Contacts of the helix formed by residues 113 - 145 (chain D) in PDB entry 3IS7
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).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D ASP* 5.6 2.8 + - + -
7D VAL* 3.5 17.4 - - + +
61D ARG* 3.0 25.6 + - - -
65D LEU* 4.0 8.5 - - - +
108D CYS* 2.9 24.4 + - + +
111D VAL* 3.2 14.1 - - + +
112D HIS* 1.3 72.0 - - - +
114D TYR* 1.3 56.2 + - - +
115D VAL 3.6 1.6 + - - -
116D SER* 2.6 27.8 + - - -
117D ARG 3.1 18.2 + - - -
102U ARG* 4.1 4.9 - - - +
128U GLU* 4.7 2.9 - - - +
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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
----------------------------------------------------------
109D GLU* 3.5 39.3 + - - -
112D HIS* 3.1 59.4 + - + -
113D ASP* 1.3 70.9 - - - +
115D VAL* 1.3 61.5 + - - +
117D ARG* 3.4 8.9 + - - +
118D ASP* 3.0 27.2 + - - +
102U ARG* 4.1 12.5 - - + +
105U ILE* 3.6 42.2 - - + -
106U VAL* 3.3 18.7 + - - +
117U ARG* 3.8 13.1 + - - +
121U LYS* 4.3 18.1 - - + +
124U LEU* 3.9 16.4 - - + -
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Residues in contact with VAL 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61D ARG* 3.5 31.0 - - - +
113D ASP* 3.3 1.2 + - - -
114D TYR* 1.3 76.5 - - - +
116D SER* 1.3 64.7 + - - +
118D ASP* 3.1 8.7 + - + +
119D LEU* 3.1 23.6 + - + +
121U LYS* 4.9 3.6 - - + +
124U LEU* 3.9 13.9 - - + -
125U GLU* 3.9 44.4 - - + +
128U GLU* 3.6 24.8 + - + +
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Residues in contact with SER 116 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D VAL* 4.0 4.9 - - - +
11D LEU* 4.1 8.6 - - - +
61D ARG* 3.0 25.9 + - - +
65D LEU* 3.9 7.1 - - - +
108D CYS* 3.8 14.4 - - - -
113D ASP* 2.6 37.0 + - - -
115D VAL* 1.3 76.8 - - - +
117D ARG* 1.3 63.2 + - - +
119D LEU* 3.4 8.3 + - - +
120D LEU* 2.9 28.8 + - - +
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Residues in contact with ARG 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105D ILE* 4.0 23.5 - - + +
106D VAL* 5.7 0.2 - - - +
108D CYS* 3.9 16.3 - - + -
109D GLU* 2.8 42.6 + - - +
113D ASP 3.1 13.8 + - - +
114D TYR* 3.5 12.6 - - - +
115D VAL 3.1 0.2 - - - -
116D SER* 1.3 79.0 - - - +
118D ASP* 1.3 57.9 + - - +
120D LEU* 3.3 6.9 + - - +
121D LYS* 3.0 34.1 + - + +
109E GLU* 2.5 43.0 + - - -
114E TYR* 3.8 19.0 + - - +
117E ARG* 4.3 14.3 - - - +
117U ARG* 4.2 14.7 - - - +
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Residues in contact with ASP 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114D TYR 3.0 14.2 + - - +
115D VAL* 3.4 11.9 - - + +
117D ARG* 1.3 76.9 - - - +
119D LEU* 1.3 64.5 + - - +
121D LYS* 3.4 23.2 + - - +
122D ASP* 3.1 35.9 + - - +
118U ASP* 5.6 0.5 - - - +
121U LYS* 3.7 27.0 - - + +
122U ASP* 5.3 2.8 - - - +
125U GLU* 4.6 12.9 - - - +
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Residues in contact with LEU 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D LEU* 5.3 1.6 - - + -
57D LYS* 3.9 24.5 - - + +
58D LEU* 3.7 28.5 - - + -
61D ARG* 3.6 42.4 - - + +
115D VAL* 3.1 12.4 + - + +
116D SER* 3.5 9.0 - - - +
118D ASP* 1.3 74.4 - - - +
120D LEU* 1.3 67.9 + - + +
122D ASP* 3.3 10.6 + - - +
123D ILE* 3.0 36.2 + - + +
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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 HIS* 5.8 0.2 - - + -
11D LEU* 3.8 26.0 - - + -
14D ILE* 4.2 6.3 - - + -
58D LEU* 4.1 16.8 - - + -
101D LEU* 4.0 23.7 - - + +
104D ALA* 3.6 33.4 - - + -
