Contacts of the helix formed by residues 127 - 157 (chain U) 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 U).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122U ASP* 5.0 0.7 - - - -
123U HIS* 2.9 21.2 + - - -
124U ALA 4.8 0.4 - - - -
125U ASP 3.4 2.2 + - - -
126U LYS* 1.3 83.2 - - - +
128U ASP* 1.3 67.0 + - - -
129U ALA 3.4 2.4 + - - -
130U LEU 3.6 0.8 + - - -
131U HIS* 3.1 19.8 + - - +
193U LYS* 4.0 17.6 - - - +
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Residues in contact with ASP 128 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190N ARG* 3.1 40.6 + - - -
69U TYR* 4.1 10.5 + - + +
70U PHE* 3.6 15.8 - - + -
75U VAL* 3.7 14.9 - - - +
77U LEU* 3.9 1.9 - - - +
121U PHE 3.5 21.9 - - - +
122U ASP* 3.8 19.3 + - - +
123U HIS 4.3 0.2 - - - +
127U GLY* 1.3 72.1 - - - -
129U ALA* 1.3 78.0 + - - +
131U HIS* 3.4 1.4 + - - +
132U ALA* 2.9 26.9 + - - +
197U VAL* 5.0 0.2 - - - +
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Residues in contact with ALA 129 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70U PHE* 4.3 1.1 - - - -
77U LEU* 4.2 4.3 - - + -
80U LEU* 3.8 29.5 - - + +
127U GLY 3.4 0.8 - - - -
128U ASP* 1.3 84.3 + - - +
130U LEU* 1.3 63.0 + - - +
132U ALA* 3.4 2.4 + - - +
133U MET* 3.0 24.8 + - - +
188U LEU* 3.8 16.8 - - + +
197U VAL* 3.6 32.8 - - + -
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Residues in contact with LEU 130 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126U LYS* 3.5 36.6 - - + +
127U GLY 3.6 1.6 + - - -
129U ALA* 1.3 79.9 - - - +
131U HIS* 1.3 58.3 + - - +
133U MET 3.3 0.5 + - - -
134U GLU* 2.9 61.2 + - + +
185U VAL* 3.9 17.7 - - + +
188U LEU* 4.0 21.9 - - + +
189U ARG* 3.9 35.0 - - + +
197U VAL* 5.7 2.4 - - + +
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Residues in contact with HIS 131 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25P LEU* 5.8 2.9 - - + +
118U LEU* 6.2 0.8 - - - +
120U ASP 5.5 1.2 + - - -
121U PHE* 3.4 29.7 - - - +
122U ASP 4.0 8.7 + - - -
123U HIS* 3.5 33.9 - + + -
126U LYS* 4.3 14.7 + - + +
127U GLY 3.1 18.9 + - - +
128U ASP 3.7 2.7 - - - +
129U ALA 3.3 0.2 - - - -
130U LEU* 1.3 77.1 - - - +
132U ALA* 1.3 57.3 + - - +
134U GLU* 3.3 6.6 + - - +
135U LEU* 2.9 64.3 + - + +
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Residues in contact with ALA 132 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66U MET* 3.1 26.5 - - + +
70U PHE* 3.4 41.1 - - + -
80U LEU* 4.8 0.2 - - + -
84U PHE* 4.2 6.1 - - + -
121U PHE* 4.5 6.7 - - + -
128U ASP 2.9 8.6 + - - +
129U ALA 3.8 2.5 - - - +
131U HIS* 1.3 77.1 - - - +
133U MET* 1.3 57.4 + - - +
135U LEU* 3.3 7.2 + - - -
136U ALA* 2.9 24.1 + - - +
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Residues in contact with MET 133 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80U LEU* 4.3 23.1 - - + -
83U PHE* 4.1 25.8 - - + -
84U PHE* 4.3 7.8 - - + -
129U ALA 3.0 15.8 + - - +
130U LEU 3.9 3.4 - - - +
132U ALA* 1.3 74.6 - - - +
134U GLU* 1.3 61.7 + - - +
136U ALA* 3.3 3.0 + - - -
137U LEU* 2.9 24.1 + - - +
181U ILE* 3.5 17.9 - - + +
184U TYR* 3.5 50.5 - - + -
185U VAL* 3.7 16.1 - - + +
188U LEU* 3.9 9.4 - - + -
200U PHE* 4.5 6.5 - - + -
204U LEU* 4.3 7.0 - - + -
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Residues in contact with GLU 134 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25P LEU* 4.0 10.1 - - + +
28P VAL* 4.8 17.1 - - + +
126U LYS* 2.8 39.8 + - - +
130U LEU* 2.9 39.4 + - + +
131U HIS* 3.7 5.3 - - - +
