Contacts of the helix formed by residues 127 - 157 (chain V) in PDB entry 3A68
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 GLY 127 (chain V).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122V ASP* 5.5 0.2 - - - -
123V HIS* 2.8 19.6 + - - -
124V ALA 4.8 0.4 - - - -
125V ASP 3.4 2.2 - - - -
126V LYS* 1.3 82.0 - - - +
128V ASP* 1.3 67.1 + - - -
129V ALA 3.4 2.8 + - - -
130V LEU 3.5 0.8 + - - -
131V HIS* 3.1 18.7 + - - +
193V LYS* 3.9 17.3 - - - +
197V VAL* 6.6 0.4 - - - -
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Residues in contact with ASP 128 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190M ARG* 3.2 39.3 + - - -
69V TYR* 4.1 15.4 + - + +
70V PHE* 3.6 16.0 - - + -
75V VAL* 3.6 15.9 - - - +
77V LEU* 3.9 1.7 - - - +
121V PHE 3.6 20.4 - - - +
122V ASP* 4.3 8.7 + - - +
123V HIS 4.1 4.8 + - - +
127V GLY* 1.3 73.3 - - - +
129V ALA* 1.3 74.1 + - - +
131V HIS* 3.7 1.4 - - - +
132V ALA* 2.9 31.4 + - - +
197V VAL* 5.0 0.3 - - - +
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Residues in contact with ALA 129 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70V PHE* 4.2 0.4 - - - -
77V LEU* 4.1 3.8 - - + -
80V LEU* 3.7 28.3 - - + +
127V GLY 3.4 0.6 - - - -
128V ASP* 1.3 84.0 + - - +
130V LEU* 1.3 63.9 + - - +
132V ALA* 3.4 1.9 + - - +
133V MET* 3.0 27.9 + - - +
188V LEU* 3.9 14.6 - - + -
197V VAL* 3.7 31.9 - - + -
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Residues in contact with LEU 130 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126V LYS* 3.6 36.8 - - + +
127V GLY 3.5 1.6 + - - -
128V ASP 3.4 0.2 - - - -
129V ALA* 1.3 75.0 - - - +
131V HIS* 1.3 67.6 + - - +
133V MET* 3.3 0.9 + - - -
134V GLU* 2.9 57.8 + - + +
185V VAL* 3.9 17.9 - - + +
188V LEU* 4.0 21.6 - - + +
189V ARG* 3.9 34.3 - - + +
197V VAL* 5.8 2.6 - - + +
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Residues in contact with HIS 131 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B LEU* 4.6 12.7 - - + +
118V LEU* 6.3 0.8 - - - +
121V PHE* 3.4 26.5 - - + +
122V ASP 3.9 10.7 + - - -
123V HIS* 3.5 35.8 - + + -
126V LYS* 4.1 15.6 - - + +
127V GLY 3.1 16.2 + - - +
128V ASP 3.7 2.2 - - - +
130V LEU* 1.3 80.5 - - - +
132V ALA* 1.3 56.6 + - - +
134V GLU* 3.3 4.4 + - - +
135V LEU* 2.9 64.0 + - + +
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Residues in contact with ALA 132 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66V MET* 3.1 33.1 - - + +
70V PHE* 3.3 35.2 - - + -
80V LEU* 4.9 0.2 - - + -
84V PHE* 4.2 4.5 - - + -
121V PHE* 4.6 5.6 - - + -
128V ASP 2.9 8.8 + - - +
129V ALA 3.8 2.5 - - - +
131V HIS* 1.3 77.8 - - - +
133V MET* 1.3 58.6 + - - +
135V LEU* 3.3 6.7 + - - +
136V ALA* 2.9 24.1 + - - +
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Residues in contact with MET 133 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80V LEU* 4.3 13.7 - - + -
83V PHE* 3.7 31.0 - - + -
84V PHE* 4.1 9.2 - - + -
129V ALA 3.0 13.3 + - - +
130V LEU 3.8 2.7 - - - +
132V ALA* 1.3 72.7 - - - +
134V GLU* 1.3 61.4 + - - +
136V ALA* 3.4 1.3 + - - -
137V LEU* 2.9 28.6 + - - +
181V ILE* 3.5 14.4 - - - +
184V TYR* 3.5 38.8 - - + -
185V VAL* 3.8 17.5 - - + -
188V LEU* 3.6 24.7 - - + -
200V PHE* 4.7 2.9 - - + -
204V LEU* 4.0 15.7 - - + -
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Residues in contact with GLU 134 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B LEU* 3.7 13.0 - - + +
28B VAL* 4.6 16.6 - - + +
126V LYS* 2.9 37.1 + - - +
130V LEU* 2.9 40.5 + - + +
131V HIS* 3.7 4.9 + - - +
