Contacts of the helix formed by residues 127 - 157 (chain X) 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 X).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122X ASP* 5.0 0.4 - - - -
123X HIS* 2.9 20.1 + - - -
124X ALA 4.4 0.2 + - - -
125X ASP 3.4 1.6 - - - -
126X LYS* 1.3 82.5 - - - +
128X ASP* 1.3 68.6 + - - -
129X ALA 3.4 2.9 + - - -
130X LEU 3.5 0.8 + - - -
131X HIS* 3.1 19.8 + - - +
193X LYS* 3.9 17.8 - - - +
197X VAL* 6.5 0.7 - - - -
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Residues in contact with ASP 128 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190Q ARG* 3.0 41.3 + - - -
69X TYR* 4.2 7.9 + - + +
70X PHE* 3.7 11.3 - - + -
75X VAL* 3.7 13.5 - - - +
77X LEU* 3.8 7.7 - - - +
121X PHE 3.6 21.2 - - - +
122X ASP* 3.9 21.1 + - - +
123X HIS 4.4 0.9 - - - +
127X GLY* 1.3 72.0 - - - +
129X ALA* 1.3 80.5 + - - +
131X HIS* 3.7 1.2 - - - +
132X ALA* 2.9 27.0 + - - +
197X VAL* 4.8 0.7 - - - +
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Residues in contact with ALA 129 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70X PHE* 4.3 0.9 - - - -
77X LEU* 4.1 4.9 - - + -
80X LEU* 3.8 25.4 - - + +
127X GLY 3.4 0.6 - - - -
128X ASP* 1.3 84.9 + - - +
130X LEU* 1.3 61.8 + - - +
132X ALA* 3.4 2.1 + - - +
133X MET* 3.1 27.9 + - - +
188X LEU* 4.0 16.4 - - + -
197X VAL* 3.7 33.0 - - + -
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Residues in contact with LEU 130 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126X LYS* 3.7 34.5 - - + +
127X GLY 3.5 1.8 + - - -
128X ASP 3.4 0.2 - - - -
129X ALA* 1.3 75.3 - - - +
131X HIS* 1.3 61.7 + - - +
133X MET* 3.2 1.2 + - - -
134X GLU* 2.9 57.6 + - - +
185X VAL* 3.9 35.2 - - + +
188X LEU* 4.0 19.0 - - + +
189X ARG* 3.9 22.9 - - + +
197X VAL* 5.7 2.6 - - + +
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Residues in contact with HIS 131 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22H LYS* 6.1 2.7 - - - -
25H LEU* 4.5 22.8 - - + +
118X LEU* 5.9 4.2 - - - +
120X ASP 5.5 1.0 + - - -
121X PHE* 3.4 35.2 - + + +
122X ASP 4.3 3.2 + - - -
123X HIS* 3.5 38.9 - + + -
126X LYS* 4.2 14.9 - - + +
127X GLY 3.1 18.7 + - - +
128X ASP 3.7 2.7 - - - +
130X LEU* 1.3 78.9 - - - +
132X ALA* 1.3 57.4 + - - +
134X GLU* 3.3 4.1 + - - +
135X LEU* 2.9 39.4 + - + +
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Residues in contact with ALA 132 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66X MET* 3.9 10.8 - - + +
70X PHE* 3.4 41.1 - - + -
80X LEU* 4.7 0.2 - - + -
84X PHE* 4.1 12.1 - - + -
121X PHE* 4.7 9.4 - - + -
128X ASP 2.9 8.6 + - - +
129X ALA 3.8 2.7 - - - +
131X HIS* 1.3 78.9 - - - +
133X MET* 1.3 58.0 + - - +
135X LEU* 3.3 8.3 + - - +
136X ALA* 2.8 27.7 + - - +
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Residues in contact with MET 133 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80X LEU* 3.8 18.6 - - + -
83X PHE* 3.8 30.1 - - + -
84X PHE* 4.0 12.3 - - + -
129X ALA 3.1 13.2 + - - +
130X LEU 3.2 4.0 + - - +
132X ALA* 1.3 74.3 - - - +
134X GLU* 1.3 61.7 + - - +
136X ALA* 3.3 1.3 + - - -
137X LEU* 2.8 25.5 + - - +
181X ILE* 3.5 16.9 - - + +
184X TYR* 3.9 26.0 - - + -
185X VAL* 3.8 17.9 - - + +
188X LEU* 3.5 25.4 - - + -
200X PHE* 4.6 2.2 - - + -
204X LEU* 3.8 22.0 - - + -
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Residues in contact with GLU 134 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25H LEU* 3.5 14.9 - - + +
28H VAL* 4.6 16.4 - - + +