133U MET* 1.3 76.7 - - - +
135U LEU* 1.3 62.1 + - - +
137U LEU* 3.3 5.9 + - - +
138U SER* 3.1 23.4 + - - -
185U VAL* 4.0 15.0 - - + -
189U ARG* 2.8 35.5 + - - +
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Residues in contact with LEU 135 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18P PHE* 5.0 13.5 - - + -
21P VAL* 4.8 6.7 - - + -
25P LEU* 3.3 37.2 - - + -
66U MET* 4.5 6.5 - - + -
118U LEU* 5.7 3.6 - - + -
121U PHE* 3.7 29.8 - - + -
131U HIS* 2.9 49.3 + - + +
132U ALA* 3.5 9.0 - - - +
133U MET 3.2 0.2 - - - -
134U GLU* 1.3 74.3 - - - +
136U ALA* 1.3 58.6 + - - +
138U SER* 2.7 20.3 + - - +
139U LEU* 2.9 23.5 + - + +
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Residues in contact with ALA 136 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63U TYR* 4.0 25.4 - - + +
66U MET* 4.4 1.3 - - + +
83U PHE* 5.3 0.2 - - + -
84U PHE* 4.0 12.8 - - + -
132U ALA 2.9 17.6 + - - +
133U MET* 3.6 10.1 - - - +
134U GLU 3.3 0.2 - - - -
135U LEU* 1.3 75.8 - - - +
137U LEU* 1.3 63.1 + - - +
139U LEU* 3.2 10.7 + - - +
140U GLU* 2.9 27.9 + - - +
181U ILE* 4.1 14.1 - - + -
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Residues in contact with LEU 137 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28P VAL* 4.3 20.4 - - + -
36P LEU* 3.9 23.1 - - + +
133U MET 2.9 16.3 + - - +
134U GLU* 3.5 5.8 - - - +
135U LEU 3.2 0.2 - - - -
136U ALA* 1.3 76.7 - - - +
138U SER* 1.3 58.9 + - - +
140U GLU* 3.2 3.5 + - + +
141U LYS* 2.9 38.1 + - + +
178U ILE* 3.8 28.0 - - + +
181U ILE* 3.6 13.8 - - + +
182U SER* 3.4 30.5 - - - +
185U VAL* 4.4 13.2 - - + -
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Residues in contact with SER 138 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21P VAL* 3.0 23.1 - - - +
24P GLU* 3.6 32.5 - - - +
25P LEU* 3.3 22.5 - - - +
28P VAL* 5.3 2.4 - - - +
134U GLU 3.1 10.6 + - - -
135U LEU* 2.7 19.9 + - - -
137U LEU* 1.3 77.7 - - - +
139U LEU* 1.3 55.3 - - - +
141U LYS* 3.4 2.2 + - - -
142U LEU* 2.9 29.5 + - - +
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Residues in contact with LEU 139 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17P PRO* 4.1 25.6 - - + +
18P PHE* 5.7 5.8 - - + -
21P VAL* 4.2 15.3 - - + -
59U VAL* 4.6 20.5 - - + +
62U VAL* 3.4 33.2 - - + -
63U TYR* 4.4 13.7 - - + +
66U MET* 4.4 8.3 - - - -
135U LEU* 2.9 19.7 + - + +
136U ALA* 3.2 15.7 + - - +
138U SER* 1.3 78.8 + - - +
140U GLU* 1.3 57.7 + - - +
142U LEU* 3.4 9.8 + - + +
143U THR* 2.9 32.0 + - - -
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Residues in contact with GLU 140 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59U VAL* 4.5 1.0 - - - +
63U TYR* 2.6 34.4 + - - +
91U GLU* 3.7 14.8 - - - +
136U ALA 2.9 19.7 + - - +
137U LEU* 3.7 5.2 - - - +
139U LEU* 1.3 74.1 - - - +
141U LYS* 1.3 60.3 + - - +
143U THR* 3.4 5.4 + - - +
144U ASN* 2.9 17.0 + - - +
174U GLN* 2.7 54.1 + - - +
177U ALA* 4.0 13.5 - - + +
178U ILE* 4.0 16.6 - - + +
181U ILE* 3.5 19.5 - - + +
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Residues in contact with LYS 141 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24P GLU* 3.3 28.7 - - + +
27P LEU 5.8 1.2 + - - -
28P VAL* 5.9 2.2 - - - +
29P PRO* 5.1 8.5 - - - +
36P LEU 2.7 30.6 + - - -
37P ALA 3.7 14.6 - - - -
38P ARG 3.4 19.1 + - - -
39P GLN* 2.9 41.3 + - + +
137U LEU* 2.9 36.8 + - + +
138U SER* 3.7 4.0 - - - +
140U GLU* 1.3 74.9 - - - +
142U LEU* 1.3 60.5 + - - +
144U ASN* 3.2 1.2 + - - +
145U GLU* 3.0 16.8 + - - +