105D ILE* 3.5 18.6 - - + -
108D CYS* 4.0 20.0 - - - -
116D SER 2.9 21.8 + - - +
117D ARG 3.3 1.1 + - - +
119D LEU* 1.3 77.3 - - + +
121D LYS* 1.3 58.0 + - - +
123D ILE* 3.2 7.5 + - + +
124D LEU* 2.8 28.4 + - - +
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Residues in contact with LYS 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105D ILE* 4.0 10.7 - - + +
117D ARG* 3.0 26.6 + - + +
118D ASP* 3.5 23.3 + - - +
120D LEU* 1.3 73.2 - - - +
122D ASP* 1.3 79.5 + - - +
124D LEU* 3.2 5.6 + - + +
125D GLU* 3.0 32.2 + - + +
114E TYR* 4.2 27.6 - - + +
115E VAL* 5.0 4.6 - - + +
118E ASP* 3.7 43.6 + - + +
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Residues in contact with ASP 122 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54D HIS* 5.0 1.5 + - - -
118D ASP* 3.1 23.9 + - - +
119D LEU* 3.5 10.8 - - - +
121D LYS* 1.3 96.6 + - - +
123D ILE* 1.3 65.8 + - + +
125D GLU* 3.5 11.0 + - - +
126D SER* 3.3 19.9 + - - -
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Residues in contact with ILE 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14D ILE* 4.9 1.6 - - + -
18D GLU* 3.5 22.0 - - - +
54D HIS* 3.9 32.3 - - + +
57D LYS* 5.8 1.6 - - + -
58D LEU* 4.0 24.0 - - + -
101D LEU* 4.1 12.8 - - + -
119D LEU* 3.0 35.1 + - + +
120D LEU* 3.2 13.4 + - + +
122D ASP* 1.3 76.5 - - + +
124D LEU* 1.3 56.5 + - - +
126D SER* 3.2 8.5 + - - -
127D GLU* 2.9 41.8 + - + +
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Residues in contact with LEU 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98D THR* 3.4 26.9 - - - +
101D LEU* 4.1 24.0 - - + +
102D ARG* 3.7 29.4 - - + +
105D ILE* 4.0 20.9 - - + -
120D LEU 2.8 19.9 + - - +
121D LYS* 3.2 6.7 + - - +
123D ILE* 1.3 69.3 - - - +
125D GLU* 1.3 61.4 + - - +
127D GLU* 3.1 1.2 + - - +
128D GLU* 2.8 49.5 + - - +
114E TYR* 4.1 19.1 - - + -
115E VAL* 4.0 8.7 - - + -
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Residues in contact with GLU 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121D LYS* 3.0 21.0 + - + +
122D ASP* 3.8 11.2 - - - +
124D LEU* 1.3 76.8 - - - +
126D SER* 1.3 59.2 + - - +
128D GLU* 3.2 3.3 + - - +
129D GLU* 2.9 48.7 + - + +
115E VAL* 3.9 31.0 - - + +
118E ASP* 4.6 12.3 - - - +
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Residues in contact with SER 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50D ASP* 5.2 5.7 + - - +
54D HIS* 3.0 31.6 + - - -
122D ASP 3.3 9.5 + - - -
123D ILE 3.2 9.2 + - - -
125D GLU* 1.3 80.8 - - - +
127D GLU* 1.3 58.3 + - - +
129D GLU* 3.4 17.0 + - - +
130D HIS* 3.0 24.9 + - - +
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Residues in contact with GLU 127 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18D GLU* 2.7 27.3 - - - +
51D GLU* 2.8 23.7 - - - +
54D HIS* 3.8 5.6 + - - -
94D GLU* 2.8 39.4 - - - +
97D ALA* 5.1 5.5 - - + +
98D THR* 4.1 13.5 - - - +
101D LEU* 3.7 20.6 - - + -
123D ILE* 2.9 25.9 + - + +
124D LEU* 3.1 6.0 + - - +
126D SER* 1.3 77.5 + - - +
128D GLU* 1.3 59.2 + - - +
130D HIS* 3.0 7.8 + - - +
131D ILE* 2.9 31.6 + - - +
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Residues in contact with GLU 128 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98D THR* 4.2 4.3 - - - +
102D ARG* 2.6 37.9 + - - +
124D LEU* 2.8 26.3 + - + +
125D GLU* 3.7 5.4 - - - +
127D GLU* 1.3 75.4 - - - +
129D GLU* 1.3 64.0 + - + +
131D ILE* 3.3 13.8 + - + +
132D ASP* 2.9 22.9 + - - +
61E ARG* 2.9 38.3 + - - +
64E PHE* 3.7 18.7 - - + -
