Contacts of the helix formed by residues 113 - 145 (chain D) in PDB entry 1EUM
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 ASP 113 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2D LEU* 3.9 16.3 - - - +
3D LYS* 5.4 1.8 + - + -
6D MET* 3.8 17.8 - - + +
60D TYR* 4.5 0.2 + - - -
108D ALA* 2.8 23.5 + - - +
111D ASN* 3.0 11.4 + - + +
112D GLN* 1.3 73.6 - - - +
114D TYR* 1.3 62.2 + - - +
115D PRO* 3.2 12.0 - - - +
116D THR* 2.7 38.7 + - - -
117D PHE* 3.1 17.5 + - - +
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Residues in contact with TYR 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108D ALA 5.7 0.4 - - - -
109D MET* 4.1 31.9 + - + -
112D GLN* 3.2 50.6 + - + +
113D ASP* 1.3 71.0 - - - +
115D PRO* 1.3 69.1 - - + +
117D PHE* 3.7 10.9 - + + +
118D ASN* 2.9 30.7 + - - +
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Residues in contact with PRO 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2D LEU* 5.9 2.0 - - + -
60D TYR* 3.6 12.8 - - + +
112D GLN 5.0 0.7 - - - +
113D ASP* 3.2 12.1 - - - +
114D TYR* 1.3 95.4 - - + +
116D THR* 1.3 57.7 + - - +
118D ASN* 3.2 9.2 + - + +
119D PHE* 2.9 27.4 + - - +
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Residues in contact with THR 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2D LEU* 3.9 4.9 - - - +
6D MET* 3.7 24.5 - - + -
10D LEU* 4.1 11.7 - - + +
60D TYR* 2.6 36.1 + - + -
108D ALA* 4.4 0.9 - - + -
113D ASP* 2.7 32.6 + - - -
115D PRO* 1.3 73.8 - - - +
117D PHE* 1.3 63.1 + - - +
119D PHE* 3.1 3.2 + - + +
120D LEU* 2.8 42.4 + - + +
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Residues in contact with PHE 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105D ALA* 3.6 24.7 - - + -
108D ALA* 3.9 12.0 - - + +
109D MET* 3.5 43.1 - - + +
113D ASP 3.1 17.6 + - - +
114D TYR* 3.7 13.9 - + + +
115D PRO 3.3 0.2 - - - -
116D THR* 1.3 76.7 - - - +
118D ASN* 1.3 66.4 + - - +
120D LEU* 3.3 8.0 + - - +
121D GLN* 2.9 51.7 + - + -
109E MET* 4.3 1.6 - - + -
114E TYR* 3.8 20.9 - + + -
117E PHE* 4.1 26.9 - + - -
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Residues in contact with ASN 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114D TYR 2.9 18.4 + - - +
115D PRO* 3.3 8.4 - - + +
117D PHE* 1.3 81.5 - - + +
119D PHE* 1.3 65.9 + - - +
121D GLN* 3.2 24.5 + - - +
122D TRP 4.5 0.5 + - - -
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Residues in contact with PHE 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D LEU* 4.9 0.7 - - + -
56D ARG* 3.6 41.9 + - + -
57D LEU* 3.9 19.1 - - + -
60D TYR* 3.6 52.5 - + + -
115D PRO 2.9 13.8 + - - +
116D THR* 3.5 9.6 - - + +
118D ASN* 1.3 82.1 + - - +
120D LEU* 1.3 71.8 + - + +
121D GLN 3.3 0.7 + - - -
122D TRP* 3.6 16.1 + - - +
123D TYR* 3.6 30.8 - + - -
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Residues in contact with LEU 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D LEU* 4.7 4.3 - - + -
57D LEU* 5.3 2.2 - - + -
101D ILE* 4.6 11.9 - - + +
104D LEU* 3.6 57.2 - - + +
105D ALA* 3.7 13.7 - - + +
108D ALA* 4.5 2.2 - - + -
116D THR* 2.8 36.5 + - + +
117D PHE* 3.8 5.8 - - - +
118D ASN 3.2 0.6 - - - -
119D PHE* 1.3 90.6 - - + +
121D GLN* 1.3 70.3 + - - +
122D TRP 3.1 0.4 - - - -
123D TYR* 2.8 28.3 + - + +
124D VAL* 3.1 14.0 + - + +
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Residues in contact with GLN 121 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105D ALA* 5.1 1.6 - - - +
117D PHE* 2.9 60.8 + - + +
