23.7 - - - +
248E GLN 4.1 5.5 + - - -
249E ALA* 3.8 11.9 + - - +
251E PHE* 3.3 41.0 - - + +
252E THR* 3.8 10.0 - - + +
255E ASP* 2.8 30.2 + - - -
273E ARG 5.0 1.2 - - - +
274E GLU 4.8 0.5 - - - +
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Residues in contact with ALA 101 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98D ILE* 3.5 20.2 - - + +
101D ALA* 3.4 32.8 - - + -
91E TYR* 4.8 2.2 - - + -
98E ILE* 3.3 18.2 + - + +
99E MSE 3.3 0.6 - - - -
100E ARG* 1.3 77.7 - - - +
102E ALA* 1.3 64.0 + - - +
104E GLN* 3.1 21.2 - - - +
105E ILE* 3.7 9.7 + - - +
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Residues in contact with ALA 102 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87E PHE* 3.5 32.5 - - + -
91E TYR* 3.7 27.5 + - + -
98E ILE 3.0 16.9 + - - +
99E MSE 3.5 2.2 - - - +
101E ALA* 1.3 75.3 - - - +
103E ASN* 1.3 66.8 + - - +
105E ILE* 2.9 14.4 + - - +
106E PHE* 2.9 23.1 + - + -
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Residues in contact with ASN 103 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99E MSE 2.8 31.9 + - - +
100E ARG* 3.2 7.3 + - - +
102E ALA* 1.3 73.6 - - - +
104E GLN* 1.3 56.8 + - - +
106E PHE* 4.5 6.5 - - - +
107E SER* 2.9 32.7 + - - -
251E PHE 4.2 0.2 + - - -
252E THR* 3.8 24.5 - - - +
273E ARG 3.8 2.4 - - - +
274E GLU 2.9 30.7 + - - +
275E ILE* 3.5 19.6 + - - +
276E GLY* 3.4 12.0 - - - +
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Residues in contact with GLN 104 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96D ALA* 4.2 10.6 - - - +
98D ILE* 3.7 23.7 - - + +
51E CYS* 3.6 16.6 - - - +
52E THR* 3.1 47.3 + - - +
53E VAL 4.0 1.0 - - - -
54E ALA* 2.9 30.2 + - - +
60E THR* 4.5 5.8 - - - +
100E ARG 3.2 8.8 + - - +
101E ALA 3.1 14.7 - - - +
102E ALA 3.0 0.6 - - - -
103E ASN* 1.3 79.5 - - - +
105E ILE* 1.3 63.8 + - + +
107E SER* 3.7 8.8 - - - -
273E ARG* 3.7 19.2 + - + +
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Residues in contact with ILE 105 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51E CYS* 3.2 25.9 - - + -
52E THR 5.1 0.2 - - - +
60E THR* 4.1 31.2 - - + +
63E ILE* 4.1 10.1 - - + -
64E LEU* 3.6 36.3 - - + +
67E LEU* 3.7 21.3 - - + -
91E TYR* 4.0 12.6 - - - +
101E ALA 3.8 12.1 - - - +
102E ALA 2.9 4.3 + - - +
104E GLN* 1.3 89.0 - - + +
106E PHE* 1.3 65.5 + - - +
107E SER 3.1 3.2 + - - -
108E GLY 3.3 2.3 + - - -
109E ILE* 3.5 10.3 + - + +
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Residues in contact with PHE 106 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67E LEU* 3.8 16.4 - - + -
83E ILE* 3.5 40.5 - - + +
86E ILE* 3.8 26.5 - - + -
87E PHE* 3.7 43.1 - + + -
91E TYR* 4.1 4.5 - + - -
102E ALA* 2.9 41.7 + - + +
103E ASN* 4.2 7.9 - - - +
105E ILE* 1.3 76.3 - - - +
107E SER* 1.3 52.9 + - - +
109E ILE* 3.6 18.1 - - + +
110E ASP* 2.7 36.9 + - - +
276E GLY* 3.8 10.3 - - - +
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Residues in contact with SER 107 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50E GLU 4.8 2.5 + - - -
51E CYS* 6.0 0.2 - - - -
103E ASN 2.9 18.2 + - - -
104E GLN 3.7 9.2 - - - -
105E ILE 3.1 0.6 - - - -
106E PHE* 1.3 76.6 - - - +
108E GLY* 1.3 62.1 + - - +
110E ASP* 3.9 1.7 - - - +
111E MSE 3.1 32.2 + - - +
272E PRO* 3.1 38.0 + - - +
273E ARG* 3.5 8.0 + - - -
276E GLY 3.6 11.9 + - - -
277E GLY* 3.6 2.3 - - - +
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Residues in contact with GLY 108 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37E ILE* 3.4 10.0 - - - +