133V MET* 1.3 74.7 - - - +
135V LEU* 1.3 59.4 + - - +
137V LEU* 3.4 6.5 + - - +
138V SER* 3.0 31.5 + - - -
185V VAL* 4.1 14.6 - - + -
189V ARG* 2.8 35.7 + - - +
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Residues in contact with LEU 135 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B PHE* 4.7 14.1 - - + -
21B VAL* 5.0 16.4 - - + +
25B LEU* 3.4 35.4 - - + -
66V MET* 4.8 5.6 - - + -
118V LEU* 5.5 4.3 - - + -
121V PHE* 3.8 29.2 - - + -
131V HIS* 2.9 43.0 + - + +
132V ALA* 3.5 8.7 - - - +
133V MET 3.3 0.2 - - - -
134V GLU* 1.3 74.9 - - - +
136V ALA* 1.3 59.6 + - - +
138V SER* 3.1 4.0 + - - +
139V LEU* 2.8 30.0 + - - +
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Residues in contact with ALA 136 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63V TYR* 3.9 29.1 + - + +
66V MET* 4.6 4.9 - - + +
84V PHE* 4.1 11.9 - - + -
132V ALA 2.9 17.3 + - - +
133V MET* 3.6 8.5 - - - +
134V GLU 3.3 0.2 - - - -
135V LEU* 1.3 76.3 - - - +
137V LEU* 1.3 62.6 + - - +
139V LEU* 3.2 8.0 + - - +
140V GLU* 2.9 28.2 + - - +
181V ILE* 4.2 12.6 - - + -
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Residues in contact with LEU 137 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B VAL* 4.2 20.9 - - + -
36B LEU* 3.8 28.0 - - + +
133V MET 2.9 17.7 + - - +
134V GLU* 3.6 6.3 - - - +
135V LEU 3.3 0.2 - - - -
136V ALA* 1.3 74.8 - - - +
138V SER* 1.3 59.4 + - - +
140V GLU* 3.2 4.4 + - + +
141V LYS* 3.0 40.3 + - + +
178V ILE* 3.8 27.6 - - + +
181V ILE* 3.6 12.7 - - + +
182V SER* 3.4 31.6 - - - +
185V VAL* 4.5 8.7 - - + -
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Residues in contact with SER 138 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B VAL* 4.1 9.4 - - - +
24B GLU* 3.2 22.8 + - - +
25B LEU* 3.0 43.2 + - - +
28B VAL* 5.0 4.5 - - - +
134V GLU 3.0 14.7 + - - -
135V LEU* 3.1 8.7 + - - -
137V LEU* 1.3 77.4 - - - +
139V LEU* 1.3 57.6 + - - +
141V LYS* 3.4 2.4 + - - -
142V LEU* 3.0 25.8 + - - +
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Residues in contact with LEU 139 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B PHE* 5.3 0.4 - - + -
17B PRO* 4.0 20.9 - - + -
21B VAL* 3.9 20.5 - - + +
59V VAL* 4.0 34.3 - - + +
62V VAL* 3.6 38.1 - - + -
63V TYR* 5.2 8.1 - - + +
66V MET* 5.9 0.9 - - - -
135V LEU 2.8 15.8 + - - +
136V ALA* 3.2 8.3 + - - +
138V SER* 1.3 78.0 - - - +
140V GLU* 1.3 58.4 + - + +
142V LEU* 3.4 12.5 + - + +
143V THR* 2.9 31.6 + - - -
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Residues in contact with GLU 140 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59V VAL* 4.1 5.8 - - - +
63V TYR* 2.5 37.9 + - - +
91V GLU* 3.7 14.5 - - - +
136V ALA 2.9 19.7 + - - +
137V LEU* 3.7 5.2 - - - +
139V LEU* 1.3 75.8 - - - +
141V LYS* 1.3 60.5 + - - +
143V THR* 3.3 4.5 + - - +
144V ASN* 2.9 25.3 + - - +
174V GLN* 2.7 45.9 + - - +
177V ALA* 4.1 12.6 - - + +
178V ILE* 3.9 13.7 - - + -
181V ILE* 3.5 17.9 - - + -
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Residues in contact with LYS 141 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B GLU* 3.5 26.9 - - + +
27B LEU 5.4 3.6 + - - -
28B VAL* 5.7 2.2 - - - +
29B PRO* 5.0 8.3 - - - +
35B SER 5.5 0.2 + - - -
36B LEU 2.8 29.6 + - - -
37B ALA 3.7 14.4 - - - -
38B ARG 3.3 19.1 + - - -
39B GLN* 3.0 43.1 + - + +
137V LEU* 3.0 35.4 + - + +
138V SER* 3.8 4.9 - - - +
139V LEU 3.3 0.2 - - - -
140V GLU* 1.3 77.5 - - - +
142V LEU* 1.3 62.4 + - - +
144V ASN* 3.1 1.7 + - - +
145V GLU* 3.0 12.1 + - - +
178V ILE* 4.2 9.0 - - + -
