Contacts of the helix formed by residues 127 - 157 (chain F) 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 F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122F ASP* 4.8 0.9 - - - -
123F HIS* 2.9 20.5 + - - -
124F ALA 4.4 0.6 + - - -
125F ASP 3.4 1.8 + - - -
126F LYS* 1.3 78.8 - - - +
128F ASP* 1.3 67.2 + - - -
129F ALA 3.4 2.9 - - - -
130F LEU 4.2 0.2 - - - -
131F HIS* 3.0 23.6 + - - +
193F LYS* 4.0 14.9 - - - +
197F VAL* 6.6 0.2 - - - -
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Residues in contact with ASP 128 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69F TYR* 4.0 13.5 + - + +
70F PHE* 3.7 16.7 - - + -
75F VAL* 3.6 14.6 - - - +
77F LEU* 3.9 2.6 - - - +
121F PHE 3.5 21.4 - - - +
122F ASP* 3.8 18.1 + - - +
127F GLY* 1.3 72.8 - - - -
129F ALA* 1.3 72.1 + - - +
131F HIS 3.3 0.2 + - - -
132F ALA* 2.8 33.3 + - - +
190V ARG* 3.2 39.8 + - - -
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Residues in contact with ALA 129 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70F PHE* 4.2 0.7 - - - -
77F LEU* 4.1 3.6 - - + -
80F LEU* 3.8 27.6 - - + +
127F GLY 3.4 0.8 - - - -
128F ASP* 1.3 83.4 + - - +
130F LEU* 1.3 64.1 + - - +
132F ALA* 3.4 1.6 + - - +
133F MET* 3.0 28.1 + - - +
188F LEU* 3.9 15.5 - - + -
197F VAL* 3.6 33.4 - - + -
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Residues in contact with LEU 130 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126F LYS* 3.6 35.4 - - + +
127F GLY 3.6 2.0 + - - -
128F ASP 3.4 0.2 - - - -
129F ALA* 1.3 78.3 - - - +
131F HIS* 1.3 64.4 + - - +
133F MET* 3.3 0.7 + - - -
134F GLU* 2.9 47.3 + - - +
185F VAL* 3.9 35.0 - - + +
188F LEU* 4.0 20.8 - - + +
189F ARG* 3.9 25.1 - - + +
197F VAL* 5.8 2.3 - - + +
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Residues in contact with HIS 131 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118F LEU* 6.0 0.8 - - - +
120F ASP 5.5 1.2 + - - -
121F PHE* 3.4 25.4 - - - +
122F ASP 3.9 11.7 + - - -
123F HIS* 3.5 33.9 + + + -
126F LYS* 4.2 15.1 + - + +
127F GLY 3.0 19.0 + - - +
128F ASP 3.8 2.7 - - - +
130F LEU* 1.3 79.1 - - - +
132F ALA* 1.3 56.5 + - - +
134F GLU* 3.3 2.5 + - - +
135F LEU* 3.0 58.7 + - + +
25O LEU* 4.1 19.9 - - + +
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Residues in contact with ALA 132 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66F MET* 4.2 8.6 - - - +
70F PHE* 3.4 31.0 - - + -
80F LEU* 4.9 0.2 - - + -
84F PHE* 4.2 12.4 - - + -
121F PHE* 4.5 9.0 - - + -
128F ASP 2.8 17.7 + - - +
129F ALA 3.8 2.7 - - - +
131F HIS* 1.3 77.5 - - - +
133F MET* 1.3 58.1 + - - +
135F LEU* 3.2 11.2 + - - +
136F ALA* 2.9 28.8 + - - +
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Residues in contact with MET 133 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80F LEU* 4.3 10.5 - - + -
83F PHE* 3.7 31.0 - - + -
84F PHE* 4.2 13.7 - - + -
129F ALA 3.0 13.6 + - - +
130F LEU* 3.9 2.9 - - - +
132F ALA* 1.3 77.1 - - - +
134F GLU* 1.3 57.9 + - - +
136F ALA* 3.3 3.5 + - - +
137F LEU* 2.9 25.5 + - - +
181F ILE* 3.5 17.1 - - - +
184F TYR* 3.6 38.8 - - + -
185F VAL* 3.9 17.5 - - + -
188F LEU* 3.6 24.5 - - + -
200F PHE* 4.8 1.8 - - + -
204F LEU* 4.0 15.9 - - + -
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Residues in contact with GLU 134 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126F LYS* 2.8 41.7 + - - +
130F LEU* 2.9 36.9 + - + +
131F HIS* 3.7 4.2 - - - +
133F MET* 1.3 77.5 - - - +
135F LEU* 1.3 57.2 + - - +
137F LEU* 3.4 4.9 + - - +
138F SER* 3.0 31.5 + - - -