113E ASP* 4.7 0.3 - - - +
115E VAL* 3.4 19.2 - - + +
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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 GLU* 2.9 35.3 + - + +
126D SER* 3.6 17.3 - - - +
128D GLU* 1.3 75.7 - - - +
130D HIS* 1.3 64.5 + - - +
132D ASP* 3.2 9.1 + - - +
133D TYR* 3.0 21.8 + - - +
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Residues in contact with HIS 130 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25D TYR* 3.7 32.6 + + - -
44D GLU* 4.7 1.4 + - - -
47D GLU* 2.9 48.5 + - + +
51D GLU* 6.0 0.4 - - - -
90D ASP* 4.5 6.8 + - + -
94D GLU* 3.3 24.0 + - - +
126D SER 3.0 14.5 + - - +
127D GLU* 3.0 12.0 + - - +
129D GLU* 1.3 76.7 - - - +
131D ILE* 1.3 61.6 + - - +
133D TYR* 3.3 12.1 + + - -
134D LEU* 3.0 43.4 + - + +
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Residues in contact with ILE 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91D LEU* 4.0 13.9 - - + -
94D GLU* 3.6 27.1 - - + +
95D LEU* 4.2 19.7 - - + -
98D THR* 3.9 24.2 - - + +
102D ARG* 6.1 0.2 - - - +
127D GLU 2.9 20.3 + - - +
128D GLU* 3.3 15.5 + - + +
130D HIS* 1.3 72.1 - - - +
132D ASP* 1.3 63.5 + - - +
134D LEU* 3.2 6.9 + - - +
135D GLU* 3.0 46.5 + - - +
64E PHE* 4.3 12.8 - - + -
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Residues in contact with ASP 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128D GLU 2.9 14.5 + - - +
129D GLU* 3.4 12.9 - - - +
130D HIS 3.2 0.2 - - - -
131D ILE* 1.3 76.9 - - - +
133D TYR* 1.3 60.2 + - - +
135D GLU* 4.0 4.6 - - - +
136D THR* 2.7 41.8 + - - -
64E PHE* 3.6 30.5 - - + +
34F ASP* 4.4 13.0 - - - +
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Residues in contact with TYR 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40D LEU* 3.7 24.4 - - - +
43D HIS* 3.3 56.1 - + + +
44D GLU* 5.6 3.1 - - - -
47D GLU* 4.8 1.1 - - - +
87D LEU* 4.7 3.5 - - + +
129D GLU 3.0 13.5 + - - +
130D HIS* 3.3 18.1 + + + +
132D ASP* 1.3 78.7 - - - +
134D LEU* 1.3 78.2 + - + +
136D THR* 3.2 6.6 + - - -
137D GLN* 2.9 71.5 + - + +
153D HIS* 5.2 2.4 + - - -
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Residues in contact with LEU 134 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44D GLU* 5.7 0.7 - - - +
87D LEU* 3.8 39.0 - - + +
90D ASP* 4.0 17.7 - - + +
91D LEU* 4.1 30.1 - - + +
94D GLU* 4.4 3.4 - - + -
130D HIS* 3.0 59.2 + - + +
131D ILE* 3.2 6.9 + - - +
133D TYR* 1.3 84.0 - - + +
135D GLU* 1.3 66.7 + - - +
137D GLN* 3.1 5.1 + - - +
138D LEU* 3.0 31.1 + - + +
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Residues in contact with GLU 135 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91D LEU* 4.2 17.2 - - + +
95D LEU* 5.5 2.9 - - - +
131D ILE* 3.0 35.9 + - + +
132D ASP* 4.0 3.5 - - - +
134D LEU* 1.3 75.7 - - - +
136D THR* 1.3 64.2 + - - +
138D LEU* 3.4 8.9 + - - +
139D GLY* 3.0 20.6 + - - -
64E PHE* 4.5 18.2 - - - +
66E GLU* 4.3 19.7 - - - +
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Residues in contact with THR 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132D ASP* 2.7 30.3 + - - -
133D TYR* 3.4 6.9 - - - -
135D GLU* 1.3 78.9 - - - +
137D GLN* 1.3 67.5 + - - +
139D GLY* 3.1 3.4 + - - -
140D LEU* 2.8 29.9 + - + +
33F ASN 5.0 1.3 + - - +
34F ASP 3.4 14.6 + - - +
35F TRP* 3.6 7.1 - - - +
36F GLY* 3.4 38.4 - - - +
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Residues in contact with GLN 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87D LEU* 4.0 16.2 - - + -