178U ILE* 4.1 8.3 - - + -
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Residues in contact with LEU 142 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15P PHE* 3.6 32.1 - - + -
17P PRO* 4.1 13.9 - - + +
20P GLU* 3.9 45.1 - - + +
21P VAL* 4.4 7.2 - - + +
24P GLU* 4.4 6.0 - - + +
59U VAL* 6.3 0.9 - - + -
138U SER 2.9 18.3 + - - +
139U LEU* 3.6 11.2 - - + +
140U GLU 3.3 0.2 - - - -
141U LYS* 1.3 76.8 - - - +
143U THR* 1.3 61.3 + - - +
145U GLU* 3.2 23.6 + - - +
146U LYS* 3.0 35.1 + - + +
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Residues in contact with THR 143 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52U GLN* 4.0 6.5 - - - +
55U VAL* 4.3 8.4 - - + +
56U GLU* 3.7 26.2 - - - +
59U VAL* 3.4 24.1 - - - +
139U LEU 2.9 24.0 + - - -
140U GLU* 3.6 8.6 + - - -
141U LYS 3.3 0.2 - - - -
142U LEU* 1.3 76.2 - - - +
144U ASN* 1.3 56.7 + - - +
146U LYS* 3.2 7.5 + - - +
147U LEU* 2.8 34.3 + - + +
174U GLN* 3.8 13.2 - - - +
213U CA 4.1 11.4 - - - -
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Residues in contact with ASN 144 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39P GLN* 2.9 31.7 + - - +
40P LYS* 5.6 0.2 - - - +
140U GLU 2.9 13.3 + - - +
141U LYS 3.2 9.4 + - - +
143U THR* 1.3 76.3 - - - +
145U GLU* 1.3 63.2 + - - +
147U LEU* 3.2 3.1 + - - +
148U LEU* 2.9 47.5 + - - +
171U LEU* 4.3 11.4 - - - +
174U GLN* 3.5 29.0 - - + +
175U VAL* 5.2 9.0 + - - +
178U ILE* 3.9 7.8 - - + +
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Residues in contact with GLU 145 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24P GLU* 3.3 28.8 - - - +
39P GLN* 3.4 19.8 + - - +
40P LYS* 3.9 24.6 + - - +
141U LYS 3.0 9.9 + - - +
142U LEU* 3.2 23.6 + - + +
144U ASN* 1.3 75.7 - - - +
146U LYS* 1.3 60.1 + - + +
148U LEU* 3.4 3.9 + - - +
149U ASN* 3.0 34.9 + - - +
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Residues in contact with LYS 146 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14P ILE* 5.9 1.6 - - - +
15P PHE* 3.8 18.0 - - - -
20P GLU* 3.0 34.7 + - - -
51U GLU* 4.8 10.7 + - + +
52U GLN* 3.3 20.8 - - - +
55U VAL* 4.0 25.4 - - + -
142U LEU* 3.0 22.9 + - + +
143U THR 3.2 6.0 + - - +
145U GLU* 1.3 76.8 - - + +
147U LEU* 1.3 59.1 + - - +
149U ASN* 3.2 23.4 - - - +
150U LEU* 3.0 24.3 + - - +
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Residues in contact with LEU 147 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52U GLN* 3.3 31.4 + - + +
56U GLU* 3.8 7.9 - - - +
98U LEU* 5.3 0.2 - - + -
143U THR* 2.8 28.4 + - + +
144U ASN* 3.6 4.7 - - - +
146U LYS* 1.3 72.9 - - - +
148U LEU* 1.3 57.3 + - - +
150U LEU* 3.2 9.1 + - + +
151U HIS* 2.9 26.7 + - - +
166U VAL* 3.9 10.2 - - + +
170U TYR* 3.8 39.5 - - + +
171U LEU* 3.8 14.6 - - + -
174U GLN* 3.9 36.1 - - + +
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Residues in contact with LEU 148 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40P LYS* 3.7 33.4 - - + -
160P VAL* 4.1 23.6 - - + +
161P GLN* 5.2 4.9 - - + +
144U ASN* 2.9 40.8 + - - +
145U GLU* 3.7 4.0 - - - +
147U LEU* 1.3 73.9 - - - +
149U ASN* 1.3 61.0 + - - +
151U HIS* 3.4 5.2 + - + +
152U SER* 2.9 31.9 + - - -
171U LEU* 3.8 29.8 - - + -
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Residues in contact with ASN 149 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145U GLU* 3.0 22.9 + - - +
146U LYS* 3.2 34.0 + - - +
148U LEU* 1.3 72.9 - - - +
150U LEU* 1.3 66.1 + - - +
152U SER* 3.0 10.4 + - - -