126X LYS* 2.8 38.3 + - - +
130X LEU* 2.9 38.0 + - + +
131X HIS* 3.8 4.5 - - - +
133X MET* 1.3 76.9 - - - +
135X LEU* 1.3 55.9 + - - +
137X LEU* 3.4 6.7 + - - +
138X SER* 3.0 31.2 + - - -
185X VAL* 4.0 15.0 - - + -
189X ARG* 2.7 36.2 + - - +
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Residues in contact with LEU 135 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18H PHE* 3.6 20.9 - - + -
21H VAL* 3.8 30.3 - - + -
25H LEU* 3.8 19.4 - - + +
66X MET* 3.5 23.3 - - + -
118X LEU* 4.9 3.4 - - + -
121X PHE* 3.6 25.1 - - + -
131X HIS* 2.9 26.0 + - + +
132X ALA* 3.5 9.0 - - - +
133X MET 3.2 0.2 - - - -
134X GLU* 1.3 74.3 - - - +
136X ALA* 1.3 59.9 + - - +
138X SER* 3.2 1.8 + - - -
139X LEU* 2.8 33.3 + - + +
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Residues in contact with ALA 136 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63X TYR* 4.0 27.6 - - + +
66X MET* 4.2 1.3 - - - +
83X PHE* 5.3 0.2 - - + -
84X PHE* 4.1 13.0 - - + -
132X ALA 2.8 17.6 + - - +
133X MET* 3.3 9.2 + - - +
135X LEU* 1.3 76.4 - - - +
137X LEU* 1.3 64.0 + - - +
139X LEU* 3.2 7.3 + - - +
140X GLU* 2.9 28.4 + - - +
181X ILE* 4.2 14.8 - - + -
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Residues in contact with LEU 137 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28H VAL* 4.4 20.0 - - + -
36H LEU* 3.8 27.6 - - + +
133X MET 2.8 17.5 + - - +
134X GLU* 3.5 6.7 - - - +
135X LEU 3.2 0.2 - - - -
136X ALA* 1.3 75.9 - - - +
138X SER* 1.3 58.2 + - - +
140X GLU* 3.2 3.8 + - + -
141X LYS* 2.9 38.2 + - + +
178X ILE* 3.8 26.9 - - + +
181X ILE* 3.7 12.9 - - + +
182X SER* 3.4 26.9 - - - +
185X VAL* 4.5 13.9 - - + -
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Residues in contact with SER 138 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21H VAL* 3.4 21.0 - - - +
24H GLU* 3.5 17.7 + - - +
25H LEU* 3.1 35.7 + - - +
28H VAL* 5.2 4.0 - - - +
134X GLU 3.0 14.8 + - - -
135X LEU* 3.2 7.8 + - - -
137X LEU* 1.3 76.1 - - - +
139X LEU* 1.3 58.6 + - - +
141X LYS* 3.3 3.4 + - - -
142X LEU* 2.9 29.3 + - - +
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Residues in contact with LEU 139 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17H PRO* 4.6 17.7 - - + +
18H PHE* 5.5 2.2 - - + -
21H VAL* 3.4 32.5 - - + -
59X VAL* 4.9 17.4 - - + +
62X VAL* 3.5 35.7 - - + -
63X TYR* 4.3 17.0 - - + +
66X MET* 4.2 12.1 - - + -
135X LEU* 2.8 21.4 + - + +
136X ALA* 3.2 8.5 + - - +
138X SER* 1.3 76.8 - - - +
140X GLU* 1.3 57.2 + - - +
142X LEU* 3.3 8.9 + - + +
143X THR* 2.9 32.9 + - - -
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Residues in contact with GLU 140 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59X VAL* 4.4 2.3 - - - +
63X TYR* 2.5 34.3 + - - +
91X GLU* 3.7 15.7 - - - +
136X ALA 2.9 20.1 + - - +
137X LEU* 3.7 4.9 - - - +
139X LEU* 1.3 73.9 - - - +
141X LYS* 1.3 61.7 + - - +
143X THR* 3.3 6.6 + - - +
144X ASN* 3.0 17.7 + - - +
174X GLN* 2.8 52.0 + - - +
177X ALA* 4.2 12.7 - - + +
178X ILE* 3.9 16.3 - - + +
181X ILE* 3.4 19.8 - - + +
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Residues in contact with LYS 141 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24H GLU* 3.8 25.7 + - + +
27H LEU* 5.7 2.0 + - - +
28H VAL* 5.7 2.8 - - - +
29H PRO* 5.0 9.1 - - - +
36H LEU 2.8 30.0 + - - -
37H ALA 3.7 13.9 - - - -
38H ARG 3.3 18.9 + - - -
39H GLN* 3.0 46.4 + - + +
137X LEU* 2.9 34.1 + - + +
138X SER* 3.7 4.9 - - - +
139X LEU 3.3 0.2 - - - -