185F VAL* 4.0 15.5 - - + -
189F ARG* 2.9 34.9 + - - +
25O LEU* 3.8 14.3 - - + +
28O VAL* 4.4 14.3 - - + +
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Residues in contact with LEU 135 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66F MET* 4.0 11.0 - - + -
118F LEU* 4.6 14.8 - - + -
121F PHE* 3.8 28.7 - - + -
131F HIS* 3.0 42.5 + - + +
132F ALA 3.6 7.0 - - - +
134F GLU* 1.3 73.1 - - - +
136F ALA* 1.3 60.9 + - - +
138F SER* 3.2 3.9 + - - -
139F LEU* 2.8 31.2 + - - +
21O VAL* 4.2 22.7 - - + +
25O LEU* 3.6 33.0 - - + -
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Residues in contact with ALA 136 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63F TYR* 4.0 28.0 - - + +
66F MET* 4.3 3.7 - - - +
83F PHE* 5.4 0.2 - - + -
84F PHE* 4.1 13.0 - - + -
132F ALA 2.9 16.5 + - - +
133F MET* 3.3 9.6 + - - +
135F LEU* 1.3 78.0 - - - +
137F LEU* 1.3 57.0 + - - +
139F LEU* 3.2 5.7 + - - +
140F GLU* 2.9 34.3 + - - +
181F ILE* 4.2 13.2 - - + -
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Residues in contact with LEU 137 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133F MET 2.9 16.7 + - - +
134F GLU* 3.6 6.1 - - - +
135F LEU 3.3 0.2 - - - -
136F ALA* 1.3 75.6 - - - +
138F SER* 1.3 58.5 + - - +
140F GLU* 3.3 3.3 + - - -
141F LYS* 2.9 39.9 + - - +
178F ILE* 3.8 27.6 - - + +
181F ILE* 3.6 12.9 - - + +
182F SER* 3.4 31.6 - - - +
185F VAL* 4.3 15.0 - - + -
28O VAL* 4.4 21.8 - - + -
36O LEU* 3.9 23.3 - - + +
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Residues in contact with SER 138 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134F GLU 3.0 15.2 + - - -
135F LEU* 3.5 5.8 - - - -
137F LEU* 1.3 77.4 - - - +
139F LEU* 1.3 58.3 + - - +
141F LYS* 3.3 1.9 + - - -
142F LEU* 2.9 28.9 + - - +
21O VAL* 3.4 23.8 - - - -
24O GLU* 3.6 24.2 + - - +
25O LEU* 3.1 26.1 + - - +
28O VAL* 3.6 9.4 - - - +
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Residues in contact with LEU 139 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59F VAL* 3.8 33.9 - - + +
62F VAL* 3.7 34.5 - - + -
63F TYR* 4.6 11.7 - - + +
66F MET* 5.1 2.5 - - + -
135F LEU 2.8 15.9 + - - +
136F ALA* 3.2 6.9 + - - +
138F SER* 1.3 76.5 - - - +
140F GLU* 1.3 59.8 + - - +
142F LEU* 3.2 10.5 + - + +
143F THR* 2.9 31.8 + - - -
15O PHE* 5.7 0.2 - - + -
17O PRO* 4.0 29.2 - - + +
18O PHE* 6.1 1.6 - - + -
21O VAL* 3.9 17.9 - - + +
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Residues in contact with GLU 140 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59F VAL* 4.3 2.6 - - - +
63F TYR* 2.5 41.7 + - - +
91F GLU* 3.6 14.9 - - - +
136F ALA 2.9 15.3 + - - +
137F LEU* 3.8 3.8 - - - +
139F LEU* 1.3 75.2 - - - +
141F LYS* 1.3 60.9 + - - +
143F THR* 3.3 6.4 + - - +
144F ASN* 3.0 17.2 + - - +
174F GLN* 2.7 54.3 + - - +
177F ALA* 4.2 12.5 - - + +
178F ILE* 3.9 15.2 - - + +
181F ILE* 3.4 20.4 - - + -
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Residues in contact with LYS 141 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137F LEU* 2.9 36.7 + - + +
138F SER* 3.7 4.7 - - - +
140F GLU* 1.3 76.3 - - - +
142F LEU* 1.3 62.5 + - - +
144F ASN* 3.2 1.0 + - - +
145F GLU* 3.0 12.5 + - - +
178F ILE* 4.1 8.1 - - + -
24O GLU* 3.6 27.9 + - - +
27O LEU 6.3 0.4 - - - -
28O VAL* 5.9 3.7 - - + +
29O PRO* 5.1 8.3 - - - +
35O SER 5.5 0.4 + - - -
36O LEU 2.8 30.1 + - - -
37O ALA 3.6 13.9 - - - -
38O ARG 3.2 20.7 + - - -
39O GLN* 3.0 48.3 + - + +
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Residues in contact with LEU 142 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138F SER 2.9 14.3 + - - +