153U VAL* 2.9 29.1 + - + +
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Residues in contact with LEU 150 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48U ALA* 3.6 37.7 - - + +
49U VAL* 3.8 16.4 - - + +
52U GLN* 3.9 29.8 - - + -
98U LEU* 4.3 15.5 - - + -
146U LYS 3.0 13.0 + - - +
147U LEU* 3.2 12.5 + - + +
149U ASN* 1.3 75.0 - - - +
151U HIS* 1.3 63.1 + - - +
153U VAL* 3.3 5.9 + - - +
154U ALA* 3.0 21.5 + - - +
162U LEU* 4.3 9.0 - - + -
166U VAL* 3.6 28.0 - - + -
170U TYR* 6.3 0.2 - - + -
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Residues in contact with HIS 151 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160P VAL* 3.3 35.4 - - + +
147U LEU 2.9 13.6 + - - +
148U LEU* 3.5 13.4 + - + +
150U LEU* 1.3 78.4 - - - +
152U SER* 1.3 57.3 + - - +
154U ALA* 3.3 5.7 + - - +
155U THR* 2.9 57.5 + - + +
163U ALA* 3.5 28.3 - - + +
166U VAL* 4.3 12.7 - - + +
167U GLU* 2.7 34.8 + - + -
171U LEU* 4.2 7.0 - - + -
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Residues in contact with SER 152 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160P VAL* 6.1 1.2 - - - +
148U LEU 2.9 17.4 + - - -
149U ASN* 3.0 13.1 + - - -
151U HIS* 1.3 75.9 + - - +
153U VAL* 1.3 61.4 + - - +
155U THR* 2.9 19.7 + - - -
156U LYS* 2.9 20.3 + - - +
----------------------------------------------------------
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Residues in contact with VAL 153 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44U GLU* 3.7 33.4 - - + +
45U SER* 4.1 4.9 - - - -
48U ALA* 3.9 19.7 - - + -
149U ASN* 2.9 21.0 + - + +
150U LEU* 3.6 6.5 - - + +
152U SER* 1.3 74.4 - - - +
154U ALA* 1.3 66.5 + - - +
156U LYS* 3.4 4.3 + - - +
157U ASN* 2.9 47.0 + - - +
----------------------------------------------------------
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Residues in contact with ALA 154 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45U SER* 4.4 2.0 - - - -
150U LEU 3.0 10.8 + - - +
151U HIS* 3.5 9.0 - - - +
153U VAL* 1.3 77.1 - - - +
155U THR* 1.3 59.6 + - - +
157U ASN 3.2 2.1 + - - -
158U GLY 3.0 3.8 + - - -
159U ASP* 2.8 38.2 + - - +
162U LEU* 3.6 35.8 - - + +
163U ALA* 3.7 19.5 - - - +
----------------------------------------------------------
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Residues in contact with THR 155 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151U HIS* 2.9 46.8 + - + +
152U SER* 2.9 23.7 + - - -
154U ALA* 1.3 73.4 - - - +
156U LYS* 1.3 64.7 + - - +
158U GLY* 3.1 13.7 + - - -
159U ASP 4.9 1.6 - - - +
163U ALA* 4.0 11.7 - - + -
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Residues in contact with LYS 156 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44U GLU* 3.3 31.1 + - - +
152U SER 2.9 18.4 + - - +
153U VAL* 3.8 4.7 - - - +
155U THR* 1.3 78.3 + - - +
157U ASN* 1.3 74.1 + - - +
158U GLY 3.3 3.3 + - - -
----------------------------------------------------------
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Residues in contact with ASN 157 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40U LYS 5.7 0.7 - - - +
42U VAL* 3.5 35.7 - - + +
44U GLU* 3.0 28.7 + - - +
45U SER* 3.8 9.3 + - - +
153U VAL* 2.9 37.6 + - - +
154U ALA 3.9 1.3 - - - +
156U LYS* 1.3 95.9 + - - +
158U GLY* 1.3 63.3 + - - +
159U ASP* 3.1 4.4 + - + +
----------------------------------------------------------
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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