140X GLU* 1.3 74.5 - - - +
142X LEU* 1.3 65.0 + - - +
144X ASN* 3.1 1.2 + - - +
145X GLU* 3.0 12.6 + - - +
178X ILE* 4.2 8.5 - - + -
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Residues in contact with LEU 142 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15H PHE* 3.5 35.0 - - + -
17H PRO* 4.3 15.0 - - + +
20H GLU* 3.4 43.3 - - + +
21H VAL* 4.7 7.6 - - + -
24H GLU* 4.6 8.8 - - + +
59X VAL* 6.4 1.1 - - + -
138X SER 2.9 13.6 + - - +
139X LEU* 3.3 12.3 + - + +
141X LYS* 1.3 76.3 - - - +
143X THR* 1.3 62.4 + - - +
145X GLU* 3.2 23.7 + - - +
146X LYS* 3.0 35.1 + - + +
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Residues in contact with THR 143 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15H PHE* 6.1 0.2 - - - -
52X GLN* 3.9 7.0 - - - +
55X VAL* 4.3 7.3 - - + +
56X GLU* 3.7 25.4 - - - +
59X VAL* 3.5 24.7 - - + +
139X LEU 2.9 19.6 + - - -
140X GLU* 3.6 9.1 + - - -
141X LYS 3.3 0.4 - - - -
142X LEU* 1.3 75.9 - - - +
144X ASN* 1.3 57.5 + - - +
146X LYS* 3.2 8.5 + - - +
147X LEU* 2.8 31.6 + - + +
174X GLN* 3.8 18.8 - - - +
242X CA 4.2 8.7 - - - -
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Residues in contact with ASN 144 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39H GLN* 2.9 31.1 + - - +
140X GLU 3.0 14.0 + - - +
141X LYS 3.1 8.9 + - - +
143X THR* 1.3 76.9 - - - +
145X GLU* 1.3 58.0 + - - +
147X LEU* 3.2 3.4 + - - +
148X LEU* 2.9 51.4 + - - +
171X LEU* 4.3 13.3 - - - +
174X GLN* 3.4 28.6 - - + +
175X VAL* 5.2 9.6 - - - +
178X ILE* 3.9 8.0 - - + +
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Residues in contact with GLU 145 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24H GLU* 4.4 13.0 - - - +
39H GLN* 4.2 4.1 + - - +
40H LYS* 4.4 30.2 + - - +
141X LYS 3.0 12.5 + - - +
142X LEU* 3.4 24.3 - - - +
144X ASN* 1.3 75.7 - - - +
146X LYS* 1.3 64.0 + - + +
148X LEU* 3.4 3.8 + - - +
149X ASN* 2.9 49.2 + - - +
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Residues in contact with LYS 146 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15H PHE* 3.7 15.6 - - - -
20H GLU* 3.1 34.9 + - - -
51X GLU* 5.7 6.1 + - + +
52X GLN* 3.4 22.2 - - - +
55X VAL* 4.1 22.2 - - + -
142X LEU* 3.0 27.3 + - + +
143X THR 3.5 6.7 - - - +
145X GLU* 1.3 79.8 + - + +
147X LEU* 1.3 59.7 + - - +
149X ASN* 3.2 19.8 + - + +
150X LEU* 2.9 24.8 + - - +
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Residues in contact with LEU 147 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52X GLN* 3.5 31.0 - - + +
56X GLU* 4.0 5.2 - - - +
98X LEU* 5.4 0.2 - - + -
143X THR* 2.8 25.4 + - + +
144X ASN* 3.6 4.3 - - - +
146X LYS* 1.3 76.0 - - - +
148X LEU* 1.3 58.3 + - - +
150X LEU* 3.3 10.3 + - + +
151X HIS* 2.9 26.7 + - - +
166X VAL* 3.8 12.0 - - + +
170X TYR* 3.8 40.8 - - + +
171X LEU* 3.8 15.5 - - + -
174X GLN* 4.0 34.1 - - + +
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Residues in contact with LEU 148 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40H LYS* 3.7 33.7 - - + -
160H VAL* 4.1 23.4 - - + +
161H GLN* 5.3 3.8 - - + +
144X ASN* 2.9 40.5 + - - +
145X GLU* 3.7 4.7 - - - +
147X LEU* 1.3 74.1 - - - +
149X ASN* 1.3 63.0 + - - +
151X HIS* 3.4 5.0 + - + +
152X SER* 3.0 30.1 + - - -
171X LEU* 3.9 29.8 - - + -
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Residues in contact with ASN 149 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145X GLU* 2.9 39.6 + - - +
146X LYS* 3.2 22.0 + - + +
148X LEU* 1.3 75.7 - - - +