139F LEU* 3.2 15.9 + - + +
141F LYS* 1.3 77.5 - - - +
143F THR* 1.3 61.9 + - - +
145F GLU* 3.3 20.0 + - - +
146F LYS* 3.0 35.0 + - + +
15O PHE* 3.5 34.5 - - + -
17O PRO* 4.2 13.7 - - + +
20O GLU* 3.4 41.5 - - + +
21O VAL* 4.7 4.3 - - + +
24O GLU* 5.0 7.5 - - + +
----------------------------------------------------------
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Residues in contact with THR 143 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52F GLN* 4.1 5.2 - - - +
55F VAL* 4.3 6.4 - - + +
56F GLU* 3.7 26.0 - - - +
59F VAL* 3.4 24.8 - - + +
139F LEU 2.9 18.2 + - - -
140F GLU* 3.6 7.9 + - - -
141F LYS 3.3 0.2 - - - -
142F LEU* 1.3 76.2 - - - +
144F ASN* 1.3 57.4 + - - +
146F LYS* 3.1 8.0 + - - +
147F LEU* 2.8 30.1 + - + +
174F GLN* 3.9 19.5 - - - +
214F CA 4.2 8.1 - - - -
15O PHE* 6.0 0.3 - - - -
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Residues in contact with ASN 144 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140F GLU 3.0 13.2 + - - +
141F LYS 3.4 8.5 - - - +
142F LEU 3.2 0.2 - - - -
143F THR* 1.3 77.8 - - - +
145F GLU* 1.3 57.8 + - - +
147F LEU* 3.2 3.4 + - - +
148F LEU* 2.9 51.8 + - - +
171F LEU* 4.3 13.9 - - - +
174F GLN* 3.4 29.5 - - + +
175F VAL* 5.2 9.4 + - - +
178F ILE* 3.9 8.4 - - + +
39O GLN* 3.0 30.1 + - - +
40O LYS* 5.6 0.2 - - - +
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Residues in contact with GLU 145 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141F LYS 3.0 12.4 + - - +
142F LEU* 3.6 22.1 - - - +
144F ASN* 1.3 76.5 - - - +
146F LYS* 1.3 62.8 + - + +
148F LEU* 3.4 10.1 + - - +
149F ASN* 2.9 43.3 + - - +
24O GLU* 5.7 0.5 - - - +
39O GLN* 4.3 9.8 + - - +
40O LYS* 4.6 16.2 - - - +
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Residues in contact with LYS 146 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51F GLU* 5.7 5.6 + - + +
52F GLN* 3.4 22.4 - - - +
55F VAL* 4.2 22.7 - - + -
142F LEU* 3.0 27.3 + - + +
143F THR 3.5 6.7 - - - +
145F GLU* 1.3 79.1 + - + +
147F LEU* 1.3 60.5 + - - +
149F ASN* 3.2 20.9 + - + +
150F LEU* 2.9 24.3 + - - +
15O PHE* 4.0 18.8 - - - +
20O GLU* 3.5 31.3 + - - -
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Residues in contact with LEU 147 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52F GLN* 3.3 30.1 - - + +
56F GLU* 3.9 7.6 - - - +
98F LEU* 5.4 0.4 - - + -
143F THR* 2.8 23.7 + - + +
144F ASN* 3.6 4.5 - - - +
146F LYS* 1.3 76.1 - - - +
148F LEU* 1.3 58.8 + - - +
150F LEU* 3.2 8.7 + - + +
151F HIS* 2.9 27.5 + - - +
166F VAL* 3.9 11.8 - - + +
170F TYR* 3.9 38.4 - - + +
171F LEU* 3.8 14.4 - - + -
174F GLN* 3.8 36.6 - - + +
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Residues in contact with LEU 148 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144F ASN* 2.9 39.9 + - - +
145F GLU* 3.8 4.5 - - - +
147F LEU* 1.3 73.8 - - - +
149F ASN* 1.3 61.8 + - - +
151F HIS* 3.3 5.8 + - + +
152F SER* 2.9 32.1 + - - -
171F LEU* 3.9 28.9 - - + -
40O LYS* 3.7 34.3 - - + -
160O VAL* 4.1 24.5 - - + +
161O GLN* 5.1 4.9 - - + +
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Residues in contact with ASN 149 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145F GLU* 2.9 34.9 + - - +
146F LYS* 3.2 30.7 - - + +
148F LEU* 1.3 74.7 - - - +
150F LEU* 1.3 65.8 + - - +
152F SER* 2.9 19.6 + - - -
153F VAL* 2.9 19.5 + - + +
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Residues in contact with LEU 150 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48F ALA* 3.7 36.6 - - + +