118D ASN* 3.5 15.9 - - - +
119D PHE 3.2 1.6 - - - -
120D LEU* 1.3 79.9 - - - +
122D TRP* 1.3 61.6 + - - +
124D VAL* 3.2 15.7 + - - +
125D SER* 3.0 24.4 + - - -
114E TYR* 4.7 3.6 - - - +
117E PHE* 5.0 2.9 - - - -
118E ASN* 3.2 38.7 + - - +
121E GLN* 5.9 0.9 - - - +
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Residues in contact with TRP 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52D THR* 5.0 4.5 - - - -
53D HIS* 3.4 34.5 - + - -
56D ARG* 3.3 60.4 - - + +
118D ASN 4.5 0.6 + - - -
119D PHE 3.6 11.5 + - - +
120D LEU 3.1 1.0 - - - -
121D GLN* 1.3 78.1 - - - +
123D TYR* 1.3 87.3 + + - +
125D SER* 3.4 7.6 + - - -
126D GLU* 3.0 54.8 + - + +
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Residues in contact with TYR 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D GLU* 4.1 10.5 - - - -
53D HIS* 2.7 44.5 + + + -
56D ARG* 2.9 20.4 - - - +
57D LEU* 3.3 18.6 + - + +
101D ILE* 3.8 34.8 - - + -
119D PHE* 3.6 35.0 - + - -
120D LEU* 2.8 19.5 + - + +
122D TRP* 1.3 103.9 - + - +
124D VAL* 1.3 61.0 + - - +
126D GLU* 3.8 2.5 - - - +
127D GLN* 2.9 37.5 + - + +
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Residues in contact with VAL 124 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101D ILE* 3.9 19.7 - - + -
102D ASN* 4.9 2.7 - - - +
105D ALA* 5.0 5.4 - - + -
120D LEU 3.1 14.9 + - - +
121D GLN* 3.2 22.9 + - - +
123D TYR* 1.3 77.3 - - - +
125D SER* 1.3 63.3 + - - +
127D GLN* 3.9 3.9 - - - +
128D HIS* 3.3 19.8 + - - +
114E TYR* 3.8 14.6 - - + +
115E PRO* 3.6 37.6 - - + +
118E ASN* 3.8 16.8 - - + +
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Residues in contact with SER 125 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121D GLN 3.0 15.5 + - - -
122D TRP* 3.8 8.3 - - - -
124D VAL* 1.3 77.3 - - - +
126D GLU* 1.3 66.8 + - - +
128D HIS* 3.1 18.5 + - - +
129D GLU* 3.3 12.7 + - - +
118E ASN* 4.2 17.4 + - - -
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Residues in contact with GLU 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49D GLU* 4.3 5.4 - - - +
53D HIS* 4.0 17.0 + - + +
122D TRP* 3.0 57.4 + - + +
123D TYR* 3.8 6.1 - - - +
125D SER* 1.3 78.7 + - - +
127D GLN* 1.3 63.0 + - - +
129D GLU* 2.9 37.1 + - - +
130D GLU* 2.9 32.3 + - - +
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Residues in contact with GLN 127 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D GLU* 5.2 0.3 - - - +
50D GLU* 4.6 1.6 - - - +
53D HIS* 4.1 16.5 + - - -
94D GLU* 3.3 36.5 + - - +
97D ILE* 3.5 23.2 - - + +
98D THR* 2.9 44.7 + - + +
101D ILE* 4.4 10.5 - - + -
123D TYR* 2.9 25.8 + - + +
124D VAL* 3.9 5.8 - - - +
126D GLU* 1.3 72.9 - - - +
128D HIS* 1.3 63.1 + - - +
130D GLU* 3.6 9.3 - - - +
131D GLU* 3.0 29.0 + - - +
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Residues in contact with HIS 128 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98D THR* 6.4 0.4 - - - -
124D VAL 3.3 9.6 + - - +
125D SER* 3.1 12.7 + - - +
126D GLU 3.1 0.6 - - - -
127D GLN* 1.3 77.5 - - - +
129D GLU* 1.3 68.8 + - + +
131D GLU* 4.0 5.3 - - - +
132D LYS* 3.3 26.1 + - + +
60E TYR* 3.6 37.3 + + - -
63E ASP* 3.5 36.1 + - + +
64E THR* 3.9 10.6 - - + +
115E PRO* 5.6 9.6 - - + +
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Residues in contact with GLU 129 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125D SER* 3.3 6.5 + - - +
126D GLU* 2.9 32.1 + - - +
128D HIS* 1.3 84.9 - - + +
130D GLU* 1.3 67.9 + - + +
132D LYS* 3.3 13.1 + - - +
133D LEU* 3.0 22.6 + - - +