150X LEU* 1.3 65.9 + - - +
152X SER* 3.1 9.9 + - - -
153X VAL* 3.0 27.9 + - + +
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Residues in contact with LEU 150 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48X ALA* 3.6 37.7 - - + +
49X VAL* 4.0 13.7 - - + +
52X GLN* 3.9 30.1 - - + +
98X LEU* 4.4 13.5 - - + -
146X LYS 2.9 13.7 + - - +
147X LEU* 3.3 11.6 + - + +
149X ASN* 1.3 75.6 - - - +
151X HIS* 1.3 63.2 + - - +
153X VAL* 3.1 8.0 + - + +
154X ALA* 3.1 19.2 + - - +
162X LEU* 4.5 10.8 - - + -
166X VAL* 3.6 29.8 - - + -
170X TYR* 6.4 0.2 - - + -
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Residues in contact with HIS 151 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160H VAL* 3.5 33.4 - - + +
147X LEU 2.9 13.3 + - - +
148X LEU* 3.5 13.7 - - + +
149X ASN 3.2 0.2 - - - -
150X LEU* 1.3 76.6 - - - +
152X SER* 1.3 59.1 + - - +
154X ALA* 3.1 8.8 + - - +
155X THR* 2.9 48.5 + - + +
163X ALA* 3.5 19.9 - - + +
166X VAL* 4.3 11.7 - - + -
167X GLU* 2.7 44.2 + - + +
171X LEU* 4.4 5.8 - - + -
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Residues in contact with SER 152 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148X LEU 3.0 16.4 + - - -
149X ASN* 3.1 13.1 + - - -
151X HIS* 1.3 79.4 + - - +
153X VAL* 1.3 52.8 + - - +
155X THR* 2.9 10.4 + - - -
156X LYS* 2.7 37.2 + - - +
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Residues in contact with VAL 153 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44X GLU* 3.7 37.9 - - + +
45X SER* 4.1 5.6 - - - -
48X ALA* 3.9 21.3 - - + -
149X ASN* 3.0 20.6 + - + +
150X LEU* 3.1 8.0 + - + +
152X SER* 1.3 77.3 - - - +
154X ALA* 1.3 62.3 + - - +
156X LYS* 3.3 8.1 + - + +
157X ASN* 2.9 46.5 + - - +
----------------------------------------------------------
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Residues in contact with ALA 154 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45X SER* 4.7 1.1 - - - -
150X LEU 3.1 9.1 + - - +
151X HIS* 3.1 9.6 + - - +
153X VAL* 1.3 78.3 - - - +
155X THR* 1.3 57.2 + - - +
157X ASN 3.2 1.7 + - - -
158X GLY 2.9 8.0 + - - -
159X ASP* 2.8 37.8 + - - +
162X LEU* 3.6 35.6 - - + +
163X ALA* 3.7 21.1 - - - +
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Residues in contact with THR 155 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151X HIS* 2.9 41.7 + - + +
152X SER* 2.9 25.5 + - - -
154X ALA* 1.3 73.0 - - - +
156X LYS* 1.3 66.1 + - - +
158X GLY* 3.2 12.8 + - - +
159X ASP 5.0 0.7 - - - +
163X ALA* 4.5 8.5 - - + -
----------------------------------------------------------
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Residues in contact with LYS 156 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44X GLU* 3.1 37.2 + - - +
152X SER 2.7 22.2 + - - +
153X VAL* 3.5 9.6 - - + +
155X THR* 1.3 74.8 + - - +
157X ASN* 1.3 65.4 + - - +
158X GLY 3.6 0.3 + - - -
----------------------------------------------------------
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Residues in contact with ASN 157 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42X VAL* 3.7 30.9 - - + +
44X GLU* 3.0 33.2 + - - +
45X SER* 3.9 9.9 + - - +
153X VAL* 2.9 36.1 + - - +
154X ALA 4.0 2.0 - - - +
156X LYS* 1.3 85.1 + - - +
158X GLY* 1.3 64.2 + - - +
159X ASP* 3.4 3.7 + - + +
----------------------------------------------------------
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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