49F VAL* 3.9 14.1 - - + +
52F GLN* 3.9 31.4 - - + +
98F LEU* 4.4 13.5 - - + -
146F LYS 2.9 12.7 + - - +
147F LEU* 3.5 11.7 - - + +
149F ASN* 1.3 74.7 - - - +
151F HIS* 1.3 64.0 + - - +
153F VAL* 3.2 7.6 + - - +
154F ALA* 3.0 19.6 + - - +
162F LEU* 4.4 10.3 - - + -
166F VAL* 3.6 29.2 - - + -
170F TYR* 6.3 0.2 - - + -
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Residues in contact with HIS 151 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147F LEU 2.9 14.1 + - - +
148F LEU* 3.4 13.0 + - + +
149F ASN 3.1 0.2 - - - -
150F LEU* 1.3 78.3 - - - +
152F SER* 1.3 63.1 + - - +
154F ALA* 3.2 7.7 + - - +
155F THR* 3.0 43.2 + - + +
163F ALA* 3.4 20.0 + - + +
166F VAL* 4.2 12.5 - - + +
167F GLU* 2.6 47.7 + - + +
171F LEU* 4.3 4.9 - - + -
160O VAL* 3.5 31.5 - - + +
----------------------------------------------------------
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Residues in contact with SER 152 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148F LEU 2.9 16.6 + - - -
149F ASN* 2.9 13.0 + - - -
151F HIS* 1.3 76.3 + - - +
153F VAL* 1.3 61.7 + - - +
155F THR* 3.2 8.5 + - - -
156F LYS* 2.8 55.6 + - - +
160O VAL* 6.1 1.4 - - - +
----------------------------------------------------------
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Residues in contact with VAL 153 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44F GLU* 3.7 49.4 - - + +
45F SER* 4.1 5.1 + - - -
48F ALA* 3.8 19.5 - - + -
149F ASN* 2.9 19.8 + - + +
150F LEU* 3.2 7.4 + - - +
152F SER* 1.3 77.0 - - - +
154F ALA* 1.3 62.6 + - - +
156F LYS* 3.3 8.6 - - - +
157F ASN* 2.8 34.3 + - - +
162F LEU* 6.0 0.2 - - + -
----------------------------------------------------------
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Residues in contact with ALA 154 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45F SER* 4.5 1.1 - - - -
150F LEU 3.0 9.4 + - - +
151F HIS* 3.2 10.1 + - - +
153F VAL* 1.3 77.1 - - - +
155F THR* 1.3 62.8 + - - +
157F ASN* 3.2 6.6 + - - -
159F ASP* 2.8 33.9 + - - +
162F LEU* 3.6 38.5 - - + +
163F ALA* 3.7 20.2 - - - +
----------------------------------------------------------
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Residues in contact with THR 155 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151F HIS* 3.0 37.3 + - + +
152F SER* 3.2 12.8 + - - -
154F ALA* 1.3 76.2 - - - +
156F LYS* 1.3 65.4 + - - +
158F GLY* 3.0 15.2 + - - +
159F ASP 4.7 2.5 - - - +
163F ALA* 3.8 13.0 - - + -
----------------------------------------------------------
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Residues in contact with LYS 156 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44F GLU* 5.0 8.1 - - - +
152F SER* 2.8 42.7 + - - +
153F VAL* 3.3 13.2 - - + +
155F THR* 1.3 79.1 + - - +
157F ASN* 1.3 67.6 + - - +
158F GLY 3.4 0.6 + - - -
----------------------------------------------------------
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Residues in contact with ASN 157 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40F LYS 5.8 0.2 - - - +
42F VAL* 3.6 34.2 - - + +
44F GLU* 2.8 39.8 + - - +
45F SER* 3.9 8.5 + - - +
153F VAL* 2.8 28.1 + - - +
154F ALA 3.2 4.2 + - - +
155F THR 3.1 0.6 - - - -
156F LYS* 1.3 81.4 - - - +
158F GLY* 1.3 63.9 + - - +
159F ASP* 3.1 4.7 + - + +
----------------------------------------------------------
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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