162D ASP* 5.3 4.3 - - - +
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Residues in contact with GLU 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46D HIS* 2.9 28.5 + - - -
49D GLU* 2.3 28.6 - - - +
50D GLU* 4.6 3.5 - - - +
53D HIS* 4.0 14.4 - - + -
94D GLU* 3.6 26.9 - - - +
126D GLU* 2.9 29.6 + - - +
127D GLN* 3.6 15.0 - - - +
129D GLU* 1.3 77.9 - - - +
131D GLU* 1.3 65.1 + - - +
133D LEU* 3.0 10.8 + - - +
134D PHE* 2.9 29.5 + - - -
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Residues in contact with GLU 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91D TYR* 3.6 23.7 + - + +
94D GLU* 4.7 11.9 - - + -
95D GLN* 4.0 22.4 + - + +
98D THR* 2.5 40.8 + - - +
127D GLN* 3.0 14.1 + - - +
128D HIS* 4.0 5.4 - - - +
130D GLU* 1.3 77.7 - - - +
132D LYS* 1.3 63.9 + - - +
134D PHE* 3.4 2.6 + - - +
135D LYS* 2.9 26.8 + - - +
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Residues in contact with LYS 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128D HIS* 3.3 15.7 + - + +
129D GLU* 3.5 16.3 - - - +
130D GLU 3.2 0.2 - - - -
131D GLU* 1.3 79.5 - - - +
133D LEU* 1.3 65.6 + - - +
135D LYS* 3.2 6.6 + - - +
136D SER* 3.0 23.4 + - - -
63E ASP* 3.6 55.5 + - + +
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Residues in contact with LEU 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42D PHE* 4.0 13.0 - - + -
46D HIS* 3.4 34.8 - - + +
129D GLU 3.0 13.5 + - - +
130D GLU* 3.0 13.2 + - - +
132D LYS* 1.3 78.8 - - - +
134D PHE* 1.3 63.7 + - + +
136D SER* 2.7 27.7 + - - +
137D ILE* 3.3 7.2 + - + +
161D LEU* 4.3 22.9 - - + -
162D ASP* 3.6 29.6 - - + +
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Residues in contact with PHE 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D TYR* 5.0 3.8 - + - -
42D PHE* 3.9 17.7 - + - -
43D LEU* 4.9 3.6 - - + -
46D HIS* 3.4 48.2 - + + -
87D PHE* 4.7 7.5 - + - +
90D THR* 3.9 36.3 - - + -
91D TYR* 3.9 22.6 - - + +
94D GLU* 3.9 29.2 - - + -
130D GLU* 2.9 34.3 + - - +
131D GLU 4.1 0.4 - - - +
133D LEU* 1.3 78.2 - - + +
135D LYS* 1.3 62.1 + - - +
137D ILE* 3.3 16.0 + - + +
138D ILE* 3.3 24.8 + - - +
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Residues in contact with LYS 135 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91D TYR* 3.8 35.3 - - + +
131D GLU 2.9 19.4 + - - +
132D LYS* 3.3 8.7 - - - +
134D PHE* 1.3 77.8 - - - +
136D SER* 1.3 62.1 + - - +
138D ILE* 3.2 14.4 + - + +
139D ASP* 2.8 52.5 + - - +
63E ASP 5.9 2.7 - - - +
65E GLY* 6.4 1.1 - - - -
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Residues in contact with SER 136 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132D LYS* 3.0 13.8 + - - -
133D LEU* 2.7 25.5 + - - +
135D LYS* 1.3 74.4 - - - +
137D ILE* 1.3 67.9 + - - +
139D ASP* 3.3 10.6 + - - +
140D LYS* 2.9 45.2 + - - +
161D LEU* 4.9 2.3 - - - +
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Residues in contact with ILE 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42D PHE* 3.4 39.7 - - + -
87D PHE* 3.6 36.3 - - + -
133D LEU* 3.3 13.9 + - + +
134D PHE* 3.5 16.8 - - + +
135D LYS 3.2 0.8 - - - -
136D SER* 1.3 79.7 + - - +
138D ILE* 1.3 65.1 + - - +
140D LYS* 3.3 9.3 + - + +
141D LEU* 3.0 30.6 + - + +
154D ILE* 5.5 1.6 - - + +
158D LEU* 3.8 17.5 - - + -
161D LEU* 3.7 22.2 - - + -
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Residues in contact with ILE 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84D ASP* 5.1 3.5 - - - +
87D PHE* 4.2 16.8 - - + +