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Residues in contact with LEU 142 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B PHE* 3.5 32.5 - - + -
17B PRO 4.1 7.0 - - - +
20B GLU* 3.5 44.2 - - + +
21B VAL* 4.1 5.4 - - + -
24B GLU* 3.8 11.1 + - + +
138V SER 3.0 17.6 + - - +
139V LEU* 3.6 20.2 - - + +
141V LYS* 1.3 74.7 - - - +
143V THR* 1.3 64.2 + - - +
145V GLU* 3.2 17.8 + - + +
146V LYS* 3.0 31.9 + - + +
----------------------------------------------------------
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Residues in contact with THR 143 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B PHE* 6.0 0.2 - - - -
52V GLN* 3.9 7.2 - - - +
55V VAL* 4.2 7.2 - - + +
56V GLU* 3.7 29.4 - - - +
59V VAL* 3.4 24.2 - - + +
139V LEU* 2.9 18.9 + - - +
140V GLU* 3.6 9.7 + - - +
141V LYS 3.2 0.2 - - - -
142V LEU* 1.3 77.9 - - - +
144V ASN* 1.3 57.5 + - - +
146V LYS* 3.2 8.7 + - - +
147V LEU* 2.8 29.1 + - + +
174V GLN* 3.7 18.2 - - - +
222V CA 4.3 2.5 - - - -
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Residues in contact with ASN 144 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B GLN* 2.9 31.6 + - - +
105B ARG* 6.1 0.4 - - - +
140V GLU 2.9 13.8 + - - +
141V LYS 3.1 9.4 + - - +
143V THR* 1.3 73.2 - - - +
145V GLU* 1.3 65.0 + - - +
147V LEU* 3.2 2.8 + - - +
148V LEU* 2.9 47.4 + - - +
171V LEU* 4.5 11.3 - - - +
174V GLN* 3.4 29.0 - - + +
175V VAL* 5.2 9.0 - - - +
178V ILE* 3.9 7.9 - - + +
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Residues in contact with GLU 145 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B GLU* 4.2 12.7 - - - +
39B GLN* 4.2 5.2 + - - +
40B LYS* 4.1 32.1 + - - +
141V LYS 3.0 11.6 + - - +
142V LEU* 3.2 20.3 + - + +
144V ASN* 1.3 77.6 - - - +
146V LYS* 1.3 57.6 + - + +
148V LEU* 3.3 4.7 + - - +
149V ASN* 2.9 45.7 + - - +
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Residues in contact with LYS 146 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B ILE 5.5 2.0 + - - -
15B PHE* 3.5 20.8 - - + -
20B GLU* 3.2 33.7 + - - -
51V GLU* 5.4 7.4 + - + +
52V GLN* 3.4 23.1 - - - +
55V VAL* 4.2 20.6 - - + -
142V LEU* 3.0 24.8 + - + +
143V THR 3.5 6.7 - - - +
145V GLU* 1.3 75.7 - - + +
147V LEU* 1.3 60.0 + - - +
149V ASN* 3.2 20.0 + - + +
150V LEU* 2.9 24.6 + - - +
----------------------------------------------------------
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Residues in contact with LEU 147 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52V GLN* 3.5 30.7 + - + +
56V GLU* 4.1 2.9 - - - +
98V LEU* 5.5 0.2 - - + -
143V THR* 2.8 21.8 + - + +
144V ASN 3.6 4.3 - - - +
146V LYS* 1.3 76.5 - - - +
148V LEU* 1.3 58.8 + - - +
150V LEU* 3.2 10.6 + - + +
151V HIS* 2.9 26.7 + - - +
166V VAL* 3.9 11.8 - - + +
170V TYR* 3.7 42.4 - - + +
171V LEU* 3.9 15.0 - - + -
174V GLN* 3.8 37.7 - - + +
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Residues in contact with LEU 148 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B LYS* 3.5 36.6 - - + -
158B GLY 5.4 2.2 - - - +
160B VAL* 3.3 34.1 - - + -
161B GLN* 5.4 2.7 - - + +
144V ASN* 2.9 38.5 + - - +
145V GLU* 3.7 4.7 - - - +
147V LEU* 1.3 76.3 - - - +
149V ASN* 1.3 57.8 + - - +
151V HIS* 3.3 5.5 + - + +
152V SER* 2.9 32.2 + - - -
171V LEU* 4.1 14.8 - - + -
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Residues in contact with ASN 149 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145V GLU* 2.9 34.3 + - - +
146V LYS* 3.3 24.3 - - + +
148V LEU* 1.3 76.9 - - - +
150V LEU* 1.3 63.9 + - - +