49E GLY* 3.8 0.2 - - - -
50E GLU 3.2 26.9 + - - -
51E CYS* 3.7 12.6 - - - -
105E ILE 3.3 4.8 + - - -
106E PHE 3.3 0.2 - - - -
107E SER* 1.3 76.6 - - - +
109E ILE* 1.3 65.4 + - - +
111E MSE 3.4 7.0 - - - +
112E ALA* 3.1 25.1 + - - +
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Residues in contact with ILE 109 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37E ILE* 4.1 9.4 - - + +
39E ILE* 3.9 2.6 - - + +
64E LEU* 3.9 18.4 - - + -
67E LEU* 4.0 23.8 - - + -
68E ALA* 4.2 12.8 - - + +
71E LEU* 3.7 27.1 - - + -
83E ILE* 4.2 17.3 - - + -
86E ILE* 5.8 1.3 - - + -
105E ILE* 3.5 13.1 + - + +
106E PHE* 3.2 30.2 + - + +
108E GLY* 1.3 76.3 - - - +
110E ASP* 1.3 57.5 + - - +
112E ALA* 3.3 5.9 + - - +
113E MSE 2.9 39.1 + - + +
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Residues in contact with ASP 110 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79E VAL* 3.3 18.8 - - - +
83E ILE* 4.1 11.5 - - + +
106E PHE 2.7 20.5 + - - +
109E ILE* 1.3 71.3 - - - +
111E MSE 1.3 65.9 + - - +
113E MSE 3.1 1.7 + - - +
114E TRP* 3.0 51.0 + - - -
276E GLY 3.8 3.1 - - - +
277E GLY* 3.8 13.0 - - - -
278E ILE* 2.6 30.2 + - - +
279E GLN* 3.1 16.9 + - - +
280E PRO* 4.2 5.0 - - - +
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Residues in contact with MSE 111 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49E GLY* 3.6 10.1 - - - -
50E GLU 3.8 22.4 - - - +
107E SER* 3.1 30.9 + - - +
108E GLY* 3.4 11.9 - - - +
110E ASP* 1.3 79.5 + - - +
112E ALA* 1.3 57.0 + - - +
114E TRP* 3.9 1.0 - - - +
115E ASP* 3.0 28.4 + - - +
272E PRO* 4.0 19.7 - - + -
278E ILE* 3.6 25.3 - - + +
305E ILE* 4.1 12.8 - - - -
306E THR* 4.1 17.9 - - + +
309E ALA* 3.7 28.7 - - + -
356E LEU* 3.6 9.6 - - + +
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Residues in contact with ALA 112 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37E ILE* 3.8 11.7 - - + +
39E ILE* 3.7 18.8 - - + -
47E GLY* 3.4 13.4 - - - +
48E ILE 3.8 12.8 - - - +
49E GLY 3.6 15.3 - - - +
108E GLY 3.1 18.1 + - - +
109E ILE 3.5 4.7 - - - +
110E ASP 3.1 0.2 - - - -
111E MSE 1.3 77.0 - - - +
113E MSE 1.3 58.9 + - - +
115E ASP* 3.3 3.6 + - - +
116E LEU* 3.0 24.6 + - - +
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Residues in contact with MSE 113 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6E ILE* 3.5 26.0 - - + -
39E ILE* 3.8 19.7 - - + -
71E LEU* 4.2 8.5 - - + -
75E SER 3.6 9.6 - - - +
76E PRO* 3.4 39.4 - - + +
79E VAL* 3.7 39.9 - - + -
82E LEU* 3.8 11.7 - - + -
109E ILE* 2.9 27.8 + - + +
110E ASP 3.1 4.7 + - - +
112E ALA* 1.3 78.2 - - - +
114E TRP* 1.3 57.1 + - + +
116E LEU* 3.4 6.7 + - - +
117E GLN* 3.0 32.2 + - - +
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Residues in contact with TRP 114 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79E VAL* 3.9 14.2 - - + +
110E ASP* 3.0 57.1 + - - +
113E MSE 1.3 76.5 - - + +
115E ASP* 1.3 61.2 + - - +
117E GLN* 3.6 31.9 - - - +
118E GLY 2.9 23.9 + - - -
125E VAL* 3.5 19.3 - - + +
128E LEU* 4.0 31.8 - - + +
129E LEU* 4.2 24.7 - - + -
278E ILE* 3.8 25.4 - - + -
279E GLN* 3.6 33.6 - - + +
128G LEU* 4.3 15.7 - - - -
129G LEU 4.7 1.3 - - - -
130G GLY* 4.3 10.8 - - - -
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Residues in contact with ASP 115 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47E GLY* 3.2 1.9 - - - -
48E ILE* 2.8 27.0 + - - +
111E MSE 3.0 18.7 + - - +
112E ALA 3.3 6.0 + - - +
114E TRP* 1.3 76.6 - - - +