88D GLN* 3.7 41.5 - - + +
91D TYR* 3.8 27.8 - - + -
134D PHE 3.3 11.0 + - - +
135D LYS* 3.2 17.1 + - + +
137D ILE* 1.3 77.7 - - - +
139D ASP* 1.3 68.9 + - - +
141D LEU* 3.2 10.6 + - + +
142D SER* 3.0 29.1 + - - +
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Residues in contact with ASP 139 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B SER 5.5 0.9 - - - +
35B THR* 3.2 42.6 + - + +
135D LYS* 2.8 52.3 + - - +
136D SER* 3.5 13.1 - - - +
137D ILE 3.2 0.2 - - - -
138D ILE* 1.3 78.1 - - - +
140D LYS* 1.3 63.2 + - + +
142D SER* 3.1 8.9 + - - -
143D LEU* 3.0 22.1 + - - +
----------------------------------------------------------
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Residues in contact with LYS 140 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B THR 6.1 0.9 - - - +
37B GLU* 6.5 1.3 - - - -
152B TYR* 4.8 13.0 - - + -
156B LYS* 6.0 0.9 - - - -
136D SER* 2.9 34.5 + - - +
137D ILE* 3.3 8.3 + - - +
139D ASP* 1.3 76.5 - - + +
141D LEU* 1.3 58.5 + - - +
143D LEU* 3.1 9.4 + - + +
144D ALA* 2.9 31.7 + - - +
145D GLY 3.7 1.2 + - - -
154D ILE* 4.0 18.3 - - + +
157D GLU* 3.6 37.2 + - + +
161D LEU* 4.3 21.0 - - + +
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Residues in contact with LEU 141 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83D LEU* 4.2 18.6 - - + +
84D ASP* 3.6 33.8 - - + +
87D PHE* 4.0 36.8 - - + -
137D ILE* 3.0 22.4 + - + +
138D ILE* 3.5 10.5 - - + +
139D ASP 3.2 0.2 - - - -
140D LYS* 1.3 77.1 - - - +
142D SER* 1.3 59.9 + - - +
145D GLY* 2.7 32.8 + - - +
146D LYS* 5.6 0.2 - - - +
151D LEU* 4.3 14.8 - - + -
154D ILE* 4.0 28.0 - - + -
----------------------------------------------------------
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Residues in contact with SER 142 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84D ASP* 4.9 6.7 + - - -
138D ILE* 3.0 21.3 + - - +
139D ASP* 3.1 10.3 + - - -
141D LEU* 1.3 79.0 - - - +
143D LEU* 1.3 61.6 + - - +
145D GLY 4.7 0.5 + - - -
146D LYS* 5.2 8.9 - - - +
----------------------------------------------------------
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Residues in contact with LEU 143 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B THR* 5.0 17.7 - - - +
36B PHE* 4.1 33.4 - - + -
148B GLY* 3.4 37.0 - - - +
149B GLU 4.3 0.2 + - - -
151B LEU* 4.3 7.9 - - + +
152B TYR* 3.8 35.4 - - + +
155B ASP* 5.5 2.9 - - + -
139D ASP 3.0 12.1 + - - +
140D LYS* 3.1 10.9 + - + +
142D SER* 1.3 80.0 - - - +
144D ALA* 1.3 59.2 + - - +
146D LYS 5.3 0.2 - - - -
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Residues in contact with ALA 144 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B GLU* 4.4 15.7 - - + +
152B TYR* 4.0 31.9 - - + -
140D LYS 2.9 8.6 + - - +
143D LEU* 1.3 75.2 - - - +
145D GLY* 1.3 59.5 + - - +
146D LYS 2.8 12.7 + - - -
147D SER* 3.7 5.4 + - - -
150D GLY* 3.3 22.5 - - - -
153D PHE* 6.2 0.2 - - + -
154D ILE* 3.7 18.2 - - + -
----------------------------------------------------------
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Residues in contact with GLY 145 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141D LEU* 2.7 32.8 + - - -
144D ALA* 1.3 70.9 - - - +
146D LYS* 1.3 64.7 + - - +
147D SER 3.3 3.5 + - - -
151D LEU* 3.7 26.9 - - - +
154D ILE* 3.6 15.0 - - - +
----------------------------------------------------------
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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