152V SER* 3.1 10.6 + - - -
153V VAL* 3.0 28.4 + - + +
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Residues in contact with LEU 150 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48V ALA* 3.5 37.9 - - + +
49V VAL* 3.9 14.4 - - + +
52V GLN* 3.9 30.3 - - + +
98V LEU* 4.6 13.9 - - + -
146V LYS 2.9 13.0 + - - +
147V LEU* 3.2 11.6 + - + +
149V ASN* 1.3 75.0 - - - +
151V HIS* 1.3 63.4 + - - +
153V VAL* 3.2 7.0 + - + +
154V ALA* 3.1 19.5 + - - +
162V LEU* 4.5 9.9 - - + -
166V VAL* 3.6 29.2 - - + -
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Residues in contact with HIS 151 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B VAL* 3.2 30.2 - - + +
147V LEU 2.9 14.4 + - - +
148V LEU* 3.5 12.3 + - + +
149V ASN 3.2 0.2 - - - -
150V LEU* 1.3 77.9 - - - +
152V SER* 1.3 59.9 + - - +
154V ALA* 3.2 7.8 + - - +
155V THR* 2.9 49.2 + - + +
163V ALA* 3.4 30.5 + - - +
166V VAL* 4.3 14.6 - - + -
167V GLU* 2.7 33.0 + - + -
171V LEU* 4.6 1.8 - - + -
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Residues in contact with SER 152 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148V LEU 2.9 16.6 + - - -
149V ASN* 3.1 14.0 + - - -
151V HIS* 1.3 77.0 + - - +
153V VAL* 1.3 59.8 + - - +
155V THR* 3.3 9.2 + - - -
156V LYS* 2.9 31.9 + - - +
----------------------------------------------------------
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Residues in contact with VAL 153 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44V GLU* 3.6 49.6 - - + +
45V SER* 4.2 4.9 - - - -
48V ALA* 3.7 19.5 - - + -
149V ASN* 3.0 21.2 + - + +
150V LEU* 3.2 7.6 + - + +
152V SER* 1.3 76.0 - - - +
154V ALA* 1.3 64.1 + - - +
156V LYS* 3.4 6.9 + - + +
157V ASN* 3.0 34.3 + - - +
162V LEU* 5.8 0.4 - - + -
----------------------------------------------------------
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Residues in contact with ALA 154 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45V SER* 4.7 1.3 - - - -
150V LEU 3.1 10.5 + - - +
151V HIS* 3.4 9.4 - - - +
153V VAL* 1.3 77.7 - - - +
155V THR* 1.3 56.9 + - - +
157V ASN 3.2 2.3 + - - -
158V GLY 2.9 8.3 + - - -
159V ASP* 2.8 33.7 + - - +
162V LEU* 3.7 25.5 - - + +
163V ALA* 3.7 32.3 - - + +
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Residues in contact with THR 155 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151V HIS* 2.9 44.0 + - + +
152V SER* 3.3 13.9 + - - -
153V VAL 3.4 0.2 - - - -
154V ALA* 1.3 73.2 - - - +
156V LYS* 1.3 67.5 + - - +
158V GLY* 3.0 14.9 + - - +
159V ASP 4.9 0.9 - - - +
163V ALA* 4.1 12.3 - - + -
----------------------------------------------------------
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Residues in contact with LYS 156 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44V GLU* 3.0 35.9 + - - +
152V SER 2.9 20.0 + - - +
153V VAL* 3.6 7.0 - - + +
155V THR* 1.3 78.8 + - - +
157V ASN* 1.3 68.1 + - - +
158V GLY 3.3 0.4 + - - -
----------------------------------------------------------
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Residues in contact with ASN 157 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42V VAL* 3.7 34.3 - - + +
44V GLU* 2.9 38.2 + - - +
45V SER* 4.1 7.3 + - - +
153V VAL* 3.0 30.0 + - - +
154V ALA 4.0 2.2 - - - +
155V THR 3.1 0.6 - - - -
156V LYS* 1.3 87.8 + - - +
158V GLY* 1.3 63.1 + - - +
159V ASP* 3.3 3.4 + - + +
----------------------------------------------------------
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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