133D TYR* 2.9 69.0 + - + +
134D LEU* 3.1 5.1 + - - +
136D THR* 1.3 87.9 - - - +
138D LEU* 1.3 64.6 + - - +
140D LEU* 3.0 13.4 + - - +
141D ILE* 3.0 27.7 + - - +
149D TYR* 2.7 41.6 + - - +
153D HIS* 3.9 11.7 + - - -
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Residues in contact with LEU 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84D GLN* 4.3 13.0 - - + +
87D LEU* 3.8 38.8 - - + +
88D GLN* 4.5 13.7 - - + +
91D LEU* 3.8 28.0 - - + -
134D LEU 3.0 27.2 + - - +
135D GLU* 3.7 6.1 - - - +
137D GLN* 1.3 77.3 - - - +
139D GLY* 1.3 63.3 + - - +
141D ILE* 3.3 22.0 + - + +
142D GLN* 3.4 17.9 + - - +
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Residues in contact with GLY 139 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135D GLU 3.0 14.1 + - - -
136D THR* 3.5 4.7 - - - -
138D LEU* 1.3 75.7 - - - +
140D LEU* 1.3 62.2 + - - +
142D GLN* 3.3 10.4 + - - +
143D LYS* 3.1 38.8 + - - +
35F TRP 5.5 0.9 - - - -
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Residues in contact with LEU 140 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136D THR* 2.8 29.0 + - + +
137D GLN* 3.0 26.2 + - - +
139D GLY* 1.3 73.2 - - - +
141D ILE* 1.3 58.6 + - - +
143D LYS* 4.3 6.3 - - + +
144D VAL* 2.8 42.1 + - + +
149D TYR* 3.8 10.5 - - + -
35F TRP 3.4 19.5 - - - +
36F GLY* 4.0 12.8 - - - +
37F LEU* 4.0 14.6 - - + -
154F MET* 3.8 42.6 - - + -
----------------------------------------------------------
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Residues in contact with ILE 141 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83D THR* 4.8 1.8 - - + -
84D GLN* 4.5 17.7 - - + -
87D LEU* 4.0 21.1 - - + -
137D GLN 3.0 15.2 + - - +
138D LEU* 3.4 15.9 - - + +
140D LEU* 1.3 77.9 - - - +
142D GLN* 1.3 75.8 + - - +
145D GLY* 3.1 22.7 + - - -
146D LEU* 3.7 32.0 + - + +
149D TYR* 3.5 39.9 - - + -
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Residues in contact with GLN 142 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138D LEU 3.7 12.1 + - - +
139D GLY* 3.3 11.4 + - - +
141D ILE* 1.3 92.4 - - - +
143D LYS* 1.3 62.9 + - + +
145D GLY* 4.2 2.6 + - - -
147F GLU* 4.7 4.3 - - - +
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Residues in contact with LYS 143 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139D GLY* 3.1 25.9 + - - +
140D LEU* 3.0 9.6 + - + +
142D GLN* 1.3 82.2 - - + +
144D VAL* 1.3 64.2 + - + +
35F TRP* 3.8 57.3 + - + +
37F LEU* 4.8 11.9 - - + -
146F LEU* 5.5 1.0 - - - +
147F GLU* 3.7 13.8 - - - +
150F LEU* 3.6 29.3 - - + +
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Residues in contact with VAL 144 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140D LEU* 2.8 33.6 + - + +
143D LYS* 1.3 77.5 - - + +
145D GLY* 1.3 68.5 + - - +
148D ASN* 3.1 33.5 + - + +
149D TYR* 3.7 21.8 - - + +
37F LEU* 4.9 0.2 - - + -
147F GLU* 3.5 25.0 - - - +
150F LEU* 3.7 12.8 - - + -
151F GLN* 3.6 25.8 - - + +
154F MET* 4.1 16.8 - - - -
----------------------------------------------------------
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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 ILE 3.1 18.1 + - - -
142D GLN 4.2 1.5 + - - -
143D LYS 3.5 1.8 - - - -
144D VAL* 1.3 80.5 - - - +
146D LEU* 1.3 60.0 + - - -
147D GLU 3.4 2.2 - - - -
148D ASN 3.4 0.8 + - - -
149D TYR* 2.9 30.5 + - - +
147F GLU* 3.9 14.5 + - - -
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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