116E LEU* 1.3 56.9 + - - +
118E GLY 3.3 1.2 + - - -
119E LYS* 2.8 71.0 + - - +
125E VAL* 4.3 0.6 - - - +
355E GLY* 3.4 6.8 - - - -
356E LEU* 2.7 42.5 + - + +
357E GLY 4.3 0.7 + - - -
358E PHE* 4.4 4.3 + - - -
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Residues in contact with LEU 116 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6E ILE* 4.4 3.1 - - + -
39E ILE* 3.8 31.9 - - + +
41E ALA* 4.1 9.6 - - + -
45E THR* 3.5 46.4 - - + +
47E GLY* 3.8 11.4 - - - +
76E PRO* 3.6 26.7 - - + -
112E ALA 3.0 12.8 + - - +
113E MSE 3.5 11.0 - - - +
114E TRP 3.2 0.2 - - - -
115E ASP* 1.3 74.5 - - - +
117E GLN* 1.3 59.7 + - - +
119E LYS* 3.3 3.1 + - - +
120E LEU* 2.8 48.6 + - + +
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Residues in contact with GLN 117 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76E PRO* 3.1 30.9 + - + +
77E HIS* 3.5 34.8 + - + +
79E VAL* 3.7 21.0 - - - +
113E MSE 3.0 19.3 + - - +
114E TRP* 3.4 37.5 + - - +
116E LEU* 1.3 75.0 - - - +
118E GLY* 1.3 57.7 + - - +
120E LEU* 3.4 9.1 + - - +
121E ALA* 2.9 32.1 + - - +
128E LEU* 3.9 13.3 - - + +
127G GLN 3.9 8.5 - - - +
128G LEU* 5.2 1.7 - - - -
130G GLY* 5.6 0.6 - - - -
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Residues in contact with GLY 118 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114E TRP 2.9 13.8 + - - -
115E ASP 3.7 1.6 - - - -
117E GLN* 1.3 76.5 - - - +
119E LYS* 1.3 50.7 + - - +
121E ALA* 3.2 1.4 + - - -
122E GLY* 2.7 31.9 + - - -
123E LEU 2.9 29.1 + - - -
128E LEU* 3.6 15.4 - - - +
354E PRO* 3.9 0.2 - - - +
355E GLY* 3.5 9.0 - - - -
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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
----------------------------------------------------------
45E THR* 3.6 22.2 - - + -
46E VAL 2.9 26.7 + - - +
47E GLY* 4.4 0.2 - - - -
48E ILE* 4.5 11.9 - - - +
115E ASP* 2.8 50.4 + - - +
116E LEU* 3.7 1.3 - - - +
118E GLY* 1.3 74.2 - - - +
120E LEU* 1.3 64.0 + - - +
122E GLY* 3.2 11.1 + - - -
354E PRO* 4.0 24.4 - - + +
355E GLY 3.7 0.2 - - - +
357E GLY 5.8 0.4 - - - +
358E PHE* 5.0 16.1 + - - +
359E GLN* 6.2 0.9 - - - +
360E LEU* 5.8 0.6 - - - +
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Residues in contact with LEU 120 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4E VAL* 4.0 24.7 - - + -
43E ASP* 3.6 16.2 - - - +
45E THR* 3.5 28.5 - - - +
76E PRO* 4.1 12.3 - - + -
77E HIS* 4.2 20.4 - - + +
116E LEU* 2.8 42.6 + - + +
117E GLN* 3.7 4.9 - - - +
119E LYS* 1.3 77.7 - - - +
121E ALA* 1.3 60.1 + - - +
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Residues in contact with ALA 121 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77E HIS* 6.0 1.3 - - - +
117E GLN 2.9 18.2 + - - +
118E GLY 4.0 1.6 - - - +
120E LEU* 1.3 76.3 - - + +
122E GLY* 1.3 64.5 + - - +
123E LEU* 3.6 28.6 - - + +
128E LEU* 4.5 8.1 - - + -
121G ALA* 5.2 12.6 - - + -
123G LEU* 6.0 4.5 - - + -
----------------------------------------------------------
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Residues in contact with GLY 122 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118E GLY 2.7 12.6 + - - -
119E LYS 3.2 11.7 + - - -
120E LEU 3.3 0.8 + - - -
121E ALA* 1.3 76.2 - - - +
123E LEU* 1.3 62.2 + - - +
124E PRO* 4.8 0.2 - - - +
354E PRO* 4.1 21.6 - - - +
----------------------------------------------------------
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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